0.7.1-dev.3

- updated all
- removed unused jest-raw-loader
- removed unused circular-dependency-plugin
- removed unused resolve-url-loader

.eslintignore

@@ -0,0 +1,3 @@
+node_modules/*
+build/*
+lib/*

.eslintrc.json

@@ -0,0 +1,75 @@
+{
+    "env": {
+        "browser": true,
+        "node": true
+    },
+    "parser": "@typescript-eslint/parser",
+    "parserOptions": {
+        "project": ["tsconfig.json", "tsconfig.servers.json"],
+        "sourceType": "module"
+    },
+    "plugins": [
+        "@typescript-eslint"
+    ],
+    "rules": {
+        "@typescript-eslint/ban-types": "warn",
+        "@typescript-eslint/class-name-casing": "off",
+        "indent": "off",
+        "@typescript-eslint/indent": [
+            "error",
+            4
+        ],
+        "@typescript-eslint/member-delimiter-style": [
+            "off",
+            {
+                "multiline": {
+                    "delimiter": "none",
+                    "requireLast": true
+                },
+                "singleline": {
+                    "delimiter": "semi",
+                    "requireLast": false
+                }
+            }
+        ],
+        "@typescript-eslint/prefer-namespace-keyword": "warn",
+        "@typescript-eslint/quotes": [
+            "error",
+            "single",
+            {
+                "avoidEscape": true,
+                "allowTemplateLiterals": true
+            }
+        ],
+        "@typescript-eslint/semi": [
+            "off",
+            null
+        ],
+        "@typescript-eslint/type-annotation-spacing": "error",
+        "arrow-parens": [
+            "off",
+            "as-needed"
+        ],
+        "brace-style": "off",
+        "@typescript-eslint/brace-style": [
+            "error",
+            "1tbs", { "allowSingleLine": true }
+        ],
+        "comma-spacing": "off",
+        "@typescript-eslint/comma-spacing": "error",
+        "space-infix-ops": "error",
+        "comma-dangle": "off",
+        "eqeqeq": [
+            "error",
+            "smart"
+        ],
+        "import/order": "off",
+        "no-eval": "warn",
+        "no-new-wrappers": "warn",
+        "no-trailing-spaces": "error",
+        "no-unsafe-finally": "warn",
+        "no-var": "error",
+        "spaced-comment": "error",
+        "semi": "warn"
+    }
+}

.github/workflows/lint.yml

@@ -0,0 +1,18 @@
+on:
+  push:
+  pull_request:
+
+jobs:
+  eslint:
+    name: eslint
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: install node v12
+      uses: actions/setup-node@v1
+      with:
+        node-version: 12
+    - name: yarn install
+      run: yarn install
+    - name: eslint
+      uses: icrawl/action-eslint@v1

.npmignore

@@ -0,0 +1 @@
+tsconfig.servers.buildinfo

.vscode/extensions.json

@@ -4,8 +4,8 @@
 
 	// List of extensions which should be recommended for users of this workspace.
 	"recommendations": [
+		"dbaeumer.vscode-eslint",
 		"firsttris.vscode-jest-runner",
-		"ms-vscode.vscode-typescript-tslint-plugin",
 		"msjsdiag.debugger-for-chrome",
 		"slevesque.shader",
 		"stpn.vscode-graphql",

.vscode/settings.json

@@ -6,4 +6,7 @@
         "*.vert.ts": "glsl",
         "*.gql.ts": "graphql"
     },
+    "eslint.options": {
+        "ignorePattern": ["webpack.config.js", "scripts/*"],
+    }
 }

.vscode/tasks.json

@@ -9,6 +9,20 @@
             "problemMatcher": [
                 "$tsc"
             ]
+        },
+        {
+            "type": "npm",
+            "script": "build-tsc",
+            "problemMatcher": [
+                "$tsc"
+            ]
+        },
+        {
+            "type": "npm",
+            "script": "watch",
+            "problemMatcher": [
+                "$tsc"
+            ]
         }
     ]
 }

README.md

@@ -5,7 +5,7 @@
 
 # Mol*
 
-The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will serve as basis for the next-generation data delivery and analysis tools for macromolecular structure data. This is a collaboration between PDBe and RCSB PDB teams and the development will be open source and available to anyone who wants to use it for developing visualisation tools for macromolecular structure data available from [PDB](https://www.wwpdb.org/) and other institutions.
+The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will serve as a basis for the next-generation data delivery and analysis tools for macromolecular structure data. This is a collaboration between PDBe and RCSB PDB teams and the development will be open-source and available to anyone who wants to use it for developing visualization tools for macromolecular structure data available from [PDB](https://www.wwpdb.org/) and other institutions.
 
 This particular project is the implementation of this technology (still under development).
 
@@ -16,27 +16,30 @@ This particular project is the implementation of this technology (still under de
 The core of Mol* currently consists of these modules (see under `src/`):
 
 - `mol-task` Computation abstraction with progress tracking and cancellation support.
-- `mol-data` Collections (integer based sets, interface to columns/tables, etc.)
+- `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
 - `mol-math` Math related (loosely) algorithms and data structures.
 - `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.
 - `mol-model` Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).
 - `mol-model-formats` Data format parsers for `mol-model`.
 - `mol-model-props` Common "custom properties".
-- `mol-script` A scriting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).
+- `mol-script` A scripting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).
 - `mol-geo` Creating (molecular) geometries.
 - `mol-theme` Theming for structure, volume and shape representations.
 - `mol-repr` Molecular representations for structures, volumes and shapes.
 - `mol-gl` A wrapper around WebGL.
-- `mol-canvas3d` A low level 3d view component. Uses `mol-geo` to generate geometries.
+- `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
 - `mol-state` State representation tree with state saving and automatic updates.
-- `mol-app` Components for builduing UIs.
+- `mol-app` Components for building UIs.
 - `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
+- `mol-plugin-state` State transformations, builders, and managers.
+- `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
 - `mol-util` Useful things that do not fit elsewhere.
 
-Moreover, the project contains the imlementation of `servers`, including
+Moreover, the project contains the implementation of `servers`, including
 
 - `servers/model` A tool for accessing coordinate and annotation data of molecular structures.
 - `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
+- `servers/plugin-state` A basic server to store Mol* Plugin states.
 
 The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `apps` (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
 
@@ -59,9 +62,13 @@ This project builds on experience from previous solutions:
 ### Build automatically on file save:
     npm run watch
 
+If working on just the viewer, ``npm run watch-viewer`` will provide shorter compile times.
+
 ### Build with debug mode enabled:
     DEBUG=molstar npm run watch
 
+Debug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.
+
 ### Build for production:
     NODE_ENV=production npm run build
 
@@ -82,20 +89,20 @@ and navigate to `build/viewer`
 
 ### Code generation
 **CIF schemas**
-Install CIFTools `npm install ciftools -g`
 
-    cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
-    cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
-    cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
+    node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
+    node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
+    node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
+    node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
 
 **GraphQL schemas**
 
-    node data/rcsb-graphql/codegen.js
+    ./node_modules/.bin/graphql-codegen -c ./src/extensions/rcsb/graphql/codegen.yml
 
 ### Other scripts
 **Create chem comp bond table**
 
-    export NODE_PATH="lib"; node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
+    node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
 
 **Test model server**
 
@@ -107,22 +114,26 @@ Install CIFTools `npm install ciftools -g`
 
 **Convert any CIF to BinaryCIF**
 
-    node build/model-server/preprocess -i file.cif -ob file.bcif
+    node lib/servers/model/preprocess -i file.cif -ob file.bcif
 
-To see all available commands, use ``node build/model-server/preprocess -h``.
+To see all available commands, use ``node lib/servers/model/preprocess -h``.
+
+Or
+
+    node ./lib/apps/cif2bcif
 
 ## Development
 
-### Intallation
+### Installation
 
-If node complains about a missine acorn peer dependency, run the following commands
+If node complains about a missing acorn peer dependency, run the following commands
 
     npm update acorn --depth 20
     npm dedupe
 
 ### Editor
 
-To get syntax highlighting for shader and graphql files add the following to Visual Code's settings files and make sure relevant extanesions are installed in the editor.
+To get syntax highlighting for shader and graphql files add the following to Visual Code's settings files and make sure relevant extensions are installed in the editor.
 
     "files.associations": {
         "*.glsl.ts": "glsl",
@@ -134,7 +145,7 @@ To get syntax highlighting for shader and graphql files add the following to Vis
 ## Publish
 
 ### Prerelease
-    npm version prerelease # asumes the current version ends with '-dev.X'
+    npm version prerelease # assumes the current version ends with '-dev.X'
     npm publish --tag next
 
 ### Release
@@ -156,4 +167,4 @@ Continually develop this prototype project. As individual modules become stable,
 Funding sources include but are not limited to:
 * [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
 * [PDBe, EMBL-EBI](https://pdbe.org)
-* [CEITEC](https://www.ceitec.eu/)
+* [CEITEC](https://www.ceitec.eu/)

data/cif-field-names/bird-field-names.csv

@@ -0,0 +1,88 @@
+pdbx_reference_molecule.prd_id
+pdbx_reference_molecule.name
+pdbx_reference_molecule.represent_as
+pdbx_reference_molecule.type
+pdbx_reference_molecule.type_evidence_code
+pdbx_reference_molecule.class
+pdbx_reference_molecule.class_evidence_code
+pdbx_reference_molecule.formula
+pdbx_reference_molecule.chem_comp_id
+pdbx_reference_molecule.formula_weight
+pdbx_reference_molecule.release_status
+pdbx_reference_molecule.replaces
+pdbx_reference_molecule.replaced_by
+pdbx_reference_molecule.compound_details
+pdbx_reference_molecule.description
+pdbx_reference_molecule.representative_PDB_id_code
+
+pdbx_reference_entity_list.prd_id
+pdbx_reference_entity_list.ref_entity_id
+pdbx_reference_entity_list.component_id
+pdbx_reference_entity_list.type
+pdbx_reference_entity_list.details
+
+pdbx_reference_entity_nonpoly.prd_id
+pdbx_reference_entity_nonpoly.ref_entity_id
+pdbx_reference_entity_nonpoly.name
+pdbx_reference_entity_nonpoly.chem_comp_id
+
+pdbx_reference_entity_link.prd_id
+pdbx_reference_entity_link.link_id
+pdbx_reference_entity_link.link_class
+pdbx_reference_entity_link.ref_entity_id_1
+pdbx_reference_entity_link.entity_seq_num_1
+pdbx_reference_entity_link.comp_id_1
+pdbx_reference_entity_link.atom_id_1
+pdbx_reference_entity_link.ref_entity_id_2
+pdbx_reference_entity_link.entity_seq_num_2
+pdbx_reference_entity_link.comp_id_2
+pdbx_reference_entity_link.atom_id_2
+pdbx_reference_entity_link.value_order
+pdbx_reference_entity_link.component_1
+pdbx_reference_entity_link.component_2
+pdbx_reference_entity_link.details
+
+pdbx_reference_entity_poly_link.prd_id
+pdbx_reference_entity_poly_link.ref_entity_id
+pdbx_reference_entity_poly_link.link_id
+pdbx_reference_entity_poly_link.atom_id_1
+pdbx_reference_entity_poly_link.comp_id_1
+pdbx_reference_entity_poly_link.entity_seq_num_1
+pdbx_reference_entity_poly_link.atom_id_2
+pdbx_reference_entity_poly_link.comp_id_2
+pdbx_reference_entity_poly_link.entity_seq_num_2
+pdbx_reference_entity_poly_link.value_order
+pdbx_reference_entity_poly_link.component_id
+
+pdbx_reference_entity_poly.prd_id
+pdbx_reference_entity_poly.ref_entity_id
+pdbx_reference_entity_poly.db_code
+pdbx_reference_entity_poly.db_name
+pdbx_reference_entity_poly.type
+
+pdbx_reference_entity_sequence.prd_id
+pdbx_reference_entity_sequence.ref_entity_id
+pdbx_reference_entity_sequence.type
+pdbx_reference_entity_sequence.NRP_flag
+pdbx_reference_entity_sequence.one_letter_codes
+
+pdbx_reference_entity_poly_seq.prd_id
+pdbx_reference_entity_poly_seq.ref_entity_id
+pdbx_reference_entity_poly_seq.num
+pdbx_reference_entity_poly_seq.mon_id
+pdbx_reference_entity_poly_seq.parent_mon_id
+pdbx_reference_entity_poly_seq.hetero
+pdbx_reference_entity_poly_seq.observed
+
+pdbx_reference_entity_src_nat.prd_id
+pdbx_reference_entity_src_nat.ref_entity_id
+pdbx_reference_entity_src_nat.ordinal
+pdbx_reference_entity_src_nat.taxid
+pdbx_reference_entity_src_nat.organism_scientific
+pdbx_reference_entity_src_nat.db_code
+pdbx_reference_entity_src_nat.db_name
+
+pdbx_prd_audit.prd_id
+pdbx_prd_audit.date
+pdbx_prd_audit.processing_site
+pdbx_prd_audit.action_type

data/cif-field-names/ccd-field-names.csv

@@ -0,0 +1,60 @@
+chem_comp.id
+chem_comp.name
+chem_comp.type
+chem_comp.pdbx_type
+chem_comp.formula
+chem_comp.mon_nstd_parent_comp_id
+chem_comp.pdbx_synonyms
+chem_comp.pdbx_formal_charge
+chem_comp.pdbx_initial_date
+chem_comp.pdbx_modified_date
+chem_comp.pdbx_ambiguous_flag
+chem_comp.pdbx_release_status
+chem_comp.pdbx_replaced_by
+chem_comp.pdbx_replaces
+chem_comp.formula_weight
+chem_comp.one_letter_code
+chem_comp.three_letter_code
+chem_comp.pdbx_model_coordinates_details
+chem_comp.pdbx_model_coordinates_missing_flag
+chem_comp.pdbx_ideal_coordinates_details
+chem_comp.pdbx_ideal_coordinates_missing_flag
+chem_comp.pdbx_model_coordinates_db_code
+chem_comp.pdbx_processing_site
+
+chem_comp_atom.comp_id
+chem_comp_atom.atom_id
+chem_comp_atom.alt_atom_id
+chem_comp_atom.type_symbol
+chem_comp_atom.charge
+chem_comp_atom.pdbx_align
+chem_comp_atom.pdbx_aromatic_flag
+chem_comp_atom.pdbx_leaving_atom_flag
+chem_comp_atom.pdbx_stereo_config
+chem_comp_atom.model_Cartn_x
+chem_comp_atom.model_Cartn_y
+chem_comp_atom.model_Cartn_z
+chem_comp_atom.pdbx_model_Cartn_x_ideal
+chem_comp_atom.pdbx_model_Cartn_y_ideal
+chem_comp_atom.pdbx_model_Cartn_z_ideal
+chem_comp_atom.pdbx_ordinal
+
+chem_comp_bond.comp_id
+chem_comp_bond.atom_id_1
+chem_comp_bond.atom_id_2
+chem_comp_bond.value_order
+chem_comp_bond.pdbx_aromatic_flag
+chem_comp_bond.pdbx_stereo_config
+chem_comp_bond.pdbx_ordinal
+
+pdbx_chem_comp_descriptor.comp_id
+pdbx_chem_comp_descriptor.type
+pdbx_chem_comp_descriptor.program
+pdbx_chem_comp_descriptor.program_version
+pdbx_chem_comp_descriptor.descriptor
+
+pdbx_chem_comp_identifier.comp_id
+pdbx_chem_comp_identifier.type
+pdbx_chem_comp_identifier.program
+pdbx_chem_comp_identifier.program_version
+pdbx_chem_comp_identifier.identifier

data/cif-field-names/cif-core-field-names.csv

@@ -0,0 +1,76 @@
+audit.block_doi
+
+database_code.depnum_ccdc_archive
+database_code.depnum_ccdc_fiz
+database_code.ICSD
+database_code.MDF
+database_code.NBS
+database_code.CSD
+database_code.COD
+
+chemical.name_systematic
+chemical.name_common
+chemical.melting_point
+
+chemical_formula.moiety
+chemical_formula.sum
+chemical_formula.weight
+
+atom_type.symbol
+atom_type.description
+
+atom_type_scat.dispersion_real
+atom_type_scat.dispersion_imag
+atom_type_scat.source
+
+space_group.crystal_system
+space_group.name_H-M_full
+space_group.IT_number
+space_group_symop.operation_xyz
+
+cell.length_a
+cell.length_b
+cell.length_c
+cell.angle_alpha
+cell.angle_beta
+cell.angle_gamma
+cell.volume
+cell.formula_units_Z
+
+atom_site.label
+atom_site.type_symbol
+atom_site.fract_x
+atom_site.fract_y
+atom_site.fract_z
+atom_site.U_iso_or_equiv
+atom_site.adp_type
+atom_site.occupancy
+atom_site.calc_flag
+atom_site.refinement_flags
+atom_site.disorder_assembly
+atom_site.disorder_group
+atom_site.site_symmetry_multiplicity
+
+atom_site_aniso.label
+atom_site_aniso.U
+atom_site_aniso.U_11
+atom_site_aniso.U_22
+atom_site_aniso.U_33
+atom_site_aniso.U_23
+atom_site_aniso.U_13
+atom_site_aniso.U_12
+atom_site_aniso.U_su
+atom_site_aniso.U_11_su
+atom_site_aniso.U_22_su
+atom_site_aniso.U_33_su
+atom_site_aniso.U_23_su
+atom_site_aniso.U_13_su
+atom_site_aniso.U_12_su
+
+geom_bond.atom_site_label_1
+geom_bond.atom_site_label_2
+geom_bond.distance
+geom_bond.site_symmetry_1
+geom_bond.site_symmetry_2
+geom_bond.publ_flag
+geom_bond.valence

data/cif-field-names/mmcif-field-names.csv

@@ -0,0 +1,805 @@
+atom_sites.entry_id
+atom_sites.fract_transf_matrix
+atom_sites.fract_transf_vector
+
+atom_site.group_PDB
+atom_site.id
+atom_site.type_symbol
+atom_site.label_atom_id
+atom_site.label_alt_id
+atom_site.label_comp_id
+atom_site.label_asym_id
+atom_site.label_entity_id
+atom_site.label_seq_id
+atom_site.pdbx_PDB_ins_code
+atom_site.pdbx_formal_charge
+atom_site.Cartn_x
+atom_site.Cartn_y
+atom_site.Cartn_z
+atom_site.occupancy
+atom_site.B_iso_or_equiv
+atom_site.auth_atom_id
+atom_site.auth_comp_id
+atom_site.auth_asym_id
+atom_site.auth_seq_id
+atom_site.pdbx_PDB_model_num
+atom_site.ihm_model_id
+
+atom_site_anisotrop.id
+atom_site_anisotrop.U
+atom_site_anisotrop.U_esd
+atom_site_anisotrop.pdbx_PDB_ins_code
+atom_site_anisotrop.pdbx_auth_asym_id
+atom_site_anisotrop.pdbx_auth_atom_id
+atom_site_anisotrop.pdbx_auth_comp_id
+atom_site_anisotrop.pdbx_auth_seq_id
+atom_site_anisotrop.pdbx_label_alt_id
+atom_site_anisotrop.pdbx_label_asym_id
+atom_site_anisotrop.pdbx_label_atom_id
+atom_site_anisotrop.pdbx_label_comp_id
+atom_site_anisotrop.pdbx_label_seq_id
+atom_site_anisotrop.type_symbol
+
+chem_comp.id
+chem_comp.type
+chem_comp.mon_nstd_flag
+chem_comp.name
+chem_comp.pdbx_synonyms
+chem_comp.formula
+chem_comp.formula_weight
+
+chem_comp_bond.comp_id
+chem_comp_bond.pdbx_stereo_config
+chem_comp_bond.pdbx_ordinal
+chem_comp_bond.pdbx_aromatic_flag
+chem_comp_bond.atom_id_1
+chem_comp_bond.atom_id_2
+chem_comp_bond.value_order
+
+pdbx_chem_comp_identifier.comp_id
+pdbx_chem_comp_identifier.type
+pdbx_chem_comp_identifier.program
+pdbx_chem_comp_identifier.program_version
+pdbx_chem_comp_identifier.identifier
+
+pdbx_chem_comp_related.comp_id
+pdbx_chem_comp_related.related_comp_id
+pdbx_chem_comp_related.relationship_type
+pdbx_chem_comp_related.details
+
+pdbx_chem_comp_synonyms.comp_id
+pdbx_chem_comp_synonyms.name
+pdbx_chem_comp_synonyms.provenance
+
+cell.entry_id
+cell.length_a
+cell.length_b
+cell.length_c
+cell.angle_alpha
+cell.angle_beta
+cell.angle_gamma
+cell.Z_PDB
+cell.pdbx_unique_axis
+
+pdbx_database_related.db_name
+pdbx_database_related.details
+pdbx_database_related.db_id
+pdbx_database_related.content_type
+
+pdbx_database_status.status_code
+pdbx_database_status.status_code_sf
+pdbx_database_status.status_code_mr
+pdbx_database_status.entry_id
+pdbx_database_status.recvd_initial_deposition_date
+pdbx_database_status.SG_entry
+pdbx_database_status.deposit_site
+pdbx_database_status.process_site
+pdbx_database_status.status_code_cs
+pdbx_database_status.methods_development_category
+pdbx_database_status.pdb_format_compatible
+
+entity.id
+entity.type
+entity.src_method
+entity.pdbx_description
+entity.formula_weight
+entity.pdbx_number_of_molecules
+entity.details
+entity.pdbx_mutation
+entity.pdbx_fragment
+entity.pdbx_ec
+
+entity_poly.entity_id
+entity_poly.type
+entity_poly.nstd_linkage
+entity_poly.nstd_monomer
+entity_poly.pdbx_seq_one_letter_code
+entity_poly.pdbx_seq_one_letter_code_can
+entity_poly.pdbx_strand_id
+entity_poly.pdbx_target_identifier
+
+entity_poly_seq.entity_id
+entity_poly_seq.num
+entity_poly_seq.mon_id
+entity_poly_seq.hetero
+
+entity_src_gen.entity_id
+entity_src_gen.pdbx_src_id
+entity_src_gen.pdbx_beg_seq_num
+entity_src_gen.pdbx_end_seq_num
+entity_src_gen.pdbx_gene_src_gene
+entity_src_gen.pdbx_gene_src_scientific_name
+entity_src_gen.plasmid_name
+
+entity_src_nat.entity_id
+entity_src_nat.pdbx_src_id
+entity_src_nat.pdbx_beg_seq_num
+entity_src_nat.pdbx_end_seq_num
+entity_src_nat.pdbx_organism_scientific
+entity_src_nat.pdbx_plasmid_name
+
+pdbx_entity_instance_feature.ordinal
+pdbx_entity_instance_feature.feature_type
+pdbx_entity_instance_feature.details
+pdbx_entity_instance_feature.asym_id
+pdbx_entity_instance_feature.comp_id
+pdbx_entity_instance_feature.seq_num
+pdbx_entity_instance_feature.auth_asym_id
+pdbx_entity_instance_feature.auth_comp_id
+pdbx_entity_instance_feature.auth_seq_num
+
+pdbx_entity_src_syn.entity_id
+pdbx_entity_src_syn.pdbx_src_id
+pdbx_entity_src_syn.pdbx_beg_seq_num
+pdbx_entity_src_syn.pdbx_end_seq_num
+pdbx_entity_src_syn.organism_scientific
+
+pdbx_entity_branch.entity_id
+pdbx_entity_branch.type
+
+pdbx_entity_branch_list.entity_id
+pdbx_entity_branch_list.comp_id
+pdbx_entity_branch_list.num
+pdbx_entity_branch_list.hetero
+
+pdbx_entity_branch_link.link_id
+pdbx_entity_branch_link.entity_id
+pdbx_entity_branch_link.entity_branch_list_num_1
+pdbx_entity_branch_link.comp_id_1
+pdbx_entity_branch_link.atom_id_1
+pdbx_entity_branch_link.leaving_atom_id_1
+pdbx_entity_branch_link.atom_stereo_config_1
+pdbx_entity_branch_link.entity_branch_list_num_2
+pdbx_entity_branch_link.comp_id_2
+pdbx_entity_branch_link.atom_id_2
+pdbx_entity_branch_link.leaving_atom_id_2
+pdbx_entity_branch_link.atom_stereo_config_2
+pdbx_entity_branch_link.value_order
+pdbx_entity_branch_link.details
+
+pdbx_branch_scheme.asym_id
+pdbx_branch_scheme.entity_id
+pdbx_branch_scheme.mon_id
+pdbx_branch_scheme.num
+pdbx_branch_scheme.auth_asym_id
+pdbx_branch_scheme.auth_mon_id
+pdbx_branch_scheme.auth_seq_num
+pdbx_branch_scheme.hetero
+pdbx_branch_scheme.pdb_mon_id
+pdbx_branch_scheme.pdb_asym_id
+pdbx_branch_scheme.pdb_seq_num
+
+pdbx_entity_branch_descriptor.ordinal
+pdbx_entity_branch_descriptor.entity_id
+pdbx_entity_branch_descriptor.descriptor
+pdbx_entity_branch_descriptor.type
+pdbx_entity_branch_descriptor.program
+pdbx_entity_branch_descriptor.program_version
+
+pdbx_entity_nonpoly.entity_id
+pdbx_entity_nonpoly.name
+pdbx_entity_nonpoly.comp_id
+
+pdbx_nonpoly_scheme.asym_id
+pdbx_nonpoly_scheme.entity_id
+pdbx_nonpoly_scheme.mon_id
+pdbx_nonpoly_scheme.ndb_seq_num
+pdbx_nonpoly_scheme.pdb_seq_num
+pdbx_nonpoly_scheme.auth_seq_num
+pdbx_nonpoly_scheme.pdb_mon_id
+pdbx_nonpoly_scheme.auth_mon_id
+pdbx_nonpoly_scheme.pdb_strand_id
+pdbx_nonpoly_scheme.pdb_ins_code
+
+entry.id
+
+audit_conform.dict_name
+audit_conform.dict_version
+audit_conform.dict_location
+
+database_2.database_id
+database_2.database_code
+
+audit_author.name
+audit_author.pdbx_ordinal
+audit_author.identifier_ORCID
+
+citation.id
+citation.title
+citation.journal_abbrev
+citation.journal_volume
+citation.page_first
+citation.page_last
+citation.year
+citation.journal_id_ASTM
+citation.country
+citation.journal_id_ISSN
+citation.journal_id_CSD
+citation.book_publisher
+citation.pdbx_database_id_PubMed
+citation.pdbx_database_id_DOI
+
+citation_author.citation_id
+citation_author.name
+citation_author.ordinal
+
+exptl.entry_id
+exptl.method
+
+struct.entry_id
+struct.title
+struct.pdbx_descriptor
+
+struct_asym.id
+struct_asym.pdbx_blank_PDB_chainid_flag
+struct_asym.pdbx_modified
+struct_asym.entity_id
+struct_asym.details
+
+struct_conf.conf_type_id
+struct_conf.id
+struct_conf.pdbx_PDB_helix_id
+struct_conf.beg_label_comp_id
+struct_conf.beg_label_asym_id
+struct_conf.beg_label_seq_id
+struct_conf.pdbx_beg_PDB_ins_code
+struct_conf.end_label_comp_id
+struct_conf.end_label_asym_id
+struct_conf.end_label_seq_id
+struct_conf.pdbx_end_PDB_ins_code
+struct_conf.beg_auth_comp_id
+struct_conf.beg_auth_asym_id
+struct_conf.beg_auth_seq_id
+struct_conf.end_auth_comp_id
+struct_conf.end_auth_asym_id
+struct_conf.end_auth_seq_id
+struct_conf.pdbx_PDB_helix_class
+struct_conf.details
+struct_conf.pdbx_PDB_helix_length
+
+struct_conn.id
+struct_conn.conn_type_id
+struct_conn.pdbx_PDB_id
+struct_conn.ptnr1_label_asym_id
+struct_conn.ptnr1_label_comp_id
+struct_conn.ptnr1_label_seq_id
+struct_conn.ptnr1_label_atom_id
+struct_conn.pdbx_ptnr1_label_alt_id
+struct_conn.pdbx_ptnr1_PDB_ins_code
+struct_conn.pdbx_ptnr1_standard_comp_id
+struct_conn.ptnr1_symmetry
+struct_conn.ptnr2_label_asym_id
+struct_conn.ptnr2_label_comp_id
+struct_conn.ptnr2_label_seq_id
+struct_conn.ptnr2_label_atom_id
+struct_conn.pdbx_ptnr2_label_alt_id
+struct_conn.pdbx_ptnr2_PDB_ins_code
+struct_conn.ptnr1_auth_asym_id
+struct_conn.ptnr1_auth_comp_id
+struct_conn.ptnr1_auth_seq_id
+struct_conn.ptnr2_auth_asym_id
+struct_conn.ptnr2_auth_comp_id
+struct_conn.ptnr2_auth_seq_id
+struct_conn.ptnr2_symmetry
+struct_conn.pdbx_ptnr3_label_atom_id
+struct_conn.pdbx_ptnr3_label_seq_id
+struct_conn.pdbx_ptnr3_label_comp_id
+struct_conn.pdbx_ptnr3_label_asym_id
+struct_conn.pdbx_ptnr3_label_alt_id
+struct_conn.pdbx_ptnr3_PDB_ins_code
+struct_conn.details
+struct_conn.pdbx_dist_value
+struct_conn.pdbx_value_order
+
+struct_conn_type.id
+struct_conn_type.criteria
+struct_conn_type.reference
+
+struct_keywords.entry_id
+struct_keywords.pdbx_keywords
+struct_keywords.text
+
+struct_ncs_oper.id
+struct_ncs_oper.code
+struct_ncs_oper.matrix
+struct_ncs_oper.vector
+struct_ncs_oper.details
+
+struct_sheet_range.sheet_id
+struct_sheet_range.id
+struct_sheet_range.beg_label_comp_id
+struct_sheet_range.beg_label_asym_id
+struct_sheet_range.beg_label_seq_id
+struct_sheet_range.pdbx_beg_PDB_ins_code
+struct_sheet_range.end_label_comp_id
+struct_sheet_range.end_label_asym_id
+struct_sheet_range.end_label_seq_id
+struct_sheet_range.pdbx_end_PDB_ins_code
+struct_sheet_range.beg_auth_comp_id
+struct_sheet_range.beg_auth_asym_id
+struct_sheet_range.beg_auth_seq_id
+struct_sheet_range.end_auth_comp_id
+struct_sheet_range.end_auth_asym_id
+struct_sheet_range.end_auth_seq_id
+
+struct_site.id
+struct_site.pdbx_evidence_code
+struct_site.pdbx_auth_asym_id
+struct_site.pdbx_auth_comp_id
+struct_site.pdbx_auth_seq_id
+struct_site.pdbx_auth_ins_code
+struct_site.pdbx_num_residues
+struct_site.details
+
+struct_site_gen.id
+struct_site_gen.site_id
+struct_site_gen.pdbx_num_res
+struct_site_gen.label_comp_id
+struct_site_gen.label_asym_id
+struct_site_gen.label_seq_id
+struct_site_gen.pdbx_auth_ins_code
+struct_site_gen.auth_comp_id
+struct_site_gen.auth_asym_id
+struct_site_gen.auth_seq_id
+struct_site_gen.label_atom_id
+struct_site_gen.label_alt_id
+struct_site_gen.symmetry
+struct_site_gen.details
+
+symmetry.entry_id
+symmetry.cell_setting
+symmetry.Int_Tables_number
+symmetry.space_group_name_Hall
+symmetry.space_group_name_H-M
+
+pdbx_molecule.instance_id
+pdbx_molecule.prd_id
+pdbx_molecule.asym_id
+
+pdbx_molecule_features.prd_id
+pdbx_molecule_features.name
+pdbx_molecule_features.type
+pdbx_molecule_features.class
+pdbx_molecule_features.details
+
+pdbx_reference_entity_link.prd_id
+pdbx_reference_entity_link.link_id
+pdbx_reference_entity_link.link_class
+pdbx_reference_entity_link.ref_entity_id_1
+pdbx_reference_entity_link.entity_seq_num_1
+pdbx_reference_entity_link.comp_id_1
+pdbx_reference_entity_link.atom_id_1
+pdbx_reference_entity_link.ref_entity_id_2
+pdbx_reference_entity_link.entity_seq_num_2
+pdbx_reference_entity_link.comp_id_2
+pdbx_reference_entity_link.atom_id_2
+pdbx_reference_entity_link.value_order
+pdbx_reference_entity_link.component_1
+pdbx_reference_entity_link.component_2
+pdbx_reference_entity_link.details
+
+pdbx_reference_entity_list.prd_id
+pdbx_reference_entity_list.ref_entity_id
+pdbx_reference_entity_list.component_id
+pdbx_reference_entity_list.type
+pdbx_reference_entity_list.details
+
+pdbx_reference_entity_poly_link.prd_id
+pdbx_reference_entity_poly_link.ref_entity_id
+pdbx_reference_entity_poly_link.link_id
+pdbx_reference_entity_poly_link.atom_id_1
+pdbx_reference_entity_poly_link.comp_id_1
+pdbx_reference_entity_poly_link.entity_seq_num_1
+pdbx_reference_entity_poly_link.atom_id_2
+pdbx_reference_entity_poly_link.comp_id_2
+pdbx_reference_entity_poly_link.entity_seq_num_2
+pdbx_reference_entity_poly_link.value_order
+pdbx_reference_entity_poly_link.component_id
+
+pdbx_struct_assembly.id
+pdbx_struct_assembly.details
+pdbx_struct_assembly.method_details
+pdbx_struct_assembly.oligomeric_details
+pdbx_struct_assembly.oligomeric_count
+
+pdbx_struct_assembly_gen.assembly_id
+pdbx_struct_assembly_gen.oper_expression
+pdbx_struct_assembly_gen.asym_id_list
+
+pdbx_struct_oper_list.id
+pdbx_struct_oper_list.type
+pdbx_struct_oper_list.name
+pdbx_struct_oper_list.symmetry_operation
+pdbx_struct_oper_list.matrix
+pdbx_struct_oper_list.vector
+
+pdbx_struct_mod_residue.id
+pdbx_struct_mod_residue.label_asym_id
+pdbx_struct_mod_residue.label_seq_id
+pdbx_struct_mod_residue.label_comp_id
+pdbx_struct_mod_residue.auth_asym_id
+pdbx_struct_mod_residue.auth_seq_id
+pdbx_struct_mod_residue.auth_comp_id
+pdbx_struct_mod_residue.PDB_ins_code
+pdbx_struct_mod_residue.parent_comp_id
+pdbx_struct_mod_residue.details
+
+pdbx_unobs_or_zero_occ_residues.id
+pdbx_unobs_or_zero_occ_residues.PDB_model_num
+pdbx_unobs_or_zero_occ_residues.polymer_flag
+pdbx_unobs_or_zero_occ_residues.occupancy_flag
+pdbx_unobs_or_zero_occ_residues.auth_asym_id
+pdbx_unobs_or_zero_occ_residues.auth_comp_id
+pdbx_unobs_or_zero_occ_residues.auth_seq_id
+pdbx_unobs_or_zero_occ_residues.PDB_ins_code
+pdbx_unobs_or_zero_occ_residues.label_asym_id
+pdbx_unobs_or_zero_occ_residues.label_comp_id
+pdbx_unobs_or_zero_occ_residues.label_seq_id
+
+ihm_struct_assembly.id
+ihm_struct_assembly.name
+ihm_struct_assembly.description
+
+ihm_struct_assembly_details.id
+ihm_struct_assembly_details.assembly_id
+ihm_struct_assembly_details.parent_assembly_id
+ihm_struct_assembly_details.entity_description
+ihm_struct_assembly_details.entity_id
+ihm_struct_assembly_details.asym_id
+ihm_struct_assembly_details.entity_poly_segment_id
+
+ihm_model_representation.id
+ihm_model_representation.name
+ihm_model_representation.details
+
+ihm_model_representation_details.id
+ihm_model_representation_details.representation_id
+ihm_model_representation_details.entity_id
+ihm_model_representation_details.entity_description
+ihm_model_representation_details.entity_asym_id
+ihm_model_representation_details.entity_poly_segment_id
+ihm_model_representation_details.model_object_primitive
+ihm_model_representation_details.starting_model_id
+ihm_model_representation_details.model_mode
+ihm_model_representation_details.model_granularity
+ihm_model_representation_details.model_object_count
+
+ihm_external_reference_info.reference_id
+ihm_external_reference_info.reference_provider
+ihm_external_reference_info.reference_type
+ihm_external_reference_info.reference
+ihm_external_reference_info.refers_to
+ihm_external_reference_info.associated_url
+
+ihm_external_files.id
+ihm_external_files.reference_id
+ihm_external_files.file_path
+ihm_external_files.content_type
+ihm_external_files.file_size_bytes
+ihm_external_files.details
+
+ihm_dataset_list.id
+ihm_dataset_list.data_type
+ihm_dataset_list.database_hosted
+
+ihm_dataset_group.id
+ihm_dataset_group.name
+ihm_dataset_group.application
+ihm_dataset_group.details
+
+ihm_dataset_group_link.group_id
+ihm_dataset_group_link.dataset_list_id
+
+ihm_dataset_external_reference.id
+ihm_dataset_external_reference.dataset_list_id
+ihm_dataset_external_reference.file_id
+
+ihm_dataset_related_db_reference.id
+ihm_dataset_related_db_reference.dataset_list_id
+ihm_dataset_related_db_reference.db_name
+ihm_dataset_related_db_reference.accession_code
+ihm_dataset_related_db_reference.version
+ihm_dataset_related_db_reference.details
+
+ihm_related_datasets.dataset_list_id_derived
+ihm_related_datasets.dataset_list_id_primary
+
+ihm_poly_residue_feature.ordinal_id
+ihm_poly_residue_feature.feature_id
+ihm_poly_residue_feature.entity_id
+ihm_poly_residue_feature.asym_id
+ihm_poly_residue_feature.seq_id_begin
+ihm_poly_residue_feature.comp_id_begin
+ihm_poly_residue_feature.seq_id_end
+ihm_poly_residue_feature.comp_id_end
+
+ihm_feature_list.feature_id
+ihm_feature_list.feature_type
+ihm_feature_list.entity_type
+
+ihm_cross_link_list.id
+ihm_cross_link_list.group_id
+ihm_cross_link_list.entity_description_1
+ihm_cross_link_list.entity_id_1
+ihm_cross_link_list.seq_id_1
+ihm_cross_link_list.comp_id_1
+ihm_cross_link_list.entity_description_2
+ihm_cross_link_list.entity_id_2
+ihm_cross_link_list.seq_id_2
+ihm_cross_link_list.comp_id_2
+ihm_cross_link_list.linker_type
+ihm_cross_link_list.dataset_list_id
+
+ihm_cross_link_restraint.id
+ihm_cross_link_restraint.group_id
+ihm_cross_link_restraint.entity_id_1
+ihm_cross_link_restraint.asym_id_1
+ihm_cross_link_restraint.seq_id_1
+ihm_cross_link_restraint.atom_id_1
+ihm_cross_link_restraint.comp_id_1
+ihm_cross_link_restraint.entity_id_2
+ihm_cross_link_restraint.asym_id_2
+ihm_cross_link_restraint.seq_id_2
+ihm_cross_link_restraint.atom_id_2
+ihm_cross_link_restraint.comp_id_2
+ihm_cross_link_restraint.restraint_type
+ihm_cross_link_restraint.conditional_crosslink_flag
+ihm_cross_link_restraint.model_granularity
+ihm_cross_link_restraint.distance_threshold
+ihm_cross_link_restraint.psi
+ihm_cross_link_restraint.sigma_1
+ihm_cross_link_restraint.sigma_2
+
+ihm_cross_link_result_parameters.id
+ihm_cross_link_result_parameters.restraint_id
+ihm_cross_link_result_parameters.model_id
+ihm_cross_link_result_parameters.psi
+ihm_cross_link_result_parameters.sigma_1
+ihm_cross_link_result_parameters.sigma_2
+
+ihm_sas_restraint.id
+ihm_sas_restraint.dataset_list_id
+ihm_sas_restraint.model_id
+ihm_sas_restraint.struct_assembly_id
+ihm_sas_restraint.profile_segment_flag
+ihm_sas_restraint.fitting_atom_type
+ihm_sas_restraint.fitting_method
+ihm_sas_restraint.fitting_state
+ihm_sas_restraint.radius_of_gyration
+ihm_sas_restraint.chi_value
+ihm_sas_restraint.details
+
+ihm_derived_distance_restraint.id
+ihm_derived_distance_restraint.group_id
+ihm_derived_distance_restraint.feature_id_1
+ihm_derived_distance_restraint.feature_id_2
+ihm_derived_distance_restraint.group_conditionality
+ihm_derived_distance_restraint.restraint_type
+ihm_derived_distance_restraint.distance_upper_limit
+ihm_derived_distance_restraint.random_exclusion_fraction
+ihm_derived_distance_restraint.dataset_list_id
+
+ihm_2dem_class_average_restraint.id
+ihm_2dem_class_average_restraint.dataset_list_id
+ihm_2dem_class_average_restraint.number_raw_micrographs
+ihm_2dem_class_average_restraint.pixel_size_width
+ihm_2dem_class_average_restraint.pixel_size_height
+ihm_2dem_class_average_restraint.image_resolution
+ihm_2dem_class_average_restraint.image_segment_flag
+ihm_2dem_class_average_restraint.number_of_projections
+ihm_2dem_class_average_restraint.struct_assembly_id
+ihm_2dem_class_average_restraint.details
+
+ihm_2dem_class_average_fitting.id
+ihm_2dem_class_average_fitting.restraint_id
+ihm_2dem_class_average_fitting.model_id
+ihm_2dem_class_average_fitting.cross_correlation_coefficient
+ihm_2dem_class_average_fitting.rot_matrix
+ihm_2dem_class_average_fitting.tr_vector
+
+ihm_3dem_restraint.id
+ihm_3dem_restraint.dataset_list_id
+ihm_3dem_restraint.fitting_method
+ihm_3dem_restraint.struct_assembly_id
+ihm_3dem_restraint.number_of_gaussians
+ihm_3dem_restraint.model_id
+ihm_3dem_restraint.cross_correlation_coefficient
+
+ihm_predicted_contact_restraint.id
+ihm_predicted_contact_restraint.group_id
+ihm_predicted_contact_restraint.entity_id_1
+ihm_predicted_contact_restraint.asym_id_1
+ihm_predicted_contact_restraint.seq_id_1
+ihm_predicted_contact_restraint.comp_id_1
+ihm_predicted_contact_restraint.rep_atom_1
+ihm_predicted_contact_restraint.entity_id_2
+ihm_predicted_contact_restraint.asym_id_2
+ihm_predicted_contact_restraint.seq_id_2
+ihm_predicted_contact_restraint.comp_id_2
+ihm_predicted_contact_restraint.rep_atom_2
+ihm_predicted_contact_restraint.restraint_type
+ihm_predicted_contact_restraint.distance_lower_limit
+ihm_predicted_contact_restraint.distance_upper_limit
+ihm_predicted_contact_restraint.probability
+ihm_predicted_contact_restraint.model_granularity
+ihm_predicted_contact_restraint.dataset_list_id
+ihm_predicted_contact_restraint.software_id
+
+ihm_starting_model_details.starting_model_id
+ihm_starting_model_details.entity_id
+ihm_starting_model_details.entity_description
+ihm_starting_model_details.asym_id
+ihm_starting_model_details.entity_poly_segment_id
+ihm_starting_model_details.starting_model_source
+ihm_starting_model_details.starting_model_auth_asym_id
+ihm_starting_model_details.starting_model_sequence_offset
+ihm_starting_model_details.dataset_list_id
+
+ihm_starting_comparative_models.id
+ihm_starting_comparative_models.starting_model_id
+ihm_starting_comparative_models.starting_model_auth_asym_id
+ihm_starting_comparative_models.starting_model_seq_id_begin
+ihm_starting_comparative_models.starting_model_seq_id_end
+ihm_starting_comparative_models.template_auth_asym_id
+ihm_starting_comparative_models.template_seq_id_begin
+ihm_starting_comparative_models.template_seq_id_end
+ihm_starting_comparative_models.template_sequence_identity
+ihm_starting_comparative_models.template_sequence_identity_denominator
+ihm_starting_comparative_models.template_dataset_list_id
+ihm_starting_comparative_models.alignment_file_id
+
+ihm_starting_model_coord.starting_model_id
+ihm_starting_model_coord.group_PDB
+ihm_starting_model_coord.id
+ihm_starting_model_coord.type_symbol
+ihm_starting_model_coord.atom_id
+ihm_starting_model_coord.comp_id
+ihm_starting_model_coord.entity_id
+ihm_starting_model_coord.asym_id
+ihm_starting_model_coord.seq_id
+ihm_starting_model_coord.Cartn_x
+ihm_starting_model_coord.Cartn_y
+ihm_starting_model_coord.Cartn_z
+ihm_starting_model_coord.B_iso_or_equiv
+ihm_starting_model_coord.ordinal_id
+
+ihm_starting_model_seq_dif.id
+ihm_starting_model_seq_dif.entity_id
+ihm_starting_model_seq_dif.asym_id
+ihm_starting_model_seq_dif.seq_id
+ihm_starting_model_seq_dif.comp_id
+ihm_starting_model_seq_dif.starting_model_id
+ihm_starting_model_seq_dif.db_asym_id
+ihm_starting_model_seq_dif.db_seq_id
+ihm_starting_model_seq_dif.db_comp_id
+ihm_starting_model_seq_dif.details
+
+ihm_modeling_protocol.id
+ihm_modeling_protocol.protocol_name
+ihm_modeling_protocol.num_steps
+
+ihm_modeling_protocol_details.id
+ihm_modeling_protocol_details.protocol_id
+ihm_modeling_protocol_details.step_id
+ihm_modeling_protocol_details.struct_assembly_id
+ihm_modeling_protocol_details.dataset_group_id
+ihm_modeling_protocol_details.struct_assembly_description
+ihm_modeling_protocol_details.step_name
+ihm_modeling_protocol_details.step_method
+ihm_modeling_protocol_details.num_models_begin
+ihm_modeling_protocol_details.num_models_end
+ihm_modeling_protocol_details.multi_scale_flag
+ihm_modeling_protocol_details.multi_state_flag
+ihm_modeling_protocol_details.ordered_flag
+ihm_modeling_protocol_details.software_id
+ihm_modeling_protocol_details.script_file_id
+
+ihm_modeling_post_process.id
+ihm_modeling_post_process.protocol_id
+ihm_modeling_post_process.analysis_id
+ihm_modeling_post_process.step_id
+ihm_modeling_post_process.type
+ihm_modeling_post_process.feature
+ihm_modeling_post_process.num_models_begin
+ihm_modeling_post_process.num_models_end
+
+ihm_ensemble_info.ensemble_id
+ihm_ensemble_info.ensemble_name
+ihm_ensemble_info.post_process_id
+ihm_ensemble_info.model_group_id
+ihm_ensemble_info.ensemble_clustering_method
+ihm_ensemble_info.ensemble_clustering_feature
+ihm_ensemble_info.num_ensemble_models
+ihm_ensemble_info.num_ensemble_models_deposited
+ihm_ensemble_info.ensemble_precision_value
+ihm_ensemble_info.ensemble_file_id
+
+ihm_localization_density_files.id
+ihm_localization_density_files.file_id
+ihm_localization_density_files.ensemble_id
+ihm_localization_density_files.entity_id
+ihm_localization_density_files.asym_id
+ihm_localization_density_files.entity_poly_segment_id
+
+ihm_model_list.model_id
+ihm_model_list.model_name
+ihm_model_list.assembly_id
+ihm_model_list.protocol_id
+ihm_model_list.representation_id
+
+ihm_model_group.id
+ihm_model_group.name
+ihm_model_group.details
+
+ihm_model_group_link.group_id
+ihm_model_group_link.model_id
+
+ihm_model_representative.id
+ihm_model_representative.model_group_id
+ihm_model_representative.model_id
+ihm_model_representative.selection_criteria
+
+ihm_sphere_obj_site.id
+ihm_sphere_obj_site.entity_id
+ihm_sphere_obj_site.seq_id_begin
+ihm_sphere_obj_site.seq_id_end
+ihm_sphere_obj_site.asym_id
+ihm_sphere_obj_site.Cartn_x
+ihm_sphere_obj_site.Cartn_y
+ihm_sphere_obj_site.Cartn_z
+ihm_sphere_obj_site.object_radius
+ihm_sphere_obj_site.rmsf
+ihm_sphere_obj_site.model_id
+
+ihm_gaussian_obj_site.id
+ihm_gaussian_obj_site.entity_id
+ihm_gaussian_obj_site.seq_id_begin
+ihm_gaussian_obj_site.seq_id_end
+ihm_gaussian_obj_site.asym_id
+ihm_gaussian_obj_site.mean_Cartn_x
+ihm_gaussian_obj_site.mean_Cartn_y
+ihm_gaussian_obj_site.mean_Cartn_z
+ihm_gaussian_obj_site.weight
+ihm_gaussian_obj_site.covariance_matrix
+ihm_gaussian_obj_site.model_id
+
+ihm_gaussian_obj_ensemble.id
+ihm_gaussian_obj_ensemble.entity_id
+ihm_gaussian_obj_ensemble.seq_id_begin
+ihm_gaussian_obj_ensemble.seq_id_end
+ihm_gaussian_obj_ensemble.asym_id
+ihm_gaussian_obj_ensemble.mean_Cartn_x
+ihm_gaussian_obj_ensemble.mean_Cartn_y
+ihm_gaussian_obj_ensemble.mean_Cartn_z
+ihm_gaussian_obj_ensemble.weight
+ihm_gaussian_obj_ensemble.covariance_matrix
+ihm_gaussian_obj_ensemble.ensemble_id
+
+ihm_multi_state_modeling.state_id
+ihm_multi_state_modeling.state_group_id
+ihm_multi_state_modeling.population_fraction
+ihm_multi_state_modeling.population_fraction_sd
+ihm_multi_state_modeling.state_type
+ihm_multi_state_modeling.state_name
+ihm_multi_state_modeling.experiment_type
+ihm_multi_state_modeling.details

data/cif-field-names/mmtf-filter.csv

@@ -0,0 +1,76 @@
+cell.length_a
+cell.length_b
+cell.length_c
+cell.angle_alpha
+cell.angle_beta
+cell.angle_gamma
+
+symmetry.space_group_name_H-M
+
+entry.id
+
+struct.title
+
+pdbx_database_status.recvd_initial_deposition_date
+
+pdbx_audit_revision_history.revision_date
+
+struct_ncs_oper
+
+pdbx_struct_assembly_gen
+
+pdbx_struct_oper_list
+
+entity.id
+entity.type
+entity.pdbx_description
+
+entity_poly.entity_id
+entity_poly.pdbx_seq_one_letter_code
+entity_poly.pdbx_strand_id
+
+exptl.method
+
+refine.ls_d_res_low
+refine.ls_R_factor_R_free
+refine.ls_R_factor_R_work
+
+atom_site.pdbx_formal_charge
+atom_site.label_atom_id
+atom_site.type_symbol
+
+chem_comp.id
+chem_comp.type
+chem_comp.name
+
+chem_comp_bond
+
+atom_site.Cartn_x
+atom_site.Cartn_y
+atom_site.Cartn_z
+atom_site.B_iso_or_equiv
+atom_site.id
+atom_site.label_alt_id
+atom_site.occupancy
+atom_site.label_seq_id
+atom_site.label_comp_id
+
+struct_sheet_range.id
+struct_sheet_range.beg_label_asym_id
+struct_sheet_range.beg_label_seq_id
+struct_sheet_range.pdbx_beg_PDB_ins_code
+struct_sheet_range.end_label_asym_id
+struct_sheet_range.end_label_seq_id
+struct_sheet_range.pdbx_end_PDB_ins_code
+struct_conf.conf_type_id
+struct_conf.id
+struct_conf.beg_label_asym_id
+struct_conf.beg_label_seq_id
+struct_conf.pdbx_beg_PDB_ins_code
+struct_conf.end_label_asym_id
+struct_conf.end_label_seq_id
+struct_conf.pdbx_end_PDB_ins_code
+
+atom_site.pdbx_PDB_ins_code
+atom_site.label_asym_id
+atom_site.auth_asym_id

data/rcsb-graphql/codegen.js

@@ -1,22 +0,0 @@
-const { generate } = require('graphql-code-generator')
-const path = require('path')
-
-const basePath = path.join(__dirname, '..', '..', 'src', 'mol-model-props', 'rcsb', 'graphql')
-
-generate({
-    schema: 'http://rest-staging.rcsb.org/graphql',
-    documents: {
-        [path.join(basePath, 'symmetry.gql.ts')]: {
-            loader: path.join(__dirname, 'loader.js')
-        },
-    },
-    generates: {
-        [path.join(basePath, 'types.ts')]: {
-            plugins: ['time', 'typescript-common', 'typescript-client']
-        }
-    },
-    overwrite: true,
-    config: path.join(__dirname, 'codegen.json')
-}, true).then(
-    () => console.log('done')
-).catch(e => console.error(e))

data/rcsb-graphql/codegen.json

@@ -1,6 +0,0 @@
-{
-    "flattenTypes": true,
-    "generatorConfig": {
-        "immutableTypes": true
-    }
-}

data/rcsb-graphql/loader.js

@@ -1,14 +0,0 @@
-const { parse } = require('graphql');
-const { readFileSync } = require('fs');
-
-module.exports = function(docString, config) {
-    const str = readFileSync(docString, { encoding: 'utf-8' }).trim()
-                    .replace(/^export default `/, '')
-                    .replace(/`$/, '')
-    return [
-        {
-            filePath: docString,
-            content: parse(str)
-        }
-    ];
-};

docs/model-server/readme.md

@@ -6,133 +6,64 @@ Model Server is a tool for preprocessing and querying macromolecular structure d
 Installing and Running
 =====================
 
-Getting the code (use node 8+):
+Requires nodejs 8+.
+
+## From GitHub
+
 ```
 git clone https://github.com/molstar/molstar
 npm install
 ```
 
-Customize configuration at ``src/server/model/config.ts`` to point to your data and which custom properties to include (see the [Custom Properties](#custom-properties) section). Alternatively, the config can be edited in the compiled version in ``build/node_modules/servers/model/config.js``.
-
-Afterwards, build the project:
+Afterwards, build the project source:
 
 ```
-npm run build
+npm run build-tsc
 ```
 
-(or run watch mode for automatic rebuilds: ``npm run watch``)
+and run the server by 
 
-Running the server locally for testing:
 ```
-npm run model-server
-```
-or
-```
-node build/node_modules/servers/model/server
+node lib/servers/model/server/server
 ```
 
-In production it is a good idea to use a service that will keep the server running, such as [forever.js](https://github.com/foreverjs/forever).
+## From NPM
+
+```
+npm install --production molstar
+./model-server 
+```
+
+(or ``node node_modules\.bin\model-server`` in Windows).
+
+The NPM package contains all the tools mentioned here as "binaries":
+
+- ``model-server``
+- ``model-server-query``
+- ``model-server-preprocess``
 
 
-## Memory issues
+### Production use
+
+In production it is required to use a service that will keep the server running, such as [forever.js](https://github.com/foreverjs/forever).
+
+
+### Memory issues
 
 Sometimes nodejs might run into problems with memory. This is usually resolved by adding the ``--max-old-space-size=8192`` parameter.
 
-Preprocessor
-============
+## Preprocessor
 
-The preprocessor application allows to add custom data to CIF files and/or convert CIF to BinaryCIF. See the [Custom Properties](#custom-properties) section for providing custom properties.
+The preprocessor application allows to add custom data to CIF files and/or convert CIF to BinaryCIF. ``node lib/servers/servers/model/preprocess`` or ``model-server-preprocess`` binary from the NPM package.
 
-## Usage
 
-The app works in two modes: single files and folders.
+## Local Mode
 
-Single files:
-
-```
-node build\node_modules\servers\model\preprocess -i input.cif [-oc output.cif] [-ob output.bcif] [--cfg config.json]
-```
-
-Folder:
-```
-node build\node_modules\servers\model\preprocess -fin input_folder [-foc output_cif_folder] [-fob output_bcif_folder] [--cfg config.json]
-```
-
-## Config
-
-The config speficies the maximum number of processes to use (in case of folder processing) and defines sources and parameters for custom properties.
-
-Example:
-```json
-{
-    "numProcesses": 4,
-    "customProperties": {
-        "sources": [
-            "./properties/pdbe"
-        ],
-        "params": {
-            "PDBe": {
-                "UseFileSource": false,
-                "API": {
-                    "residuewise_outlier_summary": "https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry",
-                    "preferred_assembly": "https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary",
-                    "struct_ref_domain": "https://www.ebi.ac.uk/pdbe/api/mappings/sequence_domains"
-                }
-            }
-        }
-    }
-}
-```
+The server can be run in local/file based mode using ``node lib/servers/servers/model/query`` (``model-server-query`` binary from the NPM package).
 
 Custom Properties
 =================
 
-It is possible to provide property descriptors that transform data to internal representation and define how it should be exported into one or mode CIF categories. Examples of this are located in the ``mol-model-props`` module and are linked to the server in the config and ``servers/model/properties``.
+This feature is still in development.
 
-Local Mode
-==========
-
-The server can be run in local/file based mode:
-
-```
-node build/node_modules/servers/model/server jobs.json
-```
-
-where ``jobs.json`` is an array of
-
-```ts
-type LocalInput = {
-    input: string,
-    output: string,
-    query: QueryName,
-    modelNums?: number[],
-    params?: any,
-    binary?: boolean
-}[]
-```
-
-For example
-
-```json
-[
-  {
-    "input": "c:/test/quick/1tqn.cif",
-    "output": "c:/test/quick/localapi/1tqn_full.cif",
-    "query": "full"
-  },
-  {
-    "input": "c:/test/quick/1tqn.cif",
-    "output": "c:/test/quick/localapi/1tqn_full.bcif",
-    "query": "full",
-    "params": {}
-  },
-  {
-    "input": "c:/test/quick/1cbs_updated.cif",
-    "output": "c:/test/quick/localapi/1cbs_ligint.cif",
-    "query": "residueInteraction",
-    "params": {
-      "atom_site": { "label_comp_id": "REA" }
-    }
-  }
-]
-```
+It is possible to provide property descriptors that transform data to internal representation and define how it should be exported into one or mode CIF categories. Examples of this are located in the ``mol-model-props`` module and are linked to the server in the config and ``servers/model/properties``.

docs/volume-server/README.md

@@ -7,107 +7,64 @@ It uses the text based CIF and BinaryCIF formats to deliver the data to the clie
 
 For quick info about the benefits of using the server, check out the [examples](examples.md).
 
-Installing the Server 
+Installing and Running
 =====================
 
-- Install [Node.js](https://nodejs.org/en/) (tested on Node 6.* and 7.*; x64 version is strongly preferred).
-- Get the code.
-- Prepare the data.
-- Run the server.
+Requires nodejs 8+.
 
-Preparing the Data
-------------------
+## From GitHub
+
+```
+git clone https://github.com/molstar/molstar
+npm install
+```
+
+Afterwards, build the project source:
+
+```
+npm run build-tsc
+```
+
+and run the server by 
+
+```
+node lib/servers/servers/volume/server
+```
+
+## From NPM
+
+```
+npm install --production molstar
+./volume-server 
+```
+
+(or ``node node_modules\.bin\volume-server`` in Windows).
+
+The NPM package contains all the tools mentioned here as "binaries":
+
+- ``volume-server``
+- ``volume-server-pack``
+- ``volume-server-query``
+
+
+### Production use
+
+In production it is required to use a service that will keep the server running, such as [forever.js](https://github.com/foreverjs/forever).
+
+
+### Memory issues
+
+Sometimes nodejs might run into problems with memory. This is usually resolved by adding the ``--max-old-space-size=8192`` parameter.
+
+
+## Preparing the Data
 
 For the server to work, CCP4/MAP (models 0, 1, 2 are supported) input data need to be converted into a custom block format. 
-To achieve this, use the ``pack`` application.
+To achieve this, use the ``pack`` application (``node lib/servers/servers/volume/pack`` or ``volume-server-pack`` binary from the NPM package).
 
-- To prepare data from x-ray based methods, use: 
+## Local Mode
 
-    ```
-    node pack -xray main.ccp4 diff.ccp4 out.mdb
-    ```
-
-- For EM data, use:
-
-    ```
-    node pack -em em.map out.mdb
-    ```
-
-Running the Server
-------------------
-
-- Install production dependencies:
-
-   ```
-   npm install --only=production
-   ```
-
-- Update ``server-config.js`` to link to your data and optionally tweak the other parameters.
-
-- Run it:
-
-    ```
-    node server
-    ```
-
-    In production it is a good idea to use a service that will keep the server running, such as [forever.js](https://github.com/foreverjs/forever).
-
-### Local Mode
-
-The program ``local`` in the build folder can be used to query the data without running a http server.
-
-- ``node local`` prints the program usage.
-- ``node local jobs.json`` takes a list of jobs to execute in JSON format. A job entry is defined by this interface:
-
-    ```TypeScript
-    interface JobEntry {
-        source: {
-            filename: string,    
-            name: string,
-            id: string
-        },
-        query: {
-            kind: 'box' | 'cell',
-            space?: 'fractional' | 'cartesian',
-            bottomLeft?: number[],
-            topRight?: number[],
-        }
-        params: {
-            /** Determines the detail level as specified in server-config */
-            detail?: number,
-            /** 
-             * Determines the sampling level:
-             * 1: Original data
-             * 2: Downsampled by factor 1/2
-             * ...
-             * N: downsampled 1/2^(N-1)
-             */
-            forcedSamplingLevel?: number,
-            asBinary: boolean,
-        },
-        outputFolder: string
-    }
-    ```
-
-    Example ``jobs.json`` file content:
-
-    ```TypeScript
-    [{
-        source: {
-            filename: `g:/test/mdb/emd-8116.mdb`,
-            name: 'em',
-            id: '8116',
-        },
-        query: {
-            kind: 'cell'
-        },
-        params: {
-            detail: 4,
-            asBinary: true
-        },
-        outputFolder: 'g:/test/local-test'
-    }]
-    ```
+The program  ``lib/servers/servers/volume/pack`` (``volume-server-query`` in NPM package) can be used to query the data without running a http server.
 
 ## Navigating the Source Code
 
@@ -122,8 +79,8 @@ The source code is split into 2 mains parts: ``pack`` and ``server``:
 Consuming the Data 
 ==================
 
-The data can be consumed in any (modern) browser using the [CIFTools.js library](https://github.com/dsehnal/CIFTools.js) (or any other piece of code that can read text or binary CIF).
+The data can be consumed in any (modern) browser using the [ciftools library](https://github.com/molstar/ciftools) (or any other piece of code that can read text or binary CIF).
 
 The [Data Format](DataFormat.md) document gives a detailed description of the server response format.
 
-As a reference/example of the server usage, please see the implementation in [LiteMol](https://github.com/dsehnal/LiteMol) ([CIF.ts + Data.ts](https://github.com/dsehnal/LiteMol/tree/master/src/lib/Core/Formats/Density), [UI](https://github.com/dsehnal/LiteMol/tree/master/src/Viewer/Extensions/DensityStreaming)) or in Mol*.
+As a reference/example of the server usage is available in Mol* ``mol-plugin`` module.

examples/867861-core.cif

@@ -0,0 +1,884 @@
+####################################################################### 
+# 
+# This file contains crystal structure data downloaded from the 
+# Cambridge Structural Database (CSD) hosted by the Cambridge 
+# Crystallographic Data Centre (CCDC).
+# 
+# Full information about CCDC data access policies and citation 
+# guidelines are available at http://www.ccdc.cam.ac.uk/access/V1 
+# 
+# Audit and citation data items may have been added by the CCDC. 
+# Please retain this information to preserve the provenance of 
+# this file and to allow appropriate attribution of the data. 
+# 
+#######################################################################
+
+data_n1379
+_audit_block_doi                 10.5517/ccy42jn
+_database_code_depnum_ccdc_archive 'CCDC 867861'
+loop_
+_citation_id
+_citation_doi
+_citation_year
+1 10.1002/chem.201202070 2012
+_audit_update_record             
+;
+2012-02-20 deposited with the CCDC.
+2016-10-08 downloaded from the CCDC.
+;
+
+_audit_creation_method           SHELXL-97
+_chemical_name_systematic        
+;
+?
+;
+_chemical_name_common            ?
+_chemical_melting_point          ?
+_chemical_formula_moiety         'C76 H90 N10 O14 4(C2 F3 O2) 4(C2 H3 N)'
+_chemical_formula_sum            'C92 H102 F12 N14 O22'
+_chemical_formula_weight         1983.88
+
+loop_
+_atom_type_symbol
+_atom_type_description
+_atom_type_scat_dispersion_real
+_atom_type_scat_dispersion_imag
+_atom_type_scat_source
+C C 0.0181 0.0091 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+F F 0.0727 0.0534 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+
+_symmetry_cell_setting           Triclinic
+_symmetry_space_group_name_H-M   P-1
+
+loop_
+_symmetry_equiv_pos_as_xyz
+'x, y, z'
+'-x, -y, -z'
+
+_cell_length_a                   11.0829(8)
+_cell_length_b                   14.6829(10)
+_cell_length_c                   16.8532(17)
+_cell_angle_alpha                105.728(6)
+_cell_angle_beta                 100.310(6)
+_cell_angle_gamma                110.620(4)
+_cell_volume                     2353.3(3)
+_cell_formula_units_Z            1
+_cell_measurement_temperature    100(2)
+_cell_measurement_reflns_used    5934
+_cell_measurement_theta_min      2.86
+_cell_measurement_theta_max      64.30
+
+_exptl_crystal_description       plate
+_exptl_crystal_colour            violet
+_exptl_crystal_size_max          0.57
+_exptl_crystal_size_mid          0.18
+_exptl_crystal_size_min          0.05
+_exptl_crystal_density_meas      ?
+_exptl_crystal_density_diffrn    1.400
+_exptl_crystal_density_method    ?
+_exptl_crystal_F_000             1036
+_exptl_absorpt_coefficient_mu    0.995
+_exptl_absorpt_correction_type   integration
+_exptl_absorpt_correction_T_min  0.6022
+_exptl_absorpt_correction_T_max  0.9482
+_exptl_absorpt_process_details   'XPREP, face-indexed'
+
+_exptl_special_details           
+;
+?
+;
+
+_diffrn_ambient_temperature      100(2)
+_diffrn_radiation_wavelength     1.54178
+_diffrn_radiation_type           CuK\a
+_diffrn_radiation_source         microsource
+_diffrn_radiation_monochromator  'Quazar optics'
+_diffrn_measurement_device_type  'Bruker APEX-II CCD'
+_diffrn_measurement_method       '\f and \w scans'
+_diffrn_detector_area_resol_mean ?
+_diffrn_reflns_number            16613
+_diffrn_reflns_av_R_equivalents  0.1477
+_diffrn_reflns_av_sigmaI/netI    0.1112
+_diffrn_reflns_limit_h_min       -12
+_diffrn_reflns_limit_h_max       8
+_diffrn_reflns_limit_k_min       -17
+_diffrn_reflns_limit_k_max       17
+_diffrn_reflns_limit_l_min       -19
+_diffrn_reflns_limit_l_max       19
+_diffrn_reflns_theta_min         2.86
+_diffrn_reflns_theta_max         64.94
+_reflns_number_total             7680
+_reflns_number_gt                5560
+_reflns_threshold_expression     >2sigma(I)
+
+_computing_data_collection       'Bruker APEX2'
+_computing_cell_refinement       'Bruker SAINT'
+_computing_data_reduction        'Bruker SAINT'
+_computing_structure_solution    'SHELXS-97 (Sheldrick, 2008)'
+_computing_structure_refinement  'SHELXL-97 (Sheldrick, 2008)'
+_computing_molecular_graphics    'Bruker SHELXTL'
+_computing_publication_material  'Bruker SHELXTL'
+
+_refine_special_details          
+;
+Refinement of F^2^ against ALL reflections. The weighted R-factor wR and
+goodness of fit S are based on F^2^, conventional R-factors R are based
+on F, with F set to zero for negative F^2^. The threshold expression of
+F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is
+not relevant to the choice of reflections for refinement. R-factors based
+on F^2^ are statistically about twice as large as those based on F, and R-
+factors based on ALL data will be even larger.
+Rigid bond restraints (esd 0.002) were imposed on the displacement parameters,
+as well as restraints on similar amplitudes (esd 0.002) separated by less
+than 1.7 Ang. on C27, C29, and N102.
+Distance restraints were refined on the bond between C28 and C29.
+;
+
+_refine_ls_structure_factor_coef Fsqd
+_refine_ls_matrix_type           full
+_refine_ls_weighting_scheme      calc
+_refine_ls_weighting_details     
+'calc w=1/[\s^2^(Fo^2^)+(0.1912P)^2^+4.8134P] where P=(Fo^2^+2Fc^2^)/3'
+_atom_sites_solution_primary     direct
+_atom_sites_solution_secondary   difmap
+_atom_sites_solution_hydrogens   geom
+_refine_ls_hydrogen_treatment    mixed
+_refine_ls_extinction_method     none
+_refine_ls_extinction_coef       ?
+_refine_ls_number_reflns         7680
+_refine_ls_number_parameters     633
+_refine_ls_number_restraints     1
+_refine_ls_R_factor_all          0.1349
+_refine_ls_R_factor_gt           0.1101
+_refine_ls_wR_factor_ref         0.3402
+_refine_ls_wR_factor_gt          0.3102
+_refine_ls_goodness_of_fit_ref   1.089
+_refine_ls_restrained_S_all      1.096
+_refine_ls_shift/su_max          0.000
+_refine_ls_shift/su_mean         0.000
+
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_U_iso_or_equiv
+_atom_site_adp_type
+_atom_site_occupancy
+_atom_site_symmetry_multiplicity
+_atom_site_calc_flag
+_atom_site_refinement_flags
+_atom_site_disorder_assembly
+_atom_site_disorder_group
+C1 C -0.3373(4) -0.2086(3) -0.2547(3) 0.0229(10) Uani 1 1 d . . .
+H1 H -0.3820 -0.2827 -0.2795 0.027 Uiso 1 1 calc R . .
+C2 C -0.1956(4) -0.0511(3) -0.2602(3) 0.0215(10) Uani 1 1 d . . .
+H2 H -0.1401 -0.0147 -0.2886 0.026 Uiso 1 1 calc R . .
+C3 C -0.3583(4) -0.1574(3) -0.1814(3) 0.0213(9) Uani 1 1 d . . .
+H3 H -0.4168 -0.1960 -0.1558 0.026 Uiso 1 1 calc R . .
+C4 C -0.2146(4) 0.0039(3) -0.1873(3) 0.0180(9) Uani 1 1 d . . .
+H4 H -0.1736 0.0780 -0.1660 0.022 Uiso 1 1 calc R . .
+C5 C -0.2943(4) -0.0488(3) -0.1440(3) 0.0163(9) Uani 1 1 d . . .
+C6 C -0.3053(4) 0.0091(3) -0.0600(3) 0.0170(9) Uani 1 1 d . . .
+C7 C -0.3538(4) -0.0444(3) -0.0071(3) 0.0193(9) Uani 1 1 d . . .
+H7 H -0.3850 -0.1181 -0.0264 0.023 Uiso 1 1 calc R . .
+C8 C -0.2620(4) 0.1168(3) -0.0291(3) 0.0194(9) Uani 1 1 d . . .
+H8 H -0.2304 0.1553 -0.0640 0.023 Uiso 1 1 calc R . .
+C9 C -0.3563(4) 0.0094(3) 0.0725(3) 0.0218(10) Uani 1 1 d . . .
+H9 H -0.3904 -0.0276 0.1077 0.026 Uiso 1 1 calc R . .
+C10 C -0.2648(4) 0.1679(3) 0.0515(3) 0.0190(9) Uani 1 1 d . . .
+H10 H -0.2340 0.2416 0.0724 0.023 Uiso 1 1 calc R . .
+C11 C -0.3024(4) 0.1707(4) 0.1919(3) 0.0227(10) Uani 1 1 d . . .
+H11A H -0.3772 0.1277 0.2088 0.027 Uiso 1 1 calc R . .
+H11B H -0.3094 0.2371 0.1964 0.027 Uiso 1 1 calc R . .
+C12 C -0.1670(4) 0.1920(3) 0.2509(2) 0.0184(9) Uani 1 1 d . . .
+C13 C -0.1547(5) 0.1179(4) 0.2849(3) 0.0223(10) Uani 1 1 d . . .
+H13 H -0.2328 0.0589 0.2788 0.027 Uiso 1 1 calc R . .
+C14 C -0.0541(4) 0.2821(3) 0.2667(2) 0.0204(9) Uani 1 1 d . . .
+H14 H -0.0631 0.3352 0.2475 0.024 Uiso 1 1 calc R . .
+C15 C -0.0272(5) 0.1313(4) 0.3277(3) 0.0231(10) Uani 1 1 d . . .
+H15 H -0.0192 0.0806 0.3506 0.028 Uiso 1 1 calc R . .
+C16 C 0.0731(4) 0.2946(3) 0.3110(2) 0.0195(9) Uani 1 1 d . . .
+C17 C 0.0890(4) 0.2163(3) 0.3381(2) 0.0204(10) Uani 1 1 d . . .
+C18 C 0.2252(5) 0.2149(4) 0.3687(3) 0.0273(11) Uani 1 1 d . . .
+H18A H 0.2965 0.2872 0.3968 0.033 Uiso 1 1 calc R . .
+H18B H 0.2237 0.1802 0.4116 0.033 Uiso 1 1 calc R . .
+C19 C 0.2862(4) 0.4582(4) 0.3974(3) 0.0247(10) Uani 1 1 d . . .
+H19 H 0.3032 0.4532 0.4530 0.030 Uiso 1 1 calc R . .
+C20 C 0.3577(5) 0.5371(4) 0.3739(3) 0.0279(11) Uani 1 1 d . . .
+C21 C 0.4805(5) 0.6358(4) 0.4267(3) 0.0333(12) Uani 1 1 d . . .
+H21A H 0.4882 0.6869 0.3975 0.040 Uiso 1 1 calc R . .
+H21B H 0.4699 0.6656 0.4837 0.040 Uiso 1 1 calc R . .
+C22 C 0.6303(6) 0.5857(4) 0.3599(3) 0.0374(12) Uani 1 1 d . . .
+H22A H 0.6523 0.6416 0.3355 0.045 Uiso 1 1 calc R . .
+H22B H 0.5494 0.5242 0.3176 0.045 Uiso 1 1 calc R . .
+C23 C 0.7460(6) 0.5575(5) 0.3762(4) 0.0413(13) Uani 1 1 d . . .
+H23A H 0.7730 0.5406 0.3231 0.050 Uiso 1 1 calc R . .
+H23B H 0.8246 0.6169 0.4226 0.050 Uiso 1 1 calc R . .
+C24 C 0.7952(6) 0.4206(5) 0.3967(4) 0.0496(16) Uani 1 1 d . . .
+H24A H 0.8893 0.4743 0.4264 0.060 Uiso 1 1 calc R . .
+H24B H 0.7870 0.3874 0.3353 0.060 Uiso 1 1 calc R . .
+C25 C 0.7663(11) 0.3428(7) 0.4361(4) 0.074(3) Uani 1 1 d . . .
+H25A H 0.8372 0.3165 0.4378 0.089 Uiso 1 1 calc R . .
+H25B H 0.7691 0.3754 0.4965 0.089 Uiso 1 1 calc R . .
+C26 C 0.6441(8) 0.1838(7) 0.4342(5) 0.071(2) Uani 1 1 d . . .
+H26A H 0.7153 0.1600 0.4249 0.085 Uiso 1 1 calc R . .
+H26B H 0.6577 0.2137 0.4970 0.085 Uiso 1 1 calc R . .
+C27 C 0.5204(10) 0.1080(8) 0.3921(7) 0.125(5) Uani 1 1 d . . .
+H27A H 0.5220 0.0408 0.3913 0.150 Uiso 1 1 calc R . .
+H27B H 0.4964 0.1039 0.3313 0.150 Uiso 1 1 calc R . .
+C28 C 0.3730(9) 0.0886(7) 0.4988(5) 0.097(4) Uani 1 1 d D . .
+H28A H 0.4284 0.0506 0.5097 0.116 Uiso 1 1 calc R . .
+H28B H 0.4078 0.1526 0.5510 0.116 Uiso 1 1 calc R . .
+C29 C 0.2559(11) 0.033(2) 0.4964(8) 0.281(16) Uani 1 1 d D . .
+H29A H 0.2452 0.0690 0.5518 0.337 Uiso 1 1 calc R . .
+H29B H 0.2589 -0.0322 0.5000 0.337 Uiso 1 1 calc R . .
+C30 C 0.0569(12) -0.1026(9) 0.4169(5) 0.089(3) Uani 1 1 d . . .
+H30A H 0.0442 -0.1134 0.4708 0.107 Uiso 1 1 calc R . .
+H30B H 0.1035 -0.1448 0.3928 0.107 Uiso 1 1 calc R . .
+C31 C -0.0702(10) -0.1360(6) 0.3569(6) 0.083(3) Uani 1 1 d . . .
+H31A H -0.1307 -0.2064 0.3530 0.100 Uiso 1 1 calc R . .
+H31B H -0.1113 -0.0878 0.3776 0.100 Uiso 1 1 calc R . .
+C32 C -0.1964(9) -0.1774(5) 0.2168(5) 0.067(2) Uani 1 1 d . . .
+H32A H -0.2564 -0.2441 0.2195 0.080 Uiso 1 1 calc R . .
+H32B H -0.2342 -0.1258 0.2343 0.080 Uiso 1 1 calc R . .
+C33 C -0.1881(7) -0.1926(5) 0.1297(4) 0.0593(19) Uani 1 1 d . . .
+H33A H -0.2803 -0.2327 0.0880 0.071 Uiso 1 1 calc R . .
+H33B H -0.1354 -0.2340 0.1169 0.071 Uiso 1 1 calc R . .
+C34 C -0.0909(4) -0.0989(4) 0.0440(3) 0.0231(10) Uani 1 1 d . . .
+C35 C -0.1178(5) -0.1907(4) -0.0206(3) 0.0290(11) Uani 1 1 d . . .
+H35 H -0.1660 -0.2560 -0.0162 0.035 Uiso 1 1 calc R . .
+C36 C -0.0214(4) -0.0005(3) 0.0371(3) 0.0182(9) Uani 1 1 d . . .
+C37 C 0.0055(4) 0.0950(3) 0.1019(3) 0.0212(10) Uani 1 1 d . . .
+H37 H -0.0240 0.0948 0.1515 0.025 Uiso 1 1 calc R . .
+C38 C 0.0734(4) 0.1868(4) 0.0931(3) 0.0249(10) Uani 1 1 d . . .
+H38 H 0.0914 0.2503 0.1372 0.030 Uiso 1 1 calc R . .
+N1 N -0.2553(3) -0.1567(3) -0.2921(2) 0.0202(8) Uani 1 1 d . . .
+N2 N -0.3112(3) 0.1137(3) 0.1013(2) 0.0181(8) Uani 1 1 d . . .
+N3 N 0.1854(4) 0.3880(3) 0.3242(2) 0.0221(8) Uani 1 1 d . . .
+N4 N 0.1947(4) 0.4236(3) 0.2574(2) 0.0281(9) Uani 1 1 d . . .
+N5 N 0.2991(4) 0.5136(3) 0.2881(3) 0.0315(10) Uani 1 1 d . . .
+O1 O 0.6028(3) 0.6210(3) 0.4395(2) 0.0301(8) Uani 1 1 d . . .
+O2 O 0.7045(4) 0.4689(3) 0.4018(2) 0.0429(10) Uani 1 1 d . . .
+O3 O 0.6381(7) 0.2580(4) 0.3907(4) 0.0743(17) Uani 1 1 d . . .
+O4 O 0.4041(4) 0.1218(3) 0.4321(2) 0.0412(10) Uani 1 1 d . . .
+O5 O 0.1363(5) 0.0023(6) 0.4355(3) 0.0786(19) Uani 1 1 d . . .
+O6 O -0.0597(6) -0.1394(4) 0.2749(3) 0.0757(17) Uani 1 1 d . . .
+O7 O -0.1244(3) -0.0939(3) 0.1185(2) 0.0320(8) Uani 1 1 d . . .
+C101 C 0.6294(5) 0.3676(4) 0.1211(3) 0.0286(11) Uani 1 1 d . . .
+C102 C 0.5798(8) 0.4458(5) 0.1022(5) 0.066(2) Uani 1 1 d . . .
+C103 C 0.5077(5) 0.8961(4) 0.2466(3) 0.0342(12) Uani 1 1 d . . .
+C104 C 0.3819(8) 0.8078(6) 0.2433(5) 0.077(3) Uani 1 1 d . . .
+C105 C 0.0707(7) 0.4215(5) 0.0313(4) 0.0516(16) Uani 1 1 d . . .
+C106 C 0.2104(7) 0.4969(6) 0.0645(5) 0.066(2) Uani 1 1 d . . .
+H10A H 0.2627 0.4718 0.0303 0.099 Uiso 1 1 calc R . .
+H10B H 0.2471 0.5066 0.1251 0.099 Uiso 1 1 calc R . .
+H10C H 0.2161 0.5637 0.0606 0.099 Uiso 1 1 calc R . .
+C107 C 0.0569(7) 0.6249(7) 0.2999(5) 0.071(2) Uani 1 1 d . . .
+C108 C 0.0316(8) 0.5978(7) 0.2128(5) 0.077(2) Uani 1 1 d . . .
+H10D H 0.0994 0.5753 0.1954 0.115 Uiso 1 1 calc R . .
+H10E H 0.0360 0.6581 0.1969 0.115 Uiso 1 1 calc R . .
+H10F H -0.0588 0.5404 0.1833 0.115 Uiso 1 1 calc R . .
+O101 O 0.5421(4) 0.2774(3) 0.0882(3) 0.0463(10) Uani 1 1 d . . .
+O102 O 0.7472(4) 0.4014(3) 0.1666(3) 0.0485(11) Uani 1 1 d . . .
+O103 O 0.4882(4) 0.9389(3) 0.1955(2) 0.0356(9) Uani 1 1 d . . .
+O104 O 0.6107(4) 0.9176(3) 0.3029(3) 0.0517(11) Uani 1 1 d . . .
+F101 F 0.4877(8) 0.4530(7) 0.1408(4) 0.148(3) Uani 1 1 d . . .
+F102 F 0.5188(6) 0.4177(4) 0.0191(3) 0.105(2) Uani 1 1 d . . .
+F103 F 0.6733(8) 0.5407(3) 0.1298(5) 0.160(4) Uani 1 1 d . . .
+F104 F 0.2811(5) 0.7655(4) 0.1734(3) 0.098(2) Uani 1 1 d . . .
+F105 F 0.3328(8) 0.8406(9) 0.3070(4) 0.233(7) Uani 1 1 d . . .
+F106 F 0.4002(9) 0.7351(6) 0.2617(7) 0.224(6) Uani 1 1 d . . .
+N101 N -0.0392(7) 0.3613(5) 0.0045(4) 0.0715(19) Uani 1 1 d . . .
+N102 N 0.0774(10) 0.6479(13) 0.3716(6) 0.185(7) Uani 1 1 d . . .
+
+loop_
+_atom_site_aniso_label
+_atom_site_aniso_U_11
+_atom_site_aniso_U_22
+_atom_site_aniso_U_33
+_atom_site_aniso_U_23
+_atom_site_aniso_U_13
+_atom_site_aniso_U_12
+C1 0.015(2) 0.023(2) 0.022(2) -0.0003(18) -0.0032(18) 0.0097(17)
+C2 0.021(2) 0.032(2) 0.012(2) 0.0047(17) -0.0022(17) 0.0168(19)
+C3 0.0099(19) 0.030(2) 0.021(2) 0.0059(18) -0.0007(17) 0.0104(17)
+C4 0.017(2) 0.027(2) 0.0111(19) 0.0045(16) -0.0012(16) 0.0157(18)
+C5 0.0087(18) 0.025(2) 0.0134(19) 0.0028(16) -0.0032(15) 0.0121(16)
+C6 0.0075(18) 0.031(2) 0.014(2) 0.0067(17) -0.0017(15) 0.0130(17)
+C7 0.0074(18) 0.029(2) 0.019(2) 0.0047(17) 0.0003(16) 0.0093(17)
+C8 0.0135(19) 0.028(2) 0.013(2) 0.0039(17) -0.0035(16) 0.0120(17)
+C9 0.013(2) 0.031(2) 0.020(2) 0.0072(18) 0.0012(17) 0.0105(18)
+C10 0.0112(19) 0.029(2) 0.018(2) 0.0066(17) 0.0025(16) 0.0122(17)
+C11 0.019(2) 0.038(2) 0.014(2) 0.0056(18) 0.0059(17) 0.0178(19)
+C12 0.019(2) 0.029(2) 0.0068(18) -0.0007(16) 0.0013(16) 0.0169(18)
+C13 0.024(2) 0.030(2) 0.013(2) 0.0023(17) 0.0047(18) 0.0159(19)
+C14 0.027(2) 0.027(2) 0.0079(19) -0.0015(16) 0.0012(17) 0.0200(19)
+C15 0.030(2) 0.034(2) 0.012(2) 0.0056(17) 0.0059(18) 0.023(2)
+C16 0.023(2) 0.028(2) 0.0057(18) -0.0018(16) 0.0027(16) 0.0154(19)
+C17 0.024(2) 0.032(2) 0.0063(18) -0.0012(16) 0.0008(16) 0.0209(19)
+C18 0.028(2) 0.040(3) 0.010(2) -0.0024(18) -0.0038(18) 0.025(2)
+C19 0.023(2) 0.034(2) 0.012(2) -0.0015(18) -0.0024(17) 0.017(2)
+C20 0.024(2) 0.031(2) 0.019(2) 0.0008(19) -0.0030(19) 0.011(2)
+C21 0.027(3) 0.034(3) 0.028(3) -0.001(2) 0.001(2) 0.014(2)
+C22 0.038(3) 0.046(3) 0.027(3) 0.011(2) 0.010(2) 0.018(2)
+C23 0.039(3) 0.054(3) 0.033(3) 0.012(3) 0.015(2) 0.022(3)
+C24 0.051(3) 0.061(4) 0.034(3) -0.002(3) 0.006(3) 0.038(3)
+C25 0.145(8) 0.082(5) 0.039(4) 0.023(4) 0.042(5) 0.090(6)
+C26 0.068(5) 0.096(6) 0.055(4) 0.020(4) 0.007(4) 0.053(5)
+C27 0.105(7) 0.115(7) 0.120(8) -0.033(6) -0.051(6) 0.106(7)
+C28 0.082(6) 0.105(6) 0.049(4) 0.052(4) -0.036(4) -0.012(5)
+C29 0.074(7) 0.62(4) 0.114(10) 0.252(18) 0.001(7) 0.029(14)
+C30 0.149(9) 0.141(9) 0.054(5) 0.065(5) 0.057(6) 0.113(8)
+C31 0.110(7) 0.062(5) 0.082(6) 0.050(4) 0.030(5) 0.021(5)
+C32 0.094(6) 0.046(4) 0.061(4) 0.021(3) 0.040(4) 0.021(4)
+C33 0.056(4) 0.048(4) 0.046(4) 0.013(3) 0.018(3) -0.007(3)
+C34 0.014(2) 0.035(2) 0.014(2) 0.0059(18) -0.0019(17) 0.0096(18)
+C35 0.025(2) 0.032(2) 0.021(2) 0.0050(19) -0.0033(19) 0.010(2)
+C36 0.0082(18) 0.030(2) 0.0130(19) 0.0013(17) -0.0030(15) 0.0125(17)
+C37 0.017(2) 0.032(2) 0.013(2) -0.0004(17) -0.0039(16) 0.0181(19)
+C38 0.024(2) 0.029(2) 0.016(2) -0.0031(18) -0.0035(18) 0.017(2)
+N1 0.0187(18) 0.032(2) 0.0087(16) -0.0003(14) -0.0050(14) 0.0193(16)
+N2 0.0109(16) 0.033(2) 0.0095(16) 0.0031(14) -0.0003(13) 0.0141(15)
+N3 0.0216(18) 0.030(2) 0.0120(17) -0.0001(15) -0.0016(14) 0.0163(16)
+N4 0.029(2) 0.029(2) 0.0150(18) 0.0034(16) -0.0032(16) 0.0089(17)
+N5 0.033(2) 0.032(2) 0.021(2) 0.0036(17) -0.0041(17) 0.0140(18)
+O1 0.0235(17) 0.0363(18) 0.0205(16) 0.0026(14) 0.0003(13) 0.0105(14)
+O2 0.054(2) 0.060(2) 0.031(2) 0.0152(18) 0.0199(18) 0.040(2)
+O3 0.137(5) 0.064(3) 0.083(4) 0.044(3) 0.084(4) 0.073(4)
+O4 0.0309(19) 0.049(2) 0.043(2) 0.0191(18) -0.0025(16) 0.0215(17)
+O5 0.045(3) 0.155(6) 0.048(3) 0.062(3) 0.024(2) 0.031(3)
+O6 0.093(4) 0.048(3) 0.058(3) 0.026(2) -0.016(3) 0.012(3)
+O7 0.0255(17) 0.045(2) 0.0179(16) 0.0091(14) 0.0051(14) 0.0090(15)
+C101 0.033(3) 0.030(3) 0.021(2) 0.0047(19) 0.011(2) 0.014(2)
+C102 0.082(5) 0.053(4) 0.047(4) 0.000(3) -0.010(4) 0.039(4)
+C103 0.041(3) 0.035(3) 0.021(2) 0.008(2) -0.002(2) 0.017(2)
+C104 0.073(5) 0.069(5) 0.048(4) 0.042(4) -0.023(4) -0.012(4)
+C105 0.055(4) 0.045(3) 0.055(4) 0.018(3) 0.001(3) 0.028(3)
+C106 0.057(4) 0.060(4) 0.070(5) 0.018(4) 0.001(4) 0.026(4)
+C107 0.041(4) 0.113(7) 0.059(5) 0.035(4) 0.016(3) 0.028(4)
+C108 0.057(4) 0.081(5) 0.061(5) 0.019(4) 0.011(4) 0.003(4)
+O101 0.033(2) 0.038(2) 0.060(3) 0.0192(19) 0.0048(19) 0.0098(17)
+O102 0.041(2) 0.038(2) 0.053(2) 0.0099(18) -0.0001(19) 0.0125(18)
+O103 0.038(2) 0.043(2) 0.0269(18) 0.0176(16) 0.0086(15) 0.0154(17)
+O104 0.043(2) 0.055(2) 0.045(2) 0.023(2) -0.0085(19) 0.0130(19)
+F101 0.159(6) 0.220(8) 0.099(4) 0.007(5) 0.016(4) 0.166(7)
+F102 0.148(5) 0.067(3) 0.074(3) 0.030(2) -0.031(3) 0.045(3)
+F103 0.177(7) 0.030(2) 0.180(6) 0.007(3) -0.087(5) 0.030(3)
+F104 0.073(3) 0.084(3) 0.072(3) 0.054(2) -0.037(2) -0.028(2)
+F105 0.132(6) 0.291(12) 0.076(4) 0.035(6) 0.034(4) -0.108(8)
+F106 0.161(7) 0.104(5) 0.286(11) 0.146(7) -0.127(7) -0.041(5)
+N101 0.063(4) 0.050(3) 0.082(4) 0.025(3) -0.013(3) 0.018(3)
+N102 0.077(6) 0.35(2) 0.072(6) 0.079(9) 0.015(5) 0.027(9)
+
+_geom_special_details            
+;
+All esds (except the esd in the dihedral angle between two l.s. planes)
+are estimated using the full covariance matrix. The cell esds are taken
+into account individually in the estimation of esds in distances, angles
+and torsion angles; correlations between esds in cell parameters are only
+used when they are defined by crystal symmetry. An approximate (isotropic)
+treatment of cell esds is used for estimating esds involving l.s. planes.
+;
+
+loop_
+_geom_bond_atom_site_label_1
+_geom_bond_atom_site_label_2
+_geom_bond_distance
+_geom_bond_site_symmetry_2
+_geom_bond_publ_flag
+C1 N1 1.334(6) . ?
+C1 C3 1.367(6) . ?
+C1 H1 0.9500 . ?
+C2 N1 1.353(6) . ?
+C2 C4 1.371(6) . ?
+C2 H2 0.9500 . ?
+C3 C5 1.394(6) . ?
+C3 H3 0.9500 . ?
+C4 C5 1.403(6) . ?
+C4 H4 0.9500 . ?
+C5 C6 1.490(6) . ?
+C6 C8 1.390(6) . ?
+C6 C7 1.397(6) . ?
+C7 C9 1.371(6) . ?
+C7 H7 0.9500 . ?
+C8 C10 1.375(6) . ?
+C8 H8 0.9500 . ?
+C9 N2 1.342(6) . ?
+C9 H9 0.9500 . ?
+C10 N2 1.352(6) . ?
+C10 H10 0.9500 . ?
+C11 N2 1.497(5) . ?
+C11 C12 1.517(6) . ?
+C11 H11A 0.9900 . ?
+C11 H11B 0.9900 . ?
+C12 C14 1.382(6) . ?
+C12 C13 1.396(6) . ?
+C13 C15 1.384(6) . ?
+C13 H13 0.9500 . ?
+C14 C16 1.395(6) . ?
+C14 H14 0.9500 . ?
+C15 C17 1.383(7) . ?
+C15 H15 0.9500 . ?
+C16 C17 1.400(6) . ?
+C16 N3 1.418(6) . ?
+C17 C18 1.515(6) . ?
+C18 N1 1.505(5) 2 ?
+C18 H18A 0.9900 . ?
+C18 H18B 0.9900 . ?
+C19 N3 1.356(5) . ?
+C19 C20 1.357(7) . ?
+C19 H19 0.9500 . ?
+C20 N5 1.366(6) . ?
+C20 C21 1.491(6) . ?
+C21 O1 1.435(6) . ?
+C21 H21A 0.9900 . ?
+C21 H21B 0.9900 . ?
+C22 O1 1.429(6) . ?
+C22 C23 1.484(8) . ?
+C22 H22A 0.9900 . ?
+C22 H22B 0.9900 . ?
+C23 O2 1.431(7) . ?
+C23 H23A 0.9900 . ?
+C23 H23B 0.9900 . ?
+C24 O2 1.420(7) . ?
+C24 C25 1.442(11) . ?
+C24 H24A 0.9900 . ?
+C24 H24B 0.9900 . ?
+C25 O3 1.416(11) . ?
+C25 H25A 0.9900 . ?
+C25 H25B 0.9900 . ?
+C26 C27 1.331(12) . ?
+C26 O3 1.481(9) . ?
+C26 H26A 0.9900 . ?
+C26 H26B 0.9900 . ?
+C27 O4 1.605(11) . ?
+C27 H27A 0.9900 . ?
+C27 H27B 0.9900 . ?
+C28 C29 1.252(12) . ?
+C28 O4 1.391(8) . ?
+C28 H28A 0.9900 . ?
+C28 H28B 0.9900 . ?
+C29 O5 1.361(11) . ?
+C29 H29A 0.9900 . ?
+C29 H29B 0.9900 . ?
+C30 O5 1.388(12) . ?
+C30 C31 1.407(13) . ?
+C30 H30A 0.9900 . ?
+C30 H30B 0.9900 . ?
+C31 O6 1.396(10) . ?
+C31 H31A 0.9900 . ?
+C31 H31B 0.9900 . ?
+C32 C33 1.449(9) . ?
+C32 O6 1.464(10) . ?
+C32 H32A 0.9900 . ?
+C32 H32B 0.9900 . ?
+C33 O7 1.453(7) . ?
+C33 H33A 0.9900 . ?
+C33 H33B 0.9900 . ?
+C34 O7 1.362(5) . ?
+C34 C35 1.377(7) . ?
+C34 C36 1.425(7) . ?
+C35 C38 1.404(7) 2 ?
+C35 H35 0.9500 . ?
+C36 C36 1.417(9) 2 ?
+C36 C37 1.417(6) . ?
+C37 C38 1.356(7) . ?
+C37 H37 0.9500 . ?
+C38 C35 1.404(7) 2 ?
+C38 H38 0.9500 . ?
+N1 C18 1.505(5) 2 ?
+N3 N4 1.370(5) . ?
+N4 N5 1.300(6) . ?
+C101 O101 1.227(6) . ?
+C101 O102 1.232(6) . ?
+C101 C102 1.518(9) . ?
+C102 F103 1.301(9) . ?
+C102 F102 1.318(8) . ?
+C102 F101 1.324(11) . ?
+C103 O104 1.224(6) . ?
+C103 O103 1.227(6) . ?
+C103 C104 1.512(9) . ?
+C104 F106 1.260(10) . ?
+C104 F104 1.290(7) . ?
+C104 F105 1.341(14) . ?
+C105 N101 1.139(9) . ?
+C105 C106 1.443(10) . ?
+C106 H10A 0.9800 . ?
+C106 H10B 0.9800 . ?
+C106 H10C 0.9800 . ?
+C107 N102 1.118(11) . ?
+C107 C108 1.360(11) . ?
+C108 H10D 0.9800 . ?
+C108 H10E 0.9800 . ?
+C108 H10F 0.9800 . ?
+
+loop_
+_geom_angle_atom_site_label_1
+_geom_angle_atom_site_label_2
+_geom_angle_atom_site_label_3
+_geom_angle
+_geom_angle_site_symmetry_1
+_geom_angle_site_symmetry_3
+_geom_angle_publ_flag
+N1 C1 C3 121.3(4) . . ?
+N1 C1 H1 119.3 . . ?
+C3 C1 H1 119.3 . . ?
+N1 C2 C4 120.4(4) . . ?
+N1 C2 H2 119.8 . . ?
+C4 C2 H2 119.8 . . ?
+C1 C3 C5 120.4(4) . . ?
+C1 C3 H3 119.8 . . ?
+C5 C3 H3 119.8 . . ?
+C2 C4 C5 120.4(4) . . ?
+C2 C4 H4 119.8 . . ?
+C5 C4 H4 119.8 . . ?
+C3 C5 C4 116.9(4) . . ?
+C3 C5 C6 121.8(4) . . ?
+C4 C5 C6 121.2(4) . . ?
+C8 C6 C7 117.6(4) . . ?
+C8 C6 C5 122.4(4) . . ?
+C7 C6 C5 119.9(4) . . ?
+C9 C7 C6 120.1(4) . . ?
+C9 C7 H7 120.0 . . ?
+C6 C7 H7 120.0 . . ?
+C10 C8 C6 120.4(4) . . ?
+C10 C8 H8 119.8 . . ?
+C6 C8 H8 119.8 . . ?
+N2 C9 C7 120.9(4) . . ?
+N2 C9 H9 119.5 . . ?
+C7 C9 H9 119.5 . . ?
+N2 C10 C8 120.3(4) . . ?
+N2 C10 H10 119.8 . . ?
+C8 C10 H10 119.8 . . ?
+N2 C11 C12 107.7(3) . . ?
+N2 C11 H11A 110.2 . . ?
+C12 C11 H11A 110.2 . . ?
+N2 C11 H11B 110.2 . . ?
+C12 C11 H11B 110.2 . . ?
+H11A C11 H11B 108.5 . . ?
+C14 C12 C13 119.9(4) . . ?
+C14 C12 C11 120.0(4) . . ?
+C13 C12 C11 120.0(4) . . ?
+C15 C13 C12 119.2(4) . . ?
+C15 C13 H13 120.4 . . ?
+C12 C13 H13 120.4 . . ?
+C12 C14 C16 119.7(4) . . ?
+C12 C14 H14 120.2 . . ?
+C16 C14 H14 120.2 . . ?
+C17 C15 C13 122.1(4) . . ?
+C17 C15 H15 118.9 . . ?
+C13 C15 H15 118.9 . . ?
+C14 C16 C17 121.1(4) . . ?
+C14 C16 N3 117.0(4) . . ?
+C17 C16 N3 121.8(4) . . ?
+C15 C17 C16 117.5(4) . . ?
+C15 C17 C18 119.0(4) . . ?
+C16 C17 C18 123.2(4) . . ?
+N1 C18 C17 109.0(3) 2 . ?
+N1 C18 H18A 109.9 2 . ?
+C17 C18 H18A 109.9 . . ?
+N1 C18 H18B 109.9 2 . ?
+C17 C18 H18B 109.9 . . ?
+H18A C18 H18B 108.3 . . ?
+N3 C19 C20 105.0(4) . . ?
+N3 C19 H19 127.5 . . ?
+C20 C19 H19 127.5 . . ?
+C19 C20 N5 108.7(4) . . ?
+C19 C20 C21 129.7(4) . . ?
+N5 C20 C21 121.6(5) . . ?
+O1 C21 C20 113.0(4) . . ?
+O1 C21 H21A 109.0 . . ?
+C20 C21 H21A 109.0 . . ?
+O1 C21 H21B 109.0 . . ?
+C20 C21 H21B 109.0 . . ?
+H21A C21 H21B 107.8 . . ?
+O1 C22 C23 109.1(4) . . ?
+O1 C22 H22A 109.9 . . ?
+C23 C22 H22A 109.9 . . ?
+O1 C22 H22B 109.9 . . ?
+C23 C22 H22B 109.9 . . ?
+H22A C22 H22B 108.3 . . ?
+O2 C23 C22 108.0(5) . . ?
+O2 C23 H23A 110.1 . . ?
+C22 C23 H23A 110.1 . . ?
+O2 C23 H23B 110.1 . . ?
+C22 C23 H23B 110.1 . . ?
+H23A C23 H23B 108.4 . . ?
+O2 C24 C25 110.9(6) . . ?
+O2 C24 H24A 109.5 . . ?
+C25 C24 H24A 109.5 . . ?
+O2 C24 H24B 109.5 . . ?
+C25 C24 H24B 109.5 . . ?
+H24A C24 H24B 108.0 . . ?
+O3 C25 C24 112.1(6) . . ?
+O3 C25 H25A 109.2 . . ?
+C24 C25 H25A 109.2 . . ?
+O3 C25 H25B 109.2 . . ?
+C24 C25 H25B 109.2 . . ?
+H25A C25 H25B 107.9 . . ?
+C27 C26 O3 98.8(7) . . ?
+C27 C26 H26A 112.0 . . ?
+O3 C26 H26A 112.0 . . ?
+C27 C26 H26B 112.0 . . ?
+O3 C26 H26B 112.0 . . ?
+H26A C26 H26B 109.7 . . ?
+C26 C27 O4 114.9(7) . . ?
+C26 C27 H27A 108.5 . . ?
+O4 C27 H27A 108.5 . . ?
+C26 C27 H27B 108.5 . . ?
+O4 C27 H27B 108.5 . . ?
+H27A C27 H27B 107.5 . . ?
+C29 C28 O4 124.1(6) . . ?
+C29 C28 H28A 106.3 . . ?
+O4 C28 H28A 106.3 . . ?
+C29 C28 H28B 106.3 . . ?
+O4 C28 H28B 106.3 . . ?
+H28A C28 H28B 106.4 . . ?
+C28 C29 O5 128.7(9) . . ?
+C28 C29 H29A 105.1 . . ?
+O5 C29 H29A 105.1 . . ?
+C28 C29 H29B 105.1 . . ?
+O5 C29 H29B 105.1 . . ?
+H29A C29 H29B 105.9 . . ?
+O5 C30 C31 110.9(6) . . ?
+O5 C30 H30A 109.5 . . ?
+C31 C30 H30A 109.5 . . ?
+O5 C30 H30B 109.5 . . ?
+C31 C30 H30B 109.5 . . ?
+H30A C30 H30B 108.1 . . ?
+O6 C31 C30 111.7(8) . . ?
+O6 C31 H31A 109.3 . . ?
+C30 C31 H31A 109.3 . . ?
+O6 C31 H31B 109.3 . . ?
+C30 C31 H31B 109.3 . . ?
+H31A C31 H31B 107.9 . . ?
+C33 C32 O6 108.1(6) . . ?
+C33 C32 H32A 110.1 . . ?
+O6 C32 H32A 110.1 . . ?
+C33 C32 H32B 110.1 . . ?
+O6 C32 H32B 110.1 . . ?
+H32A C32 H32B 108.4 . . ?
+C32 C33 O7 111.8(5) . . ?
+C32 C33 H33A 109.3 . . ?
+O7 C33 H33A 109.3 . . ?
+C32 C33 H33B 109.3 . . ?
+O7 C33 H33B 109.3 . . ?
+H33A C33 H33B 107.9 . . ?
+O7 C34 C35 124.0(4) . . ?
+O7 C34 C36 115.2(4) . . ?
+C35 C34 C36 120.8(4) . . ?
+C34 C35 C38 119.3(5) . 2 ?
+C34 C35 H35 120.4 . . ?
+C38 C35 H35 120.4 2 . ?
+C36 C36 C37 119.6(5) 2 . ?
+C36 C36 C34 118.4(5) 2 . ?
+C37 C36 C34 121.9(4) . . ?
+C38 C37 C36 119.9(4) . . ?
+C38 C37 H37 120.1 . . ?
+C36 C37 H37 120.1 . . ?
+C37 C38 C35 122.0(4) . 2 ?
+C37 C38 H38 119.0 . . ?
+C35 C38 H38 119.0 2 . ?
+C1 N1 C2 120.4(4) . . ?
+C1 N1 C18 120.5(4) . 2 ?
+C2 N1 C18 119.1(4) . 2 ?
+C9 N2 C10 120.6(4) . . ?
+C9 N2 C11 119.3(4) . . ?
+C10 N2 C11 119.9(4) . . ?
+C19 N3 N4 110.0(4) . . ?
+C19 N3 C16 130.4(4) . . ?
+N4 N3 C16 119.3(3) . . ?
+N5 N4 N3 107.0(3) . . ?
+N4 N5 C20 109.4(4) . . ?
+C22 O1 C21 112.0(4) . . ?
+C24 O2 C23 111.2(5) . . ?
+C25 O3 C26 101.1(6) . . ?
+C28 O4 C27 123.6(7) . . ?
+C29 O5 C30 109.4(11) . . ?
+C31 O6 C32 107.8(7) . . ?
+C34 O7 C33 116.5(4) . . ?
+O101 C101 O102 129.2(5) . . ?
+O101 C101 C102 113.1(5) . . ?
+O102 C101 C102 117.7(5) . . ?
+F103 C102 F102 108.6(7) . . ?
+F103 C102 F101 104.9(7) . . ?
+F102 C102 F101 105.0(7) . . ?
+F103 C102 C101 114.3(6) . . ?
+F102 C102 C101 112.4(5) . . ?
+F101 C102 C101 111.0(7) . . ?
+O104 C103 O103 130.2(5) . . ?
+O104 C103 C104 115.4(5) . . ?
+O103 C103 C104 114.3(5) . . ?
+F106 C104 F104 107.4(7) . . ?
+F106 C104 F105 99.1(9) . . ?
+F104 C104 F105 105.1(9) . . ?
+F106 C104 C103 115.6(8) . . ?
+F104 C104 C103 117.1(5) . . ?
+F105 C104 C103 110.5(7) . . ?
+N101 C105 C106 179.3(9) . . ?
+C105 C106 H10A 109.5 . . ?
+C105 C106 H10B 109.5 . . ?
+H10A C106 H10B 109.5 . . ?
+C105 C106 H10C 109.5 . . ?
+H10A C106 H10C 109.5 . . ?
+H10B C106 H10C 109.5 . . ?
+N102 C107 C108 179.3(14) . . ?
+C107 C108 H10D 109.5 . . ?
+C107 C108 H10E 109.5 . . ?
+H10D C108 H10E 109.5 . . ?
+C107 C108 H10F 109.5 . . ?
+H10D C108 H10F 109.5 . . ?
+H10E C108 H10F 109.5 . . ?
+
+loop_
+_geom_torsion_atom_site_label_1
+_geom_torsion_atom_site_label_2
+_geom_torsion_atom_site_label_3
+_geom_torsion_atom_site_label_4
+_geom_torsion
+_geom_torsion_site_symmetry_1
+_geom_torsion_site_symmetry_2
+_geom_torsion_site_symmetry_3
+_geom_torsion_site_symmetry_4
+_geom_torsion_publ_flag
+N1 C1 C3 C5 0.3(6) . . . . ?
+N1 C2 C4 C5 1.1(6) . . . . ?
+C1 C3 C5 C4 3.1(6) . . . . ?
+C1 C3 C5 C6 -174.6(4) . . . . ?
+C2 C4 C5 C3 -3.8(5) . . . . ?
+C2 C4 C5 C6 173.9(3) . . . . ?
+C3 C5 C6 C8 -168.8(4) . . . . ?
+C4 C5 C6 C8 13.6(5) . . . . ?
+C3 C5 C6 C7 14.7(5) . . . . ?
+C4 C5 C6 C7 -162.9(4) . . . . ?
+C8 C6 C7 C9 -0.6(5) . . . . ?
+C5 C6 C7 C9 176.0(3) . . . . ?
+C7 C6 C8 C10 1.4(5) . . . . ?
+C5 C6 C8 C10 -175.2(3) . . . . ?
+C6 C7 C9 N2 -0.7(6) . . . . ?
+C6 C8 C10 N2 -0.8(6) . . . . ?
+N2 C11 C12 C14 88.4(5) . . . . ?
+N2 C11 C12 C13 -87.7(5) . . . . ?
+C14 C12 C13 C15 -5.7(6) . . . . ?
+C11 C12 C13 C15 170.4(4) . . . . ?
+C13 C12 C14 C16 4.9(6) . . . . ?
+C11 C12 C14 C16 -171.2(4) . . . . ?
+C12 C13 C15 C17 0.2(6) . . . . ?
+C12 C14 C16 C17 1.4(6) . . . . ?
+C12 C14 C16 N3 179.1(3) . . . . ?
+C13 C15 C17 C16 5.9(6) . . . . ?
+C13 C15 C17 C18 -167.5(4) . . . . ?
+C14 C16 C17 C15 -6.7(6) . . . . ?
+N3 C16 C17 C15 175.7(4) . . . . ?
+C14 C16 C17 C18 166.4(4) . . . . ?
+N3 C16 C17 C18 -11.2(6) . . . . ?
+C15 C17 C18 N1 83.8(5) . . . 2 ?
+C16 C17 C18 N1 -89.3(5) . . . 2 ?
+N3 C19 C20 N5 0.2(5) . . . . ?
+N3 C19 C20 C21 -179.5(5) . . . . ?
+C19 C20 C21 O1 78.8(7) . . . . ?
+N5 C20 C21 O1 -100.9(6) . . . . ?
+O1 C22 C23 O2 66.1(5) . . . . ?
+O2 C24 C25 O3 65.4(6) . . . . ?
+O3 C26 C27 O4 -86.2(9) . . . . ?
+O4 C28 C29 O5 -7(4) . . . . ?
+O5 C30 C31 O6 69.5(9) . . . . ?
+O6 C32 C33 O7 -71.5(8) . . . . ?
+O7 C34 C35 C38 -177.1(4) . . . 2 ?
+C36 C34 C35 C38 1.4(6) . . . 2 ?
+O7 C34 C36 C36 177.6(4) . . . 2 ?
+C35 C34 C36 C36 -1.1(7) . . . 2 ?
+O7 C34 C36 C37 -2.5(6) . . . . ?
+C35 C34 C36 C37 178.9(4) . . . . ?
+C36 C36 C37 C38 -0.8(7) 2 . . . ?
+C34 C36 C37 C38 179.2(4) . . . . ?
+C36 C37 C38 C35 0.5(6) . . . 2 ?
+C3 C1 N1 C2 -3.1(6) . . . . ?
+C3 C1 N1 C18 175.3(4) . . . 2 ?
+C4 C2 N1 C1 2.4(6) . . . . ?
+C4 C2 N1 C18 -176.0(3) . . . 2 ?
+C7 C9 N2 C10 1.4(6) . . . . ?
+C7 C9 N2 C11 -173.8(3) . . . . ?
+C8 C10 N2 C9 -0.6(6) . . . . ?
+C8 C10 N2 C11 174.5(3) . . . . ?
+C12 C11 N2 C9 85.7(4) . . . . ?
+C12 C11 N2 C10 -89.6(4) . . . . ?
+C20 C19 N3 N4 -0.2(5) . . . . ?
+C20 C19 N3 C16 -174.0(4) . . . . ?
+C14 C16 N3 C19 129.4(5) . . . . ?
+C17 C16 N3 C19 -52.9(6) . . . . ?
+C14 C16 N3 N4 -43.9(5) . . . . ?
+C17 C16 N3 N4 133.8(4) . . . . ?
+C19 N3 N4 N5 0.2(5) . . . . ?
+C16 N3 N4 N5 174.8(4) . . . . ?
+N3 N4 N5 C20 -0.1(5) . . . . ?
+C19 C20 N5 N4 -0.1(6) . . . . ?
+C21 C20 N5 N4 179.7(4) . . . . ?
+C23 C22 O1 C21 -171.9(4) . . . . ?
+C20 C21 O1 C22 63.3(6) . . . . ?
+C25 C24 O2 C23 170.3(5) . . . . ?
+C22 C23 O2 C24 164.7(4) . . . . ?
+C24 C25 O3 C26 170.9(5) . . . . ?
+C27 C26 O3 C25 177.5(7) . . . . ?
+C29 C28 O4 C27 -129(2) . . . . ?
+C26 C27 O4 C28 -85.6(11) . . . . ?
+C28 C29 O5 C30 136(3) . . . . ?
+C31 C30 O5 C29 177.4(11) . . . . ?
+C30 C31 O6 C32 178.6(7) . . . . ?
+C33 C32 O6 C31 -173.5(6) . . . . ?
+C35 C34 O7 C33 2.2(7) . . . . ?
+C36 C34 O7 C33 -176.4(5) . . . . ?
+C32 C33 O7 C34 169.3(6) . . . . ?
+O101 C101 C102 F103 -174.2(7) . . . . ?
+O102 C101 C102 F103 6.5(10) . . . . ?
+O101 C101 C102 F102 -49.8(9) . . . . ?
+O102 C101 C102 F102 130.9(7) . . . . ?
+O101 C101 C102 F101 67.5(7) . . . . ?
+O102 C101 C102 F101 -111.9(7) . . . . ?
+O104 C103 C104 F106 -34.8(12) . . . . ?
+O103 C103 C104 F106 149.3(9) . . . . ?
+O104 C103 C104 F104 -163.1(8) . . . . ?
+O103 C103 C104 F104 21.0(11) . . . . ?
+O104 C103 C104 F105 76.7(10) . . . . ?
+O103 C103 C104 F105 -99.2(8) . . . . ?
+
+_diffrn_measured_fraction_theta_max 0.961
+_diffrn_reflns_theta_full        64.94
+_diffrn_measured_fraction_theta_full 0.961
+_refine_diff_density_max         1.693
+_refine_diff_density_min         -0.992
+_refine_diff_density_rms         0.109
+
+# start Validation Reply Form
+_vrf_PLAT213_I                   
+;
+PROBLEM: Atom C5 has ADP max/min Ratio ..... 5.1 oblat
+RESPONSE: The atoms of the glycol chain and of the CBPQT4+ ring showed elongated
+displacement parameters. Attempts to model this disorder did not significantly
+improve the refinement.
+;
+_vrf_PLAT222_I                   
+;
+PROBLEM: Large Non-Solvent H Uiso(max)/Uiso(min) .. 10.0 Ratio
+RESPONSE: Hydrogen atoms were refined as riding models with their isotropic
+displacement parameters linked to their parent atoms.
+In this case the parent atom exhibits disorder with an elongated
+displacement parameter and therefore the riding hydrogen atom is also large.
+;
+_vrf_PLAT241_I                   
+;
+PROBLEM: Check High Ueq as Compared to Neighbors for C27
+RESPONSE: C27 and C29 are part of the disordered glycol chain, however they
+are bonded to C26 and O5 which are relatively well-ordered parts of the
+structure.
+;
+
+# end Validation Reply Form
+
+
+

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.3.2",
+  "version": "0.7.1-dev.3",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -11,27 +11,47 @@
     "url": "https://github.com/molstar/molstar/issues"
   },
   "scripts": {
-    "lint": "tslint src/**/*.ts",
+    "lint": "eslint ./**/*.{ts,tsx}",
+    "lint-fix": "eslint ./**/*.{ts,tsx} --fix",
     "test": "npm run lint && jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
-    "build-tsc": "tsc",
-    "build-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,ico}\" lib/",
-    "build-webpack": "webpack --mode production",
-    "watch": "concurrently --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack\"",
-    "watch-tsc": "tsc -watch",
-    "watch-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,ico}\" lib/ --watch",
+    "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
+    "build-tsc": "tsc --incremental && tsc --build tsconfig.servers.json --incremental",
+    "build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
+    "build-webpack": "webpack --mode production --config ./webpack.config.production.js",
+    "build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
+    "watch": "concurrently -c \"green,green,gray,gray\" --names \"tsc,srv,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-servers\" \"npm:watch-extra\" \"npm:watch-webpack\"",
+    "watch-viewer": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer\"",
+    "watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
+    "watch-tsc": "tsc --watch --incremental",
+    "watch-servers": "tsc --build tsconfig.servers.json --watch --incremental",
+    "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
     "watch-webpack": "webpack -w --mode development --display minimal",
+    "watch-webpack-viewer": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.js",
+    "watch-webpack-viewer-debug": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.debug.js",
     "serve": "http-server -p 1338",
-    "model-server": "node lib/servers/model/server.js",
-    "model-server-watch": "nodemon --watch lib lib/servers/model/server.js",
-    "volume-server": "node lib/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort  1336",
+    "model-server": "node lib/servers/servers/model/server.js",
+    "model-server-watch": "nodemon --watch lib lib/servers/servers/model/server.js",
+    "volume-server-test": "node lib/servers/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
+    "plugin-state": "node lib/servers/servers/plugin-state/index.js",
     "preversion": "npm run test",
-    "postversion": "git push && git push --tags",
-    "prepublishOnly": "npm run test && npm run build"
+    "version": "npm run build",
+    "postversion": "git push && git push --tags"
   },
   "files": [
-    "lib/"
+    "lib/",
+    "build/viewer/"
   ],
+  "bin": {
+    "cif2bcif": "lib/apps/cif2bcif/index.js",
+    "cifschema": "lib/apps/cifschema/index.js",
+    "model-server": "lib/servers/servers/model/server.js",
+    "model-server-query": "lib/servers/servers/model/query.js",
+    "model-server-preprocess": "lib/servers/servers/model/preprocess.js",
+    "volume-server": "lib/servers/servers/volume/server.js",
+    "volume-server-query": "lib/servers/servers/volume/query.js",
+    "volume-server-pack": "lib/servers/servers/volume/pack.js"
+  },
   "nodemonConfig": {
     "ignoreRoot": [
       "./node_modules",
@@ -63,56 +83,66 @@
   ],
   "license": "MIT",
   "devDependencies": {
+    "@graphql-codegen/add": "^1.13.5",
+    "@graphql-codegen/cli": "^1.13.5",
+    "@graphql-codegen/time": "^1.13.5",
+    "@graphql-codegen/typescript": "^1.13.5",
+    "@graphql-codegen/typescript-graphql-files-modules": "^1.13.5",
+    "@graphql-codegen/typescript-graphql-request": "^1.13.5",
+    "@graphql-codegen/typescript-operations": "^1.13.5",
+    "@types/cors": "^2.8.6",
+    "@typescript-eslint/eslint-plugin": "^2.32.0",
+    "@typescript-eslint/parser": "^2.32.0",
     "benchmark": "^2.1.4",
-    "circular-dependency-plugin": "^5.2.0",
-    "concurrently": "^5.0.0",
-    "cpx": "^1.5.0",
-    "css-loader": "^3.2.0",
+    "concurrently": "^5.2.0",
+    "cpx2": "^2.0.0",
+    "css-loader": "^3.5.3",
+    "eslint": "^7.0.0",
     "extra-watch-webpack-plugin": "^1.0.3",
-    "file-loader": "^4.2.0",
-    "fs-extra": "^8.1.0",
-    "graphql-code-generator": "^0.18.2",
-    "graphql-codegen-time": "^0.18.2",
-    "graphql-codegen-typescript-template": "^0.18.2",
-    "http-server": "^0.11.1",
-    "jest": "^24.9.0",
-    "jest-raw-loader": "^1.0.1",
-    "mini-css-extract-plugin": "^0.8.0",
-    "node-sass": "^4.12.0",
-    "raw-loader": "^3.1.0",
-    "resolve-url-loader": "^3.1.0",
-    "sass-loader": "^8.0.0",
-    "simple-git": "^1.126.0",
-    "style-loader": "^1.0.0",
-    "ts-jest": "^24.1.0",
-    "tslint": "^5.20.0",
-    "typescript": "^3.6.4",
-    "webpack": "^4.41.0",
-    "webpack-cli": "^3.3.9"
+    "file-loader": "^6.0.0",
+    "fs-extra": "^9.0.0",
+    "graphql": "^15.0.0",
+    "http-server": "^0.12.3",
+    "jest": "^26.0.1",
+    "mini-css-extract-plugin": "^0.9.0",
+    "node-sass": "^4.14.1",
+    "raw-loader": "^4.0.1",
+    "sass-loader": "^8.0.2",
+    "simple-git": "^2.4.0",
+    "style-loader": "^1.2.1",
+    "ts-jest": "^25.5.1",
+    "typescript": "^3.8.3",
+    "webpack": "^4.43.0",
+    "webpack-cli": "^3.3.11",
+    "webpack-version-file-plugin": "^0.4.0"
   },
   "dependencies": {
-    "@types/argparse": "^1.0.36",
+    "@material-ui/core": "^4.9.13",
+    "@material-ui/icons": "^4.9.1",
+    "@types/argparse": "^1.0.38",
     "@types/benchmark": "^1.0.31",
-    "@types/compression": "1.0.1",
-    "@types/express": "^4.17.1",
-    "@types/jest": "^24.0.18",
-    "@types/node": "^12.7.12",
-    "@types/node-fetch": "^2.5.2",
-    "@types/react": "^16.9.5",
-    "@types/react-dom": "^16.9.1",
-    "@types/swagger-ui-dist": "3.0.3",
-    "@types/webgl2": "0.0.5",
+    "@types/compression": "1.7.0",
+    "@types/express": "^4.17.6",
+    "@types/jest": "^25.2.1",
+    "@types/node": "^13.13.5",
+    "@types/node-fetch": "^2.5.7",
+    "@types/react": "^16.9.35",
+    "@types/react-dom": "^16.9.8",
+    "@types/swagger-ui-dist": "3.0.5",
     "argparse": "^1.0.10",
+    "body-parser": "^1.19.0",
     "compression": "^1.7.4",
+    "cors": "^2.8.5",
     "express": "^4.17.1",
-    "graphql": "^14.5.8",
+    "immer": "^6.0.5",
     "immutable": "^3.8.2",
     "node-fetch": "^2.6.0",
-    "react": "^16.10.2",
-    "react-dom": "^16.10.2",
-    "rxjs": "^6.5.3",
-    "swagger-ui-dist": "^3.23.11",
-    "util.promisify": "^1.0.0",
+    "react": "^16.13.1",
+    "react-dom": "^16.13.1",
+    "rxjs": "^6.5.5",
+    "swagger-ui-dist": "^3.25.2",
+    "tslib": "^1.11.2",
+    "util.promisify": "^1.0.1",
     "xhr2": "^0.2.0"
   }
 }

src/apps/basic-wrapper/controls.tsx

@@ -1,30 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { PluginUIComponent } from '../../mol-plugin/ui/base';
-import * as React from 'react';
-import { TransformUpdaterControl } from '../../mol-plugin/ui/state/update-transform';
-
-export class BasicWrapperControls extends PluginUIComponent {
-
-    render() {
-        return <div style={{ overflowY: 'auto', display: 'block', height: '100%' }}>
-            <TransformUpdaterControl nodeRef='asm' />
-            <TransformUpdaterControl nodeRef='seq-visual' header={{ name: 'Sequence Visual' }} />
-            <TransformUpdaterControl nodeRef='het-visual' header={{ name: 'HET Visual' }} />
-            <TransformUpdaterControl nodeRef='water-visual' header={{ name: 'Water Visual' }} initiallyCollapsed={true} />
-            <TransformUpdaterControl nodeRef='ihm-visual' header={{ name: 'I/HM Visual' }} initiallyCollapsed={true} />
-        </div>;
-    }
-}
-
-export class CustomToastMessage extends PluginUIComponent {
-    render() {
-        return <>
-            Custom <i>Toast</i> content. No timeout.
-        </>;
-    }
-}

src/apps/basic-wrapper/helpers.ts

@@ -1,94 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
-import { StateTransforms } from '../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { StateBuilder } from '../../mol-state';
-import Expression from '../../mol-script/language/expression';
-import { BuiltInColorThemeName } from '../../mol-theme/color';
-type SupportedFormats = 'cif' | 'pdb'
-
-export namespace StateHelper {
-    export function download(b: StateBuilder.To<PSO.Root>, url: string, ref?: string) {
-        return b.apply(StateTransforms.Data.Download, { url, isBinary: false }, { ref });
-    }
-
-    export function getModel(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, modelIndex = 0) {
-        const parsed = format === 'cif'
-            ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
-            : b.apply(StateTransforms.Model.TrajectoryFromPDB);
-
-        return parsed.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex });
-    }
-
-    export function structure(b: StateBuilder.To<PSO.Molecule.Model>) {
-        return b.apply(StateTransforms.Model.StructureFromModel, { tags: 'structure' })
-    };
-
-    export function selectChain(b: StateBuilder.To<PSO.Molecule.Structure>, auth_asym_id: string) {
-        const expression = MS.struct.generator.atomGroups({
-            'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.auth_asym_id(), auth_asym_id])
-        })
-        return b.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression, label: `Chain ${auth_asym_id}` });
-    }
-
-    export function select(b: StateBuilder.To<PSO.Molecule.Structure>, expression: Expression) {
-        return b.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression });
-    }
-
-    export function selectSurroundingsOfFirstResidue(b: StateBuilder.To<PSO.Molecule.Structure>, comp_id: string, radius: number) {
-        const expression = MS.struct.modifier.includeSurroundings({
-            0: MS.struct.filter.first([
-                MS.struct.generator.atomGroups({
-                    'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
-                    'group-by': MS.struct.atomProperty.macromolecular.residueKey()
-                })
-            ]),
-            radius
-        })
-        return b.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression, label: `Surr. ${comp_id} (${radius} ang)` });
-    }
-
-    export function identityTransform(b: StateBuilder.To<PSO.Molecule.Structure>, m: Mat4) {
-        return b.apply(StateTransforms.Model.TransformStructureConformation,
-            { axis: Vec3.create(1, 0, 0), angle: 0, translation: Vec3.zero() },
-            { tags: 'transform' });
-    }
-
-    export function transform(b: StateBuilder.To<PSO.Molecule.Structure>, matrix: Mat4) {
-        return b.apply(StateTransforms.Model.TransformStructureConformationByMatrix, { matrix }, { tags: 'transform' });
-    }
-
-    export function assemble(b: StateBuilder.To<PSO.Molecule.Model>, id?: string) {
-        return b.apply(StateTransforms.Model.StructureAssemblyFromModel, { id: id || 'deposited' }, { tags: 'asm' })
-    }
-
-    export function visual(ctx: PluginContext, visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'cartoon'), { tags: 'seq-visual' });
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick'), { tags: 'het-visual' });
-        // visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' })
-        //     .apply(StateTransforms.Representation.StructureRepresentation3D,
-        //         StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick', { alpha: 0.51 }), { tags: 'water-visual' });
-        return visualRoot;
-    }
-
-    export function ballsAndSticks(ctx: PluginContext, visualRoot: StateBuilder.To<PSO.Molecule.Structure>, expression: Expression, coloring?: BuiltInColorThemeName) {
-        visualRoot
-            .apply(StateTransforms.Model.StructureSelectionFromExpression, { expression })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick', void 0, coloring), { tags: 'het-visual' });
-        return visualRoot;
-    }
-
-}

src/apps/basic-wrapper/index.ts

@@ -1,183 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import './index.html'
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/command';
-import { StateTransforms } from '../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
-import { Color } from '../../mol-util/color';
-import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
-import { AnimateModelIndex } from '../../mol-plugin/state/animation/built-in';
-import { StateBuilder, StateTransform } from '../../mol-state';
-import { StripedResidues } from './coloring';
-// import { BasicWrapperControls } from './controls';
-import { StaticSuperpositionTestData, buildStaticSuperposition, dynamicSuperpositionTest } from './superposition';
-import { PDBeStructureQualityReport } from '../../mol-plugin/behavior/dynamic/custom-props';
-import { CustomToastMessage } from './controls';
-require('mol-plugin/skin/light.scss')
-
-type SupportedFormats = 'cif' | 'pdb'
-type LoadParams = { url: string, format?: SupportedFormats, assemblyId?: string }
-
-class BasicWrapper {
-    plugin: PluginContext;
-
-    init(target: string | HTMLElement) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec,
-            layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
-                },
-                controls: {
-                    // left: 'none',
-                    // right: BasicWrapperControls
-                }
-            }
-        });
-
-        this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.add(StripedResidues.Descriptor.name, StripedResidues.colorTheme!);
-        this.plugin.lociLabels.addProvider(StripedResidues.labelProvider);
-        this.plugin.customModelProperties.register(StripedResidues.propertyProvider);
-    }
-
-    private download(b: StateBuilder.To<PSO.Root>, url: string) {
-        return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
-    }
-
-    private parse(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, assemblyId: string) {
-        const parsed = format === 'cif'
-            ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
-            : b.apply(StateTransforms.Model.TrajectoryFromPDB);
-
-        return parsed
-            .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
-            .apply(StateTransforms.Model.CustomModelProperties, { properties: [StripedResidues.Descriptor.name] }, { ref: 'props', state: { isGhost: false } })
-            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
-    }
-
-    private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'cartoon'), { ref: 'seq-visual' });
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'ball-and-stick'), { ref: 'het-visual' });
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'ball-and-stick', { alpha: 0.51 }), { ref: 'water-visual' });
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'spheres' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'spacefill'), { ref: 'ihm-visual' });
-        return visualRoot;
-    }
-
-    private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
-    async load({ url, format = 'cif', assemblyId = '' }: LoadParams) {
-        let loadType: 'full' | 'update' = 'full';
-
-        const state = this.plugin.state.dataState;
-
-        if (this.loadedParams.url !== url || this.loadedParams.format !== format) {
-            loadType = 'full';
-        } else if (this.loadedParams.url === url) {
-            if (state.select('asm').length > 0) loadType = 'update';
-        }
-
-        let tree: StateBuilder.Root;
-        if (loadType === 'full') {
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
-            tree = state.build();
-            this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
-        } else {
-            tree = state.build();
-            tree.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
-        }
-
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
-        this.loadedParams = { url, format, assemblyId };
-        PluginCommands.Camera.Reset.dispatch(this.plugin, { });
-    }
-
-    setBackground(color: number) {
-        const renderer = this.plugin.canvas3d.props.renderer;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
-    }
-
-    toggleSpin() {
-        const trackball = this.plugin.canvas3d.props.trackball;
-        const spinning = trackball.spin;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
-        if (!spinning) PluginCommands.Camera.Reset.dispatch(this.plugin, { });
-    }
-
-    animate = {
-        modelIndex: {
-            maxFPS: 8,
-            onceForward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }) },
-            onceBackward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }) },
-            palindrome: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }) },
-            loop: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }) },
-            stop: () => this.plugin.state.animation.stop()
-        }
-    }
-
-    coloring = {
-        applyStripes: async () => {
-            const state = this.plugin.state.dataState;
-
-            const visuals = state.selectQ(q => q.ofTransformer(StateTransforms.Representation.StructureRepresentation3D));
-            const tree = state.build();
-            const colorTheme = { name: StripedResidues.Descriptor.name, params: this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.get(StripedResidues.Descriptor.name).defaultValues };
-
-            for (const v of visuals) {
-                tree.to(v).update(old => ({ ...old, colorTheme }));
-            }
-
-            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
-        }
-    }
-
-    tests = {
-        staticSuperposition: async () => {
-            const state = this.plugin.state.dataState;
-            const tree = buildStaticSuperposition(this.plugin, StaticSuperpositionTestData);
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: StateTransform.RootRef });
-            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
-        },
-        dynamicSuperposition: async () => {
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.plugin.state.dataState, ref: StateTransform.RootRef });
-            await dynamicSuperpositionTest(this.plugin, ['1tqn', '2hhb', '4hhb'], 'HEM');
-        },
-        toggleValidationTooltip: async () => {
-            const state = this.plugin.state.behaviorState;
-            const tree = state.build().to(PDBeStructureQualityReport.id).update(PDBeStructureQualityReport, p => ({ ...p, showTooltip: !p.showTooltip }));
-            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
-        },
-        showToasts: () => {
-            PluginCommands.Toast.Show.dispatch(this.plugin, {
-                title: 'Toast 1',
-                message: 'This is an example text, timeout 3s',
-                key: 'toast-1',
-                timeoutMs: 3000
-            });
-            PluginCommands.Toast.Show.dispatch(this.plugin, {
-                title: 'Toast 2',
-                message: CustomToastMessage,
-                key: 'toast-2'
-            });
-        },
-        hideToasts: () => {
-            PluginCommands.Toast.Hide.dispatch(this.plugin, { key: 'toast-1' });
-            PluginCommands.Toast.Hide.dispatch(this.plugin, { key: 'toast-2' });
-        }
-    }
-}
-
-(window as any).BasicMolStarWrapper = new BasicWrapper();

src/apps/basic-wrapper/superposition.ts

@@ -1,108 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-// TODO: move to an "example"
-
-import { PluginContext } from '../../mol-plugin/context';
-import { Mat4 } from '../../mol-math/linear-algebra';
-import { StateHelper } from './helpers';
-import { PluginCommands } from '../../mol-plugin/command';
-import { StateSelection, StateBuilder } from '../../mol-state';
-import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { compile } from '../../mol-script/runtime/query/compiler';
-import { StructureSelection, QueryContext } from '../../mol-model/structure';
-import { superposeStructures } from '../../mol-model/structure/structure/util/superposition';
-import Expression from '../../mol-script/language/expression';
-
-export type SuperpositionTestInput = {
-    pdbId: string,
-    auth_asym_id: string,
-    matrix: Mat4
-}[];
-
-// function getAxisAngleTranslation(m: Mat4) {
-//     const translation = Mat4.getTranslation(Vec3.zero(), m);
-//     const axis = Vec3.zero();
-//     const angle = 180 / Math.PI * Quat.getAxisAngle(axis, Mat4.getRotation(Quat.zero(), m));
-//     return { translation, axis, angle };
-// }
-
-export function buildStaticSuperposition(ctx: PluginContext, src: SuperpositionTestInput) {
-    const b = ctx.state.dataState.build().toRoot();
-    for (const s of src) {
-        StateHelper.visual(ctx,
-            StateHelper.transform(
-                StateHelper.selectChain(
-                    StateHelper.structure(
-                        StateHelper.getModel(StateHelper.download(b, `https://www.ebi.ac.uk/pdbe/static/entry/${s.pdbId}_updated.cif`), 'cif')),
-                    s.auth_asym_id
-                ),
-                s.matrix
-            )
-        );
-    }
-    return b;
-}
-
-export const StaticSuperpositionTestData: SuperpositionTestInput = [
-    { pdbId: '1aj5', auth_asym_id: 'A', matrix: Mat4.identity() },
-    { pdbId: '1df0', auth_asym_id: 'B', matrix: Mat4.ofRows(
-        [[0.406, 0.879, 0.248, -200.633],
-         [0.693, -0.473, 0.544, 73.403],
-         [0.596, -0.049, -0.802, -14.209],
-         [0, 0, 0, 1]] )},
-    { pdbId: '1dvi', auth_asym_id: 'A', matrix: Mat4.ofRows(
-        [[-0.053, -0.077, 0.996, -45.633],
-         [-0.312, 0.949, 0.057, -12.255],
-         [-0.949, -0.307, -0.074, 53.562],
-         [0, 0, 0, 1]] )}
-];
-
-export async function dynamicSuperpositionTest(ctx: PluginContext, src: string[], comp_id: string) {
-    const state = ctx.state.dataState;
-
-    const structures = state.build().toRoot();
-    for (const s of src) {
-        StateHelper.structure(
-            StateHelper.getModel(StateHelper.download(structures, `https://www.ebi.ac.uk/pdbe/static/entry/${s}_updated.cif`), 'cif'));
-    }
-
-    await PluginCommands.State.Update.dispatch(ctx, { state, tree: structures });
-
-    const pivot = MS.struct.filter.first([
-        MS.struct.generator.atomGroups({
-            'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
-            'group-by': MS.struct.atomProperty.macromolecular.residueKey()
-        })
-    ]);
-    const rest = MS.struct.modifier.exceptBy({
-        0: MS.struct.generator.all(),
-        by: pivot
-    });
-
-    const query = compile<StructureSelection>(pivot);
-    const xs = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure));
-    const selections = xs.map(s => StructureSelection.toLoci(query(new QueryContext(s.obj!.data))));
-
-    const transforms = superposeStructures(selections);
-    const visuals = state.build();
-
-    siteVisual(ctx, StateHelper.selectSurroundingsOfFirstResidue(visuals.to(xs[0].transform.ref), 'HEM', 7), pivot, rest);
-    for (let i = 1; i < selections.length; i++) {
-        const root = visuals.to(xs[i].transform.ref);
-        siteVisual(ctx,
-            StateHelper.transform(StateHelper.selectSurroundingsOfFirstResidue(root, 'HEM', 7), transforms[i - 1].bTransform),
-            pivot, rest);
-    }
-
-    await PluginCommands.State.Update.dispatch(ctx, { state, tree: visuals });
-}
-
-function siteVisual(ctx: PluginContext, b: StateBuilder.To<PSO.Molecule.Structure>, pivot: Expression, rest: Expression) {
-    StateHelper.ballsAndSticks(ctx, b, pivot, 'residue-name');
-    StateHelper.ballsAndSticks(ctx, b, rest, 'uniform');
-}

src/apps/chem-comp-bond/create-table.ts

@@ -4,57 +4,57 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import * as argparse from 'argparse'
-import * as util from 'util'
-import * as path from 'path'
-import * as fs from 'fs'
-import * as zlib from 'zlib'
-import fetch from 'node-fetch'
-require('util.promisify').shim()
-const readFile = util.promisify(fs.readFile)
-const writeFile = util.promisify(fs.writeFile)
+import * as argparse from 'argparse';
+import * as util from 'util';
+import * as path from 'path';
+import * as fs from 'fs';
+import * as zlib from 'zlib';
+import fetch from 'node-fetch';
+require('util.promisify').shim();
+const readFile = util.promisify(fs.readFile);
+const writeFile = util.promisify(fs.writeFile);
 
-import { Progress } from '../../mol-task'
-import { Database, Table, DatabaseCollection } from '../../mol-data/db'
-import { CIF } from '../../mol-io/reader/cif'
-import { CifWriter } from '../../mol-io/writer/cif'
-import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd'
-import { SetUtils } from '../../mol-util/set'
-import { DefaultMap } from '../../mol-util/map'
+import { Progress } from '../../mol-task';
+import { Database, Table, DatabaseCollection } from '../../mol-data/db';
+import { CIF } from '../../mol-io/reader/cif';
+import { CifWriter } from '../../mol-io/writer/cif';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+import { SetUtils } from '../../mol-util/set';
+import { DefaultMap } from '../../mol-util/map';
 import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
 
 export async function ensureAvailable(path: string, url: string) {
     if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
-        console.log(`downloading ${url}...`)
-        const data = await fetch(url)
+        console.log(`downloading ${url}...`);
+        const data = await fetch(url);
         if (!fs.existsSync(DATA_DIR)) {
             fs.mkdirSync(DATA_DIR);
         }
         if (url.endsWith('.gz')) {
-            await writeFile(path, zlib.gunzipSync(await data.buffer()))
+            await writeFile(path, zlib.gunzipSync(await data.buffer()));
         } else {
-            await writeFile(path, await data.text())
+            await writeFile(path, await data.text());
         }
-        console.log(`done downloading ${url}`)
+        console.log(`done downloading ${url}`);
     }
 }
 
 export async function ensureDataAvailable() {
-    await ensureAvailable(CCD_PATH, CCD_URL)
-    await ensureAvailable(PVCD_PATH, PVCD_URL)
+    await ensureAvailable(CCD_PATH, CCD_URL);
+    await ensureAvailable(PVCD_PATH, PVCD_URL);
 }
 
 export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
-    const parsed = await parseCif(await readFile(path, 'utf8'))
-    return CIF.toDatabaseCollection(schema, parsed.result)
+    const parsed = await parseCif(await readFile(path, 'utf8'));
+    return CIF.toDatabaseCollection(schema, parsed.result);
 }
 
 export async function readCCD() {
-    return readFileAsCollection(CCD_PATH, CCD_Schema)
+    return readFileAsCollection(CCD_PATH, CCD_Schema);
 }
 
 export async function readPVCD() {
-    return readFileAsCollection(PVCD_PATH, CCD_Schema)
+    return readFileAsCollection(PVCD_PATH, CCD_Schema);
 }
 
 async function parseCif(data: string | Uint8Array) {
@@ -63,12 +63,12 @@ async function parseCif(data: string | Uint8Array) {
     const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
     console.timeEnd('parse cif');
     if (parsed.isError) throw parsed;
-    return parsed
+    return parsed;
 }
 
 export function getEncodedCif(name: string, database: Database<Database.Schema>, binary = false) {
     const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
-    CifWriter.Encoder.writeDatabase(encoder, name, database)
+    CifWriter.Encoder.writeDatabase(encoder, name, database);
     return encoder.getData();
 }
 
@@ -76,58 +76,58 @@ type CCB = Table<CCD_Schema['chem_comp_bond']>
 type CCA = Table<CCD_Schema['chem_comp_atom']>
 
 function ccbKey(compId: string, atomId1: string, atomId2: string) {
-    return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`
+    return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`;
 }
 
 function addChemCompBondToSet(set: Set<string>, ccb: CCB) {
     for (let i = 0, il = ccb._rowCount; i < il; ++i) {
-        set.add(ccbKey(ccb.comp_id.value(i), ccb.atom_id_1.value(i), ccb.atom_id_2.value(i)))
+        set.add(ccbKey(ccb.comp_id.value(i), ccb.atom_id_1.value(i), ccb.atom_id_2.value(i)));
     }
-    return set
+    return set;
 }
 
 function addChemCompAtomToSet(set: Set<string>, cca: CCA) {
     for (let i = 0, il = cca._rowCount; i < il; ++i) {
-        set.add(cca.atom_id.value(i))
+        set.add(cca.atom_id.value(i));
     }
-    return set
+    return set;
 }
 
 function checkAddingBondsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
-    const ccbSetByParent = DefaultMap<string, Set<string>>(() => new Set())
+    const ccbSetByParent = DefaultMap<string, Set<string>>(() => new Set());
 
     for (const k in pvcd) {
-        const { chem_comp, chem_comp_bond } = pvcd[k]
+        const { chem_comp, chem_comp_bond } = pvcd[k];
         if (chem_comp_bond._rowCount) {
-            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0)
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
             if (parentIds.length === 0) {
-                const set = ccbSetByParent.getDefault(chem_comp.id.value(0))
-                addChemCompBondToSet(set, chem_comp_bond)
+                const set = ccbSetByParent.getDefault(chem_comp.id.value(0));
+                addChemCompBondToSet(set, chem_comp_bond);
             } else {
                 for (let i = 0, il = parentIds.length; i < il; ++i) {
-                    const parentId = parentIds[i]
-                    const set = ccbSetByParent.getDefault(parentId)
-                    addChemCompBondToSet(set, chem_comp_bond)
+                    const parentId = parentIds[i];
+                    const set = ccbSetByParent.getDefault(parentId);
+                    addChemCompBondToSet(set, chem_comp_bond);
                 }
             }
         }
     }
 
     for (const k in pvcd) {
-        const { chem_comp, chem_comp_atom, chem_comp_bond } = pvcd[k]
+        const { chem_comp, chem_comp_atom, chem_comp_bond } = pvcd[k];
         if (chem_comp_bond._rowCount) {
-            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0)
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
             if (parentIds.length > 0) {
                 for (let i = 0, il = parentIds.length; i < il; ++i) {
-                    const entryBonds = addChemCompBondToSet(new Set<string>(), chem_comp_bond)
-                    const entryAtoms = addChemCompAtomToSet(new Set<string>(), chem_comp_atom)
-                    const extraBonds = SetUtils.difference(ccbSetByParent.get(parentIds[i])!, entryBonds)
+                    const entryBonds = addChemCompBondToSet(new Set<string>(), chem_comp_bond);
+                    const entryAtoms = addChemCompAtomToSet(new Set<string>(), chem_comp_atom);
+                    const extraBonds = SetUtils.difference(ccbSetByParent.get(parentIds[i])!, entryBonds);
                     extraBonds.forEach(bk => {
-                        const [a1, a2] = bk.split('|')
+                        const [a1, a2] = bk.split('|');
                         if (entryAtoms.has(a1) && entryAtoms.has(a2)) {
-                            console.error(`Adding all PVCD bonds would wrongly add bond ${bk} for ${k}`)
+                            console.error(`Adding all PVCD bonds would wrongly add bond ${bk} for ${k}`);
                         }
-                    })
+                    });
                 }
             }
         }
@@ -135,51 +135,51 @@ function checkAddingBondsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
 }
 
 async function createBonds() {
-    await ensureDataAvailable()
-    const ccd = await readCCD()
-    const pvcd = await readPVCD()
+    await ensureDataAvailable();
+    const ccd = await readCCD();
+    const pvcd = await readPVCD();
 
-    const ccbSet = new Set<string>()
+    const ccbSet = new Set<string>();
 
-    const comp_id: string[] = []
-    const atom_id_1: string[] = []
-    const atom_id_2: string[] = []
-    const value_order: string[] = []
-    const pdbx_aromatic_flag: string[] = []
-    const pdbx_stereo_config: string[] = []
-    const molstar_protonation_variant: string[] = []
+    const comp_id: string[] = [];
+    const atom_id_1: string[] = [];
+    const atom_id_2: string[] = [];
+    const value_order: typeof mmCIF_chemCompBond_schema['value_order']['T'][] = [];
+    const pdbx_aromatic_flag: typeof mmCIF_chemCompBond_schema['pdbx_aromatic_flag']['T'][] = [];
+    const pdbx_stereo_config: typeof mmCIF_chemCompBond_schema['pdbx_stereo_config']['T'][] = [];
+    const molstar_protonation_variant: string[] = [];
 
     function addBonds(compId: string, ccb: CCB, protonationVariant: boolean) {
         for (let i = 0, il = ccb._rowCount; i < il; ++i) {
-            const atomId1 = ccb.atom_id_1.value(i)
-            const atomId2 = ccb.atom_id_2.value(i)
-            const k = ccbKey(compId, atomId1, atomId2)
+            const atomId1 = ccb.atom_id_1.value(i);
+            const atomId2 = ccb.atom_id_2.value(i);
+            const k = ccbKey(compId, atomId1, atomId2);
             if (!ccbSet.has(k)) {
-                atom_id_1.push(atomId1)
-                atom_id_2.push(atomId2)
-                comp_id.push(compId)
-                value_order.push(ccb.value_order.value(i))
-                pdbx_aromatic_flag.push(ccb.pdbx_aromatic_flag.value(i))
-                pdbx_stereo_config.push(ccb.pdbx_stereo_config.value(i))
-                molstar_protonation_variant.push(protonationVariant ? 'Y' : 'N')
-                ccbSet.add(k)
+                atom_id_1.push(atomId1);
+                atom_id_2.push(atomId2);
+                comp_id.push(compId);
+                value_order.push(ccb.value_order.value(i));
+                pdbx_aromatic_flag.push(ccb.pdbx_aromatic_flag.value(i));
+                pdbx_stereo_config.push(ccb.pdbx_stereo_config.value(i));
+                molstar_protonation_variant.push(protonationVariant ? 'Y' : 'N');
+                ccbSet.add(k);
             }
         }
     }
 
     // check adding bonds from PVCD
-    checkAddingBondsFromPVCD(pvcd)
+    checkAddingBondsFromPVCD(pvcd);
 
     // add bonds from PVCD
     for (const k in pvcd) {
-        const { chem_comp, chem_comp_bond } = pvcd[k]
+        const { chem_comp, chem_comp_bond } = pvcd[k];
         if (chem_comp_bond._rowCount) {
-            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0)
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
             if (parentIds.length === 0) {
-                addBonds(chem_comp.id.value(0), chem_comp_bond, false)
+                addBonds(chem_comp.id.value(0), chem_comp_bond, false);
             } else {
                 for (let i = 0, il = parentIds.length; i < il; ++i) {
-                    addBonds(parentIds[i], chem_comp_bond, true)
+                    addBonds(parentIds[i], chem_comp_bond, true);
                 }
             }
         }
@@ -187,47 +187,47 @@ async function createBonds() {
 
     // add bonds from CCD
     for (const k in ccd) {
-        const { chem_comp, chem_comp_bond } = ccd[k]
+        const { chem_comp, chem_comp_bond } = ccd[k];
         if (chem_comp_bond._rowCount) {
-            addBonds(chem_comp.id.value(0), chem_comp_bond, false)
+            addBonds(chem_comp.id.value(0), chem_comp_bond, false);
         }
     }
 
     const bondTable = Table.ofArrays(mmCIF_chemCompBond_schema, {
         comp_id, atom_id_1, atom_id_2, value_order,
         pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant
-    })
+    });
 
     const bondDatabase =  Database.ofTables(
         TABLE_NAME,
         { chem_comp_bond: mmCIF_chemCompBond_schema },
         { chem_comp_bond: bondTable }
-    )
+    );
 
-    return bondDatabase
+    return bondDatabase;
 }
 
 async function run(out: string, binary = false) {
-    const bonds = await createBonds()
+    const bonds = await createBonds();
 
-    const cif = getEncodedCif(TABLE_NAME, bonds, binary)
+    const cif = getEncodedCif(TABLE_NAME, bonds, binary);
     if (!fs.existsSync(path.dirname(out))) {
         fs.mkdirSync(path.dirname(out));
     }
-    writeFile(out, cif)
+    writeFile(out, cif);
 }
 
-const TABLE_NAME = 'CHEM_COMP_BONDS'
+const TABLE_NAME = 'CHEM_COMP_BONDS';
 
-const DATA_DIR = path.join(__dirname, '..', '..', '..', 'build/data')
-const CCD_PATH = path.join(DATA_DIR, 'components.cif')
-const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif')
-const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif'
-const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif'
+const DATA_DIR = path.join(__dirname, '..', '..', '..', 'build/data');
+const CCD_PATH = path.join(DATA_DIR, 'components.cif');
+const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
+const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
+const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';
 
 const parser = new argparse.ArgumentParser({
-  addHelp: true,
-  description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
+    addHelp: true,
+    description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
 });
 parser.addArgument('out', {
     help: 'Generated file output path.'
@@ -247,6 +247,6 @@ interface Args {
 }
 const args: Args = parser.parseArgs();
 
-const FORCE_DOWNLOAD = args.forceDownload
+const FORCE_DOWNLOAD = args.forceDownload;
 
-run(args.out, args.binary)
+run(args.out, args.binary);

src/apps/cif2bcif/converter.ts

@@ -0,0 +1,119 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+
+import { CIF, CifCategory, getCifFieldType, CifField, CifFile } from '../../mol-io/reader/cif';
+import { CifWriter, EncodingStrategyHint } from '../../mol-io/writer/cif';
+import * as util from 'util';
+import * as fs from 'fs';
+import * as zlib from 'zlib';
+import { Progress, Task, RuntimeContext } from '../../mol-task';
+import { classifyFloatArray, classifyIntArray } from '../../mol-io/common/binary-cif';
+import { BinaryEncodingProvider } from '../../mol-io/writer/cif/encoder/binary';
+import { Category } from '../../mol-io/writer/cif/encoder';
+import { ReaderResult } from '../../mol-io/reader/result';
+
+function showProgress(p: Progress) {
+    process.stdout.write(`\r${new Array(80).join(' ')}`);
+    process.stdout.write(`\r${Progress.format(p)}`);
+}
+
+const readFileAsync = util.promisify(fs.readFile);
+const unzipAsync = util.promisify<zlib.InputType, Buffer>(zlib.unzip);
+
+async function readFile(ctx: RuntimeContext, filename: string): Promise<ReaderResult<CifFile>> {
+    const isGz = /\.gz$/i.test(filename);
+    if (filename.match(/\.bcif/)) {
+        let input = await readFileAsync(filename);
+        if (isGz) input = await unzipAsync(input);
+        return await CIF.parseBinary(new Uint8Array(input)).runInContext(ctx);
+    } else {
+        let str: string;
+        if (isGz) {
+            const data = await unzipAsync(await readFileAsync(filename));
+            str = data.toString('utf8');
+        } else {
+            str = await readFileAsync(filename, 'utf8');
+        }
+        return await CIF.parseText(str).runInContext(ctx);
+    }
+}
+
+async function getCIF(ctx: RuntimeContext, filename: string) {
+    const parsed = await readFile(ctx, filename);
+    if (parsed.isError) {
+        throw new Error(parsed.toString());
+    }
+    return parsed.result;
+}
+
+function getCategoryInstanceProvider(cat: CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
+    return {
+        name: cat.name,
+        instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
+    };
+}
+
+function classify(name: string, field: CifField): CifWriter.Field {
+    const type = getCifFieldType(field);
+    if (type['@type'] === 'str') {
+        return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
+    } else if (type['@type'] === 'float') {
+        const encoder = classifyFloatArray(field.toFloatArray({ array: Float64Array }));
+        return CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, encoder, typedArray: Float64Array });
+    } else {
+        const encoder = classifyIntArray(field.toIntArray({ array: Int32Array }));
+        return CifWriter.Field.int(name, field.int, { valueKind: field.valueKind, encoder, typedArray: Int32Array });
+    }
+}
+
+export default function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
+    return Task.create<Uint8Array>('BinaryCIF', async ctx => {
+        const encodingProvider: BinaryEncodingProvider = hints
+            ? CifWriter.createEncodingProviderFromJsonConfig(hints)
+            : { get: (c, f) => void 0 };
+        const cif = await getCIF(ctx, path);
+
+        const encoder = CifWriter.createEncoder({
+            binary: !asText,
+            encoderName: 'mol*/ciftools cif2bcif',
+            binaryAutoClassifyEncoding: true,
+            binaryEncodingPovider: encodingProvider
+        });
+
+        if (filter) {
+            encoder.setFilter(Category.filterOf(filter));
+        }
+
+        let maxProgress = 0;
+        for (const b of cif.blocks) {
+            maxProgress += b.categoryNames.length;
+            for (const c of b.categoryNames) maxProgress += b.categories[c].fieldNames.length;
+        }
+
+        let current = 0;
+        for (const b of cif.blocks) {
+            encoder.startDataBlock(b.header);
+            for (const c of b.categoryNames) {
+                const cat = b.categories[c];
+                const fields: CifWriter.Field[] = [];
+                for (const f of cat.fieldNames) {
+                    fields.push(classify(f, cat.getField(f)!));
+                    current++;
+                    if (ctx.shouldUpdate) await ctx.update({ message: 'Encoding...', current, max: maxProgress });
+                }
+
+                encoder.writeCategory(getCategoryInstanceProvider(b.categories[c], fields));
+                current++;
+                if (ctx.shouldUpdate) await ctx.update({ message: 'Encoding...', current, max: maxProgress });
+            }
+        }
+        await ctx.update('Exporting...');
+        const ret = encoder.getData() as Uint8Array;
+        await ctx.update('Done.\n');
+        return ret;
+    }).run(showProgress, 250);
+}

src/apps/cif2bcif/index.ts

@@ -0,0 +1,67 @@
+/**
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse';
+import * as util from 'util';
+import * as fs from 'fs';
+import * as zlib from 'zlib';
+import convert from './converter';
+
+require('util.promisify').shim();
+
+async function process(srcPath: string, outPath: string, configPath?: string, filterPath?: string) {
+    const config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
+    const filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
+
+    const res = await convert(srcPath, false, config, filter);
+    await write(outPath, res);
+}
+
+const zipAsync = util.promisify<zlib.InputType, Buffer>(zlib.gzip);
+
+async function write(outPath: string, res: Uint8Array) {
+    const isGz = /\.gz$/i.test(outPath);
+    if (isGz) {
+        res = await zipAsync(res);
+    }
+    fs.writeFileSync(outPath, res);
+}
+
+function run(args: Args) {
+    process(args.src, args.out, args.config, args.filter);
+}
+
+const parser = new argparse.ArgumentParser({
+    addHelp: true,
+    description: 'Convert any CIF file to a BCIF file'
+});
+parser.addArgument([ 'src' ], {
+    help: 'Source CIF path'
+});
+parser.addArgument([ 'out' ], {
+    help: 'Output BCIF path'
+});
+parser.addArgument([ '-c', '--config' ], {
+    help: 'Optional encoding strategy/precision config path',
+    required: false
+});
+parser.addArgument([ '-f', '--filter' ], {
+    help: 'Optional filter whitelist/blacklist path',
+    required: false
+});
+
+interface Args {
+    src: string
+    out: string
+    config?: string
+    filter?: string
+}
+const args: Args = parser.parseArgs();
+
+if (args) {
+    run(args);
+}

src/apps/cifschema/index.ts

@@ -0,0 +1,274 @@
+/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse';
+import * as fs from 'fs';
+import * as path from 'path';
+import fetch from 'node-fetch';
+
+import { parseCsv } from '../../mol-io/reader/csv/parser';
+import { CifFrame, CifBlock } from '../../mol-io/reader/cif';
+import parseText from '../../mol-io/reader/cif/text/parser';
+import { generateSchema } from './util/cif-dic';
+import { generate } from './util/generate';
+import { Filter, Database } from './util/schema';
+import { parseImportGet } from './util/helper';
+
+function getDicVersion(block: CifBlock) {
+    return block.categories.dictionary.getField('version')!.str(0);
+}
+
+function getDicNamespace(block: CifBlock) {
+    return block.categories.dictionary.getField('namespace')!.str(0);
+}
+
+async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
+    await ensureMmcifDicAvailable();
+    const mmcifDic = await parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
+    if (mmcifDic.isError) throw mmcifDic;
+
+    await ensureIhmDicAvailable();
+    const ihmDic = await parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
+    if (ihmDic.isError) throw ihmDic;
+
+    await ensureCarbBranchDicAvailable();
+    const carbBranchDic = await parseText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
+    if (carbBranchDic.isError) throw carbBranchDic;
+
+    await ensureCarbCompDicAvailable();
+    const carbCompDic = await parseText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
+    if (carbCompDic.isError) throw carbCompDic;
+
+    const mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
+    const ihmDicVersion = getDicVersion(ihmDic.result.blocks[0]);
+    const carbDicVersion = 'draft';
+    const version = `Dictionary versions: mmCIF ${mmcifDicVersion}, IHM ${ihmDicVersion}, CARB ${carbDicVersion}.`;
+
+    const frames: CifFrame[] = [...mmcifDic.result.blocks[0].saveFrames, ...ihmDic.result.blocks[0].saveFrames, ...carbBranchDic.result.blocks[0].saveFrames, ...carbCompDic.result.blocks[0].saveFrames];
+    const schema = generateSchema(frames);
+
+    await runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases);
+}
+
+async function runGenerateSchemaCifCore(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
+    await ensureCifCoreDicAvailable();
+    const cifCoreDic = await parseText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
+    if (cifCoreDic.isError) throw cifCoreDic;
+
+    const cifCoreDicVersion = getDicVersion(cifCoreDic.result.blocks[0]);
+    const version = `Dictionary versions: CifCore ${cifCoreDicVersion}.`;
+
+    const frames: CifFrame[] = [...cifCoreDic.result.blocks[0].saveFrames];
+    const imports = await resolveImports(frames, DIC_DIR);
+    const schema = generateSchema(frames, imports);
+
+    await runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases);
+}
+
+async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<string, CifFrame[]>> {
+    const imports = new Map<string, CifFrame[]>();
+
+    for (const d of frames) {
+        if ('import' in d.categories) {
+            const importGet = parseImportGet(d.categories['import'].getField('get')!.str(0));
+            for (const g of importGet) {
+                const { file } = g;
+                if (!file) continue;
+                if (imports.has(file)) continue;
+
+                const dic = await parseText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
+                if (dic.isError) throw dic;
+
+                imports.set(file, [...dic.result.blocks[0].saveFrames]);
+            }
+        }
+    }
+
+    return imports;
+}
+
+async function runGenerateSchemaDic(name: string, dicPath: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
+    const dic = await parseText(fs.readFileSync(dicPath, 'utf8')).run();
+    if (dic.isError) throw dic;
+
+    const dicVersion = getDicVersion(dic.result.blocks[0]);
+    const dicName = getDicNamespace(dic.result.blocks[0]);
+    const version = `Dictionary versions: ${dicName} ${dicVersion}.`;
+
+    const frames: CifFrame[] = [...dic.result.blocks[0].saveFrames];
+    const imports = await resolveImports(frames, path.dirname(dicPath));
+    const schema = generateSchema(frames, imports);
+
+    await runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases);
+}
+
+async function runGenerateSchema(name: string, version: string, schema: Database, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
+    const filter = fieldNamesPath ? await getFieldNamesFilter(fieldNamesPath) : undefined;
+    const output = typescript ? generate(name, version, schema, filter, moldbImportPath, addAliases) : JSON.stringify(schema, undefined, 4);
+
+    if (out) {
+        fs.writeFileSync(out, output);
+    } else {
+        console.log(output);
+    }
+}
+
+async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
+    const fieldNamesStr = fs.readFileSync(fieldNamesPath, 'utf8');
+    const parsed = await parseCsv(fieldNamesStr, { noColumnNames: true }).run();
+    if (parsed.isError) throw parser.error;
+    const csvFile = parsed.result;
+
+    const fieldNamesCol = csvFile.table.getColumn('0');
+    if (!fieldNamesCol) throw 'error getting fields columns';
+    const fieldNames = fieldNamesCol.toStringArray();
+
+    const filter: Filter = {};
+    fieldNames.forEach((name, i) => {
+        const [ category, field ] = name.split('.');
+        // console.log(category, field)
+        if (!filter[ category ]) filter[ category ] = {};
+        filter[ category ][ field ] = true;
+    });
+    return filter;
+}
+
+async function ensureMmcifDicAvailable() { await ensureDicAvailable(MMCIF_DIC_PATH, MMCIF_DIC_URL); }
+async function ensureIhmDicAvailable() { await ensureDicAvailable(IHM_DIC_PATH, IHM_DIC_URL); }
+async function ensureCarbBranchDicAvailable() { await ensureDicAvailable(CARB_BRANCH_DIC_PATH, CARB_BRANCH_DIC_URL); }
+async function ensureCarbCompDicAvailable() { await ensureDicAvailable(CARB_COMP_DIC_PATH, CARB_COMP_DIC_URL); }
+async function ensureCifCoreDicAvailable() {
+    await ensureDicAvailable(CIF_CORE_DIC_PATH, CIF_CORE_DIC_URL);
+    await ensureDicAvailable(CIF_CORE_ENUM_PATH, CIF_CORE_ENUM_URL);
+    await ensureDicAvailable(CIF_CORE_ATTR_PATH, CIF_CORE_ATTR_URL);
+}
+
+async function ensureDicAvailable(dicPath: string, dicUrl: string) {
+    if (FORCE_DIC_DOWNLOAD || !fs.existsSync(dicPath)) {
+        const name = dicUrl.substr(dicUrl.lastIndexOf('/') + 1);
+        console.log(`downloading ${name}...`);
+        const data = await fetch(dicUrl);
+        if (!fs.existsSync(DIC_DIR)) {
+            fs.mkdirSync(DIC_DIR);
+        }
+        fs.writeFileSync(dicPath, await data.text());
+        console.log(`done downloading ${name}`);
+    }
+}
+
+const DIC_DIR = path.resolve(__dirname, '../../../build/dics/');
+const MMCIF_DIC_PATH = `${DIC_DIR}/mmcif_pdbx_v50.dic`;
+const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic';
+const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`;
+const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic';
+const CARB_BRANCH_DIC_PATH = `${DIC_DIR}/entity_branch-extension.dic`;
+const CARB_BRANCH_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/entity_branch-extension.dic';
+const CARB_COMP_DIC_PATH = `${DIC_DIR}/chem_comp-extension.dic`;
+const CARB_COMP_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/chem_comp-extension.dic';
+
+const CIF_CORE_DIC_PATH = `${DIC_DIR}/cif_core.dic`;
+const CIF_CORE_DIC_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic';
+const CIF_CORE_ENUM_PATH = `${DIC_DIR}/templ_enum.cif`;
+const CIF_CORE_ENUM_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_enum.cif';
+const CIF_CORE_ATTR_PATH = `${DIC_DIR}/templ_attr.cif`;
+const CIF_CORE_ATTR_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif';
+
+const parser = new argparse.ArgumentParser({
+    addHelp: true,
+    description: 'Create schema from mmcif dictionary (v50 plus IHM and entity_branch extensions, downloaded from wwPDB)'
+});
+parser.addArgument([ '--preset', '-p' ], {
+    defaultValue: '',
+    choices: ['', 'mmCIF', 'CCD', 'BIRD', 'CifCore'],
+    help: 'Preset name'
+});
+parser.addArgument([ '--name', '-n' ], {
+    defaultValue: '',
+    help: 'Schema name'
+});
+parser.addArgument([ '--out', '-o' ], {
+    help: 'Generated schema output path, if not given printed to stdout'
+});
+parser.addArgument([ '--targetFormat', '-tf' ], {
+    defaultValue: 'typescript-molstar',
+    choices: ['typescript-molstar', 'json-internal'],
+    help: 'Target format'
+});
+parser.addArgument([ '--dicPath', '-d' ], {
+    defaultValue: '',
+    help: 'Path to dictionary'
+});
+parser.addArgument([ '--fieldNamesPath', '-fn' ], {
+    defaultValue: '',
+    help: 'Field names to include'
+});
+parser.addArgument([ '--forceDicDownload', '-f' ], {
+    action: 'storeTrue',
+    help: 'Force download of dictionaries'
+});
+parser.addArgument([ '--moldataImportPath', '-mip' ], {
+    defaultValue: 'molstar/lib/mol-data',
+    help: 'mol-data import path (for typescript target only)'
+});
+parser.addArgument([ '--addAliases', '-aa' ], {
+    action: 'storeTrue',
+    help: 'Add field name/path aliases'
+});
+interface Args {
+    name: string
+    preset: '' | 'mmCIF' | 'CCD' | 'BIRD' | 'CifCore'
+    forceDicDownload: boolean
+    dic: '' | 'mmCIF' | 'CifCore'
+    dicPath: string,
+    fieldNamesPath: string
+    targetFormat: 'typescript-molstar' | 'json-internal'
+    out: string,
+    moldataImportPath: string
+    addAliases: boolean
+}
+const args: Args = parser.parseArgs();
+
+const FORCE_DIC_DOWNLOAD = args.forceDicDownload;
+
+switch (args.preset) {
+    case 'mmCIF':
+        args.name = 'mmCIF';
+        args.dic = 'mmCIF';
+        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/mmcif-field-names.csv');
+        break;
+    case 'CCD':
+        args.name = 'CCD';
+        args.dic = 'mmCIF';
+        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/ccd-field-names.csv');
+        break;
+    case 'BIRD':
+        args.name = 'BIRD';
+        args.dic = 'mmCIF';
+        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/bird-field-names.csv');
+        break;
+    case 'CifCore':
+        args.name = 'CifCore';
+        args.dic = 'CifCore';
+        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/cif-core-field-names.csv');
+        break;
+}
+
+if (args.name) {
+    const typescript = args.targetFormat === 'typescript-molstar';
+    if (args.dicPath) {
+        runGenerateSchemaDic(args.name, args.dicPath, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(e => {
+            console.error(e);
+        });
+    } else if (args.dic === 'mmCIF') {
+        runGenerateSchemaMmcif(args.name, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(e => {
+            console.error(e);
+        });
+    } else if (args.dic === 'CifCore') {
+        runGenerateSchemaCifCore(args.name, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(e => {
+            console.error(e);
+        });
+    }
+}

src/apps/cifschema/util/cif-dic.ts

@@ -0,0 +1,475 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Database, Column, EnumCol, StrCol, IntCol, ListCol, FloatCol, CoordCol, MatrixCol, VectorCol } from './schema';
+import { parseImportGet } from './helper';
+import * as Data from '../../../mol-io/reader/cif/data-model';
+import { CifFrame } from '../../../mol-io/reader/cif/data-model';
+
+export function getFieldType(type: string, description: string, values?: string[], container?: string): Column {
+    switch (type) {
+        // mmCIF
+        case 'code':
+        case 'ucode':
+        case 'line':
+        case 'uline':
+        case 'text':
+        case 'char':
+        case 'uchar3':
+        case 'uchar1':
+        case 'boolean':
+            return values && values.length ? EnumCol(values, 'str', description) : StrCol(description);
+        case 'aliasname':
+        case 'name':
+        case 'idname':
+        case 'any':
+        case 'atcode':
+        case 'fax':
+        case 'phone':
+        case 'email':
+        case 'code30':
+        case 'seq-one-letter-code':
+        case 'author':
+        case 'orcid_id':
+        case 'sequence_dep':
+        case 'pdb_id':
+        case 'emd_id':
+        // todo, consider adding specialised fields
+        case 'yyyy-mm-dd':
+        case 'yyyy-mm-dd:hh:mm':
+        case 'yyyy-mm-dd:hh:mm-flex':
+        case 'int-range':
+        case 'float-range':
+        case 'binary':
+        case 'operation_expression':
+        case 'point_symmetry':
+        case '4x3_matrix':
+        case '3x4_matrices':
+        case 'point_group':
+        case 'point_group_helical':
+        case 'symmetry_operation':
+        case 'date_dep':
+        case 'url':
+        case 'symop':
+        case 'exp_data_doi':
+        case 'asym_id':
+            return StrCol(description);
+        case 'int':
+        case 'non_negative_int':
+        case 'positive_int':
+            return values && values.length ? EnumCol(values, 'int', description) : IntCol(description);
+        case 'float':
+            return FloatCol(description);
+        case 'ec-type':
+        case 'ucode-alphanum-csv':
+        case 'id_list':
+            return ListCol('str', ',', description);
+        case 'id_list_spc':
+            return ListCol('str', ' ', description);
+
+        // cif
+        case 'Text':
+        case 'Code':
+        case 'Complex':
+        case 'Symop':
+        case 'List':
+        case 'List(Real,Real)':
+        case 'List(Real,Real,Real,Real)':
+        case 'Date':
+        case 'Datetime':
+        case 'Tag':
+        case 'Implied':
+            return wrapContainer('str', ',', description, container);
+        case 'Real':
+            return wrapContainer('float', ',', description, container);
+        case 'Integer':
+            return wrapContainer('int', ',', description, container);
+
+    }
+    console.log(`unknown type '${type}'`);
+    return StrCol(description);
+}
+
+function ColFromType(type: 'int' | 'str' | 'float' | 'coord', description: string): Column {
+    switch (type) {
+        case 'int': return IntCol(description);
+        case 'str': return StrCol(description);
+        case 'float': return FloatCol(description);
+        case 'coord': return CoordCol(description);
+    }
+}
+
+function wrapContainer(type: 'int' | 'str' | 'float' | 'coord', separator: string, description: string, container?: string) {
+    return container && container === 'List' ? ListCol(type, separator, description) : ColFromType(type, description);
+}
+
+type FrameCategories = { [category: string]: Data.CifFrame }
+type FrameLinks = { [k: string]: string }
+
+interface FrameData {
+    categories: FrameCategories
+    links: FrameLinks
+}
+
+type Imports = Map<string, CifFrame[]>
+
+function getImportFrames(d: Data.CifFrame, imports: Imports) {
+    const frames: Data.CifFrame[] = [];
+    if (!('import' in d.categories)) return frames;
+
+    const importGet = parseImportGet(d.categories['import'].getField('get')!.str(0));
+    for (const g of importGet) {
+        const { file, save } = g;
+        if (!file || !save) {
+            console.warn(`missing 'save' or 'file' for import in '${d.header}'`);
+            continue;
+        }
+        const importFrames = imports.get(file);
+        if (!importFrames) {
+            console.warn(`missing '${file}' entry in imports`);
+            continue;
+        }
+        const importSave = importFrames.find(id => id.header.toLowerCase() === save.toLowerCase());
+        if (!importSave) {
+            console.warn(`missing '${save}' save frame in '${file}'`);
+            continue;
+        }
+
+        frames.push(importSave);
+    }
+
+    return frames;
+}
+
+/** get field from given or linked category */
+function getField(category: string, field: string, d: Data.CifFrame, imports: Imports, ctx: FrameData): Data.CifField|undefined {
+    const { categories, links } = ctx;
+    const cat = d.categories[category];
+    if (cat) {
+        return cat.getField(field);
+    } else if (d.header in links) {
+        const linkName = links[d.header];
+        if (linkName in categories) {
+            return getField(category, field, categories[linkName], imports, ctx);
+        } else {
+            // console.log(`link '${linkName}' not found`)
+        }
+    } else {
+        const importFrames = getImportFrames(d, imports);
+        for (const idf of importFrames) {
+            return getField(category, field, idf, imports, ctx);
+        }
+    }
+}
+
+function getEnums(d: Data.CifFrame, imports: Imports, ctx: FrameData) {
+    const value = getField('item_enumeration', 'value', d, imports, ctx);
+    const enums: string[] = [];
+    if (value) {
+        for (let i = 0; i < value.rowCount; ++i) {
+            enums.push(value.str(i));
+            // console.log(value.str(i))
+        }
+        return enums;
+    } else {
+        // console.log(`item_enumeration.value not found for '${d.header}'`)
+    }
+}
+
+function getContainer(d: Data.CifFrame, imports: Imports, ctx: FrameData) {
+    const value = getField('type', 'container', d, imports, ctx);
+    return value ? value.str(0) : undefined;
+}
+
+function getCode(d: Data.CifFrame, imports: Imports, ctx: FrameData): [string, string[] | undefined, string | undefined ] | undefined {
+    const code = getField('item_type', 'code', d, imports, ctx) || getField('type', 'contents', d, imports, ctx);
+    if (code) {
+        return [ code.str(0), getEnums(d, imports, ctx), getContainer(d, imports, ctx) ];
+    } else {
+        console.log(`item_type.code or type.contents not found for '${d.header}'`);
+    }
+}
+
+function getSubCategory(d: Data.CifFrame, imports: Imports, ctx: FrameData): string | undefined {
+    const value = getField('item_sub_category', 'id', d, imports, ctx);
+    if (value) {
+        return value.str(0);
+    }
+}
+
+function getDescription(d: Data.CifFrame, imports: Imports, ctx: FrameData): string | undefined {
+    const value = getField('item_description', 'description', d, imports, ctx) || getField('description', 'text', d, imports, ctx);
+    if (value) {
+        // trim (after newlines) and remove references to square brackets
+        return value.str(0).trim()
+            .replace(/(\r\n|\r|\n)([ \t]+)/g, '\n')
+            .replace(/(\[[1-3]\])+ element/, 'elements')
+            .replace(/(\[[1-3]\])+/, '');
+    }
+}
+
+function getAliases(d: Data.CifFrame, imports: Imports, ctx: FrameData): string[] | undefined {
+    const value = getField('item_aliases', 'alias_name', d, imports, ctx) || getField('alias', 'definition_id', d, imports, ctx);
+    return value ? value.toStringArray().map(v => v.substr(1)) : undefined;
+}
+
+const reMatrixField = /\[[1-3]\]\[[1-3]\]/;
+const reVectorField = /\[[1-3]\]/;
+
+const FORCE_INT_FIELDS = [
+    '_atom_site.id',
+    '_atom_site.auth_seq_id',
+    '_atom_site_anisotrop.id',
+    '_pdbx_struct_mod_residue.auth_seq_id',
+    '_struct_conf.beg_auth_seq_id',
+    '_struct_conf.end_auth_seq_id',
+    '_struct_conn.ptnr1_auth_seq_id',
+    '_struct_conn.ptnr2_auth_seq_id',
+    '_struct_sheet_range.beg_auth_seq_id',
+    '_struct_sheet_range.end_auth_seq_id',
+];
+
+const FORCE_MATRIX_FIELDS_MAP: { [k: string]: string } = {
+    'atom_site_aniso.U_11': 'U',
+    'atom_site_aniso.U_22': 'U',
+    'atom_site_aniso.U_33': 'U',
+    'atom_site_aniso.U_23': 'U',
+    'atom_site_aniso.U_13': 'U',
+    'atom_site_aniso.U_12': 'U',
+    'atom_site_aniso.U_11_su': 'U_su',
+    'atom_site_aniso.U_22_su': 'U_su',
+    'atom_site_aniso.U_33_su': 'U_su',
+    'atom_site_aniso.U_23_su': 'U_su',
+    'atom_site_aniso.U_13_su': 'U_su',
+    'atom_site_aniso.U_12_su': 'U_su',
+};
+const FORCE_MATRIX_FIELDS = Object.keys(FORCE_MATRIX_FIELDS_MAP);
+
+const EXTRA_ALIASES: Database['aliases'] = {
+    'atom_site_aniso.U': [
+        'atom_site_anisotrop_U'
+    ],
+    'atom_site_aniso.U_su': [
+        'atom_site_aniso_U_esd',
+        'atom_site_anisotrop_U_esd',
+    ],
+};
+
+const COMMA_SEPARATED_LIST_FIELDS = [
+    '_atom_site.pdbx_struct_group_id',
+    '_chem_comp.mon_nstd_parent_comp_id',
+    '_diffrn_radiation.pdbx_wavelength_list',
+    '_diffrn_source.pdbx_wavelength_list',
+    '_em_diffraction.tilt_angle_list', // 20,40,50,55
+    '_em_entity_assembly.entity_id_list',
+    '_entity.pdbx_description', // Endolysin,Beta-2 adrenergic receptor
+    '_entity.pdbx_ec',
+    '_entity_poly.pdbx_strand_id', // A,B
+    '_entity_src_gen.pdbx_gene_src_gene', // ADRB2, ADRB2R, B2AR
+    '_pdbx_depui_entry_details.experimental_methods',
+    '_pdbx_depui_entry_details.requested_accession_types',
+    '_pdbx_soln_scatter_model.software_list', // INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI
+    '_pdbx_soln_scatter_model.software_author_list', // MSI
+    '_pdbx_soln_scatter_model.entry_fitting_list', // Odd example: 'PDB CODE 1HFI, 1HCC, 1HFH, 1VCC'
+    '_pdbx_struct_assembly_gen.entity_inst_id',
+    '_pdbx_struct_assembly_gen.asym_id_list',
+    '_pdbx_struct_assembly_gen.auth_asym_id_list',
+    '_pdbx_struct_assembly_gen_depositor_info.asym_id_list',
+    '_pdbx_struct_assembly_gen_depositor_info.chain_id_list',
+    '_pdbx_struct_group_list.group_enumeration_type',
+    '_reflns.pdbx_diffrn_id',
+    '_refine.pdbx_diffrn_id',
+    '_reflns_shell.pdbx_diffrn_id',
+    '_struct_keywords.text',
+];
+
+const SPACE_SEPARATED_LIST_FIELDS = [
+    '_chem_comp.pdbx_subcomponent_list', // TSM DPH HIS CHF EMR
+    '_pdbx_soln_scatter.data_reduction_software_list', // OTOKO
+    '_pdbx_soln_scatter.data_analysis_software_list', // SCTPL5 GNOM
+];
+
+const SEMICOLON_SEPARATED_LIST_FIELDS = [
+    '_chem_comp.pdbx_synonyms' // GLYCERIN; PROPANE-1,2,3-TRIOL
+];
+
+/**
+ * Useful when a dictionary extension will add enum values to an existing dictionary.
+ * By adding them here, the dictionary extension can be tested before the added enum
+ * values are available in the existing dictionary.
+ */
+const EXTRA_ENUM_VALUES: { [k: string]: string[] } = {
+
+};
+
+export function generateSchema(frames: CifFrame[], imports: Imports = new Map()): Database {
+    const tables: Database['tables'] = {};
+    const aliases: Database['aliases'] = { ...EXTRA_ALIASES };
+
+    const categories: FrameCategories = {};
+    const links: FrameLinks = {};
+    const ctx = { categories, links };
+
+    // get category metadata
+    frames.forEach(d => {
+        // category definitions in mmCIF start with '_' and don't include a '.'
+        // category definitions in cifCore don't include a '.'
+        if (d.header[0] === '_'  || d.header.includes('.')) return;
+        const categoryName = d.header.toLowerCase();
+        // console.log(d.header, d.categoryNames, d.categories)
+        let descriptionField: Data.CifField | undefined;
+        const categoryKeyNames = new Set<string>();
+
+        if ('category' in d.categories && 'category_key' in d.categories) {
+            const category = d.categories['category'];
+            const categoryKey = d.categories['category_key'];
+            if (categoryKey) {
+                const categoryKey_names = categoryKey.getField('name');
+                if (categoryKey_names) {
+                    for (let i = 0, il = categoryKey_names.rowCount; i < il; ++i) {
+                        categoryKeyNames.add(categoryKey_names.str(i));
+                    }
+                }
+            }
+
+            descriptionField = category.getField('description');
+
+            if (categoryKeyNames.size === 0) {
+                console.log(`no key given for category '${categoryName}'`);
+            }
+        }
+
+        if ('description' in d.categories) {
+            descriptionField = d.categories['description'].getField('text');
+        }
+
+        let description = '';
+        if (descriptionField) {
+            description = descriptionField.str(0).trim()
+                .replace(/(\r\n|\r|\n)([ \t]+)/g, '\n'); // remove padding after newlines
+        } else {
+            console.log(`no description given for category '${categoryName}'`);
+        }
+
+        tables[categoryName] = { description, key: categoryKeyNames, columns: {} };
+
+        // console.log('++++++++++++++++++++++++++++++++++++++++++')
+        // console.log('name', categoryName)
+        // console.log('desc', description)
+        // console.log('key', categoryKeyNames)
+    });
+
+    // build list of links between categories
+    frames.forEach(d => {
+        if (d.header[0] !== '_' && !d.header.includes('.')) return;
+        categories[d.header] = d;
+        const item_linked = d.categories['item_linked'];
+        if (item_linked) {
+            const child_name = item_linked.getField('child_name');
+            const parent_name = item_linked.getField('parent_name');
+            if (child_name && parent_name) {
+                for (let i = 0; i < item_linked.rowCount; ++i) {
+                    const childName = child_name.str(i);
+                    const parentName = parent_name.str(i);
+                    if (childName in links && links[childName] !== parentName) {
+                        console.log(`${childName} linked to ${links[childName]}, ignoring link to ${parentName}`);
+                    }
+                    links[childName] = parentName;
+                }
+            }
+        }
+    });
+
+    // get field data
+    Object.keys(categories).forEach(fullName => {
+        const d = categories[fullName];
+        if (!d) {
+            console.log(`'${fullName}' not found, moving on`);
+            return;
+        }
+
+        const categoryName = d.header.substring(d.header[0] === '_' ? 1 : 0, d.header.indexOf('.'));
+        const itemName = d.header.substring(d.header.indexOf('.') + 1);
+        let fields: { [k: string]: Column };
+        if (categoryName in tables) {
+            fields = tables[categoryName].columns;
+            tables[categoryName].key.add(itemName);
+        } else if (categoryName.toLowerCase() in tables) {
+            // take case from category name in 'field' data as it is better if data is from cif dictionaries
+            tables[categoryName] = tables[categoryName.toLowerCase()];
+            fields = tables[categoryName].columns;
+        } else {
+            console.log(`category '${categoryName}' has no metadata`);
+            fields = {};
+            tables[categoryName] = {
+                description: '',
+                key: new Set(),
+                columns: fields
+            };
+        }
+
+        const itemAliases = getAliases(d, imports, ctx);
+        if (itemAliases) aliases[`${categoryName}.${itemName}`] = itemAliases;
+
+        const description = getDescription(d, imports, ctx) || '';
+
+        // need to use regex to check for matrix or vector items
+        // as sub_category assignment is missing for some entries
+        const subCategory = getSubCategory(d, imports, ctx);
+        if (subCategory === 'cartesian_coordinate' || subCategory === 'fractional_coordinate') {
+            fields[itemName] = CoordCol(description);
+        } else if (FORCE_INT_FIELDS.includes(d.header)) {
+            fields[itemName] = IntCol(description);
+            console.log(`forcing int: ${d.header}`);
+        } else if (FORCE_MATRIX_FIELDS.includes(d.header)) {
+            fields[itemName] = FloatCol(description);
+            fields[FORCE_MATRIX_FIELDS_MAP[d.header]] = MatrixCol(3, 3, description);
+            console.log(`forcing matrix: ${d.header}`);
+        } else if (subCategory === 'matrix') {
+            fields[itemName.replace(reMatrixField, '')] = MatrixCol(3, 3, description);
+        } else if (subCategory === 'vector') {
+            fields[itemName.replace(reVectorField, '')] = VectorCol(3, description);
+        } else {
+            if (itemName.match(reMatrixField)) {
+                fields[itemName.replace(reMatrixField, '')] = MatrixCol(3, 3, description);
+                console.log(`${d.header} should have 'matrix' _item_sub_category.id`);
+            } else if (itemName.match(reVectorField)) {
+                fields[itemName.replace(reVectorField, '')] = VectorCol(3, description);
+                console.log(`${d.header} should have 'vector' _item_sub_category.id`);
+            } else {
+                const code = getCode(d, imports, ctx);
+                if (code) {
+                    let fieldType = getFieldType(code[0], description, code[1], code[2]);
+                    if (fieldType.type === 'str') {
+                        if (COMMA_SEPARATED_LIST_FIELDS.includes(d.header)) {
+                            fieldType = ListCol('str', ',', description);
+                            console.log(`forcing comma separated: ${d.header}`);
+                        } else if (SPACE_SEPARATED_LIST_FIELDS.includes(d.header)) {
+                            fieldType = ListCol('str', ' ', description);
+                            console.log(`forcing space separated: ${d.header}`);
+                        } else if (SEMICOLON_SEPARATED_LIST_FIELDS.includes(d.header)) {
+                            fieldType = ListCol('str', ';', description);
+                            console.log(`forcing space separated: ${d.header}`);
+                        }
+                    }
+                    if (d.header in EXTRA_ENUM_VALUES) {
+                        if (fieldType.type === 'enum') {
+                            fieldType.values.push(...EXTRA_ENUM_VALUES[d.header]);
+                        } else {
+                            console.warn(`expected enum: ${d.header}`);
+                        }
+                    }
+                    fields[itemName] = fieldType;
+                } else {
+                    fields[itemName] = StrCol(description);
+                    // console.log(`could not determine code for '${d.header}'`)
+                }
+            }
+        }
+    });
+
+    return { tables, aliases };
+}

src/apps/cifschema/util/generate.ts

@@ -0,0 +1,151 @@
+/**
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Database, Filter, Column } from './schema';
+import { indentString } from '../../../mol-util/string';
+import { FieldPath } from '../../../mol-io/reader/cif/schema';
+
+function header (name: string, info: string, moldataImportPath: string) {
+    return `/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated '${name}' schema file. ${info}
+ *
+ * @author molstar/ciftools package
+ */
+
+import { Database, Column } from '${moldataImportPath}/db'
+
+import Schema = Column.Schema`;
+}
+
+function footer (name: string) {
+    return `
+export type ${name}_Schema = typeof ${name}_Schema;
+export interface ${name}_Database extends Database<${name}_Schema> {}`;
+}
+
+function getTypeShorthands(schema: Database, fields?: Filter) {
+    const types = new Set<string>();
+    Object.keys(schema.tables).forEach(table => {
+        if (fields && !fields[table]) return;
+        const { columns } = schema.tables[table];
+        Object.keys(columns).forEach(columnName => {
+            if (fields && !fields[table][columnName]) return;
+            types.add(schema.tables[table].columns[columnName].type);
+        });
+    });
+    const shorthands: string[] = [];
+    types.forEach(type => {
+        switch (type) {
+            case 'str': shorthands.push('const str = Schema.str;'); break;
+            case 'int': shorthands.push('const int = Schema.int;'); break;
+            case 'float': shorthands.push('const float = Schema.float;'); break;
+            case 'coord': shorthands.push('const coord = Schema.coord;'); break;
+            case 'enum': shorthands.push('const Aliased = Schema.Aliased;'); break;
+            case 'matrix': shorthands.push('const Matrix = Schema.Matrix;'); break;
+            case 'vector': shorthands.push('const Vector = Schema.Vector;'); break;
+            case 'list': shorthands.push('const List = Schema.List;'); break;
+        }
+    });
+    return shorthands.join('\n');
+}
+
+function getTypeDef(c: Column): string {
+    switch (c.type) {
+        case 'str': return 'str';
+        case 'int': return 'int';
+        case 'float': return 'float';
+        case 'coord': return 'coord';
+        case 'enum':
+            return `Aliased<'${c.values.map(v => v.replace(/'/g, '\\\'')).join(`' | '`)}'>(${c.subType})`;
+        case 'matrix':
+            return `Matrix(${c.rows}, ${c.columns})`;
+        case 'vector':
+            return `Vector(${c.length})`;
+        case 'list':
+            if (c.subType === 'int') {
+                return `List('${c.separator}', x => parseInt(x, 10))`;
+            } else if (c.subType === 'float' || c.subType === 'coord') {
+                return `List('${c.separator}', x => parseFloat(x))`;
+            } else {
+                return `List('${c.separator}', x => x)`;
+            }
+    }
+}
+
+const reSafePropertyName = /^[a-zA-Z_$][0-9a-zA-Z_$]*$/;
+function safePropertyString(name: string) { return name.match(reSafePropertyName) ? name : `'${name}'`; }
+
+function doc(description: string, spacesCount: number) {
+    const spaces = ' '.repeat(spacesCount);
+    return [
+        `${spaces}/**`,
+        `${indentString(description, 1, `${spaces} * `)}`.replace(/ +\n/g, '\n'),
+        `${spaces} */`
+    ].join('\n');
+}
+
+export function generate (name: string, info: string, schema: Database, fields: Filter | undefined, moldataImportPath: string, addAliases: boolean) {
+    const codeLines: string[] = [];
+
+    if (fields) {
+        Object.keys(fields).forEach(table => {
+            if (table in schema.tables) {
+                const schemaTable = schema.tables[table];
+                Object.keys(fields[table]).forEach(column => {
+                    if (!(column in schemaTable.columns)) {
+                        console.log(`filter field '${table}.${column}' not found in schema`);
+                    }
+                });
+            } else {
+                console.log(`filter category '${table}' not found in schema`);
+            }
+        });
+    }
+
+    codeLines.push(`export const ${name}_Schema = {`);
+    Object.keys(schema.tables).forEach(table => {
+        if (fields && !fields[table]) return;
+        const { description, columns } = schema.tables[table];
+        if (description) codeLines.push(doc(description, 4));
+        codeLines.push(`    ${safePropertyString(table)}: {`);
+        Object.keys(columns).forEach(columnName => {
+            if (fields && !fields[table][columnName]) return;
+            const c = columns[columnName];
+            const typeDef = getTypeDef(c);
+            if (c.description) codeLines.push(doc(c.description, 8));
+            codeLines.push(`        ${safePropertyString(columnName)}: ${typeDef},`);
+        });
+        codeLines.push('    },');
+    });
+    codeLines.push('}');
+
+    if (addAliases) {
+        codeLines.push('');
+        codeLines.push(`export const ${name}_Aliases = {`);
+        Object.keys(schema.aliases).forEach(path => {
+            const [ table, columnName ] = path.split('.');
+            if (fields && !fields[table]) return;
+            if (fields && !fields[table][columnName]) return;
+
+            const filteredAliases = new Set<string>();
+            schema.aliases[path].forEach(p => {
+                if (!FieldPath.equal(p, path)) filteredAliases.add(FieldPath.canonical(p));
+            });
+
+            if (filteredAliases.size === 0) return;
+            codeLines.push(`    ${safePropertyString(path)}: [`);
+            filteredAliases.forEach(alias => {
+                codeLines.push(`        '${alias}',`);
+            });
+            codeLines.push('    ],');
+        });
+        codeLines.push('}');
+    }
+
+    return `${header(name, info, moldataImportPath)}\n\n${getTypeShorthands(schema, fields)}\n\n${codeLines.join('\n')}\n${footer(name)}`;
+}

src/apps/cifschema/util/helper.ts

@@ -0,0 +1,20 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export type Import = { save?: string, file?: string }
+
+export function parseImportGet(s: string): Import[] {
+    // [{'save':hi_ang_Fox_coeffs  'file':templ_attr.cif}   {'save':hi_ang_Fox_c0  'file':templ_enum.cif}]
+    // [{"file":'templ_enum.cif' "save":'H_M_ref'}]
+    return s.trim().substring(2, s.length - 2).split(/}[ \n\t]*{/g).map(s => {
+        const save = s.match(/('save'|"save"):([^ \t\n]+)/);
+        const file = s.match(/('file'|"file"):([^ \t\n]+)/);
+        return {
+            save: save ? save[0].substr(7).replace(/['"]/g, '') : undefined,
+            file: file ? file[0].substr(7).replace(/['"]/g, '') : undefined
+        };
+    });
+}

src/apps/cifschema/util/schema.ts

@@ -0,0 +1,77 @@
+/**
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export interface Database {
+    tables: { [ tableName: string ]: Table }
+    aliases: { [ path: string ]: string[] }
+}
+export interface Table {
+    description: string
+    key: Set<string>
+    columns: { [ columnName: string ]: Column }
+}
+export type Column = IntCol | StrCol | FloatCol | CoordCol | EnumCol | VectorCol | MatrixCol | ListCol
+
+type BaseCol = { description: string }
+
+export type IntCol = { type: 'int' } & BaseCol
+export function IntCol(description: string): IntCol { return { type: 'int', description }; }
+
+export type StrCol = { type: 'str' } & BaseCol
+export function StrCol(description: string): StrCol { return { type: 'str', description }; }
+
+export type FloatCol = { type: 'float' } & BaseCol
+export function FloatCol(description: string): FloatCol { return { type: 'float', description }; }
+
+export type CoordCol = { type: 'coord' } & BaseCol
+export function CoordCol(description: string): CoordCol { return { type: 'coord', description }; }
+
+export type EnumCol = { type: 'enum', subType: 'int' | 'str', values: string[] } & BaseCol
+export function EnumCol(values: string[], subType: 'int' | 'str', description: string): EnumCol {
+    return { type: 'enum', description, values, subType };
+}
+
+export type VectorCol = { type: 'vector', length: number } & BaseCol
+export function VectorCol(length: number, description: string): VectorCol {
+    return { type: 'vector', description, length };
+}
+
+export type MatrixCol = { type: 'matrix', rows: number, columns: number } & BaseCol
+export function MatrixCol(columns: number, rows: number, description: string): MatrixCol {
+    return { type: 'matrix', description, columns, rows };
+}
+
+export type ListCol = { type: 'list', subType: 'int' | 'str' | 'float' | 'coord', separator: string } & BaseCol
+export function ListCol(subType: 'int' | 'str' | 'float' | 'coord', separator: string, description: string): ListCol {
+    return { type: 'list', description, separator, subType };
+}
+
+export type Filter = { [ table: string ]: { [ column: string ]: true } }
+
+export function mergeFilters (...filters: Filter[]) {
+    const n = filters.length;
+    const mergedFilter: Filter = {};
+    const fields: Map<string, number> = new Map();
+    filters.forEach(filter => {
+        Object.keys(filter).forEach(category => {
+            Object.keys(filter[ category ]).forEach(field => {
+                const key = `${category}.${field}`;
+                const value = fields.get(key) || 0;
+                fields.set(key, value + 1);
+            });
+        });
+    });
+    fields.forEach((v, k) => {
+        if (v !== n) return;
+        const [categoryName, fieldName] = k.split('.');
+        if (categoryName in mergedFilter) {
+            mergedFilter[categoryName][fieldName] = true;
+        } else {
+            mergedFilter[categoryName] = { fieldName: true };
+        }
+    });
+    return mergedFilter;
+}

src/apps/demos/lighting/index.ts

@@ -1,166 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { createPlugin, DefaultPluginSpec } from '../../../mol-plugin';
-import './index.html'
-import { PluginContext } from '../../../mol-plugin/context';
-import { PluginCommands } from '../../../mol-plugin/command';
-import { StateTransforms } from '../../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../../mol-plugin/state/transforms/representation';
-import { PluginStateObject as PSO } from '../../../mol-plugin/state/objects';
-import { StateBuilder } from '../../../mol-state';
-import { Canvas3DProps } from '../../../mol-canvas3d/canvas3d';
-require('mol-plugin/skin/light.scss')
-
-type SupportedFormats = 'cif' | 'pdb'
-type LoadParams = { url: string, format?: SupportedFormats, assemblyId?: string }
-
-const Canvas3DPresets = {
-    illustrative: {
-        multiSample: {
-            mode: 'temporal' as Canvas3DProps['multiSample']['mode']
-        },
-        postprocessing: {
-            occlusionEnable: true,
-            occlusionBias: 0.8,
-            occlusionKernelSize: 6,
-            outlineEnable: true,
-        },
-        renderer: {
-            ambientIntensity: 1,
-            lightIntensity: 0,
-        }
-    },
-    occlusion: {
-        multiSample: {
-            mode: 'temporal' as Canvas3DProps['multiSample']['mode']
-        },
-        postprocessing: {
-            occlusionEnable: true,
-            occlusionBias: 0.8,
-            occlusionKernelSize: 6,
-            outlineEnable: false,
-        },
-        renderer: {
-            ambientIntensity: 0.4,
-            lightIntensity: 0.6,
-        }
-    },
-    standard: {
-        multiSample: {
-            mode: 'off' as Canvas3DProps['multiSample']['mode']
-        },
-        postprocessing: {
-            occlusionEnable: false,
-            outlineEnable: false,
-        },
-        renderer: {
-            ambientIntensity: 0.4,
-            lightIntensity: 0.6,
-        }
-    }
-}
-
-type Canvas3DPreset = keyof typeof Canvas3DPresets
-
-function getPreset(preset: Canvas3DPreset) {
-    switch (preset) {
-        case 'illustrative': return Canvas3DPresets['illustrative']
-        case 'standard': return Canvas3DPresets['standard']
-        case 'occlusion': return Canvas3DPresets['occlusion']
-    }
-}
-
-class LightingDemo {
-    plugin: PluginContext;
-
-    init(target: string | HTMLElement) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec,
-            layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
-                },
-                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
-            }
-        });
-
-        this.setPreset('illustrative');
-    }
-
-    setPreset(preset: Canvas3DPreset) {
-        const props = getPreset(preset)
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
-            ...props,
-            multiSample: {
-                ...this.plugin.canvas3d.props.multiSample,
-                ...props.multiSample
-            },
-            renderer: {
-                ...this.plugin.canvas3d.props.renderer,
-                ...props.renderer
-            },
-            postprocessing: {
-                ...this.plugin.canvas3d.props.postprocessing,
-                ...props.postprocessing
-            },
-        }});
-    }
-
-    private download(b: StateBuilder.To<PSO.Root>, url: string) {
-        return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
-    }
-
-    private parse(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, assemblyId: string) {
-        const parsed = format === 'cif'
-            ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
-            : b.apply(StateTransforms.Model.TrajectoryFromPDB);
-
-        return parsed
-            .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
-            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
-    }
-
-    private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'spacefill', {}, 'illustrative'), { ref: 'seq-visual' });
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'ball-and-stick'), { ref: 'het-visual' });
-        return visualRoot;
-    }
-
-    private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
-    async load({ url, format = 'cif', assemblyId = '' }: LoadParams) {
-        let loadType: 'full' | 'update' = 'full';
-
-        const state = this.plugin.state.dataState;
-
-        if (this.loadedParams.url !== url || this.loadedParams.format !== format) {
-            loadType = 'full';
-        } else if (this.loadedParams.url === url) {
-            if (state.select('asm').length > 0) loadType = 'update';
-        }
-
-        let tree: StateBuilder.Root;
-        if (loadType === 'full') {
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
-            tree = state.build();
-            this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
-        } else {
-            tree = state.build();
-            tree.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
-        }
-
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
-        this.loadedParams = { url, format, assemblyId };
-        PluginCommands.Camera.Reset.dispatch(this.plugin, { });
-    }
-}
-
-(window as any).LightingDemo = new LightingDemo();

src/apps/model-server-query/index.html

@@ -1,12 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <title>Mol* ModelServer Query Builder</title>
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./index.js"></script>
-    </body>
-</html>

src/apps/model-server-query/index.tsx

@@ -1,134 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import * as React from 'react'
-import * as ReactDOM from 'react-dom'
-import * as Rx from 'rxjs'
-
-import { QueryDefinition, QueryList } from '../../servers/model/server/api'
-
-import './index.html'
-
-interface State {
-    query: Rx.BehaviorSubject<QueryDefinition>,
-    id: Rx.BehaviorSubject<string>,
-    params: Rx.BehaviorSubject<any>,
-    isBinary: Rx.BehaviorSubject<boolean>,
-    models: Rx.BehaviorSubject<number[]>,
-    url: Rx.Subject<string>
-}
-
-class Root extends React.Component<{ state: State }, {  }> {
-    render() {
-        return <div>
-            <div>
-                Query: <QuerySelect state={this.props.state} />
-            </div>
-            <div>
-                ID: <input type='text' onChange={t => this.props.state.id.next(t.currentTarget.value)} />
-            </div>
-            <div>
-                Params:<br/>
-                <QueryParams state={this.props.state} />
-            </div>
-            <div>
-                Model numbers (empty for all): <ModelNums state={this.props.state} />
-            </div>
-            <div>
-                <input type='checkbox' onChange={t => this.props.state.isBinary.next(!!t.currentTarget.checked)} /> Binary
-            </div>
-            <div>
-                Query string:
-                <QueryUrl state={this.props.state} />
-            </div>
-        </div>
-    }
-}
-
-class QuerySelect extends React.Component<{ state: State }> {
-    render() {
-        return <select onChange={s => this.props.state.query.next(QueryList[+s.currentTarget.value].definition)}>
-            { QueryList.map((q, i) => <option value={i} key={i} selected={i === 1}>{q.definition.niceName}</option>) }
-        </select>
-    }
-}
-
-class QueryParams extends React.Component<{ state: State }, { prms: string }> {
-    state = { prms: '' };
-
-    parseParams(str: string) {
-        this.setState({ prms: str });
-        try {
-            const params = JSON.parse(str);
-            this.props.state.params.next(params);
-        } catch {
-            this.props.state.params.next({});
-        }
-    }
-
-    componentDidMount() {
-        this.props.state.query.subscribe(q => this.setState({ prms: formatParams(q) }))
-    }
-
-    render() {
-        return <textarea style={{height: '300px'}} value={this.state.prms} cols={80} onChange={t => this.parseParams(t.currentTarget.value)} />;
-    }
-}
-
-class QueryUrl extends React.Component<{ state: State }, { queryString: string }> {
-    state = { queryString: '' };
-
-    componentDidMount() {
-        this.props.state.url.subscribe(url => this.setState({ queryString: url }))
-    }
-
-    render() {
-        return <input type='text' value={this.state.queryString} style={{ width: '800px' }} />
-    }
-}
-
-class ModelNums extends React.Component<{ state: State }> {
-    render() {
-        return <input type='text' defaultValue='1' style={{ width: '300px' }} onChange={t =>
-            this.props.state.models.next(t.currentTarget.value.split(',')
-                .map(v => v.trim())
-                .filter(v => !!v)
-                .map(v => +v)
-                )} />
-    }
-}
-
-const state: State = {
-    query: new Rx.BehaviorSubject(QueryList[1].definition),
-    id: new Rx.BehaviorSubject('1cbs'),
-    params: new Rx.BehaviorSubject({ }),
-    isBinary: new Rx.BehaviorSubject<boolean>(false),
-    models: new Rx.BehaviorSubject<number[]>([]),
-    url: new Rx.Subject()
-}
-
-function formatParams(def: QueryDefinition) {
-    const prms = Object.create(null);
-    for (const p of def.jsonParams) {
-        prms[p.name] = p.exampleValues ? p.exampleValues[0] : void 0;
-    }
-    return JSON.stringify(prms, void 0, 2);
-}
-
-function formatUrl() {
-    const json = JSON.stringify({
-        name: state.query.value.name,
-        id: state.id.value,
-        modelNums: state.models.value.length ? state.models.value : void 0,
-        binary: state.isBinary.value,
-        params: state.params.value
-    });
-    state.url.next(encodeURIComponent(json));
-}
-
-Rx.merge(state.query, state.id, state.params, state.isBinary, state.models).subscribe(s => formatUrl());
-
-ReactDOM.render(<Root state={state} />, document.getElementById('app'));

src/apps/state-docs/index.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as _ from '../../mol-plugin/state/transforms'
+import * as _ from '../../mol-plugin-state/transforms';
 import { StateTransformer, StateObject } from '../../mol-state';
 import { StringBuilder } from '../../mol-util';
 import * as fs from 'fs';
@@ -13,7 +13,7 @@ import { PluginContext } from '../../mol-plugin/context';
 import { ParamDefinition } from '../../mol-util/param-definition';
 
 // force the transform to be evaluated
-_.StateTransforms.Data.Download.id
+_.StateTransforms.Data.Download.id;
 
 // Empty plugin context
 const ctx = new PluginContext({
@@ -32,7 +32,7 @@ function writeTransformer(t: StateTransformer) {
     StringBuilder.write(builder, `## <a name="${t.id.replace('.', '-')}"></a>${t.id} :: ${typeToString(t.definition.from)} -> ${typeToString(t.definition.to)}`);
     StringBuilder.newline(builder);
     if (t.definition.display.description) {
-        StringBuilder.write(builder, `*${t.definition.display.description}*`)
+        StringBuilder.write(builder, `*${t.definition.display.description}*`);
         StringBuilder.newline(builder);
     }
     StringBuilder.newline(builder);
@@ -48,7 +48,7 @@ function writeTransformer(t: StateTransformer) {
         StringBuilder.write(builder, `\`\`\`js\n${JSON.stringify(ParamDefinition.getDefaultValues(params), null, 2)}\n\`\`\``);
         StringBuilder.newline(builder);
     }
-    StringBuilder.write(builder, '----------------------------')
+    StringBuilder.write(builder, '----------------------------');
     StringBuilder.newline(builder);
 }
 
@@ -62,7 +62,7 @@ transformers.forEach(t => {
     StringBuilder.newline(builder);
 });
 StringBuilder.newline(builder);
-StringBuilder.write(builder, '----------------------------')
+StringBuilder.write(builder, '----------------------------');
 StringBuilder.newline(builder);
 transformers.forEach(t => writeTransformer(t));
 

src/apps/state-docs/pd-to-md.ts

@@ -19,9 +19,12 @@ function paramInfo(param: PD.Any, offset: number): string {
         case 'conditioned': return getParams(param.conditionParams, offset);
         case 'multi-select': return `Array of ${oToS(param.options)}`;
         case 'color': return 'Color as 0xrrggbb';
-        case 'color-list': return `One of ${oToS(param.options)}`;
+        case 'color-list': return `A list of colors as 0xrrggbb`;
         case 'vec3': return `3D vector [x, y, z]`;
+        case 'mat4': return `4x4 transformation matrix`;
+        case 'url': return `URL couple with unique identifier`;
         case 'file': return `JavaScript File Handle`;
+        case 'file-list': return `JavaScript FileList Handle`;
         case 'select': return `One of ${oToS(param.options)}`;
         case 'text': return 'String';
         case 'interval': return `Interval [min, max]`;
@@ -38,7 +41,7 @@ function paramInfo(param: PD.Any, offset: number): string {
     }
 }
 
-function oToS(options: [string, string][]) {
+function oToS(options: readonly (readonly [string, string] | readonly [string, string, string | undefined])[]) {
     return options.map(o => `'${o[0]}'`).join(', ');
 }
 

src/apps/structure-info/helpers.ts

@@ -4,19 +4,19 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as util from 'util'
-import * as fs from 'fs'
-import fetch from 'node-fetch'
+import * as util from 'util';
+import * as fs from 'fs';
+import fetch from 'node-fetch';
 require('util.promisify').shim();
 
-import { CIF } from '../../mol-io/reader/cif'
-import { Progress } from '../../mol-task'
+import { CIF } from '../../mol-io/reader/cif';
+import { Progress } from '../../mol-task';
 
 const readFileAsync = util.promisify(fs.readFile);
 
 async function readFile(path: string) {
     if (path.match(/\.bcif$/)) {
-        const input = await readFileAsync(path)
+        const input = await readFileAsync(path);
         const data = new Uint8Array(input.byteLength);
         for (let i = 0; i < input.byteLength; i++) data[i] = input[i];
         return data;

src/apps/structure-info/model.ts

@@ -5,17 +5,19 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as argparse from 'argparse'
+import * as argparse from 'argparse';
 require('util.promisify').shim();
 
-import { CifFrame } from '../../mol-io/reader/cif'
-import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing } from '../../mol-model/structure'
+import { CifFrame } from '../../mol-io/reader/cif';
+import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing } from '../../mol-model/structure';
 // import { Run, Progress } from '../../mol-task'
 import { OrderedSet } from '../../mol-data/int';
 import { openCif, downloadCif } from './helpers';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
 import { Sequence } from '../../mol-model/sequence';
+import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 
 
 async function downloadFromPdb(pdb: string) {
@@ -30,28 +32,30 @@ export async function readCifFile(path: string) {
 }
 
 export function atomLabel(model: Model, aI: number) {
-    const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy
-    const { label_atom_id } = atoms
-    const { label_comp_id, label_seq_id } = residues
-    const { label_asym_id } = chains
-    const rI = residueAtomSegments.index[aI]
-    const cI = chainAtomSegments.index[aI]
-    return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`
+    const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
+    const { label_atom_id } = atoms;
+    const { label_comp_id, label_seq_id } = residues;
+    const { label_asym_id } = chains;
+    const rI = residueAtomSegments.index[aI];
+    const cI = chainAtomSegments.index[aI];
+    return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`;
 }
 
 export function residueLabel(model: Model, rI: number) {
-    const { residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy
-    const { label_comp_id, label_seq_id } = residues
-    const { label_asym_id } = chains
-    const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]]
-    return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`
+    const { residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
+    const { label_comp_id, label_seq_id } = residues;
+    const { label_asym_id } = chains;
+    const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]];
+    return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`;
 }
 
 export function printSecStructure(model: Model) {
     console.log('\nSecondary Structure\n=============');
     const { residues } = model.atomicHierarchy;
-    const { key, elements } = model.properties.secondaryStructure;
+    const secondaryStructure = ModelSecondaryStructure.Provider.get(model);
+    if (!secondaryStructure) return;
 
+    const { key, elements } = secondaryStructure;
     const count = residues._rowCount;
     let rI = 0;
     while (rI < count) {
@@ -65,14 +69,14 @@ export function printSecStructure(model: Model) {
     }
 }
 
-export function printLinks(structure: Structure, showIntra: boolean, showInter: boolean) {
+export function printBonds(structure: Structure, showIntra: boolean, showInter: boolean) {
     if (showIntra) {
-        console.log('\nIntra Unit Links\n=============');
+        console.log('\nIntra Unit Bonds\n=============');
         for (const unit of structure.units) {
             if (!Unit.isAtomic(unit)) continue;
 
             const elements = unit.elements;
-            const { a, b, edgeCount } = unit.links;
+            const { a, b, edgeCount } = unit.bonds;
             const { model } = unit;
 
             if (!edgeCount) continue;
@@ -86,20 +90,20 @@ export function printLinks(structure: Structure, showIntra: boolean, showInter:
     }
 
     if (showInter) {
-        console.log('\nInter Unit Links\n=============');
-        const links = structure.links;
+        console.log('\nInter Unit Bonds\n=============');
+        const bonds = structure.interUnitBonds;
         for (const unit of structure.units) {
             if (!Unit.isAtomic(unit)) continue;
 
-            for (const pairLinks of links.getLinkedUnits(unit)) {
-                if (!pairLinks.areUnitsOrdered || pairLinks.bondCount === 0) continue;
+            for (const pairBonds of bonds.getConnectedUnits(unit)) {
+                if (!pairBonds.areUnitsOrdered || pairBonds.edgeCount === 0) continue;
 
-                const { unitA, unitB } = pairLinks;
-                console.log(`${pairLinks.unitA.id} - ${pairLinks.unitB.id}: ${pairLinks.bondCount} bond(s)`);
+                const { unitA, unitB } = pairBonds;
+                console.log(`${pairBonds.unitA.id} - ${pairBonds.unitB.id}: ${pairBonds.edgeCount} bond(s)`);
 
-                for (const aI of pairLinks.linkedElementIndices) {
-                    for (const link of pairLinks.getBonds(aI)) {
-                        console.log(`${atomLabel(unitA.model, unitA.elements[aI])} -- ${atomLabel(unitB.model, unitB.elements[link.indexB])}`);
+                for (const aI of pairBonds.connectedIndices) {
+                    for (const bond of pairBonds.getEdges(aI)) {
+                        console.log(`${atomLabel(unitA.model, unitA.elements[aI])} -- ${atomLabel(unitB.model, unitB.elements[bond.indexB])}`);
                     }
                 }
             }
@@ -112,25 +116,13 @@ export function printSequence(model: Model) {
     const { byEntityKey } = model.sequence;
     for (const key of Object.keys(byEntityKey)) {
         const { sequence, entityId } = byEntityKey[+key];
-        const { seqId, compId } = sequence
-        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)} (offset ${sequence.offset}), ${seqId.value(seqId.rowCount - 1)}) (${compId.value(0)}, ${compId.value(compId.rowCount - 1)})`);
+        const { seqId, compId } = sequence;
+        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)}, ${seqId.value(seqId.rowCount - 1)}) (${compId.value(0)}, ${compId.value(compId.rowCount - 1)})`);
         console.log(`${Sequence.getSequenceString(sequence)}`);
     }
     console.log();
 }
 
-export function printModRes(model: Model) {
-    console.log('\nModified Residues\n=============');
-    const map = model.properties.modifiedResidues.parentId;
-    const { label_comp_id, _rowCount } = model.atomicHierarchy.residues;
-    for (let i = 0; i < _rowCount; i++) {
-        const comp_id = label_comp_id.value(i);
-        if (!map.has(comp_id)) continue;
-        console.log(`[${i}] ${map.get(comp_id)} -> ${comp_id}`);
-    }
-    console.log();
-}
-
 export function printRings(structure: Structure) {
     console.log('\nRings\n=============');
     for (const unit of structure.units) {
@@ -140,7 +132,7 @@ export function printRings(structure: Structure) {
         for (let i = 0, _i = Math.min(5, all.length); i < _i; i++) {
             fps[fps.length] = UnitRing.fingerprint(unit, all[i]);
         }
-        if (all.length > 5) fps.push('...')
+        if (all.length > 5) fps.push('...');
         console.log(`Unit ${unit.id}, ${all.length} ring(s), ${byFingerprint.size} different fingerprint(s).\n  ${fps.join(', ')}`);
     }
     console.log();
@@ -148,7 +140,7 @@ export function printRings(structure: Structure) {
 
 export function printUnits(structure: Structure) {
     console.log('\nUnits\n=============');
-    const l = StructureElement.Location.create();
+    const l = StructureElement.Location.create(structure);
 
     for (const unit of structure.units) {
         l.unit = unit;
@@ -179,7 +171,8 @@ export function printUnits(structure: Structure) {
 
 export function printSymmetryInfo(model: Model) {
     console.log('\nSymmetry Info\n=============');
-    const { symmetry } = model;
+    const symmetry = ModelSymmetry.Provider.get(model);
+    if (!symmetry) return;
     const { size, anglesInRadians } = symmetry.spacegroup.cell;
     console.log(`Spacegroup: ${symmetry.spacegroup.name} size: ${Vec3.toString(size)} angles: ${Vec3.toString(anglesInRadians)}`);
     console.log(`Assembly names: ${symmetry.assemblies.map(a => a.id).join(', ')}`);
@@ -214,14 +207,13 @@ async function run(frame: CifFrame, args: Args) {
     if (args.units) printUnits(structure);
     if (args.sym) printSymmetryInfo(models[0]);
     if (args.rings) printRings(structure);
-    if (args.intraLinks) printLinks(structure, true, false);
-    if (args.interLinks) printLinks(structure, false, true);
-    if (args.mod) printModRes(models[0]);
+    if (args.intraBonds) printBonds(structure, true, false);
+    if (args.interBonds) printBonds(structure, false, true);
     if (args.sec) printSecStructure(models[0]);
 }
 
 async function runDL(pdb: string, args: Args) {
-    const mmcif = await downloadFromPdb(pdb)
+    const mmcif = await downloadFromPdb(pdb);
     run(mmcif, args);
 }
 
@@ -242,8 +234,8 @@ parser.addArgument(['--seq'], { help: 'print sequence', action: 'storeTrue' });
 parser.addArgument(['--units'], { help: 'print units', action: 'storeTrue' });
 parser.addArgument(['--sym'], { help: 'print symmetry', action: 'storeTrue' });
 parser.addArgument(['--rings'], { help: 'print rings', action: 'storeTrue' });
-parser.addArgument(['--intraLinks'], { help: 'print intra unit links', action: 'storeTrue' });
-parser.addArgument(['--interLinks'], { help: 'print inter unit links', action: 'storeTrue' });
+parser.addArgument(['--intraBonds'], { help: 'print intra unit bonds', action: 'storeTrue' });
+parser.addArgument(['--interBonds'], { help: 'print inter unit bonds', action: 'storeTrue' });
 parser.addArgument(['--mod'], { help: 'print modified residues', action: 'storeTrue' });
 parser.addArgument(['--sec'], { help: 'print secoundary structure', action: 'storeTrue' });
 interface Args {
@@ -256,12 +248,12 @@ interface Args {
     units?: boolean,
     sym?: boolean,
     rings?: boolean,
-    intraLinks?: boolean,
-    interLinks?: boolean,
+    intraBonds?: boolean,
+    interBonds?: boolean,
     mod?: boolean,
     sec?: boolean,
 }
 const args: Args = parser.parseArgs();
 
-if (args.download) runDL(args.download, args)
-else if (args.file) runFile(args.file, args)
+if (args.download) runDL(args.download, args);
+else if (args.file) runFile(args.file, args);

src/apps/structure-info/volume.ts

@@ -4,43 +4,40 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as fs from 'fs'
-import * as argparse from 'argparse'
-import * as util from 'util'
+import * as fs from 'fs';
+import * as argparse from 'argparse';
+import * as util from 'util';
 
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume'
-import { downloadCif } from './helpers'
-import { CIF } from '../../mol-io/reader/cif'
-import { DensityServer_Data_Database } from '../../mol-io/reader/cif/schema/density-server';
+import { Volume } from '../../mol-model/volume';
+import { downloadCif } from './helpers';
+import { CIF } from '../../mol-io/reader/cif';
 import { Table } from '../../mol-data/db';
 import { StringBuilder } from '../../mol-util';
 import { Task } from '../../mol-task';
 import { createVolumeIsosurfaceMesh } from '../../mol-repr/volume/isosurface';
-import { createEmptyTheme } from '../../mol-theme/theme';
-import { volumeFromDensityServerData } from '../../mol-model-formats/volume/density-server';
+import { Theme } from '../../mol-theme/theme';
+import { volumeFromDensityServerData, DscifFormat } from '../../mol-model-formats/volume/density-server';
 
 require('util.promisify').shim();
 const writeFileAsync = util.promisify(fs.writeFile);
 
-type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
-
 async function getVolume(url: string): Promise<Volume> {
     const cif = await downloadCif(url, true);
     const data = CIF.schema.densityServer(cif.blocks[1]);
-    return { source: data, volume: await volumeFromDensityServerData(data).run() };
+    return await volumeFromDensityServerData(data).run();
 }
 
-function print(data: Volume) {
-    const { volume_data_3d_info } = data.source;
+function print(volume: Volume) {
+    if (!DscifFormat.is(volume.sourceData)) return;
+    const { volume_data_3d_info } = volume.sourceData.data;
     const row = Table.getRow(volume_data_3d_info, 0);
     console.log(row);
-    console.log(data.volume.cell);
-    console.log(data.volume.dataStats);
-    console.log(data.volume.fractionalBox);
+    console.log(volume.grid.transform);
+    console.log(volume.grid.stats);
 }
 
-async function doMesh(data: Volume, filename: string) {
-    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, data.volume, createEmptyTheme(), { isoValue: VolumeIsoValue.absolute(1.5) } )).run();
+async function doMesh(volume: Volume, filename: string) {
+    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) } )).run();
     console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
 
     // Export the mesh in OBJ format.
@@ -77,8 +74,8 @@ async function run(url: string, meshFilename: string) {
 }
 
 const parser = new argparse.ArgumentParser({
-addHelp: true,
-description: 'Info about VolumeData from mol-model module'
+    addHelp: true,
+    description: 'Info about VolumeData from mol-model module'
 });
 parser.addArgument([ '--emdb', '-e' ], {
     help: 'EMDB id, for example 8116',

src/apps/viewer/embedded.html

@@ -0,0 +1,63 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Embedded Mol* Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            var viewer = new molstar.Viewer('app', {
+                layoutIsExpanded: false,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
+
+                viewportShowExpand: true,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+
+                pdbProvider: 'rcsb',
+                emdbProvider: 'rcsb',
+            });
+            viewer.loadPdb('7bv2');
+            viewer.loadEmdb('EMD-30210');
+
+            // TODO add Volume.customProperty and load suggested isoValue via custom property
+            var sub = viewer.plugin.managers.volume.hierarchy.behaviors.selection.subscribe(function (value) {
+                if (value.volume?.representations[0]) {
+                    var ref = value.volume.representations[0].cell;
+                    var tree = viewer.plugin.state.data.build().to(ref).update({
+                        type: {
+                            name: 'isosurface',
+                            params: {
+                                isoValue: {
+                                    kind: 'relative',
+                                    relativeValue: 6
+                                }
+                            }
+                        },
+                        colorTheme: ref.transform.params?.colorTheme
+                    });
+                    viewer.plugin.runTask(viewer.plugin.state.data.updateTree(tree));
+                    if (typeof sub !== 'undefined') sub.unsubscribe();
+                }
+            });
+        </script>
+    </body>
+</html>

src/apps/viewer/extensions/cellpack/curve.ts

@@ -1,228 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Ludovic Autin <autin@scripps.edu>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Vec3, Quat, Mat4 } from '../../../../mol-math/linear-algebra';
-import { NumberArray } from '../../../../mol-util/type-helpers';
-
-interface Frame {
-    t: Vec3,
-    r: Vec3,
-    s: Vec3,
-}
-
-const a0Tmp = Vec3()
-const a1Tmp = Vec3()
-const a2Tmp = Vec3()
-const a3Tmp = Vec3()
-function CubicInterpolate(out: Vec3, y0: Vec3, y1: Vec3, y2: Vec3, y3: Vec3, mu: number): Vec3 {
-    const mu2 = mu * mu;
-    Vec3.sub(a0Tmp, y3, y2)
-    Vec3.sub(a0Tmp, a0Tmp, y0)
-    Vec3.add(a0Tmp, a0Tmp, y1)
-
-    Vec3.sub(a1Tmp, y0, y1)
-    Vec3.sub(a1Tmp, a1Tmp, a0Tmp)
-
-    Vec3.sub(a2Tmp, y2, y0)
-
-    Vec3.copy(a3Tmp, y1)
-
-    out[0] = a0Tmp[0] * mu * mu2 + a1Tmp[0] * mu2 + a2Tmp[0] * mu + a3Tmp[0]
-    out[1] = a0Tmp[1] * mu * mu2 + a1Tmp[1] * mu2 + a2Tmp[1] * mu + a3Tmp[1]
-    out[2] = a0Tmp[2] * mu * mu2 + a1Tmp[2] * mu2 + a2Tmp[2] * mu + a3Tmp[2]
-
-    return out
-}
-
-const cp0 = Vec3()
-const cp1 = Vec3()
-const cp2 = Vec3()
-const cp3 = Vec3()
-const currentPosition = Vec3()
-function ResampleControlPoints(points: NumberArray, segmentLength: number) {
-    const nP = points.length / 3
-    // insert a point at the end and at the begining
-    // controlPoints.Insert(0, controlPoints[0] + (controlPoints[0] - controlPoints[1]) / 2.0f);
-    // controlPoints.Add(controlPoints[nP - 1] + (controlPoints[nP - 1] - controlPoints[nP - 2]) / 2.0f);
-
-    let resampledControlPoints: Vec3[] = []
-    // resampledControlPoints.Add(controlPoints[0]);
-    // resampledControlPoints.Add(controlPoints[1]);
-
-    let idx = 1
-    // const currentPosition = Vec3.create(points[idx * 3], points[idx * 3 + 1], points[idx * 3 + 2])
-    Vec3.fromArray(currentPosition, points, idx * 3)
-
-    let lerpValue = 0.0
-
-    // Normalize the distance between control points
-    while (true) {
-        if (idx + 2 >= nP) break
-        Vec3.fromArray(cp0, points, (idx - 1) * 3)
-        Vec3.fromArray(cp1, points, idx * 3)
-        Vec3.fromArray(cp2, points, (idx + 1) * 3)
-        Vec3.fromArray(cp3, points, (idx + 2) * 3)
-        // const cp0 = Vec3.create(points[(idx-1)*3], points[(idx-1)*3+1], points[(idx-1)*3+2]) // controlPoints[currentPointId - 1];
-        // const cp1 = Vec3.create(points[idx*3], points[idx*3+1], points[idx*3+2]) // controlPoints[currentPointId];
-        // const cp2 = Vec3.create(points[(idx+1)*3], points[(idx+1)*3+1], points[(idx+1)*3+2]) // controlPoints[currentPointId + 1];
-        // const cp3 = Vec3.create(points[(idx+2)*3], points[(idx+2)*3+1], points[(idx+2)*3+2]); // controlPoints[currentPointId + 2];
-        let found = false
-        for (; lerpValue <= 1; lerpValue += 0.01) {
-            // lerp?slerp
-            // let candidate:Vec3 = Vec3.lerp(Vec3.zero(), cp0, cp1, lerpValue);
-            // const candidate:Vec3 = Vec3.bezier(Vec3.zero(), cp0, cp1, cp2, cp3, lerpValue);
-            const candidate = CubicInterpolate(Vec3(), cp0, cp1, cp2, cp3, lerpValue)
-            const d = Vec3.distance(currentPosition, candidate);
-            if (d > segmentLength) {
-                resampledControlPoints.push(candidate)
-                Vec3.copy(currentPosition, candidate)
-                found = true
-                break
-            }
-        }
-        if (!found) {
-            lerpValue = 0
-            idx += 1
-        }
-    }
-    return resampledControlPoints
-}
-
-
-const prevV = Vec3()
-const tmpV1 = Vec3()
-const tmpV2 = Vec3()
-const tmpV3 = Vec3()
-
-// easier to align to theses normals
-function GetSmoothNormals(points: Vec3[]) {
-    const nP: number = points.length;
-    const smoothNormals: Vec3[] = []
-    if (points.length < 3) {
-        for (let i = 0; i < points.length; ++i)
-            smoothNormals.push(Vec3.normalize(Vec3(), points[i]))
-        return smoothNormals;
-    }
-    let p0 = points[0]
-    let p1 = points[1]
-    let p2 = points[2]
-    const p21 = Vec3.sub(tmpV1, p2, p1)
-    const p01 =  Vec3.sub(tmpV2, p0, p1)
-    const p0121 = Vec3.cross(tmpV3, p01, p21)
-    Vec3.normalize(prevV, p0121)
-    smoothNormals.push(Vec3.clone(prevV))
-    for (let i = 1; i < points.length - 1; ++i) {
-        p0 = points[i - 1]
-        p1 = points[i]
-        p2 = points[i + 1]
-        const t = Vec3.normalize(tmpV1, Vec3.sub(tmpV1, p2 , p0))
-        const b = Vec3.normalize(tmpV2, Vec3.cross(tmpV2, t, prevV))
-        const n = Vec3.normalize(Vec3(), Vec3.cross(tmpV3, t, b))
-        Vec3.negate(n, n)
-        Vec3.copy(prevV, n)
-        smoothNormals.push(n)
-    }
-    const last = Vec3()
-    Vec3.normalize(last, Vec3.cross(last,
-        Vec3.sub(tmpV1, points[nP - 3], points[nP-2]),
-        Vec3.sub(tmpV2, points[nP-2] , points[nP-1]))
-    )
-    smoothNormals.push(last)
-    return smoothNormals;
-}
-
-const frameTmpV1 = Vec3()
-const frameTmpV2 = Vec3()
-const frameTmpV3 = Vec3()
-
-function getFrame(reference: Vec3, tangent: Vec3) {
-    const t = Vec3.normalize(Vec3(), tangent);
-    // make reference vector orthogonal to tangent
-    const proj_r_to_t = Vec3.scale(
-        frameTmpV1, tangent, Vec3.dot(reference, tangent) / Vec3.dot(tangent, tangent)
-    )
-    const r = Vec3.normalize(Vec3(), Vec3.sub(frameTmpV2, reference, proj_r_to_t))
-    // make bitangent vector orthogonal to the others
-    const s = Vec3.normalize(Vec3(), Vec3.cross(frameTmpV3, t, r))
-    return { t, r, s }
-}
-
-const mfTmpV1 = Vec3()
-const mfTmpV2 = Vec3()
-const mfTmpV3 = Vec3()
-const mfTmpV4 = Vec3()
-const mfTmpV5 = Vec3()
-const mfTmpV6 = Vec3()
-const mfTmpV7 = Vec3()
-const mfTmpV8 = Vec3()
-const mfTmpV9 = Vec3()
-
-// easier to align to theses normals
-// https://github.com/bzamecnik/gpg/blob/master/rotation-minimizing-frame/rmf.py
-function GetMiniFrame(points: Vec3[], normals: Vec3[]) {
-    const frames: Frame[] = [];
-    const t0 = Vec3.normalize(mfTmpV1, Vec3.sub(mfTmpV1, points[1], points[0]))
-    frames.push(getFrame(normals[0], t0))
-
-    for (let i = 0; i< points.length-2; ++i) {
-        const t2 = Vec3.normalize(mfTmpV1, Vec3.sub(mfTmpV1, points[i+2], points[i+1]))
-        const v1 = Vec3.sub(mfTmpV2, points[i + 1], points[i]) // this is tangeant
-        const c1 = Vec3.dot(v1, v1)
-        // compute r_i^L = R_1 * r_i
-        const v1r = Vec3.scale(mfTmpV3, v1, (2.0 / c1) * Vec3.dot(v1, frames[i].r))
-        const ref_L_i = Vec3.sub(mfTmpV4, frames[i].r, v1r)
-        // compute t_i^L = R_1 * t_i
-        const v1t = Vec3.scale(mfTmpV5, v1, (2.0 / c1) * Vec3.dot(v1, frames[i].t))
-        const tan_L_i = Vec3.sub(mfTmpV6, frames[i].t, v1t)
-        // # compute reflection vector of R_2
-        const v2 =  Vec3.sub(mfTmpV7, t2 , tan_L_i)
-        const c2 = Vec3.dot(v2, v2)
-        // compute r_(i+1) = R_2 * r_i^L
-        const v2l = Vec3.scale(mfTmpV8, v1, (2.0/c2) * Vec3.dot(v2, ref_L_i))
-        const ref_next = Vec3.sub(mfTmpV9, ref_L_i, v2l) // ref_L_i - (2 / c2) * v2.dot(ref_L_i) * v2
-        frames.push(getFrame(ref_next, t2)) // frames.append(Frame(ref_next, tangents[i+1]))
-    }
-    return frames;
-}
-
-const rpTmpVec1 = Vec3()
-
-export function getMatFromResamplePoints(points: NumberArray) {
-    const segmentLength = 3.4
-    const new_points = ResampleControlPoints(points, 3.4)
-    const npoints = new_points.length
-    const new_normal = GetSmoothNormals(new_points)
-    const frames = GetMiniFrame(new_points, new_normal)
-    const limit = npoints
-    const transforms: Mat4[] = []
-    const pti = Vec3.copy(rpTmpVec1, new_points[0]);
-    // console.log(new_points.length)
-    // console.log(points.length/3)
-    // console.log(limit)
-    // console.log(segmentLength)
-    for (let i = 0; i<npoints-2; ++i) {
-        const pti1: Vec3 = new_points[i+1] // Vec3.create(points[(i+1)*3],points[(i+1)*3+1],points[(i+1)*3+2]);
-        const d = Vec3.distance(pti, pti1)
-        if (d >= segmentLength) {
-            // use twist or random?
-            const quat = Quat.rotationTo(Quat.zero(), Vec3.create(0, 0, 1), frames[i].t) // Quat.rotationTo(Quat.zero(), Vec3.create(0,0,1),new_normal[i]);//Quat.rotationTo(Quat.zero(), Vec3.create(0,0,1),direction);new_normal
-            const rq = Quat.setAxisAngle(Quat.zero(), frames[i].t, Math.random()*3.60 ) // Quat.setAxisAngle(Quat.zero(),direction, Math.random()*3.60 );//Quat.identity();//
-            const m = Mat4.fromQuat(Mat4.zero(), Quat.multiply(Quat.zero(), rq, quat)) // Mat4.fromQuat(Mat4.zero(),Quat.multiply(Quat.zero(),quat1,quat2));//Mat4.fromQuat(Mat4.zero(),quat);//Mat4.identity();//Mat4.fromQuat(Mat4.zero(),Quat.multiply(Quat.zero(),rq,quat));
-            // let pos:Vec3 = Vec3.add(Vec3.zero(),pti1,pti)
-            // pos = Vec3.scale(pos,pos,1.0/2.0);
-            // Vec3.makeRotation(Mat4.zero(),Vec3.create(0,0,1),frames[i].t);//
-            Mat4.setTranslation(m, pti1)
-            // let m2:Mat4 = GetTubePropertiesMatrix(pti,pti1);
-            // let q:Quat = Quat.rotationTo(Quat.zero(), Vec3.create(0,1,0),Vec3.create(0,0,1))
-            // m2=Mat4.mul(Mat4.identity(),Mat4.fromQuat(Mat4.zero(),q),m2);
-            transforms.push(m)
-            Vec3.copy(pti, pti1)
-        }
-        if (transforms.length >= limit) break
-    }
-    return transforms
-}

src/apps/viewer/extensions/cellpack/data.ts

@@ -1,62 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Vec3, Quat } from '../../../../mol-math/linear-algebra';
-
-export interface CellPack {
-    cell: Cell
-    packings: CellPacking[]
-}
-
-export interface CellPacking {
-    name: string,
-    location: 'surface' | 'interior' | 'cytoplasme',
-    ingredients: Packing['ingredients']
-}
-
-//
-
-export interface Cell {
-    recipe: Recipe
-    cytoplasme?: Packing
-    compartments?: { [key: string]: Compartment }
-}
-
-export interface Recipe {
-    setupfile: string
-    /** First entry is name, secound is path: [name: string, path: string][] */
-    paths: [string, string][]
-    version: string
-    name: string
-}
-
-export interface Compartment {
-    surface?: Packing
-    interior?: Packing
-}
-
-export interface Packing {
-    ingredients: { [key: string]: Ingredient }
-}
-
-export interface Ingredient {
-    source: IngredientSource
-    results: [Vec3, Quat][]
-    name: string
-    positions?: [Vec3[]] // why wrapped in an extra array?
-    radii?: [number[]] // why wrapped in an extra array?
-
-    /** Number of `curveX` properties in the object where `X` is a 0-indexed number */
-    nbCurve?: number
-    /** Curve properties are Vec3[] but that is not expressable in TypeScript */
-    [curveX: string]: unknown
-}
-
-export interface IngredientSource {
-    pdb: string
-    transform: { center: boolean, translate?: Vec3 }
-    biomt?: boolean
-}

src/apps/viewer/extensions/cellpack/model.ts

@@ -1,474 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { StateAction } from '../../../../mol-state';
-import { PluginContext } from '../../../../mol-plugin/context';
-import { PluginStateObject as PSO } from '../../../../mol-plugin/state/objects';
-import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-import { Ingredient, CellPacking, Cell } from './data';
-import { getFromPdb, getFromCellPackDB } from './util';
-import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext } from '../../../../mol-model/structure';
-import { trajectoryFromMmCIF } from '../../../../mol-model-formats/structure/mmcif';
-import { trajectoryFromPDB } from '../../../../mol-model-formats/structure/pdb';
-import { Mat4, Vec3, Quat } from '../../../../mol-math/linear-algebra';
-import { SymmetryOperator } from '../../../../mol-math/geometry';
-import { Task } from '../../../../mol-task';
-import { StructureRepresentation3DHelpers } from '../../../../mol-plugin/state/transforms/representation';
-import { StateTransforms } from '../../../../mol-plugin/state/transforms';
-import { distinctColors } from '../../../../mol-util/color/distinct';
-import { ModelIndexColorThemeProvider } from '../../../../mol-theme/color/model-index';
-import { Hcl } from '../../../../mol-util/color/spaces/hcl';
-import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl } from './state';
-import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
-import { getMatFromResamplePoints } from './curve';
-import { compile } from '../../../../mol-script/runtime/query/compiler';
-import { UniformColorThemeProvider } from '../../../../mol-theme/color/uniform';
-import { ThemeRegistryContext } from '../../../../mol-theme/theme';
-import { ColorTheme } from '../../../../mol-theme/color';
-import { _parse_mmCif } from '../../../../mol-model-formats/structure/mmcif/parser';
-import { ModelFormat } from '../../../../mol-model-formats/structure/format';
-import { CifCategory, CifField } from '../../../../mol-io/reader/cif';
-import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
-import { Column } from '../../../../mol-data/db';
-
-function getCellPackModelUrl(fileName: string, baseUrl: string) {
-    return `${baseUrl}/results/${fileName}`
-}
-
-async function getModel(id: string, baseUrl: string) {
-    let model: Model;
-    if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
-        // return
-        const cif = await getFromPdb(id)
-        model = (await trajectoryFromMmCIF(cif).run())[0]
-    } else {
-        const pdb = await getFromCellPackDB(id, baseUrl)
-        model = (await trajectoryFromPDB(pdb).run())[0]
-    }
-    return model
-}
-
-async function getStructure(model: Model, props: { assembly?: string } = {}) {
-    let structure = Structure.ofModel(model)
-    const { assembly } = props
-
-    if (assembly) {
-        structure = await StructureSymmetry.buildAssembly(structure, assembly).run()
-    }
-
-    const query = MS.struct.modifier.union([
-        MS.struct.generator.atomGroups({
-            'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
-        })
-    ])
-    const compiled = compile<StructureSelection>(query)
-    const result = compiled(new QueryContext(structure))
-    structure = StructureSelection.unionStructure(result)
-
-    return structure
-}
-
-function getTransform(trans: Vec3, rot: Quat) {
-    const q: Quat = Quat.create(-rot[3], rot[0], rot[1], rot[2])
-    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q)
-    Mat4.transpose(m, m)
-    Mat4.scale(m, m, Vec3.create(-1.0, 1.0, -1.0))
-    Mat4.setTranslation(m, trans)
-    return m
-}
-
-function getResultTransforms(results: Ingredient['results']) {
-    return results.map((r: Ingredient['results'][0]) => getTransform(r[0], r[1]))
-}
-
-function getCurveTransforms(ingredient: Ingredient) {
-    const n = ingredient.nbCurve || 0
-    const instances: Mat4[] = []
-
-    for (let i = 0; i < n; ++i) {
-        const cname = `curve${i}`
-        if (!(cname in ingredient)) {
-            // console.warn(`Expected '${cname}' in ingredient`)
-            continue
-        }
-        const _points = ingredient[cname] as Vec3[]
-        if (_points.length <= 2) {
-            // TODO handle curve with 2 or less points
-            continue
-        }
-        const points = new Float32Array(_points.length * 3)
-        for (let i = 0, il = _points.length; i < il; ++i) Vec3.toArray(_points[i], points, i * 3)
-        const newInstances = getMatFromResamplePoints(points)
-        instances.push(...newInstances)
-    }
-
-    return instances
-}
-
-function getAssembly(transforms: Mat4[], structure: Structure) {
-    const builder = Structure.Builder()
-    const { units } = structure;
-
-    for (let i = 0, il = transforms.length; i < il; ++i) {
-        const id = `${i + 1}`
-        const op = SymmetryOperator.create(id, transforms[i], { id, operList: [ id ] })
-        for (const unit of units) {
-            builder.addWithOperator(unit, op)
-        }
-    }
-
-    return builder.getStructure();
-}
-
-function getCifCurve(name: string, transforms: Mat4[], model: Model) {
-    const d = model.sourceData.data.atom_site
-    const n = d._rowCount
-    const rowCount = n * transforms.length
-
-    const { offsets, count } = model.atomicHierarchy.chainAtomSegments
-
-    const x = d.Cartn_x.toArray()
-    const y = d.Cartn_y.toArray()
-    const z = d.Cartn_z.toArray()
-
-    const Cartn_x = new Float32Array(rowCount)
-    const Cartn_y = new Float32Array(rowCount)
-    const Cartn_z = new Float32Array(rowCount)
-    const map = new Uint32Array(rowCount)
-    const seq = new Int32Array(rowCount)
-    let offset = 0
-    for (let c = 0; c < count; ++c) {
-        const cStart = offsets[c]
-        const cEnd = offsets[c + 1]
-        const cLength = cEnd - cStart
-        for (let t = 0, tl = transforms.length; t < tl; ++t) {
-            const m = transforms[t]
-            for (let j = cStart; j < cEnd; ++j) {
-                const i = offset + j - cStart
-                const xj = x[j], yj = y[j], zj = z[j]
-                Cartn_x[i] = m[0] * xj + m[4] * yj + m[8] * zj + m[12]
-                Cartn_y[i] = m[1] * xj + m[5] * yj + m[9] * zj + m[13]
-                Cartn_z[i] = m[2] * xj + m[6] * yj + m[10] * zj + m[14]
-                map[i] = j
-                seq[i] = t + 1
-            }
-            offset += cLength
-        }
-    }
-
-    function multColumn<T>(column: Column<T>) {
-        const array = column.toArray()
-        return Column.ofLambda({
-            value: row => array[map[row]],
-            areValuesEqual: (rowA, rowB) => map[rowA] === map[rowB] || array[map[rowA]] === array[map[rowB]],
-            rowCount, schema: column.schema
-        })
-    }
-
-    const _atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
-        auth_asym_id: CifField.ofColumn(multColumn(d.auth_asym_id)),
-        auth_atom_id: CifField.ofColumn(multColumn(d.auth_atom_id)),
-        auth_comp_id: CifField.ofColumn(multColumn(d.auth_comp_id)),
-        auth_seq_id: CifField.ofNumbers(seq),
-
-        B_iso_or_equiv: CifField.ofColumn(Column.ofConst(0, rowCount, Column.Schema.float)),
-        Cartn_x: CifField.ofNumbers(Cartn_x),
-        Cartn_y: CifField.ofNumbers(Cartn_y),
-        Cartn_z: CifField.ofNumbers(Cartn_z),
-        group_PDB: CifField.ofColumn(Column.ofConst('ATOM', rowCount, Column.Schema.str)),
-        id: CifField.ofColumn(Column.ofLambda({
-            value: row => row,
-            areValuesEqual: (rowA, rowB) => rowA === rowB,
-            rowCount, schema: d.id.schema,
-        })),
-
-        label_alt_id: CifField.ofColumn(multColumn(d.label_alt_id)),
-
-        label_asym_id: CifField.ofColumn(multColumn(d.label_asym_id)),
-        label_atom_id: CifField.ofColumn(multColumn(d.label_atom_id)),
-        label_comp_id: CifField.ofColumn(multColumn(d.label_comp_id)),
-        label_seq_id: CifField.ofNumbers(seq),
-        label_entity_id: CifField.ofColumn(Column.ofConst('1', rowCount, Column.Schema.str)),
-
-        occupancy: CifField.ofColumn(Column.ofConst(1, rowCount, Column.Schema.float)),
-        type_symbol: CifField.ofColumn(multColumn(d.type_symbol)),
-
-        pdbx_PDB_ins_code: CifField.ofColumn(Column.ofConst('', rowCount, Column.Schema.str)),
-        pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst(1, rowCount, Column.Schema.int)),
-    }
-
-    const categories = {
-        entity: CifCategory.ofTable('entity', model.sourceData.data.entity),
-        chem_comp: CifCategory.ofTable('chem_comp', model.sourceData.data.chem_comp),
-        atom_site: CifCategory.ofFields('atom_site', _atom_site)
-    }
-
-    return {
-        header: name,
-        categoryNames: Object.keys(categories),
-        categories
-    };
-}
-
-async function getCurve(name: string, transforms: Mat4[], model: Model) {
-    const cif = getCifCurve(name, transforms, model)
-
-    const curveModelTask = Task.create('Curve Model', async ctx => {
-        const format = ModelFormat.mmCIF(cif)
-        const models = await _parse_mmCif(format, ctx)
-        return models[0]
-    })
-
-    const curveModel = await curveModelTask.run()
-    return getStructure(curveModel)
-}
-
-async function getIngredientStructure(ingredient: Ingredient, baseUrl: string) {
-    const { name, source, results, nbCurve } = ingredient
-
-    // TODO can these be added to the library?
-    if (name === 'HIV1_CAhex_0_1_0') return
-    if (name === 'HIV1_CAhexCyclophilA_0_1_0') return
-    if (name === 'iLDL') return
-    if (name === 'peptides') return
-    if (name === 'lypoglycane') return
-
-    if (source.pdb === 'None') return
-
-    const model = await getModel(source.pdb || name, baseUrl)
-    if (!model) return
-
-    if (nbCurve) {
-        return getCurve(name, getCurveTransforms(ingredient), model)
-    } else {
-        const structure = await getStructure(model, { assembly: source.biomt ? '1' : undefined })
-        return getAssembly(getResultTransforms(results), structure)
-    }
-}
-
-export function createStructureFromCellPack(packing: CellPacking, baseUrl: string) {
-    return Task.create('Create Packing Structure', async ctx => {
-        const { ingredients, name } = packing
-        const structures: Structure[] = []
-        for (const iName in ingredients) {
-            if (ctx.shouldUpdate) await ctx.update(iName)
-            const s = await getIngredientStructure(ingredients[iName], baseUrl)
-            if (s) structures.push(s)
-        }
-
-        if (ctx.shouldUpdate) await ctx.update(`${name} - units`)
-        const builder = Structure.Builder({ label: name })
-        let offsetInvariantId = 0
-        for (const s of structures) {
-            if (ctx.shouldUpdate) await ctx.update(`${s.label}`)
-            let maxInvariantId = 0
-            for (const u of s.units) {
-                const invariantId = u.invariantId + offsetInvariantId
-                if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId
-                builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, invariantId)
-            }
-            offsetInvariantId += maxInvariantId
-        }
-
-        if (ctx.shouldUpdate) await ctx.update(`${name} - structure`)
-        const s = builder.getStructure()
-        return s
-    })
-}
-
-export const LoadCellPackModel = StateAction.build({
-    display: { name: 'Load CellPack Model' },
-    params: {
-        id: PD.Select('influenza_model1.json', [
-            ['blood_hiv_immature_inside.json', 'blood_hiv_immature_inside'],
-            ['BloodHIV1.0_mixed_fixed_nc1.cpr', 'BloodHIV1.0_mixed_fixed_nc1'],
-            ['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV-1_0.1.6-8_mixed_radii_pdb'],
-            ['influenza_model1.json', 'influenza_model1'],
-            ['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
-            ['curveTest', 'Curve Test'],
-        ]),
-        baseUrl: PD.Text(DefaultCellPackBaseUrl),
-        preset: PD.Group({
-            traceOnly: PD.Boolean(false),
-            representation: PD.Select('spacefill', [
-                ['spacefill', 'Spacefill'],
-                ['gaussian-surface', 'Gaussian Surface'],
-                ['point', 'Point'],
-            ] as ['spacefill' | 'gaussian-surface' | 'point', string][])
-        }, { isExpanded: true })
-    },
-    from: PSO.Root
-})(({ state, params }, ctx: PluginContext) => Task.create('CellPack Loader', async taskCtx => {
-    const url = getCellPackModelUrl(params.id, params.baseUrl)
-
-    const root = state.build().toRoot();
-
-    let cellPackBuilder: any
-
-    if (params.id === 'curveTest') {
-        const url = `${params.baseUrl}/extras/rna_allpoints.json`
-        const data = await ctx.fetch({ url, type: 'string' }).runInContext(taskCtx);
-        const { points } = await (new Response(data)).json() as { points: number[] }
-        const curve0: Vec3[] = []
-        for (let j = 0, jl = Math.min(points.length, 3 * 100); j < jl; j += 3) {
-            curve0.push(Vec3.fromArray(Vec3(), points, j))
-        }
-        const cell: Cell = {
-            recipe: { setupfile: '', paths: [], version: '', name: 'Curve Test' },
-            compartments: {
-                'CurveCompartment': {
-                    interior: {
-                        ingredients: {
-                            'CurveIngredient': {
-                                source: { pdb: 'RNA_U_Base.pdb', transform: { center: false } },
-                                results: [],
-                                name: 'RNA',
-                                nbCurve: 1,
-                                curve0
-                            }
-                        }
-                    }
-                }
-            }
-        }
-
-        cellPackBuilder = root
-            .apply(StateTransforms.Data.ImportJson, { data: cell }, { state: { isGhost: true } })
-            .apply(ParseCellPack)
-    } else {
-        cellPackBuilder = root
-            .apply(StateTransforms.Data.Download, { url, isBinary: false, label: params.id }, { state: { isGhost: true } })
-            .apply(StateTransforms.Data.ParseJson, undefined, { state: { isGhost: true } })
-            .apply(ParseCellPack)
-
-
-    }
-
-    const cellPackObject = await state.updateTree(cellPackBuilder).runInContext(taskCtx)
-    const { packings } = cellPackObject.data
-    const tree = state.build().to(cellPackBuilder.ref);
-
-    const isHiv = (
-        params.id === 'BloodHIV1.0_mixed_fixed_nc1.cpr' ||
-        params.id === 'HIV-1_0.1.6-8_mixed_radii_pdb.cpr'
-    )
-
-    if (isHiv) {
-        for (let i = 0, il = packings.length; i < il; ++i) {
-            if (packings[i].name === 'HIV1_capsid_3j3q_PackInner_0_1_0') {
-                const url = `${params.baseUrl}/extras/rna_allpoints.json`
-                const data = await ctx.fetch({ url, type: 'string' }).runInContext(taskCtx);
-                const { points } = await (new Response(data)).json() as { points: number[] }
-
-                const curve0: Vec3[] = []
-                for (let j = 0, jl = points.length; j < jl; j += 3) {
-                    curve0.push(Vec3.fromArray(Vec3(), points, j))
-                }
-                packings[i].ingredients['RNA'] = {
-                    source: { pdb: 'RNA_U_Base.pdb', transform: { center: false } },
-                    results: [],
-                    name: 'RNA',
-                    nbCurve: 1,
-                    curve0
-                }
-            }
-        }
-    }
-
-    const colors = distinctColors(packings.length)
-
-    for (let i = 0, il = packings.length; i < il; ++i) {
-        const hcl = Hcl.fromColor(Hcl(), colors[i])
-        const hue = [Math.max(0, hcl[0] - 35), Math.min(360, hcl[0] + 35)] as [number, number]
-        const p = { packing: i, baseUrl: params.baseUrl }
-
-        const expression = params.preset.traceOnly
-            ? MS.struct.generator.atomGroups({
-                'atom-test': MS.core.logic.or([
-                    MS.core.rel.eq([MS.ammp('label_atom_id'), 'CA']),
-                    MS.core.rel.eq([MS.ammp('label_atom_id'), 'P'])
-                ])
-            })
-            : MS.struct.generator.all()
-
-        tree.apply(StructureFromCellpack, p)
-            .apply(StateTransforms.Model.StructureSelectionFromExpression, { expression }, { state: { isGhost: true } })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.createParams(ctx, Structure.Empty, {
-                    repr: getReprParams(ctx, params.preset),
-                    color: getColorParams(hue)
-                })
-            )
-    }
-
-    if (isHiv) {
-        const url = `${params.baseUrl}/membranes/hiv_lipids.bcif`
-        tree.apply(StateTransforms.Data.Download, { label: 'hiv_lipids', url, isBinary: true }, { state: { isGhost: true } })
-            .apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
-            .apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
-            .apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
-            .apply(StateTransforms.Model.StructureFromModel, undefined, { state: { isGhost: true } })
-            .apply(StateTransforms.Misc.CreateGroup, { label: 'HIV1_envelope_Membrane' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.createParams(ctx, Structure.Empty, {
-                    repr: getReprParams(ctx, params.preset),
-                    color: UniformColorThemeProvider
-                })
-            )
-    }
-
-    console.time('cellpack')
-    await state.updateTree(tree).runInContext(taskCtx);
-    console.timeEnd('cellpack')
-}));
-
-function getReprParams(ctx: PluginContext, params: { representation: 'spacefill' | 'gaussian-surface' | 'point', traceOnly: boolean }) {
-    const { representation, traceOnly } = params
-    switch (representation) {
-        case 'spacefill':
-            return traceOnly
-                ? [
-                    ctx.structureRepresentation.registry.get('spacefill'),
-                    () => ({ sizeFactor: 2, ignoreHydrogens: true })
-                ] as [any, any]
-                : [
-                    ctx.structureRepresentation.registry.get('spacefill'),
-                    () => ({ ignoreHydrogens: true })
-                ] as [any, any]
-        case 'gaussian-surface':
-            return [
-                ctx.structureRepresentation.registry.get('gaussian-surface'),
-                () => ({
-                    quality: 'custom', resolution: 10, radiusOffset: 2,
-                    alpha: 1.0, flatShaded: false, doubleSided: false,
-                    ignoreHydrogens: true
-                })
-            ] as [any, any]
-        case 'point':
-            return [
-                ctx.structureRepresentation.registry.get('point'),
-                () => ({ ignoreHydrogens: true })
-            ] as [any, any]
-    }
-}
-
-function getColorParams(hue: [number, number]) {
-    return [
-        ModelIndexColorThemeProvider,
-        (c: ColorTheme.Provider<any>, ctx: ThemeRegistryContext) => {
-            return {
-                palette: {
-                    name: 'generate',
-                    params: {
-                        hue, chroma: [30, 80], luminance: [15, 85],
-                        clusteringStepCount: 50, minSampleCount: 800,
-                        maxCount: 75
-                    }
-                }
-            }
-        }
-    ] as [any, any]
-}

src/apps/viewer/extensions/cellpack/state.ts

@@ -1,74 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { PluginStateObject as PSO, PluginStateTransform } from '../../../../mol-plugin/state/objects';
-import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-import { Task } from '../../../../mol-task';
-import { CellPack as _CellPack, Cell, CellPacking } from './data';
-import { createStructureFromCellPack } from './model';
-
-// export const DefaultCellPackBaseUrl = 'https://cdn.jsdelivr.net/gh/mesoscope/cellPACK_data@master/cellPACK_database_1.1.0/'
-export const DefaultCellPackBaseUrl = 'https://mgldev.scripps.edu/projects/autoPACK/web/cellpackproject/'
-
-export class CellPack extends PSO.Create<_CellPack>({ name: 'CellPack', typeClass: 'Object' }) { }
-
-export { ParseCellPack }
-type ParseCellPack = typeof ParseCellPack
-const ParseCellPack = PluginStateTransform.BuiltIn({
-    name: 'parse-cellpack',
-    display: { name: 'Parse CellPack', description: 'Parse CellPack from JSON data' },
-    from: PSO.Format.Json,
-    to: CellPack
-})({
-    apply({ a }) {
-        return Task.create('Parse CellPack', async ctx => {
-            const cell = a.data as Cell
-
-            const packings: CellPacking[] = []
-            const { compartments, cytoplasme } = cell
-            if (compartments) {
-                for (const name in compartments) {
-                    const { surface, interior } = compartments[name]
-                    if (surface) packings.push({ name, location: 'surface', ingredients: surface.ingredients })
-                    if (interior) packings.push({ name, location: 'interior', ingredients: interior.ingredients })
-                }
-            }
-            if (cytoplasme) packings.push({ name: 'Cytoplasme', location: 'cytoplasme', ingredients: cytoplasme.ingredients })
-
-            return new CellPack({ cell, packings });
-        });
-    }
-});
-
-export { StructureFromCellpack }
-type StructureFromCellpack = typeof ParseCellPack
-const StructureFromCellpack = PluginStateTransform.BuiltIn({
-    name: 'structure-from-cellpack',
-    display: { name: 'Structure from CellPack', description: 'Create Structure from CellPack Packing' },
-    from: CellPack,
-    to: PSO.Molecule.Structure,
-    params: a => {
-        if (!a) {
-            return {
-                packing: PD.Numeric(0, {}, { description: 'Packing Index' }),
-                baseUrl: PD.Text(DefaultCellPackBaseUrl)
-            };
-        }
-        const options = a.data.packings.map((d, i) => [i, d.name] as [number, string])
-        return {
-            packing: PD.Select(0, options),
-            baseUrl: PD.Text(DefaultCellPackBaseUrl)
-        }
-    }
-})({
-    apply({ a, params }) {
-        return Task.create('Structure from CellPack', async ctx => {
-            const packing = a.data.packings[params.packing]
-            const structure = await createStructureFromCellPack(packing, params.baseUrl).runInContext(ctx)
-            return new PSO.Molecule.Structure(structure, { label: packing.name })
-        });
-    }
-});

src/apps/viewer/extensions/cellpack/util.ts

@@ -1,48 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { CIF } from '../../../../mol-io/reader/cif'
-import { parsePDB } from '../../../../mol-io/reader/pdb/parser';
-
-async function parseCif(data: string|Uint8Array) {
-    const comp = CIF.parse(data);
-    const parsed = await comp.run();
-    if (parsed.isError) throw parsed;
-    return parsed.result;
-}
-
-async function parsePDBfile(data: string, id: string) {
-    const comp = parsePDB(data, id);
-    const parsed = await comp.run();
-    if (parsed.isError) throw parsed;
-    return parsed.result;
-}
-
-async function downloadCif(url: string, isBinary: boolean) {
-    const data = await fetch(url);
-    return parseCif(isBinary ? new Uint8Array(await data.arrayBuffer()) : await data.text());
-}
-
-async function downloadPDB(url: string, id: string) {
-    const data = await fetch(url);
-    return parsePDBfile(await data.text(), id);
-}
-
-export async function getFromPdb(id: string) {
-    const parsed = await downloadCif(`https://files.rcsb.org/download/${id}.cif`, false);
-    return parsed.blocks[0];
-}
-
-function getCellPackDataUrl(id: string, baseUrl: string) {
-    const url = `${baseUrl}/other/${id}`
-    return url.endsWith('.pdb') ? url : `${url}.pdb`
-}
-
-export async function getFromCellPackDB(id: string, baseUrl: string) {
-    const name = id.endsWith('.pdb') ? id.substring(0, id.length - 4) : id
-    const parsed = await downloadPDB(getCellPackDataUrl(id, baseUrl), name);
-    return parsed;
-}

src/apps/viewer/extensions/jolecule.ts

@@ -1,167 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { StateTree, StateBuilder, StateAction, State } from '../../../mol-state';
-import { StateTransforms } from '../../../mol-plugin/state/transforms';
-import { createModelTree, complexRepresentation } from '../../../mol-plugin/state/actions/structure';
-import { PluginContext } from '../../../mol-plugin/context';
-import { PluginStateObject } from '../../../mol-plugin/state/objects';
-import { ParamDefinition } from '../../../mol-util/param-definition';
-import { PluginCommands } from '../../../mol-plugin/command';
-import { Vec3 } from '../../../mol-math/linear-algebra';
-import { PluginStateSnapshotManager } from '../../../mol-plugin/state/snapshots';
-import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
-import { Text } from '../../../mol-geo/geometry/text/text';
-import { UUID } from '../../../mol-util';
-import { ColorNames } from '../../../mol-util/color/names';
-import { Camera } from '../../../mol-canvas3d/camera';
-import { StructureRepresentation3DHelpers } from '../../../mol-plugin/state/transforms/representation';
-
-export const CreateJoleculeState = StateAction.build({
-    display: { name: 'Jolecule State Import' },
-    params: { id: ParamDefinition.Text('1mbo') },
-    from: PluginStateObject.Root
-})(async ({ ref, state, params }, plugin: PluginContext) => {
-    try {
-        const id = params.id.trim().toLowerCase();
-        const data = await plugin.runTask(plugin.fetch({ url: `https://jolecule.appspot.com/pdb/${id}.views.json`, type: 'json' })) as JoleculeSnapshot[];
-
-        data.sort((a, b) => a.order - b.order);
-
-        await PluginCommands.State.RemoveObject.dispatch(plugin, { state, ref });
-        plugin.state.snapshots.clear();
-
-        const template = createTemplate(plugin, state, id);
-        const snapshots = data.map((e, idx) => buildSnapshot(plugin, template, { e, idx, len: data.length }));
-        for (const s of snapshots) {
-            plugin.state.snapshots.add(s);
-        }
-
-        PluginCommands.State.Snapshots.Apply.dispatch(plugin, { id: snapshots[0].snapshot.id });
-    } catch (e) {
-        plugin.log.error(`Jolecule Failed: ${e}`);
-    }
-});
-
-interface JoleculeSnapshot {
-    order: number,
-    distances: { i_atom1: number, i_atom2: number }[],
-    labels: { i_atom: number, text: string }[],
-    camera: { up: Vec3, pos: Vec3, in: Vec3, slab: { z_front: number, z_back: number, zoom: number } },
-    selected: number[],
-    text: string
-}
-
-function createTemplate(plugin: PluginContext, state: State, id: string) {
-    const b = new StateBuilder.Root(state.tree);
-    const data = b.toRoot().apply(StateTransforms.Data.Download, { url: `https://www.ebi.ac.uk/pdbe/static/entry/${id}_updated.cif` }, { state: { isGhost: true }});
-    const model = createModelTree(data, 'cif');
-    const structure = model.apply(StateTransforms.Model.StructureFromModel, {});
-    complexRepresentation(plugin, structure, { hideWater: true });
-    return { tree: b.getTree(), structure: structure.ref };
-}
-
-const labelOptions: ParamDefinition.Values<Text.Params> = {
-    ...ParamDefinition.getDefaultValues(Text.Params),
-    tether: true,
-    sizeFactor: 1.3,
-    attachment: 'bottom-right',
-    offsetZ: 10,
-    background: true,
-    backgroundMargin: 0.2,
-    backgroundColor: ColorNames.skyblue,
-    backgroundOpacity: 0.9
-}
-
-// const distanceLabelOptions = {
-//     ...ParamDefinition.getDefaultValues(Text.Params),
-//     sizeFactor: 1,
-//     offsetX: 0,
-//     offsetY: 0,
-//     offsetZ: 10,
-//     background: true,
-//     backgroundMargin: 0.2,
-//     backgroundColor: ColorNames.snow,
-//     backgroundOpacity: 0.9
-// }
-
-function buildSnapshot(plugin: PluginContext, template: { tree: StateTree, structure: string }, params: { e: JoleculeSnapshot, idx: number, len: number }): PluginStateSnapshotManager.Entry {
-    const b = new StateBuilder.Root(template.tree);
-
-    let i = 0;
-    for (const l of params.e.labels) {
-        const expression = createExpression([l.i_atom]);
-        const group = b.to(template.structure)
-            .group(StateTransforms.Misc.CreateGroup, { label: `Label ${++i}` });
-
-        group
-            .apply(StateTransforms.Model.StructureSelectionFromExpression, { expression, label: 'Atom' })
-            .apply(StateTransforms.Representation.StructureLabels3D, {
-                target: { name: 'static-text', params: { value: l.text || '' } },
-                options: labelOptions
-            });
-
-        group
-            .apply(StateTransforms.Model.StructureSelectionFromExpression, { expression: MS.struct.modifier.wholeResidues([ expression ]), label: 'Residue' })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'ball-and-stick', {  }));
-    }
-    if (params.e.selected && params.e.selected.length > 0) {
-        b.to(template.structure)
-            .apply(StateTransforms.Model.StructureSelectionFromExpression, { expression: createExpression(params.e.selected), label: `Selected` })
-            .apply(StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'ball-and-stick'));
-    }
-    // TODO
-    // for (const l of params.e.distances) {
-    //     b.to('structure')
-    //         .apply(StateTransforms.Model.StructureSelectionFromExpression, { query: createQuery([l.i_atom1, l.i_atom2]), label: `Distance ${++i}` })
-    //         .apply(StateTransforms.Representation.StructureLabels3D, {
-    //             target: { name: 'static-text', params: { value: l. || '' } },
-    //             options: labelOptions
-    //         });
-    // }
-    return PluginStateSnapshotManager.Entry({
-        id: UUID.create22(),
-        data: { tree: StateTree.toJSON(b.getTree()) },
-        camera: {
-            current: getCameraSnapshot(params.e.camera),
-            transitionStyle: 'animate',
-            transitionDurationInMs: 350
-        }
-    }, {
-        name:  params.e.text
-    });
-}
-
-function getCameraSnapshot(e: JoleculeSnapshot['camera']): Camera.Snapshot {
-    const direction = Vec3.sub(Vec3(), e.pos, e.in);
-    Vec3.normalize(direction, direction);
-    const up = Vec3.sub(Vec3(), e.pos, e.up);
-    Vec3.normalize(up, up);
-
-    const s: Camera.Snapshot = {
-        mode: 'perspective',
-        fov: Math.PI / 4,
-        position: Vec3.scaleAndAdd(Vec3(), e.pos, direction, e.slab.zoom),
-        target: e.pos,
-        radius: (e.slab.z_back - e.slab.z_front) / 2,
-        fog: 50,
-        up,
-    };
-    return s;
-}
-
-function createExpression(atomIndices: number[]) {
-    if (atomIndices.length === 0) return MS.struct.generator.empty();
-
-    return MS.struct.generator.atomGroups({
-        'atom-test': atomIndices.length === 1
-            ? MS.core.rel.eq([MS.struct.atomProperty.core.sourceIndex(), atomIndices[0]])
-            : MS.core.set.has([MS.set.apply(null, atomIndices), MS.struct.atomProperty.core.sourceIndex()]),
-        'group-by': 0
-    });
-}

src/apps/viewer/index.html

@@ -34,10 +34,50 @@
                 height: 600px;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="app.css" />
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
     </head>
     <body>
         <div id="app"></div>
-        <script type="text/javascript" src="./index.js"></script>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+
+            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
+            if (debugMode) molstar.setDebugMode(debugMode);
+
+            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
+            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
+            var viewer = new molstar.Viewer('app', {
+                layoutShowControls: !hideControls,
+                viewportShowExpand: false,
+                pdbProvider: pdbProvider || 'pdbe',
+                emdbProvider: emdbProvider || 'pdbe',
+            });
+
+            var snapshotId = getParam('snapshot-id', '[^&]+').trim();
+            if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
+
+            var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
+            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
+            if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
+
+            var structureUrl = getParam('structure-url', '[^&]+').trim();
+            var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
+            var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
+            if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
+
+            var pdb = getParam('pdb', '[^&]+').trim();
+            if (pdb) viewer.loadPdb(pdb);
+
+            var pdbDev = getParam('pdb-dev', '[^&]+').trim();
+            if (pdbDev) viewer.loadPdbDev(pdbDev);
+
+            var emdb = getParam('emdb', '[^&]+').trim();
+            if (emdb) viewer.loadEmdb(emdb);
+        </script>
     </body>
 </html>

src/apps/viewer/index.ts

@@ -1,67 +1,182 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
+import '../../mol-util/polyfill';
 import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import './index.html'
-import './favicon.ico'
+import './index.html';
+import './embedded.html';
+import './favicon.ico';
 import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/command';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginSpec } from '../../mol-plugin/spec';
-import { CreateJoleculeState } from './extensions/jolecule';
-import { LoadCellPackModel } from './extensions/cellpack/model';
-import { StructureFromCellpack } from './extensions/cellpack/state';
-require('mol-plugin/skin/light.scss')
+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
+import { PluginConfig } from '../../mol-plugin/config';
+import { CellPack } from '../../extensions/cellpack';
+import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { Asset } from '../../mol-util/assets';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import { PluginState } from '../../mol-plugin/state';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
 
-function getParam(name: string, regex: string): string {
-    let r = new RegExp(`${name}=(${regex})[&]?`, 'i');
-    return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-}
+require('mol-plugin-ui/skin/light.scss');
 
-const hideControls = getParam('hide-controls', `[^&]+`) === '1';
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setProductionMode, setDebugMode } from '../../mol-util/debug';
 
-function init() {
-    const spec: PluginSpec = {
-        actions: [
-            ...DefaultPluginSpec.actions,
-            PluginSpec.Action(CreateJoleculeState),
-            PluginSpec.Action(LoadCellPackModel),
-            PluginSpec.Action(StructureFromCellpack),
-        ],
-        behaviors: [...DefaultPluginSpec.behaviors],
-        animations: [...DefaultPluginSpec.animations || []],
-        customParamEditors: DefaultPluginSpec.customParamEditors,
-        layout: {
-            initial: {
-                isExpanded: true,
-                showControls: !hideControls
+const Extensions = {
+    'cellpack': PluginSpec.Behavior(CellPack),
+    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
+    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
+    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport)
+};
+
+const DefaultViewerOptions = {
+    extensions: ObjectKeys(Extensions),
+    layoutIsExpanded: true,
+    layoutShowControls: true,
+    layoutShowRemoteState: true,
+    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
+    layoutShowSequence: true,
+    layoutShowLog: true,
+    layoutShowLeftPanel: true,
+
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
+    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
+    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
+    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+};
+type ViewerOptions = typeof DefaultViewerOptions;
+
+export class Viewer {
+    plugin: PluginContext
+
+    constructor(elementId: string, options: Partial<ViewerOptions> = {}) {
+        const o = { ...DefaultViewerOptions, ...options };
+
+        const spec: PluginSpec = {
+            actions: [...DefaultPluginSpec.actions],
+            behaviors: [
+                ...DefaultPluginSpec.behaviors,
+                ...o.extensions.map(e => Extensions[e]),
+            ],
+            animations: [...DefaultPluginSpec.animations || []],
+            customParamEditors: DefaultPluginSpec.customParamEditors,
+            layout: {
+                initial: {
+                    isExpanded: o.layoutIsExpanded,
+                    showControls: o.layoutShowControls,
+                    controlsDisplay: o.layoutControlsDisplay,
+                },
+                controls: {
+                    ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
+                    top: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                }
             },
-            controls: {
-                ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls
-            }
-        }
-    };
-    const plugin = createPlugin(document.getElementById('app')!, spec);
-    trySetSnapshot(plugin);
-}
+            components: {
+                ...DefaultPluginSpec.components,
+                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
+            },
+            config: [
+                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                [PluginConfig.State.DefaultServer, o.pluginStateServer],
+                [PluginConfig.State.CurrentServer, o.pluginStateServer],
+                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
+            ]
+        };
 
-async function trySetSnapshot(ctx: PluginContext) {
-    try {
-        const snapshotUrl = getParam('snapshot-url', `[^&]+`);
-        const snapshotId = getParam('snapshot-id', `[^&]+`);
-        if (!snapshotUrl && !snapshotId) return;
-        // TODO parametrize the server
-        const url = snapshotId
-            ? `https://webchem.ncbr.muni.cz/molstar-state/get/${snapshotId}`
-            : snapshotUrl;
-        await PluginCommands.State.Snapshots.Fetch.dispatch(ctx, { url })
-    } catch (e) {
-        ctx.log.error('Failed to load snapshot.');
-        console.warn('Failed to load snapshot', e);
+        const element = document.getElementById(elementId);
+        if (!element) throw new Error(`Could not get element with id '${elementId}'`);
+        this.plugin = createPlugin(element, spec);
     }
-}
 
-init();
+    async setRemoteSnapshot(id: string) {
+        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
+        await PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
+    }
+
+    async loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
+        await PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
+    }
+
+    async loadStructureFromUrl(url: string, format = 'cif', isBinary = false) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'url',
+                params: {
+                    url: Asset.Url(url),
+                    format: format as any,
+                    isBinary,
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    async loadPdb(pdb: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb' as const,
+                params: {
+                    provider: {
+                        id: pdb,
+                        server: {
+                            name: provider,
+                            params: PdbDownloadProvider[provider].defaultValue as any
+                        }
+                    },
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    async loadPdbDev(pdbDev: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb-dev' as const,
+                params: {
+                    provider: {
+                        id: pdbDev,
+                        encoding: 'bcif',
+                    },
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    async loadEmdb(emdb: string) {
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+            source: {
+                name: 'pdb-emd-ds' as const,
+                params: {
+                    provider: {
+                        id: emdb,
+                        server: provider,
+                    },
+                    detail: 3,
+                }
+            }
+        }));
+    }
+}

src/examples/basic-wrapper/coloring.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { CustomElementProperty } from '../../mol-model-props/common/custom-element-property';
@@ -9,22 +10,21 @@ import { Model, ElementIndex } from '../../mol-model/structure';
 import { Color } from '../../mol-util/color';
 
 export const StripedResidues = CustomElementProperty.create<number>({
-    isStatic: true,
+    label: 'Residue Stripes',
     name: 'basic-wrapper-residue-striping',
-    display: 'Residue Stripes',
     getData(model: Model) {
         const map = new Map<ElementIndex, number>();
         const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
         for (let i = 0, _i = model.atomicHierarchy.atoms._rowCount; i < _i; i++) {
             map.set(i as ElementIndex, residueIndex[i] % 2);
         }
-        return map;
+        return { value: map };
     },
     coloring: {
-        getColor(e) { return e === 0 ? Color(0xff0000) : Color(0x0000ff) },
+        getColor(e) { return e === 0 ? Color(0xff0000) : Color(0x0000ff); },
         defaultColor: Color(0x777777)
     },
-    format(e) {
-        return e === 0 ? 'Odd stripe' : 'Even stripe'
+    getLabel(e) {
+        return e === 0 ? 'Odd stripe' : 'Even stripe';
     }
-})
+});

src/examples/basic-wrapper/controls.tsx

@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginUIComponent } from '../../mol-plugin-ui/base';
+import * as React from 'react';
+
+export class CustomToastMessage extends PluginUIComponent {
+    render() {
+        return <>
+            Custom <i>Toast</i> content. No timeout.
+        </>;
+    }
+}

src/examples/basic-wrapper/index.html

@@ -41,7 +41,7 @@
                 display: block;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="app.css" />
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
         <script type="text/javascript" src="./index.js"></script>
     </head>
     <body>
@@ -50,18 +50,18 @@
             <input type='text' id='url' placeholder='url' />
             <input type='text' id='assemblyId' placeholder='assembly id' />
             <select id='format'>
-                <option value='cif' selected>CIF</option>
+                <option value='mmcif' selected>mmCIF</option>
                 <option value='pdb'>PDB</option>
             </select>
         </div>
         <div id="app"></div>
-        <script>      
+        <script>
             function $(id) { return document.getElementById(id); }
-        
+
             var pdbId = '1grm', assemblyId= '1';
             var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
-            var format = 'cif';
-            
+            var format = 'mmcif';
+
             $('url').value = url;
             $('url').onchange = function (e) { url = e.target.value; }
             $('assemblyId').value = assemblyId;
@@ -69,15 +69,8 @@
             $('format').value = format;
             $('format').onchange = function (e) { format = e.target.value; }
 
-            // var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
-            // var format = 'pdb';
-            // var assemblyId = 'deposited';
-
             BasicMolStarWrapper.init('app' /** or document.getElementById('app') */);
             BasicMolStarWrapper.setBackground(0xffffff);
-            // BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId });
-            // BasicMolStarWrapper.toggleSpin();
-
 
             addControl('Load Asym Unit', () => BasicMolStarWrapper.load({ url: url, format: format }));
             addControl('Load Assembly', () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId }));
@@ -86,7 +79,7 @@
 
             addHeader('Camera');
             addControl('Toggle Spin', () => BasicMolStarWrapper.toggleSpin());
-            
+
             addSeparator();
 
             addHeader('Animation');
@@ -104,13 +97,18 @@
             addHeader('Misc');
 
             addControl('Apply Stripes', () => BasicMolStarWrapper.coloring.applyStripes());
+            addControl('Default Coloring', () => BasicMolStarWrapper.coloring.applyDefault());
+
+            addHeader('Interactivity');
+            addControl('Highlight seq_id=7', () => BasicMolStarWrapper.interactivity.highlightOn());
+            addControl('Clear Highlight', () => BasicMolStarWrapper.interactivity.clearHighlight());
 
             addHeader('Tests');
 
             addControl('Static Superposition', () => BasicMolStarWrapper.tests.staticSuperposition());
             addControl('Dynamic Superposition', () => BasicMolStarWrapper.tests.dynamicSuperposition());
             addControl('Validation Tooltip', () => BasicMolStarWrapper.tests.toggleValidationTooltip());
-            
+
             addControl('Show Toasts', () => BasicMolStarWrapper.tests.showToasts());
             addControl('Hide Toasts', () => BasicMolStarWrapper.tests.hideToasts());
 

src/examples/basic-wrapper/index.ts

@@ -0,0 +1,162 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { EmptyLoci } from '../../mol-model/loci';
+import { StructureSelection } from '../../mol-model/structure';
+import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import { Script } from '../../mol-script/script';
+import { Color } from '../../mol-util/color';
+import { StripedResidues } from './coloring';
+import { CustomToastMessage } from './controls';
+import './index.html';
+import { buildStaticSuperposition, dynamicSuperpositionTest, StaticSuperpositionTestData } from './superposition';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { Asset } from '../../mol-util/assets';
+require('mol-plugin-ui/skin/light.scss');
+
+type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
+
+class BasicWrapper {
+    plugin: PluginContext;
+
+    init(target: string | HTMLElement) {
+        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
+            ...DefaultPluginSpec,
+            layout: {
+                initial: {
+                    isExpanded: false,
+                    showControls: false
+                },
+                controls: {
+                    // left: 'none'
+                }
+            },
+            components: {
+                remoteState: 'none'
+            }
+        });
+
+        this.plugin.representation.structure.themes.colorThemeRegistry.add(StripedResidues.colorThemeProvider!);
+        this.plugin.managers.lociLabels.addProvider(StripedResidues.labelProvider!);
+        this.plugin.customModelProperties.register(StripedResidues.propertyProvider, true);
+    }
+
+    async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
+        await this.plugin.clear();
+
+        const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary }, { state: { isGhost: true } });
+        const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
+
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
+            structure: assemblyId ? {
+                name: 'assembly',
+                params: { id: assemblyId }
+            } : {
+                name: 'model',
+                params: { }
+            },
+            showUnitcell: false,
+            representationPreset: 'auto'
+        });
+    }
+
+    setBackground(color: number) {
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: props => { props.renderer.backgroundColor = Color(color); } });
+    }
+
+    toggleSpin() {
+        if (!this.plugin.canvas3d) return;
+
+        PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: props => {
+                props.trackball.spin = !props.trackball.spin;
+            }
+        });
+        if (!this.plugin.canvas3d.props.trackball.spin) PluginCommands.Camera.Reset(this.plugin, {});
+    }
+
+    animate = {
+        modelIndex: {
+            maxFPS: 8,
+            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }); },
+            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }); },
+            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }); },
+            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }); },
+            stop: () => this.plugin.managers.animation.stop()
+        }
+    }
+
+    coloring = {
+        applyStripes: async () => {
+            this.plugin.dataTransaction(async () => {
+                for (const s of this.plugin.managers.structure.hierarchy.current.structures) {
+                    await this.plugin.managers.structure.component.updateRepresentationsTheme(s.components, { color: StripedResidues.propertyProvider.descriptor.name as any });
+                }
+            });
+        },
+        applyDefault: async () => {
+            this.plugin.dataTransaction(async () => {
+                for (const s of this.plugin.managers.structure.hierarchy.current.structures) {
+                    await this.plugin.managers.structure.component.updateRepresentationsTheme(s.components, { color: 'default' });
+                }
+            });
+        }
+    }
+
+    interactivity = {
+        highlightOn: () => {
+            const seq_id = 7;
+            const data = (this.plugin.state.data.select('asm')[0].obj as PluginStateObject.Molecule.Structure).data;
+            const sel = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
+                'residue-test': Q.core.rel.eq([Q.struct.atomProperty.macromolecular.label_seq_id(), seq_id]),
+                'group-by': Q.struct.atomProperty.macromolecular.residueKey()
+            }), data);
+            const loci = StructureSelection.toLociWithSourceUnits(sel);
+            this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci });
+        },
+        clearHighlight: () => {
+            this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci });
+        }
+    }
+
+    tests = {
+        staticSuperposition: async () => {
+            await this.plugin.clear();
+            return buildStaticSuperposition(this.plugin, StaticSuperpositionTestData);
+        },
+        dynamicSuperposition: async () => {
+            await this.plugin.clear();
+            return dynamicSuperpositionTest(this.plugin, ['1tqn', '2hhb', '4hhb'], 'HEM');
+        },
+        toggleValidationTooltip: () => {
+            return this.plugin.state.updateBehavior(PDBeStructureQualityReport, params => { params.showTooltip = !params.showTooltip; });
+        },
+        showToasts: () => {
+            PluginCommands.Toast.Show(this.plugin, {
+                title: 'Toast 1',
+                message: 'This is an example text, timeout 3s',
+                key: 'toast-1',
+                timeoutMs: 3000
+            });
+            PluginCommands.Toast.Show(this.plugin, {
+                title: 'Toast 2',
+                message: CustomToastMessage,
+                key: 'toast-2'
+            });
+        },
+        hideToasts: () => {
+            PluginCommands.Toast.Hide(this.plugin, { key: 'toast-1' });
+            PluginCommands.Toast.Hide(this.plugin, { key: 'toast-2' });
+        }
+    }
+}
+
+(window as any).BasicMolStarWrapper = new BasicWrapper();

src/examples/basic-wrapper/superposition.ts

@@ -0,0 +1,119 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Mat4 } from '../../mol-math/linear-algebra';
+import { QueryContext, StructureSelection } from '../../mol-model/structure';
+import { superpose } from '../../mol-model/structure/structure/util/superposition';
+import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { PluginContext } from '../../mol-plugin/context';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import Expression from '../../mol-script/language/expression';
+import { compile } from '../../mol-script/runtime/query/compiler';
+import { StateObjectRef } from '../../mol-state';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { Asset } from '../../mol-util/assets';
+
+export type SuperpositionTestInput = {
+    pdbId: string,
+    auth_asym_id: string,
+    matrix: Mat4
+}[];
+
+export function buildStaticSuperposition(plugin: PluginContext, src: SuperpositionTestInput) {
+    return plugin.dataTransaction(async () => {
+        for (const s of src) {
+            const { structure } = await loadStructure(plugin, `https://www.ebi.ac.uk/pdbe/static/entry/${s.pdbId}_updated.cif`, 'mmcif');
+            await transform(plugin, structure, s.matrix);
+            const chain = await plugin.builders.structure.tryCreateComponentFromExpression(structure, chainSelection(s.auth_asym_id), `Chain ${s.auth_asym_id}`);
+            if (chain) await plugin.builders.structure.representation.addRepresentation(chain, { type: 'cartoon' });
+        }
+    });
+}
+
+export const StaticSuperpositionTestData: SuperpositionTestInput = [
+    {
+        pdbId: '1aj5', auth_asym_id: 'A', matrix: Mat4.identity()
+    },
+    {
+        pdbId: '1df0', auth_asym_id: 'B', matrix: Mat4.ofRows([
+            [0.406, 0.879, 0.248, -200.633],
+            [0.693, -0.473, 0.544, 73.403],
+            [0.596, -0.049, -0.802, -14.209],
+            [0, 0, 0, 1]])
+    },
+    {
+        pdbId: '1dvi', auth_asym_id: 'A', matrix: Mat4.ofRows([
+            [-0.053, -0.077, 0.996, -45.633],
+            [-0.312, 0.949, 0.057, -12.255],
+            [-0.949, -0.307, -0.074, 53.562],
+            [0, 0, 0, 1]])
+    }
+];
+
+export function dynamicSuperpositionTest(plugin: PluginContext, src: string[], comp_id: string) {
+    return plugin.dataTransaction(async () => {
+        for (const s of src) {
+            await loadStructure(plugin, `https://www.ebi.ac.uk/pdbe/static/entry/${s}_updated.cif`, 'mmcif');
+        }
+
+        const pivot = MS.struct.filter.first([
+            MS.struct.generator.atomGroups({
+                'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
+                'group-by': MS.struct.atomProperty.macromolecular.residueKey()
+            })
+        ]);
+
+        const rest = MS.struct.modifier.exceptBy({
+            0: MS.struct.modifier.includeSurroundings({
+                0: pivot,
+                radius: 5
+            }),
+            by: pivot
+        });
+
+        const query = compile<StructureSelection>(pivot);
+        const xs = plugin.managers.structure.hierarchy.current.structures;
+        const selections = xs.map(s => StructureSelection.toLociWithCurrentUnits(query(new QueryContext(s.cell.obj!.data))));
+
+        const transforms = superpose(selections);
+
+        await siteVisual(plugin, xs[0].cell, pivot, rest);
+        for (let i = 1; i < selections.length; i++) {
+            await transform(plugin, xs[i].cell, transforms[i - 1].bTransform);
+            await siteVisual(plugin, xs[i].cell, pivot, rest);
+        }
+    });
+}
+
+async function siteVisual(plugin: PluginContext, s: StateObjectRef<PSO.Molecule.Structure>, pivot: Expression, rest: Expression) {
+    const center = await plugin.builders.structure.tryCreateComponentFromExpression(s, pivot, 'pivot');
+    if (center) await plugin.builders.structure.representation.addRepresentation(center, { type: 'ball-and-stick', color: 'residue-name' });
+
+    const surr = await plugin.builders.structure.tryCreateComponentFromExpression(s, rest, 'rest');
+    if (surr) await plugin.builders.structure.representation.addRepresentation(surr, { type: 'ball-and-stick', color: 'uniform', size: 'uniform', sizeParams: { value: 0.33 } });
+}
+
+async function loadStructure(plugin: PluginContext, url: string, format: BuiltInTrajectoryFormat, assemblyId?: string) {
+    const data = await plugin.builders.data.download({ url: Asset.Url(url) });
+    const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+    const model = await plugin.builders.structure.createModel(trajectory);
+    const structure = await plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : void 0);
+
+    return { data, trajectory, model, structure };
+}
+
+function chainSelection(auth_asym_id: string) {
+    return MS.struct.generator.atomGroups({
+        'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.auth_asym_id(), auth_asym_id])
+    });
+}
+
+function transform(plugin: PluginContext, s: StateObjectRef<PSO.Molecule.Structure>, matrix: Mat4) {
+    const b = plugin.state.data.build().to(s)
+        .insert(StateTransforms.Model.TransformStructureConformation, { transform: { name: 'matrix', params: { data: matrix, transpose: false } } });
+    return plugin.runTask(plugin.state.data.updateTree(b));
+}

src/examples/domain-annotation-server/mapping.ts

@@ -4,9 +4,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Table } from '../../mol-data/db'
-import { CifWriter } from '../../mol-io/writer/cif'
-import * as S from './schemas'
+import { Table } from '../../mol-data/db';
+import { CifWriter } from '../../mol-io/writer/cif';
+import * as S from './schemas';
 // import { getCategoryInstanceProvider } from './utils'
 
 export default function create(allData: any) {

src/examples/domain-annotation-server/schemas.ts

@@ -4,21 +4,21 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Column } from '../../mol-data/db'
+import { Column } from '../../mol-data/db';
 
 import Type = Column.Schema
 
 export const Sources = {
     id: Type.str,
     count: Type.int
-}
+};
 export type Sources = typeof Sources
 
 export const Base = {
     id: Type.str,
     identifier: Type.str,
     mapping_group_id: Type.int
-}
+};
 export type Base = typeof Base
 
 export const mapping = {
@@ -36,17 +36,17 @@ export const mapping = {
     end_label_seq_id: Type.int,
     end_auth_seq_id: Type.int,
     pdbx_end_PDB_ins_code: Type.str
-}
+};
 export type mapping = typeof mapping
 
 export const Pfam = {
     description: Type.str
-}
+};
 export type Pfam = typeof Pfam
 
 export const InterPro = {
     name: Type.str
-}
+};
 export type InterPro = typeof InterPro
 
 export const CATH = {
@@ -56,32 +56,32 @@ export const CATH = {
     identifier: Type.str,
     class: Type.str,
     topology: Type.str,
-}
+};
 export type CATH = typeof CATH
 
 export const EC = {
     accepted_name: Type.str,
     reaction: Type.str,
     systematic_name: Type.str
-}
+};
 export type EC = typeof EC
 
 export const UniProt = {
     name: Type.str
-}
+};
 export type UniProt = typeof UniProt
 
 export const SCOP = {
     sccs: Type.str,
     description: Type.str
-}
+};
 export type SCOP = typeof SCOP
 
 export const GO = {
     category: Type.str,
     definition: Type.str,
     name: Type.str
-}
+};
 export type GO = typeof GO
 
 export const categories = {
@@ -92,4 +92,4 @@ export const categories = {
     UniProt,
     SCOP,
     GO
-}
+};

src/examples/domain-annotation-server/server.ts

@@ -4,9 +4,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as express from 'express'
-import fetch from 'node-fetch'
-import createMapping from './mapping'
+import express from 'express';
+import fetch from 'node-fetch';
+import createMapping from './mapping';
 
 async function getMappings(id: string) {
     const data = await fetch(`https://www.ebi.ac.uk/pdbe/api/mappings/${id}`);
@@ -19,7 +19,7 @@ let PORT = process.env.port || 1338;
 
 const app = express();
 
-const PREFIX = '/'
+const PREFIX = '/';
 
 app.get(`${PREFIX}/:id`, async (req, res) => {
     try {
@@ -41,7 +41,7 @@ app.get(`${PREFIX}/:id`, async (req, res) => {
 app.get(`${PREFIX}`, (req, res) => {
     res.writeHead(200, { 'Content-Type': 'text/plain; charset=utf-8' });
     res.end('Usage: /pdb_id, e.g. /1tqn');
-})
+});
 
 app.listen(PORT);
 

src/examples/domain-annotation-server/test.ts

@@ -4,8 +4,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import fetch from 'node-fetch'
-import createMapping from './mapping'
+import fetch from 'node-fetch';
+import createMapping from './mapping';
 
 (async function () {
     const data = await fetch('https://www.ebi.ac.uk/pdbe/api/mappings/1tqn?pretty=true');

src/examples/lighting/index.html

@@ -38,16 +38,16 @@
                 display: block;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="app.css" />
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
         <script type="text/javascript" src="./index.js"></script>
     </head>
     <body>
         <div id='controls'></div>
         <div id="app"></div>
-        <script>      
+        <script>
             LightingDemo.init('app')
             LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' })
-            
+
             addHeader('Example PDB IDs');
             addControl('1M07', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' }));
             addControl('6HY0', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/6HY0.cif', assemblyId: '1' }));

src/examples/lighting/index.ts

@@ -0,0 +1,118 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
+import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import './index.html';
+import { Asset } from '../../mol-util/assets';
+require('mol-plugin-ui/skin/light.scss');
+
+type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
+
+type _Preset = Pick<Canvas3DProps, 'multiSample' | 'postprocessing' | 'renderer'>
+type Preset = { [K in keyof _Preset]: Partial<_Preset[K]> }
+
+const Canvas3DPresets = {
+    illustrative: <Preset> {
+        multiSample: {
+            mode: 'temporal' as Canvas3DProps['multiSample']['mode']
+        },
+        postprocessing: {
+            occlusion: { name: 'on', params: { bias: 0.8, kernelSize: 6, radius: 64 } },
+            outline: { name: 'on', params: { scale: 1, threshold: 0.8 } }
+        },
+        renderer: {
+            ambientIntensity: 1,
+            lightIntensity: 0,
+        }
+    },
+    occlusion: <Preset> {
+        multiSample: {
+            mode: 'temporal' as Canvas3DProps['multiSample']['mode']
+        },
+        postprocessing: {
+            occlusion: { name: 'on', params: { bias: 0.8, kernelSize: 6, radius: 64 } },
+            outline: { name: 'off', params: { } }
+        },
+        renderer: {
+            ambientIntensity: 0.4,
+            lightIntensity: 0.6,
+        }
+    },
+    standard: <Preset> {
+        multiSample: {
+            mode: 'off' as Canvas3DProps['multiSample']['mode']
+        },
+        postprocessing: {
+            occlusion: { name: 'off', params: { } },
+            outline: { name: 'off', params: { } }
+        },
+        renderer: {
+            ambientIntensity: 0.4,
+            lightIntensity: 0.6,
+        }
+    }
+};
+
+type Canvas3DPreset = keyof typeof Canvas3DPresets
+
+class LightingDemo {
+    plugin: PluginContext;
+
+    init(target: string | HTMLElement) {
+        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
+            ...DefaultPluginSpec,
+            layout: {
+                initial: {
+                    isExpanded: false,
+                    showControls: false
+                },
+                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
+            }
+        });
+
+        this.setPreset('illustrative');
+    }
+
+    setPreset(preset: Canvas3DPreset) {
+        const props = Canvas3DPresets[preset];
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
+            ...props,
+            multiSample: {
+                ...this.plugin.canvas3d!.props.multiSample,
+                ...props.multiSample
+            },
+            renderer: {
+                ...this.plugin.canvas3d!.props.renderer,
+                ...props.renderer
+            },
+            postprocessing: {
+                ...this.plugin.canvas3d!.props.postprocessing,
+                ...props.postprocessing
+            },
+        }});
+    }
+
+    async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
+        await this.plugin.clear();
+
+        const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary }, { state: { isGhost: true } });
+        const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
+        const model = await this.plugin.builders.structure.createModel(trajectory);
+        const structure = await this.plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : { name: 'model', params: { } });
+
+        const polymer = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'polymer');
+        if (polymer) await this.plugin.builders.structure.representation.addRepresentation(polymer, { type: 'spacefill', color: 'illustrative' });
+
+        const ligand = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'ligand');
+        if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick' });
+    }
+}
+
+(window as any).LightingDemo = new LightingDemo();

src/examples/proteopedia-wrapper/annotation.ts

@@ -1,12 +1,15 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { CustomElementProperty } from '../../mol-model-props/common/custom-element-property';
 import { Model, ElementIndex, ResidueIndex } from '../../mol-model/structure';
 import { Color } from '../../mol-util/color';
+import { CustomProperty } from '../../mol-model-props/common/custom-property';
+import { Asset } from '../../mol-util/assets';
 
 const EvolutionaryConservationPalette: Color[] = [
     [255, 255, 129], // insufficient
@@ -23,14 +26,14 @@ const EvolutionaryConservationPalette: Color[] = [
 const EvolutionaryConservationDefaultColor = Color(0x999999);
 
 export const EvolutionaryConservation = CustomElementProperty.create<number>({
-    isStatic: true,
     name: 'proteopedia-wrapper-evolutionary-conservation',
-    display: 'Evolutionary Conservation',
-    async getData(model: Model) {
+    label: 'Evolutionary Conservation',
+    type: 'static',
+    async getData(model: Model, ctx: CustomProperty.Context) {
         const id = model.entryId.toLowerCase();
-        const req = await fetch(`https://proteopedia.org/cgi-bin/cnsrf?${id}`);
-        const json = await req.json();
-        const annotations = (json && json.residueAnnotations) || [];
+        const url = Asset.getUrlAsset(ctx.assetManager, `https://proteopedia.org/cgi-bin/cnsrf?${id}`);
+        const json = await ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime);
+        const annotations = json.data?.residueAnnotations || [];
 
         const conservationMap = new Map<string, number>();
 
@@ -56,7 +59,7 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
             }
         }
 
-        return map;
+        return { value: map, assets: [json] };
     },
     coloring: {
         getColor(e: number) {
@@ -65,8 +68,8 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
         },
         defaultColor: EvolutionaryConservationDefaultColor
     },
-    format(e) {
-        if (e === 10) return `Evolutionary Conservation: InsufficientData`;
+    getLabel(e) {
+        if (e === 10) return `Evolutionary Conservation: Insufficient Data`;
         return e ? `Evolutionary Conservation: ${e}` : void 0;
     }
 });

src/examples/proteopedia-wrapper/coloring.ts

@@ -6,63 +6,63 @@
  */
 
 
-import { Unit, StructureProperties, StructureElement, Link } from '../../mol-model/structure';
+import { Unit, StructureProperties, StructureElement, Bond } from '../../mol-model/structure';
 
 import { Color } from '../../mol-util/color';
 import { Location } from '../../mol-model/location';
 import { ColorTheme, LocationColor } from '../../mol-theme/color';
-import { ParamDefinition as PD } from '../../mol-util/param-definition'
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../../mol-theme/theme';
 import { Column } from '../../mol-data/db';
 
-const Description = 'Gives every chain a color from a list based on its `asym_id` value.'
+const Description = 'Gives every chain a color from a list based on its `asym_id` value.';
 
 export function createProteopediaCustomTheme(colors: number[]) {
     const ProteopediaCustomColorThemeParams = {
         colors: PD.ObjectList({ color: PD.Color(Color(0xffffff)) }, ({ color }) => Color.toHexString(color),
             { defaultValue: colors.map(c => ({ color: Color(c) })) })
-    }
+    };
     type ProteopediaCustomColorThemeParams = typeof ProteopediaCustomColorThemeParams
     function getChainIdColorThemeParams(ctx: ThemeDataContext) {
-        return ProteopediaCustomColorThemeParams // TODO return copy
+        return ProteopediaCustomColorThemeParams; // TODO return copy
     }
 
     function getAsymId(unit: Unit): StructureElement.Property<string> {
         switch (unit.kind) {
             case Unit.Kind.Atomic:
-                return StructureProperties.chain.label_asym_id
+                return StructureProperties.chain.label_asym_id;
             case Unit.Kind.Spheres:
             case Unit.Kind.Gaussians:
-                return StructureProperties.coarse.asym_id
+                return StructureProperties.coarse.asym_id;
         }
     }
 
     function addAsymIds(map: Map<string, number>, data: Column<string>) {
-        let j = map.size
+        let j = map.size;
         for (let o = 0, ol = data.rowCount; o < ol; ++o) {
-            const k = data.value(o)
+            const k = data.value(o);
             if (!map.has(k)) {
-                map.set(k, j)
-                j += 1
+                map.set(k, j);
+                j += 1;
             }
         }
     }
 
     function ProteopediaCustomColorTheme(ctx: ThemeDataContext, props: PD.Values<ProteopediaCustomColorThemeParams>): ColorTheme<ProteopediaCustomColorThemeParams> {
-        let color: LocationColor
+        let color: LocationColor;
 
         const colors = props.colors, colorCount = colors.length, defaultColor = colors[0].color;
 
         if (ctx.structure) {
-            const l = StructureElement.Location.create()
-            const { models } = ctx.structure
-            const asymIdSerialMap = new Map<string, number>()
+            const l = StructureElement.Location.create(ctx.structure);
+            const { models } = ctx.structure;
+            const asymIdSerialMap = new Map<string, number>();
             for (let i = 0, il = models.length; i < il; ++i) {
-                const m = models[i]
-                addAsymIds(asymIdSerialMap, m.atomicHierarchy.chains.label_asym_id)
+                const m = models[i];
+                addAsymIds(asymIdSerialMap, m.atomicHierarchy.chains.label_asym_id);
                 if (m.coarseHierarchy.isDefined) {
-                    addAsymIds(asymIdSerialMap, m.coarseHierarchy.spheres.asym_id)
-                    addAsymIds(asymIdSerialMap, m.coarseHierarchy.gaussians.asym_id)
+                    addAsymIds(asymIdSerialMap, m.coarseHierarchy.spheres.asym_id);
+                    addAsymIds(asymIdSerialMap, m.coarseHierarchy.gaussians.asym_id);
                 }
             }
 
@@ -71,17 +71,17 @@ export function createProteopediaCustomTheme(colors: number[]) {
                     const asym_id = getAsymId(location.unit);
                     const o = asymIdSerialMap.get(asym_id(location)) || 0;
                     return colors[o % colorCount].color;
-                } else if (Link.isLocation(location)) {
-                    const asym_id = getAsymId(location.aUnit)
-                    l.unit = location.aUnit
-                    l.element = location.aUnit.elements[location.aIndex]
+                } else if (Bond.isLocation(location)) {
+                    const asym_id = getAsymId(location.aUnit);
+                    l.unit = location.aUnit;
+                    l.element = location.aUnit.elements[location.aIndex];
                     const o = asymIdSerialMap.get(asym_id(l)) || 0;
                     return colors[o % colorCount].color;
                 }
-                return defaultColor
-            }
+                return defaultColor;
+            };
         } else {
-            color = () => defaultColor
+            color = () => defaultColor;
         }
 
         return {
@@ -91,16 +91,16 @@ export function createProteopediaCustomTheme(colors: number[]) {
             props,
             description: Description,
             legend: undefined
-        }
+        };
     }
 
-    const ProteopediaCustomColorThemeProvider: ColorTheme.Provider<ProteopediaCustomColorThemeParams> = {
+    return {
+        name: 'proteopedia-custom',
         label: 'Proteopedia Custom',
+        category: 'Custom',
         factory: ProteopediaCustomColorTheme,
         getParams: getChainIdColorThemeParams,
         defaultValues: PD.getDefaultValues(ProteopediaCustomColorThemeParams),
         isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
-    }
-
-    return ProteopediaCustomColorThemeProvider;
+    };
 }

src/examples/proteopedia-wrapper/helpers.ts

@@ -4,11 +4,11 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { ResidueIndex, Model } from '../../mol-model/structure';
-import { BuiltInStructureRepresentationsName } from '../../mol-repr/structure/registry';
-import { BuiltInColorThemeName } from '../../mol-theme/color';
-import { AminoAcidNames } from '../../mol-model/structure/model/types';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+import { Model, ResidueIndex } from '../../mol-model/structure';
 import { PluginContext } from '../../mol-plugin/context';
+import { StructureRepresentationRegistry } from '../../mol-repr/structure/registry';
+import { ColorTheme } from '../../mol-theme/color';
 
 export interface ModelInfo {
     hetResidues: { name: string, indices: ResidueIndex[] }[],
@@ -53,14 +53,12 @@ export namespace ModelInfo {
         const hetMap = new Map<string, ModelInfo['hetResidues'][0]>();
 
         for (let rI = 0 as ResidueIndex; rI < residueCount; rI++) {
-            const comp_id = model.atomicHierarchy.residues.label_comp_id.value(rI);
-            if (AminoAcidNames.has(comp_id)) continue;
-            const mod_parent = model.properties.modifiedResidues.parentId.get(comp_id);
-            if (mod_parent && AminoAcidNames.has(mod_parent)) continue;
-
             const cI = chainIndex[residueOffsets[rI]];
             const eI = model.atomicHierarchy.index.getEntityFromChain(cI);
-            if (model.entities.data.type.value(eI) === 'water') continue;
+            const entityType = model.entities.data.type.value(eI);
+            if (entityType !== 'non-polymer' && entityType !== 'branched') continue;
+
+            const comp_id = model.atomicHierarchy.residues.label_comp_id.value(rI);
 
             let lig = hetMap.get(comp_id);
             if (!lig) {
@@ -72,10 +70,11 @@ export namespace ModelInfo {
         }
 
         const preferredAssemblyId = await pref;
+        const symmetry = ModelSymmetry.Provider.get(model);
 
         return {
             hetResidues: hetResidues,
-            assemblies: model.symmetry.assemblies.map(a => ({ id: a.id, details: a.details, isPreferred: a.id === preferredAssemblyId })),
+            assemblies: symmetry ? symmetry.assemblies.map(a => ({ id: a.id, details: a.details, isPreferred: a.id === preferredAssemblyId })) : [],
             preferredAssemblyId
         };
     }
@@ -85,6 +84,7 @@ export type SupportedFormats = 'cif' | 'pdb'
 export interface LoadParams {
     url: string,
     format?: SupportedFormats,
+    isBinary?: boolean,
     assemblyId?: string,
     representationStyle?: RepresentationStyle
 }
@@ -97,7 +97,7 @@ export interface RepresentationStyle {
 }
 
 export namespace RepresentationStyle {
-    export type Entry = { hide?: boolean, kind?: BuiltInStructureRepresentationsName, coloring?: BuiltInColorThemeName }
+    export type Entry = { hide?: boolean, kind?: StructureRepresentationRegistry.BuiltIn, coloring?: ColorTheme.BuiltIn }
 }
 
 export enum StateElements {

src/examples/proteopedia-wrapper/index.html

@@ -48,7 +48,7 @@
                 width: 300px;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="app.css" />
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
         <script type="text/javascript" src="./index.js"></script>
     </head>
     <body>
@@ -60,11 +60,12 @@
                 <option value='cif' selected>CIF</option>
                 <option value='pdb'>PDB</option>
             </select>
+            <input type='checkbox' id='isBinary' style="display: inline-block; width: auto" /> <label for="isBinary"> Binary</label><br />
         </div>
         <div id="app"></div>
         <div id="volume-streaming-wrapper"></div>
         <script>
-            // it might be a good idea to define these colors in a separate script file 
+            // it might be a good idea to define these colors in a separate script file
             var CustomColors = [0x00ff00, 0x0000ff];
 
             // create an instance of the plugin
@@ -73,24 +74,28 @@
             console.log('Wrapper version', MolStarProteopediaWrapper.VERSION_MAJOR, MolStarProteopediaWrapper.VERSION_MINOR);
 
             function $(id) { return document.getElementById(id); }
-        
-            var pdbId = '1cbs', assemblyId= 'preferred';
-            var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
+
+            var pdbId = '1cbs', assemblyId= 'preferred', isBinary = true;
+            var url = 'https://www.ebi.ac.uk/pdbe/entry-files/download/' + pdbId + '.bcif'
             var format = 'cif';
-            
+
             $('url').value = url;
             $('url').onchange = function (e) { url = e.target.value; }
             $('assemblyId').value = assemblyId;
             $('assemblyId').onchange = function (e) { assemblyId = e.target.value; }
             $('format').value = format;
             $('format').onchange = function (e) { format = e.target.value; }
+            $('isBinary').checked = isBinary;
+            $('isBinary').onchange = function (e) { isBinary = !!e.target.checked; };
 
-            // var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
-            // var format = 'pdb';
-            // var assemblyId = 'deposited';
+            function loadAndSnapshot(params) {
+                PluginWrapper.load(params).then(() => {
+                    setTimeout(() => snapshot = PluginWrapper.plugin.state.getSnapshot({ canvas3d: false /* do not save spinning state */ }), 500);
+                });
+            }
 
             var representationStyle = {
-                sequence: { coloring: 'proteopedia-custom' }, // or just { }
+                // sequence: { coloring: 'proteopedia-custom' }, // or just { }
                 hetGroups: { kind: 'ball-and-stick' }, // or 'spacefill
                 water: { hide: true },
                 snfg3d: { hide: false }
@@ -100,7 +105,7 @@
                 customColorList: CustomColors
             });
             PluginWrapper.setBackground(0xffffff);
-            PluginWrapper.load({ url: url, format: format, assemblyId: assemblyId, representationStyle: representationStyle });
+            loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
             PluginWrapper.toggleSpin();
 
             PluginWrapper.events.modelInfo.subscribe(function (info) {
@@ -108,8 +113,8 @@
                 listHetGroups(info);
             });
 
-            addControl('Load Asym Unit', () => PluginWrapper.load({ url: url, format: format }));
-            addControl('Load Assembly', () => PluginWrapper.load({ url: url, format: format, assemblyId: assemblyId }));
+            addControl('Load Asym Unit', () => loadAndSnapshot({ url: url, format: format, isBinary }));
+            addControl('Load Assembly', () => loadAndSnapshot({ url: url, format: format, isBinary, assemblyId: assemblyId }));
 
             addSeparator();
 
@@ -135,7 +140,7 @@
             // Same as "wheel icon" and Viewport options
             // addControl('Clip', () => PluginWrapper.viewport.setSettings({ clip: [33, 66] }));
             // addControl('Reset Clip', () => PluginWrapper.viewport.setSettings({ clip: [1, 100] }));
-            
+
             addSeparator();
 
             addHeader('Animation');
@@ -168,20 +173,24 @@
             addControl('Init', () => PluginWrapper.experimentalData.init($('volume-streaming-wrapper')));
             addControl('Remove', () => PluginWrapper.experimentalData.remove());
 
-            addSeparator(); 
+            addSeparator();
             addHeader('State');
 
             var snapshot;
-            addControl('Create Snapshot', () => {
-                snapshot = PluginWrapper.snapshot.get();
-                // could use JSON.stringify(snapshot) and upload the data
+            addControl('Set Snapshot', () => {
+                // const options = { data: true, behavior: false, animation: false, interactivity: false, canvas3d: false, camera: false, cameraTransition: false };
+                snapshot = PluginWrapper.plugin.state.getSnapshot(/** options */);
+                // console.log(JSON.stringify(snapshot, null, 2));
             });
-            addControl('Apply Snapshot', () => {
+            addControl('Restore Snapshot', () => {
                 if (!snapshot) return;
                 PluginWrapper.snapshot.set(snapshot);
-
-                // or download snapshot using fetch or ajax or whatever
-                // or PluginWrapper.snapshot.download(url);
+            });
+            addControl('Download State', () => {
+                PluginWrapper.snapshot.download('molj');
+            });
+            addControl('Download Session', () => {
+                PluginWrapper.snapshot.download('molx');
             });
 
             ////////////////////////////////////////////////////////
@@ -217,7 +226,7 @@
                     var l = document.createElement('button');
                     l.innerText = r.name;
                     l.onclick = function () {
-                        PluginWrapper.hetGroups.focusFirst(r.name);
+                        PluginWrapper.hetGroups.focusFirst(r.name, { doNotLabelWaters: true });
                     };
                     div.appendChild(l);
                 });

src/examples/proteopedia-wrapper/index.ts

@@ -5,39 +5,34 @@
  */
 
 import * as ReactDOM from 'react-dom';
+import { Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
 import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import './index.html'
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
+import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
+import { PluginStateObject, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/command';
-import { StateTransforms } from '../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
-import { Color } from '../../mol-util/color';
-import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin/state/objects';
-import { AnimateModelIndex } from '../../mol-plugin/state/animation/built-in';
-import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
-import { EvolutionaryConservation } from './annotation';
-import { LoadParams, SupportedFormats, RepresentationStyle, ModelInfo, StateElements } from './helpers';
-import { RxEventHelper } from '../../mol-util/rx-event-helper';
-import { ControlsWrapper, volumeStreamingControls } from './ui/controls';
 import { PluginState } from '../../mol-plugin/state';
-import { Scheduler } from '../../mol-task';
-import { createProteopediaCustomTheme } from './coloring';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { BuiltInStructureRepresentations } from '../../mol-repr/structure/registry';
-import { BuiltInColorThemes } from '../../mol-theme/color';
-import { BuiltInSizeThemes } from '../../mol-theme/size';
+import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
+import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
 import { ColorNames } from '../../mol-util/color/names';
-import { InitVolumeStreaming, CreateVolumeStreamingInfo } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
-import { ParamDefinition } from '../../mol-util/param-definition';
-import { DefaultCanvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
-// import { Vec3 } from 'mol-math/linear-algebra';
-// import { ParamDefinition } from 'mol-util/param-definition';
-// import { Text } from 'mol-geo/geometry/text/text';
-require('../../mol-plugin/skin/light.scss')
+import { getFormattedTime } from '../../mol-util/date';
+import { download } from '../../mol-util/download';
+import { RxEventHelper } from '../../mol-util/rx-event-helper';
+import { EvolutionaryConservation } from './annotation';
+import { createProteopediaCustomTheme } from './coloring';
+import { LoadParams, ModelInfo, RepresentationStyle, StateElements, SupportedFormats } from './helpers';
+import './index.html';
+import { volumeStreamingControls } from './ui/controls';
+require('../../mol-plugin-ui/skin/light.scss');
 
 class MolStarProteopediaWrapper {
-    static VERSION_MAJOR = 3;
-    static VERSION_MINOR = 4;
+    static VERSION_MAJOR = 5;
+    static VERSION_MINOR = 5;
 
     private _ev = RxEventHelper.create();
 
@@ -59,27 +54,27 @@ class MolStarProteopediaWrapper {
                 initial: {
                     isExpanded: false,
                     showControls: false
-                },
-                controls: {
-                    right: ControlsWrapper
                 }
+            },
+            components: {
+                remoteState: 'none'
             }
         });
 
         const customColoring = createProteopediaCustomTheme((options && options.customColorList) || []);
 
-        this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.add('proteopedia-custom', customColoring);
-        this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.add(EvolutionaryConservation.Descriptor.name, EvolutionaryConservation.colorTheme!);
-        this.plugin.lociLabels.addProvider(EvolutionaryConservation.labelProvider);
-        this.plugin.customModelProperties.register(EvolutionaryConservation.propertyProvider);
+        this.plugin.representation.structure.themes.colorThemeRegistry.add(customColoring);
+        this.plugin.representation.structure.themes.colorThemeRegistry.add(EvolutionaryConservation.colorThemeProvider!);
+        this.plugin.managers.lociLabels.addProvider(EvolutionaryConservation.labelProvider!);
+        this.plugin.customModelProperties.register(EvolutionaryConservation.propertyProvider, true);
     }
 
     get state() {
-        return this.plugin.state.dataState;
+        return this.plugin.state.data;
     }
 
-    private download(b: StateBuilder.To<PSO.Root>, url: string) {
-        return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
+    private download(b: StateBuilder.To<PSO.Root>, url: string, isBinary: boolean) {
+        return b.apply(StateTransforms.Data.Download, { url: Asset.Url(url), isBinary });
     }
 
     private model(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats) {
@@ -93,10 +88,18 @@ class MolStarProteopediaWrapper {
 
     private structure(assemblyId: string) {
         const model = this.state.build().to(StateElements.Model);
+        const props = {
+            type: assemblyId ? {
+                name: 'assembly' as const,
+                params: { id: assemblyId }
+            } : {
+                name: 'model' as const,
+                params: { }
+            }
+        };
 
         const s = model
-            .apply(StateTransforms.Model.CustomModelProperties, { properties: [EvolutionaryConservation.Descriptor.name] }, { ref: StateElements.ModelProps, state: { isGhost: false } })
-            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: StateElements.Assembly });
+            .apply(StateTransforms.Model.StructureFromModel, props, { ref: StateElements.Assembly });
 
         s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' }, { ref: StateElements.Sequence });
         s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' }, { ref: StateElements.Het });
@@ -119,9 +122,10 @@ class MolStarProteopediaWrapper {
                 root.delete(StateElements.SequenceVisual);
             } else {
                 root.applyOrUpdate(StateElements.SequenceVisual, StateTransforms.Representation.StructureRepresentation3D,
-                    StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
-                        (style.sequence && style.sequence.kind) || 'cartoon',
-                        (style.sequence && style.sequence.coloring) || 'unit-index', structure));
+                    createStructureRepresentationParams(this.plugin, structure, {
+                        type: (style.sequence && style.sequence.kind) || 'cartoon',
+                        color: (style.sequence && style.sequence.coloring) || 'unit-index'
+                    }));
             }
         }
 
@@ -134,9 +138,10 @@ class MolStarProteopediaWrapper {
                     root.delete(StateElements.HetVisual);
                 } else {
                     root.applyOrUpdate(StateElements.HetVisual, StateTransforms.Representation.StructureRepresentation3D,
-                        StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
-                            (style.hetGroups && style.hetGroups.kind) || 'ball-and-stick',
-                            (style.hetGroups && style.hetGroups.coloring), structure));
+                        createStructureRepresentationParams(this.plugin, structure, {
+                            type: (style.hetGroups && style.hetGroups.kind) || 'ball-and-stick',
+                            color: style.hetGroups && style.hetGroups.coloring
+                        }));
                 }
             }
         }
@@ -150,7 +155,7 @@ class MolStarProteopediaWrapper {
                     root.delete(StateElements.Het3DSNFG);
                 } else {
                     root.applyOrUpdate(StateElements.Het3DSNFG, StateTransforms.Representation.StructureRepresentation3D,
-                        StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin, 'carbohydrate', void 0, structure));
+                        createStructureRepresentationParams(this.plugin, structure, { type: 'carbohydrate' }));
                 }
             }
         }
@@ -161,9 +166,11 @@ class MolStarProteopediaWrapper {
                 root.delete(StateElements.WaterVisual);
             } else {
                 root.applyOrUpdate(StateElements.WaterVisual, StateTransforms.Representation.StructureRepresentation3D,
-                        StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
-                            (style.water && style.water.kind) || 'ball-and-stick',
-                            (style.water && style.water.coloring), structure, { alpha: 0.51 }));
+                    createStructureRepresentationParams(this.plugin, structure, {
+                        type: (style.water && style.water.kind) || 'ball-and-stick',
+                        typeParams: { alpha: 0.51 },
+                        color: style.water && style.water.coloring
+                    }));
             }
         }
 
@@ -181,20 +188,21 @@ class MolStarProteopediaWrapper {
         const model = this.getObj<PluginStateObject.Molecule.Model>('model');
         if (!model) return;
 
-        const info = await ModelInfo.get(this.plugin, model, checkPreferredAssembly)
+        const info = await ModelInfo.get(this.plugin, model, checkPreferredAssembly);
         this.events.modelInfo.next(info);
         return info;
     }
 
     private applyState(tree: StateBuilder) {
-        return PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
+        return PluginCommands.State.Update(this.plugin, { state: this.plugin.state.data, tree });
     }
 
-    private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
-    async load({ url, format = 'cif', assemblyId = 'deposited', representationStyle }: LoadParams) {
+    private emptyLoadedParams: LoadParams = { url: '', format: 'cif', isBinary: false, assemblyId: '' };
+    private loadedParams: LoadParams = { url: '', format: 'cif', isBinary: false, assemblyId: '' };
+    async load({ url, format = 'cif', assemblyId = '', isBinary = false, representationStyle }: LoadParams) {
         let loadType: 'full' | 'update' = 'full';
 
-        const state = this.plugin.state.dataState;
+        const state = this.plugin.state.data;
 
         if (this.loadedParams.url !== url || this.loadedParams.format !== format) {
             loadType = 'full';
@@ -203,8 +211,8 @@ class MolStarProteopediaWrapper {
         }
 
         if (loadType === 'full') {
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
-            const modelTree = this.model(this.download(state.build().toRoot(), url), format);
+            await PluginCommands.State.RemoveObject(this.plugin, { state, ref: state.tree.root.ref });
+            const modelTree = this.model(this.download(state.build().toRoot(), url, isBinary), format);
             await this.applyState(modelTree);
             const info = await this.doInfo(true);
             const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
@@ -214,37 +222,45 @@ class MolStarProteopediaWrapper {
             const tree = state.build();
             const info = await this.doInfo(true);
             const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
-            tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: asmId }));
+            const props = {
+                type: assemblyId ? {
+                    name: 'assembly' as const,
+                    params: { id: asmId }
+                } : {
+                    name: 'model' as const,
+                    params: { }
+                }
+            };
+            tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
             await this.applyState(tree);
         }
 
         await this.updateStyle(representationStyle);
 
         this.loadedParams = { url, format, assemblyId };
-        Scheduler.setImmediate(() => PluginCommands.Camera.Reset.dispatch(this.plugin, { }));
     }
 
     async updateStyle(style?: RepresentationStyle, partial?: boolean) {
         const tree = this.visual(style, partial);
         if (!tree) return;
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
+        await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.data, tree });
     }
 
     setBackground(color: number) {
+        if (!this.plugin.canvas3d) return;
         const renderer = this.plugin.canvas3d.props.renderer;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
     }
 
     toggleSpin() {
+        if (!this.plugin.canvas3d) return;
         const trackball = this.plugin.canvas3d.props.trackball;
-        const spinning = trackball.spin;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
-        if (!spinning) PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
     }
 
     viewport = {
         setSettings: (settings?: Canvas3DProps) => {
-            PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, {
+            PluginCommands.Canvas3D.SetSettings(this.plugin, {
                 settings: settings || DefaultCanvas3DParams
             });
         }
@@ -252,36 +268,17 @@ class MolStarProteopediaWrapper {
 
     camera = {
         toggleSpin: () => this.toggleSpin(),
-        resetPosition: () => PluginCommands.Camera.Reset.dispatch(this.plugin, { }),
-        // setClip: (options?: { distance?: number, near?: number, far?: number }) => {
-        //     if (!options) {
-        //         PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, {
-        //             settings: {
-        //                 cameraClipDistance: DefaultCanvas3DParams.cameraClipDistance,
-        //                 clip: DefaultCanvas3DParams.clip
-        //             }
-        //         });
-        //         return;
-        //     }
-
-        //     options = options || { };
-        //     const props = this.plugin.canvas3d.props;
-        //     const clipNear = typeof options.near === 'undefined' ? props.clip[0] : options.near;
-        //     const clipFar = typeof options.far === 'undefined' ? props.clip[1] : options.far;
-        //     PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, {
-        //         settings: { cameraClipDistance: options.distance, clip: [clipNear, clipFar] }
-        //     });
-        // }
+        resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { })
     }
 
     animate = {
         modelIndex: {
             maxFPS: 8,
-            onceForward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }) },
-            onceBackward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }) },
-            palindrome: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }) },
-            loop: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }) },
-            stop: () => this.plugin.state.animation.stop()
+            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }); },
+            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }); },
+            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }); },
+            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }); },
+            stop: () => this.plugin.managers.animation.stop()
         }
     }
 
@@ -292,13 +289,8 @@ class MolStarProteopediaWrapper {
             }
 
             const state = this.state;
-
-            // const visuals = state.selectQ(q => q.ofType(PluginStateObject.Molecule.Structure.Representation3D).filter(c => c.transform.transformer === StateTransforms.Representation.StructureRepresentation3D));
-            // for (const v of visuals) {
-            // }
-
             const tree = state.build();
-            const colorTheme = { name: EvolutionaryConservation.Descriptor.name, params: this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.get(EvolutionaryConservation.Descriptor.name).defaultValues };
+            const colorTheme = { name: EvolutionaryConservation.propertyProvider.descriptor.name, params: this.plugin.representation.structure.themes.colorThemeRegistry.get(EvolutionaryConservation.propertyProvider.descriptor.name).defaultValues };
 
             if (!params || !!params.sequence) {
                 tree.to(StateElements.SequenceVisual).update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
@@ -307,7 +299,7 @@ class MolStarProteopediaWrapper {
                 tree.to(StateElements.HetVisual).update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
             }
 
-            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
+            await PluginCommands.State.Update(this.plugin, { state, tree });
         }
     }
 
@@ -315,9 +307,11 @@ class MolStarProteopediaWrapper {
     experimentalData = {
         init: async (parent: Element) => {
             const asm = this.state.select(StateElements.Assembly)[0].obj!;
-            const params = ParamDefinition.getDefaultValues(InitVolumeStreaming.definition.params!(asm, this.plugin));
-            params.behaviorRef = StateElements.VolumeStreaming;
+            const params = InitVolumeStreaming.createDefaultParams(asm, this.plugin);
+            params.options.behaviorRef = StateElements.VolumeStreaming;
             params.defaultView = 'box';
+            params.options.channelParams['fo-fc(+ve)'] = { wireframe: true };
+            params.options.channelParams['fo-fc(-ve)'] = { wireframe: true };
             await this.plugin.runTask(this.state.applyAction(InitVolumeStreaming, params, StateElements.Assembly));
             this.experimentalDataElement = parent;
             volumeStreamingControls(this.plugin, parent);
@@ -325,7 +319,7 @@ class MolStarProteopediaWrapper {
         remove: () => {
             const r = this.state.select(StateSelection.Generators.ofTransformer(CreateVolumeStreamingInfo))[0];
             if (!r) return;
-            PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.state, ref: r.transform.ref });
+            PluginCommands.State.RemoveObject(this.plugin, { state: this.state, ref: r.transform.ref });
             if (this.experimentalDataElement) {
                 ReactDOM.unmountComponentAtNode(this.experimentalDataElement);
                 this.experimentalDataElement = void 0;
@@ -336,14 +330,12 @@ class MolStarProteopediaWrapper {
     hetGroups = {
         reset: () => {
             const update = this.state.build().delete(StateElements.HetGroupFocusGroup);
-            PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
-            PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+            PluginCommands.State.Update(this.plugin, { state: this.state, tree: update });
+            PluginCommands.Camera.Reset(this.plugin, { });
         },
-        focusFirst: async (compId: string) => {
+        focusFirst: async (compId: string, options?: { hideLabels: boolean, doNotLabelWaters: boolean }) => {
             if (!this.state.transforms.has(StateElements.Assembly)) return;
-            await PluginCommands.Camera.Reset.dispatch(this.plugin, { });
-
-            // const asm = (this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure).data;
+            await PluginCommands.Camera.Reset(this.plugin, { });
 
             const update = this.state.build();
 
@@ -358,65 +350,66 @@ class MolStarProteopediaWrapper {
             const surroundings = MS.struct.modifier.includeSurroundings({ 0: core, radius: 5, 'as-whole-residues': true });
 
             const group = update.to(StateElements.Assembly).group(StateTransforms.Misc.CreateGroup, { label: compId }, { ref: StateElements.HetGroupFocusGroup });
+            const asm = this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure;
+            const coreSel = group.apply(StateTransforms.Model.StructureSelectionFromExpression, { label: 'Core', expression: core }, { ref: StateElements.HetGroupFocus });
+
+
+            coreSel.apply(StateTransforms.Representation.StructureRepresentation3D, createStructureRepresentationParams(this.plugin, asm.data, {
+                type: 'ball-and-stick'
+            }));
+            coreSel.apply(StateTransforms.Representation.StructureRepresentation3D, createStructureRepresentationParams(this.plugin, asm.data, {
+                type: 'label',
+                typeParams: { level: 'element' }
+            }), { tags: ['proteopedia-labels'] });
 
-            group.apply(StateTransforms.Model.StructureSelectionFromExpression, { label: 'Core', expression: core }, { ref: StateElements.HetGroupFocus })
-                .apply(StateTransforms.Representation.StructureRepresentation3D, this.createCoreVisualParams());
             group.apply(StateTransforms.Model.StructureSelectionFromExpression, { label: 'Surroundings', expression: surroundings })
-                .apply(StateTransforms.Representation.StructureRepresentation3D, this.createSurVisualParams());
-            // sel.apply(StateTransforms.Representation.StructureLabels3D, {
-            //     target: { name: 'residues', params: { } },
-            //     options: {
-            //         ...ParamDefinition.getDefaultValues(Text.Params),
-            //         background: true,
-            //         backgroundMargin: 0.2,
-            //         backgroundColor: ColorNames.snow,
-            //         backgroundOpacity: 0.9,
-            //     }
-            // });
+                .apply(StateTransforms.Representation.StructureRepresentation3D, createStructureRepresentationParams(this.plugin, asm.data, {
+                    type: 'ball-and-stick',
+                    color: 'uniform', colorParams: { value: ColorNames.gray },
+                    size: 'uniform', sizeParams: { value: 0.33 }
+                }));
 
-            await PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
+            if (!options?.hideLabels) {
+                // Labels
+                const waters = MS.struct.generator.atomGroups({
+                    'entity-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.entityType(), 'water']),
+                });
+                const exclude = options?.doNotLabelWaters ? MS.struct.combinator.merge([core, waters]) : core;
+                const onlySurroundings = MS.struct.modifier.exceptBy({ 0: surroundings, by: exclude });
+
+                group.apply(StateTransforms.Model.StructureSelectionFromExpression, { label: 'Surroundings (only)', expression: onlySurroundings })
+                    .apply(StateTransforms.Representation.StructureRepresentation3D, createStructureRepresentationParams(this.plugin, asm.data, {
+                        type: 'label',
+                        typeParams: { level: 'residue' }
+                    }), { tags: ['proteopedia-labels'] }); // the tag can later be used to toggle the labels
+            }
+
+            await PluginCommands.State.Update(this.plugin, { state: this.state, tree: update });
 
             const focus = (this.state.select(StateElements.HetGroupFocus)[0].obj as PluginStateObject.Molecule.Structure).data;
             const sphere = focus.boundary.sphere;
-            // const asmCenter = asm.boundary.sphere.center;
-            // const position = Vec3.sub(Vec3.zero(), sphere.center, asmCenter);
-            // Vec3.normalize(position, position);
-            // Vec3.scaleAndAdd(position, sphere.center, position, sphere.radius);
-            const snapshot = this.plugin.canvas3d.camera.getFocus(sphere.center, Math.max(sphere.radius, 5));
-            PluginCommands.Camera.SetSnapshot.dispatch(this.plugin, { snapshot, durationMs: 250 });
+            const radius = Math.max(sphere.radius, 5);
+            const snapshot = this.plugin.canvas3d!.camera.getFocus(sphere.center, radius);
+            PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: 250 });
         }
     }
 
-    private createSurVisualParams() {
-        const asm = this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure;
-        return StructureRepresentation3DHelpers.createParams(this.plugin, asm.data, {
-            repr: BuiltInStructureRepresentations['ball-and-stick'],
-            color: [BuiltInColorThemes.uniform, () => ({ value: ColorNames.gray })],
-            size: [BuiltInSizeThemes.uniform, () => ({ value: 0.33 } )]
-        });
-    }
-
-    private createCoreVisualParams() {
-        const asm = this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure;
-        return StructureRepresentation3DHelpers.createParams(this.plugin, asm.data, {
-            repr: BuiltInStructureRepresentations['ball-and-stick'],
-            // color: [BuiltInColorThemes.uniform, () => ({ value: ColorNames.gray })],
-            // size: [BuiltInSizeThemes.uniform, () => ({ value: 0.33 } )]
-        });
-    }
-
     snapshot = {
-        get: () => {
-            return this.plugin.state.getSnapshot();
+        get: (params?: PluginState.SnapshotParams) => {
+            return this.plugin.state.getSnapshot(params);
         },
         set: (snapshot: PluginState.Snapshot) => {
             return this.plugin.state.setSnapshot(snapshot);
         },
-        download: async (url: string) => {
+        download: async (type: 'molj' | 'molx' = 'molj', params?: PluginState.SnapshotParams) => {
+            const data = await this.plugin.managers.snapshot.serialize({ type, params });
+            download(data, `mol-star_state_${(name || getFormattedTime())}.${type}`);
+        },
+        fetch: async (url: string, type: 'molj' | 'molx' = 'molj') => {
             try {
-                const data = await this.plugin.runTask(this.plugin.fetch({ url }));
-                const snapshot = JSON.parse(data);
-                await this.plugin.state.setSnapshot(snapshot);
+                const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'binary' }));
+                this.loadedParams = { ...this.emptyLoadedParams };
+                return await this.plugin.managers.snapshot.open(new File([data], `state.${type}`));
             } catch (e) {
                 console.log(e);
             }

src/examples/proteopedia-wrapper/ui/controls.tsx

@@ -6,27 +6,13 @@
 
 import * as React from 'react';
 import * as ReactDOM from 'react-dom';
-import { PluginUIComponent } from '../../../mol-plugin/ui/base';
-import { CurrentObject, PluginContextContainer } from '../../../mol-plugin/ui/plugin';
-import { AnimationControls } from '../../../mol-plugin/ui/state/animation';
-import { CameraSnapshots } from '../../../mol-plugin/ui/camera';
+import { PluginContextContainer } from '../../../mol-plugin-ui/plugin';
+import { TransformUpdaterControl } from '../../../mol-plugin-ui/state/update-transform';
 import { PluginContext } from '../../../mol-plugin/context';
-import { TransformUpdaterControl } from '../../../mol-plugin/ui/state/update-transform';
 import { StateElements } from '../helpers';
 
-export class ControlsWrapper extends PluginUIComponent {
-    render() {
-        return <div className='msp-scrollable-container msp-right-controls'>
-            <CurrentObject />
-            <AnimationControls />
-            <CameraSnapshots />
-        </div>;
-    }
-}
-
 export function volumeStreamingControls(plugin: PluginContext, parent: Element) {
     ReactDOM.render(<PluginContextContainer plugin={plugin}>
-            <TransformUpdaterControl nodeRef={StateElements.VolumeStreaming} />
-        </PluginContextContainer>,
-        parent);
+        <TransformUpdaterControl nodeRef={StateElements.VolumeStreaming} />
+    </PluginContextContainer>, parent);
 }

src/examples/task.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Task, Progress, Scheduler, MultistepTask, chunkedSubtask } from '../mol-task'
+import { Task, Progress, Scheduler, MultistepTask, chunkedSubtask } from '../mol-task';
 import { now } from '../mol-util/now';
 
 export async function test1() {
@@ -28,9 +28,9 @@ function messageTree(root: Progress.Node, prefix = ''): string {
 
 function createTask<T>(delayMs: number, r: T): Task<T> {
     return Task.create('delayed value ' + r, async ctx => {
-        ctx.update('Processing delayed... ' + r, true);
+        ctx.update(`Processing delayed ${r} after ${delayMs}ms`, true);
         await Scheduler.delay(delayMs);
-        if (ctx.shouldUpdate) await ctx.update({ message: 'hello from delayed... ' });
+        if (ctx.shouldUpdate) await ctx.update({ message: `hello from delayed ${r} ${delayMs}` });
         return r;
     }, () => console.log('On abort called ' + r));
 }
@@ -63,7 +63,7 @@ export function testTree() {
         const r = await c1 + await c2 + await c3;
         if (ctx.shouldUpdate) await ctx.update({ message: 'Almost done...' });
         return r + 1;
-    });
+    }, () => console.log('On abort O'));
 }
 
 export type ChunkedState = { i: number, current: number, total: number }
@@ -85,19 +85,19 @@ export const ms = MultistepTask('ms-task', ['step 1', 'step 2', 'step 3'], async
     await step(0);
 
     const child = Task.create('chunked', async ctx => {
-        const s = await chunkedSubtask(ctx, 25, { i: 0, current: 0, total: 125 }, processChunk, (ctx, s, p) => ctx.update('chunk test ' + p))
+        const s = await chunkedSubtask(ctx, 25, { i: 0, current: 0, total: 125 }, processChunk, (ctx, s, p) => ctx.update('chunk test ' + p));
         return s.i;
     });
 
     await child.runAsChild(ctx);
     await Scheduler.delay(250);
     await step(1);
-    await chunkedSubtask(ctx, 25, { i: 0, current: 0, total: 80 }, processChunk, (ctx, s, p) => ctx.update('chunk test ' + p))
+    await chunkedSubtask(ctx, 25, { i: 0, current: 0, total: 80 }, processChunk, (ctx, s, p) => ctx.update('chunk test ' + p));
     await Scheduler.delay(250);
     await step(2);
     await Scheduler.delay(250);
     return p.i + 3;
-})
+});
 
 
 export function abortingObserver(p: Progress) {
@@ -115,7 +115,7 @@ async function test() {
         // const r = await Run(testTree(), abortingObserver, 250);
         // console.log(r);
 
-        const m = await ms({ i: 10 }).run(logP);
+        const m = await testTree().run(abortingObserver, 50);
         console.log(m);
     } catch (e) {
         console.error(e);

src/extensions/cellpack/color/generate.ts

@@ -0,0 +1,97 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Color } from '../../../mol-util/color';
+import { getPalette } from '../../../mol-util/color/palette';
+import { ColorTheme, LocationColor } from '../../../mol-theme/color';
+import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
+import { StructureElement, Bond } from '../../../mol-model/structure';
+import { Location } from '../../../mol-model/location';
+import { CellPackInfoProvider } from '../property';
+import { distinctColors } from '../../../mol-util/color/distinct';
+import { Hcl } from '../../../mol-util/color/spaces/hcl';
+
+const DefaultColor = Color(0xCCCCCC);
+const Description = 'Gives every model in a CellPack packing a unique generated color similar to other models in the packing.';
+
+export const CellPackGenerateColorThemeParams = {};
+export type CellPackGenerateColorThemeParams = typeof CellPackGenerateColorThemeParams
+export function getCellPackGenerateColorThemeParams(ctx: ThemeDataContext) {
+    return CellPackGenerateColorThemeParams; // TODO return copy
+}
+
+export function CellPackGenerateColorTheme(ctx: ThemeDataContext, props: PD.Values<CellPackGenerateColorThemeParams>): ColorTheme<CellPackGenerateColorThemeParams> {
+    let color: LocationColor;
+    let legend: ScaleLegend | TableLegend | undefined;
+
+    const info = ctx.structure && CellPackInfoProvider.get(ctx.structure).value;
+
+    if (ctx.structure && info) {
+        const colors = distinctColors(info.packingsCount);
+        let hcl = Hcl.fromColor(Hcl(), colors[info.packingIndex]);
+
+        const hue = [Math.max(0, hcl[0] - 35), Math.min(360, hcl[0] + 35)] as [number, number];
+
+        const { models } = ctx.structure.root;
+
+        let size = 0;
+        for (const m of models) size = Math.max(size, m.trajectoryInfo.size);
+
+        const palette = getPalette(size, { palette: {
+            name: 'generate',
+            params: {
+                hue, chroma: [30, 80], luminance: [15, 85],
+                clusteringStepCount: 50, minSampleCount: 800, maxCount: 75,
+                minLabel: 'Min', maxLabel: 'Max', valueLabel: (i: number) => `${i + 1}`,
+            }
+        }});
+        legend = palette.legend;
+        const modelColor = new Map<number, Color>();
+        for (let i = 0, il = models.length; i < il; ++i) {
+            const idx = models[i].trajectoryInfo.index;
+            modelColor.set(models[i].trajectoryInfo.index, palette.color(idx));
+        }
+
+        color = (location: Location): Color => {
+            if (StructureElement.Location.is(location)) {
+                return modelColor.get(location.unit.model.trajectoryInfo.index)!;
+            } else if (Bond.isLocation(location)) {
+                return modelColor.get(location.aUnit.model.trajectoryInfo.index)!;
+            }
+            return DefaultColor;
+        };
+    } else {
+        color = () => DefaultColor;
+    }
+
+    return {
+        factory: CellPackGenerateColorTheme,
+        granularity: 'instance',
+        color,
+        props,
+        description: Description,
+        legend
+    };
+}
+
+export const CellPackGenerateColorThemeProvider: ColorTheme.Provider<CellPackGenerateColorThemeParams, 'cellpack-generate'> = {
+    name: 'cellpack-generate',
+    label: 'CellPack Generate',
+    category: ColorTheme.Category.Chain,
+    factory: CellPackGenerateColorTheme,
+    getParams: getCellPackGenerateColorThemeParams,
+    defaultValues: PD.getDefaultValues(CellPackGenerateColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => {
+        return (
+            !!ctx.structure && ctx.structure.elementCount > 0 &&
+            ctx.structure.models[0].trajectoryInfo.size > 1 &&
+            !!CellPackInfoProvider.get(ctx.structure).value
+        );
+    }
+};
+

src/extensions/cellpack/color/provided.ts

@@ -0,0 +1,72 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Color } from '../../../mol-util/color';
+import { ColorTheme, LocationColor } from '../../../mol-theme/color';
+import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
+import { StructureElement } from '../../../mol-model/structure';
+import { Location } from '../../../mol-model/location';
+import { CellPackInfoProvider } from '../property';
+
+const DefaultColor = Color(0xCCCCCC);
+const Description = 'Gives every model in a CellPack the color provied in the packing data.';
+
+export const CellPackProvidedColorThemeParams = {};
+export type CellPackProvidedColorThemeParams = typeof CellPackProvidedColorThemeParams
+export function getCellPackProvidedColorThemeParams(ctx: ThemeDataContext) {
+    return CellPackProvidedColorThemeParams; // TODO return copy
+}
+
+export function CellPackProvidedColorTheme(ctx: ThemeDataContext, props: PD.Values<CellPackProvidedColorThemeParams>): ColorTheme<CellPackProvidedColorThemeParams> {
+    let color: LocationColor;
+    let legend: ScaleLegend | TableLegend | undefined;
+
+    const info = ctx.structure && CellPackInfoProvider.get(ctx.structure).value;
+
+    if (ctx.structure && info?.colors) {
+        const { models } = ctx.structure.root;
+        const modelColor = new Map<number, Color>();
+        for (let i = 0, il = models.length; i < il; ++i) {
+            const idx = models[i].trajectoryInfo.index;
+            modelColor.set(models[i].trajectoryInfo.index, info.colors[idx]);
+        }
+
+        color = (location: Location): Color => {
+            return StructureElement.Location.is(location)
+                ? modelColor.get(location.unit.model.trajectoryInfo.index)!
+                : DefaultColor;
+        };
+    } else {
+        color = () => DefaultColor;
+    }
+
+    return {
+        factory: CellPackProvidedColorTheme,
+        granularity: 'instance',
+        color,
+        props,
+        description: Description,
+        legend
+    };
+}
+
+export const CellPackProvidedColorThemeProvider: ColorTheme.Provider<CellPackProvidedColorThemeParams, 'cellpack-provided'> = {
+    name: 'cellpack-provided',
+    label: 'CellPack Provided',
+    category: ColorTheme.Category.Chain,
+    factory: CellPackProvidedColorTheme,
+    getParams: getCellPackProvidedColorThemeParams,
+    defaultValues: PD.getDefaultValues(CellPackProvidedColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => {
+        return (
+            !!ctx.structure && ctx.structure.elementCount > 0 &&
+            ctx.structure.models[0].trajectoryInfo.size > 1 &&
+            !!CellPackInfoProvider.get(ctx.structure).value?.colors
+        );
+    }
+};

src/extensions/cellpack/curve.ts

@@ -0,0 +1,229 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Ludovic Autin <autin@scripps.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec3, Quat, Mat4 } from '../../mol-math/linear-algebra';
+import { NumberArray } from '../../mol-util/type-helpers';
+
+interface Frame {
+    t: Vec3,
+    r: Vec3,
+    s: Vec3,
+}
+
+const a0Tmp = Vec3();
+const a1Tmp = Vec3();
+const a2Tmp = Vec3();
+const a3Tmp = Vec3();
+function CubicInterpolate(out: Vec3, y0: Vec3, y1: Vec3, y2: Vec3, y3: Vec3, mu: number): Vec3 {
+    const mu2 = mu * mu;
+    Vec3.sub(a0Tmp, y3, y2);
+    Vec3.sub(a0Tmp, a0Tmp, y0);
+    Vec3.add(a0Tmp, a0Tmp, y1);
+
+    Vec3.sub(a1Tmp, y0, y1);
+    Vec3.sub(a1Tmp, a1Tmp, a0Tmp);
+
+    Vec3.sub(a2Tmp, y2, y0);
+
+    Vec3.copy(a3Tmp, y1);
+
+    out[0] = a0Tmp[0] * mu * mu2 + a1Tmp[0] * mu2 + a2Tmp[0] * mu + a3Tmp[0];
+    out[1] = a0Tmp[1] * mu * mu2 + a1Tmp[1] * mu2 + a2Tmp[1] * mu + a3Tmp[1];
+    out[2] = a0Tmp[2] * mu * mu2 + a1Tmp[2] * mu2 + a2Tmp[2] * mu + a3Tmp[2];
+
+    return out;
+}
+
+const cp0 = Vec3();
+const cp1 = Vec3();
+const cp2 = Vec3();
+const cp3 = Vec3();
+const currentPosition = Vec3();
+function ResampleControlPoints(points: NumberArray, segmentLength: number) {
+    const nP = points.length / 3;
+    // insert a point at the end and at the begining
+    // controlPoints.Insert(0, controlPoints[0] + (controlPoints[0] - controlPoints[1]) / 2.0f);
+    // controlPoints.Add(controlPoints[nP - 1] + (controlPoints[nP - 1] - controlPoints[nP - 2]) / 2.0f);
+
+    let resampledControlPoints: Vec3[] = [];
+    // resampledControlPoints.Add(controlPoints[0]);
+    // resampledControlPoints.Add(controlPoints[1]);
+
+    let idx = 1;
+    // const currentPosition = Vec3.create(points[idx * 3], points[idx * 3 + 1], points[idx * 3 + 2])
+    Vec3.fromArray(currentPosition, points, idx * 3);
+
+    let lerpValue = 0.0;
+
+    // Normalize the distance between control points
+    while (true) {
+        if (idx + 2 >= nP) break;
+        Vec3.fromArray(cp0, points, (idx - 1) * 3);
+        Vec3.fromArray(cp1, points, idx * 3);
+        Vec3.fromArray(cp2, points, (idx + 1) * 3);
+        Vec3.fromArray(cp3, points, (idx + 2) * 3);
+        // const cp0 = Vec3.create(points[(idx-1)*3], points[(idx-1)*3+1], points[(idx-1)*3+2]) // controlPoints[currentPointId - 1];
+        // const cp1 = Vec3.create(points[idx*3], points[idx*3+1], points[idx*3+2]) // controlPoints[currentPointId];
+        // const cp2 = Vec3.create(points[(idx+1)*3], points[(idx+1)*3+1], points[(idx+1)*3+2]) // controlPoints[currentPointId + 1];
+        // const cp3 = Vec3.create(points[(idx+2)*3], points[(idx+2)*3+1], points[(idx+2)*3+2]); // controlPoints[currentPointId + 2];
+        let found = false;
+        for (; lerpValue <= 1; lerpValue += 0.01) {
+            // lerp?slerp
+            // let candidate:Vec3 = Vec3.lerp(Vec3.zero(), cp0, cp1, lerpValue);
+            // const candidate:Vec3 = Vec3.bezier(Vec3.zero(), cp0, cp1, cp2, cp3, lerpValue);
+            const candidate = CubicInterpolate(Vec3(), cp0, cp1, cp2, cp3, lerpValue);
+            const d = Vec3.distance(currentPosition, candidate);
+            if (d > segmentLength) {
+                resampledControlPoints.push(candidate);
+                Vec3.copy(currentPosition, candidate);
+                found = true;
+                break;
+            }
+        }
+        if (!found) {
+            lerpValue = 0;
+            idx += 1;
+        }
+    }
+    return resampledControlPoints;
+}
+
+
+const prevV = Vec3();
+const tmpV1 = Vec3();
+const tmpV2 = Vec3();
+const tmpV3 = Vec3();
+
+// easier to align to theses normals
+function GetSmoothNormals(points: Vec3[]) {
+    const nP: number = points.length;
+    const smoothNormals: Vec3[] = [];
+    if (points.length < 3) {
+        for (let i = 0; i < points.length; ++i)
+            smoothNormals.push(Vec3.normalize(Vec3(), points[i]));
+        return smoothNormals;
+    }
+    let p0 = points[0];
+    let p1 = points[1];
+    let p2 = points[2];
+    const p21 = Vec3.sub(tmpV1, p2, p1);
+    const p01 =  Vec3.sub(tmpV2, p0, p1);
+    const p0121 = Vec3.cross(tmpV3, p01, p21);
+    Vec3.normalize(prevV, p0121);
+    smoothNormals.push(Vec3.clone(prevV));
+    for (let i = 1; i < points.length - 1; ++i) {
+        p0 = points[i - 1];
+        p1 = points[i];
+        p2 = points[i + 1];
+        const t = Vec3.normalize(tmpV1, Vec3.sub(tmpV1, p2, p0));
+        const b = Vec3.normalize(tmpV2, Vec3.cross(tmpV2, t, prevV));
+        const n = Vec3.normalize(Vec3(), Vec3.cross(tmpV3, t, b));
+        Vec3.negate(n, n);
+        Vec3.copy(prevV, n);
+        smoothNormals.push(n);
+    }
+    const last = Vec3();
+    Vec3.normalize(last, Vec3.cross(last,
+        Vec3.sub(tmpV1, points[nP - 3], points[nP - 2]),
+        Vec3.sub(tmpV2, points[nP - 2], points[nP - 1]))
+    );
+    smoothNormals.push(last);
+    return smoothNormals;
+}
+
+const frameTmpV1 = Vec3();
+const frameTmpV2 = Vec3();
+const frameTmpV3 = Vec3();
+
+function getFrame(reference: Vec3, tangent: Vec3) {
+    const t = Vec3.normalize(Vec3(), tangent);
+    // make reference vector orthogonal to tangent
+    const proj_r_to_t = Vec3.scale(
+        frameTmpV1, tangent, Vec3.dot(reference, tangent) / Vec3.dot(tangent, tangent)
+    );
+    const r = Vec3.normalize(Vec3(), Vec3.sub(frameTmpV2, reference, proj_r_to_t));
+    // make bitangent vector orthogonal to the others
+    const s = Vec3.normalize(Vec3(), Vec3.cross(frameTmpV3, t, r));
+    return { t, r, s };
+}
+
+const mfTmpV1 = Vec3();
+const mfTmpV2 = Vec3();
+const mfTmpV3 = Vec3();
+const mfTmpV4 = Vec3();
+const mfTmpV5 = Vec3();
+const mfTmpV6 = Vec3();
+const mfTmpV7 = Vec3();
+const mfTmpV8 = Vec3();
+const mfTmpV9 = Vec3();
+
+// easier to align to theses normals
+// https://github.com/bzamecnik/gpg/blob/master/rotation-minimizing-frame/rmf.py
+function GetMiniFrame(points: Vec3[], normals: Vec3[]) {
+    const frames: Frame[] = [];
+    const t0 = Vec3.normalize(mfTmpV1, Vec3.sub(mfTmpV1, points[1], points[0]));
+    frames.push(getFrame(normals[0], t0));
+
+    for (let i = 0; i < points.length - 2; ++i) {
+        const t2 = Vec3.normalize(mfTmpV1, Vec3.sub(mfTmpV1, points[i + 2], points[i + 1]));
+        const v1 = Vec3.sub(mfTmpV2, points[i + 1], points[i]); // this is tangeant
+        const c1 = Vec3.dot(v1, v1);
+        // compute r_i^L = R_1 * r_i
+        const v1r = Vec3.scale(mfTmpV3, v1, (2.0 / c1) * Vec3.dot(v1, frames[i].r));
+        const ref_L_i = Vec3.sub(mfTmpV4, frames[i].r, v1r);
+        // compute t_i^L = R_1 * t_i
+        const v1t = Vec3.scale(mfTmpV5, v1, (2.0 / c1) * Vec3.dot(v1, frames[i].t));
+        const tan_L_i = Vec3.sub(mfTmpV6, frames[i].t, v1t);
+        // # compute reflection vector of R_2
+        const v2 =  Vec3.sub(mfTmpV7, t2, tan_L_i);
+        const c2 = Vec3.dot(v2, v2);
+        // compute r_(i+1) = R_2 * r_i^L
+        const v2l = Vec3.scale(mfTmpV8, v1, (2.0 / c2) * Vec3.dot(v2, ref_L_i));
+        const ref_next = Vec3.sub(mfTmpV9, ref_L_i, v2l); // ref_L_i - (2 / c2) * v2.dot(ref_L_i) * v2
+        frames.push(getFrame(ref_next, t2)); // frames.append(Frame(ref_next, tangents[i+1]))
+    }
+    return frames;
+}
+
+const rpTmpVec1 = Vec3();
+
+export function getMatFromResamplePoints(points: NumberArray, segmentLength: number, resample: boolean) {
+    let new_points: Vec3[] = [];
+    if (resample) new_points = ResampleControlPoints(points, segmentLength);
+    else {
+        for (let idx = 0; idx < points.length / 3; ++idx){
+            new_points.push(Vec3.fromArray(Vec3.zero(), points, idx * 3));
+        }
+    }
+    const npoints = new_points.length;
+    const new_normal = GetSmoothNormals(new_points);
+    const frames = GetMiniFrame(new_points, new_normal);
+    const limit = npoints;
+    const transforms: Mat4[] = [];
+    const pti = Vec3.copy(rpTmpVec1, new_points[0]);
+    for (let i = 0; i < npoints - 2; ++i) {
+        const pti1: Vec3 = new_points[i + 1]; // Vec3.create(points[(i+1)*3],points[(i+1)*3+1],points[(i+1)*3+2]);
+        const d = Vec3.distance(pti, pti1);
+        if (d >= segmentLength) {
+            // use twist or random?
+            const quat = Quat.rotationTo(Quat.zero(), Vec3.create(0, 0, 1), frames[i].t); // Quat.rotationTo(Quat.zero(), Vec3.create(0,0,1),new_normal[i]);//Quat.rotationTo(Quat.zero(), Vec3.create(0,0,1),direction);new_normal
+            const rq = Quat.setAxisAngle(Quat.zero(), frames[i].t, Math.random() * 3.60 ); // Quat.setAxisAngle(Quat.zero(),direction, Math.random()*3.60 );//Quat.identity();//
+            const m = Mat4.fromQuat(Mat4.zero(), Quat.multiply(Quat.zero(), rq, quat)); // Mat4.fromQuat(Mat4.zero(),Quat.multiply(Quat.zero(),quat1,quat2));//Mat4.fromQuat(Mat4.zero(),quat);//Mat4.identity();//Mat4.fromQuat(Mat4.zero(),Quat.multiply(Quat.zero(),rq,quat));
+            // let pos:Vec3 = Vec3.add(Vec3.zero(),pti1,pti)
+            // pos = Vec3.scale(pos,pos,1.0/2.0);
+            // Vec3.makeRotation(Mat4.zero(),Vec3.create(0,0,1),frames[i].t);//
+            Mat4.setTranslation(m, pti1);
+            // let m2:Mat4 = GetTubePropertiesMatrix(pti,pti1);
+            // let q:Quat = Quat.rotationTo(Quat.zero(), Vec3.create(0,1,0),Vec3.create(0,0,1))
+            // m2=Mat4.mul(Mat4.identity(),Mat4.fromQuat(Mat4.zero(),q),m2);
+            transforms.push(m);
+            Vec3.copy(pti, pti1);
+        }
+        if (transforms.length >= limit) break;
+    }
+    return transforms;
+}

src/extensions/cellpack/data.ts

@@ -0,0 +1,84 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec3, Quat } from '../../mol-math/linear-algebra';
+
+export interface CellPack {
+    cell: Cell
+    packings: CellPacking[]
+}
+
+export interface CellPacking {
+    name: string,
+    location: 'surface' | 'interior' | 'cytoplasme',
+    ingredients: Packing['ingredients']
+}
+
+//
+
+export interface Cell {
+    recipe: Recipe
+    cytoplasme?: Packing
+    compartments?: { [key: string]: Compartment }
+}
+
+export interface Recipe {
+    setupfile: string
+    paths: [string, string][] // [name: string, path: string][]
+    version: string
+    name: string
+}
+
+export interface Compartment {
+    surface?: Packing
+    interior?: Packing
+}
+
+export interface Packing {
+    ingredients: { [key: string]: Ingredient }
+}
+
+export interface Positions {
+    coords?: Vec3[];
+}
+
+export interface Radii {
+    radii?: number[];
+}
+
+export interface Ingredient {
+    source: IngredientSource;
+    results: [Vec3, Quat][];
+    name: string;
+    /** Vec3[]];CoarseGraind Beads coordinates LOD */
+    positions?: [Positions];
+    /** number[]];CoarseGraind Beads radii LOD */
+    radii?: [Radii];
+    /** Number of `curveX` properties in the object where `X` is a 0-indexed number */
+    nbCurve?: number;
+    uLength?: number;
+    /** Curve properties are Vec3[] but that is not expressable in TypeScript */
+    [curveX: string]: unknown;
+    /** the orientation in the membrane */
+    principalAxis?: Vec3;
+    /** offset along membrane */
+    offset?: Vec3;
+    ingtype?: string;
+    color?: Vec3;
+    confidence?: number;
+}
+
+export interface IngredientSource {
+    pdb: string;
+    bu?: string;  /** biological unit e.g AU,BU1,etc.. */
+    selection?: string; /** NGL selection or :A or :B etc.. */
+    model?: string;     /** model number e.g 0,1,2... */
+    transform: {
+        center: boolean;
+        translate?: Vec3;
+    };
+    biomt?: boolean;
+}

src/extensions/cellpack/index.ts

@@ -0,0 +1,32 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior';
+import { LoadCellPackModel } from './model';
+import { CellPackGenerateColorThemeProvider } from './color/generate';
+import { CellPackProvidedColorThemeProvider } from './color/provided';
+
+export const CellPack = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'cellpack',
+    category: 'custom-props',
+    display: {
+        name: 'CellPack',
+        description: 'CellPack Model Loading and Viewing.'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
+        register(): void {
+            this.ctx.state.data.actions.add(LoadCellPackModel);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(CellPackGenerateColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(CellPackProvidedColorThemeProvider);
+        }
+
+        unregister() {
+            this.ctx.state.data.actions.remove(LoadCellPackModel);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(CellPackGenerateColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(CellPackProvidedColorThemeProvider);
+        }
+    }
+});

src/extensions/cellpack/model.ts

@@ -0,0 +1,584 @@
+/**
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StateAction, StateBuilder, StateTransformer, State } from '../../mol-state';
+import { PluginContext } from '../../mol-plugin/context';
+import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Ingredient, IngredientSource, CellPacking } from './data';
+import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile, getStructureMean, getFromOPM } from './util';
+import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../mol-model/structure';
+import { trajectoryFromMmCIF, MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { trajectoryFromPDB } from '../../mol-model-formats/structure/pdb';
+import { Mat4, Vec3, Quat } from '../../mol-math/linear-algebra';
+import { SymmetryOperator } from '../../mol-math/geometry';
+import { Task, RuntimeContext } from '../../mol-task';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl, StructureFromAssemblies } from './state';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { getMatFromResamplePoints } from './curve';
+import { compile } from '../../mol-script/runtime/query/compiler';
+import { CifCategory, CifField } from '../../mol-io/reader/cif';
+import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { Column } from '../../mol-data/db';
+import { createModels } from '../../mol-model-formats/structure/basic/parser';
+import { CellpackPackingPreset, CellpackMembranePreset } from './preset';
+import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
+import { readFromFile } from '../../mol-util/data-source';
+import { objectForEach } from '../../mol-util/object';
+
+function getCellPackModelUrl(fileName: string, baseUrl: string) {
+    return `${baseUrl}/results/${fileName}`;
+}
+
+class TrajectoryCache {
+    private map = new Map<string, Model.Trajectory>();
+    set(id: string, trajectory: Model.Trajectory) { this.map.set(id, trajectory); }
+    get(id: string) { return this.map.get(id); }
+}
+
+async function getModel(plugin: PluginContext, id: string, ingredient: Ingredient, baseUrl: string, trajCache: TrajectoryCache, file?: Asset.File) {
+    const assetManager = plugin.managers.asset;
+    const modelIndex = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
+    const surface = (ingredient.ingtype) ? (ingredient.ingtype === 'transmembrane') : false;
+    let trajectory = trajCache.get(id);
+    let assets: Asset.Wrapper[] = [];
+    if (!trajectory) {
+        if (file) {
+            if (file.name.endsWith('.cif')) {
+                const text = await plugin.runTask(assetManager.resolve(file, 'string'));
+                assets.push(text);
+                const cif = (await parseCif(plugin, text.data)).blocks[0];
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(cif));
+            } else if (file.name.endsWith('.bcif')) {
+                const binary = await plugin.runTask(assetManager.resolve(file, 'binary'));
+                assets.push(binary);
+                const cif = (await parseCif(plugin, binary.data)).blocks[0];
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(cif));
+            } else if (file.name.endsWith('.pdb')) {
+                const text = await plugin.runTask(assetManager.resolve(file, 'string'));
+                assets.push(text);
+                const pdb = await parsePDBfile(plugin, text.data, id);
+                trajectory = await plugin.runTask(trajectoryFromPDB(pdb));
+            } else {
+                throw new Error(`unsupported file type '${file.name}'`);
+            }
+        } else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
+            if (surface){
+                try {
+                    const data = await getFromOPM(plugin, id, assetManager);
+                    assets.push(data.asset);
+                    trajectory = await plugin.runTask(trajectoryFromPDB(data.pdb));
+                } catch (e) {
+                    // fallback to getFromPdb
+                    // console.error(e);
+                    const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
+                    assets.push(asset);
+                    trajectory = await plugin.runTask(trajectoryFromMmCIF(mmcif));
+                }
+            } else {
+                const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
+                assets.push(asset);
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(mmcif));
+            }
+        } else {
+            const data = await getFromCellPackDB(plugin, id, baseUrl, assetManager);
+            assets.push(data.asset);
+            if ('pdb' in data) {
+                trajectory = await plugin.runTask(trajectoryFromPDB(data.pdb));
+            } else {
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(data.mmcif));
+            }
+        }
+        trajCache.set(id, trajectory);
+    }
+    const model = trajectory[modelIndex];
+    return { model, assets };
+}
+
+async function getStructure(plugin: PluginContext, model: Model, source: IngredientSource, props: { assembly?: string } = {}) {
+    let structure = Structure.ofModel(model);
+    const { assembly } = props;
+
+    if (assembly) {
+        structure = await plugin.runTask(StructureSymmetry.buildAssembly(structure, assembly));
+    }
+    let query;
+    if (source.selection){
+        const asymIds: string[] = source.selection.replace(' ', '').replace(':', '').split('or');
+        query = MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
+                'chain-test': MS.core.set.has([MS.set(...asymIds), MS.ammp('auth_asym_id')])
+            })
+        ]);
+    } else {
+        query = MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
+            })
+        ]);
+    }
+
+    const compiled = compile<StructureSelection>(query);
+    const result = compiled(new QueryContext(structure));
+    structure = StructureSelection.unionStructure(result);
+
+    return structure;
+}
+
+function getTransformLegacy(trans: Vec3, rot: Quat) {
+    const q: Quat = Quat.create(-rot[3], rot[0], rot[1], rot[2]);
+    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+    Mat4.transpose(m, m);
+    Mat4.scale(m, m, Vec3.create(-1.0, 1.0, -1.0));
+    Mat4.setTranslation(m, trans);
+    return m;
+}
+
+function getTransform(trans: Vec3, rot: Quat) {
+    const q: Quat = Quat.create(rot[0], rot[1], rot[2], rot[3]);
+    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+    const p: Vec3 = Vec3.create(trans[0], trans[1], trans[2]);
+    Mat4.setTranslation(m, p);
+    return m;
+}
+
+function getResultTransforms(results: Ingredient['results'], legacy: boolean) {
+    if (legacy) return results.map((r: Ingredient['results'][0]) => getTransformLegacy(r[0], r[1]));
+    else return results.map((r: Ingredient['results'][0]) => getTransform(r[0], r[1]));
+}
+
+function getCurveTransforms(ingredient: Ingredient) {
+    const n = ingredient.nbCurve || 0;
+    const instances: Mat4[] = [];
+    let segmentLength = 3.4;
+    if (ingredient.uLength){
+        segmentLength = ingredient.uLength;
+    } else if (ingredient.radii){
+        segmentLength = ingredient.radii[0].radii
+            ? ingredient.radii[0].radii[0] * 2.0
+            : 3.4;
+    }
+    let resampling: boolean = false;
+    for (let i = 0; i < n; ++i) {
+        const cname = `curve${i}`;
+        if (!(cname in ingredient)) {
+            // console.warn(`Expected '${cname}' in ingredient`)
+            continue;
+        }
+        const _points = ingredient[cname] as Vec3[];
+        if (_points.length <= 2) {
+            // TODO handle curve with 2 or less points
+            continue;
+        }
+        // test for resampling
+        let distance: number = Vec3.distance(_points[0], _points[1]);
+        if (distance >= segmentLength + 2.0) {
+            console.info(distance);
+            resampling = true;
+        }
+        const points = new Float32Array(_points.length * 3);
+        for (let i = 0, il = _points.length; i < il; ++i) Vec3.toArray(_points[i], points, i * 3);
+        const newInstances = getMatFromResamplePoints(points, segmentLength, resampling);
+        instances.push(...newInstances);
+    }
+    return instances;
+}
+
+function getAssembly(transforms: Mat4[], structure: Structure) {
+    const builder = Structure.Builder();
+    const { units } = structure;
+
+    for (let i = 0, il = transforms.length; i < il; ++i) {
+        const id = `${i + 1}`;
+        const op = SymmetryOperator.create(id, transforms[i], { assembly: { id, operId: i, operList: [ id ] } });
+        for (const unit of units) {
+            builder.addWithOperator(unit, op);
+        }
+    }
+
+    return builder.getStructure();
+}
+
+function getCifCurve(name: string, transforms: Mat4[], model: Model) {
+    if (!MmcifFormat.is(model.sourceData)) throw new Error('mmcif source data needed');
+
+    const { db } = model.sourceData.data;
+    const d = db.atom_site;
+    const n = d._rowCount;
+    const rowCount = n * transforms.length;
+
+    const { offsets, count } = model.atomicHierarchy.chainAtomSegments;
+
+    const x = d.Cartn_x.toArray();
+    const y = d.Cartn_y.toArray();
+    const z = d.Cartn_z.toArray();
+
+    const Cartn_x = new Float32Array(rowCount);
+    const Cartn_y = new Float32Array(rowCount);
+    const Cartn_z = new Float32Array(rowCount);
+    const map = new Uint32Array(rowCount);
+    const seq = new Int32Array(rowCount);
+    let offset = 0;
+    for (let c = 0; c < count; ++c) {
+        const cStart = offsets[c];
+        const cEnd = offsets[c + 1];
+        const cLength = cEnd - cStart;
+        for (let t = 0, tl = transforms.length; t < tl; ++t) {
+            const m = transforms[t];
+            for (let j = cStart; j < cEnd; ++j) {
+                const i = offset + j - cStart;
+                const xj = x[j], yj = y[j], zj = z[j];
+                Cartn_x[i] = m[0] * xj + m[4] * yj + m[8] * zj + m[12];
+                Cartn_y[i] = m[1] * xj + m[5] * yj + m[9] * zj + m[13];
+                Cartn_z[i] = m[2] * xj + m[6] * yj + m[10] * zj + m[14];
+                map[i] = j;
+                seq[i] = t + 1;
+            }
+            offset += cLength;
+        }
+    }
+
+    function multColumn<T>(column: Column<T>) {
+        const array = column.toArray();
+        return Column.ofLambda({
+            value: row => array[map[row]],
+            areValuesEqual: (rowA, rowB) => map[rowA] === map[rowB] || array[map[rowA]] === array[map[rowB]],
+            rowCount, schema: column.schema
+        });
+    }
+
+    const _atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
+        auth_asym_id: CifField.ofColumn(multColumn(d.auth_asym_id)),
+        auth_atom_id: CifField.ofColumn(multColumn(d.auth_atom_id)),
+        auth_comp_id: CifField.ofColumn(multColumn(d.auth_comp_id)),
+        auth_seq_id: CifField.ofNumbers(seq),
+
+        B_iso_or_equiv: CifField.ofColumn(Column.ofConst(0, rowCount, Column.Schema.float)),
+        Cartn_x: CifField.ofNumbers(Cartn_x),
+        Cartn_y: CifField.ofNumbers(Cartn_y),
+        Cartn_z: CifField.ofNumbers(Cartn_z),
+        group_PDB: CifField.ofColumn(Column.ofConst('ATOM', rowCount, Column.Schema.str)),
+        id: CifField.ofColumn(Column.ofLambda({
+            value: row => row,
+            areValuesEqual: (rowA, rowB) => rowA === rowB,
+            rowCount, schema: d.id.schema,
+        })),
+
+        label_alt_id: CifField.ofColumn(multColumn(d.label_alt_id)),
+
+        label_asym_id: CifField.ofColumn(multColumn(d.label_asym_id)),
+        label_atom_id: CifField.ofColumn(multColumn(d.label_atom_id)),
+        label_comp_id: CifField.ofColumn(multColumn(d.label_comp_id)),
+        label_seq_id: CifField.ofNumbers(seq),
+        label_entity_id: CifField.ofColumn(Column.ofConst('1', rowCount, Column.Schema.str)),
+
+        occupancy: CifField.ofColumn(Column.ofConst(1, rowCount, Column.Schema.float)),
+        type_symbol: CifField.ofColumn(multColumn(d.type_symbol)),
+
+        pdbx_PDB_ins_code: CifField.ofColumn(Column.ofConst('', rowCount, Column.Schema.str)),
+        pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst(1, rowCount, Column.Schema.int)),
+    };
+
+    const categories = {
+        entity: CifCategory.ofTable('entity', db.entity),
+        chem_comp: CifCategory.ofTable('chem_comp', db.chem_comp),
+        atom_site: CifCategory.ofFields('atom_site', _atom_site)
+    };
+
+    return {
+        header: name,
+        categoryNames: Object.keys(categories),
+        categories
+    };
+}
+
+async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredient, transforms: Mat4[], model: Model) {
+    const cif = getCifCurve(name, transforms, model);
+    const curveModelTask = Task.create('Curve Model', async ctx => {
+        const format = MmcifFormat.fromFrame(cif);
+        const models = await createModels(format.data.db, format, ctx);
+        return models[0];
+    });
+
+    const curveModel = await plugin.runTask(curveModelTask);
+    return getStructure(plugin, curveModel, ingredient.source);
+}
+
+async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles, trajCache: TrajectoryCache) {
+    const { name, source, results, nbCurve } = ingredient;
+    if (source.pdb === 'None') return;
+
+    const file = ingredientFiles[source.pdb];
+    if (!file) {
+        // TODO can these be added to the library?
+        if (name === 'HIV1_CAhex_0_1_0') return; // 1VU4CtoH_hex.pdb
+        if (name === 'HIV1_CAhexCyclophilA_0_1_0') return; // 1AK4fitTo1VU4hex.pdb
+        if (name === 'iLDL') return; // EMD-5239
+        if (name === 'peptides') return; // peptide.pdb
+        if (name === 'lypoglycane') return;
+    }
+
+    // model id in case structure is NMR
+    const { model, assets } = await getModel(plugin, source.pdb || name, ingredient, baseUrl, trajCache, file);
+    if (!model) return;
+
+    let structure: Structure;
+    if (nbCurve) {
+        structure = await getCurve(plugin, name, ingredient, getCurveTransforms(ingredient), model);
+    } else {
+        let bu: string|undefined = source.bu ? source.bu : undefined;
+        if (bu){
+            if (bu === 'AU') {
+                bu = undefined;
+            } else {
+                bu = bu.slice(2);
+            }
+        }
+        structure = await getStructure(plugin, model, source, { assembly: bu });
+        // transform with offset and pcp
+        let legacy: boolean = true;
+        if (ingredient.offset || ingredient.principalAxis){
+            legacy = false;
+            const structureMean = getStructureMean(structure);
+            Vec3.negate(structureMean, structureMean);
+            const m1: Mat4 = Mat4.identity();
+            Mat4.setTranslation(m1, structureMean);
+            structure = Structure.transform(structure, m1);
+            if (ingredient.offset){
+                if (!Vec3.exactEquals(ingredient.offset, Vec3.zero())){
+                    const m: Mat4 = Mat4.identity();
+                    Mat4.setTranslation(m, ingredient.offset);
+                    structure = Structure.transform(structure, m);
+                }
+            }
+            if (ingredient.principalAxis){
+                if (!Vec3.exactEquals(ingredient.principalAxis, Vec3.unitZ)){
+                    const q: Quat = Quat.identity();
+                    Quat.rotationTo(q, ingredient.principalAxis, Vec3.unitZ);
+                    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+                    structure = Structure.transform(structure, m);
+                }
+            }
+        }
+        structure = getAssembly(getResultTransforms(results, legacy), structure);
+    }
+
+    return { structure, assets };
+}
+
+export function createStructureFromCellPack(plugin: PluginContext, packing: CellPacking, baseUrl: string, ingredientFiles: IngredientFiles) {
+    return Task.create('Create Packing Structure', async ctx => {
+        const { ingredients, name } = packing;
+        const assets: Asset.Wrapper[] = [];
+        const trajCache = new TrajectoryCache();
+        const structures: Structure[] = [];
+        const colors: Color[] = [];
+        let skipColors: boolean = false;
+        for (const iName in ingredients) {
+            if (ctx.shouldUpdate) await ctx.update(iName);
+            const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache);
+            if (ingredientStructure) {
+                structures.push(ingredientStructure.structure);
+                assets.push(...ingredientStructure.assets);
+                const c = ingredients[iName].color;
+                if (c){
+                    colors.push(Color.fromNormalizedRgb(c[0], c[1], c[2]));
+                } else {
+                    skipColors = true;
+                }
+            }
+        }
+
+        if (ctx.shouldUpdate) await ctx.update(`${name} - units`);
+        const builder = Structure.Builder({ label: name });
+        let offsetInvariantId = 0;
+        for (const s of structures) {
+            if (ctx.shouldUpdate) await ctx.update(`${s.label}`);
+            let maxInvariantId = 0;
+            for (const u of s.units) {
+                const invariantId = u.invariantId + offsetInvariantId;
+                if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId;
+                builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId);
+            }
+            offsetInvariantId += maxInvariantId + 1;
+        }
+
+        if (ctx.shouldUpdate) await ctx.update(`${name} - structure`);
+        const structure = builder.getStructure();
+        for( let i = 0, il = structure.models.length; i < il; ++i) {
+            const { trajectoryInfo } = structure.models[i];
+            trajectoryInfo.size = il;
+            trajectoryInfo.index = i;
+        }
+        return { structure, assets, colors: skipColors ? undefined : colors };
+    });
+}
+
+async function handleHivRna(plugin: PluginContext, packings: CellPacking[], baseUrl: string) {
+    for (let i = 0, il = packings.length; i < il; ++i) {
+        if (packings[i].name === 'HIV1_capsid_3j3q_PackInner_0_1_0') {
+            const url = Asset.getUrlAsset(plugin.managers.asset, `${baseUrl}/extras/rna_allpoints.json`);
+            const json = await plugin.runTask(plugin.managers.asset.resolve(url, 'json', false));
+            const points = json.data.points as number[];
+
+            const curve0: Vec3[] = [];
+            for (let j = 0, jl = points.length; j < jl; j += 3) {
+                curve0.push(Vec3.fromArray(Vec3(), points, j));
+            }
+            packings[i].ingredients['RNA'] = {
+                source: { pdb: 'RNA_U_Base.pdb', transform: { center: false } },
+                results: [],
+                name: 'RNA',
+                nbCurve: 1,
+                curve0
+            };
+        }
+    }
+}
+
+async function loadMembrane(plugin: PluginContext, name: string, state: State, params: LoadCellPackModelParams) {
+    let file: Asset.File | undefined = undefined;
+    if (params.ingredients.files !== null) {
+        const fileName = `${name}.bcif`;
+        for (const f of params.ingredients.files) {
+            if (fileName === f.name) {
+                file = f;
+                break;
+            }
+        }
+        if (!file){
+            // check for cif directly
+            const cifileName = `${name}.cif`;
+            for (const f of params.ingredients.files) {
+                if (cifileName === f.name) {
+                    file = f;
+                    break;
+                }
+            }
+        }
+    }
+
+    let b = state.build().toRoot();
+    if (file) {
+        if (file.name.endsWith('.cif')) {
+            b = b.apply(StateTransforms.Data.ReadFile, { file, isBinary: false, label: file.name }, { state: { isGhost: true } });
+        } else if (file.name.endsWith('.bcif')) {
+            b = b.apply(StateTransforms.Data.ReadFile, { file, isBinary: true, label: file.name }, { state: { isGhost: true } });
+        }
+    } else {
+        const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/membranes/${name}.bcif`);
+        b = b.apply(StateTransforms.Data.Download, { url, isBinary: true, label: name }, { state: { isGhost: true } });
+    }
+
+    const membrane = await b.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
+        .apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
+        .apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
+        .apply(StructureFromAssemblies, undefined, { state: { isGhost: true } })
+        .commit({ revertOnError: true });
+
+    const membraneParams = {
+        representation: params.preset.representation,
+    };
+
+    await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
+}
+
+async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
+    const ingredientFiles = params.ingredients.files || [];
+
+    let cellPackJson: StateBuilder.To<PSO.Format.Json, StateTransformer<PSO.Data.String, PSO.Format.Json>>;
+    if (params.source.name === 'id') {
+        const url = Asset.getUrlAsset(plugin.managers.asset, getCellPackModelUrl(params.source.params, params.baseUrl));
+        cellPackJson = state.build().toRoot()
+            .apply(StateTransforms.Data.Download, { url, isBinary: false, label: params.source.params }, { state: { isGhost: true } });
+    } else {
+        const file = params.source.params;
+        if (!file?.file) {
+            plugin.log.error('No file selected');
+            return;
+        }
+
+        let jsonFile: Asset.File;
+        if (file.name.toLowerCase().endsWith('.zip')) {
+            const data = await readFromFile(file.file, 'zip').runInContext(runtime);
+            jsonFile = Asset.File(new File([data['model.json']], 'model.json'));
+            objectForEach(data, (v, k) => {
+                if (k === 'model.json') return;
+                ingredientFiles.push(Asset.File(new File([v], k)));
+            });
+        } else {
+            jsonFile = file;
+        }
+
+        cellPackJson = state.build().toRoot()
+            .apply(StateTransforms.Data.ReadFile, { file: jsonFile, isBinary: false, label: jsonFile.name }, { state: { isGhost: true } });
+    }
+
+    const cellPackBuilder = cellPackJson
+        .apply(StateTransforms.Data.ParseJson, undefined, { state: { isGhost: true } })
+        .apply(ParseCellPack);
+
+    const cellPackObject = await state.updateTree(cellPackBuilder).runInContext(runtime);
+    const { packings } = cellPackObject.obj!.data;
+
+    await handleHivRna(plugin, packings, params.baseUrl);
+
+    for (let i = 0, il = packings.length; i < il; ++i) {
+        const p = { packing: i, baseUrl: params.baseUrl, ingredientFiles };
+
+        const packing = await state.build()
+            .to(cellPackBuilder.ref)
+            .apply(StructureFromCellpack, p)
+            .commit({ revertOnError: true });
+
+        const packingParams = {
+            traceOnly: params.preset.traceOnly,
+            representation: params.preset.representation,
+        };
+        await CellpackPackingPreset.apply(packing, packingParams, plugin);
+        if ( packings[i].location === 'surface' && params.membrane){
+            await loadMembrane(plugin, packings[i].name, state, params);
+        }
+    }
+}
+
+const LoadCellPackModelParams = {
+    source: PD.MappedStatic('id', {
+        'id': PD.Select('InfluenzaModel2.json', [
+            ['blood_hiv_immature_inside.json', 'Blood HIV immature'],
+            ['HIV_immature_model.json', 'HIV immature'],
+            ['BloodHIV1.0_mixed_fixed_nc1.cpr', 'Blood HIV'],
+            ['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV'],
+            ['influenza_model1.json', 'Influenza envelope'],
+            ['InfluenzaModel2.json', 'Influenza Complete'],
+            ['ExosomeModel.json', 'Exosome Model'],
+            ['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma simple'],
+            ['MycoplasmaModel.json', 'Mycoplasma WholeCell model'],
+        ] as const, { description: 'Download the model definition with `id` from the server at `baseUrl.`' }),
+        'file': PD.File({ accept: '.json,.cpr,.zip', description: 'Open model definition from .json/.cpr file or open .zip file containing model definition plus ingredients.' }),
+    }, { options: [['id', 'Id'], ['file', 'File']] }),
+    baseUrl: PD.Text(DefaultCellPackBaseUrl),
+    membrane: PD.Boolean(true),
+    ingredients : PD.Group({
+        files: PD.FileList({ accept: '.cif,.bcif,.pdb' })
+    }, { isExpanded: true }),
+    preset: PD.Group({
+        traceOnly: PD.Boolean(false),
+        representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation']))
+    }, { isExpanded: true })
+};
+type LoadCellPackModelParams = PD.Values<typeof LoadCellPackModelParams>
+
+export const LoadCellPackModel = StateAction.build({
+    display: { name: 'Load CellPack', description: 'Open or download a model' },
+    params: LoadCellPackModelParams,
+    from: PSO.Root
+})(({ state, params }, ctx: PluginContext) => Task.create('CellPack Loader', async taskCtx => {
+    await loadPackings(ctx, taskCtx, state, params);
+}));

src/extensions/cellpack/preset.ts

@@ -0,0 +1,95 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StateObjectRef } from '../../mol-state';
+import { StructureRepresentationPresetProvider, presetStaticComponent } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { ColorNames } from '../../mol-util/color/names';
+import { CellPackGenerateColorThemeProvider } from './color/generate';
+import { CellPackInfoProvider } from './property';
+import { CellPackProvidedColorThemeProvider } from './color/provided';
+
+export const CellpackPackingPresetParams = {
+    traceOnly: PD.Boolean(true),
+    representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'])),
+};
+export type CellpackPackingPresetParams = PD.ValuesFor<typeof CellpackPackingPresetParams>
+
+export const CellpackPackingPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-cellpack-packing',
+    display: { name: 'CellPack Packing' },
+    params: () => CellpackPackingPresetParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        if (!structureCell) return {};
+
+        const reprProps = {
+            ignoreHydrogens: true,
+            traceOnly: params.traceOnly
+        };
+        const components = {
+            polymer: await presetStaticComponent(plugin, structureCell, 'polymer')
+        };
+
+        if (params.representation === 'gaussian-surface') {
+            Object.assign(reprProps, {
+                quality: 'custom', resolution: 10, radiusOffset: 2, doubleSided: false
+            });
+        } else if (params.representation === 'spacefill' && params.traceOnly) {
+            Object.assign(reprProps, { sizeFactor: 2 });
+        }
+
+        const info = structureCell.obj?.data && CellPackInfoProvider.get(structureCell.obj?.data).value;
+        const color = info?.colors ? CellPackProvidedColorThemeProvider.name : CellPackGenerateColorThemeProvider.name;
+
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, {});
+        const representations = {
+            polymer: builder.buildRepresentation<any>(update, components.polymer, { type: params.representation, typeParams: { ...typeParams, ...reprProps }, color }, { tag: 'polymer' })
+        };
+
+        await update.commit({ revertOnError: true });
+        return { components, representations };
+    }
+});
+
+//
+
+export const CellpackMembranePresetParams = {
+    representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'])),
+};
+export type CellpackMembranePresetParams = PD.ValuesFor<typeof CellpackMembranePresetParams>
+
+export const CellpackMembranePreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-cellpack-membrane',
+    display: { name: 'CellPack Membrane' },
+    params: () => CellpackMembranePresetParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        if (!structureCell) return {};
+
+        const reprProps = {
+            ignoreHydrogens: true,
+        };
+        const components = {
+            membrane: await presetStaticComponent(plugin, structureCell, 'all', { label: 'Membrane' })
+        };
+
+        if (params.representation === 'gaussian-surface') {
+            Object.assign(reprProps, {
+                quality: 'custom', resolution: 10, radiusOffset: 2, doubleSided: false
+            });
+        }
+
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, {});
+        const representations = {
+            membrane: builder.buildRepresentation(update, components.membrane, { type: 'gaussian-surface', typeParams: { ...typeParams, ...reprProps }, color: 'uniform', colorParams: { value: ColorNames.lightgrey } }, { tag: 'all' })
+        };
+
+        await update.commit({ revertOnError: true });
+
+        return { components, representations };
+    }
+});

src/extensions/cellpack/property.ts

@@ -0,0 +1,37 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
+import { Structure } from '../../mol-model/structure';
+import { CustomProperty } from '../../mol-model-props/common/custom-property';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Color } from '../../mol-util/color';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
+
+export type CellPackInfoValue = {
+    packingsCount: number
+    packingIndex: number
+    colors?: Color[]
+}
+
+const CellPackInfoParams = {
+    info: PD.Value<CellPackInfoValue>({ packingsCount: 1, packingIndex: 0, colors: undefined }, { isHidden: true })
+};
+type CellPackInfoParams = PD.Values<typeof CellPackInfoParams>
+
+export const CellPackInfoProvider: CustomStructureProperty.Provider<typeof CellPackInfoParams, CellPackInfoValue> = CustomStructureProperty.createProvider({
+    label: 'CellPack Info',
+    descriptor: CustomPropertyDescriptor({ name: 'cellpack-info' }),
+    type: 'root',
+    defaultParams: CellPackInfoParams,
+    getParams: (data: Structure) => CellPackInfoParams,
+    isApplicable: (data: Structure) => true,
+    obtain: async (ctx: CustomProperty.Context, data: Structure, props: CellPackInfoParams) => {
+        return {
+            value: { ...CellPackInfoParams.info.defaultValue, ...props.info }
+        };
+    }
+});

src/extensions/cellpack/state.ts

@@ -0,0 +1,204 @@
+/**
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginStateObject as PSO, PluginStateTransform } from '../../mol-plugin-state/objects';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Task } from '../../mol-task';
+import { CellPack as _CellPack, Cell, CellPacking } from './data';
+import { createStructureFromCellPack } from './model';
+import { IngredientFiles } from './util';
+import { Asset } from '../../mol-util/assets';
+import { PluginContext } from '../../mol-plugin/context';
+import { CellPackInfoProvider } from './property';
+import { Structure, StructureSymmetry, Unit } from '../../mol-model/structure';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+
+export const DefaultCellPackBaseUrl = 'https://mesoscope.scripps.edu/data/cellPACK_data/cellPACK_database_1.1.0/';
+
+export class CellPack extends PSO.Create<_CellPack>({ name: 'CellPack', typeClass: 'Object' }) { }
+
+export { ParseCellPack };
+type ParseCellPack = typeof ParseCellPack
+const ParseCellPack = PluginStateTransform.BuiltIn({
+    name: 'parse-cellpack',
+    display: { name: 'Parse CellPack', description: 'Parse CellPack from JSON data' },
+    from: PSO.Format.Json,
+    to: CellPack
+})({
+    apply({ a }) {
+        return Task.create('Parse CellPack', async ctx => {
+            const cell = a.data as Cell;
+
+            const packings: CellPacking[] = [];
+            const { compartments, cytoplasme } = cell;
+            if (compartments) {
+                for (const name in compartments) {
+                    const { surface, interior } = compartments[name];
+                    if (surface) packings.push({ name, location: 'surface', ingredients: surface.ingredients });
+                    if (interior) packings.push({ name, location: 'interior', ingredients: interior.ingredients });
+                }
+            }
+            if (cytoplasme) packings.push({ name: 'Cytoplasme', location: 'cytoplasme', ingredients: cytoplasme.ingredients });
+
+            return new CellPack({ cell, packings });
+        });
+    }
+});
+
+export { StructureFromCellpack };
+type StructureFromCellpack = typeof ParseCellPack
+const StructureFromCellpack = PluginStateTransform.BuiltIn({
+    name: 'structure-from-cellpack',
+    display: { name: 'Structure from CellPack', description: 'Create Structure from CellPack Packing' },
+    from: CellPack,
+    to: PSO.Molecule.Structure,
+    params: a => {
+        const options = a ? a.data.packings.map((d, i) => [i, d.name] as const) : [];
+        return {
+            packing: PD.Select(0, options),
+            baseUrl: PD.Text(DefaultCellPackBaseUrl),
+            ingredientFiles: PD.FileList({ accept: '.cif,.bcif,.pdb' })
+        };
+    }
+})({
+    apply({ a, params, cache }, plugin: PluginContext) {
+        return Task.create('Structure from CellPack', async ctx => {
+            const packing = a.data.packings[params.packing];
+            const ingredientFiles: IngredientFiles = {};
+            if (params.ingredientFiles !== null) {
+                for (const file of params.ingredientFiles) {
+                    ingredientFiles[file.name] = file;
+                }
+            }
+            const { structure, assets, colors } = await createStructureFromCellPack(plugin, packing, params.baseUrl, ingredientFiles).runInContext(ctx);
+            await CellPackInfoProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, structure, {
+                info: { packingsCount: a.data.packings.length, packingIndex: params.packing, colors }
+            });
+
+            (cache as any).assets = assets;
+            return new PSO.Molecule.Structure(structure, { label: packing.name });
+        });
+    },
+    dispose({ b, cache }) {
+        const assets = (cache as any).assets as Asset.Wrapper[];
+        if(assets) {
+            for (const a of assets) a.dispose();
+        }
+
+        if (b) {
+            b.data.customPropertyDescriptors.dispose();
+            for (const m of b.data.models) {
+                m.customProperties.dispose();
+            }
+        }
+    }
+});
+
+export { StructureFromAssemblies };
+type StructureFromAssemblies = typeof StructureFromAssemblies
+const StructureFromAssemblies = PluginStateTransform.BuiltIn({
+    name: 'Structure from all assemblies',
+    display: { name: 'Structure from all assemblies' },
+    from: PSO.Molecule.Model,
+    to: PSO.Molecule.Structure,
+    params: {
+    }
+})({
+    canAutoUpdate({ newParams }) {
+        return true;
+    },
+    apply({ a, params }) {
+        return Task.create('Build Structure', async ctx => {
+            // TODO: optimze
+            // TODO: think of ways how to fast-track changes to this for animations
+            const model = a.data;
+            let initial_structure = Structure.ofModel(model);
+            const structures: Structure[] = [];
+            let structure: Structure = initial_structure;
+            // the list of asambly *?
+            const symmetry = ModelSymmetry.Provider.get(model);
+            if (symmetry && symmetry.assemblies.length !== 0){
+                for (const a of symmetry.assemblies) {
+                    const s = await StructureSymmetry.buildAssembly(initial_structure, a.id).runInContext(ctx);
+                    structures.push(s);
+                }
+                const builder = Structure.Builder({ label: name });
+                let offsetInvariantId = 0;
+                for (const s of structures) {
+                    let maxInvariantId = 0;
+                    for (const u of s.units) {
+                        const invariantId = u.invariantId + offsetInvariantId;
+                        if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId;
+                        builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId);
+                    }
+                    offsetInvariantId += maxInvariantId + 1;
+                }
+                structure = builder.getStructure();
+                for( let i = 0, il = structure.models.length; i < il; ++i) {
+                    const { trajectoryInfo } = structure.models[i];
+                    trajectoryInfo.size = il;
+                    trajectoryInfo.index = i;
+                }
+            }
+            return new PSO.Molecule.Structure(structure, { label: a.label, description: `${a.description}` });
+        });
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});
+
+// export { GetAllAssamblyinOneStructure };
+// type GetAllAssamblyinOneStructure = typeof GetAllAssamblyinOneStructure
+// const GetAllAssamblyinOneStructure = PluginStateTransform.BuiltIn({
+//     name: 'get assambly from structure',
+//     display: { name: 'get assambly from structure' },
+//     isDecorator: true,
+//     from: PSO.Molecule.Structure,
+//     to: PSO.Molecule.Structure,
+//     params(a) {
+//         return { };
+//     }
+// })({
+//     apply({ a, params }) {
+//         return Task.create('Build Structure Assemblies', async ctx => {
+//             // TODO: optimze
+//             // TODO: think of ways how to fast-track changes to this for animations
+//             const initial_structure = a.data;
+//             const structures: Structure[] = [];
+//             let structure: Structure = initial_structure;
+//             // the list of asambly *?
+//             const symmetry = ModelSymmetry.Provider.get(initial_structure.model);
+//             if (symmetry){
+//                 if (symmetry.assemblies.length !== 0) {
+//                     for (const a of symmetry.assemblies) {
+//                         const s = await StructureSymmetry.buildAssembly(initial_structure, a.id!).runInContext(ctx);
+//                         structures.push(s);
+//                     }
+//                     const builder = Structure.Builder({ label: name });
+//                     let offsetInvariantId = 0;
+//                     for (const s of structures) {
+//                         let maxInvariantId = 0;
+//                         for (const u of s.units) {
+//                             const invariantId = u.invariantId + offsetInvariantId;
+//                             if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId;
+//                             builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId);
+//                         }
+//                         offsetInvariantId += maxInvariantId + 1;
+//                     }
+//                     structure = builder.getStructure();
+//                     for( let i = 0, il = structure.models.length; i < il; ++i) {
+//                         const { trajectoryInfo } = structure.models[i];
+//                         trajectoryInfo.size = il;
+//                         trajectoryInfo.index = i;
+//                     }
+//                 }
+//             }
+//             return new PSO.Molecule.Structure(structure, { label: a.label, description: `${a.description}` });
+//         });
+//     }
+// });
+

src/extensions/cellpack/util.ts

@@ -0,0 +1,77 @@
+/**
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CIF } from '../../mol-io/reader/cif';
+import { parsePDB } from '../../mol-io/reader/pdb/parser';
+import { AssetManager, Asset } from '../../mol-util/assets';
+import { Structure } from '../../mol-model/structure';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { PluginContext } from '../../mol-plugin/context';
+
+export async function parseCif(plugin: PluginContext, data: string | Uint8Array) {
+    const comp = CIF.parse(data);
+    const parsed = await plugin.runTask(comp);
+    if (parsed.isError) throw parsed;
+    return parsed.result;
+}
+
+export async function parsePDBfile(plugin: PluginContext, data: string, id: string) {
+    const comp = parsePDB(data, id);
+    const parsed = await plugin.runTask(comp);
+    if (parsed.isError) throw parsed;
+    return parsed.result;
+}
+
+async function downloadCif(plugin: PluginContext, url: string, isBinary: boolean, assetManager: AssetManager) {
+    const type = isBinary ? 'binary' : 'string';
+    const asset = await plugin.runTask(assetManager.resolve(Asset.getUrlAsset(assetManager, url), type));
+    return { cif: await parseCif(plugin, asset.data), asset };
+}
+
+async function downloadPDB(plugin: PluginContext, url: string, id: string, assetManager: AssetManager) {
+    const asset = await assetManager.resolve(Asset.getUrlAsset(assetManager, url), 'string').run();
+    return { pdb: await parsePDBfile(plugin, asset.data, id), asset };
+}
+
+export async function getFromPdb(plugin: PluginContext, pdbId: string, assetManager: AssetManager) {
+    const { cif, asset } = await downloadCif(plugin, `https://models.rcsb.org/${pdbId.toUpperCase()}.bcif`, true, assetManager);
+    return { mmcif: cif.blocks[0], asset };
+}
+
+export async function getFromOPM(plugin: PluginContext, pdbId: string, assetManager: AssetManager){
+    const asset = await plugin.runTask(assetManager.resolve(Asset.getUrlAsset(assetManager, `https://opm-assets.storage.googleapis.com/pdb/${pdbId.toLowerCase()}.pdb`), 'string'));
+    return { pdb: await parsePDBfile(plugin, asset.data, pdbId), asset };
+}
+
+export async function getFromCellPackDB(plugin: PluginContext, id: string, baseUrl: string, assetManager: AssetManager) {
+    if (id.toLowerCase().endsWith('.cif') || id.toLowerCase().endsWith('.bcif')) {
+        const isBinary = id.toLowerCase().endsWith('.bcif');
+        const { cif, asset } = await downloadCif(plugin, `${baseUrl}/other/${id}`, isBinary, assetManager);
+        return { mmcif: cif.blocks[0], asset };
+    } else {
+        const name = id.endsWith('.pdb') ? id.substring(0, id.length - 4) : id;
+        return await downloadPDB(plugin, `${baseUrl}/other/${name}.pdb`, name, assetManager);
+    }
+}
+
+export type IngredientFiles = { [name: string]: Asset.File }
+
+export function getStructureMean(structure: Structure) {
+    let xSum = 0, ySum = 0, zSum = 0;
+    for (let i = 0, il = structure.units.length; i < il; ++i) {
+        const unit = structure.units[i];
+        const { elements } = unit;
+        const { x, y, z } = unit.conformation;
+        for (let j = 0, jl = elements.length; j < jl; ++j) {
+            const eI = elements[j];
+            xSum += x(eI);
+            ySum += y(eI);
+            zSum += z(eI);
+        }
+    }
+    const { elementCount } = structure;
+    return Vec3.create(xSum / elementCount, ySum / elementCount, zSum / elementCount);
+}

src/extensions/pdbe/index.ts

@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export { PDBeStructureQualityReport } from './structure-quality-report/behavior';
+export { PDBePreferredAssembly } from './preferred-assembly';
+export { PDBeStructRefDomain } from './struct-ref-domain';

src/extensions/pdbe/preferred-assembly.ts

@@ -7,14 +7,17 @@
 import { Column, Table } from '../../mol-data/db';
 import { toTable } from '../../mol-io/reader/cif/schema';
 import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export namespace PDBePreferredAssembly {
     export type Property = string
 
     export function getFirstFromModel(model: Model): Property {
-        const asm = model.symmetry.assemblies;
-        return asm.length ? asm[0].id : '';
+        const symmetry = ModelSymmetry.Provider.get(model);
+        return symmetry?.assemblies.length ? symmetry.assemblies[0].id : '';
     }
 
     export function get(model: Model): Property {
@@ -32,7 +35,6 @@ export namespace PDBePreferredAssembly {
     export type Schema = typeof Schema
 
     export const Descriptor = CustomPropertyDescriptor({
-        isStatic: true,
         name: 'pdbe_preferred_assembly',
         cifExport: {
             prefix: 'pdbe',
@@ -47,8 +49,8 @@ export namespace PDBePreferredAssembly {
     });
 
     function fromCifData(model: Model): string | undefined {
-        if (model.sourceData.kind !== 'mmCIF') return void 0;
-        const cat = model.sourceData.frame.categories.pdbe_preferred_assembly;
+        if (!MmcifFormat.is(model.sourceData)) return void 0;
+        const cat = model.sourceData.data.frame.categories.pdbe_preferred_assembly;
         if (!cat) return void 0;
         return toTable(Schema.pdbe_preferred_assembly, cat).assembly_id.value(0) || getFirstFromModel(model);
     }

src/extensions/pdbe/struct-ref-domain.ts

@@ -7,8 +7,10 @@
 import { Column, Table } from '../../mol-data/db';
 import { toTable } from '../../mol-io/reader/cif/schema';
 import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
-import { PropertyWrapper } from '../common/wrapper';
+import { Model } from '../../mol-model/structure';
+import { PropertyWrapper } from '../../mol-model-props/common/wrapper';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export namespace PDBeStructRefDomain {
     export type Property = PropertyWrapper<Table<Schema['pdbe_struct_ref_domain']> | undefined>
@@ -40,7 +42,6 @@ export namespace PDBeStructRefDomain {
     export type Schema = typeof Schema
 
     export const Descriptor = CustomPropertyDescriptor({
-        isStatic: true,
         name: 'pdbe_struct_ref_domain',
         cifExport: {
             prefix: 'pdbe',
@@ -58,8 +59,8 @@ export namespace PDBeStructRefDomain {
     });
 
     function fromCifData(model: Model): Property['data'] {
-        if (model.sourceData.kind !== 'mmCIF') return void 0;
-        const cat = model.sourceData.frame.categories.pdbe_struct_ref_domain;
+        if (!MmcifFormat.is(model.sourceData)) return void 0;
+        const cat = model.sourceData.data.frame.categories.pdbe_struct_ref_domain;
         if (!cat) return void 0;
         return toTable(Schema.pdbe_struct_ref_domain, cat);
     }
@@ -111,7 +112,7 @@ function fromPDBeJson(modelData: Model, data: any): PDBeStructRefDomain.Property
                     beg_pdbx_PDB_ins_code: map.start.author_insertion_code,
                     end_label_seq_id: map.end.residue_number,
                     end_pdbx_PDB_ins_code: map.end.author_insertion_code,
-                })
+                });
             }
         }
     }

src/extensions/pdbe/structure-quality-report/behavior.ts

@@ -0,0 +1,72 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { OrderedSet } from '../../../mol-data/int';
+import { StructureQualityReport, StructureQualityReportProvider } from './prop';
+import { StructureQualityReportColorThemeProvider } from './color';
+import { Loci } from '../../../mol-model/loci';
+import { StructureElement } from '../../../mol-model/structure';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
+
+export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'pdbe-structure-quality-report-prop',
+    category: 'custom-props',
+    display: {
+        name: 'Structure Quality Report',
+        description: 'Data from wwPDB Validation Report, obtained via PDBe.'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
+
+        private provider = StructureQualityReportProvider
+
+        private labelPDBeValidation = {
+            label: (loci: Loci): string | undefined => {
+                if (!this.params.showTooltip) return void 0;
+
+                switch (loci.kind) {
+                    case 'element-loci':
+                        if (loci.elements.length === 0) return void 0;
+                        const e = loci.elements[0];
+                        const u = e.unit;
+                        if (!u.model.customProperties.hasReference(StructureQualityReportProvider.descriptor)) return void 0;
+
+                        const se = StructureElement.Location.create(loci.structure, u, u.elements[OrderedSet.getAt(e.indices, 0)]);
+                        const issues = StructureQualityReport.getIssues(se);
+                        if (issues.length === 0) return 'Validation: No Issues';
+                        return `Validation: ${issues.join(', ')}`;
+
+                    default: return void 0;
+                }
+            }
+        }
+
+        register(): void {
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+            this.ctx.managers.lociLabels.addProvider(this.labelPDBeValidation);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(StructureQualityReportColorThemeProvider);
+        }
+
+        update(p: { autoAttach: boolean, showTooltip: boolean }) {
+            let updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.params.showTooltip = p.showTooltip;
+            this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+
+        unregister() {
+            this.ctx.customModelProperties.unregister(StructureQualityReportProvider.descriptor.name);
+            this.ctx.managers.lociLabels.removeProvider(this.labelPDBeValidation);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(StructureQualityReportColorThemeProvider);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(false),
+        showTooltip: PD.Boolean(true)
+    })
+});

src/extensions/pdbe/structure-quality-report/color.ts

@@ -0,0 +1,110 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { StructureQualityReport, StructureQualityReportProvider } from './prop';
+import { Location } from '../../../mol-model/location';
+import { StructureElement } from '../../../mol-model/structure';
+import { ColorTheme, LocationColor } from '../../../mol-theme/color';
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { Color } from '../../../mol-util/color';
+import { TableLegend } from '../../../mol-util/legend';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+
+const ValidationColors = [
+    Color.fromRgb(170, 170, 170), // not applicable
+    Color.fromRgb(0, 255, 0), // 0 issues
+    Color.fromRgb(255, 255, 0), // 1
+    Color.fromRgb(255, 128, 0), // 2
+    Color.fromRgb(255, 0, 0), // 3 or more
+];
+
+const ValidationColorTable: [string, Color][] = [
+    ['No Issues', ValidationColors[1]],
+    ['One Issue', ValidationColors[2]],
+    ['Two Issues', ValidationColors[3]],
+    ['Three Or More Issues', ValidationColors[4]],
+    ['Not Applicable', ValidationColors[9]]
+];
+
+export const StructureQualityReportColorThemeParams = {
+    type: PD.MappedStatic('issue-count', {
+        'issue-count': PD.Group({}),
+        'specific-issue': PD.Group({
+            kind: PD.Text()
+        })
+    })
+};
+
+type Params = typeof StructureQualityReportColorThemeParams
+
+export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: PD.Values<Params>): ColorTheme<Params> {
+    let color: LocationColor;
+
+    if (ctx.structure && !ctx.structure.isEmpty && ctx.structure.models[0].customProperties.has(StructureQualityReportProvider.descriptor)) {
+        const getIssues = StructureQualityReport.getIssues;
+
+        if (props.type.name === 'issue-count') {
+            color = (location: Location) => {
+                if (StructureElement.Location.is(location)) {
+                    return ValidationColors[Math.min(3, getIssues(location).length) + 1];
+                }
+                return ValidationColors[0];
+            };
+        } else {
+            const issue = props.type.params.kind;
+            color = (location: Location) => {
+                if (StructureElement.Location.is(location) && getIssues(location).indexOf(issue) >= 0) {
+                    return ValidationColors[4];
+                }
+                return ValidationColors[0];
+            };
+        }
+    } else {
+        color = () => ValidationColors[0];
+    }
+
+    return {
+        factory: StructureQualityReportColorTheme,
+        granularity: 'group',
+        color: color,
+        props: props,
+        description: 'Assigns residue colors according to the number of quality issues or a specific quality issue. Data from wwPDB Validation Report, obtained via PDBe.',
+        legend: TableLegend(ValidationColorTable)
+    };
+}
+
+export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Params, 'pdbe-structure-quality-report'> =  {
+    name: 'pdbe-structure-quality-report',
+    label: 'Structure Quality Report',
+    category: ColorTheme.Category.Validation,
+    factory: StructureQualityReportColorTheme,
+    getParams: ctx => {
+        const issueTypes = StructureQualityReport.getIssueTypes(ctx.structure);
+        if (issueTypes.length === 0) {
+            return {
+                type: PD.MappedStatic('issue-count', {
+                    'issue-count': PD.Group({})
+                })
+            };
+        }
+
+        return {
+            type: PD.MappedStatic('issue-count', {
+                'issue-count': PD.Group({}),
+                'specific-issue': PD.Group({
+                    kind: PD.Select(issueTypes[0], PD.arrayToOptions(issueTypes))
+                }, { isFlat: true })
+            })
+        };
+    },
+    defaultValues: PD.getDefaultValues(StructureQualityReportColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => StructureQualityReport.isApplicable(ctx.structure?.models[0]),
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? StructureQualityReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
+        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(StructureQualityReportProvider.descriptor, false)
+    }
+};

src/extensions/pdbe/structure-quality-report/prop.ts

@@ -1,29 +1,44 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Column, Table } from '../../mol-data/db';
-import { toTable } from '../../mol-io/reader/cif/schema';
-import { mmCIF_residueId_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
-import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from '../../mol-model/structure';
-import { residueIdFields } from '../../mol-model/structure/export/categories/atom_site';
-import { StructureElement, CifExportContext } from '../../mol-model/structure/structure';
-import { CustomPropSymbol } from '../../mol-script/language/symbol';
-import Type from '../../mol-script/language/type';
-import { QuerySymbolRuntime } from '../../mol-script/runtime/query/compiler';
-import { PropertyWrapper } from '../common/wrapper';
-import { Task } from '../../mol-task';
+import { Column, Table } from '../../../mol-data/db';
+import { toTable } from '../../../mol-io/reader/cif/schema';
+import { mmCIF_residueId_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { CifWriter } from '../../../mol-io/writer/cif';
+import { Model, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-model/structure';
+import { residueIdFields } from '../../../mol-model/structure/export/categories/atom_site';
+import { StructureElement, CifExportContext, Structure } from '../../../mol-model/structure/structure';
+import { CustomPropSymbol } from '../../../mol-script/language/symbol';
+import Type from '../../../mol-script/language/type';
+import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { arraySetAdd } from '../../../mol-util/array';
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
+import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { Asset } from '../../../mol-util/assets';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
-export namespace StructureQualityReport {
-    export type IssueMap = IndexedCustomProperty.Residue<string[]>
-    export type Property = PropertyWrapper<IssueMap | undefined>
+export { StructureQualityReport };
 
-    export function get(model: Model): Property | undefined {
-        // must be defined before the descriptor so it's not undefined.
-        return model._dynamicPropertyData.__PDBeStructureQualityReport__;
+type StructureQualityReport = PropertyWrapper<{
+    issues: IndexedCustomProperty.Residue<string[]>,
+    issueTypes: string[]
+}| undefined>
+
+namespace StructureQualityReport {
+    export const DefaultServerUrl = 'https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/';
+    export function getEntryUrl(pdbId: string, serverUrl: string) {
+        return `${serverUrl}/${pdbId.toLowerCase()}`;
+    }
+
+    export function isApplicable(model?: Model): boolean {
+        return !!model && Model.isFromPdbArchive(model);
     }
 
     export const Schema = {
@@ -43,12 +58,71 @@ export namespace StructureQualityReport {
     };
     export type Schema = typeof Schema
 
-    export const Descriptor = CustomPropertyDescriptor({
-        isStatic: false,
+    export function fromJson(model: Model, data: any) {
+        const info = PropertyWrapper.createInfo();
+        const issueMap = createIssueMapFromJson(model, data);
+        return { info, data: issueMap };
+    }
+
+    export async function fromServer(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): Promise<CustomProperty.Data<StructureQualityReport>> {
+        const url = Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.serverUrl));
+        const json = await ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime);
+        const data = json.data[model.entryId.toLowerCase()];
+        if (!data) throw new Error('missing data');
+        return { value: fromJson(model, data), assets: [json] };
+    }
+
+    export function fromCif(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): StructureQualityReport | undefined {
+        let info = PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model);
+        if (!info) return;
+        const data = getCifData(model);
+        const issueMap = createIssueMapFromCif(model, data.residues, data.groups);
+        return { info, data: issueMap };
+    }
+
+    export async function fromCifOrServer(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): Promise<CustomProperty.Data<StructureQualityReport>> {
+        const cif = fromCif(ctx, model, props);
+        return cif ? { value: cif } : fromServer(ctx, model, props);
+    }
+
+    const _emptyArray: string[] = [];
+    export function getIssues(e: StructureElement.Location) {
+        if (!Unit.isAtomic(e.unit)) return _emptyArray;
+        const prop = StructureQualityReportProvider.get(e.unit.model).value;
+        if (!prop || !prop.data) return _emptyArray;
+        const rI = e.unit.residueIndex[e.element];
+        return prop.data.issues.has(rI) ? prop.data.issues.get(rI)! : _emptyArray;
+    }
+
+    export function getIssueTypes(structure?: Structure) {
+        if (!structure) return _emptyArray;
+        const prop = StructureQualityReportProvider.get(structure.models[0]).value;
+        if (!prop || !prop.data) return _emptyArray;
+        return prop.data.issueTypes;
+    }
+
+    function getCifData(model: Model) {
+        if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF.');
+        return {
+            residues: toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.data.frame.categories.pdbe_structure_quality_report_issues),
+            groups: toTable(Schema.pdbe_structure_quality_report_issue_types, model.sourceData.data.frame.categories.pdbe_structure_quality_report_issue_types),
+        };
+    }
+}
+
+export const StructureQualityReportParams = {
+    serverUrl: PD.Text(StructureQualityReport.DefaultServerUrl, { description: 'JSON API Server URL' })
+};
+export type StructureQualityReportParams = typeof StructureQualityReportParams
+export type StructureQualityReportProps = PD.Values<StructureQualityReportParams>
+
+export const StructureQualityReportProvider: CustomModelProperty.Provider<StructureQualityReportParams, StructureQualityReport> = CustomModelProperty.createProvider({
+    label: 'Structure Quality Report',
+    descriptor: CustomPropertyDescriptor<ReportExportContext, any>({
         name: 'pdbe_structure_quality_report',
         cifExport: {
             prefix: 'pdbe',
-            context(ctx) {
+            context(ctx: CifExportContext) {
                 return createExportContext(ctx);
             },
             categories: [
@@ -59,7 +133,7 @@ export namespace StructureQualityReport {
                         return {
                             fields: _structure_quality_report_issues_fields,
                             source: ctx.models.map(data => ({ data, rowCount: data.elements.length }))
-                        }
+                        };
                     }
                 }, {
                     name: 'pdbe_structure_quality_report_issue_types',
@@ -73,86 +147,16 @@ export namespace StructureQualityReport {
                 ctx => StructureQualityReport.getIssues(ctx.element).length),
             // TODO: add (hasIssue :: IssueType(extends string) -> boolean) symbol
         }
-    });
-
-    function getCifData(model: Model) {
-        if (model.sourceData.kind !== 'mmCIF') throw new Error('Data format must be mmCIF.');
-        return {
-            residues: toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report_issues),
-            groups: toTable(Schema.pdbe_structure_quality_report_issue_types, model.sourceData.frame.categories.pdbe_structure_quality_report_issue_types),
-        }
+    }),
+    type: 'static',
+    defaultParams: StructureQualityReportParams,
+    getParams: (data: Model) => StructureQualityReportParams,
+    isApplicable: (data: Model) => StructureQualityReport.isApplicable(data),
+    obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<StructureQualityReportProps>) => {
+        const p = { ...PD.getDefaultValues(StructureQualityReportParams), ...props };
+        return await StructureQualityReport.fromCifOrServer(ctx, data, p);
     }
-
-    export function createAttachTask(mapUrl: (model: Model) => string, fetch: import('../../mol-util/data-source').AjaxTask) {
-        return (model: Model) => Task.create('PDBe Structure Quality Report', async ctx => {
-            if (get(model)) return true;
-
-            let issueMap: IssueMap | undefined;
-            let info;
-            // TODO: return from CIF support once the data is recomputed
-            //  = PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model);
-            // if (info) {
-            //     const data = getCifData(model);
-            //     issueMap = createIssueMapFromCif(model, data.residues, data.groups);
-            // } else
-            {
-                const url = mapUrl(model);
-                const dataStr = await fetch({ url }).runInContext(ctx) as string;
-                const data = JSON.parse(dataStr)[model.entryId.toLowerCase()];
-                if (!data) return false;
-                info = PropertyWrapper.createInfo();
-                issueMap = createIssueMapFromJson(model, data);
-            }
-
-            model.customProperties.add(Descriptor);
-            set(model, { info, data: issueMap });
-            return false;
-        });
-    }
-
-    export async function attachFromCifOrApi(model: Model, params: {
-        // optional JSON source
-        PDBe_apiSourceJson?: (model: Model) => Promise<any>
-    }) {
-        if (get(model)) return true;
-
-        let issueMap: IssueMap | undefined;
-        let info = PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model);
-        if (info) {
-            const data = getCifData(model);
-            issueMap = createIssueMapFromCif(model, data.residues, data.groups);
-        } else if (params.PDBe_apiSourceJson) {
-            const data = await params.PDBe_apiSourceJson(model);
-            if (!data) return false;
-            info = PropertyWrapper.createInfo();
-            issueMap = createIssueMapFromJson(model, data);
-        } else {
-            return false;
-        }
-
-        model.customProperties.add(Descriptor);
-        set(model, { info, data: issueMap });
-        return true;
-    }
-
-    function set(model: Model, prop: Property) {
-        (model._dynamicPropertyData.__PDBeStructureQualityReport__ as Property) = prop;
-    }
-
-    export function getIssueMap(model: Model): IssueMap | undefined {
-        const prop = get(model);
-        return prop && prop.data;
-    }
-
-    const _emptyArray: string[] = [];
-    export function getIssues(e: StructureElement.Location) {
-        if (!Unit.isAtomic(e.unit)) return _emptyArray;
-        const prop = StructureQualityReport.get(e.unit.model);
-        if (!prop || !prop.data) return _emptyArray;
-        const rI = e.unit.residueIndex[e.element];
-        return prop.data.has(rI) ? prop.data.get(rI)! : _emptyArray;
-    }
-}
+});
 
 const _structure_quality_report_issues_fields = CifWriter.fields<number, ReportExportContext['models'][0]>()
     .index('id')
@@ -176,11 +180,11 @@ function createExportContext(ctx: CifExportContext): ReportExportContext {
     let info: PropertyWrapper.Info = PropertyWrapper.createInfo();
 
     for (const s of ctx.structures) {
-        const prop = StructureQualityReport.get(s.model);
+        const prop = StructureQualityReportProvider.get(s.model).value;
         if (prop) info = prop.info;
         if (!prop || !prop.data) continue;
 
-        const { elements, property } = prop.data.getElements(s);
+        const { elements, property } = prop.data.issues.getElements(s);
         if (elements.length === 0) continue;
 
         const elementGroupId: number[] = [];
@@ -204,13 +208,15 @@ function createExportContext(ctx: CifExportContext): ReportExportContext {
         info,
         models,
         issueTypes: Table.ofArrays(StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types, { group_id, issue_type })
-    }
+    };
 }
 
-function createIssueMapFromJson(modelData: Model, data: any): StructureQualityReport.IssueMap | undefined {
+function createIssueMapFromJson(modelData: Model, data: any): StructureQualityReport['data'] | undefined {
     const ret = new Map<ResidueIndex, string[]>();
     if (!data.molecules) return;
 
+    const issueTypes: string[] = [];
+
     for (const entity of data.molecules) {
         const entity_id = entity.entity_id.toString();
         for (const chain of entity.chains) {
@@ -223,17 +229,24 @@ function createIssueMapFromJson(modelData: Model, data: any): StructureQualityRe
                     const auth_seq_id = residue.author_residue_number, ins_code = residue.author_insertion_code || '';
                     const idx = modelData.atomicHierarchy.index.findResidue(entity_id, asym_id, auth_seq_id, ins_code);
                     ret.set(idx, residue.outlier_types);
+
+                    for (const t of residue.outlier_types) {
+                        arraySetAdd(issueTypes, t);
+                    }
                 }
             }
         }
     }
 
-    return IndexedCustomProperty.fromResidueMap(ret);
+    return {
+        issues: IndexedCustomProperty.fromResidueMap(ret),
+        issueTypes
+    };
 }
 
 function createIssueMapFromCif(modelData: Model,
     residueData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issues>,
-    groupData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types>): StructureQualityReport.IssueMap | undefined {
+    groupData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types>): StructureQualityReport['data'] | undefined {
 
     const ret = new Map<ResidueIndex, string[]>();
     const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issue_type_group_id, pdbx_PDB_model_num, _rowCount } = residueData;
@@ -246,7 +259,17 @@ function createIssueMapFromCif(modelData: Model,
         ret.set(idx, groups.get(issue_type_group_id.value(i))!);
     }
 
-    return IndexedCustomProperty.fromResidueMap(ret);
+    const issueTypes: string[] = [];
+    groups.forEach(issues => {
+        for (const t of issues) {
+            arraySetAdd(issueTypes, t);
+        }
+    });
+
+    return {
+        issues: IndexedCustomProperty.fromResidueMap(ret),
+        issueTypes
+    };
 }
 
 function parseIssueTypes(groupData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types>): Map<number, string[]> {

src/extensions/rcsb/README.md

@@ -0,0 +1,4 @@
+### Code generation
+**GraphQL schemas**
+
+    ./node_modules/.bin/graphql-codegen -c ./src/extensions/rcsb/graphql/codegen.yml

src/extensions/rcsb/assembly-symmetry/behavior.ts

@@ -0,0 +1,196 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { AssemblySymmetryProvider, AssemblySymmetry, AssemblySymmetryDataProvider } from './prop';
+import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
+import { AssemblySymmetryParams, AssemblySymmetryRepresentation } from './representation';
+import { AssemblySymmetryClusterColorThemeProvider } from './color';
+import { PluginStateTransform, PluginStateObject } from '../../../mol-plugin-state/objects';
+import { Task } from '../../../mol-task';
+import { PluginContext } from '../../../mol-plugin/context';
+import { StateTransformer, StateAction, StateObject, StateTransform, StateObjectRef } from '../../../mol-state';
+import { GenericRepresentationRef } from '../../../mol-plugin-state/manager/structure/hierarchy-state';
+import { AssemblySymmetryControls } from './ui';
+import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
+
+const Tag = AssemblySymmetry.Tag;
+
+export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean }>({
+    name: 'rcsb-assembly-symmetry-prop',
+    category: 'custom-props',
+    display: {
+        name: 'Assembly Symmetry',
+        description: 'Assembly Symmetry data calculated with BioJava, obtained via RCSB PDB.'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
+        private provider = AssemblySymmetryProvider
+
+        register(): void {
+            this.ctx.state.data.actions.add(InitAssemblySymmetry3D);
+            this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(AssemblySymmetryClusterColorThemeProvider);
+
+            this.ctx.genericRepresentationControls.set(Tag.Representation, selection => {
+                const refs: GenericRepresentationRef[] = [];
+                selection.structures.forEach(structure => {
+                    const symmRepr = structure.genericRepresentations?.filter(r => r.cell.transform.transformer.id === AssemblySymmetry3D.id)[0];
+                    if (symmRepr) refs.push(symmRepr);
+                });
+                return [refs, 'Symmetries'];
+            });
+            this.ctx.customStructureControls.set(Tag.Representation, AssemblySymmetryControls as any);
+            this.ctx.builders.structure.representation.registerPreset(AssemblySymmetryPreset);
+        }
+
+        update(p: { autoAttach: boolean }) {
+            let updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+
+        unregister() {
+            this.ctx.state.data.actions.remove(InitAssemblySymmetry3D);
+            this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(AssemblySymmetryClusterColorThemeProvider);
+
+            this.ctx.genericRepresentationControls.delete(Tag.Representation);
+            this.ctx.customStructureControls.delete(Tag.Representation);
+            this.ctx.builders.structure.representation.unregisterPreset(AssemblySymmetryPreset);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(false),
+        serverUrl: PD.Text(AssemblySymmetry.DefaultServerUrl)
+    })
+});
+
+//
+
+export const InitAssemblySymmetry3D = StateAction.build({
+    display: {
+        name: 'Assembly Symmetry',
+        description: 'Initialize Assembly Symmetry axes and cage. Data calculated with BioJava, obtained via RCSB PDB.'
+    },
+    from: PluginStateObject.Molecule.Structure,
+    isApplicable: (a) => AssemblySymmetry.isApplicable(a.data)
+})(({ a, ref, state }, plugin: PluginContext) => Task.create('Init Assembly Symmetry', async ctx => {
+    try {
+        const propCtx = { runtime: ctx, assetManager: plugin.managers.asset };
+        await AssemblySymmetryDataProvider.attach(propCtx, a.data);
+        const assemblySymmetryData = AssemblySymmetryDataProvider.get(a.data).value;
+        const symmetryIndex = assemblySymmetryData ? AssemblySymmetry.firstNonC1(assemblySymmetryData) : -1;
+        await AssemblySymmetryProvider.attach(propCtx, a.data, { symmetryIndex });
+    } catch(e) {
+        plugin.log.error(`Assembly Symmetry: ${e}`);
+        return;
+    }
+    const tree = state.build().to(ref)
+        .applyOrUpdateTagged(AssemblySymmetry.Tag.Representation, AssemblySymmetry3D);
+    await state.updateTree(tree).runInContext(ctx);
+}));
+
+export { AssemblySymmetry3D };
+
+type AssemblySymmetry3D = typeof AssemblySymmetry3D
+const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
+    name: Tag.Representation,
+    display: {
+        name: 'Assembly Symmetry',
+        description: 'Assembly Symmetry axes and cage. Data calculated with BioJava, obtained via RCSB PDB.'
+    },
+    from: PluginStateObject.Molecule.Structure,
+    to: PluginStateObject.Shape.Representation3D,
+    params: (a) => {
+        return {
+            ...AssemblySymmetryParams,
+        };
+    }
+})({
+    canAutoUpdate({ oldParams, newParams }) {
+        return true;
+    },
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Assembly Symmetry', async ctx => {
+            await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
+            const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value;
+            if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
+                return StateObject.Null;
+            }
+            const repr = AssemblySymmetryRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => AssemblySymmetryParams);
+            await repr.createOrUpdate(params, a.data).runInContext(ctx);
+            const { type, kind, symbol } = assemblySymmetry;
+            return new PluginStateObject.Shape.Representation3D({ repr, source: a }, { label: kind, description: `${type} (${symbol})` });
+        });
+    },
+    update({ a, b, newParams }, plugin: PluginContext) {
+        return Task.create('Assembly Symmetry', async ctx => {
+            await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
+            const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value;
+            if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
+                // this should NOT be StateTransformer.UpdateResult.Null
+                // because that keeps the old object
+                return StateTransformer.UpdateResult.Recreate;
+            }
+            const props = { ...b.data.repr.props, ...newParams };
+            await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
+            const { type, kind, symbol } = assemblySymmetry;
+            b.label = kind;
+            b.description = `${type} (${symbol})`;
+            return StateTransformer.UpdateResult.Updated;
+        });
+    },
+    isApplicable(a) {
+        return AssemblySymmetry.isApplicable(a.data);
+    }
+});
+
+//
+
+export const AssemblySymmetryPresetParams = {
+    ...StructureRepresentationPresetProvider.CommonParams,
+};
+
+export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-rcsb-assembly-symmetry',
+    display: {
+        name: 'Assembly Symmetry', group: 'Annotation',
+        description: 'Shows Assembly Symmetry axes and cage; colors structure according to assembly symmetry cluster membership. Data calculated with BioJava, obtained via RCSB PDB.'
+    },
+    isApplicable(a) {
+        return AssemblySymmetry.isApplicable(a.data);
+    },
+    params: () => AssemblySymmetryPresetParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        if (!AssemblySymmetryDataProvider.get(structure).value) {
+            await plugin.runTask(Task.create('Assembly Symmetry', async runtime => {
+                const propCtx = { runtime, assetManager: plugin.managers.asset };
+                await AssemblySymmetryDataProvider.attach(propCtx, structure);
+                const assemblySymmetryData = AssemblySymmetryDataProvider.get(structure).value;
+                const symmetryIndex = assemblySymmetryData ? AssemblySymmetry.firstNonC1(assemblySymmetryData) : -1;
+                await AssemblySymmetryProvider.attach(propCtx, structure, { symmetryIndex });
+            }));
+        }
+
+        const assemblySymmetry = await tryCreateAssemblySymmetry(plugin, structureCell);
+        const globalThemeName = assemblySymmetry.isOk ? Tag.Cluster as any : undefined;
+        const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName }, plugin);
+
+        return { components: preset.components, representations: { ...preset.representations, assemblySymmetry } };
+    }
+});
+
+export function tryCreateAssemblySymmetry(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<AssemblySymmetry3D>, initialState?: Partial<StateTransform.State>) {
+    const state = plugin.state.data;
+    const assemblySymmetry = state.build().to(structure)
+        .applyOrUpdateTagged(AssemblySymmetry.Tag.Representation, AssemblySymmetry3D, params, { state: initialState });
+    return assemblySymmetry.commit({ revertOnError: true });
+}

src/extensions/rcsb/assembly-symmetry/color.ts

@@ -0,0 +1,104 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { ColorTheme, LocationColor } from '../../../mol-theme/color';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { AssemblySymmetryProvider, AssemblySymmetry } from './prop';
+import { Color } from '../../../mol-util/color';
+import { Unit, StructureElement, StructureProperties } from '../../../mol-model/structure';
+import { Location } from '../../../mol-model/location';
+import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
+import { getPalette, getPaletteParams } from '../../../mol-util/color/palette';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+
+const DefaultColor = Color(0xCCCCCC);
+
+function getAsymId(unit: Unit): StructureElement.Property<string> {
+    switch (unit.kind) {
+        case Unit.Kind.Atomic:
+            return StructureProperties.chain.label_asym_id;
+        case Unit.Kind.Spheres:
+        case Unit.Kind.Gaussians:
+            return StructureProperties.coarse.asym_id;
+    }
+}
+
+function clusterMemberKey(asymId: string, operList: string[]) {
+    return `${asymId}-${operList.join('|')}`;
+}
+
+export const AssemblySymmetryClusterColorThemeParams = {
+    ...getPaletteParams({ colorList: 'red-yellow-blue' }),
+};
+export type AssemblySymmetryClusterColorThemeParams = typeof AssemblySymmetryClusterColorThemeParams
+export function getAssemblySymmetryClusterColorThemeParams(ctx: ThemeDataContext) {
+    const params = PD.clone(AssemblySymmetryClusterColorThemeParams);
+    return params;
+}
+
+export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props: PD.Values<AssemblySymmetryClusterColorThemeParams>): ColorTheme<AssemblySymmetryClusterColorThemeParams> {
+    let color: LocationColor = () => DefaultColor;
+    let legend: ScaleLegend | TableLegend | undefined;
+
+    const assemblySymmetry = ctx.structure && AssemblySymmetryProvider.get(ctx.structure);
+    const contextHash = assemblySymmetry?.version;
+
+    const clusters = assemblySymmetry?.value?.clusters;
+
+    if (clusters?.length && ctx.structure) {
+        const clusterByMember = new Map<string, number>();
+        for (let i = 0, il = clusters.length; i < il; ++i) {
+            const { members } = clusters[i]!;
+            for (let j = 0, jl = members.length; j < jl; ++j) {
+                const asymId = members[j]!.asym_id;
+                const operList = [...members[j]!.pdbx_struct_oper_list_ids || []] as string[];
+                clusterByMember.set(clusterMemberKey(asymId, operList), i);
+                if (operList.length === 0) {
+                    operList.push('1'); // TODO hack assuming '1' is the id of the identity operator
+                    clusterByMember.set(clusterMemberKey(asymId, operList), i);
+                }
+            }
+        }
+        const palette = getPalette(clusters.length, props);
+        legend = palette.legend;
+
+        const _emptyList: any[] = [];
+        color = (location: Location): Color => {
+            if (StructureElement.Location.is(location)) {
+                const { assembly } = location.unit.conformation.operator;
+                const asymId = getAsymId(location.unit)(location);
+                const cluster = clusterByMember.get(clusterMemberKey(asymId, assembly?.operList || _emptyList));
+                return cluster !== undefined ? palette.color(cluster) : DefaultColor;
+            }
+            return DefaultColor;
+        };
+    }
+
+    return {
+        factory: AssemblySymmetryClusterColorTheme,
+        granularity: 'instance',
+        color,
+        props,
+        contextHash,
+        description: 'Assigns chain colors according to assembly symmetry cluster membership calculated with BioJava and obtained via RCSB PDB.',
+        legend
+    };
+}
+
+export const AssemblySymmetryClusterColorThemeProvider: ColorTheme.Provider<AssemblySymmetryClusterColorThemeParams, AssemblySymmetry.Tag.Cluster> = {
+    name: AssemblySymmetry.Tag.Cluster,
+    label: 'Assembly Symmetry Cluster',
+    category: ColorTheme.Category.Symmetry,
+    factory: AssemblySymmetryClusterColorTheme,
+    getParams: getAssemblySymmetryClusterColorThemeParams,
+    defaultValues: PD.getDefaultValues(AssemblySymmetryClusterColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => AssemblySymmetry.isApplicable(ctx.structure),
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? AssemblySymmetryProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
+        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(AssemblySymmetryProvider.descriptor, false)
+    }
+};

src/extensions/rcsb/assembly-symmetry/prop.ts

@@ -0,0 +1,202 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from '../graphql/types';
+import query from '../graphql/symmetry.gql';
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
+import { Database as _Database, Column } from '../../../mol-data/db';
+import { GraphQLClient } from '../../../mol-util/graphql-client';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { NonNullableArray } from '../../../mol-util/type-helpers';
+import { CustomStructureProperty } from '../../../mol-model-props/common/custom-structure-property';
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
+import { ReadonlyVec3 } from '../../../mol-math/linear-algebra/3d/vec3';
+import { SetUtils } from '../../../mol-util/set';
+import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
+import { compile } from '../../../mol-script/runtime/query/compiler';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
+
+const BiologicalAssemblyNames = new Set([
+    'author_and_software_defined_assembly',
+    'author_defined_assembly',
+    'complete icosahedral assembly',
+    'complete point assembly',
+    'representative helical assembly',
+    'software_defined_assembly'
+]);
+
+export function isBiologicalAssembly(structure: Structure): boolean {
+    if (!MmcifFormat.is(structure.models[0].sourceData)) return false;
+    const mmcif = structure.models[0].sourceData.data.db;
+    if (!mmcif.pdbx_struct_assembly.details.isDefined) return false;
+    const id = structure.units[0].conformation.operator.assembly?.id || '';
+    if (id === '') return true;
+    const indices = Column.indicesOf(mmcif.pdbx_struct_assembly.id, e => e === id);
+    if (indices.length !== 1) return false;
+    const details = mmcif.pdbx_struct_assembly.details.value(indices[0]);
+    return BiologicalAssemblyNames.has(details);
+}
+
+export namespace AssemblySymmetry {
+    export enum Tag {
+        Cluster = 'rcsb-assembly-symmetry-cluster',
+        Representation = 'rcsb-assembly-symmetry-3d'
+    }
+
+    export const DefaultServerUrl = 'https://data.rcsb.org/graphql';
+
+    export function isApplicable(structure?: Structure): boolean {
+        return (
+            !!structure && structure.models.length === 1 &&
+            Model.isFromPdbArchive(structure.models[0]) &&
+            isBiologicalAssembly(structure)
+        );
+    }
+
+    export async function fetch(ctx: CustomProperty.Context, structure: Structure, props: AssemblySymmetryDataProps): Promise<CustomProperty.Data<AssemblySymmetryDataValue>> {
+        if (!isApplicable(structure)) return { value: [] };
+
+        const client = new GraphQLClient(props.serverUrl, ctx.assetManager);
+        const variables: AssemblySymmetryQueryVariables = {
+            assembly_id: structure.units[0].conformation.operator.assembly?.id || '',
+            entry_id: structure.units[0].model.entryId
+        };
+        const result = await client.request(ctx.runtime, query, variables);
+        let value: AssemblySymmetryDataValue = [];
+
+        if (!result.data.assembly?.rcsb_struct_symmetry) {
+            console.error('expected `rcsb_struct_symmetry` field');
+        } else {
+            value = result.data.assembly.rcsb_struct_symmetry as AssemblySymmetryDataValue;
+        }
+        return { value, assets: [result] };
+    }
+
+    /** Returns the index of the first non C1 symmetry or -1 */
+    export function firstNonC1(assemblySymmetryData: AssemblySymmetryDataValue) {
+        for (let i = 0, il = assemblySymmetryData.length; i < il; ++i) {
+            if (assemblySymmetryData[i].symbol !== 'C1') return i;
+        }
+        return -1;
+    }
+
+    export type RotationAxes = ReadonlyArray<{ order: number, start: ReadonlyVec3, end: ReadonlyVec3 }>
+    export function isRotationAxes(x: AssemblySymmetryValue['rotation_axes']): x is RotationAxes {
+        return !!x && x.length > 0;
+    }
+
+    export function getAsymIds(assemblySymmetry: AssemblySymmetryValue) {
+        const asymIds = new Set<string>();
+        for (const c of assemblySymmetry.clusters) {
+            if (!c?.members) continue;
+            for (const m of c.members) {
+                if (m?.asym_id) asymIds.add(m.asym_id);
+            }
+        }
+        return SetUtils.toArray(asymIds);
+    }
+
+    function getAsymIdsStructure(structure: Structure, asymIds: string[]) {
+        const query = MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'chain-test': MS.core.set.has([MS.set(...asymIds), MS.ammp('label_asym_id')])
+            })
+        ]);
+        const compiled = compile<StructureSelection>(query);
+        const result = compiled(new QueryContext(structure));
+        return StructureSelection.unionStructure(result);
+    }
+
+    /** Returns structure limited to all cluster member chains */
+    export function getStructure(structure: Structure, assemblySymmetry: AssemblySymmetryValue) {
+        const asymIds = AssemblySymmetry.getAsymIds(assemblySymmetry);
+        return asymIds.length > 0 ? getAsymIdsStructure(structure, asymIds) : structure;
+    }
+}
+
+export function getSymmetrySelectParam(structure?: Structure) {
+    const param = PD.Select<number>(0, [[0, 'First Symmetry']]);
+    if (structure) {
+        const assemblySymmetryData = AssemblySymmetryDataProvider.get(structure).value;
+        if (assemblySymmetryData) {
+            const options: [number, string][] = [];
+            for (let i = 0, il = assemblySymmetryData.length; i < il; ++i) {
+                const { symbol, kind } = assemblySymmetryData[i];
+                if (symbol !== 'C1') {
+                    options.push([ i, `${i + 1}: ${symbol} ${kind}` ]);
+                }
+            }
+            if (options.length) {
+                param.options = options;
+                param.defaultValue = options[0][0];
+            }
+        }
+    }
+    return param;
+}
+
+//
+
+export const AssemblySymmetryDataParams = {
+    serverUrl: PD.Text(AssemblySymmetry.DefaultServerUrl, { description: 'GraphQL endpoint URL' })
+};
+export type AssemblySymmetryDataParams = typeof AssemblySymmetryDataParams
+export type AssemblySymmetryDataProps = PD.Values<AssemblySymmetryDataParams>
+
+export type AssemblySymmetryDataValue = NonNullableArray<NonNullable<NonNullable<AssemblySymmetryQuery['assembly']>['rcsb_struct_symmetry']>>
+
+export const AssemblySymmetryDataProvider: CustomStructureProperty.Provider<AssemblySymmetryDataParams, AssemblySymmetryDataValue> = CustomStructureProperty.createProvider({
+    label: 'Assembly Symmetry Data',
+    descriptor: CustomPropertyDescriptor({
+        name: 'rcsb_struct_symmetry_data',
+        // TODO `cifExport` and `symbol`
+    }),
+    type: 'root',
+    defaultParams: AssemblySymmetryDataParams,
+    getParams: (data: Structure) => AssemblySymmetryDataParams,
+    isApplicable: (data: Structure) => AssemblySymmetry.isApplicable(data),
+    obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<AssemblySymmetryDataProps>) => {
+        const p = { ...PD.getDefaultValues(AssemblySymmetryDataParams), ...props };
+        return await AssemblySymmetry.fetch(ctx, data, p);
+    }
+});
+
+//
+
+function getAssemblySymmetryParams(data?: Structure) {
+    return {
+        ... AssemblySymmetryDataParams,
+        symmetryIndex: getSymmetrySelectParam(data)
+    };
+}
+
+export const AssemblySymmetryParams = getAssemblySymmetryParams();
+export type AssemblySymmetryParams = typeof AssemblySymmetryParams
+export type AssemblySymmetryProps = PD.Values<AssemblySymmetryParams>
+
+export type AssemblySymmetryValue = AssemblySymmetryDataValue[0]
+
+export const AssemblySymmetryProvider: CustomStructureProperty.Provider<AssemblySymmetryParams, AssemblySymmetryValue> = CustomStructureProperty.createProvider({
+    label: 'Assembly Symmetry',
+    descriptor: CustomPropertyDescriptor({
+        name: 'rcsb_struct_symmetry',
+        // TODO `cifExport` and `symbol`
+    }),
+    type: 'root',
+    defaultParams: AssemblySymmetryParams,
+    getParams: getAssemblySymmetryParams,
+    isApplicable: (data: Structure) => AssemblySymmetry.isApplicable(data),
+    obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<AssemblySymmetryProps>) => {
+        const p = { ...PD.getDefaultValues(getAssemblySymmetryParams(data)), ...props };
+        await AssemblySymmetryDataProvider.attach(ctx, data, p);
+        const assemblySymmetryData = AssemblySymmetryDataProvider.get(data).value;
+        const assemblySymmetry = assemblySymmetryData?.[p.symmetryIndex];
+        if (!assemblySymmetry) new Error(`No assembly symmetry found for index ${p.symmetryIndex}`);
+        return { value: assemblySymmetry };
+    }
+});

src/extensions/rcsb/assembly-symmetry/representation.ts

@@ -0,0 +1,384 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { AssemblySymmetryValue, AssemblySymmetryProvider, AssemblySymmetry } from './prop';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { Vec3, Mat4, Mat3 } from '../../../mol-math/linear-algebra';
+import { addCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { RuntimeContext } from '../../../mol-task';
+import { Shape } from '../../../mol-model/shape';
+import { ColorNames } from '../../../mol-util/color/names';
+import { ShapeRepresentation } from '../../../mol-repr/shape/representation';
+import { MarkerActions } from '../../../mol-util/marker-action';
+import { Prism, PrismCage } from '../../../mol-geo/primitive/prism';
+import { Wedge, WedgeCage } from '../../../mol-geo/primitive/wedge';
+import { Primitive, transformPrimitive } from '../../../mol-geo/primitive/primitive';
+import { memoize1 } from '../../../mol-util/memoize';
+import { polygon } from '../../../mol-geo/primitive/polygon';
+import { ColorMap, Color } from '../../../mol-util/color';
+import { TableLegend } from '../../../mol-util/legend';
+import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
+import { Cage, transformCage, cloneCage } from '../../../mol-geo/primitive/cage';
+import { OctahedronCage } from '../../../mol-geo/primitive/octahedron';
+import { TetrahedronCage } from '../../../mol-geo/primitive/tetrahedron';
+import { IcosahedronCage } from '../../../mol-geo/primitive/icosahedron';
+import { degToRad, radToDeg } from '../../../mol-math/misc';
+import { Mutable } from '../../../mol-util/type-helpers';
+import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
+import { Structure } from '../../../mol-model/structure';
+import { isInteger } from '../../../mol-util/number';
+import { Sphere3D } from '../../../mol-math/geometry';
+
+const OrderColors = ColorMap({
+    '2': ColorNames.deepskyblue,
+    '3': ColorNames.lime,
+    'N': ColorNames.red,
+});
+const OrderColorsLegend = TableLegend(Object.keys(OrderColors).map(name => {
+    return [name, (OrderColors as any)[name] as Color] as [string, Color];
+}));
+
+function axesColorHelp(value: { name: string, params: {} }) {
+    return value.name === 'byOrder'
+        ? { description: 'Color axes by their order', legend: OrderColorsLegend }
+        : {};
+}
+
+const SharedParams = {
+    ...Mesh.Params,
+    scale: PD.Numeric(2, { min: 0.1, max: 5, step: 0.1 }),
+};
+
+const AxesParams = {
+    ...SharedParams,
+    axesColor: PD.MappedStatic('byOrder', {
+        byOrder: PD.EmptyGroup(),
+        uniform: PD.Group({
+            colorValue: PD.Color(ColorNames.orange),
+        }, { isFlat: true })
+    }, { help: axesColorHelp }),
+};
+type AxesParams = typeof AxesParams
+
+const CageParams = {
+    ...SharedParams,
+    cageColor: PD.Color(ColorNames.orange),
+};
+type CageParams = typeof CageParams
+
+const AssemblySymmetryVisuals = {
+    // cage should come before 'axes' so that the representative loci uses the cage shape
+    'cage': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CageParams>) => ShapeRepresentation(getCageShape, Mesh.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }) }),
+    'axes': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, AxesParams>) => ShapeRepresentation(getAxesShape, Mesh.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }) }),
+};
+
+export const AssemblySymmetryParams = {
+    ...AxesParams,
+    ...CageParams,
+    visuals: PD.MultiSelect(['axes', 'cage'], PD.objectToOptions(AssemblySymmetryVisuals)),
+};
+export type AssemblySymmetryParams = typeof AssemblySymmetryParams
+export type AssemblySymmetryProps = PD.Values<AssemblySymmetryParams>
+
+//
+
+function getAssemblyName(s: Structure) {
+    const id = s.units[0].conformation.operator.assembly?.id || '';
+    return isInteger(id) ? `Assembly ${id}` : id;
+}
+
+const t = Mat4.identity();
+const tmpV = Vec3();
+const tmpCenter = Vec3();
+const tmpScale = Vec3();
+
+const getOrderPrimitive = memoize1((order: number): Primitive | undefined => {
+    if (order < 2) {
+        return Prism(polygon(48, false));
+    } else if (order === 2) {
+        const lens = Prism(polygon(48, false));
+        const m = Mat4.identity();
+        Mat4.scale(m, m, Vec3.create(1, 0.35, 1));
+        transformPrimitive(lens, m);
+        return lens;
+    } else if (order === 3) {
+        return Wedge();
+    } else {
+        return Prism(polygon(order, false));
+    }
+});
+
+function getAxesMesh(data: AssemblySymmetryValue, props: PD.Values<AxesParams>, mesh?: Mesh) {
+    const { scale } = props;
+
+    const { rotation_axes } = data;
+    if (!AssemblySymmetry.isRotationAxes(rotation_axes)) return Mesh.createEmpty(mesh);
+
+    const { start, end } = rotation_axes[0];
+    const radius = (Vec3.distance(start, end) / 500) * scale;
+
+    Vec3.set(tmpScale, radius * 7, radius * 7, radius * 0.4);
+
+    const cylinderProps = { radiusTop: radius, radiusBottom: radius };
+    const builderState = MeshBuilder.createState(256, 128, mesh);
+
+    builderState.currentGroup = 0;
+    Vec3.scale(tmpCenter, Vec3.add(tmpCenter, start, end), 0.5);
+
+    for (let i = 0, il = rotation_axes.length; i < il; ++i) {
+        const { order, start, end } = rotation_axes[i];
+        builderState.currentGroup = i;
+        addCylinder(builderState, start, end, 1, cylinderProps);
+
+        const primitive = getOrderPrimitive(order);
+        if (primitive) {
+            Vec3.scale(tmpCenter, Vec3.add(tmpCenter, start, end), 0.5);
+            if (Vec3.dot(Vec3.unitY, Vec3.sub(tmpV, start, tmpCenter)) === 0) {
+                Mat4.targetTo(t, start, tmpCenter, Vec3.unitY);
+            } else {
+                Mat4.targetTo(t, start, tmpCenter, Vec3.unitX);
+            }
+            Mat4.scale(t, t, tmpScale);
+
+            Mat4.setTranslation(t, start);
+            MeshBuilder.addPrimitive(builderState, t, primitive);
+            Mat4.setTranslation(t, end);
+            MeshBuilder.addPrimitive(builderState, t, primitive);
+        }
+    }
+    return MeshBuilder.getMesh(builderState);
+}
+
+function getAxesShape(ctx: RuntimeContext, data: Structure, props: AssemblySymmetryProps, shape?: Shape<Mesh>) {
+    const assemblySymmetry = AssemblySymmetryProvider.get(data).value!;
+    const geo = getAxesMesh(assemblySymmetry, props, shape && shape.geometry);
+    const getColor = (groupId: number) => {
+        if (props.axesColor.name === 'byOrder') {
+            const { rotation_axes } = assemblySymmetry;
+            const order = rotation_axes![groupId]?.order;
+            if (order === 2) return OrderColors[2];
+            else if (order === 3) return OrderColors[3];
+            else return OrderColors.N;
+        } else {
+            return props.axesColor.params.colorValue;
+        }
+    };
+    const getLabel = (groupId: number) => {
+        const { type, symbol, kind, rotation_axes } = assemblySymmetry;
+        const order = rotation_axes![groupId]?.order;
+        return [
+            `<small>${data.model.entryId}</small>`,
+            `<small>${getAssemblyName(data)}</small>`,
+            `Axis ${groupId + 1} with Order ${order} of ${type} ${kind} (${symbol})`
+        ].join(' | ');
+    };
+    return Shape.create('Axes', data, geo, getColor, () => 1, getLabel);
+}
+
+//
+
+const getSymbolCage = memoize1((symbol: string): Cage | undefined => {
+    if (symbol.startsWith('D') || symbol.startsWith('C')) {
+        // z axis is prism axis, x/y axes cut through edge midpoints
+        const fold = parseInt(symbol.substr(1));
+        let cage: Cage;
+        if (fold === 2) {
+            cage = PrismCage(polygon(4, false));
+        } else if (fold === 3) {
+            cage = WedgeCage();
+        } else if (fold > 3) {
+            cage = PrismCage(polygon(fold, false));
+        } else {
+            return;
+        }
+        if (fold % 2 === 0) {
+            return cage;
+        } else {
+            const m = Mat4.identity();
+            Mat4.rotate(m, m, 1 / fold * Math.PI / 2, Vec3.unitZ);
+            return transformCage(cloneCage(cage), m);
+        }
+    } else if (symbol === 'O') {
+        // x/y/z axes cut through order 4 vertices
+        return OctahedronCage();
+    } else if (symbol === 'I') {
+        // z axis cut through order 5 vertex
+        // x axis cut through edge midpoint
+        const cage = IcosahedronCage();
+        const m = Mat4.identity();
+        Mat4.rotate(m, m, degToRad(31.7), Vec3.unitX);
+        return transformCage(cloneCage(cage), m);
+    } else if (symbol === 'T') {
+        // x/y/z axes cut through edge midpoints
+        return TetrahedronCage();
+    }
+});
+
+function getSymbolScale(symbol: string) {
+    if (symbol.startsWith('D') || symbol.startsWith('C')) {
+        return 0.75;
+    } else if (symbol === 'O') {
+        return 1.2;
+    } else if (symbol === 'I') {
+        return 0.25;
+    } else if (symbol === 'T') {
+        return 0.8;
+    }
+    return 1;
+}
+
+function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.RotationAxes, size: number, structure: Structure) {
+    const eye = Vec3();
+    const target = Vec3();
+    const dir = Vec3();
+    const up = Vec3();
+    let pair: Mutable<AssemblySymmetry.RotationAxes> | undefined = undefined;
+
+    if (symbol.startsWith('C')) {
+        pair = [axes[0]];
+    } else if (symbol.startsWith('D')) {
+        const fold = parseInt(symbol.substr(1));
+        if (fold === 2) {
+            pair = axes.filter(a => a.order === 2);
+        } else if (fold >= 3) {
+            const aN = axes.filter(a => a.order === fold)[0];
+            const a2 = axes.filter(a => a.order === 2)[1];
+            pair = [aN, a2];
+        }
+    } else if (symbol === 'O') {
+        pair = axes.filter(a => a.order === 4);
+    } else if (symbol === 'I') {
+        const a5 = axes.filter(a => a.order === 5)[0];
+        const a5dir = Vec3.sub(Vec3(), a5.end, a5.start);
+        pair = [a5];
+        for (const a of axes.filter(a => a.order === 3)) {
+            const d = radToDeg(Vec3.angle(Vec3.sub(up, a.end, a.start), a5dir));
+            if (!pair[1] && (equalEps(d, 100.81, 0.1) || equalEps(d, 79.19, 0.1))) {
+                pair[1] = a;
+                break;
+            }
+        }
+    } else if (symbol === 'T') {
+        pair = axes.filter(a => a.order === 2);
+    }
+
+    Mat4.setIdentity(t);
+    if (pair) {
+        const [aA, aB] = pair;
+        Vec3.scale(eye, Vec3.add(eye, aA.end, aA.start), 0.5);
+        Vec3.copy(target, aA.end);
+        if (aB) {
+            Vec3.sub(up, aB.end, aB.start);
+            Vec3.sub(dir, eye, target);
+            if (Vec3.dot(dir, up) < 0) Vec3.negate(up, up);
+            Mat4.targetTo(t, eye, target, up);
+
+            if (symbol.startsWith('D')) {
+                const { sphere } = structure.lookup3d.boundary;
+                let sizeXY = (sphere.radius * 2) * 0.8; // fallback for missing extrema
+                if (Sphere3D.hasExtrema(sphere)) {
+                    const n = Mat3.directionTransform(Mat3(), t);
+                    const dirs = unitCircleDirections.map(d => Vec3.transformMat3(Vec3(), d, n));
+                    sizeXY = getMaxProjectedDistance(sphere.extrema, dirs, sphere.center) * 1.6;
+                }
+                Mat4.scale(t, t, Vec3.create(sizeXY, sizeXY, Vec3.distance(aA.start, aA.end) * 0.9));
+            } else {
+                Mat4.scaleUniformly(t, t, size * getSymbolScale(symbol));
+            }
+        } else {
+            if (Vec3.dot(Vec3.unitY, Vec3.sub(tmpV, aA.end, aA.start)) === 0) {
+                Vec3.copy(up, Vec3.unitY);
+            } else {
+                Vec3.copy(up, Vec3.unitX);
+            }
+            Mat4.targetTo(t, eye, target, up);
+
+            const { sphere } = structure.lookup3d.boundary;
+            let sizeXY = (sphere.radius * 2) * 0.8; // fallback for missing extrema
+            if (Sphere3D.hasExtrema(sphere)) {
+                const n = Mat3.directionTransform(Mat3(), t);
+                const dirs = unitCircleDirections.map(d => Vec3.transformMat3(Vec3(), d, n));
+                sizeXY = getMaxProjectedDistance(sphere.extrema, dirs, sphere.center);
+            }
+            Mat4.scale(t, t, Vec3.create(sizeXY, sizeXY, size * 0.9));
+        }
+    }
+}
+
+const unitCircleDirections = (function() {
+    const dirs: Vec3[] = [];
+    const circle = polygon(12, false, 1);
+    for (let i = 0, il = circle.length; i < il; i += 3) {
+        dirs.push(Vec3.fromArray(Vec3(), circle, i));
+    }
+    return dirs;
+})();
+const tmpProj = Vec3();
+
+function getMaxProjectedDistance(points: Vec3[], directions: Vec3[], center: Vec3) {
+    let maxDist = 0;
+    for (const p of points) {
+        for (const d of directions) {
+            Vec3.projectPointOnVector(tmpProj, p, d, center);
+            const dist = Vec3.distance(tmpProj, center);
+            if (dist > maxDist) maxDist = dist;
+        }
+    }
+    return maxDist;
+}
+
+function getCageMesh(data: Structure, props: PD.Values<CageParams>, mesh?: Mesh) {
+    const assemblySymmetry = AssemblySymmetryProvider.get(data).value!;
+    const { scale } = props;
+
+    const { rotation_axes, symbol } = assemblySymmetry;
+    if (!AssemblySymmetry.isRotationAxes(rotation_axes)) return Mesh.createEmpty(mesh);
+
+    const structure = AssemblySymmetry.getStructure(data, assemblySymmetry);
+
+    const cage = getSymbolCage(symbol);
+    if (!cage) return Mesh.createEmpty(mesh);
+
+    const { start, end } = rotation_axes[0];
+    const size = Vec3.distance(start, end);
+    const radius = (size / 500) * scale;
+
+    const builderState = MeshBuilder.createState(256, 128, mesh);
+    builderState.currentGroup = 0;
+    setSymbolTransform(t, symbol, rotation_axes, size, structure);
+    Vec3.scale(tmpCenter, Vec3.add(tmpCenter, start, end), 0.5);
+    Mat4.setTranslation(t, tmpCenter);
+    MeshBuilder.addCage(builderState, t, cage, radius, 1, 8);
+
+    return MeshBuilder.getMesh(builderState);
+}
+
+function getCageShape(ctx: RuntimeContext, data: Structure, props: AssemblySymmetryProps, shape?: Shape<Mesh>) {
+    const assemblySymmetry = AssemblySymmetryProvider.get(data).value!;
+    const geo = getCageMesh(data, props, shape && shape.geometry);
+    const getColor = (groupId: number) => {
+        return props.cageColor;
+    };
+    const getLabel = (groupId: number) => {
+        const { type, symbol, kind } = assemblySymmetry;
+        data.model.entryId;
+        return [
+            `<small>${data.model.entryId}</small>`,
+            `<small>${getAssemblyName(data)}</small>`,
+            `Cage of ${type} ${kind} (${symbol})`
+        ].join(' | ');
+    };
+    return Shape.create('Cage', data, geo, getColor, () => 1, getLabel);
+}
+
+//
+
+export type AssemblySymmetryRepresentation = Representation<Structure, AssemblySymmetryParams>
+export function AssemblySymmetryRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, AssemblySymmetryParams>): AssemblySymmetryRepresentation {
+    return Representation.createMulti('Assembly Symmetry', ctx, getParams, Representation.StateBuilder, AssemblySymmetryVisuals as unknown as Representation.Def<Structure, AssemblySymmetryParams>);
+}

src/extensions/rcsb/assembly-symmetry/ui.tsx

@@ -0,0 +1,158 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as React from 'react';
+import { CollapsableState, CollapsableControls } from '../../../mol-plugin-ui/base';
+import { ApplyActionControl } from '../../../mol-plugin-ui/state/apply-action';
+import { InitAssemblySymmetry3D, AssemblySymmetry3D, AssemblySymmetryPreset, tryCreateAssemblySymmetry } from './behavior';
+import { AssemblySymmetryProvider,  AssemblySymmetryProps, AssemblySymmetryDataProvider, AssemblySymmetry } from './prop';
+import { ParameterControls } from '../../../mol-plugin-ui/controls/parameters';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { StructureHierarchyManager } from '../../../mol-plugin-state/manager/structure/hierarchy';
+import { StateAction, StateSelection } from '../../../mol-state';
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { PluginContext } from '../../../mol-plugin/context';
+import { Task } from '../../../mol-task';
+import Check from '@material-ui/icons/Check';
+import Extension from '@material-ui/icons/Extension';
+
+interface AssemblySymmetryControlState extends CollapsableState {
+    isBusy: boolean
+}
+
+export class AssemblySymmetryControls extends CollapsableControls<{}, AssemblySymmetryControlState> {
+    protected defaultState(): AssemblySymmetryControlState {
+        return {
+            header: 'Assembly Symmetry',
+            isCollapsed: false,
+            isBusy: false,
+            isHidden: true,
+            brand: { accent: 'cyan', svg: Extension }
+        };
+    }
+
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, () => {
+            this.setState({
+                isHidden: !this.canEnable(),
+                description: StructureHierarchyManager.getSelectedStructuresDescription(this.plugin)
+            });
+        });
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (e.cell.transform.transformer === AssemblySymmetry3D) this.forceUpdate();
+        });
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => this.setState({ isBusy: v }));
+    }
+
+    get pivot() {
+        return this.plugin.managers.structure.hierarchy.selection.structures[0];
+    }
+
+    canEnable() {
+        const { selection } = this.plugin.managers.structure.hierarchy;
+        if (selection.structures.length !== 1) return false;
+        const pivot = this.pivot.cell;
+        if (!pivot.obj) return false;
+        return !!InitAssemblySymmetry3D.definition.isApplicable?.(pivot.obj, pivot.transform, this.plugin);
+    }
+
+    renderEnable() {
+        const pivot = this.pivot;
+        if (!pivot.cell.parent) return null;
+        return <ApplyActionControl state={pivot.cell.parent} action={EnableAssemblySymmetry3D} initiallyCollapsed={true} nodeRef={pivot.cell.transform.ref} simpleApply={{ header: 'Enable', icon: Check }} />;
+    }
+
+    renderNoSymmetries() {
+        return <div className='msp-row-text'>
+            <div>No Symmetries for Assembly</div>
+        </div>;
+    }
+
+    get params() {
+        const structure = this.pivot.cell.obj?.data;
+        const params = PD.clone(structure ? AssemblySymmetryProvider.getParams(structure) : AssemblySymmetryProvider.defaultParams);
+        params.serverUrl.isHidden = true;
+        params.symmetryIndex.options = [[-1, 'Off'], ...params.symmetryIndex.options];
+        return params;
+    }
+
+    get values() {
+        const structure = this.pivot.cell.obj?.data;
+        if (structure) {
+            return AssemblySymmetryProvider.props(structure);
+        } else {
+            return { ...PD.getDefaultValues(AssemblySymmetryProvider.defaultParams), symmetryIndex: -1 };
+        }
+    }
+
+    async updateAssemblySymmetry(values: AssemblySymmetryProps) {
+        const s = this.pivot;
+        const currValues = AssemblySymmetryProvider.props(s.cell.obj!.data);
+        if (PD.areEqual(AssemblySymmetryProvider.defaultParams, currValues, values)) return;
+
+        if (s.properties) {
+            const b = this.plugin.state.data.build();
+            b.to(s.properties.cell).update(old => {
+                old.properties[AssemblySymmetryProvider.descriptor.name] = values;
+            });
+            await b.commit();
+        } else {
+            const pd = this.plugin.customStructureProperties.getParams(s.cell.obj?.data);
+            const params = PD.getDefaultValues(pd);
+            params.properties[AssemblySymmetryProvider.descriptor.name] = values;
+            await this.plugin.builders.structure.insertStructureProperties(s.cell, params);
+        }
+
+        for (const components of this.plugin.managers.structure.hierarchy.currentComponentGroups) {
+            if (values.symmetryIndex === -1) {
+                const name = components[0]?.representations[0]?.cell.transform.params?.colorTheme.name;
+                if (name === AssemblySymmetry.Tag.Cluster) {
+                    await this.plugin.managers.structure.component.updateRepresentationsTheme(components, { color: 'default' });
+                }
+            } else {
+                tryCreateAssemblySymmetry(this.plugin, s.cell);
+                await this.plugin.managers.structure.component.updateRepresentationsTheme(components, { color: AssemblySymmetry.Tag.Cluster as any });
+            }
+        }
+    }
+
+    paramsOnChange = (options: AssemblySymmetryProps) => {
+        this.updateAssemblySymmetry(options);
+    }
+
+    get hasAssemblySymmetry3D() {
+        return !this.pivot.cell.parent || !!StateSelection.findTagInSubtree(this.pivot.cell.parent.tree, this.pivot.cell.transform.ref, AssemblySymmetry.Tag.Representation);
+    }
+
+    get enable() {
+        return !this.hasAssemblySymmetry3D && this.values.symmetryIndex !== -1;
+    }
+
+    get noSymmetries() {
+        const structure = this.pivot.cell.obj?.data;
+        const data = structure && AssemblySymmetryDataProvider.get(structure).value;
+        return data && data.filter(sym => sym.symbol !== 'C1').length === 0;
+    }
+
+    renderParams() {
+        return <>
+            <ParameterControls params={this.params} values={this.values} onChangeValues={this.paramsOnChange} />
+        </>;
+    }
+
+    renderControls() {
+        if (!this.pivot) return null;
+        if (this.noSymmetries) return this.renderNoSymmetries();
+        if (this.enable) return this.renderEnable();
+        return this.renderParams();
+    }
+}
+
+const EnableAssemblySymmetry3D = StateAction.build({
+    from: PluginStateObject.Molecule.Structure,
+})(({ a, ref, state }, plugin: PluginContext) => Task.create('Enable Assembly Symmetry', async ctx => {
+    await AssemblySymmetryPreset.apply(ref, Object.create(null), plugin);
+}));

src/extensions/rcsb/graphql/codegen.yml

@@ -0,0 +1,12 @@
+schema: https://data.rcsb.org/graphql
+documents: './src/extensions/rcsb/graphql/symmetry.gql.ts'
+generates:
+  './src/extensions/rcsb/graphql/types.ts':
+    plugins:
+      - add: '/* eslint-disable */'
+      - time
+      - typescript
+      - typescript-operations
+    config:
+      immutableTypes: true
+      skipTypename: true

src/extensions/rcsb/graphql/symmetry.gql.ts

@@ -0,0 +1,25 @@
+export default /* GraphQL */ `
+query AssemblySymmetry($assembly_id: String!, $entry_id: String!) {
+    assembly(assembly_id: $assembly_id, entry_id: $entry_id) {
+        rcsb_struct_symmetry {
+            clusters {
+                avg_rmsd
+                members {
+                    asym_id
+                    pdbx_struct_oper_list_ids
+                }
+            }
+            kind
+            oligomeric_state
+            rotation_axes {
+                order
+                start
+                end
+            }
+            stoichiometry
+            symbol
+            type
+        }
+    }
+}
+`;

src/extensions/rcsb/index.ts

@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export { RCSBAssemblySymmetry } from './assembly-symmetry/behavior';
+export { RCSBValidationReport } from './validation-report/behavior';

src/extensions/rcsb/validation-report/behavior.ts

@@ -0,0 +1,382 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
+import { ValidationReport, ValidationReportProvider } from './prop';
+import { RandomCoilIndexColorThemeProvider } from './color/random-coil-index';
+import { GeometryQualityColorThemeProvider } from './color/geometry-quality';
+import { Loci } from '../../../mol-model/loci';
+import { OrderedSet } from '../../../mol-data/int';
+import { ClashesRepresentationProvider } from './representation';
+import { DensityFitColorThemeProvider } from './color/density-fit';
+import { cantorPairing } from '../../../mol-data/util';
+import { DefaultQueryRuntimeTable } from '../../../mol-script/runtime/query/compiler';
+import { StructureSelectionQuery, StructureSelectionCategory } from '../../../mol-plugin-state/helpers/structure-selection-query';
+import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
+import { Task } from '../../../mol-task';
+import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
+import { StateObjectRef } from '../../../mol-state';
+import { Model } from '../../../mol-model/structure';
+
+export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'rcsb-validation-report-prop',
+    category: 'custom-props',
+    display: {
+        name: 'Validation Report',
+        description: 'Data from wwPDB Validation Report, obtained via RCSB PDB.'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
+        private provider = ValidationReportProvider
+
+        private labelProvider = {
+            label: (loci: Loci): string | undefined => {
+                if (!this.params.showTooltip) return;
+                return [
+                    geometryQualityLabel(loci),
+                    densityFitLabel(loci),
+                    randomCoilIndexLabel(loci)
+                ].filter(l => !!l).join('</br>');
+            }
+        }
+
+        register(): void {
+            DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);
+
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+
+            this.ctx.managers.lociLabels.addProvider(this.labelProvider);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(DensityFitColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(GeometryQualityColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(RandomCoilIndexColorThemeProvider);
+
+            this.ctx.representation.structure.registry.add(ClashesRepresentationProvider);
+            this.ctx.query.structure.registry.add(hasClash);
+
+            this.ctx.builders.structure.representation.registerPreset(ValidationReportGeometryQualityPreset);
+            this.ctx.builders.structure.representation.registerPreset(ValidationReportDensityFitPreset);
+            this.ctx.builders.structure.representation.registerPreset(ValidationReportRandomCoilIndexPreset);
+        }
+
+        update(p: { autoAttach: boolean, showTooltip: boolean }) {
+            let updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.params.showTooltip = p.showTooltip;
+            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+
+        unregister() {
+            DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+
+            this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
+
+            this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(DensityFitColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(GeometryQualityColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(RandomCoilIndexColorThemeProvider);
+
+            this.ctx.representation.structure.registry.remove(ClashesRepresentationProvider);
+            this.ctx.query.structure.registry.remove(hasClash);
+
+            this.ctx.builders.structure.representation.unregisterPreset(ValidationReportGeometryQualityPreset);
+            this.ctx.builders.structure.representation.unregisterPreset(ValidationReportDensityFitPreset);
+            this.ctx.builders.structure.representation.unregisterPreset(ValidationReportRandomCoilIndexPreset);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(false),
+        showTooltip: PD.Boolean(true),
+        baseUrl: PD.Text(ValidationReport.DefaultBaseUrl)
+    })
+});
+
+//
+
+function geometryQualityLabel(loci: Loci): string | undefined {
+    if (loci.kind === 'element-loci') {
+        if (loci.elements.length === 0) return;
+
+        if (loci.elements.length === 1 && OrderedSet.size(loci.elements[0].indices) === 1) {
+            const { unit, indices } = loci.elements[0];
+
+            const validationReport = ValidationReportProvider.get(unit.model).value;
+            if (!validationReport) return;
+            if (!unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) return;
+
+            const { bondOutliers, angleOutliers } = validationReport;
+            const eI = unit.elements[OrderedSet.start(indices)];
+            const issues = new Set<string>();
+
+            const bonds = bondOutliers.index.get(eI);
+            if (bonds) bonds.forEach(b => issues.add(bondOutliers.data[b].tag));
+
+            const angles = angleOutliers.index.get(eI);
+            if (angles) angles.forEach(a => issues.add(angleOutliers.data[a].tag));
+
+            if (issues.size === 0) {
+                return `Geometry Quality <small>(1 Atom)</small>: no issues`;
+            }
+
+            const summary: string[] = [];
+            issues.forEach(name => summary.push(name));
+            return `Geometry Quality <small>(1 Atom)</small>: ${summary.join(', ')}`;
+        }
+
+        let hasValidationReport = false;
+        const seen = new Set<number>();
+        const cummulativeIssues = new Map<string, number>();
+
+        for (const { indices, unit } of loci.elements) {
+            const validationReport = ValidationReportProvider.get(unit.model).value;
+            if (!validationReport) continue;
+            if (!unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) continue;
+            hasValidationReport = true;
+
+            const { geometryIssues } = validationReport;
+            const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index;
+            const { elements } = unit;
+
+            OrderedSet.forEach(indices, idx => {
+                const eI = elements[idx];
+
+                const rI = residueIndex[eI];
+                const residueKey = cantorPairing(rI, unit.id);
+                if (!seen.has(residueKey)) {
+                    const issues = geometryIssues.get(rI);
+                    if (issues) {
+                        issues.forEach(name => {
+                            const count = cummulativeIssues.get(name) || 0;
+                            cummulativeIssues.set(name, count + 1);
+                        });
+                    }
+                    seen.add(residueKey);
+                }
+            });
+        }
+
+        if (!hasValidationReport) return;
+
+        const residueCount = `<small>(${seen.size} ${seen.size > 1 ? 'Residues' : 'Residue'})</small>`;
+
+        if (cummulativeIssues.size === 0) {
+            return `Geometry Quality ${residueCount}: no issues`;
+        }
+
+        const summary: string[] = [];
+        cummulativeIssues.forEach((count, name) => {
+            summary.push(`${name}${count > 1 ? ` \u00D7 ${count}` : ''}`);
+        });
+        return `Geometry Quality ${residueCount}: ${summary.join(', ')}`;
+    }
+}
+
+function densityFitLabel(loci: Loci): string | undefined {
+    if (loci.kind === 'element-loci') {
+        if (loci.elements.length === 0) return;
+
+        const seen = new Set<number>();
+        const rsrzSeen = new Set<number>();
+        const rsccSeen = new Set<number>();
+        let rsrzSum = 0;
+        let rsccSum = 0;
+
+        for (const { indices, unit } of loci.elements) {
+            const validationReport = ValidationReportProvider.get(unit.model).value;
+            if (!validationReport) continue;
+            if (!unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) continue;
+
+            const { rsrz, rscc } = validationReport;
+            const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index;
+            const { elements } = unit;
+
+            OrderedSet.forEach(indices, idx => {
+                const eI = elements[idx];
+                const rI = residueIndex[eI];
+
+                const residueKey = cantorPairing(rI, unit.id);
+                if (!seen.has(residueKey)) {
+                    const rsrzValue = rsrz.get(rI);
+                    const rsccValue = rscc.get(rI);
+                    if (rsrzValue !== undefined) {
+                        rsrzSum += rsrzValue;
+                        rsrzSeen.add(residueKey);
+                    } else if (rsccValue !== undefined) {
+                        rsccSum += rsccValue;
+                        rsccSeen.add(residueKey);
+                    }
+                    seen.add(residueKey);
+                }
+            });
+        }
+
+        if (seen.size === 0) return;
+
+        const summary: string[] = [];
+
+        if (rsrzSeen.size) {
+            const rsrzCount = `<small>(${rsrzSeen.size} ${rsrzSeen.size > 1 ? 'Residues avg.' : 'Residue'})</small>`;
+            const rsrzAvg = rsrzSum / rsrzSeen.size;
+            summary.push(`Real-Space R Z-score ${rsrzCount}: ${rsrzAvg.toFixed(2)}`);
+        }
+        if (rsccSeen.size) {
+            const rsccCount = `<small>(${rsccSeen.size} ${rsccSeen.size > 1 ? 'Residues avg.' : 'Residue'})</small>`;
+            const rsccAvg = rsccSum / rsccSeen.size;
+            summary.push(`Real-Space Correlation Coefficient ${rsccCount}: ${rsccAvg.toFixed(2)}`);
+        }
+
+        if (summary.length) {
+            return summary.join('</br>');
+        }
+    }
+}
+
+function randomCoilIndexLabel(loci: Loci): string | undefined {
+    if (loci.kind === 'element-loci') {
+        if (loci.elements.length === 0) return;
+
+        const seen = new Set<number>();
+        let sum = 0;
+
+        for (const { indices, unit } of loci.elements) {
+            const validationReport = ValidationReportProvider.get(unit.model).value;
+            if (!validationReport) continue;
+            if (!unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) continue;
+
+            const { rci } = validationReport;
+            const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index;
+            const { elements } = unit;
+
+            OrderedSet.forEach(indices, idx => {
+                const eI = elements[idx];
+                const rI = residueIndex[eI];
+
+                const residueKey = cantorPairing(rI, unit.id);
+                if (!seen.has(residueKey)) {
+                    const rciValue = rci.get(rI);
+                    if (rciValue !== undefined) {
+                        sum += rciValue;
+                        seen.add(residueKey);
+                    }
+                }
+            });
+        }
+
+        if (seen.size === 0) return;
+
+        const residueCount = `<small>(${seen.size} ${seen.size > 1 ? 'Residues avg.' : 'Residue'})</small>`;
+        const rciAvg = sum / seen.size;
+
+        return `Random Coil Index ${residueCount}: ${rciAvg.toFixed(2)}`;
+    }
+}
+
+//
+
+const hasClash = StructureSelectionQuery('Residues with Clashes', MS.struct.modifier.union([
+    MS.struct.modifier.wholeResidues([
+        MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'atom-test': ValidationReport.symbols.hasClash.symbol(),
+            })
+        ])
+    ])
+]), {
+    description: 'Select residues with clashes in the wwPDB validation report.',
+    category: StructureSelectionCategory.Residue,
+    ensureCustomProperties: (ctx, structure) => {
+        return ValidationReportProvider.attach(ctx, structure.models[0]);
+    }
+});
+
+//
+
+export const ValidationReportGeometryQualityPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-rcsb-validation-report-geometry-uality',
+    display: {
+        name: 'Validation Report (Geometry Quality)', group: 'Annotation',
+        description: 'Color structure based on geometry quality; show geometry clashes. Data from wwPDB Validation Report, obtained via RCSB PDB.'
+    },
+    isApplicable(a) {
+        return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]);
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const model = structureCell?.obj?.data.model;
+        if (!structureCell || !model) return {};
+
+        await plugin.runTask(Task.create('Validation Report', async runtime => {
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+        }));
+
+        const colorTheme = GeometryQualityColorThemeProvider.name as any;
+        const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin);
+
+        const clashes = await plugin.builders.structure.tryCreateComponentFromExpression(structureCell, hasClash.expression, 'clashes', { label: 'Clashes' });
+
+        const { update, builder, typeParams, color } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+        let clashesBallAndStick, clashesSnfg3d;
+        if (representations) {
+            clashesBallAndStick = builder.buildRepresentation(update, clashes, { type: 'ball-and-stick', typeParams, color: colorTheme }, { tag: 'clashes-ball-and-stick' });
+            clashesSnfg3d = builder.buildRepresentation<any>(update, clashes, { type: ClashesRepresentationProvider.name, typeParams, color }, { tag: 'clashes-snfg-3d' });
+        }
+
+        await update.commit({ revertOnError: true });
+        return { components: { ...components, clashes }, representations: { ...representations, clashesBallAndStick, clashesSnfg3d } };
+    }
+});
+
+export const ValidationReportDensityFitPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-rcsb-validation-report-density-fit',
+    display: {
+        name: 'Validation Report (Density Fit)', group: 'Annotation',
+        description: 'Color structure based on density fit. Data from wwPDB Validation Report, obtained via RCSB PDB.'
+    },
+    isApplicable(a) {
+        return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]) && Model.isFromXray(a.data.models[0]) && Model.probablyHasDensityMap(a.data.models[0]);
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const model = structureCell?.obj?.data.model;
+        if (!structureCell || !model) return {};
+
+        await plugin.runTask(Task.create('Validation Report', async runtime => {
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+        }));
+
+        const colorTheme = DensityFitColorThemeProvider.name as any;
+        return await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin);
+    }
+});
+
+export const ValidationReportRandomCoilIndexPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-rcsb-validation-report-random-coil-index',
+    display: {
+        name: 'Validation Report (Random Coil Index)', group: 'Annotation',
+        description: 'Color structure based on Random Coil Index. Data from wwPDB Validation Report, obtained via RCSB PDB.'
+    },
+    isApplicable(a) {
+        return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]) && Model.isFromNmr(a.data.models[0]);
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const model = structureCell?.obj?.data.model;
+        if (!structureCell || !model) return {};
+
+        await plugin.runTask(Task.create('Validation Report', async runtime => {
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+        }));
+
+        const colorTheme = RandomCoilIndexColorThemeProvider.name as any;
+        return await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin);
+    }
+});

src/extensions/rcsb/validation-report/color/density-fit.ts

@@ -0,0 +1,75 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ThemeDataContext } from '../../../../mol-theme/theme';
+import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { Color, ColorScale } from '../../../../mol-util/color';
+import { StructureElement, Model } from '../../../../mol-model/structure';
+import { Location } from '../../../../mol-model/location';
+import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
+import { ValidationReportProvider, ValidationReport } from '../prop';
+
+const DefaultColor = Color(0xCCCCCC);
+
+export function DensityFitColorTheme(ctx: ThemeDataContext, props: {}): ColorTheme<{}> {
+    let color: LocationColor = () => DefaultColor;
+    const scaleRsrz = ColorScale.create({
+        minLabel: 'Poor',
+        maxLabel: 'Better',
+        domain: [2, 0],
+        listOrName: 'red-yellow-blue',
+    });
+    const scaleRscc = ColorScale.create({
+        minLabel: 'Poor',
+        maxLabel: 'Better',
+        domain: [0.678, 1.0],
+        listOrName: 'red-yellow-blue',
+    });
+
+    const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]);
+    const contextHash = validationReport?.version;
+    const model = ctx.structure?.models[0];
+
+    if (validationReport?.value && model) {
+        const { rsrz, rscc } = validationReport.value;
+        const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
+        color = (location: Location): Color => {
+            if (StructureElement.Location.is(location) && location.unit.model === model) {
+                const rsrzValue = rsrz.get(residueIndex[location.element]);
+                if (rsrzValue !== undefined) return scaleRsrz.color(rsrzValue);
+                const rsccValue = rscc.get(residueIndex[location.element]);
+                if (rsccValue !== undefined) return scaleRscc.color(rsccValue);
+                return DefaultColor;
+            }
+            return DefaultColor;
+        };
+    }
+
+    return {
+        factory: DensityFitColorTheme,
+        granularity: 'group',
+        color,
+        props,
+        contextHash,
+        description: 'Assigns residue colors according to the density fit using normalized Real Space R (RSRZ) for polymer residues and real space correlation coefficient (RSCC) for ligands. Colors range from poor (RSRZ = 2 or RSCC = 0.678) - to better (RSRZ = 0 or RSCC = 1.0). Data from wwPDB Validation Report, obtained via RCSB PDB.',
+        legend: scaleRsrz.legend
+    };
+}
+
+export const DensityFitColorThemeProvider: ColorTheme.Provider<{}, ValidationReport.Tag.DensityFit> = {
+    name: ValidationReport.Tag.DensityFit,
+    label: 'Density Fit',
+    category: ColorTheme.Category.Validation,
+    factory: DensityFitColorTheme,
+    getParams: () => ({}),
+    defaultValues: PD.getDefaultValues({}),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromXray(ctx.structure.models[0]) && Model.probablyHasDensityMap(ctx.structure.models[0]),
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
+        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+    }
+};

src/extensions/rcsb/validation-report/color/geometry-quality.ts

@@ -0,0 +1,115 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ThemeDataContext } from '../../../../mol-theme/theme';
+import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { Color } from '../../../../mol-util/color';
+import { StructureElement } from '../../../../mol-model/structure';
+import { Location } from '../../../../mol-model/location';
+import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
+import { ValidationReportProvider, ValidationReport } from '../prop';
+import { TableLegend } from '../../../../mol-util/legend';
+import { PolymerType } from '../../../../mol-model/structure/model/types';
+import { SetUtils } from '../../../../mol-util/set';
+
+const DefaultColor = Color(0x909090);
+
+const NoIssuesColor = Color(0x2166ac);
+const OneIssueColor = Color(0xfee08b);
+const TwoIssuesColor = Color(0xf46d43);
+const ThreeOrMoreIssuesColor = Color(0xa50026);
+
+const ColorLegend = TableLegend([
+    ['Data unavailable', DefaultColor],
+    ['No issues', NoIssuesColor],
+    ['One issue', OneIssueColor],
+    ['Two issues', TwoIssuesColor],
+    ['Three or more issues', ThreeOrMoreIssuesColor],
+]);
+
+export function getGeometricQualityColorThemeParams(ctx: ThemeDataContext) {
+    const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]).value;
+    const options: [string, string][] = [];
+    if (validationReport) {
+        const kinds = new Set<string>();
+        validationReport.geometryIssues.forEach(v => v.forEach(k => kinds.add(k)));
+        kinds.forEach(k => options.push([k, k]));
+    }
+    return {
+        ignore: PD.MultiSelect([] as string[], options)
+    };
+}
+export type GeometricQualityColorThemeParams = ReturnType<typeof getGeometricQualityColorThemeParams>
+
+export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: PD.Values<GeometricQualityColorThemeParams>): ColorTheme<GeometricQualityColorThemeParams> {
+    let color: LocationColor = () => DefaultColor;
+
+    const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]);
+    const contextHash = validationReport?.version;
+
+    const value = validationReport?.value;
+    const model = ctx.structure?.models[0];
+
+    if (value && model) {
+        const { geometryIssues, clashes, bondOutliers, angleOutliers } = value;
+        const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
+        const { polymerType } = model.atomicHierarchy.derived.residue;
+        const ignore = new Set(props.ignore);
+
+        color = (location: Location): Color => {
+            if (StructureElement.Location.is(location) && location.unit.model === model) {
+                const { element } = location;
+                const rI = residueIndex[element];
+
+                const value = geometryIssues.get(rI);
+                if (value === undefined) return DefaultColor;
+
+                let count = SetUtils.differenceSize(value, ignore);
+
+                if (count > 0 && polymerType[rI] === PolymerType.NA) {
+                    count = 0;
+                    if (!ignore.has('clash') && clashes.getVertexEdgeCount(element) > 0) count += 1;
+                    if (!ignore.has('mog-bond-outlier') && bondOutliers.index.has(element)) count += 1;
+                    if (!ignore.has('mog-angle-outlier') && angleOutliers.index.has(element)) count += 1;
+                }
+
+                switch (count) {
+                    case undefined: return DefaultColor;
+                    case 0: return NoIssuesColor;
+                    case 1: return OneIssueColor;
+                    case 2: return TwoIssuesColor;
+                    default: return ThreeOrMoreIssuesColor;
+                }
+            }
+            return DefaultColor;
+        };
+    }
+
+    return {
+        factory: GeometryQualityColorTheme,
+        granularity: 'group',
+        color,
+        props,
+        contextHash,
+        description: 'Assigns residue colors according to the number of (filtered) geometry issues. Data from wwPDB Validation Report, obtained via RCSB PDB.',
+        legend: ColorLegend
+    };
+}
+
+export const GeometryQualityColorThemeProvider: ColorTheme.Provider<GeometricQualityColorThemeParams, ValidationReport.Tag.GeometryQuality> = {
+    name: ValidationReport.Tag.GeometryQuality,
+    label: 'Geometry Quality',
+    category: ColorTheme.Category.Validation,
+    factory: GeometryQualityColorTheme,
+    getParams: getGeometricQualityColorThemeParams,
+    defaultValues: PD.getDefaultValues(getGeometricQualityColorThemeParams({})),
+    isApplicable: (ctx: ThemeDataContext) => ValidationReport.isApplicable(ctx.structure?.models[0]),
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
+        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+    }
+};

src/extensions/rcsb/validation-report/color/random-coil-index.ts

@@ -0,0 +1,66 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ThemeDataContext } from '../../../../mol-theme/theme';
+import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { Color, ColorScale } from '../../../../mol-util/color';
+import { StructureElement, Model } from '../../../../mol-model/structure';
+import { Location } from '../../../../mol-model/location';
+import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
+import { ValidationReportProvider, ValidationReport } from '../prop';
+
+const DefaultColor = Color(0xCCCCCC);
+
+export function RandomCoilIndexColorTheme(ctx: ThemeDataContext, props: {}): ColorTheme<{}> {
+    let color: LocationColor = () => DefaultColor;
+    const scale = ColorScale.create({
+        reverse: true,
+        domain: [0, 0.6],
+        listOrName: 'red-yellow-blue',
+    });
+
+    const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]);
+    const contextHash = validationReport?.version;
+
+    const rci = validationReport?.value?.rci;
+    const model = ctx.structure?.models[0];
+
+    if (rci && model) {
+        const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
+        color = (location: Location): Color => {
+            if (StructureElement.Location.is(location) && location.unit.model === model) {
+                const value = rci.get(residueIndex[location.element]);
+                return value === undefined ? DefaultColor : scale.color(value);
+            }
+            return DefaultColor;
+        };
+    }
+
+    return {
+        factory: RandomCoilIndexColorTheme,
+        granularity: 'group',
+        color,
+        props,
+        contextHash,
+        description: 'Assigns residue colors according to the Random Coil Index value. Data from wwPDB Validation Report, obtained via RCSB PDB.',
+        legend: scale.legend
+    };
+}
+
+export const RandomCoilIndexColorThemeProvider: ColorTheme.Provider<{}, ValidationReport.Tag.RandomCoilIndex> = {
+    name: ValidationReport.Tag.RandomCoilIndex,
+    label: 'Random Coil Index',
+    category: ColorTheme.Category.Validation,
+    factory: RandomCoilIndexColorTheme,
+    getParams: () => ({}),
+    defaultValues: PD.getDefaultValues({}),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromNmr(ctx.structure.models[0]),
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
+        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+    }
+};

src/extensions/rcsb/validation-report/prop.ts

@@ -0,0 +1,574 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Structure, Unit } from '../../../mol-model/structure';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { Model, ElementIndex, ResidueIndex } from '../../../mol-model/structure/model';
+import { IntAdjacencyGraph } from '../../../mol-math/graph';
+import { CustomStructureProperty } from '../../../mol-model-props/common/custom-structure-property';
+import { InterUnitGraph } from '../../../mol-math/graph/inter-unit-graph';
+import { UnitIndex } from '../../../mol-model/structure/structure/element/element';
+import { IntMap, SortedArray } from '../../../mol-data/int';
+import { arrayMax } from '../../../mol-util/array';
+import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
+import { CustomPropSymbol } from '../../../mol-script/language/symbol';
+import Type from '../../../mol-script/language/type';
+import { Asset } from '../../../mol-util/assets';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
+
+export { ValidationReport };
+
+interface ValidationReport {
+    /**
+     * Real Space R (RSRZ) for residues,
+     * defined for polymer residues in X-ray structures
+     */
+    rsrz: Map<ResidueIndex, number>
+    /**
+     * Real Space Correlation Coefficient (RSCC) for residues,
+     * defined for each non-polymer residue in X-ray structures
+     */
+    rscc: Map<ResidueIndex, number>
+    /**
+     * Random Coil Index (RCI) for residues,
+     * defined for polymer residues in NMR structures
+     */
+    rci: Map<ResidueIndex, number>
+    /**
+     * Set of geometry issues for residues
+     */
+    geometryIssues: Map<ResidueIndex, Set<string>>
+
+    /**
+     * Set of bond outliers
+     */
+    bondOutliers: {
+        index: Map<ElementIndex, number[]>
+        data: {
+            tag: string, atomA: ElementIndex, atomB: ElementIndex
+            z: number, mean: number, obs: number, stdev: number
+        }[]
+    }
+    /**
+     * Set of angle outliers
+     */
+    angleOutliers: {
+        index: Map<ElementIndex, number[]>
+        data: {
+            tag: string, atomA: ElementIndex, atomB: ElementIndex, atomC: ElementIndex,
+            z: number, mean: number, obs: number, stdev: number
+        }[]
+    }
+
+    /**
+     * Clashes between atoms, including id, magniture and distance
+     */
+    clashes: IntAdjacencyGraph<ElementIndex, {
+        readonly id: ArrayLike<number>
+        readonly magnitude: ArrayLike<number>
+        readonly distance: ArrayLike<number>
+    }>
+}
+
+namespace ValidationReport {
+    export enum Tag {
+        DensityFit = 'rcsb-density-fit',
+        GeometryQuality = 'rcsb-geometry-quality',
+        RandomCoilIndex = 'rcsb-random-coil-index',
+        Clashes = 'rcsb-clashes',
+    }
+
+    export const DefaultBaseUrl = '//ftp.rcsb.org/pub/pdb/validation_reports';
+    export function getEntryUrl(pdbId: string, baseUrl: string) {
+        const id = pdbId.toLowerCase();
+        return `${baseUrl}/${id.substr(1, 2)}/${id}/${id}_validation.xml.gz`;
+    }
+
+    export function isApplicable(model?: Model): boolean {
+        return !!model && Model.isFromPdbArchive(model);
+    }
+
+    export function fromXml(xml: XMLDocument, model: Model): ValidationReport {
+        return parseValidationReportXml(xml, model);
+    }
+
+    export async function fetch(ctx: CustomProperty.Context, model: Model, props: ServerSourceProps): Promise<CustomProperty.Data<ValidationReport>> {
+        const url = Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.baseUrl));
+        const xml = await ctx.assetManager.resolve(url, 'xml').runInContext(ctx.runtime);
+        return { value: fromXml(xml.data, model), assets: [xml] };
+    }
+
+    export async function open(ctx: CustomProperty.Context, model: Model, props: FileSourceProps): Promise<CustomProperty.Data<ValidationReport>> {
+        if (props.input === null) throw new Error('No file given');
+        const xml = await ctx.assetManager.resolve(props.input, 'xml').runInContext(ctx.runtime);
+        return { value: fromXml(xml.data, model), assets: [xml] };
+    }
+
+    export async function obtain(ctx: CustomProperty.Context, model: Model, props: ValidationReportProps): Promise<CustomProperty.Data<ValidationReport>> {
+        switch(props.source.name) {
+            case 'file': return open(ctx, model, props.source.params);
+            case 'server': return fetch(ctx, model, props.source.params);
+        }
+    }
+
+    export const symbols = {
+        hasClash: QuerySymbolRuntime.Dynamic(CustomPropSymbol('rcsb', 'validation-report.has-clash', Type.Bool),
+            ctx => {
+                const { unit, element } = ctx.element;
+                if (!Unit.isAtomic(unit)) return 0;
+                const validationReport = ValidationReportProvider.get(unit.model).value;
+                return validationReport && validationReport.clashes.getVertexEdgeCount(element) > 0;
+            }
+        ),
+        issueCount: QuerySymbolRuntime.Dynamic(CustomPropSymbol('rcsb', 'validation-report.issue-count', Type.Num),
+            ctx => {
+                const { unit, element } = ctx.element;
+                if (!Unit.isAtomic(unit)) return 0;
+                const validationReport = ValidationReportProvider.get(unit.model).value;
+                return validationReport?.geometryIssues.get(unit.residueIndex[element])?.size || 0;
+            }
+        ),
+    };
+}
+
+const FileSourceParams = {
+    input: PD.File({ accept: '.xml,.gz,.zip' })
+};
+type FileSourceProps = PD.Values<typeof FileSourceParams>
+
+const ServerSourceParams = {
+    baseUrl: PD.Text(ValidationReport.DefaultBaseUrl, { description: 'Base URL to directory tree' })
+};
+type ServerSourceProps = PD.Values<typeof ServerSourceParams>
+
+export const ValidationReportParams = {
+    source: PD.MappedStatic('server', {
+        'file': PD.Group(FileSourceParams, { label: 'File', isFlat: true }),
+        'server': PD.Group(ServerSourceParams, { label: 'Server', isFlat: true }),
+    }, { options: [['file', 'File'], ['server', 'Server']] })
+};
+export type ValidationReportParams = typeof ValidationReportParams
+export type ValidationReportProps = PD.Values<ValidationReportParams>
+
+export const ValidationReportProvider: CustomModelProperty.Provider<ValidationReportParams, ValidationReport> = CustomModelProperty.createProvider({
+    label: 'Validation Report',
+    descriptor: CustomPropertyDescriptor({
+        name: 'rcsb_validation_report',
+        symbols: ValidationReport.symbols
+    }),
+    type: 'dynamic',
+    defaultParams: ValidationReportParams,
+    getParams: (data: Model) => ValidationReportParams,
+    isApplicable: (data: Model) => ValidationReport.isApplicable(data),
+    obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<ValidationReportProps>) => {
+        const p = { ...PD.getDefaultValues(ValidationReportParams), ...props };
+        return await ValidationReport.obtain(ctx, data, p);
+    }
+});
+
+//
+
+type IntraUnitClashesProps = {
+    readonly id: ArrayLike<number>
+    readonly magnitude: ArrayLike<number>
+    readonly distance: ArrayLike<number>
+}
+type InterUnitClashesProps = {
+    readonly id: number
+    readonly magnitude: number
+    readonly distance: number
+}
+
+export type IntraUnitClashes = IntAdjacencyGraph<UnitIndex, IntraUnitClashesProps>
+export type InterUnitClashes = InterUnitGraph<Unit.Atomic, UnitIndex, InterUnitClashesProps>
+
+export interface Clashes {
+    readonly interUnit: InterUnitClashes
+    readonly intraUnit: IntMap<IntraUnitClashes>
+}
+
+function createInterUnitClashes(structure: Structure, clashes: ValidationReport['clashes']) {
+    const builder = new InterUnitGraph.Builder<Unit.Atomic, UnitIndex, InterUnitClashesProps>();
+    const { a, b, edgeProps: { id, magnitude, distance } } = clashes;
+
+    const pA = Vec3(), pB = Vec3();
+
+    Structure.eachUnitPair(structure, (unitA: Unit, unitB: Unit) => {
+        const elementsA = unitA.elements;
+        const elementsB = unitB.elements;
+
+        builder.startUnitPair(unitA as Unit.Atomic, unitB as Unit.Atomic);
+
+        for (let i = 0, il = clashes.edgeCount * 2; i < il; ++i) {
+            // TODO create lookup
+            let indexA = SortedArray.indexOf(elementsA, a[i]);
+            let indexB = SortedArray.indexOf(elementsB, b[i]);
+
+            if (indexA !== -1 && indexB !== -1) {
+                unitA.conformation.position(a[i], pA);
+                unitB.conformation.position(b[i], pB);
+
+                // check actual distance to avoid clashes between unrelated chain instances
+                if (equalEps(distance[i], Vec3.distance(pA, pB), 0.1)) {
+                    builder.add(indexA as UnitIndex, indexB as UnitIndex, {
+                        id: id[i],
+                        magnitude: magnitude[i],
+                        distance: distance[i],
+                    });
+                }
+            }
+        }
+
+        builder.finishUnitPair();
+    }, {
+        maxRadius: arrayMax(clashes.edgeProps.distance),
+        validUnit: (unit: Unit) => Unit.isAtomic(unit),
+        validUnitPair: (unitA: Unit, unitB: Unit) => unitA.model === unitB.model
+    });
+
+    return new InterUnitGraph(builder.getMap());
+}
+
+function createIntraUnitClashes(unit: Unit.Atomic, clashes: ValidationReport['clashes']): IntraUnitClashes {
+    const aIndices: UnitIndex[] = [];
+    const bIndices: UnitIndex[] = [];
+    const ids: number[] = [];
+    const magnitudes: number[] = [];
+    const distances: number[] = [];
+
+    const pA = Vec3(), pB = Vec3();
+
+    const { elements } = unit;
+    const { a, b, edgeCount, edgeProps } = clashes;
+
+    for (let i = 0, il = edgeCount * 2; i < il; ++i) {
+        // TODO create lookup
+        let indexA = SortedArray.indexOf(elements, a[i]);
+        let indexB = SortedArray.indexOf(elements, b[i]);
+
+        if (indexA !== -1 && indexB !== -1) {
+            unit.conformation.position(a[i], pA);
+            unit.conformation.position(b[i], pB);
+
+            // check actual distance to avoid clashes between unrelated chain instances
+            if (equalEps(edgeProps.distance[i], Vec3.distance(pA, pB), 0.1)) {
+                aIndices.push(indexA as UnitIndex);
+                bIndices.push(indexB as UnitIndex);
+                ids.push(edgeProps.id[i]);
+                magnitudes.push(edgeProps.magnitude[i]);
+                distances.push(edgeProps.distance[i]);
+            }
+        }
+    }
+
+    const builder = new IntAdjacencyGraph.EdgeBuilder(elements.length, aIndices, bIndices);
+    const id = new Int32Array(builder.slotCount);
+    const magnitude = new Float32Array(builder.slotCount);
+    const distance = new Float32Array(builder.slotCount);
+    for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
+        builder.addNextEdge();
+        builder.assignProperty(id, ids[i]);
+        builder.assignProperty(magnitude, magnitudes[i]);
+        builder.assignProperty(distance, distances[i]);
+    }
+    return builder.createGraph({ id, magnitude, distance });
+}
+
+function createClashes(structure: Structure, clashes: ValidationReport['clashes']): Clashes {
+    const intraUnit = IntMap.Mutable<IntraUnitClashes>();
+
+    for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
+        const group = structure.unitSymmetryGroups[i];
+        if (!Unit.isAtomic(group.units[0])) continue;
+
+        const intraClashes = createIntraUnitClashes(group.units[0], clashes);
+        for (let j = 0, jl = group.units.length; j < jl; ++j) {
+            intraUnit.set(group.units[j].id, intraClashes);
+        }
+    }
+
+    return {
+        interUnit: createInterUnitClashes(structure, clashes),
+        intraUnit
+    };
+}
+
+export const ClashesProvider: CustomStructureProperty.Provider<{}, Clashes> = CustomStructureProperty.createProvider({
+    label: 'Clashes',
+    descriptor: CustomPropertyDescriptor({
+        name: 'rcsb_clashes',
+        // TODO `cifExport` and `symbol`
+    }),
+    type: 'local',
+    defaultParams: {},
+    getParams: (data: Structure) => ({}),
+    isApplicable: (data: Structure) => true,
+    obtain: async (ctx: CustomProperty.Context, data: Structure) => {
+        await ValidationReportProvider.attach(ctx, data.models[0]);
+        const validationReport = ValidationReportProvider.get(data.models[0]).value!;
+        return {
+            value: createClashes(data, validationReport.clashes)
+        };
+    }
+});
+
+//
+
+function getItem(a: NamedNodeMap, name: string) {
+    const item = a.getNamedItem(name);
+    return item !== null ? item.value : '';
+}
+
+function hasAttr(a: NamedNodeMap, name: string, value: string) {
+    const item = a.getNamedItem(name);
+    return item !== null && item.value === value;
+}
+
+function getMogInfo(a: NamedNodeMap) {
+    return {
+        mean: parseFloat(getItem(a, 'mean')),
+        obs: parseFloat(getItem(a, 'obsval')),
+        stdev: parseFloat(getItem(a, 'stdev')),
+        z: parseFloat(getItem(a, 'Zscore')),
+    };
+}
+
+function getMolInfo(a: NamedNodeMap) {
+    return {
+        mean: parseFloat(getItem(a, 'mean')),
+        obs: parseFloat(getItem(a, 'obs')),
+        stdev: parseFloat(getItem(a, 'stdev')),
+        z: parseInt(getItem(a, 'z')),
+    };
+}
+
+function addIndex(index: number, element: ElementIndex, map: Map<ElementIndex, number[]>) {
+    if (map.has(element)) map.get(element)!.push(index);
+    else map.set(element, [index]);
+}
+
+function ClashesBuilder(elementsCount: number) {
+    const aIndices: ElementIndex[] = [];
+    const bIndices: ElementIndex[] = [];
+    const ids: number[] = [];
+    const magnitudes: number[] = [];
+    const distances: number[] = [];
+
+    const seen = new Map<string, ElementIndex>();
+
+    return {
+        add(element: ElementIndex, id: number, magnitude: number, distance: number, isSymop: boolean) {
+            const hash = `${id}|${isSymop ? 's' : ''}`;
+            const other = seen.get(hash);
+            if (other !== undefined) {
+                aIndices[aIndices.length] = element;
+                bIndices[bIndices.length] = other;
+                ids[ids.length] = id;
+                magnitudes[magnitudes.length] = magnitude;
+                distances[distances.length] = distance;
+            } else {
+                seen.set(hash, element);
+            }
+        },
+        get() {
+            const builder = new IntAdjacencyGraph.EdgeBuilder(elementsCount, aIndices, bIndices);
+            const id = new Int32Array(builder.slotCount);
+            const magnitude = new Float32Array(builder.slotCount);
+            const distance = new Float32Array(builder.slotCount);
+            for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
+                builder.addNextEdge();
+                builder.assignProperty(id, ids[i]);
+                builder.assignProperty(magnitude, magnitudes[i]);
+                builder.assignProperty(distance, distances[i]);
+            }
+            return builder.createGraph({ id, magnitude, distance });
+        }
+    };
+}
+
+function parseValidationReportXml(xml: XMLDocument, model: Model): ValidationReport {
+    const rsrz = new Map<ResidueIndex, number>();
+    const rscc = new Map<ResidueIndex, number>();
+    const rci = new Map<ResidueIndex, number>();
+    const geometryIssues = new Map<ResidueIndex, Set<string>>();
+
+    const bondOutliers = {
+        index: new Map<ElementIndex, number[]>(),
+        data: [] as ValidationReport['bondOutliers']['data']
+    };
+    const angleOutliers = {
+        index: new Map<ElementIndex, number[]>(),
+        data: [] as ValidationReport['angleOutliers']['data']
+    };
+
+    const clashesBuilder = ClashesBuilder(model.atomicHierarchy.atoms._rowCount);
+
+    const { index } = model.atomicHierarchy;
+
+    const entries = xml.getElementsByTagName('Entry');
+    if (entries.length === 1) {
+        const chemicalShiftLists = entries[0].getElementsByTagName('chemical_shift_list');
+        if (chemicalShiftLists.length === 1) {
+            const randomCoilIndices = chemicalShiftLists[0].getElementsByTagName('random_coil_index');
+            for (let j = 0, jl = randomCoilIndices.length; j < jl; ++j) {
+                const { attributes } = randomCoilIndices[j];
+                const value = parseFloat(getItem(attributes, 'value'));
+                const auth_asym_id = getItem(attributes, 'chain');
+                const auth_comp_id = getItem(attributes, 'rescode');
+                const auth_seq_id = parseInt(getItem(attributes, 'resnum'));
+                const rI = index.findResidueAuth({ auth_asym_id, auth_comp_id, auth_seq_id });
+                if (rI !== -1) rci.set(rI, value);
+            }
+        }
+    }
+
+    const groups = xml.getElementsByTagName('ModelledSubgroup');
+    for (let i = 0, il = groups.length; i < il; ++i) {
+        const g = groups[ i ];
+        const ga = g.attributes;
+
+        const pdbx_PDB_model_num = parseInt(getItem(ga, 'model'));
+        if (model.modelNum !== pdbx_PDB_model_num) continue;
+
+        const auth_asym_id = getItem(ga, 'chain');
+        const auth_comp_id = getItem(ga, 'resname');
+        const auth_seq_id = parseInt(getItem(ga, 'resnum'));
+        const pdbx_PDB_ins_code = getItem(ga, 'icode').trim() || undefined;
+        const label_alt_id = getItem(ga, 'altcode').trim() || undefined;
+
+        const rI = index.findResidueAuth({ auth_asym_id, auth_comp_id, auth_seq_id, pdbx_PDB_ins_code });
+
+        // continue if no residue index is found
+        if (rI === -1) continue;
+
+        if (ga.getNamedItem('rsrz') !== null) rsrz.set(rI, parseFloat(getItem(ga, 'rsrz')));
+        if (ga.getNamedItem('rscc') !== null) rscc.set(rI, parseFloat(getItem(ga, 'rscc')));
+
+        const isPolymer = getItem(ga, 'seq') !== '.';
+        const issues = new Set<string>();
+
+        if (isPolymer) {
+            const molBondOutliers = g.getElementsByTagName('bond-outlier');
+            if (molBondOutliers.length) issues.add('bond-outlier');
+
+            for (let j = 0, jl = molBondOutliers.length; j < jl; ++j) {
+                const bo = molBondOutliers[j].attributes;
+                const idx = bondOutliers.data.length;
+                const atomA = index.findAtomOnResidue(rI, getItem(bo, 'atom0'));
+                const atomB = index.findAtomOnResidue(rI, getItem(bo, 'atom1'));
+                addIndex(idx, atomA, bondOutliers.index);
+                addIndex(idx, atomB, bondOutliers.index);
+                bondOutliers.data.push({
+                    tag: 'bond-outlier', atomA, atomB, ...getMolInfo(bo)
+                });
+            }
+
+            const molAngleOutliers = g.getElementsByTagName('angle-outlier');
+            if (molAngleOutliers.length) issues.add('angle-outlier');
+
+            for (let j = 0, jl = molAngleOutliers.length; j < jl; ++j) {
+                const ao = molAngleOutliers[j].attributes;
+                const idx = bondOutliers.data.length;
+                const atomA = index.findAtomOnResidue(rI, getItem(ao, 'atom0'));
+                const atomB = index.findAtomOnResidue(rI, getItem(ao, 'atom1'));
+                const atomC = index.findAtomOnResidue(rI, getItem(ao, 'atom2'));
+                addIndex(idx, atomA, angleOutliers.index);
+                addIndex(idx, atomB, angleOutliers.index);
+                addIndex(idx, atomC, angleOutliers.index);
+                angleOutliers.data.push({
+                    tag: 'angle-outlier', atomA, atomB, atomC, ...getMolInfo(ao)
+                });
+            }
+
+            const planeOutliers = g.getElementsByTagName('plane-outlier');
+            if (planeOutliers.length) issues.add('plane-outlier');
+
+            if (hasAttr(ga, 'rota', 'OUTLIER')) issues.add('rotamer-outlier');
+            if (hasAttr(ga, 'rama', 'OUTLIER')) issues.add('ramachandran-outlier');
+            if (hasAttr(ga, 'RNApucker', 'outlier')) issues.add('RNApucker-outlier');
+        } else {
+            const mogBondOutliers = g.getElementsByTagName('mog-bond-outlier');
+            if (mogBondOutliers.length) issues.add('mog-bond-outlier');
+
+            for (let j = 0, jl = mogBondOutliers.length; j < jl; ++j) {
+                const mbo = mogBondOutliers[j].attributes;
+                const atoms = getItem(mbo, 'atoms').split(',');
+                const idx = bondOutliers.data.length;
+                const atomA = index.findAtomOnResidue(rI, atoms[0]);
+                const atomB = index.findAtomOnResidue(rI, atoms[1]);
+                addIndex(idx, atomA, bondOutliers.index);
+                addIndex(idx, atomB, bondOutliers.index);
+                bondOutliers.data.push({
+                    tag: 'mog-bond-outlier', atomA, atomB, ...getMogInfo(mbo)
+                });
+            }
+
+            const mogAngleOutliers = g.getElementsByTagName('mog-angle-outlier');
+            if (mogAngleOutliers.length) issues.add('mog-angle-outlier');
+
+            for (let j = 0, jl = mogAngleOutliers.length; j < jl; ++j) {
+                const mao = mogAngleOutliers[j].attributes;
+                const atoms = getItem(mao, 'atoms').split(',');
+                const idx = angleOutliers.data.length;
+                const atomA = index.findAtomOnResidue(rI, atoms[0]);
+                const atomB = index.findAtomOnResidue(rI, atoms[1]);
+                const atomC = index.findAtomOnResidue(rI, atoms[2]);
+                addIndex(idx, atomA, angleOutliers.index);
+                addIndex(idx, atomB, angleOutliers.index);
+                addIndex(idx, atomC, angleOutliers.index);
+                angleOutliers.data.push({
+                    tag: 'mog-angle-outlier', atomA, atomB, atomC, ...getMogInfo(mao)
+                });
+            }
+        }
+
+        const clashes = g.getElementsByTagName('clash');
+        if (clashes.length) issues.add('clash');
+
+        for (let j = 0, jl = clashes.length; j < jl; ++j) {
+            const ca = clashes[j].attributes;
+            const id = parseInt(getItem(ca, 'cid'));
+            const magnitude = parseFloat(getItem(ca, 'clashmag'));
+            const distance = parseFloat(getItem(ca, 'dist'));
+            const label_atom_id = getItem(ca, 'atom');
+            const element = index.findAtomOnResidue(rI, label_atom_id, label_alt_id);
+            if (element !== -1) {
+                clashesBuilder.add(element, id, magnitude, distance, false);
+            }
+        }
+
+        const symmClashes = g.getElementsByTagName('symm-clash');
+        if (symmClashes.length) issues.add('symm-clash');
+
+        for (let j = 0, jl = symmClashes.length; j < jl; ++j) {
+            const sca = symmClashes[j].attributes;
+            const id = parseInt(getItem(sca, 'scid'));
+            const magnitude = parseFloat(getItem(sca, 'clashmag'));
+            const distance = parseFloat(getItem(sca, 'dist'));
+            const label_atom_id = getItem(sca, 'atom');
+            const element = index.findAtomOnResidue(rI, label_atom_id, label_alt_id);
+            if (element !== -1) {
+                clashesBuilder.add(element, id, magnitude, distance, true);
+            }
+        }
+
+        geometryIssues.set(rI, issues);
+    }
+
+    const clashes = clashesBuilder.get();
+
+    const validationReport = {
+        rsrz, rscc, rci, geometryIssues,
+        bondOutliers, angleOutliers,
+        clashes
+    };
+
+    return validationReport;
+}

src/extensions/rcsb/validation-report/representation.ts

@@ -0,0 +1,295 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Unit, Structure, StructureElement, Bond } from '../../../mol-model/structure';
+import { Theme, ThemeRegistryContext } from '../../../mol-theme/theme';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { PickingId } from '../../../mol-geo/geometry/picking';
+import { EmptyLoci, Loci, DataLoci } from '../../../mol-model/loci';
+import { Interval } from '../../../mol-data/int';
+import { RepresentationContext, RepresentationParamsGetter, Representation } from '../../../mol-repr/representation';
+import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation } from '../../../mol-repr/structure/representation';
+import { VisualContext } from '../../../mol-repr/visual';
+import { createLinkCylinderMesh, LinkCylinderParams, LinkCylinderStyle } from '../../../mol-repr/structure/visual/util/link';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '../../../mol-repr/structure/units-visual';
+import { VisualUpdateState } from '../../../mol-repr/util';
+import { LocationIterator } from '../../../mol-geo/util/location-iterator';
+import { ClashesProvider, IntraUnitClashes, InterUnitClashes, ValidationReport } from './prop';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { ComplexMeshParams, ComplexVisual, ComplexMeshVisual } from '../../../mol-repr/structure/complex-visual';
+import { Color } from '../../../mol-util/color';
+import { MarkerActions } from '../../../mol-util/marker-action';
+import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { bondLabel } from '../../../mol-theme/label';
+import { getUnitKindsParam } from '../../../mol-repr/structure/params';
+
+//
+
+function createIntraUnitClashCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<IntraUnitClashParams>, mesh?: Mesh) {
+    if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh);
+
+    const clashes = ClashesProvider.get(structure).value!.intraUnit.get(unit.id);
+    const { edgeCount, a, b, edgeProps } = clashes;
+    const { magnitude } = edgeProps;
+    const { sizeFactor } = props;
+
+    if (!edgeCount) return Mesh.createEmpty(mesh);
+
+    const { elements } = unit;
+    const pos = unit.conformation.invariantPosition;
+
+    const builderProps = {
+        linkCount: edgeCount * 2,
+        position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
+            pos(elements[a[edgeIndex]], posA);
+            pos(elements[b[edgeIndex]], posB);
+        },
+        style: (edgeIndex: number) => LinkCylinderStyle.Disk,
+        radius: (edgeIndex: number) => magnitude[edgeIndex] * sizeFactor,
+    };
+
+    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+}
+
+export const IntraUnitClashParams = {
+    ...UnitsMeshParams,
+    ...LinkCylinderParams,
+    linkCap: PD.Boolean(true),
+    sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.01 }),
+};
+export type IntraUnitClashParams = typeof IntraUnitClashParams
+
+export function IntraUnitClashVisual(materialId: number): UnitsVisual<IntraUnitClashParams> {
+    return UnitsMeshVisual<IntraUnitClashParams>({
+        defaultProps: PD.getDefaultValues(IntraUnitClashParams),
+        createGeometry: createIntraUnitClashCylinderMesh,
+        createLocationIterator: createIntraClashIterator,
+        getLoci: getIntraClashLoci,
+        eachLocation: eachIntraClash,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IntraUnitClashParams>, currentProps: PD.Values<IntraUnitClashParams>) => {
+            state.createGeometry = (
+                newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.radialSegments !== currentProps.radialSegments ||
+                newProps.linkScale !== currentProps.linkScale ||
+                newProps.linkSpacing !== currentProps.linkSpacing ||
+                newProps.linkCap !== currentProps.linkCap
+            );
+        }
+    }, materialId);
+}
+
+function getIntraClashBoundingSphere(unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[], boundingSphere: Sphere3D) {
+    return CentroidHelper.fromPairProvider(elements.length, (i, pA, pB) => {
+        unit.conformation.position(unit.elements[clashes.a[elements[i]]], pA);
+        unit.conformation.position(unit.elements[clashes.b[elements[i]]], pB);
+    }, boundingSphere);
+}
+
+function getIntraClashLabel(structure: Structure, unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[]) {
+    const idx = elements[0];
+    if (idx === undefined) return '';
+    const { edgeProps: { id, magnitude, distance } } = clashes;
+    const mag = magnitude[idx].toFixed(2);
+    const dist = distance[idx].toFixed(2);
+
+    return [
+        `Clash id: ${id[idx]} | Magnitude: ${mag} \u212B | Distance: ${dist} \u212B`,
+        bondLabel(Bond.Location(structure, unit, clashes.a[idx], structure, unit, clashes.b[idx]))
+    ].join('</br>');
+}
+
+function IntraClashLoci(structure: Structure, unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[]) {
+    return DataLoci('intra-clashes', { unit, clashes }, elements,
+        (boundingSphere: Sphere3D) =>  getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere),
+        () => getIntraClashLabel(structure, unit, clashes, elements));
+}
+
+function getIntraClashLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number) {
+    const { objectId, instanceId, groupId } = pickingId;
+    if (id === objectId) {
+        const { structure, group } = structureGroup;
+        const unit = group.units[instanceId];
+        if (Unit.isAtomic(unit)) {
+            const clashes = ClashesProvider.get(structure).value!.intraUnit.get(unit.id);
+            return IntraClashLoci(structure, unit, clashes, [groupId]);
+        }
+    }
+    return EmptyLoci;
+}
+
+function eachIntraClash(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+    let changed = false;
+    // TODO
+    return changed;
+}
+
+function createIntraClashIterator(structureGroup: StructureGroup): LocationIterator {
+    const { structure, group } = structureGroup;
+    const unit = group.units[0];
+    const clashes = ClashesProvider.get(structure).value!.intraUnit.get(unit.id);
+    const { a } = clashes;
+    const groupCount = clashes.edgeCount * 2;
+    const instanceCount = group.units.length;
+    const location = StructureElement.Location.create(structure);
+    const getLocation = (groupIndex: number, instanceIndex: number) => {
+        const unit = group.units[instanceIndex];
+        location.unit = unit;
+        location.element = unit.elements[a[groupIndex]];
+        return location;
+    };
+    return LocationIterator(groupCount, instanceCount, getLocation);
+}
+
+//
+
+function createInterUnitClashCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitClashParams>, mesh?: Mesh) {
+    const clashes = ClashesProvider.get(structure).value!.interUnit;
+    const { edges, edgeCount } = clashes;
+    const { sizeFactor } = props;
+
+    if (!edgeCount) return Mesh.createEmpty(mesh);
+
+    const builderProps = {
+        linkCount: edgeCount,
+        position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
+            const b = edges[edgeIndex];
+            const uA = b.unitA, uB = b.unitB;
+            uA.conformation.position(uA.elements[b.indexA], posA);
+            uB.conformation.position(uB.elements[b.indexB], posB);
+        },
+        style: (edgeIndex: number) => LinkCylinderStyle.Disk,
+        radius: (edgeIndex: number) => edges[edgeIndex].props.magnitude * sizeFactor
+    };
+
+    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+}
+
+export const InterUnitClashParams = {
+    ...ComplexMeshParams,
+    ...LinkCylinderParams,
+    linkCap: PD.Boolean(true),
+    sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.01 }),
+};
+export type InterUnitClashParams = typeof InterUnitClashParams
+
+export function InterUnitClashVisual(materialId: number): ComplexVisual<InterUnitClashParams> {
+    return ComplexMeshVisual<InterUnitClashParams>({
+        defaultProps: PD.getDefaultValues(InterUnitClashParams),
+        createGeometry: createInterUnitClashCylinderMesh,
+        createLocationIterator: createInterClashIterator,
+        getLoci: getInterClashLoci,
+        eachLocation: eachInterClash,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitClashParams>, currentProps: PD.Values<InterUnitClashParams>) => {
+            state.createGeometry = (
+                newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.radialSegments !== currentProps.radialSegments ||
+                newProps.linkScale !== currentProps.linkScale ||
+                newProps.linkSpacing !== currentProps.linkSpacing ||
+                newProps.linkCap !== currentProps.linkCap
+            );
+        }
+    }, materialId);
+}
+
+function getInterClashBoundingSphere(clashes: InterUnitClashes, elements: number[], boundingSphere: Sphere3D) {
+    return CentroidHelper.fromPairProvider(elements.length, (i, pA, pB) => {
+        const c = clashes.edges[elements[i]];
+        c.unitA.conformation.position(c.unitA.elements[c.indexA], pA);
+        c.unitB.conformation.position(c.unitB.elements[c.indexB], pB);
+    }, boundingSphere);
+}
+
+function getInterClashLabel(structure: Structure, clashes: InterUnitClashes, elements: number[]) {
+    const idx = elements[0];
+    if (idx === undefined) return '';
+    const c = clashes.edges[idx];
+    const mag = c.props.magnitude.toFixed(2);
+    const dist = c.props.distance.toFixed(2);
+
+    return [
+        `Clash id: ${c.props.id} | Magnitude: ${mag} \u212B | Distance: ${dist} \u212B`,
+        bondLabel(Bond.Location(structure, c.unitA, c.indexA, structure, c.unitB, c.indexB))
+    ].join('</br>');
+}
+
+function InterClashLoci(structure: Structure, clashes: InterUnitClashes, elements: number[]) {
+    return DataLoci('inter-clashes', clashes, elements,
+        (boundingSphere: Sphere3D) =>  getInterClashBoundingSphere(clashes, elements, boundingSphere),
+        () => getInterClashLabel(structure, clashes, elements));
+}
+
+function getInterClashLoci(pickingId: PickingId, structure: Structure, id: number) {
+    const { objectId, groupId } = pickingId;
+    if (id === objectId) {
+        const clashes = ClashesProvider.get(structure).value!.interUnit;
+        return InterClashLoci(structure, clashes, [groupId]);
+    }
+    return EmptyLoci;
+}
+
+function eachInterClash(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+    let changed = false;
+    // TODO
+    return changed;
+}
+
+function createInterClashIterator(structure: Structure): LocationIterator {
+    const clashes = ClashesProvider.get(structure).value!.interUnit;
+    const groupCount = clashes.edgeCount;
+    const instanceCount = 1;
+    const location = StructureElement.Location.create(structure);
+    const getLocation = (groupIndex: number) => {
+        const clash = clashes.edges[groupIndex];
+        location.unit = clash.unitA;
+        location.element = clash.unitA.elements[clash.indexA];
+        return location;
+    };
+    return LocationIterator(groupCount, instanceCount, getLocation, true);
+}
+
+//
+
+const ClashesVisuals = {
+    'intra-clash': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, IntraUnitClashParams>) => UnitsRepresentation('Intra-unit clash cylinder', ctx, getParams, IntraUnitClashVisual),
+    'inter-clash': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, InterUnitClashParams>) => ComplexRepresentation('Inter-unit clash cylinder', ctx, getParams, InterUnitClashVisual),
+};
+
+export const ClashesParams = {
+    ...IntraUnitClashParams,
+    ...InterUnitClashParams,
+    unitKinds: getUnitKindsParam(['atomic']),
+    visuals: PD.MultiSelect(['intra-clash', 'inter-clash'], PD.objectToOptions(ClashesVisuals))
+};
+export type ClashesParams = typeof ClashesParams
+export function getClashesParams(ctx: ThemeRegistryContext, structure: Structure) {
+    return PD.clone(ClashesParams);
+}
+
+export type ClashesRepresentation = StructureRepresentation<ClashesParams>
+export function ClashesRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ClashesParams>): ClashesRepresentation {
+    const repr = Representation.createMulti('Clashes', ctx, getParams, StructureRepresentationStateBuilder, ClashesVisuals as unknown as Representation.Def<Structure, ClashesParams>);
+    repr.setState({ markerActions: MarkerActions.Highlighting });
+    return repr;
+}
+
+export const ClashesRepresentationProvider = StructureRepresentationProvider({
+    name: ValidationReport.Tag.Clashes,
+    label: 'Validation Clashes',
+    description: 'Displays clashes between atoms as disks. Data from wwPDB Validation Report, obtained via RCSB PDB.',
+    factory: ClashesRepresentation,
+    getParams: getClashesParams,
+    defaultValues: PD.getDefaultValues(ClashesParams),
+    defaultColorTheme: { name: 'uniform', props: { value: Color(0xFA28FF) } },
+    defaultSizeTheme: { name: 'physical' },
+    isApplicable: (structure: Structure) => structure.elementCount > 0,
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, structure: Structure) => ClashesProvider.attach(ctx, structure, void 0, true),
+        detach: (data) => ClashesProvider.ref(data, false)
+    }
+});