0.4.5

.eslintignore

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

.eslintrc.json

@@ -1,96 +0,0 @@
-{
-    "env": {
-        "browser": true,
-        "node": true
-    },
-    "parserOptions": {
-        "ecmaVersion": 2018,
-        "sourceType": "module",
-        "ecmaFeatures": {
-            "impliedStrict": true
-        }
-    },
-    "rules": {
-        "indent": "off",
-        "arrow-parens": [
-            "off",
-            "as-needed"
-        ],
-        "brace-style": "off",
-        "comma-spacing": "off",
-        "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",
-        "no-restricted-syntax": [
-            "error",
-            {
-                "selector": "ExportDefaultDeclaration",
-                "message": "Default exports are not allowed"
-            }
-        ]
-    },
-    "overrides": [
-        {
-            "files": ["**/*.ts", "**/*.tsx"],
-            "parser": "@typescript-eslint/parser",
-            "parserOptions": {
-                "project": ["tsconfig.json", "tsconfig.commonjs.json"],
-                "sourceType": "module"
-            },
-            "plugins": [
-                "@typescript-eslint"
-            ],
-            "rules": {
-                "@typescript-eslint/ban-types": "off",
-                "@typescript-eslint/class-name-casing": "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",
-                "@typescript-eslint/brace-style": [
-                    "error",
-                    "1tbs", { "allowSingleLine": true }
-                ],
-                "@typescript-eslint/comma-spacing": "error"
-            }
-        }
-    ]
-}

.github/workflows/lint.yml

@@ -1,18 +0,0 @@
-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

.gitignore

@@ -5,7 +5,6 @@ node_modules/
 debug.log
 npm-debug.log
 tsconfig.tsbuildinfo
-tsconfig.commonjs.tsbuildinfo
 
 *.sublime-workspace
 .idea

.npmignore

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

.travis.yml

@@ -14,5 +14,6 @@ before_install:
 node_js:
   - "12"
   - "10"
+  - "8"
 before_script:
   - export DISPLAY=:99.0; sh -e /etc/init.d/xvfb start

.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

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

.vscode/tasks.json

@@ -9,20 +9,6 @@
             "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 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.
+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.
 
 This particular project is the implementation of this technology (still under development).
 
@@ -16,32 +16,29 @@ 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 scripting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).
+- `mol-script` A scriting 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 building UIs.
+- `mol-app` Components for builduing 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 implementation of `servers`, including
+Moreover, the project contains the imlementation 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 `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+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).
 
 ## Previous Work
 This project builds on experience from previous solutions:
@@ -62,8 +59,6 @@ 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
 
@@ -89,29 +84,20 @@ and navigate to `build/viewer`
 
 ### Code generation
 **CIF schemas**
+Install CIFTools `npm install ciftools -g`
 
-    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
-    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
-    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
-    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
-
-**Lipid names**
-
-    node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
-
-**Ion names**
-
-    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
-
+    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
 
 **GraphQL schemas**
 
-    node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
+    node data/rcsb-graphql/codegen.js
 
 ### Other scripts
 **Create chem comp bond table**
 
-    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
+    export NODE_PATH="lib"; node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
 
 **Test model server**
 
@@ -123,26 +109,22 @@ and navigate to `build/viewer`
 
 **Convert any CIF to BinaryCIF**
 
-    node lib/servers/model/preprocess -i file.cif -ob file.bcif
+    node build/model-server/preprocess -i file.cif -ob file.bcif
 
-To see all available commands, use ``node lib/servers/model/preprocess -h``.
-
-Or
-
-    node lib/commonjs/cli/cif2bcif
+To see all available commands, use ``node build/model-server/preprocess -h``.
 
 ## Development
 
-### Installation
+### Intallation
 
-If node complains about a missing acorn peer dependency, run the following commands
+If node complains about a missine 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 extensions 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 extanesions are installed in the editor.
 
     "files.associations": {
         "*.glsl.ts": "glsl",
@@ -154,7 +136,7 @@ To get syntax highlighting for shader and graphql files add the following to Vis
 ## Publish
 
 ### Prerelease
-    npm version prerelease # assumes the current version ends with '-dev.X'
+    npm version prerelease # asumes the current version ends with '-dev.X'
     npm publish --tag next
 
 ### Release
@@ -176,5 +158,4 @@ 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/)
-* [EntosAI](https://www.entos.ai) (``alpha-orbitals`` extension)
+* [CEITEC](https://www.ceitec.eu/)

data/cif-core.csv

@@ -1,12 +1,6 @@
 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
@@ -25,7 +19,6 @@ 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
@@ -49,28 +42,19 @@ 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
+geom_bond.publ_flag

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

@@ -1,88 +0,0 @@
-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

@@ -1,60 +0,0 @@
-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/mmcif-field-names.csv

@@ -1,805 +0,0 @@
-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

@@ -1,76 +0,0 @@
-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

@@ -0,0 +1,22 @@
+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

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

data/rcsb-graphql/loader.js

@@ -0,0 +1,14 @@
+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/interesting-pdb-entries.md

@@ -1,28 +0,0 @@
-* Cyclic polymers (1sfi, 6dny, 1HVZ)
-* B-DNA (1bna)
-* Missing carbonyl oxygen (1gfl)
-* Mono-saccharides with alt locs (1B5F)
-* Microheterogeneity
-    * Protein (1EJG, 3NIR)
-    * DNA (3VOK)
-* PNA: peptide nucleic acid (5eme, 1xj9)
-* Peptide derived residues
-    * GFP chromophores (5Z6Y)
-* Nucleotides that don’t have a parent base set, i.e. detect purine/pyrimidine from geometry (THX in 1AUL, OMC in e.g. 5D3G)
-* Bases with modified ring atoms
-    * DZ has C1 instead of N1 (e.g. 6I4N)
-    * DP has N5 instead of C5 and C7 instead of N7 (e.g. 6I4N)
-* Beta & Gamma peptides (e.g. 1GAC, 6PQF)
-* Mixed (heterogeneous) all-atom/trace-only RNA model (1JGQ)
-* Polymers with residues with missing trace atoms (e.g. 2QFJ)
-* Modified RNA bases (1y26, 5L4O)
-* Discontinuous chains, i.e. gaps in the sequence (3sn6)
-* Lots of sheets (1cbs)
-* DNA (2np2, 1d66)
-* C-alpha only (2rcj)
-* Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible (6SW3)
-* Close backbone atoms but not linked (e.g. 4HIV)
-* Non-standard residues
-    * Protein (1BRR, 5Z6Y)
-    * DNA (5D3G)
-* Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)

docs/model-server/readme.md

@@ -6,64 +6,133 @@ Model Server is a tool for preprocessing and querying macromolecular structure d
 Installing and Running
 =====================
 
-Requires nodejs 8+.
-
-## From GitHub
-
+Getting the code (use node 8+):
 ```
 git clone https://github.com/molstar/molstar
 npm install
 ```
 
-Afterwards, build the project source:
+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:
 
 ```
-npm run build-tsc
+npm run build
 ```
 
-and run the server by 
+(or run watch mode for automatic rebuilds: ``npm run watch``)
 
+Running the server locally for testing:
 ```
-node lib/commonjs/servers/model/server/server
+npm run model-server
+```
+or
+```
+node build/node_modules/servers/model/server
 ```
 
-## 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``
+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).
 
 
-### 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
+## 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. ``node lib/commonjs/servers/model/preprocess`` or ``model-server-preprocess`` binary from the NPM package.
+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.
 
+## Usage
 
-## Local Mode
+The app works in two modes: single files and folders.
 
-The server can be run in local/file based mode using ``node lib/commonjs/servers/model/query`` (``model-server-query`` binary from the NPM package).
+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"
+                }
+            }
+        }
+    }
+}
+```
 
 Custom Properties
 =================
 
-This feature is still in development.
+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``.
 
-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``.
+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" }
+    }
+  }
+]
+```

docs/volume-server/README.md

@@ -7,64 +7,107 @@ 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 and Running
+Installing the Server 
 =====================
 
-Requires nodejs 8+.
+- 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.
 
-## 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/commonjs/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
+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 (``node lib/commonjs/servers/volume/pack`` or ``volume-server-pack`` binary from the NPM package).
+To achieve this, use the ``pack`` application.
 
-## Local Mode
+- To prepare data from x-ray based methods, use: 
 
-The program  ``lib/commonjs/servers/volume/pack`` (``volume-server-query`` in NPM package) can be used to query the data without running a http server.
+    ```
+    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'
+    }]
+    ```
 
 ## Navigating the Source Code
 
@@ -79,8 +122,8 @@ 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 library](https://github.com/molstar/ciftools) (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.js library](https://github.com/dsehnal/CIFTools.js) (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 is available in Mol* ``mol-plugin`` module.
+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*.

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.2",
+  "version": "0.4.5",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -11,47 +11,27 @@
     "url": "https://github.com/molstar/molstar/issues"
   },
   "scripts": {
-    "lint": "eslint .",
-    "lint-fix": "eslint . --fix",
+    "lint": "tslint src/**/*.ts",
     "test": "npm run lint && jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
-    "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
-    "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.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.commonjs.json --watch --incremental",
-    "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
+    "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",
     "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 -g",
-    "model-server": "node lib/commonjs/servers/model/server.js",
-    "model-server-watch": "nodemon --watch lib lib/commonjs/servers/model/server.js",
-    "volume-server-test": "node lib/commonjs/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
-    "plugin-state": "node lib/commonjs/servers/plugin-state/index.js --working-folder ./build/state --port 1339",
+    "serve": "http-server -p 1338",
+    "model-server": "node lib/servers/model/server.js",
+    "model-server-watch": "nodemon --watch lib lib/servers/model/server.js",
+    "volume-server": "node lib/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort  1336",
     "preversion": "npm run test",
-    "version": "npm run build",
-    "postversion": "git push && git push --tags"
+    "postversion": "git push && git push --tags",
+    "prepublishOnly": "npm run test && npm run build"
   },
   "files": [
-    "lib/",
-    "build/viewer/"
+    "lib/"
   ],
-  "bin": {
-    "cif2bcif": "lib/commonjs/cli/cif2bcif/index.js",
-    "cifschema": "lib/commonjs/cli/cifschema/index.js",
-    "model-server": "lib/commonjs/servers/model/server.js",
-    "model-server-query": "lib/commonjs/servers/model/query.js",
-    "model-server-preprocess": "lib/commonjs/servers/model/preprocess.js",
-    "volume-server": "lib/commonjs/servers/volume/server.js",
-    "volume-server-query": "lib/commonjs/servers/volume/query.js",
-    "volume-server-pack": "lib/commonjs/servers/volume/pack.js"
-  },
   "nodemonConfig": {
     "ignoreRoot": [
       "./node_modules",
@@ -79,73 +59,59 @@
   "contributors": [
     "Alexander Rose <alexander.rose@weirdbyte.de>",
     "David Sehnal <david.sehnal@gmail.com>",
-    "Sebastian Bittrich <sebastian.bittrich@rcsb.org>",
-    "Áron Samuel Kovács <aron.kovacs@mail.muni.cz>",
-    "Ludovic Autin <autin@scripps.edu>",
-    "Michal Malý <michal.maly@ibt.cas.cz>",
-    "Jiří Černý <jiri.cerny@ibt.cas.cz>"
+    "Sebastian Bittrich <sebastian.bittrich@rcsb.org>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^2.0.2",
-    "@graphql-codegen/cli": "^1.19.4",
-    "@graphql-codegen/time": "^2.0.2",
-    "@graphql-codegen/typescript": "^1.19.0",
-    "@graphql-codegen/typescript-graphql-files-modules": "^1.18.1",
-    "@graphql-codegen/typescript-graphql-request": "^2.0.3",
-    "@graphql-codegen/typescript-operations": "^1.17.12",
-    "@types/cors": "^2.8.8",
-    "@typescript-eslint/eslint-plugin": "^4.9.1",
-    "@typescript-eslint/parser": "^4.9.1",
     "benchmark": "^2.1.4",
-    "concurrently": "^5.3.0",
-    "cpx2": "^3.0.0",
-    "css-loader": "^5.0.1",
-    "eslint": "^7.15.0",
+    "circular-dependency-plugin": "^5.2.0",
+    "concurrently": "^5.0.0",
+    "cpx": "^1.5.0",
+    "css-loader": "^3.2.0",
     "extra-watch-webpack-plugin": "^1.0.3",
-    "file-loader": "^6.2.0",
-    "fs-extra": "^9.0.1",
-    "graphql": "^15.4.0",
-    "http-server": "^0.12.3",
-    "jest": "^26.6.3",
-    "mini-css-extract-plugin": "^1.3.2",
-    "node-sass": "^5.0.0",
-    "raw-loader": "^4.0.2",
-    "sass-loader": "^10.1.0",
-    "simple-git": "^2.25.0",
-    "style-loader": "^2.0.0",
-    "ts-jest": "^26.4.4",
-    "typescript": "^4.1.2",
-    "webpack": "^4.44.1",
-    "webpack-cli": "^3.3.12",
-    "webpack-version-file-plugin": "^0.4.0"
+    "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": "^4.13.0",
+    "raw-loader": "^3.1.0",
+    "resolve-url-loader": "^3.1.1",
+    "sass-loader": "^8.0.0",
+    "simple-git": "^1.126.0",
+    "style-loader": "^1.0.0",
+    "ts-jest": "^24.1.0",
+    "tslint": "^5.20.1",
+    "typescript": "^3.7.2",
+    "webpack": "^4.41.2",
+    "webpack-cli": "^3.3.10"
   },
   "dependencies": {
-    "@types/argparse": "^1.0.38",
-    "@types/benchmark": "^2.1.0",
-    "@types/compression": "1.7.0",
-    "@types/express": "^4.17.9",
-    "@types/jest": "^26.0.18",
-    "@types/node": "^14.14.11",
-    "@types/node-fetch": "^2.5.7",
-    "@types/react": "^17.0.0",
-    "@types/react-dom": "^17.0.0",
-    "@types/swagger-ui-dist": "3.30.0",
+    "@types/argparse": "^1.0.36",
+    "@types/benchmark": "^1.0.31",
+    "@types/compression": "1.0.1",
+    "@types/express": "^4.17.2",
+    "@types/jest": "^24.0.23",
+    "@types/node": "^12.12.9",
+    "@types/node-fetch": "^2.5.3",
+    "@types/react": "^16.9.11",
+    "@types/react-dom": "^16.9.4",
+    "@types/swagger-ui-dist": "3.0.3",
     "argparse": "^1.0.10",
-    "body-parser": "^1.19.0",
     "compression": "^1.7.4",
-    "cors": "^2.8.5",
     "express": "^4.17.1",
-    "h264-mp4-encoder": "^1.0.12",
-    "immer": "^8.0.0",
+    "graphql": "^14.5.8",
     "immutable": "^3.8.2",
-    "node-fetch": "^2.6.1",
-    "react": "^17.0.1",
-    "react-dom": "^17.0.1",
-    "rxjs": "^6.6.3",
-    "swagger-ui-dist": "^3.37.2",
-    "tslib": "^2.0.3",
-    "util.promisify": "^1.0.1",
+    "node-fetch": "^2.6.0",
+    "react": "^16.12.0",
+    "react-dom": "^16.12.0",
+    "rxjs": "^6.5.3",
+    "swagger-ui-dist": "^3.24.3",
+    "util.promisify": "^1.0.0",
     "xhr2": "^0.2.0"
   }
 }

scripts/deploy.js

@@ -4,40 +4,40 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-const git = require('simple-git');
-const path = require('path');
-const fs = require("fs");
-const fse = require("fs-extra");
+const git = require('simple-git')
+const path = require('path')
+const fs = require("fs")
+const fse = require("fs-extra")
 
-const remoteUrl = "https://github.com/molstar/molstar.github.io.git";
-const buildDir = path.resolve(__dirname, '../build/');
-const deployDir = path.resolve(buildDir, 'deploy/');
-const localPath = path.resolve(deployDir, 'molstar.github.io/');
+const remoteUrl = "https://github.com/molstar/molstar.github.io.git"
+const buildDir = path.resolve(__dirname, '../build/')
+const deployDir = path.resolve(buildDir, 'deploy/')
+const localPath = path.resolve(deployDir, 'molstar.github.io/')
 
 function log(command, stdout, stderr) {
     if (command) {
-        console.log('\n###', command);
-        stdout.pipe(process.stdout);
-        stderr.pipe(process.stderr);
+        console.log('\n###', command)
+        stdout.pipe(process.stdout)
+        stderr.pipe(process.stderr)
     }
 }
 
 function copyViewer() {
-    console.log('\n###', 'copy viewer files');
-    const viewerBuildPath = path.resolve(buildDir, '../build/viewer/');
-    const viewerDeployPath = path.resolve(localPath, 'viewer/');
-    fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true });
+    console.log('\n###', 'copy viewer files')
+    const viewerBuildPath = path.resolve(buildDir, '../build/viewer/')
+    const viewerDeployPath = path.resolve(localPath, 'viewer/')
+    fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true })
 }
 
 if (!fs.existsSync(localPath)) {
-    console.log('\n###', 'create localPath');
-    fs.mkdirSync(localPath, { recursive: true });
+    console.log('\n###', 'create localPath')
+    fs.mkdirSync(localPath, { recursive: true })
 }
 
 process.chdir(localPath);
 
 if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
-    console.log('\n###', 'clone repository');
+    console.log('\n###', 'clone repository')
     git()
         .outputHandler(log)
         .clone(remoteUrl, localPath)
@@ -45,9 +45,9 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .exec(copyViewer)
         .add(['-A'])
         .commit('updated viewer')
-        .push();
+        .push()
 } else {
-    console.log('\n###', 'update repository');
+    console.log('\n###', 'update repository')
     git()
         .outputHandler(log)
         .fetch(['--all'])
@@ -55,5 +55,5 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .exec(copyViewer)
         .add(['-A'])
         .commit('updated viewer')
-        .push();
+        .push()
 }

src/apps/basic-wrapper/coloring.ts

@@ -1,8 +1,7 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 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 { CustomElementProperty } from '../../mol-model-props/common/custom-element-property';
@@ -10,21 +9,22 @@ import { Model, ElementIndex } from '../../mol-model/structure';
 import { Color } from '../../mol-util/color';
 
 export const StripedResidues = CustomElementProperty.create<number>({
-    label: 'Residue Stripes',
+    isStatic: true,
     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 { value: map };
+        return map;
     },
     coloring: {
-        getColor(e) { return e === 0 ? Color(0xff0000) : Color(0x0000ff); },
+        getColor(e) { return e === 0 ? Color(0xff0000) : Color(0x0000ff) },
         defaultColor: Color(0x777777)
     },
-    getLabel(e) {
-        return e === 0 ? 'Odd stripe' : 'Even stripe';
+    format(e) {
+        return e === 0 ? 'Odd stripe' : 'Even stripe'
     }
-});
+})

src/apps/basic-wrapper/controls.tsx

@@ -0,0 +1,30 @@
+/**
+ * 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

@@ -0,0 +1,94 @@
+/**
+ * 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.html

@@ -41,7 +41,7 @@
                 display: block;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
+        <link rel="stylesheet" type="text/css" href="app.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='mmcif' selected>mmCIF</option>
+                <option value='cif' selected>CIF</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 = 'mmcif';
-
+            var format = 'cif';
+            
             $('url').value = url;
             $('url').onchange = function (e) { url = e.target.value; }
             $('assemblyId').value = assemblyId;
@@ -69,8 +69,15 @@
             $('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 }));
@@ -79,14 +86,14 @@
 
             addHeader('Camera');
             addControl('Toggle Spin', () => BasicMolStarWrapper.toggleSpin());
-
+            
             addSeparator();
 
             addHeader('Animation');
 
             // adjust this number to make the animation faster or slower
             // requires to "restart" the animation if changed
-            BasicMolStarWrapper.animate.modelIndex.targetFps = 30;
+            BasicMolStarWrapper.animate.modelIndex.maxFPS = 30;
 
             addControl('Play To End', () => BasicMolStarWrapper.animate.modelIndex.onceForward());
             addControl('Play To Start', () => BasicMolStarWrapper.animate.modelIndex.onceBackward());
@@ -97,7 +104,6 @@
             addHeader('Misc');
 
             addControl('Apply Stripes', () => BasicMolStarWrapper.coloring.applyStripes());
-            addControl('Default Coloring', () => BasicMolStarWrapper.coloring.applyDefault());
 
             addHeader('Interactivity');
             addControl('Highlight seq_id=7', () => BasicMolStarWrapper.interactivity.highlightOn());
@@ -108,7 +114,7 @@
             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/apps/basic-wrapper/index.ts

@@ -0,0 +1,201 @@
+/**
+ * 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, PluginStateObject } 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 { StaticSuperpositionTestData, buildStaticSuperposition, dynamicSuperpositionTest } from './superposition';
+import { PDBeStructureQualityReport } from '../../mol-plugin/behavior/dynamic/custom-props';
+import { CustomToastMessage } from './controls';
+import { EmptyLoci } from '../../mol-model/loci';
+import { StructureSelection } from '../../mol-model/structure';
+import { Script } from '../../mol-script/script';
+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' }, { ref: 'seq' })
+            .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 });
+        }
+    }
+
+    interactivity = {
+        highlightOn: () => {
+            const seq_id = 7;
+            const data = (this.plugin.state.dataState.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.interactivity.lociHighlights.highlightOnly({ loci });
+        },
+        clearHighlight: () => {
+            this.plugin.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci });
+        }
+    }
+
+    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

@@ -0,0 +1,108 @@
+/**
+ * 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.toLociWithCurrentUnits(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

@@ -0,0 +1,252 @@
+/**
+ * Copyright (c) 2018-2019 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 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 { 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)
+        if (!fs.existsSync(DATA_DIR)) {
+            fs.mkdirSync(DATA_DIR);
+        }
+        if (url.endsWith('.gz')) {
+            await writeFile(path, zlib.gunzipSync(await data.buffer()))
+        } else {
+            await writeFile(path, await data.text())
+        }
+        console.log(`done downloading ${url}`)
+    }
+}
+
+export async function ensureDataAvailable() {
+    await ensureAvailable(CCD_PATH, CCD_URL)
+    await ensureAvailable(PVCD_PATH, PVCD_URL)
+}
+
+export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
+    const parsed = await parseCif(await readFile(path, 'utf8'))
+    return CIF.toDatabaseCollection(schema, parsed.result)
+}
+
+export async function readCCD() {
+    return readFileAsCollection(CCD_PATH, CCD_Schema)
+}
+
+export async function readPVCD() {
+    return readFileAsCollection(PVCD_PATH, CCD_Schema)
+}
+
+async function parseCif(data: string | Uint8Array) {
+    const comp = CIF.parse(data);
+    console.time('parse cif');
+    const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
+    console.timeEnd('parse cif');
+    if (parsed.isError) throw parsed;
+    return parsed
+}
+
+export function getEncodedCif(name: string, database: Database<Database.Schema>, binary = false) {
+    const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
+    CifWriter.Encoder.writeDatabase(encoder, name, database)
+    return encoder.getData();
+}
+
+type CCB = Table<CCD_Schema['chem_comp_bond']>
+type CCA = Table<CCD_Schema['chem_comp_atom']>
+
+function ccbKey(compId: string, atomId1: string, atomId2: string) {
+    return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`
+}
+
+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)))
+    }
+    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))
+    }
+    return set
+}
+
+function checkAddingBondsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
+    const ccbSetByParent = DefaultMap<string, Set<string>>(() => new Set())
+
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_bond } = pvcd[k]
+        if (chem_comp_bond._rowCount) {
+            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)
+            } 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)
+                }
+            }
+        }
+    }
+
+    for (const k in pvcd) {
+        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)
+            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)
+                    extraBonds.forEach(bk => {
+                        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}`)
+                        }
+                    })
+                }
+            }
+        }
+    }
+}
+
+async function createBonds() {
+    await ensureDataAvailable()
+    const ccd = await readCCD()
+    const pvcd = await readPVCD()
+
+    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[] = []
+
+    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)
+            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)
+            }
+        }
+    }
+
+    // check adding bonds from PVCD
+    checkAddingBondsFromPVCD(pvcd)
+
+    // add bonds from PVCD
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_bond } = pvcd[k]
+        if (chem_comp_bond._rowCount) {
+            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)
+            } else {
+                for (let i = 0, il = parentIds.length; i < il; ++i) {
+                    addBonds(parentIds[i], chem_comp_bond, true)
+                }
+            }
+        }
+    }
+
+    // add bonds from CCD
+    for (const k in ccd) {
+        const { chem_comp, chem_comp_bond } = ccd[k]
+        if (chem_comp_bond._rowCount) {
+            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
+}
+
+async function run(out: string, binary = false) {
+    const bonds = await createBonds()
+
+    const cif = getEncodedCif(TABLE_NAME, bonds, binary)
+    if (!fs.existsSync(path.dirname(out))) {
+        fs.mkdirSync(path.dirname(out));
+    }
+    writeFile(out, cif)
+}
+
+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 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.'
+});
+parser.addArgument('out', {
+    help: 'Generated file output path.'
+});
+parser.addArgument([ '--forceDownload', '-f' ], {
+    action: 'storeTrue',
+    help: 'Force download of CCD and PVCD.'
+});
+parser.addArgument([ '--binary', '-b' ], {
+    action: 'storeTrue',
+    help: 'Output as BinaryCIF.'
+});
+interface Args {
+    out: string
+    forceDownload?: boolean
+    binary?: boolean
+}
+const args: Args = parser.parseArgs();
+
+const FORCE_DOWNLOAD = args.forceDownload
+
+run(args.out, args.binary)

src/apps/demos/lighting/index.html

@@ -38,16 +38,16 @@
                 display: block;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
+        <link rel="stylesheet" type="text/css" href="app.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/apps/demos/lighting/index.ts

@@ -0,0 +1,166 @@
+/**
+ * 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/docking-viewer/index.html

@@ -1,37 +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* Docking 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 DockingViewer('app', [0x33DD22, 0x1133EE], true);
-
-            function getParam(name, regex) {
-                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
-                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-            }
-            var pdbqt = getParam('pdbqt', '[^&]+').trim();
-            var mol2 = getParam('mol2', '[^&]+').trim();
-
-            viewer.loadStructuresFromUrlsAndMerge([
-                { url: pdbqt, format: 'pdbqt' },
-                { url: mol2, format: 'mol2' }
-            ]);
-        </script>
-    </body>
-</html>

src/apps/docking-viewer/index.ts

@@ -1,213 +0,0 @@
-/**
- * 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 } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
-import './index.html';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { PluginConfig } from '../../mol-plugin/config';
-import { ObjectKeys } from '../../mol-util/type-helpers';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { Structure } from '../../mol-model/structure';
-import { PluginStateTransform, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Task } from '../../mol-task';
-import { StateObject } from '../../mol-state';
-import { ViewportComponent, StructurePreset, ShowButtons } from './viewport';
-import { PluginBehaviors } from '../../mol-plugin/behavior';
-import { ColorNames } from '../../mol-util/color/names';
-import { Color } from '../../mol-util/color';
-
-require('mol-plugin-ui/skin/light.scss');
-
-export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setProductionMode, setDebugMode } from '../../mol-util/debug';
-
-const DefaultViewerOptions = {
-    extensions: ObjectKeys({}),
-    layoutIsExpanded: true,
-    layoutShowControls: true,
-    layoutShowRemoteState: true,
-    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
-    layoutShowSequence: true,
-    layoutShowLog: true,
-    layoutShowLeftPanel: true,
-
-    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
-    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
-    viewportShowSettings: PluginConfig.Viewport.ShowSettings.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,
-};
-
-class Viewer {
-    plugin: PluginContext
-
-    constructor(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
-        const o = { ...DefaultViewerOptions, ...{
-            layoutIsExpanded: false,
-            layoutShowControls: false,
-            layoutShowRemoteState: false,
-            layoutShowSequence: true,
-            layoutShowLog: false,
-            layoutShowLeftPanel: true,
-
-            viewportShowExpand: true,
-            viewportShowControls: false,
-            viewportShowSettings: false,
-            viewportShowSelectionMode: false,
-            viewportShowAnimation: false,
-        } };
-        const defaultSpec = DefaultPluginSpec();
-
-        const spec: PluginSpec = {
-            actions: [...defaultSpec.actions],
-            behaviors: [
-                PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci, { mark: false }),
-                PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
-                PluginSpec.Behavior(PluginBehaviors.Camera.FocusLoci),
-
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.StructureInfo),
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
-            ],
-            animations: [...defaultSpec.animations || []],
-            customParamEditors: defaultSpec.customParamEditors,
-            layout: {
-                initial: {
-                    isExpanded: o.layoutIsExpanded,
-                    showControls: o.layoutShowControls,
-                    controlsDisplay: o.layoutControlsDisplay,
-                },
-                controls: {
-                    ...defaultSpec.layout && defaultSpec.layout.controls,
-                    top: o.layoutShowSequence ? undefined : 'none',
-                    bottom: o.layoutShowLog ? undefined : 'none',
-                    left: o.layoutShowLeftPanel ? undefined : 'none',
-                }
-            },
-            components: {
-                ...defaultSpec.components,
-                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
-                viewport: {
-                    view: ViewportComponent
-                }
-            },
-            config: [
-                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
-                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
-                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
-                [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],
-                [ShowButtons, showButtons]
-            ]
-        };
-
-        const element = typeof elementOrId === 'string'
-            ? document.getElementById(elementOrId)
-            : elementOrId;
-        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
-        this.plugin = createPlugin(element, spec);
-
-        (this.plugin.customState as any) = {
-            colorPalette: {
-                name: 'colors',
-                params: { list: { colors } }
-            }
-        };
-
-        this.plugin.behaviors.canvas3d.initialized.subscribe(v => {
-            if (v) {
-                PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
-                    renderer: {
-                        ...this.plugin.canvas3d!.props.renderer,
-                        backgroundColor: ColorNames.white,
-                    },
-                    camera: {
-                        ...this.plugin.canvas3d!.props.camera,
-                        helper: { axes: { name: 'off', params: {} } }
-                    }
-                } });
-            }
-        });
-    }
-
-    async loadStructuresFromUrlsAndMerge(sources: { url: string, format: BuiltInTrajectoryFormat, isBinary?: boolean }[]) {
-        const structures: { ref: string }[] = [];
-        for (const { url, format, isBinary } of sources) {
-            const data = await this.plugin.builders.data.download({ url, isBinary });
-            const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
-            const model = await this.plugin.builders.structure.createModel(trajectory);
-            const modelProperties = await this.plugin.builders.structure.insertModelProperties(model);
-            const structure = await this.plugin.builders.structure.createStructure(modelProperties || model);
-            const structureProperties = await this.plugin.builders.structure.insertStructureProperties(structure);
-
-            structures.push({ ref: structureProperties?.ref || structure.ref });
-        }
-
-        // remove current structuresfrom hierarchy as they will be merged
-        // TODO only works with using loadStructuresFromUrlsAndMerge once
-        //      need some more API metho to work with the hierarchy
-        this.plugin.managers.structure.hierarchy.updateCurrent(this.plugin.managers.structure.hierarchy.current.structures, 'remove');
-
-        const dependsOn = structures.map(({ ref }) => ref);
-        const data = this.plugin.state.data.build().toRoot().apply(MergeStructures, { structures }, { dependsOn });
-        const structure = await data.commit();
-        const structureProperties = await this.plugin.builders.structure.insertStructureProperties(structure);
-        this.plugin.behaviors.canvas3d.initialized.subscribe(async v => {
-            await this.plugin.builders.structure.representation.applyPreset(structureProperties || structure, StructurePreset);
-        });
-    }
-}
-
-type MergeStructures = typeof MergeStructures
-const MergeStructures = PluginStateTransform.BuiltIn({
-    name: 'merge-structures',
-    display: { name: 'Merge Structures', description: 'Merge Structure' },
-    from: PSO.Root,
-    to: PSO.Molecule.Structure,
-    params: {
-        structures: PD.ObjectList({
-            ref: PD.Text('')
-        }, ({ ref }) => ref, { isHidden: true })
-    }
-})({
-    apply({ params, dependencies }) {
-        return Task.create('Merge Structures', async ctx => {
-            if (params.structures.length === 0) return StateObject.Null;
-
-            const first = dependencies![params.structures[0].ref].data as Structure;
-            const builder = Structure.Builder({ masterModel: first.models[0] });
-            for (const { ref } of params.structures) {
-                const s = dependencies![ref].data as Structure;
-                for (const unit of s.units) {
-                    // TODO invariantId
-                    builder.addUnit(unit.kind, unit.model, unit.conformation.operator, unit.elements, unit.traits);
-                }
-            }
-
-            const structure = builder.getStructure();
-            return new PSO.Molecule.Structure(structure, { label: 'Merged Structure' });
-        });
-    }
-});
-
-(window as any).DockingViewer = Viewer;
-export { Viewer as DockingViewer };

src/apps/docking-viewer/viewport.tsx

@@ -1,276 +0,0 @@
-/**
- * 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 { PluginUIComponent } from '../../mol-plugin-ui/base';
-import { Viewport, ViewportControls } from '../../mol-plugin-ui/viewport';
-import { BackgroundTaskProgress } from '../../mol-plugin-ui/task';
-import { LociLabels } from '../../mol-plugin-ui/controls';
-import { Toasts } from '../../mol-plugin-ui/toast';
-import { Button } from '../../mol-plugin-ui/controls/common';
-import { StructureRepresentationPresetProvider, presetStaticComponent } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { StateObjectRef } from '../../mol-state';
-import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { InteractionsRepresentationProvider } from '../../mol-model-props/computed/representations/interactions';
-import { InteractionTypeColorThemeProvider } from '../../mol-model-props/computed/themes/interaction-type';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginContext } from '../../mol-plugin/context';
-import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
-import { Color } from '../../mol-util/color';
-import { PluginConfig } from '../../mol-plugin/config';
-
-function shinyStyle(plugin: PluginContext) {
-    return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
-        renderer: {
-            ...plugin.canvas3d!.props.renderer,
-            style: { name: 'plastic', params: {} },
-        },
-        postprocessing: {
-            ...plugin.canvas3d!.props.postprocessing,
-            occlusion: { name: 'off', params: {} },
-            outline: { name: 'off', params: {} }
-        }
-    } });
-}
-
-function occlusionStyle(plugin: PluginContext) {
-    return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
-        renderer: {
-            ...plugin.canvas3d!.props.renderer,
-            style: { name: 'flat', params: {} }
-        },
-        postprocessing: {
-            ...plugin.canvas3d!.props.postprocessing,
-            occlusion: { name: 'on', params: {
-                samples: 64,
-                radius: 8,
-                bias: 1.0,
-                blurKernelSize: 13
-            } },
-            outline: { name: 'on', params: {
-                scale: 1.0,
-                threshold: 0.33
-            } }
-        }
-    } });
-}
-
-const ligandPlusSurroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of Ligand plus Ligand itself', MS.struct.modifier.union([
-    MS.struct.modifier.includeSurroundings({
-        0: StructureSelectionQueries.ligand.expression,
-        radius: 5,
-        'as-whole-residues': true
-    })
-]));
-
-const ligandSurroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of Ligand', MS.struct.modifier.union([
-    MS.struct.modifier.exceptBy({
-        0: ligandPlusSurroundings.expression,
-        by: StructureSelectionQueries.ligand.expression
-    })
-]));
-
-const PresetParams = {
-    ...StructureRepresentationPresetProvider.CommonParams,
-};
-
-
-
-export const StructurePreset = StructureRepresentationPresetProvider({
-    id: 'preset-structure',
-    display: { name: 'Structure' },
-    params: () => PresetParams,
-    async apply(ref, params, plugin) {
-        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        if (!structureCell) return {};
-
-        const components = {
-            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
-            polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
-        };
-
-        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
-        const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.35 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams }, color: 'chain-id', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
-        };
-
-        await update.commit({ revertOnError: true });
-        await shinyStyle(plugin);
-        plugin.managers.interactivity.setProps({ granularity: 'residue' });
-
-        return { components, representations };
-    }
-});
-
-export const IllustrativePreset = StructureRepresentationPresetProvider({
-    id: 'preset-illustrative',
-    display: { name: 'Illustrative' },
-    params: () => PresetParams,
-    async apply(ref, params, plugin) {
-        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        if (!structureCell) return {};
-
-        const components = {
-            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
-            polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
-        };
-
-        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
-        const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'spacefill', typeParams: { ...typeParams }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'spacefill', typeParams: { ...typeParams }, color: 'illustrative', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
-        };
-
-        await update.commit({ revertOnError: true });
-        await occlusionStyle(plugin);
-        plugin.managers.interactivity.setProps({ granularity: 'residue' });
-
-        return { components, representations };
-    }
-});
-
-const SurfacePreset = StructureRepresentationPresetProvider({
-    id: 'preset-surface',
-    display: { name: 'Surface' },
-    params: () => PresetParams,
-    async apply(ref, params, plugin) {
-        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const structure = structureCell?.obj?.data;
-        if (!structureCell || !structure) return {};
-
-        const components = {
-            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
-            polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
-        };
-
-        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
-        const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: { ...typeParams, quality: 'custom', resolution: 0.5, doubleSided: true }, color: 'partial-charge' }, { tag: 'polymer' }),
-        };
-
-        await update.commit({ revertOnError: true });
-        await shinyStyle(plugin);
-        plugin.managers.interactivity.setProps({ granularity: 'residue' });
-
-        return { components, representations };
-    }
-});
-
-const PocketPreset = StructureRepresentationPresetProvider({
-    id: 'preset-pocket',
-    display: { name: 'Pocket' },
-    params: () => PresetParams,
-    async apply(ref, params, plugin) {
-        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const structure = structureCell?.obj?.data;
-        if (!structureCell || !structure) return {};
-
-        const components = {
-            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
-            surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
-        };
-
-        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
-        const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: { ...typeParams, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }, color: 'partial-charge' }, { tag: 'surroundings' }),
-        };
-
-        await update.commit({ revertOnError: true });
-        await shinyStyle(plugin);
-        plugin.managers.interactivity.setProps({ granularity: 'element' });
-
-        return { components, representations };
-    }
-});
-
-const InteractionsPreset = StructureRepresentationPresetProvider({
-    id: 'preset-interactions',
-    display: { name: 'Interactions' },
-    params: () => PresetParams,
-    async apply(ref, params, plugin) {
-        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const structure = structureCell?.obj?.data;
-        if (!structureCell || !structure) return {};
-
-        const components = {
-            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
-            surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
-            interactions: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandPlusSurroundings, `interactions`)
-        };
-
-        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
-        const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.3 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.1, sizeAspectRatio: 1 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
-            interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
-            label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
-        };
-
-        await update.commit({ revertOnError: true });
-        await shinyStyle(plugin);
-        plugin.managers.interactivity.setProps({ granularity: 'element' });
-
-        return { components, representations };
-    }
-});
-
-export const ShowButtons = PluginConfig.item('showButtons', true);
-
-export class ViewportComponent extends PluginUIComponent {
-    async _set(structures: readonly StructureRef[], preset: StructureRepresentationPresetProvider) {
-        await this.plugin.managers.structure.component.clear(structures);
-        await this.plugin.managers.structure.component.applyPreset(structures, preset);
-    }
-
-    set = async (preset: StructureRepresentationPresetProvider) => {
-        await this._set(this.plugin.managers.structure.hierarchy.selection.structures, preset);
-    }
-
-    structurePreset = () => this.set(StructurePreset);
-    illustrativePreset = () => this.set(IllustrativePreset);
-    surfacePreset = () => this.set(SurfacePreset);
-    pocketPreset = () => this.set(PocketPreset);
-    interactionsPreset = () => this.set(InteractionsPreset);
-
-    get showButtons () {
-        return this.plugin.config.get(ShowButtons);
-    }
-
-    render() {
-        const VPControls = this.plugin.spec.components?.viewport?.controls || ViewportControls;
-
-        return <>
-            <Viewport />
-            {this.showButtons && <div className='msp-viewport-top-left-controls'>
-                <div style={{ marginBottom: '4px' }}>
-                    <Button onClick={this.structurePreset} >Structure</Button>
-                </div>
-                <div style={{ marginBottom: '4px' }}>
-                    <Button onClick={this.illustrativePreset}>Illustrative</Button>
-                </div>
-                <div style={{ marginBottom: '4px' }}>
-                    <Button onClick={this.surfacePreset}>Surface</Button>
-                </div>
-                {/* <div style={{ marginBottom: '4px' }}>
-                    <Button onClick={this.pocketPreset}>Pocket</Button>
-                </div> */}
-                <div style={{ marginBottom: '4px' }}>
-                    <Button onClick={this.interactionsPreset}>Interactions</Button>
-                </div>
-            </div>}
-            <VPControls />
-            <BackgroundTaskProgress />
-            <div className='msp-highlight-toast-wrapper'>
-                <LociLabels />
-                <Toasts />
-            </div>
-        </>;
-    }
-}

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

@@ -4,12 +4,12 @@
  * @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 function createMapping(allData: any) {
+export default function create(allData: any) {
     const mols = Object.keys(allData);
     const enc = CifWriter.createEncoder();
     enc.startDataBlock(mols[0]);

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

@@ -4,9 +4,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import express from 'express';
-import fetch from 'node-fetch';
-import { createMapping } from './mapping';
+import * as 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/apps/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/apps/model-server-query/index.html

@@ -0,0 +1,12 @@
+<!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

@@ -0,0 +1,134 @@
+/**
+ * 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

@@ -1,11 +1,10 @@
-#!/usr/bin/env node
 /**
  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @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';
@@ -14,7 +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({
@@ -33,7 +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, `*${t.definition.display.description}*`)
         StringBuilder.newline(builder);
     }
     StringBuilder.newline(builder);
@@ -49,7 +48,7 @@ function writeTransformer(t: StateTransformer) {
         StringBuilder.write(builder, `\`\`\`js\n${JSON.stringify(ParamDefinition.getDefaultValues(params), null, 2)}\n\`\`\``);
         StringBuilder.newline(builder);
     }
-    StringBuilder.write(builder, '----------------------------');
+    StringBuilder.write(builder, '----------------------------')
     StringBuilder.newline(builder);
 }
 
@@ -63,7 +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

@@ -19,15 +19,10 @@ 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 `A list of colors as 0xrrggbb`;
+        case 'color-list': return `One of ${oToS(param.options)}`;
         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 ${oToS(param.options)}`;
-        case 'value-ref': return `Reference to a runtime defined value.`;
-        case 'data-ref': return `Reference to a computed data value.`;
         case 'text': return 'String';
         case 'interval': return `Interval [min, max]`;
         case 'group': return `Object with:\n${getParams(param.params, offset + 2)}`;
@@ -43,7 +38,7 @@ function paramInfo(param: PD.Any, offset: number): string {
     }
 }
 
-function oToS(options: readonly (readonly [string, string] | readonly [string, string, string | undefined])[]) {
+function oToS(options: [string, string][]) {
     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

@@ -1,4 +1,3 @@
-#!/usr/bin/env node
 /**
  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
@@ -6,20 +5,17 @@
  * @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, Trajectory } 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';
-import { Task } from '../../mol-task';
 
 
 async function downloadFromPdb(pdb: string) {
@@ -34,32 +30,28 @@ 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, label_comp_id } = atoms;
-    const { 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(aI)} ${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 { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
-    const { label_comp_id } = atoms;
-    const { label_seq_id } = residues;
-    const { label_asym_id } = chains;
-    const aI = residueAtomSegments.offsets[rI];
-    const cI = chainAtomSegments.index[aI];
-    return `${label_asym_id.value(cI)} ${label_comp_id.value(aI)} ${label_seq_id.value(rI)}`;
+    const { residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy
+    const { label_comp_id, label_seq_id } = residues
+    const { label_asym_id } = chains
+    const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]]
+    return `${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 secondaryStructure = ModelSecondaryStructure.Provider.get(model);
-    if (!secondaryStructure) return;
+    const { key, elements } = model.properties.secondaryStructure;
 
-    const { key, elements } = secondaryStructure;
     const count = residues._rowCount;
     let rI = 0;
     while (rI < count) {
@@ -73,14 +65,14 @@ export function printSecStructure(model: Model) {
     }
 }
 
-export function printBonds(structure: Structure, showIntra: boolean, showInter: boolean) {
+export function printLinks(structure: Structure, showIntra: boolean, showInter: boolean) {
     if (showIntra) {
-        console.log('\nIntra Unit Bonds\n=============');
+        console.log('\nIntra Unit Links\n=============');
         for (const unit of structure.units) {
             if (!Unit.isAtomic(unit)) continue;
 
             const elements = unit.elements;
-            const { a, b, edgeCount } = unit.bonds;
+            const { a, b, edgeCount } = unit.links;
             const { model } = unit;
 
             if (!edgeCount) continue;
@@ -94,22 +86,20 @@ export function printBonds(structure: Structure, showIntra: boolean, showInter:
     }
 
     if (showInter) {
-        console.log('\nInter Unit Bonds\n=============');
-        const bonds = structure.interUnitBonds;
+        console.log('\nInter Unit Links\n=============');
+        const links = structure.links;
         for (const unit of structure.units) {
             if (!Unit.isAtomic(unit)) continue;
 
-            for (const pairBonds of bonds.getConnectedUnits(unit.id)) {
-                if (!pairBonds.areUnitsOrdered || pairBonds.edgeCount === 0) continue;
+            for (const pairLinks of links.getLinkedUnits(unit)) {
+                if (!pairLinks.areUnitsOrdered || pairLinks.bondCount === 0) continue;
 
-                const { unitA, unitB, edgeCount } = pairBonds;
-                const uA = structure.unitMap.get(unitA);
-                const uB = structure.unitMap.get(unitB);
-                console.log(`${unitA} - ${unitB}: ${edgeCount} bond(s)`);
+                const { unitA, unitB } = pairLinks;
+                console.log(`${pairLinks.unitA.id} - ${pairLinks.unitB.id}: ${pairLinks.bondCount} bond(s)`);
 
-                for (const aI of pairBonds.connectedIndices) {
-                    for (const bond of pairBonds.getEdges(aI)) {
-                        console.log(`${atomLabel(uA.model, uA.elements[aI])} -- ${atomLabel(uB.model, uB.elements[bond.indexB])}`);
+                for (const aI of pairLinks.linkedElementIndices) {
+                    for (const link of pairLinks.getBonds(aI)) {
+                        console.log(`${atomLabel(unitA.model, unitA.elements[aI])} -- ${atomLabel(unitB.model, unitB.elements[link.indexB])}`);
                     }
                 }
             }
@@ -122,13 +112,25 @@ export function printSequence(model: Model) {
     const { byEntityKey } = model.sequence;
     for (const key of Object.keys(byEntityKey)) {
         const { sequence, entityId } = byEntityKey[+key];
-        const { seqId, compId } = sequence;
-        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)}, ${seqId.value(seqId.rowCount - 1)}) (${compId.value(0)}, ${compId.value(compId.rowCount - 1)})`);
+        const { seqId, compId } = sequence
+        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)} (offset ${sequence.offset}), ${seqId.value(seqId.rowCount - 1)}) (${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) {
@@ -138,7 +140,7 @@ 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();
@@ -146,7 +148,7 @@ export function printRings(structure: Structure) {
 
 export function printUnits(structure: Structure) {
     console.log('\nUnits\n=============');
-    const l = StructureElement.Location.create(structure);
+    const l = StructureElement.Location.create();
 
     for (const unit of structure.units) {
         l.unit = unit;
@@ -177,8 +179,7 @@ export function printUnits(structure: Structure) {
 
 export function printSymmetryInfo(model: Model) {
     console.log('\nSymmetry Info\n=============');
-    const symmetry = ModelSymmetry.Provider.get(model);
-    if (!symmetry) return;
+    const { symmetry } = model;
     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(', ')}`);
@@ -186,11 +187,10 @@ export function printSymmetryInfo(model: Model) {
     console.log(`NCS operators: ${symmetry.ncsOperators && symmetry.ncsOperators.map(a => a.name).join(', ')}`);
 }
 
-export async function printModelStats(models: Trajectory) {
+export function printModelStats(models: ReadonlyArray<Model>) {
     console.log('\nModels\n=============');
 
-    for (let i = 0; i < models.frameCount; i++) {
-        const m = await Task.resolveInContext(models.getFrameAtIndex(i));
+    for (const m of models) {
         if (m.coarseHierarchy.isDefined) {
             console.log(`${m.label} ${m.modelNum}: ${m.atomicHierarchy.atoms._rowCount} atom(s), ${m.coarseHierarchy.spheres.count} sphere(s), ${m.coarseHierarchy.gaussians.count} gaussian(s)`);
         } else {
@@ -202,7 +202,7 @@ export async function printModelStats(models: Trajectory) {
 
 export async function getModelsAndStructure(frame: CifFrame) {
     const models = await trajectoryFromMmCIF(frame).run();
-    const structure = Structure.ofModel(models.representative);
+    const structure = Structure.ofModel(models[0]);
     return { models, structure };
 }
 
@@ -210,17 +210,18 @@ async function run(frame: CifFrame, args: Args) {
     const { models, structure } = await getModelsAndStructure(frame);
 
     if (args.models) printModelStats(models);
-    if (args.seq) printSequence(models.representative);
+    if (args.seq) printSequence(models[0]);
     if (args.units) printUnits(structure);
-    if (args.sym) printSymmetryInfo(models.representative);
+    if (args.sym) printSymmetryInfo(models[0]);
     if (args.rings) printRings(structure);
-    if (args.intraBonds) printBonds(structure, true, false);
-    if (args.interBonds) printBonds(structure, false, true);
-    if (args.sec) printSecStructure(models.representative);
+    if (args.intraLinks) printLinks(structure, true, false);
+    if (args.interLinks) printLinks(structure, false, true);
+    if (args.mod) printModRes(models[0]);
+    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);
 }
 
@@ -241,8 +242,8 @@ 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(['--intraBonds'], { help: 'print intra unit bonds', action: 'storeTrue' });
-parser.addArgument(['--interBonds'], { help: 'print inter unit bonds', action: 'storeTrue' });
+parser.addArgument(['--intraLinks'], { help: 'print intra unit links', action: 'storeTrue' });
+parser.addArgument(['--interLinks'], { help: 'print inter unit links', action: 'storeTrue' });
 parser.addArgument(['--mod'], { help: 'print modified residues', action: 'storeTrue' });
 parser.addArgument(['--sec'], { help: 'print secoundary structure', action: 'storeTrue' });
 interface Args {
@@ -255,12 +256,12 @@ interface Args {
     units?: boolean,
     sym?: boolean,
     rings?: boolean,
-    intraBonds?: boolean,
-    interBonds?: boolean,
+    intraLinks?: boolean,
+    interLinks?: 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

@@ -1,44 +1,46 @@
-#!/usr/bin/env node
 /**
  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @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 { Volume } from '../../mol-model/volume';
-import { downloadCif } from './helpers';
-import { CIF } from '../../mol-io/reader/cif';
+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 { Table } from '../../mol-data/db';
 import { StringBuilder } from '../../mol-util';
 import { Task } from '../../mol-task';
 import { createVolumeIsosurfaceMesh } from '../../mol-repr/volume/isosurface';
-import { Theme } from '../../mol-theme/theme';
-import { volumeFromDensityServerData, DscifFormat } from '../../mol-model-formats/volume/density-server';
+import { createEmptyTheme } from '../../mol-theme/theme';
+import { volumeFromDensityServerData } 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 await volumeFromDensityServerData(data).run();
+    return { source: data, volume: await volumeFromDensityServerData(data).run() };
 }
 
-function print(volume: Volume) {
-    if (!DscifFormat.is(volume.sourceData)) return;
-    const { volume_data_3d_info } = volume.sourceData.data;
+function print(data: Volume) {
+    const { volume_data_3d_info } = data.source;
     const row = Table.getRow(volume_data_3d_info, 0);
     console.log(row);
-    console.log(volume.grid.transform);
-    console.log(volume.grid.stats);
+    console.log(data.volume.cell);
+    console.log(data.volume.dataStats);
+    console.log(data.volume.fractionalBox);
 }
 
-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();
+async function doMesh(data: Volume, filename: string) {
+    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, data.volume, createEmptyTheme(), { isoValue: VolumeIsoValue.absolute(1.5) } )).run();
     console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
 
     // Export the mesh in OBJ format.
@@ -75,8 +77,8 @@ 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

@@ -1,43 +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">
-        <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', { detail: 6 });
-            // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
-        </script>
-    </body>
-</html>

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

@@ -0,0 +1,228 @@
+/**
+ * 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

@@ -0,0 +1,62 @@
+/**
+ * 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

@@ -0,0 +1,474 @@
+/**
+ * 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, Unit } 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, Unit.Trait.None, 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 }
+
+        let cellpackTree = tree.apply(StructureFromCellpack, p)
+        if (params.preset.traceOnly) {
+            const expression = 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'])
+                ])
+            })
+            cellpackTree = cellpackTree.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression }, { state: { isGhost: true } })
+        }
+        cellpackTree
+            .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

@@ -0,0 +1,74 @@
+/**
+ * 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

@@ -0,0 +1,48 @@
+/**
+ * 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

@@ -0,0 +1,167 @@
+/**
+ * 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

@@ -34,56 +34,10 @@
                 height: 600px;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
+        <link rel="stylesheet" type="text/css" href="app.css" />
     </head>
     <body>
         <div id="app"></div>
-        <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, debugMode);
-
-            var disableAntialiasing = getParam('disable-antialiasing', '[^&]+').trim() === '1';
-            var pixelScale = parseFloat(getParam('pixel-scale', '[^&]+').trim() || '1');
-            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            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', {
-                disableAntialiasing: disableAntialiasing,
-                pixelScale: pixelScale,
-                enableWboit: !disableWboit,
-                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>
+        <script type="text/javascript" src="./index.js"></script>
     </body>
 </html>

src/apps/viewer/index.ts

@@ -1,279 +1,67 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 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 '../../mol-util/polyfill';
-import { createPlugin } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
-import './index.html';
-import './embedded.html';
-import './favicon.ico';
+import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import './index.html'
+import './favicon.ico'
 import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginCommands } from '../../mol-plugin/command';
 import { PluginSpec } from '../../mol-plugin/spec';
-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';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
-import { DnatcoConfalPyramids } from '../../extensions/dnatco';
-import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
-import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
-import { Color } from '../../mol-util/color';
-import { StateObjectSelector } from '../../mol-state';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
-import { Mp4Export } from '../../extensions/mp4-export';
-import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { CreateJoleculeState } from './extensions/jolecule';
+import { LoadCellPackModel } from './extensions/cellpack/model';
+import { StructureFromCellpack } from './extensions/cellpack/state';
+require('mol-plugin/skin/light.scss')
 
-require('mol-plugin-ui/skin/light.scss');
+function getParam(name: string, regex: string): string {
+    let r = new RegExp(`${name}=(${regex})[&]?`, 'i');
+    return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+}
 
-export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setProductionMode, setDebugMode } from '../../mol-util/debug';
+const hideControls = getParam('hide-controls', `[^&]+`) === '1';
 
-const CustomFormats = [
-    ['g3d', G3dProvider] as const
-];
-
-const Extensions = {
-    'cellpack': PluginSpec.Behavior(CellPack),
-    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
-    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
-    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
-    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
-    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
-    'g3d': PluginSpec.Behavior(G3DFormat),
-    'mp4-export': PluginSpec.Behavior(Mp4Export)
-};
-
-const DefaultViewerOptions = {
-    customFormats: CustomFormats as [string, DataFormatProvider][],
-    extensions: ObjectKeys(Extensions),
-    layoutIsExpanded: true,
-    layoutShowControls: true,
-    layoutShowRemoteState: true,
-    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
-    layoutShowSequence: true,
-    layoutShowLog: true,
-    layoutShowLeftPanel: true,
-    disableAntialiasing: false,
-    pixelScale: 1,
-    enableWboit: true,
-
-    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
-    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
-    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
-    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
-    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
-    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
-    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
-    volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
-    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
-    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
-};
-type ViewerOptions = typeof DefaultViewerOptions;
-
-export class Viewer {
-    plugin: PluginContext
-
-    constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
-        const o = { ...DefaultViewerOptions, ...options };
-        const defaultSpec = DefaultPluginSpec();
-
-        const spec: PluginSpec = {
-            actions: [...defaultSpec.actions],
-            behaviors: [
-                ...defaultSpec.behaviors,
-                ...o.extensions.map(e => Extensions[e]),
-            ],
-            animations: [...defaultSpec.animations || []],
-            customParamEditors: defaultSpec.customParamEditors,
-            customFormats: o?.customFormats,
-            layout: {
-                initial: {
-                    isExpanded: o.layoutIsExpanded,
-                    showControls: o.layoutShowControls,
-                    controlsDisplay: o.layoutControlsDisplay,
-                },
-                controls: {
-                    ...defaultSpec.layout && defaultSpec.layout.controls,
-                    top: o.layoutShowSequence ? undefined : 'none',
-                    bottom: o.layoutShowLog ? undefined : 'none',
-                    left: o.layoutShowLeftPanel ? undefined : 'none',
-                }
+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
             },
-            components: {
-                ...defaultSpec.components,
-                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
-            },
-            config: [
-                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
-                [PluginConfig.General.PixelScale, o.pixelScale],
-                [PluginConfig.General.EnableWboit, o.enableWboit],
-                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
-                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
-                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
-                [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.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
-                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
-                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
-            ]
-        };
-
-        const element = typeof elementOrId === 'string'
-            ? document.getElementById(elementOrId)
-            : elementOrId;
-        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
-        this.plugin = createPlugin(element, spec);
-    }
-
-    setRemoteSnapshot(id: string) {
-        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
-        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
-    }
-
-    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
-        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
-    }
-
-    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
-        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, representationParams: options?.representationParams as any },
-                }
+            controls: {
+                ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls
             }
-        }));
-    }
-
-    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
-        const plugin = this.plugin;
-
-        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
-        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
-
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
-    }
-
-    async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
-        const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
-        const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
-    }
-
-    loadPdb(pdb: string, options?: LoadStructureOptions) {
-        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, representationParams: options?.representationParams as any },
-                }
-            }
-        }));
-    }
-
-    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,
-                }
-            }
-        }));
-    }
-
-    loadEmdb(emdb: string, options?: { detail?: number }) {
-        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: options?.detail ?? 3,
-                }
-            }
-        }));
-    }
-
-    async loadVolumeFromUrl(url: string, format: BuildInVolumeFormat, isBinary: boolean, isovalues: VolumeIsovalueInfo[], entryId?: string) {
-        const plugin = this.plugin;
-
-        if (!plugin.dataFormats.get(format)) {
-            throw new Error(`Unknown density format: ${format}`);
         }
+    };
+    const plugin = createPlugin(document.getElementById('app')!, spec);
+    trySetSnapshot(plugin);
+}
 
-        return plugin.dataTransaction(async () => {
-            const data = await plugin.builders.data.download({ url, isBinary, label: entryId }, { state: { isGhost: true } });
-
-            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId });
-            const volume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
-            if (!volume?.isOk) throw new Error('Failed to parse any volume.');
-
-            const repr = plugin.build().to(volume);
-            for (const iso of isovalues) {
-                repr.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, volume.data!, {
-                    type: 'isosurface',
-                    typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ?  { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
-                    color: 'uniform',
-                    colorParams: { value: iso.color }
-                }));
-            }
-
-            await repr.commit();
-        });
-    }
-
-    handleResize() {
-        this.plugin.layout.events.updated.next();
+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);
     }
 }
 
-export interface LoadStructureOptions {
-    representationParams?: StructureRepresentationPresetProvider.CommonParams
-}
-
-export interface VolumeIsovalueInfo {
-    type: 'absolute' | 'relative',
-    value: number,
-    color: Color,
-    alpha?: number
-}
+init();

src/cli/chem-comp-dict/create-ions.ts

@@ -1,73 +0,0 @@
-#!/usr/bin/env node
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Josh McMenemy <josh.mcmenemy@gmail.com>
- */
-
-import * as argparse from 'argparse';
-import * as path from 'path';
-import util from 'util';
-import fs from 'fs';
-require('util.promisify').shim();
-const writeFile = util.promisify(fs.writeFile);
-
-import { DatabaseCollection } from '../../mol-data/db';
-import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
-import { ensureDataAvailable, readCCD } from './util';
-
-function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
-    const ionNames: string[] = [];
-    for (const k in ccd) {
-        const {chem_comp} = ccd[k];
-        if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
-            ionNames.push(chem_comp.id.value(0));
-        }
-    }
-    // these are extra ions that don't have ION in their name
-    ionNames.push('NCO', 'OHX');
-    return ionNames;
-}
-
-function writeIonNamesFile(filePath: string, ionNames: string[]) {
-    const output = `/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated ion names params file. Names extracted from CCD components.
- *
- * @author molstar/chem-comp-dict/create-table cli
- */
-
-export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
-`;
-    writeFile(filePath, output);
-}
-
-async function run(out: string, forceDownload = false) {
-    await ensureDataAvailable(forceDownload);
-    const ccd = await readCCD();
-    const ionNames = extractIonNames(ccd);
-    if (!fs.existsSync(path.dirname(out))) {
-        fs.mkdirSync(path.dirname(out));
-    }
-    writeIonNamesFile(out, ionNames);
-}
-
-const parser = new argparse.ArgumentParser({
-    addHelp: true,
-    description: 'Extract and save IonNames from CCD.'
-});
-parser.addArgument('out', {
-    help: 'Generated file output path.'
-});
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
-    help: 'Force download of CCD and PVCD.'
-});
-interface Args {
-    out: string,
-    forceDownload?: boolean,
-}
-const args: Args = parser.parseArgs();
-
-run(args.out, args.forceDownload);

src/cli/chem-comp-dict/create-table.ts

@@ -1,294 +0,0 @@
-#!/usr/bin/env node
-/**
- * Copyright (c) 2018-2020 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 util from 'util';
-import * as path from 'path';
-import * as fs from 'fs';
-require('util.promisify').shim();
-const writeFile = util.promisify(fs.writeFile);
-
-import { Database, Table, DatabaseCollection } from '../../mol-data/db';
-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';
-import { ccd_chemCompAtom_schema } from '../../mol-io/reader/cif/schema/ccd-extras';
-import { ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
-
-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}`;
-}
-
-function ccaKey(compId: string, atomId: string) {
-    return `${compId}:${atomId}`;
-}
-
-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)));
-    }
-    return set;
-}
-
-function addChemCompAtomToSet(set: Set<string>, cca: CCA) {
-    for (let i = 0, il = cca._rowCount; i < il; ++i) {
-        set.add(ccaKey(cca.comp_id.value(i), cca.atom_id.value(i)));
-    }
-    return set;
-}
-
-function checkAddingBondsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
-    const ccbSetByParent = DefaultMap<string, Set<string>>(() => new Set());
-
-    for (const k in pvcd) {
-        const { chem_comp, chem_comp_bond } = pvcd[k];
-        if (chem_comp_bond._rowCount) {
-            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);
-            } 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);
-                }
-            }
-        }
-    }
-
-    for (const k in pvcd) {
-        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);
-            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);
-                    extraBonds.forEach(bk => {
-                        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}`);
-                        }
-                    });
-                }
-            }
-        }
-    }
-}
-
-function checkAddingAtomsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
-    const ccaSetByParent = DefaultMap<string, Set<string>>(() => new Set());
-
-    for (const k in pvcd) {
-        const { chem_comp, chem_comp_atom } = pvcd[k];
-        if (chem_comp_atom._rowCount) {
-            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
-            if (parentIds.length === 0) {
-                const set = ccaSetByParent.getDefault(chem_comp.id.value(0));
-                addChemCompAtomToSet(set, chem_comp_atom);
-            } else {
-                for (let i = 0, il = parentIds.length; i < il; ++i) {
-                    const parentId = parentIds[i];
-                    const set = ccaSetByParent.getDefault(parentId);
-                    addChemCompAtomToSet(set, chem_comp_atom);
-                }
-            }
-        }
-    }
-}
-
-async function createBonds(
-    ccd: DatabaseCollection<CCD_Schema>,
-    pvcd: DatabaseCollection<CCD_Schema>,
-    atomsRequested: boolean
-) {
-    const ccbSet = new Set<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);
-            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);
-            }
-        }
-    }
-
-    // check adding bonds from PVCD
-    checkAddingBondsFromPVCD(pvcd);
-
-    // add bonds from PVCD
-    for (const k in pvcd) {
-        const { chem_comp, chem_comp_bond } = pvcd[k];
-        if (chem_comp_bond._rowCount) {
-            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);
-            } else {
-                for (let i = 0, il = parentIds.length; i < il; ++i) {
-                    addBonds(parentIds[i], chem_comp_bond, true);
-                }
-            }
-        }
-    }
-
-    // add bonds from CCD
-    for (const k in ccd) {
-        const { chem_comp, chem_comp_bond } = ccd[k];
-        if (chem_comp_bond._rowCount) {
-            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(
-        CCB_TABLE_NAME,
-        { chem_comp_bond: mmCIF_chemCompBond_schema },
-        { chem_comp_bond: bondTable }
-    );
-
-    return { bonds: bondDatabase, atoms: atomsRequested ? createAtoms(ccd, pvcd) : void 0 };
-}
-
-function createAtoms(ccd: DatabaseCollection<CCD_Schema>, pvcd: DatabaseCollection<CCD_Schema>) {
-    const ccaSet = new Set<string>();
-
-    const comp_id: string[] = [];
-    const atom_id: string[] = [];
-    const charge: number[] = [];
-    const pdbx_stereo_config: typeof CCD_Schema.chem_comp_atom['pdbx_stereo_config']['T'][] = [];
-
-    function addAtoms(compId: string, cca: CCA) {
-        for (let i = 0, il = cca._rowCount; i < il; ++i) {
-            const atomId = cca.atom_id.value(i);
-            const k = ccaKey(compId, atomId);
-            if (!ccaSet.has(k)) {
-                atom_id.push(atomId);
-                comp_id.push(compId);
-                charge.push(cca.charge.value(i));
-                pdbx_stereo_config.push(cca.pdbx_stereo_config.value(i));
-                ccaSet.add(k);
-            }
-        }
-    }
-
-    // check adding atoms from PVCD
-    checkAddingAtomsFromPVCD(pvcd);
-
-    // add atoms from PVCD
-    for (const k in pvcd) {
-        const { chem_comp, chem_comp_atom } = pvcd[k];
-        if (chem_comp_atom._rowCount) {
-            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
-            if (parentIds.length === 0) {
-                addAtoms(chem_comp.id.value(0), chem_comp_atom);
-            } else {
-                for (let i = 0, il = parentIds.length; i < il; ++i) {
-                    addAtoms(parentIds[i], chem_comp_atom);
-                }
-            }
-        }
-    }
-
-    // add atoms from CCD
-    for (const k in ccd) {
-        const { chem_comp, chem_comp_atom } = ccd[k];
-        if (chem_comp_atom._rowCount) {
-            addAtoms(chem_comp.id.value(0), chem_comp_atom);
-        }
-    }
-
-    const atomTable = Table.ofArrays(ccd_chemCompAtom_schema, {
-        comp_id, atom_id, charge, pdbx_stereo_config
-    });
-
-    return Database.ofTables(
-        CCA_TABLE_NAME,
-        { chem_comp_atom: ccd_chemCompAtom_schema },
-        { chem_comp_atom: atomTable }
-    );
-}
-
-async function run(out: string, binary = false, forceDownload = false, ccaOut?: string) {
-    await ensureDataAvailable(forceDownload);
-    const ccd = await readCCD();
-    const pvcd = await readPVCD();
-
-    const { bonds, atoms } = await createBonds(ccd, pvcd, !!ccaOut);
-
-    const ccbCif = getEncodedCif(CCB_TABLE_NAME, bonds, binary);
-    if (!fs.existsSync(path.dirname(out))) {
-        fs.mkdirSync(path.dirname(out));
-    }
-    writeFile(out, ccbCif);
-
-    if (!!ccaOut) {
-        const ccaCif = getEncodedCif(CCA_TABLE_NAME, atoms, binary);
-        if (!fs.existsSync(path.dirname(ccaOut))) {
-            fs.mkdirSync(path.dirname(ccaOut));
-        }
-        writeFile(ccaOut, ccaCif);
-    }
-}
-
-const CCB_TABLE_NAME = 'CHEM_COMP_BONDS';
-const CCA_TABLE_NAME = 'CHEM_COMP_ATOMS';
-
-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.'
-});
-parser.addArgument('out', {
-    help: 'Generated file output path.'
-});
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
-    help: 'Force download of CCD and PVCD.'
-});
-parser.addArgument([ '--binary', '-b' ], {
-    action: 'storeTrue',
-    help: 'Output as BinaryCIF.'
-});
-parser.addArgument(['--ccaOut', '-a'], {
-    help: 'Optional generated file output path for chem_comp_atom data.',
-    required: false
-});
-interface Args {
-    out: string,
-    forceDownload?: boolean,
-    binary?: boolean,
-    ccaOut?: string
-}
-const args: Args = parser.parseArgs();
-
-run(args.out, args.binary, args.forceDownload, args.ccaOut);

src/cli/chem-comp-dict/util.ts

@@ -1,75 +0,0 @@
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-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 } 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';
-
-export async function ensureAvailable(path: string, url: string, forceDownload = false) {
-    if (forceDownload || !fs.existsSync(path)) {
-        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()));
-        } else {
-            await writeFile(path, await data.text());
-        }
-        console.log(`done downloading ${url}`);
-    }
-}
-
-export async function ensureDataAvailable(forceDownload = false) {
-    await ensureAvailable(CCD_PATH, CCD_URL, forceDownload);
-    await ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload);
-}
-
-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);
-}
-
-export async function readCCD() {
-    return readFileAsCollection(CCD_PATH, CCD_Schema);
-}
-
-export async function readPVCD() {
-    return readFileAsCollection(PVCD_PATH, CCD_Schema);
-}
-
-async function parseCif(data: string | Uint8Array) {
-    const comp = CIF.parse(data);
-    console.time('parse cif');
-    const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
-    console.timeEnd('parse cif');
-    if (parsed.isError) throw 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);
-    return encoder.getData();
-}
-
-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';

src/cli/cif2bcif/converter.ts

@@ -1,119 +0,0 @@
-/**
- * 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 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/cli/cif2bcif/index.ts

@@ -1,68 +0,0 @@
-#!/usr/bin/env node
-/**
- * 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/cli/cifschema/index.ts

@@ -1,275 +0,0 @@
-#!/usr/bin/env node
-/**
- * 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 { parseCifText } 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 parseCifText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
-    if (mmcifDic.isError) throw mmcifDic;
-
-    await ensureIhmDicAvailable();
-    const ihmDic = await parseCifText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
-    if (ihmDic.isError) throw ihmDic;
-
-    await ensureCarbBranchDicAvailable();
-    const carbBranchDic = await parseCifText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
-    if (carbBranchDic.isError) throw carbBranchDic;
-
-    await ensureCarbCompDicAvailable();
-    const carbCompDic = await parseCifText(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 parseCifText(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 parseCifText(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 parseCifText(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/cli/cifschema/util/cif-dic.ts

@@ -1,475 +0,0 @@
-/**
- * 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/cli/cifschema/util/generate.ts

@@ -1,151 +0,0 @@
-/**
- * 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/cli/cifschema/util/helper.ts

@@ -1,20 +0,0 @@
-/**
- * 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/cli/cifschema/util/schema.ts

@@ -1,77 +0,0 @@
-/**
- * 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/cli/lipid-params/index.ts

@@ -1,93 +0,0 @@
-#!/usr/bin/env node
-/**
- * Copyright (c) 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 { UniqueArray } from '../../mol-data/generic';
-
-const LIPIDS_DIR = path.resolve(__dirname, '../../../../build/lipids/');
-
-const MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids.itp');
-const MARTINI_LIPIDS_URL = 'http://www.cgmartini.nl/images/parameters/lipids/Collections/martini_v2.0_lipids_all_201506.itp';
-
-async function ensureAvailable(path: string, url: string) {
-    if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
-        const name = url.substr(url.lastIndexOf('/') + 1);
-        console.log(`downloading ${name}...`);
-        const data = await fetch(url);
-        if (!fs.existsSync(LIPIDS_DIR)) {
-            fs.mkdirSync(LIPIDS_DIR);
-        }
-        fs.writeFileSync(path, await data.text());
-        console.log(`done downloading ${name}`);
-    }
-}
-
-async function ensureLipidsAvailable() { await ensureAvailable(MARTINI_LIPIDS_PATH, MARTINI_LIPIDS_URL); }
-
-const extraLipids = ['DMPC'];
-
-async function run(out: string) {
-    await ensureLipidsAvailable();
-    const lipidsItpStr = fs.readFileSync(MARTINI_LIPIDS_PATH, 'utf8');
-
-    const lipids = UniqueArray.create<string>();
-    const reLipid = /\[moleculetype\]\n; molname      nrexcl\n +([a-zA-Z]{3,5})/g;
-    let m: RegExpExecArray | null;
-
-    while ((m = reLipid.exec(lipidsItpStr)) !== null) {
-        const v = m[0].substr(m[0].lastIndexOf(' ') + 1);
-        UniqueArray.add(lipids, v, v);
-    }
-
-    for (const v of extraLipids) {
-        UniqueArray.add(lipids, v, v);
-    }
-
-    const lipidNames = JSON.stringify(lipids.array);
-
-    if (out) {
-        const output = `/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
- *
- * @author molstar/lipid-params cli
- */
-
-export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
-`;
-        fs.writeFileSync(out, output);
-    } else {
-        console.log(lipidNames);
-    }
-}
-
-const parser = new argparse.ArgumentParser({
-    addHelp: true,
-    description: 'Create lipid params (from martini lipids itp)'
-});
-parser.addArgument([ '--out', '-o' ], {
-    help: 'Generated lipid params output path, if not given printed to stdout'
-});
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
-    help: 'Force download of martini lipids itp'
-});
-interface Args {
-    out: string
-    forceDownload: boolean
-}
-const args: Args = parser.parseArgs();
-
-const FORCE_DOWNLOAD = args.forceDownload;
-
-run(args.out || '').catch(e => {
-    console.error(e);
-});

src/examples/alpha-orbitals/controls.tsx

@@ -1,25 +0,0 @@
-/**
- * Copyright (c) 2020 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 { AlphaOrbitalsExample } from '.';
-import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
-import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
-import { PluginContextContainer } from '../../mol-plugin-ui/plugin';
-
-export function mountControls(orbitals: AlphaOrbitalsExample, parent: Element) {
-    ReactDOM.render(<PluginContextContainer plugin={orbitals.plugin}>
-        <Controls orbitals={orbitals} />
-    </PluginContextContainer>, parent);
-}
-
-function Controls({ orbitals }: { orbitals: AlphaOrbitalsExample }) {
-    const params = useBehavior(orbitals.params);
-    const values = useBehavior(orbitals.state);
-
-    return <ParameterControls params={params as any} values={values} onChangeValues={(vs: any) => orbitals.state.next(vs)} />;
-}

src/examples/alpha-orbitals/index.html

@@ -1,37 +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* Alpha Orbitals Example</title>
-        <style>
-            * {
-                margin: 0;
-                padding: 0;
-                box-sizing: border-box;
-            }
-            #app {
-                position: absolute;
-                left: 0;
-                top: 0;
-                bottom: 0;
-                right: 0;
-            }
-            #controls {
-                position: absolute;
-                left: 8px;
-                top: 8px;
-                width: 300px;
-            }            
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-        <script type="text/javascript" src="./index.js"></script>
-    </head>
-    <body>
-        <div id="app"></div>
-        <div id='controls'></div>
-        <script>
-            AlphaOrbitalsExample.init('app')
-        </script>
-    </body>
-</html>

src/examples/alpha-orbitals/index.ts

@@ -1,213 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { SphericalBasisOrder } from '../../extensions/alpha-orbitals/spherical-functions';
-import { BasisAndOrbitals, CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
-import { createPluginAsync } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { PluginConfig } from '../../mol-plugin/config';
-import { PluginContext } from '../../mol-plugin/context';
-import { StateObjectSelector, StateTransformer } from '../../mol-state';
-import { Color } from '../../mol-util/color';
-import { ColorNames } from '../../mol-util/color/names';
-import { ParamDefinition } from '../../mol-util/param-definition';
-import { mountControls } from './controls';
-import { DemoMoleculeSDF, DemoOrbitals } from './example-data';
-import { BehaviorSubject } from 'rxjs';
-import { debounceTime, skip } from 'rxjs/operators';
-import './index.html';
-import { Basis, AlphaOrbital } from '../../extensions/alpha-orbitals/data-model';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
-require('mol-plugin-ui/skin/light.scss');
-
-interface DemoInput {
-    moleculeSdf: string,
-    basis: Basis,
-    order: SphericalBasisOrder,
-    orbitals: AlphaOrbital[]
-}
-
-interface Params {
-    show: { name: 'orbital', params: { index: number } } | { name: 'density', params: {} },
-    isoValue: number,
-    gpuSurface: boolean
-}
-
-type Selectors = {
-    type: 'orbital',
-    volume: StateObjectSelector<PluginStateObject.Volume.Data, typeof CreateOrbitalVolume>,
-    positive: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
-    negative: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
-} | {
-    type: 'density',
-    volume: StateObjectSelector<PluginStateObject.Volume.Data, typeof CreateOrbitalDensityVolume>,
-    positive: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
-}
-
-export class AlphaOrbitalsExample {
-    plugin: PluginContext;
-
-    async init(target: string | HTMLElement) {
-        this.plugin = await createPluginAsync(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec(),
-            layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
-                },
-                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' },
-            },
-            config: [
-                [PluginConfig.Viewport.ShowExpand, false],
-                [PluginConfig.Viewport.ShowControls, false],
-                [PluginConfig.Viewport.ShowSelectionMode, false],
-                [PluginConfig.Viewport.ShowAnimation, false],
-            ]
-        });
-
-        this.plugin.managers.interactivity.setProps({ granularity: 'element' });
-
-        if (!canComputeGrid3dOnGPU(this.plugin.canvas3d?.webgl)) {
-            PluginCommands.Toast.Show(this.plugin, {
-                title: 'Error',
-                message: `Browser/device does not support required WebGL extension (OES_texture_float).`
-            });
-            return;
-        }
-
-        this.load({
-            moleculeSdf: DemoMoleculeSDF,
-            ...DemoOrbitals
-        });
-
-        mountControls(this, document.getElementById('controls')!);
-    }
-
-    readonly params = new BehaviorSubject<ParamDefinition.For<Params>>({} as any);
-    readonly state = new BehaviorSubject<Params>({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: false });
-
-    private selectors?: Selectors = void 0;
-    private basis?: StateObjectSelector<BasisAndOrbitals> = void 0;
-
-    private currentParams: Params = { ...this.state.value };
-
-    private clearVolume() {
-        if (!this.selectors) return;
-        const v = this.selectors.volume;
-        this.selectors = void 0;
-        return this.plugin.build().delete(v).commit();
-    }
-
-    private async syncVolume() {
-        if (!this.basis?.isOk) return;
-
-        const state = this.state.value;
-
-        if (state.show.name !== this.selectors?.type) {
-            await this.clearVolume();
-        }
-
-        const update = this.plugin.build();
-        if (state.show.name === 'orbital') {
-            if (!this.selectors) {
-                const volume = update
-                    .to(this.basis)
-                    .apply(CreateOrbitalVolume, { index: state.show.params.index });
-
-                const positive = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('positive', ColorNames.blue)).selector;
-                const negative = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('negative', ColorNames.red)).selector;
-
-                this.selectors = { type: 'orbital', volume: volume.selector, positive, negative };
-            } else {
-                const index = state.show.params.index;
-                update.to(this.selectors.volume).update(CreateOrbitalVolume, () => ({ index }));
-            }
-        } else {
-            if (!this.selectors) {
-                const volume = update
-                    .to(this.basis)
-                    .apply(CreateOrbitalDensityVolume);
-                const positive = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('positive', ColorNames.blue)).selector;
-                this.selectors = { type: 'density', volume: volume.selector, positive };
-            }
-        }
-
-        await update.commit();
-
-        if (this.currentParams.gpuSurface !== this.state.value.gpuSurface) {
-            await this.setIsovalue();
-        }
-
-        this.currentParams = this.state.value;
-    }
-
-    private setIsovalue() {
-        if (!this.selectors) return;
-
-        this.currentParams = this.state.value;
-        const update = this.plugin.build();
-        update.to(this.selectors.positive).update(this.volumeParams('positive', ColorNames.blue));
-        if (this.selectors?.type === 'orbital') {
-            update.to(this.selectors.negative).update(this.volumeParams('negative', ColorNames.red));
-        }
-        return update.commit();
-    }
-
-    private volumeParams(kind: 'positive' | 'negative', color: Color): StateTransformer.Params<typeof CreateOrbitalRepresentation3D> {
-        return {
-            alpha: 0.85,
-            color,
-            directVolume: this.state.value.gpuSurface,
-            kind,
-            relativeIsovalue: this.state.value.isoValue,
-            pickable: false,
-            xrayShaded: true
-        };
-    }
-
-    async load(input: DemoInput) {
-        await this.plugin.clear();
-
-        const data = await this.plugin.builders.data.rawData({ data: input.moleculeSdf }, { state: { isGhost: true } });
-        const trajectory = await this.plugin.builders.structure.parseTrajectory(data, 'mol');
-        const model = await this.plugin.builders.structure.createModel(trajectory);
-        const structure = await this.plugin.builders.structure.createStructure(model);
-
-        const all = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'all');
-        if (all) await this.plugin.builders.structure.representation.addRepresentation(all, { type: 'ball-and-stick', color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } });
-
-
-        this.basis = await this.plugin.build().toRoot()
-            .apply(StaticBasisAndOrbitals, { basis: input.basis, order: input.order, orbitals: input.orbitals })
-            .commit();
-
-        await this.syncVolume();
-
-        this.params.next({
-            show: ParamDefinition.MappedStatic('orbital', {
-                'orbital': ParamDefinition.Group({
-                    index: ParamDefinition.Numeric(32, { min: 0, max: input.orbitals.length - 1 }, { immediateUpdate: true, isEssential: true }),
-                }),
-                'density': ParamDefinition.EmptyGroup()
-            }, { cycle: true }),
-            isoValue: ParamDefinition.Numeric(this.currentParams.isoValue, { min: 0.5, max: 3, step: 0.1 }, { immediateUpdate: true, isEssential: false }),
-            gpuSurface: ParamDefinition.Boolean(this.currentParams.gpuSurface, { isHidden: true })
-        });
-
-        this.state.pipe(skip(1), debounceTime(1000 / 24)).subscribe(async params => {
-            if (params.show.name !== this.currentParams.show.name
-                || (params.show.name === 'orbital' && this.currentParams.show.name === 'orbital' && params.show.params.index !== this.currentParams.show.params.index)) {
-                this.syncVolume();
-            } else if (params.isoValue !== this.currentParams.isoValue || params.gpuSurface !== this.currentParams.gpuSurface) {
-                this.setIsovalue();
-            }
-        });
-    }
-}
-
-(window as any).AlphaOrbitalsExample = new AlphaOrbitalsExample();

src/examples/basic-wrapper/controls.tsx

@@ -1,16 +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';
-
-export class CustomToastMessage extends PluginUIComponent {
-    render() {
-        return <>
-            Custom <i>Toast</i> content. No timeout.
-        </>;
-    }
-}

src/examples/basic-wrapper/index.ts

@@ -1,168 +0,0 @@
-/**
- * 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 } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
-import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-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, {});
-    }
-
-    private animateModelIndexTargetFps() {
-        return Math.max(1, this.animate.modelIndex.targetFps | 0);
-    }
-
-    animate = {
-        modelIndex: {
-            targetFps: 8,
-            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'forward' } } }); },
-            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'backward' } } }); },
-            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'palindrome', params: {} } }); },
-            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, 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 data = this.plugin.managers.structure.hierarchy.current.structures[0]?.cell.obj?.data;
-            if (!data) return;
-
-            const seq_id = 7;
-            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

@@ -1,119 +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 } 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/lighting/index.ts

@@ -1,119 +0,0 @@
-/**
- * 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 } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
-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: { samples: 64, radius: 8, bias: 1.0, blurKernelSize: 13 } },
-            outline: { name: 'on', params: { scale: 1, threshold: 0.33 } }
-        },
-        renderer: {
-            ambientIntensity: 1,
-            lightIntensity: 0,
-        }
-    },
-    occlusion: <Preset> {
-        multiSample: {
-            mode: 'temporal' as Canvas3DProps['multiSample']['mode']
-        },
-        postprocessing: {
-            occlusion: { name: 'on', params: { samples: 64, radius: 8, bias: 1.0, blurKernelSize: 13 } },
-            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

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

src/examples/proteopedia-wrapper/coloring.ts

@@ -6,63 +6,63 @@
  */
 
 
-import { Unit, StructureProperties, StructureElement, Bond } from '../../mol-model/structure';
+import { Unit, StructureProperties, StructureElement, Link } 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(ctx.structure);
-            const { models } = ctx.structure;
-            const asymIdSerialMap = new Map<string, number>();
+            const l = StructureElement.Location.create()
+            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 (Bond.isLocation(location)) {
-                    const asym_id = getAsymId(location.aUnit);
-                    l.unit = location.aUnit;
-                    l.element = location.aUnit.elements[location.aIndex];
+                } else if (Link.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
-        };
+        }
     }
 
-    return {
-        name: 'proteopedia-custom',
+    const ProteopediaCustomColorThemeProvider: ColorTheme.Provider<ProteopediaCustomColorThemeParams> = {
         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 { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
-import { Model, ResidueIndex } from '../../mol-model/structure';
+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 { 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[] }[],
@@ -53,12 +53,14 @@ 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);
-            const entityType = model.entities.data.type.value(eI);
-            if (entityType !== 'non-polymer' && entityType !== 'branched') continue;
-
-            const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(residueOffsets[rI]);
+            if (model.entities.data.type.value(eI) === 'water') continue;
 
             let lig = hetMap.get(comp_id);
             if (!lig) {
@@ -70,11 +72,10 @@ export namespace ModelInfo {
         }
 
         const preferredAssemblyId = await pref;
-        const symmetry = ModelSymmetry.Provider.get(model);
 
         return {
             hetResidues: hetResidues,
-            assemblies: symmetry ? symmetry.assemblies.map(a => ({ id: a.id, details: a.details, isPreferred: a.id === preferredAssemblyId })) : [],
+            assemblies: model.symmetry.assemblies.map(a => ({ id: a.id, details: a.details, isPreferred: a.id === preferredAssemblyId })),
             preferredAssemblyId
         };
     }
@@ -84,7 +85,6 @@ 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?: StructureRepresentationRegistry.BuiltIn, coloring?: ColorTheme.BuiltIn }
+    export type Entry = { hide?: boolean, kind?: BuiltInStructureRepresentationsName, coloring?: BuiltInColorThemeName }
 }
 
 export enum StateElements {

src/examples/proteopedia-wrapper/index.html

@@ -48,7 +48,7 @@
                 width: 300px;
             }
         </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
+        <link rel="stylesheet" type="text/css" href="app.css" />
         <script type="text/javascript" src="./index.js"></script>
     </head>
     <body>
@@ -60,12 +60,11 @@
                 <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
@@ -74,28 +73,24 @@
             console.log('Wrapper version', MolStarProteopediaWrapper.VERSION_MAJOR, MolStarProteopediaWrapper.VERSION_MINOR);
 
             function $(id) { return document.getElementById(id); }
-
-            var pdbId = '1cbs', assemblyId= 'preferred', isBinary = true;
-            var url = 'https://www.ebi.ac.uk/pdbe/entry-files/download/' + pdbId + '.bcif'
+        
+            var pdbId = '1cbs', assemblyId= 'preferred';
+            var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
             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; };
 
-            function loadAndSnapshot(params) {
-                PluginWrapper.load(params).then(() => {
-                    setTimeout(() => snapshot = PluginWrapper.plugin.state.getSnapshot({ canvas3d: false /* do not save spinning state */ }), 500);
-                });
-            }
+            // var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
+            // var format = 'pdb';
+            // var assemblyId = 'deposited';
 
             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 }
@@ -105,7 +100,7 @@
                 customColorList: CustomColors
             });
             PluginWrapper.setBackground(0xffffff);
-            loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
+            PluginWrapper.load({ url: url, format: format, assemblyId: assemblyId, representationStyle: representationStyle });
             PluginWrapper.toggleSpin();
 
             PluginWrapper.events.modelInfo.subscribe(function (info) {
@@ -113,8 +108,8 @@
                 listHetGroups(info);
             });
 
-            addControl('Load Asym Unit', () => loadAndSnapshot({ url: url, format: format, isBinary }));
-            addControl('Load Assembly', () => loadAndSnapshot({ url: url, format: format, isBinary, assemblyId: assemblyId }));
+            addControl('Load Asym Unit', () => PluginWrapper.load({ url: url, format: format }));
+            addControl('Load Assembly', () => PluginWrapper.load({ url: url, format: format, assemblyId: assemblyId }));
 
             addSeparator();
 
@@ -140,14 +135,14 @@
             // 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');
 
             // adjust this number to make the animation faster or slower
             // requires to "restart" the animation if changed
-            PluginWrapper.animate.modelIndex.targetFps = 30;
+            PluginWrapper.animate.modelIndex.maxFPS = 30;
 
             addControl('Play To End', () => PluginWrapper.animate.modelIndex.onceForward());
             addControl('Play To Start', () => PluginWrapper.animate.modelIndex.onceBackward());
@@ -173,24 +168,20 @@
             addControl('Init', () => PluginWrapper.experimentalData.init($('volume-streaming-wrapper')));
             addControl('Remove', () => PluginWrapper.experimentalData.remove());
 
-            addSeparator();
+            addSeparator(); 
             addHeader('State');
 
             var snapshot;
-            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('Create Snapshot', () => {
+                snapshot = PluginWrapper.snapshot.get();
+                // could use JSON.stringify(snapshot) and upload the data
             });
-            addControl('Restore Snapshot', () => {
+            addControl('Apply Snapshot', () => {
                 if (!snapshot) return;
                 PluginWrapper.snapshot.set(snapshot);
-            });
-            addControl('Download State', () => {
-                PluginWrapper.snapshot.download('molj');
-            });
-            addControl('Download Session', () => {
-                PluginWrapper.snapshot.download('molx');
+
+                // or download snapshot using fetch or ajax or whatever
+                // or PluginWrapper.snapshot.download(url);
             });
 
             ////////////////////////////////////////////////////////
@@ -226,7 +217,7 @@
                     var l = document.createElement('button');
                     l.innerText = r.name;
                     l.onclick = function () {
-                        PluginWrapper.hetGroups.focusFirst(r.name, { doNotLabelWaters: true });
+                        PluginWrapper.hetGroups.focusFirst(r.name);
                     };
                     div.appendChild(l);
                 });

src/examples/proteopedia-wrapper/index.ts

@@ -5,35 +5,38 @@
  */
 
 import * as ReactDOM from 'react-dom';
-import { Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
-import { createPlugin } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
-import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
-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 { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import './index.html'
 import { PluginContext } from '../../mol-plugin/context';
-import { PluginState } from '../../mol-plugin/state';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
-import { Asset } from '../../mol-util/assets';
+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 { ColorNames } from '../../mol-util/color/names';
-import { getFormattedTime } from '../../mol-util/date';
-import { download } from '../../mol-util/download';
-import { RxEventHelper } from '../../mol-util/rx-event-helper';
+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 { LoadParams, ModelInfo, RepresentationStyle, StateElements, SupportedFormats } from './helpers';
-import './index.html';
-import { volumeStreamingControls } from './ui/controls';
-require('../../mol-plugin-ui/skin/light.scss');
+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 { ColorNames } from '../../mol-util/color/names';
+import { InitVolumeStreaming, CreateVolumeStreamingInfo } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
+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')
 
 class MolStarProteopediaWrapper {
-    static VERSION_MAJOR = 5;
-    static VERSION_MINOR = 5;
+    static VERSION_MAJOR = 3;
+    static VERSION_MINOR = 4;
 
     private _ev = RxEventHelper.create();
 
@@ -47,7 +50,7 @@ class MolStarProteopediaWrapper {
         customColorList?: number[]
     }) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec(),
+            ...DefaultPluginSpec,
             animations: [
                 AnimateModelIndex
             ],
@@ -55,27 +58,27 @@ class MolStarProteopediaWrapper {
                 initial: {
                     isExpanded: false,
                     showControls: false
+                },
+                controls: {
+                    right: ControlsWrapper
                 }
-            },
-            components: {
-                remoteState: 'none'
             }
         });
 
         const customColoring = createProteopediaCustomTheme((options && options.customColorList) || []);
 
-        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);
+        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);
     }
 
     get state() {
-        return this.plugin.state.data;
+        return this.plugin.state.dataState;
     }
 
-    private download(b: StateBuilder.To<PSO.Root>, url: string, isBinary: boolean) {
-        return b.apply(StateTransforms.Data.Download, { url: Asset.Url(url), isBinary });
+    private download(b: StateBuilder.To<PSO.Root>, url: string) {
+        return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
     }
 
     private model(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats) {
@@ -89,18 +92,10 @@ 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.StructureFromModel, props, { ref: StateElements.Assembly });
+            .apply(StateTransforms.Model.CustomModelProperties, { properties: [EvolutionaryConservation.Descriptor.name] }, { ref: StateElements.ModelProps, state: { isGhost: false } })
+            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { 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 });
@@ -123,10 +118,9 @@ class MolStarProteopediaWrapper {
                 root.delete(StateElements.SequenceVisual);
             } else {
                 root.applyOrUpdate(StateElements.SequenceVisual, StateTransforms.Representation.StructureRepresentation3D,
-                    createStructureRepresentationParams(this.plugin, structure, {
-                        type: (style.sequence && style.sequence.kind) || 'cartoon',
-                        color: (style.sequence && style.sequence.coloring) || 'unit-index'
-                    }));
+                    StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
+                        (style.sequence && style.sequence.kind) || 'cartoon',
+                        (style.sequence && style.sequence.coloring) || 'unit-index', structure));
             }
         }
 
@@ -139,10 +133,9 @@ class MolStarProteopediaWrapper {
                     root.delete(StateElements.HetVisual);
                 } else {
                     root.applyOrUpdate(StateElements.HetVisual, StateTransforms.Representation.StructureRepresentation3D,
-                        createStructureRepresentationParams(this.plugin, structure, {
-                            type: (style.hetGroups && style.hetGroups.kind) || 'ball-and-stick',
-                            color: style.hetGroups && style.hetGroups.coloring
-                        }));
+                        StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
+                            (style.hetGroups && style.hetGroups.kind) || 'ball-and-stick',
+                            (style.hetGroups && style.hetGroups.coloring), structure));
                 }
             }
         }
@@ -156,7 +149,7 @@ class MolStarProteopediaWrapper {
                     root.delete(StateElements.Het3DSNFG);
                 } else {
                     root.applyOrUpdate(StateElements.Het3DSNFG, StateTransforms.Representation.StructureRepresentation3D,
-                        createStructureRepresentationParams(this.plugin, structure, { type: 'carbohydrate' }));
+                        StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin, 'carbohydrate', void 0, structure));
                 }
             }
         }
@@ -167,11 +160,9 @@ class MolStarProteopediaWrapper {
                 root.delete(StateElements.WaterVisual);
             } else {
                 root.applyOrUpdate(StateElements.WaterVisual, StateTransforms.Representation.StructureRepresentation3D,
-                    createStructureRepresentationParams(this.plugin, structure, {
-                        type: (style.water && style.water.kind) || 'ball-and-stick',
-                        typeParams: { alpha: 0.51 },
-                        color: style.water && style.water.coloring
-                    }));
+                        StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
+                            (style.water && style.water.kind) || 'ball-and-stick',
+                            (style.water && style.water.coloring), structure, { alpha: 0.51 }));
             }
         }
 
@@ -189,21 +180,20 @@ 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(this.plugin, { state: this.plugin.state.data, tree });
+        return PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
     }
 
-    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) {
+    private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
+    async load({ url, format = 'cif', assemblyId = 'deposited', representationStyle }: LoadParams) {
         let loadType: 'full' | 'update' = 'full';
 
-        const state = this.plugin.state.data;
+        const state = this.plugin.state.dataState;
 
         if (this.loadedParams.url !== url || this.loadedParams.format !== format) {
             loadType = 'full';
@@ -212,8 +202,8 @@ class MolStarProteopediaWrapper {
         }
 
         if (loadType === 'full') {
-            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 PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
+            const modelTree = this.model(this.download(state.build().toRoot(), url), format);
             await this.applyState(modelTree);
             const info = await this.doInfo(true);
             const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
@@ -223,45 +213,37 @@ class MolStarProteopediaWrapper {
             const tree = state.build();
             const info = await this.doInfo(true);
             const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
-            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 }));
+            tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: asmId }));
             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(this.plugin, { state: this.plugin.state.data, tree });
+        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
     }
 
     setBackground(color: number) {
-        if (!this.plugin.canvas3d) return;
         const renderer = this.plugin.canvas3d.props.renderer;
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
+        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
     }
 
     toggleSpin() {
-        if (!this.plugin.canvas3d) return;
         const trackball = this.plugin.canvas3d.props.trackball;
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
+        const spinning = trackball.spin;
+        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
+        if (!spinning) PluginCommands.Camera.Reset.dispatch(this.plugin, { });
     }
 
     viewport = {
         setSettings: (settings?: Canvas3DProps) => {
-            PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, {
                 settings: settings || DefaultCanvas3DParams
             });
         }
@@ -269,21 +251,36 @@ class MolStarProteopediaWrapper {
 
     camera = {
         toggleSpin: () => this.toggleSpin(),
-        resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { })
-    }
+        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;
+        //     }
 
-    private animateModelIndexTargetFps() {
-        return Math.max(1, this.animate.modelIndex.targetFps | 0);
+        //     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] }
+        //     });
+        // }
     }
 
     animate = {
         modelIndex: {
-            targetFps: 8,
-            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'forward' } } }); },
-            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'backward' } } }); },
-            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'palindrome', params: {} } }); },
-            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: {} } }); },
-            stop: () => this.plugin.managers.animation.stop()
+            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()
         }
     }
 
@@ -294,8 +291,13 @@ 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.propertyProvider.descriptor.name, params: this.plugin.representation.structure.themes.colorThemeRegistry.get(EvolutionaryConservation.propertyProvider.descriptor.name).defaultValues };
+            const colorTheme = { name: EvolutionaryConservation.Descriptor.name, params: this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.get(EvolutionaryConservation.Descriptor.name).defaultValues };
 
             if (!params || !!params.sequence) {
                 tree.to(StateElements.SequenceVisual).update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
@@ -304,7 +306,7 @@ class MolStarProteopediaWrapper {
                 tree.to(StateElements.HetVisual).update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
             }
 
-            await PluginCommands.State.Update(this.plugin, { state, tree });
+            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
         }
     }
 
@@ -324,7 +326,7 @@ class MolStarProteopediaWrapper {
         remove: () => {
             const r = this.state.select(StateSelection.Generators.ofTransformer(CreateVolumeStreamingInfo))[0];
             if (!r) return;
-            PluginCommands.State.RemoveObject(this.plugin, { state: this.state, ref: r.transform.ref });
+            PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.state, ref: r.transform.ref });
             if (this.experimentalDataElement) {
                 ReactDOM.unmountComponentAtNode(this.experimentalDataElement);
                 this.experimentalDataElement = void 0;
@@ -335,12 +337,14 @@ class MolStarProteopediaWrapper {
     hetGroups = {
         reset: () => {
             const update = this.state.build().delete(StateElements.HetGroupFocusGroup);
-            PluginCommands.State.Update(this.plugin, { state: this.state, tree: update });
-            PluginCommands.Camera.Reset(this.plugin, { });
+            PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
+            PluginCommands.Camera.Reset.dispatch(this.plugin, { });
         },
-        focusFirst: async (compId: string, options?: { hideLabels: boolean, doNotLabelWaters: boolean }) => {
+        focusFirst: async (compId: string) => {
             if (!this.state.transforms.has(StateElements.Assembly)) return;
-            await PluginCommands.Camera.Reset(this.plugin, { });
+            await PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+
+            // const asm = (this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure).data;
 
             const update = this.state.build();
 
@@ -355,66 +359,65 @@ 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, createStructureRepresentationParams(this.plugin, asm.data, {
-                    type: 'ball-and-stick',
-                    color: 'uniform', colorParams: { value: ColorNames.gray },
-                    size: 'uniform', sizeParams: { value: 0.33 }
-                }));
+                .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,
+            //     }
+            // });
 
-            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 });
+            await PluginCommands.State.Update.dispatch(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 radius = Math.max(sphere.radius, 5);
-            const snapshot = this.plugin.canvas3d!.camera.getFocus(sphere.center, radius);
-            PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: 250 });
+            // 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 });
         }
     }
 
+    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: (params?: PluginState.SnapshotParams) => {
-            return this.plugin.state.getSnapshot(params);
+        get: () => {
+            return this.plugin.state.getSnapshot();
         },
         set: (snapshot: PluginState.Snapshot) => {
             return this.plugin.state.setSnapshot(snapshot);
         },
-        download: async (type: 'molj' | 'molx' = 'molj', params?: PluginState.SnapshotParams) => {
-            const data = await this.plugin.managers.snapshot.serialize({ type, params });
-            download(data, `mol-star_state_${getFormattedTime()}.${type}`);
-        },
-        fetch: async (url: string, type: 'molj' | 'molx' = 'molj') => {
+        download: async (url: string) => {
             try {
-                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}`));
+                const data = await this.plugin.runTask(this.plugin.fetch({ url }));
+                const snapshot = JSON.parse(data);
+                await this.plugin.state.setSnapshot(snapshot);
             } catch (e) {
                 console.log(e);
             }

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

@@ -6,13 +6,27 @@
 
 import * as React from 'react';
 import * as ReactDOM from 'react-dom';
-import { PluginContextContainer } from '../../../mol-plugin-ui/plugin';
-import { TransformUpdaterControl } from '../../../mol-plugin-ui/state/update-transform';
+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 { 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() {
@@ -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) {

src/extensions/alpha-orbitals/_spec/collocation.spec.ts

@@ -1,214 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { Box3D } from '../../../mol-math/geometry';
-import { Vec3 } from '../../../mol-math/linear-algebra';
-import { RuntimeContext } from '../../../mol-task';
-import { sphericalCollocation } from '../collocation';
-import { Basis, CubeGridInfo } from '../data-model';
-
-describe('alpha-orbitals-cubes', () => {
-    it('water', async () => {
-        const grid: CubeGridInfo = {
-            params: {
-                basis: _testBasis,
-                cutoffThreshold: 0,
-                sphericalOrder: 'cca-reverse',
-                boxExpand: 0,
-                gridSpacing: []
-            },
-            box: Box3D.create(Vec3.create(-1, -1, -1), Vec3.create(1, 1, 1)),
-            delta: Vec3.create(2, 2, 2),
-            dimensions: Vec3.create(2, 2, 2),
-            npoints: 8,
-            size: Vec3.create(2, 2, 2)
-        };
-
-        const matrix = await sphericalCollocation(grid, {
-            energy: 0,
-            occupancy: 0,
-            alpha: [-2.2623991420609075e-16, 0.6360205395000592, 0.6672122399886391, -0.3876927909355508, -1.6780131293332933e-16, 2.844782862661151e-16, 4.977960694176068e-19, -2.3945919908996803e-16]
-        }, RuntimeContext.Synchronous);
-
-        const expected = [-0.1451730622877498, 0.06479453956039086, -0.2777738736440713, -0.057116584776260436, 0.05929916178822645, 0.2742903371231049, -0.07221698722165386, 0.15389180241391376];
-
-        expect(matrix.length).toBe(expected.length);
-
-        for (let i = 0; i < matrix.length; i++) {
-            expect(Math.abs(matrix[i] - expected[i]) < 1e-6).toBe(true);
-        }
-    });
-});
-
-const _testBasis: Basis = {
-    'atoms': [
-        {
-            'center': [
-                0.025886090588624934,
-                0.019164790004065606,
-                -0.013539970104105408
-            ] as Vec3,
-            'shells': [
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            -0.004151277818987536,
-                            -0.02067024147993795,
-                            -0.05150303336984537,
-                            0.33462711739899537,
-                            0.5621061300983125,
-                            0.17129946969948573
-                        ]
-                    ],
-                    'exponents': [
-                        152.28769660788095,
-                        27.928015215973073,
-                        7.848374792384515,
-                        1.1223350202705642,
-                        0.5093846587907856,
-                        0.24292266532510307
-                    ]
-                },
-                {
-                    'angularMomentum': [1],
-                    'coefficients': [
-                        [
-                            0.007924233646294425,
-                            0.051441048251911314,
-                            0.18984000600705359,
-                            0.4049863191150474,
-                            0.40123628611490797,
-                            0.1051855189039082
-                        ]
-                    ],
-                    'exponents': [
-                        27.203421487167727,
-                        7.09409912597673,
-                        2.5383362605345954,
-                        1.0610730767843852,
-                        0.4851948916410433,
-                        0.22938302550642545
-                    ]
-                }
-            ]
-        },
-        {
-            'center': [
-                0.5082729578468134,
-                1.6880351220025265,
-                0.4963443067810461
-            ] as Vec3,
-            'shells': [
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            0.009163596280542963,
-                            0.04936149294292479,
-                            0.16853830490998634,
-                            0.37056279972195677,
-                            0.4164915298246781,
-                            0.13033408410772263
-                        ]
-                    ],
-                    'exponents': [
-                        33.710073211949485,
-                        6.180705022740464,
-                        1.7291385346152253,
-                        0.5940057549921978,
-                        0.2306698170449518,
-                        0.09500256906284119
-                    ]
-                },
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            -0.32279868167000036,
-                            3.209629817295221,
-                            2.4672629224617935,
-                            -0.048487066612842224,
-                            -0.2611850111200143,
-                            -0.8917817597810863,
-                            -1.9607480081275706,
-                            -2.203769342520311,
-                            -0.6896328935259993
-                        ]
-                    ],
-                    'exponents': [
-                        10.256286070314905,
-                        0.6227965325875392,
-                        0.2391007667853915,
-                        33.710073211949485,
-                        6.180705022740464,
-                        1.7291385346152253,
-                        0.5940057549921978,
-                        0.2306698170449518,
-                        0.09500256906284119
-                    ]
-                }
-            ]
-        },
-        {
-            'center': [
-                1.1367367844436005,
-                -0.47018519422670163,
-                -1.356802622574504
-            ] as Vec3,
-            'shells': [
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            0.009163596280542963,
-                            0.04936149294292479,
-                            0.16853830490998634,
-                            0.37056279972195677,
-                            0.4164915298246781,
-                            0.13033408410772263
-                        ]
-                    ],
-                    'exponents': [
-                        33.710073211949485,
-                        6.180705022740464,
-                        1.7291385346152253,
-                        0.5940057549921978,
-                        0.2306698170449518,
-                        0.09500256906284119
-                    ]
-                },
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            -0.32279868167000036,
-                            3.209629817295221,
-                            2.4672629224617935,
-                            -0.048487066612842224,
-                            -0.2611850111200143,
-                            -0.8917817597810863,
-                            -1.9607480081275706,
-                            -2.203769342520311,
-                            -0.6896328935259993
-                        ]
-                    ],
-                    'exponents': [
-                        10.256286070314905,
-                        0.6227965325875392,
-                        0.2391007667853915,
-                        33.710073211949485,
-                        6.180705022740464,
-                        1.7291385346152253,
-                        0.5940057549921978,
-                        0.2306698170449518,
-                        0.09500256906284119
-                    ]
-                }
-            ]
-        }
-    ]
-};

src/extensions/alpha-orbitals/collocation.ts

@@ -1,162 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Inspired by https://github.com/dgasmith/gau2grid.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { Vec3 } from '../../mol-math/linear-algebra';
-import { RuntimeContext } from '../../mol-task';
-import { arrayMin } from '../../mol-util/array';
-import { AlphaOrbital, CubeGridInfo } from './data-model';
-import { normalizeBasicOrder, SphericalFunctions } from './spherical-functions';
-
-export async function sphericalCollocation(
-    grid: CubeGridInfo,
-    orbital: AlphaOrbital,
-    taskCtx: RuntimeContext
-) {
-    const { basis, sphericalOrder, cutoffThreshold } = grid.params;
-    let baseCount = 0;
-
-    for (const atom of basis.atoms) {
-        for (const shell of atom.shells) {
-            for (const L of shell.angularMomentum) {
-                if (L > 4) {
-                    // TODO: will L > 4 be required? Would need to precompute more functions in that case.
-                    throw new Error('Angular momentum L > 4 not supported.');
-                }
-
-                baseCount += 2 * L + 1;
-            }
-        }
-    }
-
-    const matrix = new Float32Array(grid.npoints);
-
-    let baseIndex = 0;
-    for (const atom of basis.atoms) {
-        for (const shell of atom.shells) {
-            let amIndex = 0;
-            for (const L of shell.angularMomentum) {
-                const alpha = normalizeBasicOrder(
-                    L,
-                    orbital.alpha.slice(baseIndex, baseIndex + 2 * L + 1),
-                    sphericalOrder
-                );
-                baseIndex += 2 * L + 1;
-
-                collocationBasis(
-                    matrix,
-                    grid,
-                    L,
-                    shell.coefficients[amIndex++],
-                    shell.exponents,
-                    atom.center,
-                    cutoffThreshold,
-                    alpha
-                );
-
-                if (taskCtx.shouldUpdate) {
-                    await taskCtx.update({
-                        message: 'Computing...',
-                        current: baseIndex,
-                        max: baseCount,
-                        isIndeterminate: false,
-                    });
-                }
-            }
-        }
-    }
-
-    return matrix;
-}
-
-function collocationBasis(
-    matrix: Float32Array,
-    grid: CubeGridInfo,
-    L: number,
-    coefficients: number[],
-    exponents: number[],
-    center: Vec3,
-    cutoffThreshold: number,
-    alpha: number[]
-) {
-    const ncoeff = exponents.length;
-    const sphericalFunc = SphericalFunctions[L];
-
-    const cx = center[0],
-        cy = center[1],
-        cz = center[2];
-    const ny = grid.dimensions[1],
-        nz = grid.dimensions[2];
-    const gdx = grid.delta[0],
-        gdy = grid.delta[1],
-        gdz = grid.delta[2];
-    const sx = grid.box.min[0],
-        sy = grid.box.min[1],
-        sz = grid.box.min[2];
-
-    const cutoffRadius =
-        cutoffThreshold > 0
-            ? Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(exponents))
-            : 10000;
-    const cutoffSquared = cutoffRadius * cutoffRadius;
-
-    const radiusBox = getRadiusBox(grid, center, cutoffRadius);
-    const iMin = radiusBox[0][0],
-        jMin = radiusBox[0][1],
-        kMin = radiusBox[0][2];
-    const iMax = radiusBox[1][0],
-        jMax = radiusBox[1][1],
-        kMax = radiusBox[1][2];
-
-    for (let i = iMin; i <= iMax; i++) {
-        const x = sx + gdx * i - cx;
-        const oX = i * ny * nz;
-
-        for (let j = jMin; j <= jMax; j++) {
-            const y = sy + gdy * j - cy;
-            const oY = oX + j * nz;
-            for (let k = kMin; k <= kMax; k++) {
-                const z = sz + gdz * k - cz;
-                const R2 = x * x + y * y + z * z;
-
-                if (R2 > cutoffSquared) {
-                    continue;
-                }
-
-                let gaussianSum = 0;
-                for (let c = 0; c < ncoeff; c++) {
-                    gaussianSum +=
-                        coefficients[c] * Math.exp(-exponents[c] * R2);
-                }
-
-                const sphericalSum = L === 0 ? alpha[0] : sphericalFunc(alpha, x, y, z);
-
-
-                matrix[k + oY] += gaussianSum * sphericalSum;
-            }
-        }
-    }
-}
-
-function getRadiusBox(grid: CubeGridInfo, center: Vec3, radius: number) {
-    const r = Vec3.create(radius, radius, radius);
-    const min = Vec3.scaleAndAdd(Vec3(), center, r, -1);
-    const max = Vec3.add(Vec3(), center, r);
-
-    Vec3.sub(min, min, grid.box.min);
-    Vec3.sub(max, max, grid.box.min);
-
-    Vec3.div(min, min, grid.delta);
-    Vec3.floor(min, min);
-    Vec3.max(min, min, Vec3());
-
-    Vec3.div(max, max, grid.delta);
-    Vec3.ceil(max, max);
-    Vec3.min(max, max, Vec3.subScalar(Vec3(), grid.dimensions, 1));
-
-    return [min, max];
-}

src/extensions/alpha-orbitals/data-model.ts

@@ -1,131 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { Mat4, Tensor, Vec3 } from '../../mol-math/linear-algebra';
-import { Grid } from '../../mol-model/volume';
-import { SphericalBasisOrder } from './spherical-functions';
-import { Box3D, RegularGrid3d } from '../../mol-math/geometry';
-import { arrayMin, arrayMax, arrayRms, arrayMean } from '../../mol-util/array';
-
-// Note: generally contracted gaussians are currently not supported.
-export interface SphericalElectronShell {
-    exponents: number[];
-    angularMomentum: number[];
-    // number[] for each angular momentum
-    coefficients: number[][];
-}
-
-export interface Basis {
-    atoms: {
-        // in Bohr units!
-        center: Vec3;
-        shells: SphericalElectronShell[];
-    }[];
-}
-
-export interface AlphaOrbital {
-    energy: number;
-    occupancy: number;
-    alpha: number[];
-}
-
-export interface CubeGridComputationParams {
-    basis: Basis;
-    /**
-     * for each electron shell compute a cutoff radius as
-     *    const cutoffRadius = Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(exponents));
-     */
-    cutoffThreshold: number;
-    sphericalOrder: SphericalBasisOrder;
-    boxExpand: number;
-    gridSpacing: number | [atomCountThreshold: number, spacing: number][];
-    doNotComputeIsovalues?: boolean;
-}
-
-export interface CubeGridInfo {
-    params: CubeGridComputationParams;
-    dimensions: Vec3;
-    box: Box3D;
-    size: Vec3;
-    npoints: number;
-    delta: Vec3;
-}
-
-export interface CubeGrid {
-    grid: Grid;
-    isovalues?: { negative?: number; positive?: number };
-}
-
-export function initCubeGrid(params: CubeGridComputationParams): CubeGridInfo {
-    const geometry = params.basis.atoms.map(a => a.center);
-    const { gridSpacing: spacing, boxExpand: expand } = params;
-
-    const count = geometry.length;
-    const box = Box3D.expand(
-        Box3D(),
-        Box3D.fromVec3Array(Box3D(), geometry),
-        Vec3.create(expand, expand, expand)
-    );
-    const size = Box3D.size(Vec3(), box);
-
-    const spacingThresholds =
-        typeof spacing === 'number' ? [[0, spacing]] : [...spacing];
-    spacingThresholds.sort((a, b) => b[0] - a[0]);
-
-    let s = 0.4;
-    for (let i = 0; i <= spacingThresholds.length; i++) {
-        s = spacingThresholds[i][1];
-        if (spacingThresholds[i][0] <= count) break;
-    }
-
-    const dimensions = Vec3.ceil(Vec3(), Vec3.scale(Vec3(), size, 1 / s));
-
-    return {
-        params,
-        box,
-        dimensions,
-        size,
-        npoints: dimensions[0] * dimensions[1] * dimensions[2],
-        delta: Vec3.div(Vec3(), size, Vec3.subScalar(Vec3(), dimensions, 1)),
-    };
-}
-
-const BohrToAngstromFactor = 0.529177210859;
-
-export function createGrid(gridInfo: RegularGrid3d, values: Float32Array, axisOrder: number[]) {
-    const boxSize = Box3D.size(Vec3(), gridInfo.box);
-    const boxOrigin = Vec3.clone(gridInfo.box.min);
-
-    Vec3.scale(boxSize, boxSize, BohrToAngstromFactor);
-    Vec3.scale(boxOrigin, boxOrigin, BohrToAngstromFactor);
-
-    const scale = Mat4.fromScaling(
-        Mat4(),
-        Vec3.div(
-            Vec3(),
-            boxSize,
-            Vec3.sub(Vec3(), gridInfo.dimensions, Vec3.create(1, 1, 1))
-        )
-    );
-    const translate = Mat4.fromTranslation(Mat4(), boxOrigin);
-    const matrix = Mat4.mul(Mat4(), translate, scale);
-
-    const grid: Grid = {
-        transform: { kind: 'matrix', matrix },
-        cells: Tensor.create(
-            Tensor.Space(gridInfo.dimensions, axisOrder, Float32Array),
-            (values as any) as Tensor.Data
-        ),
-        stats: {
-            min: arrayMin(values),
-            max: arrayMax(values),
-            mean: arrayMean(values),
-            sigma: arrayRms(values),
-        },
-    };
-
-    return grid;
-}

src/extensions/alpha-orbitals/density.ts

@@ -1,124 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { sortArray } from '../../mol-data/util';
-import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
-import { WebGLContext } from '../../mol-gl/webgl/context';
-import { Task } from '../../mol-task';
-import { AlphaOrbital, createGrid, CubeGrid, CubeGridComputationParams, initCubeGrid } from './data-model';
-import { gpuComputeAlphaOrbitalsDensityGridValues } from './gpu/compute';
-
-export function createSphericalCollocationDensityGrid(
-    params: CubeGridComputationParams, orbitals: AlphaOrbital[], webgl?: WebGLContext
-): Task<CubeGrid> {
-    return Task.create('Spherical Collocation Grid', async (ctx) => {
-        const cubeGrid = initCubeGrid(params);
-
-        let matrix: Float32Array;
-        if (canComputeGrid3dOnGPU(webgl)) {
-            // console.time('gpu');
-            matrix = await gpuComputeAlphaOrbitalsDensityGridValues(ctx, webgl!, cubeGrid, orbitals);
-            // console.timeEnd('gpu');
-        } else {
-            throw new Error('Missing OES_texture_float WebGL extension.');
-        }
-
-        const grid = createGrid(cubeGrid, matrix, [0, 1, 2]);
-        let isovalues: { negative?: number, positive?: number } | undefined;
-
-        if (!params.doNotComputeIsovalues) {
-            isovalues = computeDensityIsocontourValues(matrix, 0.85);
-        }
-
-        return { grid, isovalues };
-    });
-}
-
-export function computeDensityIsocontourValues(input: Float32Array, cumulativeThreshold: number) {
-    let weightSum = 0;
-    for (let i = 0, _i = input.length; i < _i; i++) {
-        const v = input[i];
-        const w = Math.abs(v);
-        weightSum += w;
-    }
-    const avgWeight = weightSum / input.length;
-    let minWeight = 3 * avgWeight;
-
-    // do not try to identify isovalues for degenerate data
-    // e.g. all values are almost same
-    if (Math.abs(avgWeight - input[0] * input[0]) < 1e-5) {
-        return { negative: void 0, positive: void 0 };
-    }
-
-    let size = 0;
-    while (true) {
-        let csum = 0;
-        size = 0;
-        for (let i = 0, _i = input.length; i < _i; i++) {
-            const v = input[i];
-            const w = Math.abs(v);
-            if (w >= minWeight) {
-                csum += w;
-                size++;
-            }
-        }
-
-        if (csum / weightSum > cumulativeThreshold) {
-            break;
-        }
-
-        minWeight -= avgWeight;
-    }
-
-    const values = new Float32Array(size);
-    const weights = new Float32Array(size);
-    const indices = new Int32Array(size);
-
-    let o = 0;
-    for (let i = 0, _i = input.length; i < _i; i++) {
-        const v = input[i];
-        const w = Math.abs(v);
-        if (w >= minWeight) {
-            values[o] = v;
-            weights[o] = w;
-            indices[o] = o;
-            o++;
-        }
-    }
-
-    sortArray(
-        indices,
-        (indices, i, j) => weights[indices[j]] - weights[indices[i]]
-    );
-
-    let cweight = 0,
-        cutoffIndex = 0;
-    for (let i = 0; i < size; i++) {
-        cweight += weights[indices[i]];
-
-        if (cweight / weightSum >= cumulativeThreshold) {
-            cutoffIndex = i;
-            break;
-        }
-    }
-
-    let positive = Number.POSITIVE_INFINITY,
-        negative = Number.NEGATIVE_INFINITY;
-
-    for (let i = 0; i < cutoffIndex; i++) {
-        const v = values[indices[i]];
-        if (v > 0) {
-            if (v < positive) positive = v;
-        } else if (v < 0) {
-            if (v > negative) negative = v;
-        }
-    }
-
-    return {
-        negative: negative !== Number.NEGATIVE_INFINITY ? negative : void 0,
-        positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
-    };
-}

src/extensions/alpha-orbitals/gpu/compute.ts

@@ -1,170 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { createGrid3dComputeRenderable } from '../../../mol-gl/compute/grid3d';
-import { TextureSpec, UnboxedValues, UniformSpec } from '../../../mol-gl/renderable/schema';
-import { WebGLContext } from '../../../mol-gl/webgl/context';
-import { RuntimeContext } from '../../../mol-task';
-import { ValueCell } from '../../../mol-util';
-import { arrayMin } from '../../../mol-util/array';
-import { AlphaOrbital, Basis, CubeGridInfo } from '../data-model';
-import { normalizeBasicOrder, SphericalBasisOrder } from '../spherical-functions';
-import { MAIN, UTILS } from './shader.frag';
-
-const Schema = {
-    tCenters: TextureSpec('image-float32', 'rgba', 'float', 'nearest'),
-    tInfo: TextureSpec('image-float32', 'rgba', 'float', 'nearest'),
-    tCoeff: TextureSpec('image-float32', 'rgb', 'float', 'nearest'),
-    tAlpha: TextureSpec('image-float32', 'alpha', 'float', 'nearest'),
-    uNCenters: UniformSpec('i'),
-    uNAlpha: UniformSpec('i'),
-    uNCoeff: UniformSpec('i'),
-    uMaxCoeffs: UniformSpec('i'),
-};
-
-const Orbitals = createGrid3dComputeRenderable({
-    schema: Schema,
-    loopBounds: ['uNCenters', 'uMaxCoeffs'],
-    mainCode: MAIN,
-    utilCode: UTILS,
-    returnCode: 'v',
-    values(params: { grid: CubeGridInfo, orbital: AlphaOrbital }) {
-        return createTextureData(params.grid, params.orbital);
-    }
-});
-
-const Density = createGrid3dComputeRenderable({
-    schema: {
-        ...Schema,
-        uOccupancy: UniformSpec('f'),
-    },
-    loopBounds: ['uNCenters', 'uMaxCoeffs'],
-    mainCode: MAIN,
-    utilCode: UTILS,
-    returnCode: 'current + uOccupancy * v * v',
-    values(params: { grid: CubeGridInfo, orbitals: AlphaOrbital[] }) {
-        return {
-            ...createTextureData(params.grid, params.orbitals[0]),
-            uOccupancy: 0
-        };
-    },
-    cumulative: {
-        states(params: { grid: CubeGridInfo, orbitals: AlphaOrbital[] }) {
-            return params.orbitals.filter(o => o.occupancy !== 0);
-        },
-        update({ grid }, state: AlphaOrbital, values) {
-            const alpha = getNormalizedAlpha(grid.params.basis, state.alpha, grid.params.sphericalOrder);
-            ValueCell.updateIfChanged(values.uOccupancy, state.occupancy);
-            ValueCell.update(values.tAlpha, { width: alpha.length, height: 1, array: alpha });
-        }
-    }
-});
-
-export function gpuComputeAlphaOrbitalsGridValues(ctx: RuntimeContext, webgl: WebGLContext, grid: CubeGridInfo, orbital: AlphaOrbital) {
-    return Orbitals(ctx, webgl, grid, { grid, orbital });
-}
-
-export function gpuComputeAlphaOrbitalsDensityGridValues(ctx: RuntimeContext, webgl: WebGLContext, grid: CubeGridInfo, orbitals: AlphaOrbital[]) {
-    return Density(ctx, webgl, grid, { grid, orbitals });
-}
-
-function getNormalizedAlpha(basis: Basis, alphaOrbitals: number[], sphericalOrder: SphericalBasisOrder) {
-    const alpha = new Float32Array(alphaOrbitals.length);
-
-    let aO = 0;
-    for (const atom of basis.atoms) {
-        for (const shell of atom.shells) {
-            for (const L of shell.angularMomentum) {
-                const a0 = normalizeBasicOrder(L, alphaOrbitals.slice(aO, aO + 2 * L + 1), sphericalOrder);
-                for (let i = 0; i < a0.length; i++) alpha[aO + i] = a0[i];
-                aO += 2 * L + 1;
-            }
-        }
-    }
-
-    return alpha;
-}
-
-function createTextureData(grid: CubeGridInfo, orbital: AlphaOrbital): UnboxedValues<typeof Schema> {
-    const { basis, sphericalOrder, cutoffThreshold } = grid.params;
-
-    let centerCount = 0;
-    let baseCount = 0;
-    let coeffCount = 0;
-    for (const atom of basis.atoms) {
-        for (const shell of atom.shells) {
-            for (const L of shell.angularMomentum) {
-                if (L > 4) {
-                    // TODO: will L > 4 be required? Would need to precompute more functions in that case.
-                    throw new Error('Angular momentum L > 4 not supported.');
-                }
-
-                centerCount++;
-                baseCount += 2 * L + 1;
-                coeffCount += shell.exponents.length;
-            }
-        }
-    }
-
-    const centers = new Float32Array(4 * centerCount);
-    // L, alpha_offset, coeff_offset_start, coeff_offset_end
-    const info = new Float32Array(4 * centerCount);
-    const alpha = new Float32Array(baseCount);
-    const coeff = new Float32Array(3 * coeffCount);
-
-    let maxCoeffs = 0;
-    let cO = 0, aO = 0, coeffO = 0;
-    for (const atom of basis.atoms) {
-        for (const shell of atom.shells) {
-
-            let amIndex = 0;
-            for (const L of shell.angularMomentum) {
-                const a0 = normalizeBasicOrder(L, orbital.alpha.slice(aO, aO + 2 * L + 1), sphericalOrder);
-
-                const cutoffRadius = cutoffThreshold > 0
-                    ? Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(shell.exponents))
-                    : 10000;
-
-                centers[4 * cO + 0] = atom.center[0];
-                centers[4 * cO + 1] = atom.center[1];
-                centers[4 * cO + 2] = atom.center[2];
-                centers[4 * cO + 3] = cutoffRadius * cutoffRadius;
-
-                info[4 * cO + 0] = L;
-                info[4 * cO + 1] = aO;
-                info[4 * cO + 2] = coeffO;
-                info[4 * cO + 3] = coeffO + shell.exponents.length;
-
-                for (let i = 0; i < a0.length; i++) alpha[aO + i] = a0[i];
-
-                const c0 = shell.coefficients[amIndex++];
-                for (let i = 0; i < shell.exponents.length; i++) {
-                    coeff[3 * (coeffO + i) + 0] = c0[i];
-                    coeff[3 * (coeffO + i) + 1] = shell.exponents[i];
-                }
-
-                if (c0.length > maxCoeffs) {
-                    maxCoeffs = c0.length;
-                }
-
-                cO++;
-                aO += 2 * L + 1;
-                coeffO += shell.exponents.length;
-            }
-        }
-    }
-
-    return {
-        uNCenters: centerCount,
-        uNAlpha: baseCount,
-        uNCoeff: coeffCount,
-        uMaxCoeffs: maxCoeffs,
-        tCenters: { width: centerCount, height: 1, array: centers },
-        tInfo: { width: centerCount, height: 1, array: info },
-        tCoeff: { width: coeffCount, height: 1, array: coeff },
-        tAlpha: { width: baseCount, height: 1, array: alpha },
-    };
-}

src/extensions/alpha-orbitals/gpu/shader.frag.ts

@@ -1,145 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-export const UTILS = `
-float L1(vec3 p, float a0, float a1, float a2) {
-    return a0 * p.z + a1 * p.x + a2 * p.y;
-}
-
-float L2(vec3 p, float a0, float a1, float a2, float a3, float a4) {
-    float x = p.x, y = p.y, z = p.z;
-    float xx = x * x, yy = y * y, zz = z * z;
-    return (
-        a0 * (-0.5 * xx - 0.5 * yy + zz) +
-        a1 * (1.7320508075688772 * x * z) +
-        a2 * (1.7320508075688772 * y * z) +
-        a3 * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
-        a4 * (1.7320508075688772 * x * y)
-    );
-}
-
-float L3(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6) {
-    float x = p.x, y = p.y, z = p.z;
-    float xx = x * x, yy = y * y, zz = z * z;
-    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
-    return (
-        a0 * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
-        a1 * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
-        a2 * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
-        a3 * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
-        a4 * (3.872983346207417 * x * y * z) +
-        a5 * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
-        a6 * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
-    );
-}
-
-float L4(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6, float a7, float a8) {
-    float x = p.x, y = p.y, z = p.z;
-    float xx = x * x, yy = y * y, zz = z * z;
-    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
-    float xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
-    return (
-        a0 * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
-        a1 * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
-        a2 * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
-        a3 * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
-        a4 * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
-        a5 * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
-        a6 * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
-        a7 * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
-        a8 * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
-    );
-}
-
-float alpha(float offset, float f) {
-    #ifdef WEBGL1
-        // in webgl1, the value is in the alpha channel!
-        return texture2D(tAlpha, vec2(offset * f, 0.5)).a;
-    #else
-        return texture2D(tAlpha, vec2(offset * f, 0.5)).x;
-    #endif
-}
-
-float Y(int L, vec3 X, float aO, float fA) {
-    if (L == 0) {
-        return alpha(aO, fA);
-    } else if (L == 1) {
-        return L1(X,
-            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA)
-        );
-    } else if (L == 2) {
-        return L2(X,
-            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA)
-        );
-    } else if (L == 3) {
-        return L3(X,
-            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
-            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA)
-        );
-    } else if (L == 4) {
-        return L4(X,
-            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
-            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA), alpha(aO + 7.0, fA), alpha(aO + 8.0, fA)
-        );
-    }
-    // TODO: do we need L > 4?
-    return 0.0;
-}
-
-#ifndef WEBGL1
-    float R(float R2, int start, int end, float fCoeff) {
-        float gauss = 0.0;
-        for (int i = start; i < end; i++) {
-            vec2 c = texture2D(tCoeff, vec2(float(i) * fCoeff, 0.5)).xy;
-            gauss += c.x * exp(-c.y * R2);
-        }
-        return gauss;
-    }
-#else
-    float R(float R2, int start, int end, float fCoeff) {
-        float gauss = 0.0;
-        int o = start;
-        for (int i = 0; i < uMaxCoeffs; i++) {
-            if (o >= end) break;
-
-            vec2 c = texture2D(tCoeff, vec2(float(o) * fCoeff, 0.5)).xy;
-            gauss += c.x * exp(-c.y * R2);
-            o++;
-        }
-        return gauss;
-    }
-#endif
-`;
-
-export const MAIN = `
-    float fCenter = 1.0 / float(uNCenters - 1);
-    float fCoeff = 1.0 / float(uNCoeff - 1);
-    float fA = 1.0 / float(uNAlpha - 1);
-
-    float v = 0.0;
-
-    for (int i = 0; i < uNCenters; i++) {
-        vec2 cCoord = vec2(float(i) * fCenter, 0.5);
-
-        vec4 center = texture2D(tCenters, cCoord);
-        vec3 X = xyz - center.xyz;
-        float R2 = dot(X, X);
-
-        // center.w is squared cutoff radius
-        if (R2 > center.w) {
-            continue;
-        }
-
-        vec4 info = texture2D(tInfo, cCoord);
-
-        int L = int(info.x);
-        float aO = info.y;
-        int coeffStart = int(info.z);
-        int coeffEnd = int(info.w);
-
-        v += R(R2, coeffStart, coeffEnd, fCoeff) * Y(L, X, aO, fA);
-    }
-`;

src/extensions/alpha-orbitals/orbitals.ts

@@ -1,131 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Inspired by https://github.com/dgasmith/gau2grid.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { sortArray } from '../../mol-data/util';
-import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
-import { WebGLContext } from '../../mol-gl/webgl/context';
-import { Task } from '../../mol-task';
-import { sphericalCollocation } from './collocation';
-import { AlphaOrbital, createGrid, CubeGrid, CubeGridComputationParams, initCubeGrid } from './data-model';
-import { gpuComputeAlphaOrbitalsGridValues } from './gpu/compute';
-
-// setDebugMode(true);
-
-export function createSphericalCollocationGrid(
-    params: CubeGridComputationParams, orbital: AlphaOrbital, webgl?: WebGLContext
-): Task<CubeGrid> {
-    return Task.create('Spherical Collocation Grid', async (ctx) => {
-        const cubeGrid = initCubeGrid(params);
-
-        let matrix: Float32Array;
-        if (canComputeGrid3dOnGPU(webgl)) {
-            // console.time('gpu');
-            matrix = await gpuComputeAlphaOrbitalsGridValues(ctx, webgl!, cubeGrid, orbital);
-            // console.timeEnd('gpu');
-        } else {
-            // console.time('cpu');
-            matrix = await sphericalCollocation(cubeGrid, orbital, ctx);
-            // console.timeEnd('cpu');
-        }
-
-        const grid = createGrid(cubeGrid, matrix, [0, 1, 2]);
-        let isovalues: { negative?: number, positive?: number } | undefined;
-
-        if (!params.doNotComputeIsovalues) {
-            isovalues = computeOrbitalIsocontourValues(matrix, 0.85);
-        }
-
-        return { grid, isovalues };
-    });
-}
-
-export function computeOrbitalIsocontourValues(input: Float32Array, cumulativeThreshold: number) {
-    let weightSum = 0;
-    for (let i = 0, _i = input.length; i < _i; i++) {
-        const v = input[i];
-        const w = v * v;
-        weightSum += w;
-    }
-    const avgWeight = weightSum / input.length;
-    let minWeight = 3 * avgWeight;
-
-    // do not try to identify isovalues for degenerate data
-    // e.g. all values are almost same
-    if (Math.abs(avgWeight - input[0] * input[0]) < 1e-5) {
-        return { negative: void 0, positive: void 0 };
-    }
-
-    let size = 0;
-    while (true) {
-        let csum = 0;
-        size = 0;
-        for (let i = 0, _i = input.length; i < _i; i++) {
-            const v = input[i];
-            const w = v * v;
-            if (w >= minWeight) {
-                csum += w;
-                size++;
-            }
-        }
-
-        if (csum / weightSum > cumulativeThreshold) {
-            break;
-        }
-
-        minWeight -= avgWeight;
-    }
-
-    const values = new Float32Array(size);
-    const weights = new Float32Array(size);
-    const indices = new Int32Array(size);
-
-    let o = 0;
-    for (let i = 0, _i = input.length; i < _i; i++) {
-        const v = input[i];
-        const w = v * v;
-        if (w >= minWeight) {
-            values[o] = v;
-            weights[o] = w;
-            indices[o] = o;
-            o++;
-        }
-    }
-
-    sortArray(
-        indices,
-        (indices, i, j) => weights[indices[j]] - weights[indices[i]]
-    );
-
-    let cweight = 0,
-        cutoffIndex = 0;
-    for (let i = 0; i < size; i++) {
-        cweight += weights[indices[i]];
-
-        if (cweight / weightSum >= cumulativeThreshold) {
-            cutoffIndex = i;
-            break;
-        }
-    }
-
-    let positive = Number.POSITIVE_INFINITY,
-        negative = Number.NEGATIVE_INFINITY;
-
-    for (let i = 0; i < cutoffIndex; i++) {
-        const v = values[indices[i]];
-        if (v > 0) {
-            if (v < positive) positive = v;
-        } else if (v < 0) {
-            if (v > negative) negative = v;
-        }
-    }
-
-    return {
-        negative: negative !== Number.NEGATIVE_INFINITY ? negative : void 0,
-        positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
-    };
-}

src/extensions/alpha-orbitals/spherical-functions.ts

@@ -1,93 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Inspired by https://github.com/dgasmith/gau2grid.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-// gaussian:
-//     R_0, R^+_1, R^-_1, ..., R^+_l, R^-_l
-// cca:
-//     R^-_(l), R^-_(l-1), ..., R_0, ..., R^+_(l-1), R^+_l
-// cca-reverse:
-//     R^+_(l), R^+_(l-1), ..., R_0, ..., R^-_(l-1), R^-_l
-export type SphericalBasisOrder = 'gaussian' | 'cca' | 'cca-reverse';
-
-export function normalizeBasicOrder(
-    L: number,
-    alpha: number[],
-    order: SphericalBasisOrder
-) {
-    if (order === 'gaussian' || L === 0) return alpha;
-
-    const ret: number[] = [alpha[L]];
-    for (let l = 0; l < L; l++) {
-        const a = alpha[L - l - 1],
-            b = alpha[L + l + 1];
-        if (order === 'cca') ret.push(b, a);
-        else ret.push(a, b);
-    }
-    return ret;
-}
-
-export type SphericalFunc = (
-    alpha: number[],
-    x: number,
-    y: number,
-    z: number
-) => number;
-
-export const SphericalFunctions: SphericalFunc[] = [L0, L1, L2, L3, L4];
-
-// L_i functions were auto-generated.
-
-function L0(alpha: number[], x: number, y: number, z: number) {
-    return alpha[0];
-}
-
-function L1(alpha: number[], x: number, y: number, z: number) {
-    return alpha[0] * z + alpha[1] * x + alpha[2] * y;
-}
-
-function L2(alpha: number[], x: number, y: number, z: number) {
-    const xx = x * x, yy = y * y, zz = z * z;
-    return (
-        alpha[0] * (-0.5 * xx - 0.5 * yy + zz) +
-        alpha[1] * (1.7320508075688772 * x * z) +
-        alpha[2] * (1.7320508075688772 * y * z) +
-        alpha[3] * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
-        alpha[4] * (1.7320508075688772 * x * y)
-    );
-}
-
-function L3(alpha: number[], x: number, y: number, z: number) {
-    const xx = x * x, yy = y * y, zz = z * z;
-    const xxx = xx * x, yyy = yy * y, zzz = zz * z;
-    return (
-        alpha[0] * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
-        alpha[1] * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
-        alpha[2] * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
-        alpha[3] * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
-        alpha[4] * (3.872983346207417 * x * y * z) +
-        alpha[5] * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
-        alpha[6] * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
-    );
-}
-
-function L4(alpha: number[], x: number, y: number, z: number) {
-    const xx = x * x, yy = y * y, zz = z * z;
-    const xxx = xx * x, yyy = yy * y, zzz = zz * z;
-    const xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
-    return (
-        alpha[0] * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
-        alpha[1] * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
-        alpha[2] * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
-        alpha[3] * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
-        alpha[4] * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
-        alpha[5] * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
-        alpha[6] * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
-        alpha[7] * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
-        alpha[8] * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
-    );
-}

src/extensions/alpha-orbitals/transforms.ts

@@ -1,236 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects';
-import { createSphericalCollocationGrid } from './orbitals';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Task } from '../../mol-task';
-import { CustomProperties } from '../../mol-model/custom-property';
-import { SphericalBasisOrder } from './spherical-functions';
-import { Volume } from '../../mol-model/volume';
-import { PluginContext } from '../../mol-plugin/context';
-import { ColorNames } from '../../mol-util/color/names';
-import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
-import { StateTransformer } from '../../mol-state';
-import { Theme } from '../../mol-theme/theme';
-import { VolumeRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
-import { AlphaOrbital, Basis, CubeGrid } from './data-model';
-import { createSphericalCollocationDensityGrid } from './density';
-import { Tensor } from '../../mol-math/linear-algebra';
-
-export class BasisAndOrbitals extends PluginStateObject.Create<{ basis: Basis, order: SphericalBasisOrder, orbitals: AlphaOrbital[] }>({ name: 'Basis', typeClass: 'Object' }) { }
-
-export const StaticBasisAndOrbitals = PluginStateTransform.BuiltIn({
-    name: 'static-basis-and-orbitals',
-    display: 'Basis and Orbitals',
-    from: PluginStateObject.Root,
-    to: BasisAndOrbitals,
-    params: {
-        label: PD.Text('Orbital Data', { isHidden: true }),
-        basis: PD.Value<Basis>(void 0 as any, { isHidden: true }),
-        order: PD.Text<SphericalBasisOrder>('gaussian' as SphericalBasisOrder, { isHidden: true }),
-        orbitals: PD.Value<AlphaOrbital[]>([], { isHidden: true })
-    },
-})({
-    apply({ params }) {
-        return new BasisAndOrbitals({ basis: params.basis, order: params.order, orbitals: params.orbitals }, { label: params.label });
-    }
-});
-
-const CreateOrbitalVolumeParamBase = {
-    cutoffThreshold: PD.Numeric(0.0015, { min: 0, max: 0.1, step: 0.0001 }),
-    boxExpand: PD.Numeric(4.5, { min: 0, max: 7, step: 0.1 }),
-    gridSpacing: PD.ObjectList({ atomCount: PD.Numeric(0), spacing: PD.Numeric(0.35, { min: 0.1, max: 2, step: 0.01 }) }, e => `Atoms ${e.atomCount}: ${e.spacing}`, {
-        defaultValue: [
-            { atomCount: 55, spacing: 0.5 },
-            { atomCount: 40, spacing: 0.45 },
-            { atomCount: 25, spacing: 0.4 },
-            { atomCount: 0, spacing: 0.35 },
-        ]
-    }),
-    clampValues: PD.MappedStatic('off', {
-        off: PD.EmptyGroup(),
-        on: PD.Group({
-            sigma: PD.Numeric(8, { min: 1, max: 20 }, { description: 'Clamp values to range [sigma * negIsoValue, sigma * posIsoValue].' })
-        })
-    })
-};
-
-function clampData(matrix: Tensor.Data, min: number, max: number) {
-    for (let i = 0, _i = matrix.length; i < _i; i++) {
-        const v = matrix[i];
-        if (v < min) matrix[i] = min;
-        else if (v > max) matrix[i] = max;
-    }
-}
-
-function clampGrid(data: CubeGrid, v: number) {
-    const grid = data.grid;
-    const min = (data.isovalues?.negative ?? data.grid.stats.min) * v;
-    const max = (data.isovalues?.positive ?? data.grid.stats.max) * v;
-
-    // clamp values for better direct volume resolution
-    // current implementation uses Byte array for values
-    // if this is not enough, update mol* to use float
-    // textures instead
-    if (grid.stats.min < min || grid.stats.max > max) {
-        clampData(data.grid.cells.data, min, max);
-        if (grid.stats.min < min) {
-            (grid.stats.min as number) = min;
-        }
-        if (grid.stats.max > max) {
-            (grid.stats.max as number) = max;
-        }
-    }
-}
-
-export const CreateOrbitalVolume = PluginStateTransform.BuiltIn({
-    name: 'create-orbital-volume',
-    display: 'Orbital Volume',
-    from: BasisAndOrbitals,
-    to: PluginStateObject.Volume.Data,
-    params: (a) => {
-        if (!a) {
-            return { index: PD.Numeric(0), ...CreateOrbitalVolumeParamBase };
-        }
-
-        return {
-            index: PD.Select(0, a.data.orbitals.map((o, i) => [i, `[${i + 1}] ${o.energy.toFixed(4)}`])),
-            ...CreateOrbitalVolumeParamBase
-        };
-    }
-})({
-    apply({ a, params }, plugin: PluginContext) {
-        return Task.create('Orbital Volume', async ctx => {
-            const data = await createSphericalCollocationGrid({
-                basis: a.data.basis,
-                cutoffThreshold: params.cutoffThreshold,
-                sphericalOrder: a.data.order,
-                boxExpand: params.boxExpand,
-                gridSpacing: params.gridSpacing.map(e => [e.atomCount, e.spacing] as [number, number])
-            }, a.data.orbitals[params.index], plugin.canvas3d?.webgl).runInContext(ctx);
-            const volume: Volume = {
-                grid: data.grid,
-                sourceData: { name: 'custom grid', kind: 'alpha-orbitals', data },
-                customProperties: new CustomProperties(),
-                _propertyData: Object.create(null),
-            };
-
-            if (params.clampValues?.name === 'on') {
-                clampGrid(data, params.clampValues?.params?.sigma ?? 8);
-            }
-
-            return new PluginStateObject.Volume.Data(volume, { label: 'Orbital Volume' });
-        });
-    }
-});
-
-export const CreateOrbitalDensityVolume = PluginStateTransform.BuiltIn({
-    name: 'create-orbital-density-volume',
-    display: 'Orbital Density Volume',
-    from: BasisAndOrbitals,
-    to: PluginStateObject.Volume.Data,
-    params: CreateOrbitalVolumeParamBase
-})({
-    apply({ a, params }, plugin: PluginContext) {
-        return Task.create('Orbital Volume', async ctx => {
-            const data = await createSphericalCollocationDensityGrid({
-                basis: a.data.basis,
-                cutoffThreshold: params.cutoffThreshold,
-                sphericalOrder: a.data.order,
-                boxExpand: params.boxExpand,
-                gridSpacing: params.gridSpacing.map(e => [e.atomCount, e.spacing] as [number, number])
-            }, a.data.orbitals, plugin.canvas3d?.webgl).runInContext(ctx);
-            const volume: Volume = {
-                grid: data.grid,
-                sourceData: { name: 'custom grid', kind: 'alpha-orbitals', data },
-                customProperties: new CustomProperties(),
-                _propertyData: Object.create(null),
-            };
-
-            if (params.clampValues?.name === 'on') {
-                clampGrid(data, params.clampValues?.params?.sigma ?? 8);
-            }
-
-            return new PluginStateObject.Volume.Data(volume, { label: 'Orbital Volume' });
-        });
-    }
-});
-
-export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
-    name: 'create-orbital-representation-3d',
-    display: 'Orbital Representation 3D',
-    from: PluginStateObject.Volume.Data,
-    to: PluginStateObject.Volume.Representation3D,
-    params: {
-        directVolume: PD.Boolean(false),
-        relativeIsovalue: PD.Numeric(1, { min: 0.01, max: 5, step: 0.01 }),
-        kind: PD.Select<'positive' | 'negative'>('positive', [['positive', 'Positive'], ['negative', 'Negative']]),
-        color: PD.Color(ColorNames.blue),
-        alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
-        xrayShaded: PD.Boolean(false),
-        pickable: PD.Boolean(true)
-    }
-})({
-    canAutoUpdate() {
-        return true;
-    },
-    apply({ a, params: srcParams }, plugin: PluginContext) {
-        return Task.create('Orbitals Representation 3D', async ctx => {
-            const params = volumeParams(plugin, a, srcParams);
-
-            const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
-            const provider = plugin.representation.volume.registry.get(params.type.name);
-            if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
-            const props = params.type.params || {};
-            const repr = provider.factory({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.volume.themes }, provider.getParams);
-            repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, params));
-            await repr.createOrUpdate(props, a.data).runInContext(ctx);
-            repr.setState({ pickable: srcParams.pickable });
-            return new PluginStateObject.Volume.Representation3D({ repr, source: a }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
-        });
-    },
-    update({ a, b, newParams: srcParams }, plugin: PluginContext) {
-        return Task.create('Orbitals Representation 3D', async ctx => {
-            const newParams = volumeParams(plugin, a, srcParams);
-
-            const props = { ...b.data.repr.props, ...newParams.type.params };
-            b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
-            await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
-            b.data.repr.setState({ pickable: srcParams.pickable });
-            b.description = VolumeRepresentation3DHelpers.getDescription(props);
-            return StateTransformer.UpdateResult.Updated;
-        });
-    }
-});
-
-function volumeParams(plugin: PluginContext, volume: PluginStateObject.Volume.Data, params: StateTransformer.Params<typeof CreateOrbitalRepresentation3D>) {
-    if (volume.data.sourceData.kind !== 'alpha-orbitals') throw new Error('Invalid data source kind.');
-
-    const { isovalues } = volume.data.sourceData.data as CubeGrid;
-    if (!isovalues) throw new Error('Isovalues are not computed.');
-
-    const value = isovalues[params.kind];
-
-    return createVolumeRepresentationParams(plugin, volume.data, params.directVolume ? {
-        type: 'direct-volume',
-        typeParams: {
-            alpha: params.alpha,
-            renderMode: {
-                name: 'isosurface',
-                params: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, singleLayer: false }
-            },
-            xrayShaded: params.xrayShaded
-        },
-        color: 'uniform',
-        colorParams: { value: params.color }
-    } : {
-        type: 'isosurface',
-        typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded },
-        color: 'uniform',
-        colorParams: { value: params.color }
-    });
-}

src/extensions/anvil/algorithm.ts

@@ -1,370 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Structure, StructureElement, StructureProperties } from '../../mol-model/structure';
-import { Task, RuntimeContext } from '../../mol-task';
-import { CentroidHelper } from '../../mol-math/geometry/centroid-helper';
-import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area';
-import { Vec3 } from '../../mol-math/linear-algebra';
-import { getElementMoleculeType } from '../../mol-model/structure/util';
-import { MoleculeType } from '../../mol-model/structure/model/types';
-import { AccessibleSurfaceArea } from '../../mol-model-props/computed/accessible-surface-area/shrake-rupley';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { MembraneOrientation } from './prop';
-
-interface ANVILContext {
-    structure: Structure,
-
-    numberOfSpherePoints: number,
-    stepSize: number,
-    minThickness: number,
-    maxThickness: number,
-    asaCutoff: number,
-
-    offsets: ArrayLike<number>,
-    exposed: ArrayLike<boolean>,
-    centroid: Vec3,
-    extent: number
-};
-
-export const ANVILParams = {
-    numberOfSpherePoints: PD.Numeric(120, { min: 35, max: 700, step: 1 }, { description: 'Number of spheres/directions to test for membrane placement. Original value is 350.' }),
-    stepSize: PD.Numeric(1, { min: 0.25, max: 4, step: 0.25 }, { description: 'Thickness of membrane slices that will be tested' }),
-    minThickness: PD.Numeric(20, { min: 10, max: 30, step: 1}, { description: 'Minimum membrane thickness used during refinement' }),
-    maxThickness: PD.Numeric(40, { min: 30, max: 50, step: 1}, { description: 'Maximum membrane thickness used during refinement' }),
-    asaCutoff: PD.Numeric(40, { min: 10, max: 100, step: 1 }, { description: 'Absolute ASA cutoff above which residues will be considered' })
-};
-export type ANVILParams = typeof ANVILParams
-export type ANVILProps = PD.Values<ANVILParams>
-
-/**
- * Implements:
- * Membrane positioning for high- and low-resolution protein structures through a binary classification approach
- * Guillaume Postic, Yassine Ghouzam, Vincent Guiraud, and Jean-Christophe Gelly
- * Protein Engineering, Design & Selection, 2015, 1–5
- * doi: 10.1093/protein/gzv063
- */
-export function computeANVIL(structure: Structure, props: ANVILProps) {
-    return Task.create('Compute Membrane Orientation', async runtime => {
-        return await calculate(runtime, structure, props);
-    });
-}
-
-
-const centroidHelper = new CentroidHelper();
-function initialize(structure: Structure, props: ANVILProps): ANVILContext {
-    const l = StructureElement.Location.create(structure);
-    const { label_atom_id, x, y, z } = StructureProperties.atom;
-    const elementCount = structure.polymerResidueCount;
-    centroidHelper.reset();
-
-    let offsets = new Int32Array(elementCount);
-    let exposed = new Array<boolean>(elementCount);
-
-    const accessibleSurfaceArea = structure && AccessibleSurfaceAreaProvider.get(structure);
-    const asa = accessibleSurfaceArea.value!;
-
-    const vec = Vec3();
-    let m = 0;
-    for (let i = 0, il = structure.units.length; i < il; ++i) {
-        const unit = structure.units[i];
-        const { elements } = unit;
-        l.unit = unit;
-
-        for (let j = 0, jl = elements.length; j < jl; ++j) {
-            const eI = elements[j];
-            l.element = eI;
-
-            // consider only amino acids
-            if (getElementMoleculeType(unit, eI) !== MoleculeType.Protein) {
-                continue;
-            }
-
-            // only CA is considered for downstream operations
-            if (label_atom_id(l) !== 'CA') {
-                continue;
-            }
-
-            // while iterating use first pass to compute centroid
-            Vec3.set(vec, x(l), y(l), z(l));
-            centroidHelper.includeStep(vec);
-
-            // keep track of offsets and exposed state to reuse
-            offsets[m] = structure.serialMapping.getSerialIndex(l.unit, l.element);
-            exposed[m] = AccessibleSurfaceArea.getValue(l, asa) > props.asaCutoff;
-
-            m++;
-        }
-    }
-
-    // omit potentially empty tail1
-    offsets = offsets.slice(0, m);
-    exposed = exposed.slice(0, m);
-
-    // calculate centroid and extent
-    centroidHelper.finishedIncludeStep();
-    const centroid = centroidHelper.center;
-    for (let k = 0, kl = offsets.length; k < kl; k++) {
-        setLocation(l, structure, offsets[k]);
-        Vec3.set(vec, x(l), y(l), z(l));
-        centroidHelper.radiusStep(vec);
-    }
-    const extent = 1.2 * Math.sqrt(centroidHelper.radiusSq);
-
-    return {
-        ...props,
-        structure: structure,
-
-        offsets: offsets,
-        exposed: exposed,
-        centroid: centroid,
-        extent: extent
-    };
-}
-
-export async function calculate(runtime: RuntimeContext, structure: Structure, params: ANVILProps): Promise<MembraneOrientation> {
-    const { label_comp_id } = StructureProperties.atom;
-
-    const ctx = initialize(structure, params);
-    const initialHphobHphil = HphobHphil.filtered(ctx, label_comp_id);
-
-    const initialMembrane = findMembrane(ctx, generateSpherePoints(ctx, ctx.numberOfSpherePoints), initialHphobHphil, label_comp_id);
-    const alternativeMembrane = findMembrane(ctx, findProximateAxes(ctx, initialMembrane), initialHphobHphil, label_comp_id);
-
-    const membrane = initialMembrane.qmax! > alternativeMembrane.qmax! ? initialMembrane : alternativeMembrane;
-
-    return {
-        planePoint1: membrane.planePoint1,
-        planePoint2: membrane.planePoint2,
-        normalVector: membrane.normalVector!,
-        radius: ctx.extent,
-        centroid: ctx.centroid
-    };
-}
-
-interface MembraneCandidate {
-    planePoint1: Vec3,
-    planePoint2: Vec3,
-    stats: HphobHphil,
-    normalVector?: Vec3,
-    spherePoint?: Vec3,
-    qmax?: number
-}
-
-namespace MembraneCandidate {
-    export function initial(c1: Vec3, c2: Vec3, stats: HphobHphil): MembraneCandidate {
-        return {
-            planePoint1: c1,
-            planePoint2: c2,
-            stats: stats
-        };
-    }
-
-    export function scored(spherePoint: Vec3, c1: Vec3, c2: Vec3, stats: HphobHphil, qmax: number, centroid: Vec3): MembraneCandidate {
-        const diam_vect = Vec3();
-        Vec3.sub(diam_vect, centroid, spherePoint);
-        return {
-            planePoint1: c1,
-            planePoint2: c2,
-            stats: stats,
-            normalVector: diam_vect,
-            spherePoint: spherePoint,
-            qmax: qmax
-        };
-    }
-}
-
-function findMembrane(ctx: ANVILContext, spherePoints: Vec3[], initialStats: HphobHphil, label_comp_id: StructureElement.Property<string>): MembraneCandidate {
-    const { centroid, stepSize, minThickness, maxThickness } = ctx;
-    // best performing membrane
-    let membrane: MembraneCandidate;
-    // score of the best performing membrane
-    let qmax = 0;
-
-    // construct slices of thickness 1.0 along the axis connecting the centroid and the spherePoint
-    const diam = Vec3();
-    for (let i = 0, il = spherePoints.length; i < il; i++) {
-        const spherePoint = spherePoints[i];
-        Vec3.sub(diam, centroid, spherePoint);
-        Vec3.scale(diam, diam, 2);
-        const diamNorm = Vec3.magnitude(diam);
-        const qvartemp = [];
-
-        for (let i = 0, il = diamNorm - stepSize; i < il; i += stepSize) {
-            const c1 = Vec3();
-            const c2 = Vec3();
-            Vec3.scaleAndAdd(c1, spherePoint, diam, i / diamNorm);
-            Vec3.scaleAndAdd(c2, spherePoint, diam, (i + stepSize) / diamNorm);
-
-            // evaluate how well this membrane slice embeddeds the peculiar residues
-            const stats = HphobHphil.filtered(ctx, label_comp_id, (testPoint: Vec3) => isInMembranePlane(testPoint, diam, c1, c2));
-            qvartemp.push(MembraneCandidate.initial(c1, c2, stats));
-        }
-
-        let jmax = (minThickness / stepSize) - 1;
-
-        for (let width = 0, widthl = maxThickness; width < widthl;) {
-            const imax = qvartemp.length - 1 - jmax;
-
-            for (let i = 0, il = imax; i < il; i++) {
-                const c1 = qvartemp[i].planePoint1;
-                const c2 = qvartemp[i + jmax].planePoint2;
-
-                let hphob = 0;
-                let hphil = 0;
-                let total = 0;
-                for (let j = 0; j < jmax; j++) {
-                    const ij = qvartemp[i + j];
-                    if (j === 0 || j === jmax - 1) {
-                        hphob += 0.5 * ij.stats.hphob;
-                        hphil += 0.5 * ij.stats.hphil;
-                    } else {
-                        hphob += ij.stats.hphob;
-                        hphil += ij.stats.hphil;
-                    }
-                    total += ij.stats.total;
-                }
-
-                const stats = HphobHphil.of(hphob, hphil, total);
-
-                if (hphob !== 0) {
-                    const qvaltest = qValue(stats, initialStats);
-                    if (qvaltest > qmax) {
-                        qmax = qvaltest;
-                        membrane = MembraneCandidate.scored(spherePoint, c1, c2, HphobHphil.of(hphob, hphil, total), qmax, centroid);
-                    }
-                }
-            }
-            jmax++;
-            width = (jmax + 1) * stepSize;
-        }
-    }
-
-    return membrane!;
-}
-
-function qValue(currentStats: HphobHphil, initialStats: HphobHphil): number {
-    if(initialStats.hphob < 1) {
-        initialStats.hphob = 0.1;
-    }
-
-    if(initialStats.hphil < 1) {
-        initialStats.hphil += 1;
-    }
-
-    const part_tot = currentStats.hphob + currentStats.hphil;
-    return (currentStats.hphob * (initialStats.hphil - currentStats.hphil) - currentStats.hphil * (initialStats.hphob - currentStats.hphob)) /
-            Math.sqrt(part_tot * initialStats.hphob * initialStats.hphil * (initialStats.hphob + initialStats.hphil - part_tot));
-}
-
-export function isInMembranePlane(testPoint: Vec3, normalVector: Vec3, planePoint1: Vec3, planePoint2: Vec3): boolean {
-    const d1 = -Vec3.dot(normalVector, planePoint1);
-    const d2 = -Vec3.dot(normalVector, planePoint2);
-    const d = -Vec3.dot(normalVector, testPoint);
-    return d > Math.min(d1, d2) && d < Math.max(d1, d2);
-}
-
-// generates a defined number of points on a sphere with radius = extent around the specified centroid
-function generateSpherePoints(ctx: ANVILContext, numberOfSpherePoints: number): Vec3[] {
-    const { centroid, extent } = ctx;
-    const points = [];
-    let oldPhi = 0, h, theta, phi;
-    for(let k = 1, kl = numberOfSpherePoints + 1; k < kl; k++) {
-        h = -1 + 2 * (k - 1) / (numberOfSpherePoints - 1);
-        theta = Math.acos(h);
-        phi = (k === 1 || k === numberOfSpherePoints) ? 0 : (oldPhi + 3.6 / Math.sqrt(numberOfSpherePoints * (1 - h * h))) % (2 * Math.PI);
-
-        const point = Vec3.create(
-            extent * Math.sin(phi) * Math.sin(theta) + centroid[0],
-            extent * Math.cos(theta) + centroid[1],
-            extent * Math.cos(phi) * Math.sin(theta) + centroid[2]
-        );
-        points[k - 1] = point;
-        oldPhi = phi;
-    }
-
-    return points;
-}
-
-// generates sphere points close to that of the initial membrane
-function findProximateAxes(ctx: ANVILContext, membrane: MembraneCandidate): Vec3[] {
-    const { numberOfSpherePoints, extent } = ctx;
-    const points = generateSpherePoints(ctx, 30000);
-    let j = 4;
-    let sphere_pts2: Vec3[] = [];
-    while (sphere_pts2.length < numberOfSpherePoints) {
-        const d = 2 * extent / numberOfSpherePoints + j;
-        const dsq = d * d;
-        sphere_pts2 = [];
-        for (let i = 0, il = points.length; i < il; i++) {
-            if (Vec3.squaredDistance(points[i], membrane.spherePoint!) < dsq) {
-                sphere_pts2.push(points[i]);
-            }
-        }
-        j += 0.2;
-    }
-    return sphere_pts2;
-}
-
-interface HphobHphil {
-    hphob: number,
-    hphil: number,
-    total: number
-}
-
-namespace HphobHphil {
-    export function of(hphob: number, hphil: number, total?: number) {
-        return {
-            hphob: hphob,
-            hphil: hphil,
-            total: !!total ? total : hphob + hphil
-        };
-    }
-
-    const testPoint = Vec3();
-    export function filtered(ctx: ANVILContext, label_comp_id: StructureElement.Property<string>, filter?: (test: Vec3) => boolean): HphobHphil {
-        const { offsets, exposed, structure } = ctx;
-        const l = StructureElement.Location.create(structure);
-        const { x, y, z } = StructureProperties.atom;
-        let hphob = 0;
-        let hphil = 0;
-        for (let k = 0, kl = offsets.length; k < kl; k++) {
-            // ignore buried residues
-            if (!exposed[k]) {
-                continue;
-            }
-
-            setLocation(l, structure, offsets[k]);
-            Vec3.set(testPoint, x(l), y(l), z(l));
-
-            // testPoints have to be in putative membrane layer
-            if (filter && !filter(testPoint)) {
-                continue;
-            }
-
-            if (isHydrophobic(label_comp_id(l))) {
-                hphob++;
-            } else {
-                hphil++;
-            }
-        }
-        return of(hphob, hphil);
-    }
-}
-
-// ANVIL-specific (not general) definition of membrane-favoring amino acids
-const HYDROPHOBIC_AMINO_ACIDS = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'THR', 'VAL']);
-export function isHydrophobic(label_comp_id: string): boolean {
-    return HYDROPHOBIC_AMINO_ACIDS.has(label_comp_id);
-}
-
-function setLocation(l: StructureElement.Location, structure: Structure, serialIndex: number) {
-    l.structure = structure;
-    l.unit = structure.units[structure.serialMapping.unitIndices[serialIndex]];
-    l.element = structure.serialMapping.elementIndices[serialIndex];
-    return l;
-}

src/extensions/anvil/behavior.ts

@@ -1,174 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { MembraneOrientationProvider, MembraneOrientation } from './prop';
-import { StateObjectRef, StateTransformer, StateTransform } from '../../mol-state';
-import { Task } from '../../mol-task';
-import { PluginBehavior } from '../../mol-plugin/behavior';
-import { MembraneOrientationRepresentationProvider, MembraneOrientationParams, MembraneOrientationRepresentation } from './representation';
-import { HydrophobicityColorThemeProvider } from '../../mol-theme/color/hydrophobicity';
-import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects';
-import { PluginContext } from '../../mol-plugin/context';
-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 { GenericRepresentationRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
-
-const Tag = MembraneOrientation.Tag;
-
-export const ANVILMembraneOrientation = PluginBehavior.create<{ autoAttach: boolean }>({
-    name: 'anvil-membrane-orientation-prop',
-    category: 'custom-props',
-    display: {
-        name: 'Membrane Orientation',
-        description: 'Data calculated with ANVIL algorithm.'
-    },
-    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
-        private provider = MembraneOrientationProvider
-
-        register(): void {
-            DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);
-
-            this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach);
-
-            this.ctx.representation.structure.registry.add(MembraneOrientationRepresentationProvider);
-            this.ctx.query.structure.registry.add(isTransmembrane);
-
-            this.ctx.genericRepresentationControls.set(Tag.Representation, selection => {
-                const refs: GenericRepresentationRef[] = [];
-                selection.structures.forEach(structure => {
-                    const memRepr = structure.genericRepresentations?.filter(r => r.cell.transform.transformer.id === MembraneOrientation3D.id)[0];
-                    if (memRepr) refs.push(memRepr);
-                });
-                return [refs, 'Membrane Orientation'];
-            });
-            this.ctx.builders.structure.representation.registerPreset(MembraneOrientationPreset);
-        }
-
-        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() {
-            DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
-
-            this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
-
-            this.ctx.representation.structure.registry.remove(MembraneOrientationRepresentationProvider);
-            this.ctx.query.structure.registry.remove(isTransmembrane);
-
-            this.ctx.genericRepresentationControls.delete(Tag.Representation);
-            this.ctx.builders.structure.representation.unregisterPreset(MembraneOrientationPreset);
-        }
-    },
-    params: () => ({
-        autoAttach: PD.Boolean(false)
-    })
-});
-
-//
-
-export const isTransmembrane = StructureSelectionQuery('Residues Embedded in Membrane', 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': MembraneOrientation.symbols.isTransmembrane.symbol(),
-            })
-        ])
-    ])
-]), {
-    description: 'Select residues that are embedded between the membrane layers.',
-    category: StructureSelectionCategory.Residue,
-    ensureCustomProperties: (ctx, structure) => {
-        return MembraneOrientationProvider.attach(ctx, structure);
-    }
-});
-
-//
-
-export { MembraneOrientation3D };
-
-type MembraneOrientation3D = typeof MembraneOrientation3D
-const MembraneOrientation3D = PluginStateTransform.BuiltIn({
-    name: 'membrane-orientation-3d',
-    display: {
-        name: 'Membrane Orientation',
-        description: 'Membrane Orientation planes and rims. Data calculated with ANVIL algorithm.'
-    },
-    from: PluginStateObject.Molecule.Structure,
-    to: PluginStateObject.Shape.Representation3D,
-    params: (a) => {
-        return {
-            ...MembraneOrientationParams,
-        };
-    }
-})({
-    canAutoUpdate({ oldParams, newParams }) {
-        return true;
-    },
-    apply({ a, params }, plugin: PluginContext) {
-        return Task.create('Membrane Orientation', async ctx => {
-            await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
-            const repr = MembraneOrientationRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => MembraneOrientationParams);
-            await repr.createOrUpdate(params, a.data).runInContext(ctx);
-            return new PluginStateObject.Shape.Representation3D({ repr, source: a }, { label: 'Membrane Orientation' });
-        });
-    },
-    update({ a, b, newParams }, plugin: PluginContext) {
-        return Task.create('Membrane Orientation', async ctx => {
-            await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
-            const props = { ...b.data.repr.props, ...newParams };
-            await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
-            return StateTransformer.UpdateResult.Updated;
-        });
-    },
-    isApplicable(a) {
-        return MembraneOrientationProvider.isApplicable(a.data);
-    }
-});
-
-export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
-    id: 'preset-membrane-orientation',
-    display: {
-        name: 'Membrane Orientation', group: 'Annotation',
-        description: 'Shows orientation of membrane layers. Data calculated with ANVIL algorithm.' // TODO add ' or obtained via RCSB PDB'
-    },
-    isApplicable(a) {
-        return MembraneOrientationProvider.isApplicable(a.data);
-    },
-    params: () => StructureRepresentationPresetProvider.CommonParams,
-    async apply(ref, params, plugin) {
-        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const structure  = structureCell?.obj?.data;
-        if (!structureCell || !structure) return {};
-
-        if (!MembraneOrientationProvider.get(structure).value) {
-            await plugin.runTask(Task.create('Membrane Orientation', async runtime => {
-                await MembraneOrientationProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure);
-            }));
-        }
-
-        const membraneOrientation = await tryCreateMembraneOrientation(plugin, structureCell);
-        const colorTheme = HydrophobicityColorThemeProvider.name as any;
-        const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
-
-        return { components: preset.components, representations: { ...preset.representations, membraneOrientation } };
-    }
-});
-
-export function tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<MembraneOrientation3D>, initialState?: Partial<StateTransform.State>) {
-    const state = plugin.state.data;
-    const membraneOrientation = state.build().to(structure)
-        .applyOrUpdateTagged('membrane-orientation-3d', MembraneOrientation3D, params, { state: initialState });
-    return membraneOrientation.commit({ revertOnError: true });
-}

src/extensions/anvil/prop.ts

@@ -1,82 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Structure, StructureProperties, Unit } from '../../mol-model/structure';
-import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
-import { ANVILParams, ANVILProps, computeANVIL, isInMembranePlane } from './algorithm';
-import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
-import { CustomProperty } from '../../mol-model-props/common/custom-property';
-import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area';
-import { Vec3 } from '../../mol-math/linear-algebra';
-import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
-import { CustomPropSymbol } from '../../mol-script/language/symbol';
-import { Type } from '../../mol-script/language/type';
-
-export const MembraneOrientationParams = {
-    ...ANVILParams
-};
-export type MembraneOrientationParams = typeof MembraneOrientationParams
-export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
-
-export { MembraneOrientation };
-
-interface MembraneOrientation {
-    // point in membrane boundary
-    readonly planePoint1: Vec3,
-    // point in opposite side of membrane boundary
-    readonly planePoint2: Vec3,
-    // normal vector of membrane layer
-    readonly normalVector: Vec3,
-    // the radius of the membrane layer
-    readonly radius: number,
-    readonly centroid: Vec3
-}
-
-namespace MembraneOrientation {
-    export enum Tag {
-        Representation = 'membrane-orientation-3d'
-    }
-
-    const pos = Vec3();
-    export const symbols = {
-        isTransmembrane: QuerySymbolRuntime.Dynamic(CustomPropSymbol('computed', 'membrane-orientation.is-transmembrane', Type.Bool),
-            ctx => {
-                const { unit, structure } = ctx.element;
-                const { x, y, z } = StructureProperties.atom;
-                if (!Unit.isAtomic(unit)) return 0;
-                const membraneOrientation = MembraneOrientationProvider.get(structure).value;
-                if (!membraneOrientation) return 0;
-                Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
-                const { normalVector, planePoint1, planePoint2 } = membraneOrientation!;
-                return isInMembranePlane(pos, normalVector, planePoint1, planePoint2);
-            })
-    };
-}
-
-export const MembraneOrientationProvider: CustomStructureProperty.Provider<MembraneOrientationParams, MembraneOrientation> = CustomStructureProperty.createProvider({
-    label: 'Membrane Orientation',
-    descriptor: CustomPropertyDescriptor({
-        name: 'anvil_computed_membrane_orientation',
-        symbols: MembraneOrientation.symbols,
-        // TODO `cifExport`
-    }),
-    type: 'root',
-    defaultParams: MembraneOrientationParams,
-    getParams: (data: Structure) => MembraneOrientationParams,
-    isApplicable: (data: Structure) => true,
-    obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<MembraneOrientationProps>) => {
-        const p = { ...PD.getDefaultValues(MembraneOrientationParams), ...props };
-        return { value: await computeAnvil(ctx, data, p) };
-    }
-});
-
-async function computeAnvil(ctx: CustomProperty.Context, data: Structure, props: Partial<ANVILProps>): Promise<MembraneOrientation> {
-    await AccessibleSurfaceAreaProvider.attach(ctx, data);
-    const p = { ...PD.getDefaultValues(ANVILParams), ...props };
-    return await computeANVIL(data, p).runInContext(ctx.runtime);
-}

src/extensions/anvil/representation.ts

@@ -1,156 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
-import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../mol-repr/representation';
-import { Structure } from '../../mol-model/structure';
-import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
-import { StructureRepresentationProvider, StructureRepresentation, StructureRepresentationStateBuilder } from '../../mol-repr/structure/representation';
-import { MembraneOrientation } from './prop';
-import { ThemeRegistryContext } from '../../mol-theme/theme';
-import { ShapeRepresentation } from '../../mol-repr/shape/representation';
-import { Shape } from '../../mol-model/shape';
-import { RuntimeContext } from '../../mol-task';
-import { Lines } from '../../mol-geo/geometry/lines/lines';
-import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
-import { LinesBuilder } from '../../mol-geo/geometry/lines/lines-builder';
-import { Circle } from '../../mol-geo/primitive/circle';
-import { transformPrimitive } from '../../mol-geo/primitive/primitive';
-import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
-import { MembraneOrientationProvider } from './prop';
-import { MarkerActions } from '../../mol-util/marker-action';
-import { lociLabel } from '../../mol-theme/label';
-import { ColorNames } from '../../mol-util/color/names';
-import { CustomProperty } from '../../mol-model-props/common/custom-property';
-
-const SharedParams = {
-    color: PD.Color(ColorNames.lightgrey),
-    radiusFactor: PD.Numeric(0.8333, { min: 0.1, max: 3.0, step: 0.01 }, { description: 'Scale the radius of the membrane layer' })
-};
-
-const BilayerSpheresParams = {
-    ...Spheres.Params,
-    ...SharedParams,
-    sphereSize: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }, { description: 'Size of spheres that represent membrane planes' }),
-    density: PD.Numeric(1, { min: 0.25, max: 10, step: 0.25 }, { description: 'Distance between spheres'})
-};
-export type BilayerSpheresParams = typeof BilayerSpheresParams
-export type BilayerSpheresProps = PD.Values<BilayerSpheresParams>
-
-const BilayerPlanesParams = {
-    ...Mesh.Params,
-    ...SharedParams,
-    sectorOpacity: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
-};
-export type BilayerPlanesParams = typeof BilayerPlanesParams
-export type BilayerPlanesProps = PD.Values<BilayerPlanesParams>
-
-const BilayerRimsParams = {
-    ...Lines.Params,
-    ...SharedParams,
-    lineSizeAttenuation: PD.Boolean(true),
-    linesSize: PD.Numeric(0.3, { min: 0.01, max: 50, step: 0.01 }),
-    dashedLines: PD.Boolean(true),
-};
-export type BilayerRimsParams = typeof BilayerRimsParams
-export type BilayerRimsProps = PD.Values<BilayerRimsParams>
-
-const MembraneOrientationVisuals = {
-    'bilayer-planes': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneOrientation, BilayerPlanesParams>) => ShapeRepresentation(getBilayerPlanes, Mesh.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }), modifyProps: p => ({ ...p, alpha: p.sectorOpacity, ignoreLight: true, doubleSided: false }) }),
-    'bilayer-rims': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneOrientation, BilayerRimsParams>) => ShapeRepresentation(getBilayerRims, Lines.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }) })
-};
-
-export const MembraneOrientationParams = {
-    ...BilayerSpheresParams,
-    ...BilayerPlanesParams,
-    ...BilayerRimsParams,
-    visuals: PD.MultiSelect(['bilayer-planes', 'bilayer-rims'], PD.objectToOptions(MembraneOrientationVisuals)),
-};
-export type MembraneOrientationParams = typeof MembraneOrientationParams
-export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
-
-export function getMembraneOrientationParams(ctx: ThemeRegistryContext, structure: Structure) {
-    return PD.clone(MembraneOrientationParams);
-}
-
-export type MembraneOrientationRepresentation = StructureRepresentation<MembraneOrientationParams>
-export function MembraneOrientationRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MembraneOrientationParams>): MembraneOrientationRepresentation {
-    return Representation.createMulti('Membrane Orientation', ctx, getParams, StructureRepresentationStateBuilder, MembraneOrientationVisuals as unknown as Representation.Def<Structure, MembraneOrientationParams>);
-}
-
-export const MembraneOrientationRepresentationProvider = StructureRepresentationProvider({
-    name: 'membrane-orientation',
-    label: 'Membrane Orientation',
-    description: 'Displays a grid of points representing membrane layers.',
-    factory: MembraneOrientationRepresentation,
-    getParams: getMembraneOrientationParams,
-    defaultValues: PD.getDefaultValues(MembraneOrientationParams),
-    defaultColorTheme: { name: 'shape-group' },
-    defaultSizeTheme: { name: 'shape-group' },
-    isApplicable: (structure: Structure) => structure.elementCount > 0,
-    ensureCustomProperties: {
-        attach: (ctx: CustomProperty.Context, structure: Structure) => MembraneOrientationProvider.attach(ctx, structure, void 0, true),
-        detach: (data) => MembraneOrientationProvider.ref(data, false)
-    }
-});
-
-function membraneLabel(data: Structure) {
-    return `${lociLabel(Structure.Loci(data))} | Membrane Orientation`;
-}
-
-function getBilayerRims(ctx: RuntimeContext, data: Structure, props: BilayerRimsProps, shape?: Shape<Lines>): Shape<Lines> {
-    const { planePoint1: p1, planePoint2: p2, centroid, normalVector: normal, radius } = MembraneOrientationProvider.get(data).value!;
-    const scaledRadius = props.radiusFactor * radius;
-    const builder = LinesBuilder.create(128, 64, shape?.geometry);
-    getLayerCircle(builder, p1, centroid, normal, scaledRadius, props);
-    getLayerCircle(builder, p2, centroid, normal, scaledRadius, props);
-    return Shape.create('Bilayer rims', data, builder.getLines(), () => props.color, () => props.linesSize, () => membraneLabel(data));
-}
-
-function getLayerCircle(builder: LinesBuilder, p: Vec3, centroid: Vec3, normal: Vec3, radius: number, props: BilayerRimsProps, shape?: Shape<Lines>) {
-    const circle = getCircle(p, centroid, normal, radius);
-    const { indices, vertices } = circle;
-    for (let j = 0, jl = indices.length; j < jl; j += 3) {
-        if (props.dashedLines && j % 2 === 1) continue; // draw every other segment to get dashes
-        const start = indices[j] * 3;
-        const end = indices[j + 1] * 3;
-        const startX = vertices[start];
-        const startY = vertices[start + 1];
-        const startZ = vertices[start + 2];
-        const endX = vertices[end];
-        const endY = vertices[end + 1];
-        const endZ = vertices[end + 2];
-        builder.add(startX, startY, startZ, endX, endY, endZ, 0);
-    }
-}
-
-const tmpMat = Mat4();
-function getCircle(p: Vec3, centroid: Vec3, normal: Vec3, radius: number) {
-    Mat4.targetTo(tmpMat, p, centroid, normal);
-    Mat4.setTranslation(tmpMat, p);
-    Mat4.mul(tmpMat, tmpMat, Mat4.rotX90);
-
-    const circle = Circle({ radius, segments: 64 });
-    return transformPrimitive(circle, tmpMat);
-}
-
-function getBilayerPlanes(ctx: RuntimeContext, data: Structure, props: BilayerPlanesProps, shape?: Shape<Mesh>): Shape<Mesh> {
-    const { planePoint1: p1, planePoint2: p2, centroid, normalVector: normal, radius } = MembraneOrientationProvider.get(data).value!;
-    const state = MeshBuilder.createState(128, 64, shape && shape.geometry);
-    const scaledRadius = props.radiusFactor * radius;
-    getLayerPlane(state, p1, centroid, normal, scaledRadius);
-    getLayerPlane(state, p2, centroid, normal, scaledRadius);
-    return Shape.create('Bilayer planes', data, MeshBuilder.getMesh(state), () => props.color, () => 1, () => membraneLabel(data));
-}
-
-function getLayerPlane(state: MeshBuilder.State, p: Vec3, centroid: Vec3, normal: Vec3, radius: number) {
-    const circle = getCircle(p, centroid, normal, radius);
-    state.currentGroup = 0;
-    MeshBuilder.addPrimitive(state, Mat4.id, circle);
-    MeshBuilder.addPrimitiveFlipped(state, Mat4.id, circle);
-}

src/extensions/cellpack/color/generate.ts

@@ -1,95 +0,0 @@
-/**
- * Copyright (c) 2020-2021 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, Model } 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, Model.TrajectoryInfo.get(m).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' });
-        legend = palette.legend;
-        const modelColor = new Map<number, Color>();
-        for (let i = 0, il = models.length; i < il; ++i) {
-            const idx = Model.TrajectoryInfo.get(models[i]).index;
-            modelColor.set(Model.TrajectoryInfo.get(models[i]).index, palette.color(idx));
-        }
-
-        color = (location: Location): Color => {
-            if (StructureElement.Location.is(location)) {
-                return modelColor.get(Model.TrajectoryInfo.get(location.unit.model).index)!;
-            } else if (Bond.isLocation(location)) {
-                return modelColor.get(Model.TrajectoryInfo.get(location.aUnit.model).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 &&
-            !!CellPackInfoProvider.get(ctx.structure).value
-        );
-    }
-};
-

src/extensions/cellpack/color/provided.ts

@@ -1,75 +0,0 @@
-/**
- * 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, Model, Bond } 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 = Model.TrajectoryInfo.get(models[i]).index;
-            modelColor.set(Model.TrajectoryInfo.get(models[i]).index, info.colors[idx]);
-        }
-
-        color = (location: Location): Color => {
-            if (StructureElement.Location.is(location)) {
-                return modelColor.get(Model.TrajectoryInfo.get(location.unit.model).index)!;
-            } else if (Bond.isLocation(location)) {
-                return modelColor.get(Model.TrajectoryInfo.get(location.aUnit.model).index)!;
-            }
-            return 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 &&
-            Model.TrajectoryInfo.get(ctx.structure.models[0]).size > 1 &&
-            !!CellPackInfoProvider.get(ctx.structure).value?.colors
-        );
-    }
-};

src/extensions/cellpack/curve.ts

@@ -1,229 +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, 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

@@ -1,84 +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
-    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

@@ -1,32 +0,0 @@
-/**
- * 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);
-        }
-    }
-});