3.3.0

Coordinate trajectory related improvements

CHANGELOG.md

@@ -6,6 +6,49 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [v3.3.0] - 2022-02-27
+
+- Fix parsing contour-level from emdb v3 header files
+- Fix invalid CSS (#376)
+- Fix "texture not renderable" & "texture not bound" warnings (#319)
+- Fix visual for bonds between two aromatic rings
+- Fix visual for delocalized bonds (parsed from mmcif and mol2)
+- Fix ring computation algorithm
+- Add ``UnitResonance`` property with info about delocalized triplets
+- Resolve marking in main renderer loop to improve overall performance
+- Use ``throttleTime`` instead of ``debounceTime`` in sequence viewer for better responsiveness
+- Change line geometry default ``scaleFactor`` to 2 (3 is too big after fixing line rendering)
+- Trajectory animation performance improvements
+    - Reuse ``Model.CoarseGrained`` for coordinate trajectories
+    - Avoid calculating ``InterUnitBonds`` when ``Structure.parent`` ones are empty
+    - Reuse unit boundary if sphere has not changed too much
+    - Don't show 'inter-bond' and 'element-cross' visuals in line representations of polymerAndLigand preset
+- Fix additional mononucleotides detected as polymer components
+- Fix and improve ``canRemap`` handling in ``IntraUnitBonds``
+- Reuse occlusion for secondary passes during multi-sampling
+- Check if marking passes are needed before doing them
+- Add ``resolutionScale`` parameter to allow trading quality of occlusion for performance
+
+## [v3.2.0] - 2022-02-17
+
+- Rename "best database mapping" to "SIFTS Mapping"
+- Add schema and export support for ``atom_site.pdbx_sifts_xref_*`` fields
+- Add schema export support for ``atom_site.pdbx_label_index`` field
+- Add `traceOnly` parameter to chain/UniProt-based structure alignment
+- Store ``IndexPairBonds`` as a dynamic property.
+
+## [v3.1.0] - 2022-02-06
+
+- Fix ``xrayShaded`` & ``ignoreLight`` params not working at the same time
+- Add ``ignoreLight`` to component params
+- Tweaks for cleaner default representation style
+    - Cartoon: use ``nucleotide-ring`` instead of ``nucleotide-block``
+    - Focus: use ``xrayShaded`` instead of opacity; adjust target size; don't show non-covalent interactions twice
+- Fix representation preset side effects (changing post-processing parameters, see #363)
+- Add Quick Styles panel (default, illustrative, stylized)
+- Fix exported structure missing secondary-structure categories (#364)
+- Fix volume streaming error message: distinguish between missing data and server error (#364)
+
 ## [v3.0.2] - 2022-01-30
 
 - Fix color smoothing of elongated structures (by fixing ``Sphere.expand`` for spheres with highly directional extrema)

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

@@ -24,6 +24,11 @@ atom_site.auth_asym_id
 atom_site.auth_seq_id
 atom_site.pdbx_PDB_model_num
 atom_site.ihm_model_id
+atom_site.pdbx_label_index
+atom_site.pdbx_sifts_xref_db_name
+atom_site.pdbx_sifts_xref_db_acc
+atom_site.pdbx_sifts_xref_db_num
+atom_site.pdbx_sifts_xref_db_res
 
 atom_site_anisotrop.id
 atom_site_anisotrop.U

docs/interesting-pdb-entries.md

@@ -34,6 +34,14 @@
     * ACE (many, e.g. 5AGU, 1E1X)
     * ACY in 7ABY
     * NH2 (many, e.g. 6Y13)
+* Ligands with many rings
+    * STU (e.g. 1U59) - many fused rings
+    * HT (e.g. 127D) - rings connected by a single bond
+    * J2C (e.g. 7EFJ) - rings connected by a single atom
+    * RBF (e.g. 7QF2) - three linearly fused rings
+    * TA1 (e.g. 1JFF) - many fused rings (incl. a 8-member rings)
+    * BPA (e.g. 1JDG) - many fused rings
+    * CLR (e.g. 3GKI) - four fused rings
 
 Assembly symmetries
 * 5M30 (Assembly 1, C3 local and pseudo)

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.0.2",
+  "version": "3.3.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -92,69 +92,69 @@
   "license": "MIT",
   "devDependencies": {
     "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.4.0",
+    "@graphql-codegen/cli": "^2.6.2",
     "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.2",
+    "@graphql-codegen/typescript": "^2.4.5",
     "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.3.3",
-    "@graphql-codegen/typescript-operations": "^2.2.2",
+    "@graphql-codegen/typescript-graphql-request": "^4.3.7",
+    "@graphql-codegen/typescript-operations": "^2.3.2",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.0",
-    "@types/jest": "^27.4.0",
-    "@typescript-eslint/eslint-plugin": "^5.10.0",
-    "@typescript-eslint/parser": "^5.10.0",
+    "@types/jest": "^27.4.1",
+    "@typescript-eslint/eslint-plugin": "^5.12.1",
+    "@typescript-eslint/parser": "^5.12.1",
     "benchmark": "^2.1.4",
     "concurrently": "^7.0.0",
-    "cpx2": "^4.1.2",
+    "cpx2": "^4.2.0",
     "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.5.1",
-    "eslint": "^8.7.0",
+    "css-loader": "^6.6.0",
+    "eslint": "^8.10.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
-    "fs-extra": "^10.0.0",
-    "graphql": "^16.2.0",
+    "fs-extra": "^10.0.1",
+    "graphql": "^16.3.0",
     "http-server": "^14.1.0",
-    "jest": "^27.4.7",
-    "mini-css-extract-plugin": "^2.5.2",
+    "jest": "^27.5.1",
+    "mini-css-extract-plugin": "^2.5.3",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass": "^1.49.0",
-    "sass-loader": "^12.4.0",
-    "simple-git": "^2.48.0",
+    "sass": "^1.49.9",
+    "sass-loader": "^12.6.0",
+    "simple-git": "^3.2.6",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
     "ts-jest": "^27.1.3",
     "typescript": "^4.5.5",
-    "webpack": "^5.67.0",
-    "webpack-cli": "^4.9.1"
+    "webpack": "^5.69.1",
+    "webpack-cli": "^4.9.2"
   },
   "dependencies": {
     "@types/argparse": "^2.0.10",
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.11.21",
-    "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.38",
+    "@types/node": "^16.11.26",
+    "@types/node-fetch": "^2.6.1",
+    "@types/react": "^17.0.39",
     "@types/react-dom": "^17.0.11",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
-    "body-parser": "^1.19.1",
+    "body-parser": "^1.19.2",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
-    "express": "^4.17.2",
+    "express": "^4.17.3",
     "h264-mp4-encoder": "^1.0.12",
     "immer": "^9.0.12",
     "immutable": "^4.0.0",
     "node-fetch": "^2.6.7",
-    "rxjs": "^7.5.2",
-    "swagger-ui-dist": "^4.2.1",
+    "rxjs": "^7.5.4",
+    "swagger-ui-dist": "^4.5.2",
     "tslib": "^2.3.1",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"
   },
   "peerDependencies": {
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2"
+    "react": "^17.0.2 || ^16.14.0",
+    "react-dom": "^17.0.2 || ^16.14.0"
   }
 }

src/apps/docking-viewer/viewport.tsx

@@ -44,10 +44,11 @@ function occlusionStyle(plugin: PluginContext) {
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
             occlusion: { name: 'on', params: {
-                samples: 64,
-                radius: 8,
-                bias: 1.0,
-                blurKernelSize: 13
+                bias: 0.8,
+                blurKernelSize: 15,
+                radius: 5,
+                samples: 32,
+                resolutionScale: 1
             } },
             outline: { name: 'on', params: {
                 scale: 1.0,

src/examples/lighting/index.ts

@@ -24,7 +24,7 @@ const Canvas3DPresets = {
     illustrative: {
         canvas3d: <Preset>{
             postprocessing: {
-                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
                 outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: Color(0x000000) } }
             },
             renderer: {
@@ -36,7 +36,7 @@ const Canvas3DPresets = {
     occlusion: {
         canvas3d: <Preset>{
             postprocessing: {
-                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
                 outline: { name: 'off', params: {} }
             },
             renderer: {

src/extensions/rcsb/graphql/types.ts

@@ -4,7 +4,7 @@ export type InputMaybe<T> = Maybe<T>;
 export type Exact<T extends { [key: string]: unknown }> = { [K in keyof T]: T[K] };
 export type MakeOptional<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]?: Maybe<T[SubKey]> };
 export type MakeMaybe<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]: Maybe<T[SubKey]> };
-// Generated on 2022-01-15T19:52:34-08:00
+// Generated on 2022-02-27T12:49:36-08:00
 
 /** All built-in and custom scalars, mapped to their actual values */
 export type Scalars = {
@@ -477,6 +477,8 @@ export type ClustersMembers = {
 export type CoreAssembly = {
   /** Get PDB entry that includes this assembly. */
   readonly entry?: Maybe<CoreEntry>;
+  /** Get all pairwise polymer interfaces for this PDB assembly. */
+  readonly interfaces?: Maybe<ReadonlyArray<Maybe<CoreInterface>>>;
   readonly pdbx_struct_assembly?: Maybe<PdbxStructAssembly>;
   readonly pdbx_struct_assembly_auth_evidence?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyAuthEvidence>>>;
   readonly pdbx_struct_assembly_gen?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyGen>>>;
@@ -724,6 +726,16 @@ export type CoreEntry = {
   readonly symmetry?: Maybe<Symmetry>;
 };
 
+export type CoreInterface = {
+  readonly rcsb_id: Scalars['String'];
+  readonly rcsb_interface_container_identifiers: RcsbInterfaceContainerIdentifiers;
+  readonly rcsb_interface_info?: Maybe<RcsbInterfaceInfo>;
+  /** List of operations for each interface partner. */
+  readonly rcsb_interface_operator: ReadonlyArray<Maybe<ReadonlyArray<Maybe<ReadonlyArray<Maybe<Scalars['String']>>>>>>;
+  readonly rcsb_interface_partner: ReadonlyArray<Maybe<RcsbInterfacePartner>>;
+  readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+};
+
 export type CoreNonpolymerEntity = {
   /** Get PDB entry that contains this non-polymer entity. */
   readonly entry?: Maybe<CoreEntry>;
@@ -3186,6 +3198,28 @@ export type GeneName = {
   readonly value?: Maybe<Scalars['String']>;
 };
 
+export type InterfacePartnerFeatureAdditionalProperties = {
+  /**
+   * The additional property name.
+   *
+   * Allowable values:
+   * TO_BE_DEFINED
+   *
+   */
+  readonly name?: Maybe<Scalars['String']>;
+  /** The value(s) of the additional property. */
+  readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
+};
+
+export type InterfacePartnerFeatureFeaturePositions = {
+  /** An identifier for the monomer at which this segment of the feature begins. */
+  readonly beg_seq_id: Scalars['Int'];
+  /** An identifier for the monomer at which this segment of the feature ends. */
+  readonly end_seq_id?: Maybe<Scalars['Int']>;
+  /** The value(s) of the feature over the monomer segment. */
+  readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
+};
+
 export type PdbxAuditRevisionCategory = {
   /**
    * The category updated in the pdbx_audit_revision_category record.
@@ -6745,6 +6779,10 @@ export type Query = {
   readonly entries?: Maybe<ReadonlyArray<Maybe<CoreEntry>>>;
   /** Get PDB entry given the PDB id. */
   readonly entry?: Maybe<CoreEntry>;
+  /** Get a pairwise polymeric interface given the PDB ID, ASSEMBLY ID and INTERFACE ID. */
+  readonly interface?: Maybe<CoreInterface>;
+  /** Get a list of pairwise polymeric interfaces given a list of INTERFACE IDs. Here INTERFACE ID is a compound identifier that includes entry_id, assembly_id and interface_id e.g. 1XXX-1.1. */
+  readonly interfaces?: Maybe<ReadonlyArray<Maybe<CoreInterface>>>;
   /** Get a list of PDB non-polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
   readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
   /** Get a PDB non-polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
@@ -6831,6 +6869,20 @@ export type QueryEntryArgs = {
 };
 
 
+/** Query root */
+export type QueryInterfaceArgs = {
+  assembly_id: Scalars['String'];
+  entry_id: Scalars['String'];
+  interface_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryInterfacesArgs = {
+  interface_ids: ReadonlyArray<Scalars['String']>;
+};
+
+
 /** Query root */
 export type QueryNonpolymer_EntitiesArgs = {
   entity_ids: ReadonlyArray<Scalars['String']>;
@@ -6952,6 +7004,8 @@ export type RcsbAssemblyContainerIdentifiers = {
   readonly assembly_id: Scalars['String'];
   /** Entry identifier for the container. */
   readonly entry_id: Scalars['String'];
+  /** List of binary interface Ids within the assembly (it points to interface id collection). */
+  readonly interface_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
   /**
    * A unique identifier for each object in this assembly container formed by
    *  a dash separated concatenation of entry and assembly identifiers.
@@ -7010,6 +7064,24 @@ export type RcsbAssemblyInfo = {
    *  This is the total count of non-polymer entity instances generated in the assembly coordinate data.
    */
   readonly nonpolymer_entity_instance_count?: Maybe<Scalars['Int']>;
+  /** Number of heterologous (both binding sites are different) interface entities */
+  readonly num_heterologous_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of heteromeric (both partners are different polymeric entities) interface entities */
+  readonly num_heteromeric_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of homomeric (both partners are the same polymeric entity) interface entities */
+  readonly num_homomeric_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of polymer-polymer interface entities, grouping equivalent interfaces at the entity level (i.e. same entity_ids on either side, with similar but not identical binding sites) */
+  readonly num_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of geometrically equivalent (i.e. same asym_ids on either side) polymer-polymer interfaces in the assembly */
+  readonly num_interfaces?: Maybe<Scalars['Int']>;
+  /** Number of isologous (both binding sites are same, i.e. interface is symmetric) interface entities */
+  readonly num_isologous_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of nucleic acid-nucleic acid interface entities */
+  readonly num_na_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of protein-nucleic acid interface entities */
+  readonly num_prot_na_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of protein-protein interface entities */
+  readonly num_protein_interface_entities?: Maybe<Scalars['Int']>;
   /** The assembly non-hydrogen polymer entity atomic coordinate count. */
   readonly polymer_atom_count?: Maybe<Scalars['Int']>;
   /**
@@ -7085,6 +7157,10 @@ export type RcsbAssemblyInfo = {
    *  This is the total count of solvent entity instances generated in the assembly coordinate data.
    */
   readonly solvent_entity_instance_count?: Maybe<Scalars['Int']>;
+  /** Total buried surface area calculated as the sum of buried surface areas over all interfaces */
+  readonly total_assembly_buried_surface_area?: Maybe<Scalars['Float']>;
+  /** Total number of interfacing residues in the assembly, calculated as the sum of interfacing residues over all interfaces */
+  readonly total_number_interface_residues?: Maybe<Scalars['Int']>;
   /**
    * The number of unmodeled polymer monomers in the assembly coordinate data. This is
    *  the total count of monomers with unreported coordinate data for all polymer
@@ -8817,6 +8893,99 @@ export type RcsbGenomicLineage = {
   readonly name?: Maybe<Scalars['String']>;
 };
 
+export type RcsbInterfaceContainerIdentifiers = {
+  /** This item references an assembly in pdbx_struct_assembly */
+  readonly assembly_id: Scalars['String'];
+  /** Entry identifier for the container. */
+  readonly entry_id: Scalars['String'];
+  /**
+   * Identifier for NCS-equivalent interfaces within the assembly (same entity_ids on both sides)
+   *
+   * Examples:
+   * 1, 2
+   *
+   */
+  readonly interface_entity_id?: Maybe<Scalars['String']>;
+  /**
+   * Identifier for the geometrically equivalent (same asym_ids on either side) interfaces within the assembly
+   *
+   * Examples:
+   * 1, 2
+   *
+   */
+  readonly interface_id: Scalars['String'];
+  /**
+   * Unique identifier for the document
+   *
+   * Examples:
+   * 2UZI-1.A.B?1
+   *
+   */
+  readonly rcsb_id: Scalars['String'];
+};
+
+export type RcsbInterfaceInfo = {
+  /** Total interface buried surface area */
+  readonly interface_area?: Maybe<Scalars['Float']>;
+  /** Allowable values: homo, hetero. */
+  readonly interface_character?: Maybe<Scalars['String']>;
+  /** Number of core interface residues, defined as those that bury >90% accessible surface area with respect to the unbound state */
+  readonly num_core_interface_residues?: Maybe<Scalars['Int']>;
+  /** Number of interface residues, defined as those with burial fraction > 0 */
+  readonly num_interface_residues?: Maybe<Scalars['Int']>;
+  /** Allowable values: Nucleic acid (only), Protein (only), Protein/NA. */
+  readonly polymer_composition?: Maybe<Scalars['String']>;
+  /** The Jaccard score (intersection over union) of interface contacts in homomeric interfaces, comparing contact sets left-right vs right-left. High values indicate isologous (symmetric) interfaces, with value=1 if perfectly symmetric (e.g. crystallographic symmetry) */
+  readonly self_jaccard_contact_score?: Maybe<Scalars['Float']>;
+};
+
+export type RcsbInterfacePartner = {
+  readonly interface_partner_feature?: Maybe<ReadonlyArray<Maybe<RcsbInterfacePartnerInterfacePartnerFeature>>>;
+  readonly interface_partner_identifier?: Maybe<RcsbInterfacePartnerInterfacePartnerIdentifier>;
+};
+
+export type RcsbInterfacePartnerInterfacePartnerFeature = {
+  readonly additional_properties?: Maybe<ReadonlyArray<Maybe<InterfacePartnerFeatureAdditionalProperties>>>;
+  /**
+   * Identifies the version of the feature assignment.
+   *
+   * Examples:
+   * V4_0_2
+   *
+   */
+  readonly assignment_version?: Maybe<Scalars['String']>;
+  /** A description for the feature. */
+  readonly description?: Maybe<Scalars['String']>;
+  /** An identifier for the feature. */
+  readonly feature_id?: Maybe<Scalars['String']>;
+  readonly feature_positions?: Maybe<ReadonlyArray<Maybe<InterfacePartnerFeatureFeaturePositions>>>;
+  /** A name for the feature. */
+  readonly name?: Maybe<Scalars['String']>;
+  /**
+   * Code identifying the individual, organization or program that assigned the feature.
+   *
+   * Examples:
+   * NACCESS
+   *
+   */
+  readonly provenance_source?: Maybe<Scalars['String']>;
+  /**
+   * A type or category of the feature.
+   *
+   * Allowable values:
+   * ASA_UNBOUND, ASA_BOUND
+   *
+   */
+  readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbInterfacePartnerInterfacePartnerIdentifier = {
+  /** Instance identifier for this container. */
+  readonly asym_id: Scalars['String'];
+  /** Polymer entity identifier for the container. */
+  readonly entity_id: Scalars['String'];
+};
+
 export type RcsbLatestRevision = {
   /** The major version number of the latest revision. */
   readonly major_revision?: Maybe<Scalars['Int']>;
@@ -10263,7 +10432,7 @@ export type RcsbPolymerInstanceFeature = {
    * A type or category of the feature.
    *
    * Allowable values:
-   * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+   * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ, ASA
    *
    */
   readonly type?: Maybe<Scalars['String']>;
@@ -13145,4 +13314,4 @@ export type AssemblySymmetryQueryVariables = Exact<{
 }>;
 
 
-export type AssemblySymmetryQuery = { readonly assembly?: { readonly rcsb_struct_symmetry?: ReadonlyArray<{ readonly kind: string, readonly oligomeric_state: string, readonly stoichiometry: ReadonlyArray<string | null | undefined>, readonly symbol: string, readonly type: string, readonly clusters: ReadonlyArray<{ readonly avg_rmsd?: number | null | undefined, readonly members: ReadonlyArray<{ readonly asym_id: string, readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null | undefined> | null | undefined } | null | undefined> } | null | undefined>, readonly rotation_axes?: ReadonlyArray<{ readonly order?: number | null | undefined, readonly start: ReadonlyArray<number | null | undefined>, readonly end: ReadonlyArray<number | null | undefined> } | null | undefined> | null | undefined } | null | undefined> | null | undefined } | null | undefined };
+export type AssemblySymmetryQuery = { readonly assembly?: { readonly rcsb_struct_symmetry?: ReadonlyArray<{ readonly kind: string, readonly oligomeric_state: string, readonly stoichiometry: ReadonlyArray<string | null>, readonly symbol: string, readonly type: string, readonly clusters: ReadonlyArray<{ readonly avg_rmsd?: number | null, readonly members: ReadonlyArray<{ readonly asym_id: string, readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null> | null } | null> } | null>, readonly rotation_axes?: ReadonlyArray<{ readonly order?: number | null, readonly start: ReadonlyArray<number | null>, readonly end: ReadonlyArray<number | null> } | null> | null } | null> | null } | null };

src/mol-canvas3d/canvas3d.ts

@@ -236,7 +236,7 @@ interface Canvas3D {
     /** Sets drawPaused = false without starting the built in animation loop */
     resume(): void
     identify(x: number, y: number): PickData | undefined
-    mark(loci: Representation.Loci, action: MarkerAction, noDraw?: boolean): void
+    mark(loci: Representation.Loci, action: MarkerAction): void
     getLoci(pickingId: PickingId | undefined): Representation.Loci
 
     notifyDidDraw: boolean,
@@ -345,7 +345,30 @@ namespace Canvas3D {
             return { loci, repr };
         }
 
-        function mark(reprLoci: Representation.Loci, action: MarkerAction, noDraw = false) {
+        let markBuffer: [reprLoci: Representation.Loci, action: MarkerAction][] = [];
+
+        function mark(reprLoci: Representation.Loci, action: MarkerAction) {
+            // NOTE: might try to optimize a case with opposite actions for the
+            //       same loci. Tho this might end up being more expensive (and error prone)
+            //       then just applying everything "naively".
+            markBuffer.push([reprLoci, action]);
+        }
+
+        function resolveMarking() {
+            let changed = false;
+            for (const [r, l] of markBuffer) {
+                changed = applyMark(r, l) || changed;
+            }
+            markBuffer = [];
+            if (changed) {
+                scene.update(void 0, true);
+                helper.handle.scene.update(void 0, true);
+                helper.camera.scene.update(void 0, true);
+            }
+            return changed;
+        }
+
+        function applyMark(reprLoci: Representation.Loci, action: MarkerAction) {
             const { repr, loci } = reprLoci;
             let changed = false;
             if (repr) {
@@ -355,24 +378,10 @@ namespace Canvas3D {
                 changed = helper.camera.mark(loci, action) || changed;
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
-            if (changed) {
-                if (noDraw) {
-                    // Even with `noDraw` make sure changes will be rendered.
-                    // Note that with this calling mark (with or without `noDraw`) multiple times
-                    // during a JS event loop iteration will only result in a single render call.
-                    forceNextRender = true;
-                } else {
-                    scene.update(void 0, true);
-                    helper.handle.scene.update(void 0, true);
-                    helper.camera.scene.update(void 0, true);
-                    const prevPickDirty = pickHelper.dirty;
-                    draw({ force: true, allowMulti: true });
-                    pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
-                }
-            }
+            return changed;
         }
 
-        function render(force: boolean, allowMulti: boolean) {
+        function render(force: boolean) {
             if (webgl.isContextLost) return false;
 
             let resized = false;
@@ -386,6 +395,8 @@ namespace Canvas3D {
                 y > gl.drawingBufferHeight || y + height < 0
             ) return false;
 
+            const markingUpdated = resolveMarking();
+
             let didRender = false;
             controls.update(currentTime);
             const cameraChanged = camera.update();
@@ -393,9 +404,9 @@ namespace Canvas3D {
             const shouldRender = force || cameraChanged || resized || forceNextRender;
             forceNextRender = false;
 
-            const multiSampleChanged = multiSampleHelper.update(shouldRender, p.multiSample);
+            const multiSampleChanged = multiSampleHelper.update(markingUpdated || shouldRender, p.multiSample);
 
-            if (shouldRender || multiSampleChanged) {
+            if (shouldRender || multiSampleChanged || markingUpdated) {
                 let cam: Camera | StereoCamera = camera;
                 if (p.camera.stereo.name === 'on') {
                     stereoCamera.update();
@@ -404,12 +415,13 @@ namespace Canvas3D {
 
                 const ctx = { renderer, camera: cam, scene, helper };
                 if (MultiSamplePass.isEnabled(p.multiSample)) {
-                    const forceOn = !cameraChanged && allowMulti && !controls.isAnimating;
+                    const forceOn = !cameraChanged && markingUpdated && !controls.isAnimating;
                     multiSampleHelper.render(ctx, p, true, forceOn);
                 } else {
                     passes.draw.render(ctx, p, true);
                 }
-                pickHelper.dirty = true;
+                // if only marking has updated, do not set the flag to dirty
+                pickHelper.dirty = pickHelper.dirty || shouldRender;
                 didRender = true;
             }
 
@@ -421,9 +433,9 @@ namespace Canvas3D {
         let currentTime = 0;
         let drawPaused = false;
 
-        function draw(options?: { force?: boolean, allowMulti?: boolean }) {
+        function draw(options?: { force?: boolean }) {
             if (drawPaused) return;
-            if (render(!!options?.force, !!options?.allowMulti) && notifyDidDraw) {
+            if (render(!!options?.force) && notifyDidDraw) {
                 didDraw.next(now() - startTime as now.Timestamp);
             }
         }
@@ -831,6 +843,8 @@ namespace Canvas3D {
             dispose: () => {
                 contextRestoredSub.unsubscribe();
 
+                markBuffer = [];
+
                 scene.clear();
                 helper.debug.clear();
                 controls.dispose();

src/mol-canvas3d/passes/draw.ts

@@ -307,19 +307,22 @@ export class DrawPass {
         }
 
         if (markingEnabled) {
-            const markingDepthTest = props.marking.ghostEdgeStrength < 1;
-            if (markingDepthTest) {
-                this.marking.depthTarget.bind();
+            const markerAverage = scene.getMarkerAverage();
+            if (markerAverage > 0) {
+                const markingDepthTest = props.marking.ghostEdgeStrength < 1;
+                if (markingDepthTest && markerAverage !== 1) {
+                    this.marking.depthTarget.bind();
+                    renderer.clear(false, true);
+                    renderer.renderMarkingDepth(scene.primitives, camera, null);
+                }
+
+                this.marking.maskTarget.bind();
                 renderer.clear(false, true);
-                renderer.renderMarkingDepth(scene.primitives, camera, null);
+                renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
+
+                this.marking.update(props.marking);
+                this.marking.render(camera.viewport, postprocessingEnabled ? this.postprocessing.target : this.colorTarget);
             }
-
-            this.marking.maskTarget.bind();
-            renderer.clear(false, true);
-            renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
-
-            this.marking.update(props.marking);
-            this.marking.render(camera.viewport, postprocessingEnabled ? this.postprocessing.target : this.colorTarget);
         }
 
         if (helper.debug.isEnabled) {

src/mol-canvas3d/passes/multi-sample.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -157,6 +157,14 @@ export class MultiSamplePass {
             ValueCell.update(compose.values.uWeight, sampleWeight);
 
             // render scene
+            if (i === 0) {
+                drawPass.postprocessing.setOcclusionOffset(0, 0);
+            } else {
+                drawPass.postprocessing.setOcclusionOffset(
+                    offset[0] / width,
+                    offset[1] / height
+                );
+            }
             drawPass.render(ctx, props, false);
 
             // compose rendered scene with compose target
@@ -175,6 +183,8 @@ export class MultiSamplePass {
             compose.render();
         }
 
+        drawPass.postprocessing.setOcclusionOffset(0, 0);
+
         ValueCell.update(compose.values.uWeight, 1.0);
         ValueCell.update(compose.values.tColor, composeTarget.texture);
         compose.update();
@@ -236,6 +246,14 @@ export class MultiSamplePass {
                 camera.update();
 
                 // render scene
+                if (sampleIndex === 0) {
+                    drawPass.postprocessing.setOcclusionOffset(0, 0);
+                } else {
+                    drawPass.postprocessing.setOcclusionOffset(
+                        offset[0] / width,
+                        offset[1] / height
+                    );
+                }
                 drawPass.render(ctx, props, false);
 
                 // compose rendered scene with compose target
@@ -258,6 +276,8 @@ export class MultiSamplePass {
             }
         }
 
+        drawPass.postprocessing.setOcclusionOffset(0, 0);
+
         this.bindOutputTarget(toDrawingBuffer);
         gl.viewport(x, y, width, height);
         gl.scissor(x, y, width, height);
@@ -291,23 +311,23 @@ const JitterVectors = [
         [0, 0]
     ],
     [
-        [4, 4], [-4, -4]
+        [0, 0], [-4, -4]
     ],
     [
-        [-2, -6], [6, -2], [-6, 2], [2, 6]
+        [0, 0], [6, -2], [-6, 2], [2, 6]
     ],
     [
-        [1, -3], [-1, 3], [5, 1], [-3, -5],
+        [0, 0], [-1, 3], [5, 1], [-3, -5],
         [-5, 5], [-7, -1], [3, 7], [7, -7]
     ],
     [
-        [1, 1], [-1, -3], [-3, 2], [4, -1],
+        [0, 0], [-1, -3], [-3, 2], [4, -1],
         [-5, -2], [2, 5], [5, 3], [3, -5],
         [-2, 6], [0, -7], [-4, -6], [-6, 4],
         [-8, 0], [7, -4], [6, 7], [-7, -8]
     ],
     [
-        [-4, -7], [-7, -5], [-3, -5], [-5, -4],
+        [0, 0], [-7, -5], [-3, -5], [-5, -4],
         [-1, -4], [-2, -2], [-6, -1], [-4, 0],
         [-7, 1], [-1, 2], [-6, 3], [-3, 3],
         [-7, 6], [-3, 6], [-5, 7], [-1, 7],

src/mol-canvas3d/passes/postprocessing.ts

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
  */
 
-import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { CopyRenderable, createCopyRenderable, QuadSchema, QuadValues } from '../../mol-gl/compute/util';
 import { TextureSpec, Values, UniformSpec, DefineSpec } from '../../mol-gl/renderable/schema';
 import { ShaderCode } from '../../mol-gl/shader-code';
 import { WebGLContext } from '../../mol-gl/webgl/context';
@@ -199,6 +199,7 @@ const PostprocessingSchema = {
     uMaxPossibleViewZDiff: UniformSpec('f'),
 
     dOcclusionEnable: DefineSpec('boolean'),
+    uOcclusionOffset: UniformSpec('v2'),
 
     dOutlineEnable: DefineSpec('boolean'),
     dOutlineScale: DefineSpec('number'),
@@ -227,6 +228,7 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
         uMaxPossibleViewZDiff: ValueCell.create(0.5),
 
         dOcclusionEnable: ValueCell.create(true),
+        uOcclusionOffset: ValueCell.create(Vec2.create(0, 0)),
 
         dOutlineEnable: ValueCell.create(false),
         dOutlineScale: ValueCell.create(1),
@@ -244,9 +246,10 @@ export const PostprocessingParams = {
     occlusion: PD.MappedStatic('on', {
         on: PD.Group({
             samples: PD.Numeric(32, { min: 1, max: 256, step: 1 }),
-            radius: PD.Numeric(5, { min: 0, max: 10, step: 0.1 }, { description: 'Final radius is 2^x.' }),
+            radius: PD.Numeric(5, { min: 0, max: 10, step: 0.1 }, { description: 'Final occlusion radius is 2^x' }),
             bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
             blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
+            resolutionScale: PD.Numeric(1, { min: 0.1, max: 1, step: 0.05 }, { description: 'Adjust resolution of occlusion calculation' }),
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
@@ -281,6 +284,9 @@ export class PostprocessingPass {
     private readonly ssaoBlurFirstPassFramebuffer: Framebuffer;
     private readonly ssaoBlurSecondPassFramebuffer: Framebuffer;
 
+    private readonly downsampledDepthTarget: RenderTarget;
+    private readonly downsampleDepthRenderable: CopyRenderable;
+
     private readonly ssaoDepthTexture: Texture;
     private readonly ssaoDepthBlurProxyTexture: Texture;
 
@@ -290,24 +296,25 @@ export class PostprocessingPass {
 
     private nSamples: number;
     private blurKernelSize: number;
+    private downsampleFactor: number;
 
     private readonly renderable: PostprocessingRenderable;
 
     private ssaoScale: number;
     private calcSsaoScale() {
         // downscale ssao for high pixel-ratios
-        return Math.min(1, 1 / this.webgl.pixelRatio);
+        return Math.min(1, 1 / this.webgl.pixelRatio) * this.downsampleFactor;
     }
 
-    constructor(private webgl: WebGLContext, drawPass: DrawPass) {
-        this.ssaoScale = this.calcSsaoScale();
-
+    constructor(private webgl: WebGLContext, private drawPass: DrawPass) {
         const { colorTarget, depthTexture } = drawPass;
         const width = colorTarget.getWidth();
         const height = colorTarget.getHeight();
 
         this.nSamples = 1;
         this.blurKernelSize = 1;
+        this.downsampleFactor = 1;
+        this.ssaoScale = this.calcSsaoScale();
 
         // needs to be linear for anti-aliasing pass
         this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
@@ -332,17 +339,20 @@ export class PostprocessingPass {
         const sw = Math.floor(width * this.ssaoScale);
         const sh = Math.floor(height * this.ssaoScale);
 
-        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+        this.downsampledDepthTarget = webgl.createRenderTarget(sw, sh, false, 'uint8', 'linear');
+        this.downsampleDepthRenderable = createCopyRenderable(webgl, depthTexture);
+
+        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
         this.ssaoDepthTexture.define(sw, sh);
         this.ssaoDepthTexture.attachFramebuffer(this.ssaoFramebuffer, 'color0');
 
-        this.ssaoDepthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+        this.ssaoDepthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
         this.ssaoDepthBlurProxyTexture.define(sw, sh);
         this.ssaoDepthBlurProxyTexture.attachFramebuffer(this.ssaoBlurFirstPassFramebuffer, 'color0');
 
         this.ssaoDepthTexture.attachFramebuffer(this.ssaoBlurSecondPassFramebuffer, 'color0');
 
-        this.ssaoRenderable = getSsaoRenderable(webgl, depthTexture);
+        this.ssaoRenderable = getSsaoRenderable(webgl, this.downsampleFactor === 1 ? depthTexture : this.downsampledDepthTarget.texture);
         this.ssaoBlurFirstPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthTexture, 'horizontal');
         this.ssaoBlurSecondPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthBlurProxyTexture, 'vertical');
         this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTexture, this.outlinesTarget.texture, this.ssaoDepthTexture);
@@ -359,11 +369,13 @@ export class PostprocessingPass {
             const sh = Math.floor(height * this.ssaoScale);
             this.target.setSize(width, height);
             this.outlinesTarget.setSize(width, height);
+            this.downsampledDepthTarget.setSize(sw, sh);
             this.ssaoDepthTexture.define(sw, sh);
             this.ssaoDepthBlurProxyTexture.define(sw, sh);
 
             ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
             ValueCell.update(this.outlinesRenderable.values.uTexSize, Vec2.set(this.outlinesRenderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
             ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
             ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
             ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
@@ -434,6 +446,30 @@ export class PostprocessingPass {
                 ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
             }
 
+            if (this.downsampleFactor !== props.occlusion.params.resolutionScale) {
+                needsUpdateSsao = true;
+
+                this.downsampleFactor = props.occlusion.params.resolutionScale;
+                this.ssaoScale = this.calcSsaoScale();
+
+                const sw = Math.floor(w * this.ssaoScale);
+                const sh = Math.floor(h * this.ssaoScale);
+
+                this.downsampledDepthTarget.setSize(sw, sh);
+                this.ssaoDepthTexture.define(sw, sh);
+                this.ssaoDepthBlurProxyTexture.define(sw, sh);
+
+                if (this.ssaoScale === 1) {
+                    ValueCell.update(this.ssaoRenderable.values.tDepth, this.drawPass.depthTexture);
+                } else {
+                    ValueCell.update(this.ssaoRenderable.values.tDepth, this.downsampledDepthTarget.texture);
+                }
+
+                ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
+            }
         }
 
         if (props.outline.name === 'on') {
@@ -494,6 +530,13 @@ export class PostprocessingPass {
         gl.scissor(x, y, width, height);
     }
 
+    private occlusionOffset: [x: number, y: number] = [0, 0];
+    setOcclusionOffset(x: number, y: number) {
+        this.occlusionOffset[0] = x;
+        this.occlusionOffset[1] = y;
+        ValueCell.update(this.renderable.values.uOcclusionOffset, Vec2.set(this.renderable.values.uOcclusionOffset.ref.value, x, y));
+    }
+
     render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
         this.updateState(camera, transparentBackground, backgroundColor, props);
 
@@ -502,14 +545,13 @@ export class PostprocessingPass {
             this.outlinesRenderable.render();
         }
 
-        if (props.occlusion.name === 'on') {
-            const { x, y, width, height } = camera.viewport;
-            const sx = Math.floor(x * this.ssaoScale);
-            const sy = Math.floor(y * this.ssaoScale);
-            const sw = Math.ceil(width * this.ssaoScale);
-            const sh = Math.ceil(height * this.ssaoScale);
-            this.webgl.gl.viewport(sx, sy, sw, sh);
-            this.webgl.gl.scissor(sx, sy, sw, sh);
+        // don't render occlusion if offset is given,
+        // which will reuse the existing occlusion
+        if (props.occlusion.name === 'on' && this.occlusionOffset[0] === 0 && this.occlusionOffset[1] === 0) {
+            if (this.ssaoScale < 1) {
+                this.downsampledDepthTarget.bind();
+                this.downsampleDepthRenderable.render();
+            }
 
             this.ssaoFramebuffer.bind();
             this.ssaoRenderable.render();
@@ -519,9 +561,6 @@ export class PostprocessingPass {
 
             this.ssaoBlurSecondPassFramebuffer.bind();
             this.ssaoBlurSecondPassRenderable.render();
-
-            this.webgl.gl.viewport(x, y, width, height);
-            this.webgl.gl.scissor(x, y, width, height);
         }
 
         if (toDrawingBuffer) {

src/mol-geo/geometry/lines/lines.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -165,7 +165,7 @@ export namespace Lines {
 
     export const Params = {
         ...BaseGeometry.Params,
-        sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
+        sizeFactor: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }),
         lineSizeAttenuation: PD.Boolean(false),
     };
     export type Params = typeof Params

src/mol-gl/_spec/renderer.spec.ts

@@ -31,7 +31,7 @@ describe('renderer', () => {
         expect(ctx.gl.drawingBufferHeight).toBe(32);
 
         expect(ctx.stats.resourceCounts.attribute).toBe(0);
-        expect(ctx.stats.resourceCounts.texture).toBe(0);
+        expect(ctx.stats.resourceCounts.texture).toBe(1);
         expect(ctx.stats.resourceCounts.vertexArray).toBe(0);
         expect(ctx.stats.resourceCounts.program).toBe(0);
         expect(ctx.stats.resourceCounts.shader).toBe(0);
@@ -52,7 +52,7 @@ describe('renderer', () => {
         scene.add(points);
         scene.commit();
         expect(ctx.stats.resourceCounts.attribute).toBe(ctx.isWebGL2 ? 4 : 5);
-        expect(ctx.stats.resourceCounts.texture).toBe(8);
+        expect(ctx.stats.resourceCounts.texture).toBe(9);
         expect(ctx.stats.resourceCounts.vertexArray).toBe(ctx.extensions.vertexArrayObject ? 5 : 0);
         expect(ctx.stats.resourceCounts.program).toBe(5);
         expect(ctx.stats.resourceCounts.shader).toBe(10);
@@ -60,7 +60,7 @@ describe('renderer', () => {
         scene.remove(points);
         scene.commit();
         expect(ctx.stats.resourceCounts.attribute).toBe(0);
-        expect(ctx.stats.resourceCounts.texture).toBe(0);
+        expect(ctx.stats.resourceCounts.texture).toBe(1);
         expect(ctx.stats.resourceCounts.vertexArray).toBe(0);
         expect(ctx.stats.resourceCounts.program).toBe(5);
         expect(ctx.stats.resourceCounts.shader).toBe(10);

src/mol-gl/renderer.ts

@@ -16,7 +16,7 @@ import { GlobalUniformValues } from './renderable/schema';
 import { GraphicsRenderVariant } from './webgl/render-item';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { degToRad } from '../mol-math/misc';
-import { createNullTexture, Texture, Textures } from './webgl/texture';
+import { Texture, Textures } from './webgl/texture';
 import { arrayMapUpsert } from '../mol-util/array';
 import { clamp } from '../mol-math/interpolate';
 
@@ -146,9 +146,9 @@ namespace Renderer {
 
         let transparentBackground = false;
 
-        const nullDepthTexture = createNullTexture(gl);
+        const emptyDepthTexture = ctx.resources.texture('image-depth', 'depth', 'ushort', 'nearest');
         const sharedTexturesList: Textures = [
-            ['tDepth', nullDepthTexture]
+            ['tDepth', emptyDepthTexture]
         ];
 
         const view = Mat4();
@@ -309,7 +309,7 @@ namespace Renderer {
         };
 
         const updateInternal = (group: Scene.Group, camera: ICamera, depthTexture: Texture | null, renderWboit: boolean, markingDepthTest: boolean) => {
-            arrayMapUpsert(sharedTexturesList, 'tDepth', depthTexture || nullDepthTexture);
+            arrayMapUpsert(sharedTexturesList, 'tDepth', depthTexture || emptyDepthTexture);
 
             ValueCell.update(globalUniforms.uModel, group.view);
             ValueCell.update(globalUniforms.uModelView, Mat4.mul(modelView, group.view, camera.view));

src/mol-gl/scene.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -79,6 +79,7 @@ interface Scene extends Object3D {
     has: (o: GraphicsRenderObject) => boolean
     clear: () => void
     forEach: (callbackFn: (value: GraphicsRenderable, key: GraphicsRenderObject) => void) => void
+    getMarkerAverage: () => number
 }
 
 namespace Scene {
@@ -243,7 +244,18 @@ namespace Scene {
                     visibleHash = computeVisibleHash();
                 }
                 return boundingSphereVisible;
-            }
+            },
+            getMarkerAverage() {
+                if (primitives.length === 0 && volumes.length === 0) return 0;
+                let markerAverage = 0;
+                for (let i = 0, il = primitives.length; i < il; ++i) {
+                    markerAverage += primitives[i].values.markerAverage.ref.value;
+                }
+                for (let i = 0, il = volumes.length; i < il; ++i) {
+                    markerAverage += volumes[i].values.markerAverage.ref.value;
+                }
+                return markerAverage / (primitives.length + volumes.length);
+            },
         };
     }
 }

src/mol-gl/shader/chunks/apply-light-color.glsl.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  *
@@ -8,61 +8,65 @@
  */
 
 export const apply_light_color = `
-#ifdef bumpEnabled
-    if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {
-        vec3 bumpNormal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);
-        #ifdef enabledFragDepth
-            if (!isNaN(bumpNormal.x) && !isNaN(bumpNormal.y) && !isNaN(bumpNormal.z)) {
-                normal = bumpNormal;
-            }
-        #else
-            normal = bumpNormal;
-        #endif
-    }
-#endif
-
-vec4 color = material;
-
-ReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));
-
-PhysicalMaterial physicalMaterial;
-physicalMaterial.diffuseColor = color.rgb * (1.0 - metalness);
-#ifdef enabledFragDepth
-    physicalMaterial.roughness = min(max(roughness, 0.0525), 1.0);
+#ifdef dIgnoreLight
+    gl_FragColor = material;
 #else
-    vec3 dxy = max(abs(dFdx(normal)), abs(dFdy(normal)));
-    float geometryRoughness = max(max(dxy.x, dxy.y), dxy.z);
-    physicalMaterial.roughness = min(max(roughness, 0.0525) + geometryRoughness, 1.0);
+    #ifdef bumpEnabled
+        if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {
+            vec3 bumpNormal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);
+            #ifdef enabledFragDepth
+                if (!isNaN(bumpNormal.x) && !isNaN(bumpNormal.y) && !isNaN(bumpNormal.z)) {
+                    normal = bumpNormal;
+                }
+            #else
+                normal = bumpNormal;
+            #endif
+        }
+    #endif
+
+    vec4 color = material;
+
+    ReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));
+
+    PhysicalMaterial physicalMaterial;
+    physicalMaterial.diffuseColor = color.rgb * (1.0 - metalness);
+    #ifdef enabledFragDepth
+        physicalMaterial.roughness = min(max(roughness, 0.0525), 1.0);
+    #else
+        vec3 dxy = max(abs(dFdx(normal)), abs(dFdy(normal)));
+        float geometryRoughness = max(max(dxy.x, dxy.y), dxy.z);
+        physicalMaterial.roughness = min(max(roughness, 0.0525) + geometryRoughness, 1.0);
+    #endif
+    physicalMaterial.specularColor = mix(vec3(0.04), color.rgb, metalness);
+    physicalMaterial.specularF90 = 1.0;
+
+    GeometricContext geometry;
+    geometry.position = -vViewPosition;
+    geometry.normal = normal;
+    geometry.viewDir = normalize(vViewPosition);
+
+    IncidentLight directLight;
+    #pragma unroll_loop_start
+    for (int i = 0; i < dLightCount; ++i) {
+        directLight.direction = uLightDirection[i];
+        directLight.color = uLightColor[i] * PI; // * PI for punctual light
+        RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);
+    }
+    #pragma unroll_loop_end
+
+    vec3 irradiance = uAmbientColor * PI; // * PI for punctual light
+    RE_IndirectDiffuse_Physical(irradiance, geometry, physicalMaterial, reflectedLight);
+
+    // indirect specular only metals
+    vec3 radiance = uAmbientColor * metalness;
+    vec3 iblIrradiance = uAmbientColor * metalness;
+    vec3 clearcoatRadiance = vec3(0.0);
+    RE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);
+
+    vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;
+
+    gl_FragColor = vec4(outgoingLight, color.a);
 #endif
-physicalMaterial.specularColor = mix(vec3(0.04), color.rgb, metalness);
-physicalMaterial.specularF90 = 1.0;
-
-GeometricContext geometry;
-geometry.position = -vViewPosition;
-geometry.normal = normal;
-geometry.viewDir = normalize(vViewPosition);
-
-IncidentLight directLight;
-#pragma unroll_loop_start
-for (int i = 0; i < dLightCount; ++i) {
-    directLight.direction = uLightDirection[i];
-    directLight.color = uLightColor[i] * PI; // * PI for punctual light
-    RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);
-}
-#pragma unroll_loop_end
-
-vec3 irradiance = uAmbientColor * PI; // * PI for punctual light
-RE_IndirectDiffuse_Physical(irradiance, geometry, physicalMaterial, reflectedLight);
-
-// indirect specular only metals
-vec3 radiance = uAmbientColor * metalness;
-vec3 iblIrradiance = uAmbientColor * metalness;
-vec3 clearcoatRadiance = vec3(0.0);
-RE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);
-
-vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;
-
-gl_FragColor = vec4(outgoingLight, color.a);
 
 #ifdef dXrayShaded
     gl_FragColor.a *= 1.0 - pow(abs(dot(normal, vec3(0.0, 0.0, 1.0))), uXrayEdgeFalloff);

src/mol-gl/shader/cylinders.frag.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -127,13 +127,9 @@ void main() {
     #elif defined(dRenderVariant_marking)
         gl_FragColor = material;
     #elif defined(dRenderVariant_color)
-        #ifdef dIgnoreLight
-            gl_FragColor = material;
-        #else
-            mat3 normalMatrix = transpose3(inverse3(mat3(uView)));
-            vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));
-            #include apply_light_color
-        #endif
+        mat3 normalMatrix = transpose3(inverse3(mat3(uView)));
+        vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));
+        #include apply_light_color
 
         #include apply_interior_color
         #include apply_marker_color

src/mol-gl/shader/direct-volume.frag.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
@@ -166,9 +166,7 @@ vec3 v3m4(vec3 p, mat4 m) {
 float preFogAlphaBlended = 0.0;
 
 vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {
-    #if !defined(dIgnoreLight)
-        mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));
-    #endif
+    mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));
     mat4 cartnToUnit = uCartnToUnit * inverse4(vTransform);
     #if defined(dClipVariant_pixel) && dClipObjectCount != 0
         mat4 modelTransform = uModel * vTransform * uTransform;
@@ -296,24 +294,20 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {
             material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);
         #endif
 
-        #ifdef dIgnoreLight
+        if (material.a >= 0.01) {
+            #ifdef dPackedGroup
+                // compute gradient by central differences
+                gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;
+                gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;
+                gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;
+            #else
+                gradient = cell.xyz * 2.0 - 1.0;
+            #endif
+            vec3 normal = -normalize(normalMatrix * normalize(gradient));
+            #include apply_light_color
+        } else {
             gl_FragColor.rgb = material.rgb;
-        #else
-            if (material.a >= 0.01) {
-                #ifdef dPackedGroup
-                    // compute gradient by central differences
-                    gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;
-                    gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;
-                    gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;
-                #else
-                    gradient = cell.xyz * 2.0 - 1.0;
-                #endif
-                vec3 normal = -normalize(normalMatrix * normalize(gradient));
-                #include apply_light_color
-            } else {
-                gl_FragColor.rgb = material.rgb;
-            }
-        #endif
+        }
 
         gl_FragColor.a = material.a * uAlpha * uTransferScale;
 

src/mol-gl/shader/mesh.frag.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -43,17 +43,13 @@ void main() {
     #elif defined(dRenderVariant_marking)
         gl_FragColor = material;
     #elif defined(dRenderVariant_color)
-        #ifdef dIgnoreLight
-            gl_FragColor = material;
+        #if defined(dFlatShaded)
+            vec3 normal = -faceNormal;
         #else
-            #if defined(dFlatShaded)
-                vec3 normal = -faceNormal;
-            #else
-                vec3 normal = -normalize(vNormal);
-                if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;
-            #endif
-            #include apply_light_color
+            vec3 normal = -normalize(vNormal);
+            if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;
         #endif
+        #include apply_light_color
 
         #include apply_interior_color
         #include apply_marker_color

src/mol-gl/shader/postprocessing.frag.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -24,8 +24,7 @@ uniform vec3 uFogColor;
 uniform vec3 uOutlineColor;
 uniform bool uTransparentBackground;
 
-uniform float uOcclusionBias;
-uniform float uOcclusionRadius;
+uniform vec2 uOcclusionOffset;
 
 uniform float uMaxPossibleViewZDiff;
 
@@ -102,7 +101,7 @@ void main(void) {
         if (!isBackground(depth)) {
             viewDist = abs(getViewZ(depth));
             fogFactor = smoothstep(uFogNear, uFogFar, viewDist);
-            float occlusionFactor = getSsao(coords);
+            float occlusionFactor = getSsao(coords + uOcclusionOffset);
             if (!uTransparentBackground) {
                 color.rgb = mix(mix(occlusionColor, uFogColor, fogFactor), color.rgb, occlusionFactor);
             } else {

src/mol-gl/shader/spheres.frag.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -92,12 +92,8 @@ void main(void){
     #elif defined(dRenderVariant_marking)
         gl_FragColor = material;
     #elif defined(dRenderVariant_color)
-        #ifdef dIgnoreLight
-            gl_FragColor = material;
-        #else
-            vec3 normal = -cameraNormal;
-            #include apply_light_color
-        #endif
+        vec3 normal = -cameraNormal;
+        #include apply_light_color
 
         #include apply_interior_color
         #include apply_marker_color

src/mol-gl/webgl/texture.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -176,7 +176,7 @@ function isTexture2d(x: TextureImage<any> | TextureVolume<any>, target: number,
     return target === gl.TEXTURE_2D;
 }
 
-function isTexture3d(x: TextureImage<any> | TextureVolume<any>, target: number, gl: WebGL2RenderingContext): x is TextureImage<any> {
+function isTexture3d(x: TextureImage<any> | TextureVolume<any>, target: number, gl: WebGL2RenderingContext): x is TextureVolume<any> {
     return target === gl.TEXTURE_3D;
 }
 
@@ -260,6 +260,10 @@ export function createTexture(gl: GLRenderingContext, extensions: WebGLExtension
     let destroyed = false;
 
     function define(_width: number, _height: number, _depth?: number) {
+        if (_width === 0 || _height === 0 || (isWebGL2(gl) && target === gl.TEXTURE_3D && _depth === 0)) {
+            throw new Error('empty textures are not allowed');
+        }
+
         if (width === _width && height === _height && depth === (_depth || 0)) return;
 
         width = _width, height = _height, depth = _depth || 0;
@@ -272,14 +276,20 @@ export function createTexture(gl: GLRenderingContext, extensions: WebGLExtension
             throw new Error('unknown texture target');
         }
     }
+    define(1, 1, isWebGL2(gl) && target === gl.TEXTURE_3D ? 1 : 0);
 
     function load(data: TextureImage<any> | TextureVolume<any> | HTMLImageElement, sub = false) {
+        if (data.width === 0 || data.height === 0 || (!isImage(data) && isWebGL2(gl) && isTexture3d(data, target, gl) && data.depth === 0)) {
+            throw new Error('empty textures are not allowed');
+        }
+
         gl.bindTexture(target, texture);
         // unpack alignment of 1 since we use textures only for data
         gl.pixelStorei(gl.UNPACK_ALIGNMENT, 1);
         gl.pixelStorei(gl.UNPACK_COLORSPACE_CONVERSION_WEBGL, gl.NONE);
         gl.pixelStorei(gl.UNPACK_PREMULTIPLY_ALPHA_WEBGL, 0);
         if (isImage(data)) {
+            width = data.width, height = data.height;
             gl.pixelStorei(gl.UNPACK_FLIP_Y_WEBGL, false);
             gl.bindTexture(gl.TEXTURE_2D, texture);
             gl.texImage2D(gl.TEXTURE_2D, 0, internalFormat, format, type, data);

src/mol-io/common/_spec/encoder.spec.ts

@@ -0,0 +1,28 @@
+import { ArrayEncoding } from '../binary-cif/array-encoder';
+import { decode } from '../binary-cif/decoder';
+
+const E = ArrayEncoding;
+
+test('fixedPoint2', async () => {
+    const fixedPoint2 = E.by(E.fixedPoint(100)).and(E.delta).and(E.integerPacking);
+
+    const x = [1.092, 1.960, 0.666, 0.480, 1.267];
+    const y = [7.428, 7.026, 6.851, 7.524, 8.333];
+    const z = [26.270, 26.561, 25.573, 27.055, 25.881];
+
+    const xEnc = fixedPoint2.encode(new Float32Array(x));
+    const yEnc = fixedPoint2.encode(new Float32Array(y));
+    const zEnc = fixedPoint2.encode(new Float32Array(z));
+
+    expect(xEnc.data.length).toEqual(6);
+    expect(yEnc.data.length).toEqual(5);
+    expect(zEnc.data.length).toEqual(6);
+
+    const xDec = decode(xEnc);
+    const yDec = decode(yEnc);
+    const zDec = decode(zEnc);
+
+    x.forEach((a, i) => expect(xDec[i]).toBeCloseTo(a, 2));
+    y.forEach((a, i) => expect(yDec[i]).toBeCloseTo(a, 2));
+    z.forEach((a, i) => expect(zDec[i]).toBeCloseTo(a, 2));
+});

src/mol-io/reader/cif/schema/bird.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
  *
  * @author molstar/ciftools package
  */

src/mol-io/reader/cif/schema/ccd.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
  *
  * @author molstar/ciftools package
  */

src/mol-io/reader/cif/schema/mmcif.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
  *
  * @author molstar/ciftools package
  */
@@ -215,6 +215,28 @@ export const mmCIF_Schema = {
          * formal charge assignment normally found in chemical diagrams.
          */
         pdbx_formal_charge: int,
+        /**
+         * This data item is an ordinal which identifies distinct chemical components in the atom_site category, both
+         * polymeric and non-polymeric.
+         */
+        pdbx_label_index: int,
+        /**
+         * The name of additional external databases with residue level mapping.
+         */
+        pdbx_sifts_xref_db_name: str,
+        /**
+         * The accession code related to the additional external database entry.
+         */
+        pdbx_sifts_xref_db_acc: str,
+        /**
+         * The sequence position of the external database entry that corresponds
+         * to the residue mapping defined by the SIFTS process.
+         */
+        pdbx_sifts_xref_db_num: str,
+        /**
+         * Describes the residue type of the given UniProt match
+         */
+        pdbx_sifts_xref_db_res: str,
         /**
          * The model id corresponding to the atom site.
          * This data item is a pointer to _ihm_model_list.model_id
@@ -682,7 +704,7 @@ export const mmCIF_Schema = {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Aliased<'AFDB' | 'CAS' | 'CSD' | 'EMDB' | 'ICSD' | 'MA' | 'MDF' | 'MODBASE' | 'NDB' | 'NBS' | 'PDB' | 'PDF' | 'RCSB' | 'SMR' | 'EBI' | 'PDBE' | 'BMRB' | 'WWPDB' | 'PDB_ACC'>(str),
+        database_id: Aliased<'AlphaFoldDB' | 'CAS' | 'CSD' | 'EMDB' | 'ICSD' | 'ModelArchive' | 'MDF' | 'MODBASE' | 'NDB' | 'NBS' | 'PDB' | 'PDF' | 'RCSB' | 'SWISS-MODEL_REPOSITORY' | 'EBI' | 'PDBE' | 'BMRB' | 'WWPDB' | 'PDB_ACC'>(str),
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.
@@ -2211,6 +2233,10 @@ export const mmCIF_Schema = {
         oligomeric_count: int,
         /**
          * A description of special aspects of the macromolecular assembly.
+         *
+         * In the PDB, 'representative helical assembly', 'complete point assembly',
+         * 'complete icosahedral assembly', 'software_defined_assembly', 'author_defined_assembly',
+         * and 'author_and_software_defined_assembly' are considered "biologically relevant assemblies.
          */
         details: str,
         /**

src/mol-model-formats/structure/common/component.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -30,7 +30,7 @@ const DnaAtomIdsList = [
 
 /** Used to reduce false positives for atom name-based type guessing */
 const NonPolymerNames = new Set([
-    'FMN', 'NCN', 'FNS', 'FMA' // Mononucleotides
+    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP' // Mononucleotides
 ]);
 
 const StandardComponents = (function () {
@@ -156,7 +156,7 @@ export class ComponentBuilder {
                 this.set(StandardComponents.get(compId)!);
             } else if (WaterNames.has(compId)) {
                 this.set({ id: compId, name: 'WATER', type: 'non-polymer' });
-            } else if (NonPolymerNames.has(compId)) {
+            } else if (NonPolymerNames.has(compId.toUpperCase())) {
                 this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
             } else {
                 const atomIds = this.getAtomIds(index);

src/mol-model-formats/structure/common/property.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { Model } from '../../../mol-model/structure';
@@ -44,7 +45,7 @@ interface FormatPropertyProvider<T> {
 }
 
 namespace FormatPropertyProvider {
-    export function create<T>(descriptor: CustomPropertyDescriptor): FormatPropertyProvider<T> {
+    export function create<T>(descriptor: CustomPropertyDescriptor, options?: { asDynamic?: boolean }): FormatPropertyProvider<T> {
         const { name } = descriptor;
         const formatRegistry = new FormatRegistry<T>();
 
@@ -55,21 +56,31 @@ namespace FormatPropertyProvider {
                 return formatRegistry.isApplicable(model);
             },
             get(model: Model): T | undefined {
-                if (model._staticPropertyData[name]) return model._staticPropertyData[name];
+                const store = options?.asDynamic ? model._dynamicPropertyData : model._staticPropertyData;
+
+                if (store[name]) return store[name];
                 if (model.customProperties.has(descriptor)) return;
 
                 const obtain = formatRegistry.get(model.sourceData.kind);
                 if (!obtain) return;
 
-                model._staticPropertyData[name] = obtain(model);
+                store[name] = obtain(model);
                 model.customProperties.add(descriptor);
-                return model._staticPropertyData[name];
+                return store[name];
             },
             set(model: Model, value: T) {
-                model._staticPropertyData[name] = value;
+                if (options?.asDynamic) {
+                    model._dynamicPropertyData[name] = value;
+                } else {
+                    model._staticPropertyData[name] = value;
+                }
             },
             delete(model: Model) {
-                delete model._staticPropertyData[name];
+                if (options?.asDynamic) {
+                    delete model._dynamicPropertyData[name];
+                } else {
+                    delete model._staticPropertyData[name];
+                }
             }
         };
     }

src/mol-model-formats/structure/mol2.ts

@@ -103,11 +103,11 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
             const flag = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => {
                 switch (x) {
                     case 'ar': // aromatic
+                    case 'am': // amide
                         return BondType.Flag.Aromatic | BondType.Flag.Covalent;
                     case 'du': // dummy
                     case 'nc': // not connected
                         return BondType.Flag.None;
-                    case 'am': // amide
                     case 'un': // unknown
                     default:
                         return BondType.Flag.Covalent;

src/mol-model-formats/structure/property/bonds/chem_comp.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -56,10 +56,10 @@ export namespace ComponentBond {
         const entries: Map<string, Entry> = new Map();
 
         function addEntry(id: string) {
-            // weird behavior when 'PRO' is requested - will report a single bond between N and H because a later operation would override real content
-            if (entries.has(id)) {
-                return entries.get(id)!;
-            }
+            // weird behavior when 'PRO' is requested - will report a single bond
+            // between N and H because a later operation would override real content
+            if (entries.has(id)) return entries.get(id)!;
+
             const e = new Entry(id);
             entries.set(id, e);
             return e;
@@ -83,10 +83,8 @@ export namespace ComponentBond {
             let ord = 1;
             if (aromatic) flags |= BondType.Flag.Aromatic;
             switch (order.toLowerCase()) {
-                case 'doub':
-                case 'delo':
-                    ord = 2;
-                    break;
+                case 'delo': flags |= BondType.Flag.Aromatic; break;
+                case 'doub': ord = 2; break;
                 case 'trip': ord = 3; break;
                 case 'quad': ord = 4; break;
             }

src/mol-model-formats/structure/property/bonds/index-pair.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2019-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
@@ -42,7 +43,7 @@ export namespace IndexPairBonds {
         name: 'index_pair_bonds',
     };
 
-    export const Provider = FormatPropertyProvider.create<IndexPairBonds>(Descriptor);
+    export const Provider = FormatPropertyProvider.create<IndexPairBonds>(Descriptor, { asDynamic: true });
 
     export type Data = {
         pairs: {

src/mol-model-props/sequence/sifts-mapping.ts

@@ -11,30 +11,43 @@ import { Model } from '../../mol-model/structure';
 import { StructureElement } from '../../mol-model/structure/structure';
 import { CustomModelProperty } from '../common/custom-model-property';
 
-export { BestDatabaseSequenceMapping };
+export { SIFTSMapping as SIFTSMapping };
 
-interface BestDatabaseSequenceMapping {
+interface SIFTSMappingMapping {
     readonly dbName: string[],
     readonly accession: string[],
-    readonly num: number[],
+    readonly num: string[],
     readonly residue: string[]
 }
 
-namespace BestDatabaseSequenceMapping {
-    export const Provider: CustomModelProperty.Provider<{}, BestDatabaseSequenceMapping> = CustomModelProperty.createProvider({
-        label: 'Best Database Sequence Mapping',
+namespace SIFTSMapping {
+    export const Provider: CustomModelProperty.Provider<{}, SIFTSMappingMapping> = CustomModelProperty.createProvider({
+        label: 'SIFTS Mapping',
         descriptor: CustomPropertyDescriptor({
-            name: 'molstar_best_database_sequence_mapping'
+            name: 'sifts_sequence_mapping'
         }),
         type: 'static',
         defaultParams: {},
         getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('pdbx_sifts_xref_db_name') >= 0,
+        isApplicable: (data: Model) => isAvailable(data),
         obtain: async (ctx, data) => {
             return { value: fromCif(data) };
         }
     });
 
+    export function isAvailable(model: Model) {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+
+        const {
+            pdbx_sifts_xref_db_name: db_name,
+            pdbx_sifts_xref_db_acc: db_acc,
+            pdbx_sifts_xref_db_num: db_num,
+            pdbx_sifts_xref_db_res: db_res
+        } = model.sourceData.data.db.atom_site;
+
+        return db_name.isDefined && db_acc.isDefined && db_num.isDefined && db_res.isDefined;
+    }
+
     export function getKey(loc: StructureElement.Location) {
         const model = loc.unit.model;
         const data = Provider.get(model).value;
@@ -55,22 +68,23 @@ namespace BestDatabaseSequenceMapping {
         return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${data.residue[rI]}`;
     }
 
-    function fromCif(model: Model): BestDatabaseSequenceMapping | undefined {
+    function fromCif(model: Model): SIFTSMappingMapping | undefined {
         if (!MmcifFormat.is(model.sourceData)) return;
 
-        const { atom_site } = model.sourceData.data.frame.categories;
-        const db_name = atom_site.getField('pdbx_sifts_xref_db_name');
-        const db_acc = atom_site.getField('pdbx_sifts_xref_db_acc');
-        const db_num = atom_site.getField('pdbx_sifts_xref_db_num');
-        const db_res = atom_site.getField('pdbx_sifts_xref_db_res');
+        const {
+            pdbx_sifts_xref_db_name: db_name,
+            pdbx_sifts_xref_db_acc: db_acc,
+            pdbx_sifts_xref_db_num: db_num,
+            pdbx_sifts_xref_db_res: db_res
+        } = model.sourceData.data.db.atom_site;
 
-        if (!db_name || !db_acc || !db_num || !db_res) return;
+        if (!db_name.isDefined || !db_acc.isDefined || !db_num.isDefined || !db_res.isDefined) return;
 
         const { atomSourceIndex } = model.atomicHierarchy;
         const { count, offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
         const dbName = new Array<string>(count);
         const accession = new Array<string>(count);
-        const num = new Array<number>(count);
+        const num = new Array<string>(count);
         const residue = new Array<string>(count);
 
         for (let i = 0; i < count; i++) {
@@ -79,15 +93,15 @@ namespace BestDatabaseSequenceMapping {
             if (db_name.valueKind(row) !== Column.ValueKind.Present) {
                 dbName[i] = '';
                 accession[i] = '';
-                num[i] = 0;
+                num[i] = '';
                 residue[i] = '';
                 continue;
             }
 
-            dbName[i] = db_name.str(row);
-            accession[i] = db_acc.str(row);
-            num[i] = db_num.int(row);
-            residue[i] = db_res.str(row);
+            dbName[i] = db_name.value(row);
+            accession[i] = db_acc.value(row);
+            num[i] = db_num.value(row);
+            residue[i] = db_res.value(row);
         }
 
         return { dbName, accession, num, residue };

src/mol-model-props/sequence/themes/sifts-mapping.ts

@@ -12,27 +12,27 @@ import { Color } from '../../../mol-util/color';
 import { getPalette, getPaletteParams } from '../../../mol-util/color/palette';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { CustomProperty } from '../../common/custom-property';
-import { BestDatabaseSequenceMapping } from '../best-database-mapping';
+import { SIFTSMapping } from '../sifts-mapping';
 
 const DefaultColor = Color(0xFAFAFA);
-const Description = 'Assigns a color based on best dababase sequence mapping.';
+const Description = 'Assigns a color based on SIFTS mapping.';
 
 // same colors for same accessions
 const globalAccessionMap = new Map<string, number>();
 
-export const BestDatabaseSequenceMappingColorThemeParams = {
+export const SIFTSMappingColorThemeParams = {
     ...getPaletteParams({ type: 'colors', colorList: 'set-1' }),
 };
-export type BestDatabaseSequenceMappingColorThemeParams = typeof BestDatabaseSequenceMappingColorThemeParams
-export function getBestDatabaseSequenceMappingColorThemeParams(ctx: ThemeDataContext) {
-    return BestDatabaseSequenceMappingColorThemeParams; // TODO return copy
+export type SIFTSMappingColorThemeParams = typeof SIFTSMappingColorThemeParams
+export function getSIFTSMappingColorThemeParams(ctx: ThemeDataContext) {
+    return SIFTSMappingColorThemeParams; // TODO return copy
 }
-export function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, props: PD.Values<BestDatabaseSequenceMappingColorThemeParams>): ColorTheme<BestDatabaseSequenceMappingColorThemeParams> {
+export function SIFTSMappingColorTheme(ctx: ThemeDataContext, props: PD.Values<SIFTSMappingColorThemeParams>): ColorTheme<SIFTSMappingColorThemeParams> {
     let color: LocationColor;
 
     if (ctx.structure) {
         for (const m of ctx.structure.models) {
-            const mapping = BestDatabaseSequenceMapping.Provider.get(m).value;
+            const mapping = SIFTSMapping.Provider.get(m).value;
             if (!mapping) continue;
             for (const acc of mapping.accession) {
                 if (!acc || globalAccessionMap.has(acc)) continue;
@@ -45,7 +45,7 @@ export function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, pro
         const colorMap = new Map<string, Color>();
 
         const getColor = (location: StructureElement.Location) => {
-            const key = BestDatabaseSequenceMapping.getKey(location);
+            const key = SIFTSMapping.getKey(location);
             if (!key) return DefaultColor;
 
             if (colorMap.has(key)) return colorMap.get(key)!;
@@ -70,7 +70,7 @@ export function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, pro
     }
 
     return {
-        factory: BestDatabaseSequenceMappingColorTheme,
+        factory: SIFTSMappingColorTheme,
         granularity: 'group',
         preferSmoothing: true,
         color,
@@ -79,26 +79,26 @@ export function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, pro
     };
 }
 
-export const BestDatabaseSequenceMappingColorThemeProvider: ColorTheme.Provider<BestDatabaseSequenceMappingColorThemeParams, 'best-sequence-database-mapping'> = {
-    name: 'best-sequence-database-mapping',
-    label: 'Best Database Sequence Mapping',
+export const SIFTSMappingColorThemeProvider: ColorTheme.Provider<SIFTSMappingColorThemeParams, 'sifts-mapping'> = {
+    name: 'sifts-mapping',
+    label: 'SIFTS Mapping',
     category: ColorTheme.Category.Residue,
-    factory: BestDatabaseSequenceMappingColorTheme,
-    getParams: getBestDatabaseSequenceMappingColorThemeParams,
-    defaultValues: PD.getDefaultValues(BestDatabaseSequenceMappingColorThemeParams),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => BestDatabaseSequenceMapping.Provider.isApplicable(m)),
+    factory: SIFTSMappingColorTheme,
+    getParams: getSIFTSMappingColorThemeParams,
+    defaultValues: PD.getDefaultValues(SIFTSMappingColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => SIFTSMapping.Provider.isApplicable(m)),
     ensureCustomProperties: {
         attach: async (ctx: CustomProperty.Context, data: ThemeDataContext) => {
             if (!data.structure) return;
 
             for (const m of data.structure.models) {
-                await BestDatabaseSequenceMapping.Provider.attach(ctx, m, void 0, true);
+                await SIFTSMapping.Provider.attach(ctx, m, void 0, true);
             }
         },
         detach: (data) => {
             if (!data.structure) return;
             for (const m of data.structure.models) {
-                BestDatabaseSequenceMapping.Provider.ref(m, false);
+                SIFTSMapping.Provider.ref(m, false);
             }
         }
     }

src/mol-model/structure/export/categories/atom_site.ts

@@ -5,7 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
+import { Column } from '../../../../mol-data/db';
+import { mmCIF_Database } from '../../../../mol-io/reader/cif/schema/mmcif';
 import { CifWriter } from '../../../../mol-io/writer/cif';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
 import { StructureElement, Structure, StructureProperties as P } from '../../structure';
 import { CifExportContext } from '../mmcif';
 import CifField = CifWriter.Field
@@ -26,7 +30,64 @@ function atom_site_auth_asym_id(e: StructureElement.Location) {
     return l + suffix;
 }
 
-const atom_site_fields = () => CifWriter.fields<StructureElement.Location, Structure>()
+
+const atom_site_pdbx_label_index = {
+    shouldInclude(s: AtomSiteData) {
+        return !!s.atom_site?.pdbx_label_index.isDefined;
+    },
+    value(e: StructureElement.Location, d: AtomSiteData) {
+        const srcIndex = d.sourceIndex.value(e.element);
+        return d.atom_site!.pdbx_label_index.value(srcIndex);
+    },
+};
+
+const SIFTS = {
+    shouldInclude(s: AtomSiteData) {
+        return SIFTSMapping.isAvailable(s.structure.models[0]);
+    },
+    pdbx_sifts_xref_db_name: {
+        value(e: StructureElement.Location, d: AtomSiteData) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_name.value(srcIndex);
+        },
+        valueKind(e: StructureElement.Location, d: any) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_name.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_acc: {
+        value(e: StructureElement.Location, d: AtomSiteData) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_acc.value(srcIndex);
+        },
+        valueKind(e: StructureElement.Location, d: any) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_acc.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_num: {
+        value(e: StructureElement.Location, d: AtomSiteData) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_num.value(srcIndex);
+        },
+        valueKind(e: StructureElement.Location, d: any) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_num.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_res: {
+        value(e: StructureElement.Location, d: AtomSiteData) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_res.value(srcIndex);
+        },
+        valueKind(e: StructureElement.Location, d: any) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_res.valueKind(srcIndex);
+        },
+    }
+};
+
+const atom_site_fields = () => CifWriter.fields<StructureElement.Location, AtomSiteData>()
     .str('group_PDB', P.residue.group_PDB)
     .index('id')
     .str('type_symbol', P.atom.type_symbol as any)
@@ -62,18 +123,37 @@ const atom_site_fields = () => CifWriter.fields<StructureElement.Location, Struc
     .str('auth_asym_id', atom_site_auth_asym_id)
 
     .int('pdbx_PDB_model_num', P.unit.model_num, { encoder: E.deltaRLE })
+
+    .int('pdbx_label_index', atom_site_pdbx_label_index.value, { shouldInclude: atom_site_pdbx_label_index.shouldInclude })
+
+    // SIFTS
+    .str('pdbx_sifts_xref_db_name', SIFTS.pdbx_sifts_xref_db_name.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_name.valueKind })
+    .str('pdbx_sifts_xref_db_acc', SIFTS.pdbx_sifts_xref_db_acc.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_acc.valueKind })
+    .str('pdbx_sifts_xref_db_num', SIFTS.pdbx_sifts_xref_db_num.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_num.valueKind })
+    .str('pdbx_sifts_xref_db_res', SIFTS.pdbx_sifts_xref_db_res.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_res.valueKind })
+
     // .str('operator_name', P.unit.operator_name, {
     //     shouldInclude: structure => structure.units.some(u => !u.conformation.operator.isIdentity)
     // })
     .getFields();
 
+interface AtomSiteData {
+    structure: Structure,
+    sourceIndex: Column<number>,
+    atom_site?: mmCIF_Database['atom_site']
+}
+
 export const _atom_site: CifCategory<CifExportContext> = {
     name: 'atom_site',
     instance({ structures }: CifExportContext) {
         return {
             fields: atom_site_fields(),
             source: structures.map(s => ({
-                data: s,
+                data: {
+                    structure: s,
+                    sourceIndex: s.model.atomicHierarchy.atomSourceIndex,
+                    atom_site: MmcifFormat.is(s.model.sourceData) ? s.model.sourceData.data.db.atom_site : void 0
+                } as AtomSiteData,
                 rowCount: s.elementCount,
                 keys: () => s.elementLocations()
             }))

src/mol-model/structure/export/categories/secondary-structure.ts

@@ -78,12 +78,12 @@ function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContex
     const ssElements: SSElement<any>[] = [];
 
     const structure = ctx.structures[0];
-    for (const unit of structure.units) {
-        // currently can only support this for "identity" operators.
-        if (!Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity) continue;
+    for (const { units } of structure.unitSymmetryGroups) {
+        const u = units[0];
+        if (!Unit.isAtomic(u)) continue;
 
-        const segs = unit.model.atomicHierarchy.residueAtomSegments;
-        const residues = Segmentation.transientSegments(segs, unit.elements);
+        const segs = u.model.atomicHierarchy.residueAtomSegments;
+        const residues = Segmentation.transientSegments(segs, u.elements);
 
         let current: Segmentation.Segment, move = true;
         while (residues.hasNext) {
@@ -104,8 +104,8 @@ function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContex
                 if (startIdx !== key[current.index]) {
                     move = false;
                     ssElements[ssElements.length] = {
-                        start: StructureElement.Location.create(structure, unit, segs.offsets[start]),
-                        end: StructureElement.Location.create(structure, unit, segs.offsets[prev]),
+                        start: StructureElement.Location.create(structure, u, segs.offsets[start]),
+                        end: StructureElement.Location.create(structure, u, segs.offsets[prev]),
                         length: prev - start + 1,
                         element
                     };

src/mol-model/structure/model/model.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -98,6 +98,7 @@ export namespace Model {
         const srcIndex = model.atomicHierarchy.atomSourceIndex;
         const isIdentity = Column.isIdentity(srcIndex);
         const srcIndexArray = isIdentity ? void 0 : srcIndex.toArray({ array: Int32Array });
+        const coarseGrained = isCoarseGrained(model);
 
         for (let i = 0, il = frames.length; i < il; ++i) {
             const f = frames[i];
@@ -119,6 +120,7 @@ export namespace Model {
             }
 
             TrajectoryInfo.set(m, { index: i, size: frames.length });
+            CoarseGrained.set(m, coarseGrained);
 
             trajectory.push(m);
         }
@@ -138,11 +140,13 @@ export namespace Model {
 
             const bondData = { pairs: topology.bonds, count: model.atomicHierarchy.atoms._rowCount };
             const indexPairBonds = IndexPairBonds.fromData(bondData);
+            const coarseGrained = isCoarseGrained(model);
 
             let index = 0;
             for (const m of trajectory) {
                 IndexPairBonds.Provider.set(m, indexPairBonds);
                 TrajectoryInfo.set(m, { index: index++, size: trajectory.length });
+                CoarseGrained.set(m, coarseGrained);
             }
             return new ArrayTrajectory(trajectory);
         });
@@ -225,35 +229,44 @@ export namespace Model {
     };
 
     const CoarseGrainedProp = '__CoarseGrained__';
+    export const CoarseGrained = {
+        get(model: Model): boolean | undefined {
+            return model._staticPropertyData[CoarseGrainedProp];
+        },
+        set(model: Model, coarseGrained: boolean) {
+            return model._staticPropertyData[CoarseGrainedProp] = coarseGrained;
+        }
+    };
     /**
      * Has typical coarse grained atom names (BB, SC1) or less than three times as many
      * atoms as polymer residues (C-alpha only models).
      */
     export function isCoarseGrained(model: Model): boolean {
-        if (model._staticPropertyData[CoarseGrainedProp] !== undefined) return model._staticPropertyData[CoarseGrainedProp];
+        let coarseGrained = CoarseGrained.get(model);
+        if (coarseGrained === undefined) {
+            let polymerResidueCount = 0;
+            const { polymerType } = model.atomicHierarchy.derived.residue;
+            for (let i = 0; i < polymerType.length; ++i) {
+                if (polymerType[i] !== PolymerType.NA) polymerResidueCount += 1;
+            }
 
-        let polymerResidueCount = 0;
-        const { polymerType } = model.atomicHierarchy.derived.residue;
-        for (let i = 0; i < polymerType.length; ++i) {
-            if (polymerType[i] !== PolymerType.NA) polymerResidueCount += 1;
+            // check for coarse grained atom names
+            let hasBB = false, hasSC1 = false;
+            const { label_atom_id, _rowCount: atomCount } = model.atomicHierarchy.atoms;
+            for (let i = 0; i < atomCount; ++i) {
+                const atomName = label_atom_id.value(i);
+                if (!hasBB && atomName === 'BB') hasBB = true;
+                if (!hasSC1 && atomName === 'SC1') hasSC1 = true;
+                if (hasBB && hasSC1) break;
+            }
+
+            coarseGrained = (hasBB && hasSC1) || (
+                polymerResidueCount && atomCount
+                    ? atomCount / polymerResidueCount < 3
+                    : false
+            );
+            CoarseGrained.set(model, coarseGrained);
         }
-
-        // check for coarse grained atom names
-        let hasBB = false, hasSC1 = false;
-        const { label_atom_id, _rowCount: atomCount } = model.atomicHierarchy.atoms;
-        for (let i = 0; i < atomCount; ++i) {
-            const atomName = label_atom_id.value(i);
-            if (!hasBB && atomName === 'BB') hasBB = true;
-            if (!hasSC1 && atomName === 'SC1') hasSC1 = true;
-            if (hasBB && hasSC1) break;
-        }
-
-        const coarseGrained = (hasBB && hasSC1) || (
-            polymerResidueCount && atomCount
-                ? atomCount / polymerResidueCount < 3
-                : false
-        );
-        model._staticPropertyData[CoarseGrainedProp] = coarseGrained;
         return coarseGrained;
     }
 

src/mol-model/structure/structure/structure.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -232,7 +232,14 @@ class Structure {
 
     get interUnitBonds() {
         if (this.state.interUnitBonds) return this.state.interUnitBonds;
-        this.state.interUnitBonds = computeInterUnitBonds(this, { ignoreWater: !this.dynamicBonds });
+        if (this.parent && this.state.dynamicBonds === this.parent.state.dynamicBonds &&
+            this.parent.state.interUnitBonds && this.parent.state.interUnitBonds.edgeCount === 0
+        ) {
+            // no need to compute InterUnitBonds if parent's ones are empty
+            this.state.interUnitBonds = new InterUnitBonds(new Map());
+        } else {
+            this.state.interUnitBonds = computeInterUnitBonds(this, { ignoreWater: !this.dynamicBonds });
+        }
         return this.state.interUnitBonds;
     }
 

src/mol-model/structure/structure/unit.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -25,6 +25,10 @@ import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
 import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bonds/index-pair';
 import { ElementSetIntraBondCache } from './unit/bonds/element-set-intra-bond-cache';
 import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
+import { getResonance, UnitResonance } from './unit/resonance';
+
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3add = Vec3.add;
 
 /**
  * A building block of a structure that corresponds to an atomic or
@@ -220,9 +224,32 @@ namespace Unit {
 
         remapModel(model: Model, dynamicBonds: boolean, props?: AtomicProperties) {
             if (!props) {
-                props = { ...this.props, bonds: dynamicBonds ? undefined : tryRemapBonds(this, this.props.bonds, model) };
+                props = {
+                    ...this.props,
+                    bonds: dynamicBonds && !this.props.bonds?.props?.canRemap
+                        ? undefined
+                        : tryRemapBonds(this, this.props.bonds, model, dynamicBonds)
+                };
                 if (!Unit.isSameConformation(this, model)) {
-                    props.boundary = undefined;
+                    const b = props.boundary;
+                    if (b) {
+                        const { elements } = this;
+                        const pos = this.conformation.invariantPosition;
+                        const v = Vec3();
+                        const center = Vec3();
+
+                        for (let i = 0, il = elements.length; i < il; i++) {
+                            pos(elements[i], v);
+                            v3add(center, center, v);
+                        }
+                        Vec3.scale(center, center, 1 / elements.length);
+
+                        // only invalidate boundary if sphere has changed too much
+                        if (Vec3.distance(center, b.sphere.center) / b.sphere.radius >= 1.0) {
+                            props.boundary = undefined;
+                        }
+                    }
+
                     props.lookup3d = undefined;
                     props.principalAxes = undefined;
                 }
@@ -282,6 +309,12 @@ namespace Unit {
             return this.props.rings;
         }
 
+        get resonance() {
+            if (this.props.resonance) return this.props.resonance;
+            this.props.resonance = getResonance(this);
+            return this.props.resonance;
+        }
+
         get polymerElements() {
             if (this.props.polymerElements) return this.props.polymerElements;
             this.props.polymerElements = getAtomicPolymerElements(this);
@@ -342,6 +375,7 @@ namespace Unit {
     interface AtomicProperties extends BaseProperties {
         bonds?: IntraUnitBonds
         rings?: UnitRings
+        resonance?: UnitResonance
         nucleotideElements?: SortedArray<ElementIndex>
         proteinElements?: SortedArray<ElementIndex>
         residueCount?: number
@@ -481,7 +515,7 @@ namespace Unit {
         return isSameConformation(a, b.model);
     }
 
-    function tryRemapBonds(a: Atomic, old: IntraUnitBonds | undefined, model: Model) {
+    function tryRemapBonds(a: Atomic, old: IntraUnitBonds | undefined, model: Model, dynamicBonds: boolean) {
         // TODO: should include additional checks?
 
         if (!old) return void 0;
@@ -495,7 +529,7 @@ namespace Unit {
             return void 0;
         }
 
-        if (old.props?.canRemap) {
+        if (old.props?.canRemap || !dynamicBonds) {
             return old;
         }
         return isSameConformation(a, model) ? old : void 0;

src/mol-model/structure/structure/unit/bonds/data.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -12,7 +12,13 @@ import { StructureElement } from '../../element';
 import { Bond } from '../bonds';
 import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';
 
-type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, { readonly order: ArrayLike<number>, readonly flags: ArrayLike<BondType.Flag> }, { readonly canRemap?: boolean }>
+type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, {
+    readonly order: ArrayLike<number>,
+    readonly flags: ArrayLike<BondType.Flag>
+}, {
+    /** can remap even with dynamicBonds on, e.g., for water molecules */
+    readonly canRemap?: boolean
+}>
 
 namespace IntraUnitBonds {
     export const Empty: IntraUnitBonds = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [] });

src/mol-model/structure/structure/unit/bonds/intra-compute.ts

@@ -141,7 +141,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
         const aI = atoms[_aI];
 
         const elemA = type_symbol.value(aI);
-        if (isWatery && (elemA !== 'H' || elemA !== 'O')) isWatery = false;
+        if (isWatery && (elemA !== 'H' && elemA !== 'O')) isWatery = false;
 
         const structConnEntries = props.forceCompute ? void 0 : structConn && structConn.byAtomIndex.get(aI);
         let hasStructConn = false;

src/mol-model/structure/structure/unit/resonance.ts

@@ -0,0 +1,83 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { SortedArray } from '../../../../mol-data/int/sorted-array';
+import { sortedCantorPairing } from '../../../../mol-data/util';
+import { BondType } from '../../model/types';
+import { StructureElement } from '../element';
+import { Unit } from '../unit';
+
+export type UnitResonance = {
+    /**
+     * Lookup for triplets of atoms in delocalized bonds.
+     *
+     * Does not include triplets that are part of aromatic rings.
+     */
+    readonly delocalizedTriplets: {
+        /** Return 3rd element in triplet or undefined if `a` and `b` are not part of a triplet */
+        readonly getThirdElement: (a: StructureElement.UnitIndex, b: StructureElement.UnitIndex) => StructureElement.UnitIndex | undefined
+        /** Return index into `triplets` or undefined if `a` is not part of any triplet */
+        readonly getTripletIndices: (a: StructureElement.UnitIndex) => number[] | undefined
+        readonly triplets: SortedArray<StructureElement.UnitIndex>[]
+    }
+}
+
+export function getResonance(unit: Unit.Atomic): UnitResonance {
+    return {
+        delocalizedTriplets: getDelocalizedTriplets(unit)
+    };
+}
+
+function getDelocalizedTriplets(unit: Unit.Atomic) {
+    const bonds = unit.bonds;
+    const { b, edgeProps, offset } = bonds;
+    const { order: _order, flags: _flags } = edgeProps;
+    const { elementAromaticRingIndices } = unit.rings;
+
+    const triplets: SortedArray<StructureElement.UnitIndex>[] = [];
+    const thirdElementMap = new Map<number, StructureElement.UnitIndex>();
+    const indicesMap = new Map<number, number[]>();
+
+    const add = (a: StructureElement.UnitIndex, b: StructureElement.UnitIndex, c: StructureElement.UnitIndex) => {
+        const index = triplets.length;
+        triplets.push(SortedArray.ofUnsortedArray([a, b, c]));
+        thirdElementMap.set(sortedCantorPairing(a, b), c);
+        if (indicesMap.has(a)) indicesMap.get(a)!.push(index);
+        else indicesMap.set(a, [index]);
+    };
+
+    for (let i = 0 as StructureElement.UnitIndex; i < unit.elements.length; i++) {
+        if (elementAromaticRingIndices.has(i)) continue;
+
+        const count = offset[i + 1] - offset[i] + 1;
+        if (count < 2) continue;
+
+        const deloBonds: StructureElement.UnitIndex[] = [];
+        for (let t = offset[i], _t = offset[i + 1]; t < _t; t++) {
+            const f = _flags[t];
+            if (!BondType.is(f, BondType.Flag.Aromatic)) continue;
+
+            deloBonds.push(b[t]);
+        }
+
+        if (deloBonds.length >= 2) {
+            add(i, deloBonds[0], deloBonds[1]);
+            for (let j = 1, jl = deloBonds.length; j < jl; j++) {
+                add(i, deloBonds[j], deloBonds[0]);
+            }
+        }
+    }
+
+    return {
+        getThirdElement: (a: StructureElement.UnitIndex, b: StructureElement.UnitIndex) => {
+            return thirdElementMap.get(sortedCantorPairing(a, b));
+        },
+        getTripletIndices: (a: StructureElement.UnitIndex) => {
+            return indicesMap.get(a);
+        },
+        triplets,
+    };
+}

src/mol-model/structure/structure/unit/rings/compute.ts

@@ -28,17 +28,19 @@ export function computeRings(unit: Unit.Atomic) {
 }
 
 const enum Constants {
-    MaxDepth = 4
+    MaxDepth = 5
 }
 
 interface State {
     startVertex: number,
     endVertex: number,
     count: number,
-    visited: Int32Array,
+    isRingAtom: Int32Array,
+    marked: Int32Array,
     queue: Int32Array,
     color: Int32Array,
     pred: Int32Array,
+    depth: Int32Array,
 
     left: Int32Array,
     right: Int32Array,
@@ -59,9 +61,11 @@ function State(unit: Unit.Atomic, capacity: number): State {
         startVertex: 0,
         endVertex: 0,
         count: 0,
-        visited: new Int32Array(capacity),
+        isRingAtom: new Int32Array(capacity),
+        marked: new Int32Array(capacity),
         queue: new Int32Array(capacity),
         pred: new Int32Array(capacity),
+        depth: new Int32Array(capacity),
         left: new Int32Array(Constants.MaxDepth),
         right: new Int32Array(Constants.MaxDepth),
         color: new Int32Array(capacity),
@@ -78,17 +82,26 @@ function State(unit: Unit.Atomic, capacity: number): State {
 
 function resetState(state: State) {
     state.count = state.endVertex - state.startVertex;
-    const { visited, pred, color } = state;
+    const { isRingAtom, pred, color, depth, marked } = state;
     for (let i = 0; i < state.count; i++) {
-        visited[i] = -1;
+        isRingAtom[i] = 0;
         pred[i] = -1;
+        marked[i] = -1;
         color[i] = 0;
+        depth[i] = 0;
     }
     state.currentColor = 0;
     state.currentAltLoc = '';
     state.hasAltLoc = false;
 }
 
+function resetDepth(state: State) {
+    const { depth } = state;
+    for (let i = 0; i < state.count; i++) {
+        depth[i] = state.count + 1;
+    }
+}
+
 function largestResidue(unit: Unit.Atomic) {
     const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
     let size = 0;
@@ -99,8 +112,16 @@ function largestResidue(unit: Unit.Atomic) {
     return size;
 }
 
+function isStartIndex(state: State, i: number) {
+    const bondOffset = state.bonds.offset;
+    const a = state.startVertex + i;
+    const bStart = bondOffset[a], bEnd = bondOffset[a + 1];
+    const bondCount = bEnd - bStart;
+    if (bondCount <= 1 || (state.isRingAtom[i] && bondCount === 2)) return false;
+    return true;
+}
+
 function processResidue(state: State, start: number, end: number) {
-    const { visited } = state;
     state.startVertex = start;
     state.endVertex = end;
 
@@ -117,11 +138,13 @@ function processResidue(state: State, start: number, end: number) {
     }
     arraySetRemove(altLocs, '');
 
+    let mark = 1;
     if (altLocs.length === 0) {
         resetState(state);
         for (let i = 0; i < state.count; i++) {
-            if (visited[i] >= 0) continue;
-            findRings(state, i);
+            if (!isStartIndex(state, i)) continue;
+            resetDepth(state);
+            mark = findRings(state, i, mark);
         }
     } else {
         for (let aI = 0; aI < altLocs.length; aI++) {
@@ -129,12 +152,13 @@ function processResidue(state: State, start: number, end: number) {
             state.hasAltLoc = true;
             state.currentAltLoc = altLocs[aI];
             for (let i = 0; i < state.count; i++) {
-                if (visited[i] >= 0) continue;
+                if (!isStartIndex(state, i)) continue;
                 const altLoc = state.altLoc.value(elements[state.startVertex + i]);
                 if (altLoc && altLoc !== state.currentAltLoc) {
                     continue;
                 }
-                findRings(state, i);
+                resetDepth(state);
+                mark = findRings(state, i, mark);
             }
         }
     }
@@ -144,10 +168,10 @@ function processResidue(state: State, start: number, end: number) {
     }
 }
 
-function addRing(state: State, a: number, b: number) {
+function addRing(state: State, a: number, b: number, isRingAtom: Int32Array) {
     // only "monotonous" rings
     if (b < a) {
-        return;
+        return false;
     }
 
     const { pred, color, left, right } = state;
@@ -176,7 +200,7 @@ function addRing(state: State, a: number, b: number) {
         if (current < 0) break;
     }
     if (!found) {
-        return;
+        return false;
     }
 
     current = a;
@@ -190,50 +214,50 @@ function addRing(state: State, a: number, b: number) {
     const len = leftOffset + rightOffset;
     // rings must have at least three elements
     if (len < 3) {
-        return;
+        return false;
     }
 
     const ring = new Int32Array(len);
     let ringOffset = 0;
-    for (let t = 0; t < leftOffset; t++) ring[ringOffset++] = state.startVertex + left[t];
-    for (let t = rightOffset - 1; t >= 0; t--) ring[ringOffset++] = state.startVertex + right[t];
+    for (let t = 0; t < leftOffset; t++) {
+        ring[ringOffset++] = state.startVertex + left[t];
+        isRingAtom[left[t]] = 1;
+    }
+    for (let t = rightOffset - 1; t >= 0; t--) {
+        ring[ringOffset++] = state.startVertex + right[t];
+        isRingAtom[right[t]] = 1;
+    }
 
     sortArray(ring);
 
-    if (state.hasAltLoc) {
-        // we need to check if the ring was already added because alt locs are present.
+    // Check if the ring is unique and another one is not it's subset
+    for (let rI = 0, _rI = state.currentRings.length; rI < _rI; rI++) {
+        const r = state.currentRings[rI];
 
-        for (let rI = 0, _rI = state.currentRings.length; rI < _rI; rI++) {
-            const r = state.currentRings[rI];
-            if (ring[0] !== r[0]) continue;
-            if (ring.length !== r.length) continue;
-
-            let areSame = true;
-            for (let aI = 0, _aI = ring.length; aI < _aI; aI++) {
-                if (ring[aI] !== r[aI]) {
-                    areSame = false;
-                    break;
-                }
-            }
-            if (areSame) {
-                return;
-            }
+        if (ring.length === r.length) {
+            if (SortedArray.areEqual(ring as any, r)) return false;
+        } else if (ring.length > r.length) {
+            if (SortedArray.isSubset(ring as any, r)) return false;
         }
     }
 
     state.currentRings.push(SortedArray.ofSortedArray(ring));
+
+    return true;
 }
 
-function findRings(state: State, from: number) {
-    const { bonds, startVertex, endVertex, visited, queue, pred } = state;
+function findRings(state: State, from: number, mark: number) {
+    const { bonds, startVertex, endVertex, isRingAtom, marked, queue, pred, depth } = state;
     const { elements } = state.unit;
     const { b: neighbor, edgeProps: { flags: bondFlags }, offset } = bonds;
-    visited[from] = 1;
+    marked[from] = mark;
+    depth[from] = 0;
     queue[0] = from;
     let head = 0, size = 1;
 
     while (head < size) {
         const top = queue[head++];
+        const d = depth[top];
         const a = startVertex + top;
         const start = offset[a], end = offset[a + 1];
 
@@ -250,18 +274,25 @@ function findRings(state: State, from: number) {
 
             const other = b - startVertex;
 
-            if (visited[other] > 0) {
+            if (marked[other] === mark) {
                 if (pred[other] !== top && pred[top] !== other) {
-                    addRing(state, top, other);
+                    if (addRing(state, top, other, isRingAtom)) {
+                        return mark + 1;
+                    }
                 }
                 continue;
             }
 
-            visited[other] = 1;
+            const newDepth = Math.min(depth[other], d + 1);
+            if (newDepth > Constants.MaxDepth) continue;
+
+            depth[other] = newDepth;
+            marked[other] = mark;
             queue[size++] = other;
             pred[other] = top;
         }
     }
+    return mark + 1;
 }
 
 export function getFingerprint(elements: string[]) {

src/mol-model/structure/structure/util/superposition-sifts-mapping.ts

@@ -1,28 +1,34 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 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 { Segmentation } from '../../../../mol-data/int';
-import { Mat4 } from '../../../../mol-math/linear-algebra';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
-import { BestDatabaseSequenceMapping } from '../../../../mol-model-props/sequence/best-database-mapping';
+import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
 import { ElementIndex } from '../../model/indexing';
 import { Structure } from '../structure';
 import { Unit } from '../unit';
 
-export interface AlignmentResult {
+export interface AlignmentResultEntry {
     transform: MinimizeRmsd.Result,
     pivot: number,
     other: number
 }
 
-export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]): AlignmentResult[] {
+export interface AlignmentResult {
+    entries: AlignmentResultEntry[],
+    zeroOverlapPairs: [number, number][],
+    failedPairs: [number, number][]
+}
+
+export function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: { traceOnly?: boolean }): AlignmentResult {
     const indexMap = new Map<string, IndexEntry>();
 
     for (let i = 0; i < structures.length; i++) {
-        buildIndex(structures[i], indexMap, i);
+        buildIndex(structures[i], indexMap, i, options?.traceOnly ?? true);
     }
 
     const index = Array.from(indexMap.values());
@@ -30,15 +36,26 @@ export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]
     // TODO: support non-first structure pivots
     const pairs = findPairs(structures.length, index);
 
-    const ret: AlignmentResult[] = [];
+    const zeroOverlapPairs: AlignmentResult['zeroOverlapPairs'] = [];
+    const failedPairs: AlignmentResult['failedPairs'] = [];
+
+
+    const entries: AlignmentResultEntry[] = [];
     for (const p of pairs) {
-        const [a, b] = getPositionTables(index, p.i, p.j, p.count);
-        const transform = MinimizeRmsd.compute({ a, b });
-        console.log(Mat4.makeTable(transform.bTransform), transform.rmsd);
-        ret.push({ transform, pivot: p.i, other: p.j });
+        if (p.count === 0) {
+            zeroOverlapPairs.push([p.i, p.j]);
+        } else {
+            const [a, b] = getPositionTables(index, p.i, p.j, p.count);
+            const transform = MinimizeRmsd.compute({ a, b });
+            if (Number.isNaN(transform.rmsd)) {
+                failedPairs.push([p.i, p.j]);
+            } else {
+                entries.push({ transform, pivot: p.i, other: p.j });
+            }
+        }
     }
 
-    return ret;
+    return { entries, zeroOverlapPairs, failedPairs };
 }
 
 function getPositionTables(index: IndexEntry[], pivot: number, other: number, N: number) {
@@ -53,7 +70,6 @@ function getPositionTables(index: IndexEntry[], pivot: number, other: number, N:
 
         const l = Math.min(a[2] - a[1], b[2] - b[1]);
 
-        // TODO: allow to use just backbone atoms?
         // TODO: check if residue types match?
         for (let i = 0; i < l; i++) {
             let eI = (a[1] + i) as ElementIndex;
@@ -121,19 +137,20 @@ interface IndexEntry {
     pivots: { [i: number]: [unit: Unit.Atomic, start: ElementIndex, end: ElementIndex] | undefined }
 }
 
-function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: number) {
+function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: number, traceOnly: boolean) {
     for (const unit of structure.units) {
         if (unit.kind !== Unit.Kind.Atomic) continue;
 
         const { elements, model } = unit;
 
-        const map = BestDatabaseSequenceMapping.Provider.get(model).value;
+        const map = SIFTSMapping.Provider.get(model).value;
         if (!map) return;
 
         const { dbName, accession, num } = map;
 
         const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
         const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+        const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
 
         while (chainsIt.hasNext) {
             const chainSegment = chainsIt.move();
@@ -144,8 +161,15 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
 
                 if (!dbName[rI]) continue;
 
-                const start = elements[residueSegment.start];
-                const end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+                let start, end;
+                if (traceOnly) {
+                    start = traceElementIndex[rI];
+                    if (start === -1) continue;
+                    end = start + 1 as ElementIndex;
+                } else {
+                    start = elements[residueSegment.start];
+                    end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+                }
 
                 const key = `${dbName[rI]}-${accession[rI]}-${num[rI]}`;
 
@@ -161,6 +185,4 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
             }
         }
     }
-
-    console.log(index);
 }

src/mol-plugin-state/builder/structure/representation-preset.ts

@@ -24,8 +24,6 @@ import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bo
 import { StructConn } from '../../../mol-model-formats/structure/property/bonds/struct_conn';
 import { StructureRepresentationRegistry } from '../../../mol-repr/structure/registry';
 import { assertUnreachable } from '../../../mol-util/type-helpers';
-import { Color } from '../../../mol-util/color';
-import { PostprocessingParams } from '../../../mol-canvas3d/passes/postprocessing';
 
 export interface StructureRepresentationPresetProvider<P = any, S extends _Result = _Result> extends PresetProvider<PluginStateObject.Molecule.Structure, P, S> { }
 export function StructureRepresentationPresetProvider<P, S extends _Result>(repr: StructureRepresentationPresetProvider<P, S>) { return repr; }
@@ -39,6 +37,7 @@ export namespace StructureRepresentationPresetProvider {
 
     export const CommonParams = {
         ignoreHydrogens: PD.Optional(PD.Boolean(false)),
+        ignoreLight: PD.Optional(PD.Boolean(false)),
         quality: PD.Optional(PD.Select<VisualQuality>('auto', VisualQualityOptions)),
         theme: PD.Optional(PD.Group({
             globalName: PD.Optional(PD.Text<ColorTheme.BuiltIn>('')),
@@ -70,9 +69,11 @@ export namespace StructureRepresentationPresetProvider {
         const typeParams = {
             quality: plugin.managers.structure.component.state.options.visualQuality,
             ignoreHydrogens: !plugin.managers.structure.component.state.options.showHydrogens,
+            ignoreLight: plugin.managers.structure.component.state.options.ignoreLight,
         };
         if (params.quality && params.quality !== 'auto') typeParams.quality = params.quality;
         if (params.ignoreHydrogens !== void 0) typeParams.ignoreHydrogens = !!params.ignoreHydrogens;
+        if (params.ignoreLight !== void 0) typeParams.ignoreLight = !!params.ignoreLight;
         const color: ColorTheme.BuiltIn | undefined = params.theme?.globalName ? params.theme?.globalName : void 0;
         const ballAndStickColor: ColorTheme.BuiltInParams<'element-symbol'> = params.theme?.carbonColor !== undefined
             ? { carbonColor: getCarbonColorParams(params.theme?.carbonColor) }
@@ -100,15 +101,6 @@ type CommonParams = StructureRepresentationPresetProvider.CommonParams
 const reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
 const updateFocusRepr = StructureRepresentationPresetProvider.updateFocusRepr;
 
-function resetPostprocessingProps(plugin: PluginContext) {
-    if (plugin.canvas3d) {
-        const p = PD.getDefaultValues(PostprocessingParams);
-        plugin.canvas3d.setProps({
-            postprocessing: { outline: p.outline, occlusion: p.occlusion }
-        });
-    }
-}
-
 const auto = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-auto',
     display: {
@@ -148,7 +140,6 @@ const empty = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-empty',
     display: { name: 'Empty', description: 'Removes all existing representations.' },
     async apply(ref, params, plugin) {
-        resetPostprocessingProps(plugin);
         return { };
     }
 });
@@ -194,17 +185,15 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
             nonStandard: builder.buildRepresentation(update, components.nonStandard, { type: 'ball-and-stick', typeParams, color, colorParams: ballAndStickColor }, { tag: 'non-standard' }),
             branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.3 }, color, colorParams: ballAndStickColor }, { tag: 'branched-ball-and-stick' }),
             branchedSnfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams, color }, { tag: 'branched-snfg-3d' }),
-            water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6 }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
+            water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6, visuals: waterType === 'line' ? ['intra-bond', 'element-point'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
             ion: builder.buildRepresentation(update, components.ion, { type: 'ball-and-stick', typeParams, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ion' }),
-            lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6 }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
+            lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6, visuals: lipidType === 'line' ? ['intra-bond'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
             coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams, color: color || 'chain-id' }, { tag: 'coarse' })
         };
 
         await update.commit({ revertOnError: false });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -244,8 +233,6 @@ const proteinAndNucleic = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -298,8 +285,6 @@ const coarseSurface = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -333,8 +318,6 @@ const polymerCartoon = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -401,8 +384,6 @@ const atomicDetail = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name ?? color, params.theme?.focus?.params ?? colorParams);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -436,21 +417,6 @@ const illustrative = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name ?? color, params.theme?.focus?.params);
 
-        if (plugin.canvas3d) {
-            plugin.canvas3d.setProps({
-                postprocessing: {
-                    outline: {
-                        name: 'on',
-                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
-                    },
-                    occlusion: {
-                        name: 'on',
-                        params: { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
-                    },
-                }
-            });
-        }
-
         return { components, representations };
     }
 });
@@ -471,6 +437,6 @@ export const PresetStructureRepresentations = {
     'polymer-and-ligand': polymerAndLigand,
     'protein-and-nucleic': proteinAndNucleic,
     'coarse-surface': coarseSurface,
-    'illustrative': illustrative,
+    illustrative,
 };
 export type PresetStructureRepresentations = typeof PresetStructureRepresentations;

src/mol-plugin-state/builder/structure/representation.ts

@@ -29,7 +29,7 @@ export class StructureRepresentationBuilder {
 
     readonly defaultProvider = PresetStructureRepresentations.auto;
 
-    private resolveProvider(ref: StructureRepresentationPresetProviderRef) {
+    resolveProvider(ref: StructureRepresentationPresetProviderRef) {
         return typeof ref === 'string'
             ? PresetStructureRepresentations[ref as keyof PresetStructureRepresentations] ?? arrayFind(this._providers, p => p.id === ref)
             : ref;

src/mol-plugin-state/manager/interactivity.ts

@@ -76,9 +76,11 @@ namespace InteractivityManager {
 
     /**
      * The `noRender` argument indicates that the action should only update the internal
-     * data structure but not render anything user visible. For example 1) no drawing of
-     * the canvas3d scene or 2) no ui update of loci labels. This is useful because some
-     * actions require clearing any markings before they can be applied.
+     * data structure but not render anything user visible. For example, no ui update of
+     * loci labels.
+     *
+     * This is useful because some actions require clearing any markings before
+     * they can be applied.
      */
     export type LociMarkProvider = (loci: Representation.Loci, action: MarkerAction, /* test */ noRender?: boolean) => void
 

src/mol-plugin-state/manager/structure/component.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 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>
@@ -71,6 +71,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
             await update.commit();
             await this.plugin.state.updateBehavior(StructureFocusRepresentation, p => {
                 p.ignoreHydrogens = !options.showHydrogens;
+                p.ignoreLight = options.ignoreLight;
                 p.material = options.materialStyle;
                 p.clip = options.clipObjects;
             });
@@ -79,16 +80,17 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
     }
 
     private updateReprParams(update: StateBuilder.Root, component: StructureComponentRef) {
-        const { showHydrogens, visualQuality: quality, materialStyle: material, clipObjects: clip } = this.state.options;
+        const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
         const ignoreHydrogens = !showHydrogens;
         for (const r of component.representations) {
             if (r.cell.transform.transformer !== StructureRepresentation3D) continue;
 
             const params = r.cell.transform.params as StateTransformer.Params<StructureRepresentation3D>;
-            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
+            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || params.type.params.ignoreLight !== ignoreLight || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
                 update.to(r.cell).update(old => {
                     old.type.params.ignoreHydrogens = ignoreHydrogens;
                     old.type.params.quality = quality;
+                    old.type.params.ignoreLight = ignoreLight;
                     old.type.params.material = material;
                     old.type.params.clip = clip;
                 });
@@ -309,9 +311,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
     addRepresentation(components: ReadonlyArray<StructureComponentRef>, type: string) {
         if (components.length === 0) return;
 
-        const { showHydrogens, visualQuality: quality, materialStyle: material, clipObjects: clip } = this.state.options;
+        const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
         const ignoreHydrogens = !showHydrogens;
-        const typeParams = { ignoreHydrogens, quality, material, clip };
+        const typeParams = { ignoreHydrogens, quality, ignoreLight, material, clip };
 
         return this.plugin.dataTransaction(async () => {
             for (const component of components) {
@@ -346,9 +348,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
             const xs = structures || this.currentStructures;
             if (xs.length === 0) return;
 
-            const { showHydrogens, visualQuality: quality, materialStyle: material, clipObjects: clip } = this.state.options;
+            const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
             const ignoreHydrogens = !showHydrogens;
-            const typeParams = { ignoreHydrogens, quality, material, clip };
+            const typeParams = { ignoreHydrogens, quality, ignoreLight, material, clip };
 
             const componentKey = UUID.create22();
             for (const s of xs) {
@@ -458,6 +460,7 @@ namespace StructureComponentManager {
     export const OptionsParams = {
         showHydrogens: PD.Boolean(true, { description: 'Toggle display of hydrogen atoms in representations' }),
         visualQuality: PD.Select('auto', VisualQualityOptions, { description: 'Control the visual/rendering quality of representations' }),
+        ignoreLight: PD.Boolean(false, { description: 'Ignore light for stylized rendering of representtions' }),
         materialStyle: Material.getParam(),
         clipObjects: PD.Group(Clip.Params),
         interactions: PD.Group(InteractionsProvider.defaultParams, { label: 'Non-covalent Interactions' }),

src/mol-plugin-ui/controls.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -24,6 +24,7 @@ import { StructureSourceControls } from './structure/source';
 import { VolumeStreamingControls, VolumeSourceControls } from './structure/volume';
 import { PluginConfig } from '../mol-plugin/config';
 import { StructureSuperpositionControls } from './structure/superposition';
+import { StructureQuickStylesControls } from './structure/quick-styles';
 
 export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: boolean, label: string }> {
     state = { show: false, label: '' };
@@ -292,6 +293,7 @@ export class DefaultStructureTools extends PluginUIComponent {
             <StructureSourceControls />
             <StructureMeasurementsControls />
             <StructureSuperpositionControls />
+            <StructureQuickStylesControls />
             <StructureComponentControls />
             {this.plugin.config.get(PluginConfig.VolumeStreaming.Enabled) && <VolumeStreamingControls />}
             <VolumeSourceControls />

src/mol-plugin-ui/controls/icons.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
@@ -38,10 +38,10 @@ export function MoleculeSvg() { return _Molecule; }
 // The following icons are adapted from https://materialdesignicons.com/ and
 // licensed with https://github.com/Templarian/MaterialDesign/blob/master/LICENSE
 
-const _CubeOutline = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M21,16.5C21,16.88 20.79,17.21 20.47,17.38L12.57,21.82C12.41,21.94 12.21,22 12,22C11.79,22 11.59,21.94 11.43,21.82L3.53,17.38C3.21,17.21 3,16.88 3,16.5V7.5C3,7.12 3.21,6.79 3.53,6.62L11.43,2.18C11.59,2.06 11.79,2 12,2C12.21,2 12.41,2.06 12.57,2.18L20.47,6.62C20.79,6.79 21,7.12 21,7.5V16.5M12,4.15L6.04,7.5L12,10.85L17.96,7.5L12,4.15M5,15.91L11,19.29V12.58L5,9.21V15.91M19,15.91V9.21L13,12.58V19.29L19,15.91Z" /></svg>;
+const _CubeOutline = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d='M21,16.5C21,16.88 20.79,17.21 20.47,17.38L12.57,21.82C12.41,21.94 12.21,22 12,22C11.79,22 11.59,21.94 11.43,21.82L3.53,17.38C3.21,17.21 3,16.88 3,16.5V7.5C3,7.12 3.21,6.79 3.53,6.62L11.43,2.18C11.59,2.06 11.79,2 12,2C12.21,2 12.41,2.06 12.57,2.18L20.47,6.62C20.79,6.79 21,7.12 21,7.5V16.5M12,4.15L6.04,7.5L12,10.85L17.96,7.5L12,4.15M5,15.91L11,19.29V12.58L5,9.21V15.91M19,15.91V9.21L13,12.58V19.29L19,15.91Z' /></svg>;
 export function CubeOutlineSvg() { return _CubeOutline; }
 
-const _CubeScan = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M17,22V20H20V17H22V20.5C22,20.89 21.84,21.24 21.54,21.54C21.24,21.84 20.89,22 20.5,22H17M7,22H3.5C3.11,22 2.76,21.84 2.46,21.54C2.16,21.24 2,20.89 2,20.5V17H4V20H7V22M17,2H20.5C20.89,2 21.24,2.16 21.54,2.46C21.84,2.76 22,3.11 22,3.5V7H20V4H17V2M7,2V4H4V7H2V3.5C2,3.11 2.16,2.76 2.46,2.46C2.76,2.16 3.11,2 3.5,2H7M13,17.25L17,14.95V10.36L13,12.66V17.25M12,10.92L16,8.63L12,6.28L8,8.63L12,10.92M7,14.95L11,17.25V12.66L7,10.36V14.95M18.23,7.59C18.73,7.91 19,8.34 19,8.91V15.23C19,15.8 18.73,16.23 18.23,16.55L12.75,19.73C12.25,20.05 11.75,20.05 11.25,19.73L5.77,16.55C5.27,16.23 5,15.8 5,15.23V8.91C5,8.34 5.27,7.91 5.77,7.59L11.25,4.41C11.5,4.28 11.75,4.22 12,4.22C12.25,4.22 12.5,4.28 12.75,4.41L18.23,7.59Z" /></svg>;
+const _CubeScan = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d='M17,22V20H20V17H22V20.5C22,20.89 21.84,21.24 21.54,21.54C21.24,21.84 20.89,22 20.5,22H17M7,22H3.5C3.11,22 2.76,21.84 2.46,21.54C2.16,21.24 2,20.89 2,20.5V17H4V20H7V22M17,2H20.5C20.89,2 21.24,2.16 21.54,2.46C21.84,2.76 22,3.11 22,3.5V7H20V4H17V2M7,2V4H4V7H2V3.5C2,3.11 2.16,2.76 2.46,2.46C2.76,2.16 3.11,2 3.5,2H7M13,17.25L17,14.95V10.36L13,12.66V17.25M12,10.92L16,8.63L12,6.28L8,8.63L12,10.92M7,14.95L11,17.25V12.66L7,10.36V14.95M18.23,7.59C18.73,7.91 19,8.34 19,8.91V15.23C19,15.8 18.73,16.23 18.23,16.55L12.75,19.73C12.25,20.05 11.75,20.05 11.25,19.73L5.77,16.55C5.27,16.23 5,15.8 5,15.23V8.91C5,8.34 5.27,7.91 5.77,7.59L11.25,4.41C11.5,4.28 11.75,4.22 12,4.22C12.25,4.22 12.5,4.28 12.75,4.41L18.23,7.59Z' /></svg>;
 export function CubeScanSvg() { return _CubeScan; }
 
 const _CubeSend = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M16,4L9,8.04V15.96L16,20L23,15.96V8.04M16,6.31L19.8,8.5L16,10.69L12.21,8.5M0,7V9H7V7M11,10.11L15,12.42V17.11L11,14.81M21,10.11V14.81L17,17.11V12.42M2,11V13H7V11M4,15V17H7V15" /></svg>;
@@ -53,9 +53,12 @@ export function CursorDefaultOutlineSvg() { return _CursorDefaultOutline; }
 const _FileOutline = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path fill='currentColor' d='M14,2H6A2,2 0 0,0 4,4V20A2,2 0 0,0 6,22H18A2,2 0 0,0 20,20V8L14,2M18,20H6V4H13V9H18V20Z' /></svg>;
 export function FileOutlineSvg() { return _FileOutline; }
 
-const _PencilRuler = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M3 17.25V21H6.75L17.81 9.93L14.06 6.18L3 17.25M22.61 18.36L18.36 22.61L13.16 17.41L14.93 15.64L15.93 16.64L18.4 14.16L19.82 15.58L18.36 17L19.42 18L20.84 16.6L22.61 18.36M6.61 10.83L1.39 5.64L5.64 1.39L7.4 3.16L4.93 5.64L6 6.7L8.46 4.22L9.88 5.64L8.46 7.05L9.46 8.05L6.61 10.83M20.71 7C21.1 6.61 21.1 6 20.71 5.59L18.37 3.29C18 2.9 17.35 2.9 16.96 3.29L15.12 5.12L18.87 8.87L20.71 7Z" /></svg>;
+const _PencilRuler = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d='M3 17.25V21H6.75L17.81 9.93L14.06 6.18L3 17.25M22.61 18.36L18.36 22.61L13.16 17.41L14.93 15.64L15.93 16.64L18.4 14.16L19.82 15.58L18.36 17L19.42 18L20.84 16.6L22.61 18.36M6.61 10.83L1.39 5.64L5.64 1.39L7.4 3.16L4.93 5.64L6 6.7L8.46 4.22L9.88 5.64L8.46 7.05L9.46 8.05L6.61 10.83M20.71 7C21.1 6.61 21.1 6 20.71 5.59L18.37 3.29C18 2.9 17.35 2.9 16.96 3.29L15.12 5.12L18.87 8.87L20.71 7Z' /></svg>;
 export function PencilRulerSvg() { return _PencilRuler; }
 
+const _MagicWand = <svg width='24px' height='24px' viewBox='0 0 24 24'><path fill='currentColor' d='M7.5,5.6L5,7L6.4,4.5L5,2L7.5,3.4L10,2L8.6,4.5L10,7L7.5,5.6M19.5,15.4L22,14L20.6,16.5L22,19L19.5,17.6L17,19L18.4,16.5L17,14L19.5,15.4M22,2L20.6,4.5L22,7L19.5,5.6L17,7L18.4,4.5L17,2L19.5,3.4L22,2M13.34,12.78L15.78,10.34L13.66,8.22L11.22,10.66L13.34,12.78M14.37,7.29L16.71,9.63C17.1,10 17.1,10.65 16.71,11.04L5.04,22.71C4.65,23.1 4,23.1 3.63,22.71L1.29,20.37C0.9,20 0.9,19.35 1.29,18.96L12.96,7.29C13.35,6.9 14,6.9 14.37,7.29Z' /></svg>;
+export function MagicWandSvg() { return _MagicWand; }
+
 // The following icons are adapted from https://material-ui.com/components/material-icons/ and
 // licensed with https://github.com/mui-org/material-ui/blob/master/LICENSE
 

src/mol-plugin-ui/sequence/sequence.tsx

@@ -6,15 +6,15 @@
  */
 
 import * as React from 'react';
-import { PluginUIComponent } from '../base';
-import { MarkerAction } from '../../mol-util/marker-action';
-import { ButtonsType, ModifiersKeys, getButtons, getModifiers, getButton } from '../../mol-util/input/input-observer';
-import { SequenceWrapper } from './wrapper';
-import { StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
 import { Subject } from 'rxjs';
-import { debounceTime } from 'rxjs/operators';
+import { throttleTime } from 'rxjs/operators';
 import { OrderedSet } from '../../mol-data/int';
+import { StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
 import { Representation } from '../../mol-repr/representation';
+import { ButtonsType, getButton, getButtons, getModifiers, ModifiersKeys } from '../../mol-util/input/input-observer';
+import { MarkerAction } from '../../mol-util/marker-action';
+import { PluginUIComponent } from '../base';
+import { SequenceWrapper } from './wrapper';
 
 type SequenceProps = {
     sequenceWrapper: SequenceWrapper.Any,
@@ -55,12 +55,10 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
         this.plugin.managers.interactivity.lociHighlights.addProvider(this.lociHighlightProvider);
         this.plugin.managers.interactivity.lociSelects.addProvider(this.lociSelectionProvider);
 
-        this.subscribe(debounceTime<{ seqIdx: number, buttons: number, button: number, modifiers: ModifiersKeys }>(15)(this.highlightQueue), (e) => {
+        this.subscribe(this.highlightQueue.pipe(throttleTime(3 * 16.666, void 0, { leading: true, trailing: true })), (e) => {
             const loci = this.getLoci(e.seqIdx < 0 ? void 0 : e.seqIdx);
             this.hover(loci, e.buttons, e.button, e.modifiers);
         });
-
-        // this.updateMarker()
     }
 
     componentWillUnmount() {

src/mol-plugin-ui/skin/base/components/misc.scss

@@ -490,7 +490,7 @@
     }
 }
 
-.msp-action-menu-options {   
+.msp-action-menu-options {
     &-no-header, .msp-control-group-children {
         max-height: 300px;
         overflow: hidden;
@@ -602,10 +602,10 @@
     }
 
     .msp-slider {
-        > div:first-child() {
+        > div:first-child {
             right: 42px;
         }
-        > div:last-child() {
+        > div:last-child {
             width: 30px;
         }
     }

src/mol-plugin-ui/skin/base/components/viewport.scss

@@ -24,6 +24,7 @@
     right: 0;
     bottom: 0;
     -webkit-user-select: none;
+    user-select: none;
     -webkit-tap-highlight-color: rgba(0,0,0,0);
     -webkit-touch-callout: none;
     touch-action: manipulation;
@@ -71,7 +72,7 @@
     }
 }
 
-.msp-semi-transparent-background {    
+.msp-semi-transparent-background {
     background: $default-background;
     opacity: 0.5;
     position: absolute;
@@ -94,7 +95,7 @@
 
     .msp-viewport-controls-panel-controls {
         overflow-y: auto;
-        max-height: 400px;    
+        max-height: 400px;
     }
 }
 

src/mol-plugin-ui/structure/quick-styles.tsx

@@ -0,0 +1,107 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { Color } from '../../mol-util/color';
+import { CollapsableControls, PurePluginUIComponent } from '../base';
+import { Button } from '../controls/common';
+import { MagicWandSvg } from '../controls/icons';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PostprocessingParams } from '../../mol-canvas3d/passes/postprocessing';
+import { PluginConfig } from '../../mol-plugin/config';
+import { StructureComponentManager } from '../../mol-plugin-state/manager/structure/component';
+
+export class StructureQuickStylesControls extends CollapsableControls {
+    defaultState() {
+        return {
+            isCollapsed: false,
+            header: 'Quick Styles',
+            brand: { accent: 'gray' as const, svg: MagicWandSvg }
+        };
+    }
+
+    renderControls() {
+        return <>
+            <QuickStyles />
+        </>;
+    }
+}
+
+export class QuickStyles extends PurePluginUIComponent {
+    async default() {
+        const { structures } = this.plugin.managers.structure.hierarchy.selection;
+        const preset = this.plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+        const provider = this.plugin.builders.structure.representation.resolveProvider(preset);
+        await this.plugin.managers.structure.component.applyPreset(structures, provider);
+
+        this.plugin.managers.structure.component.setOptions(PD.getDefaultValues(StructureComponentManager.OptionsParams));
+
+        if (this.plugin.canvas3d) {
+            const p = PD.getDefaultValues(PostprocessingParams);
+            this.plugin.canvas3d.setProps({
+                postprocessing: { outline: p.outline, occlusion: p.occlusion }
+            });
+        }
+    }
+
+    async illustrative() {
+        const { structures } = this.plugin.managers.structure.hierarchy.selection;
+        await this.plugin.managers.structure.component.applyPreset(structures, PresetStructureRepresentations.illustrative);
+
+        if (this.plugin.canvas3d) {
+            this.plugin.canvas3d.setProps({
+                postprocessing: {
+                    outline: {
+                        name: 'on',
+                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
+                    },
+                    occlusion: {
+                        name: 'on',
+                        params: { bias: 0.8, blurKernelSize: 15, radius: 5, samples: 32, resolutionScale: 1 }
+                    },
+                }
+            });
+        }
+    }
+
+    async stylized() {
+        this.plugin.managers.structure.component.setOptions({ ...this.plugin.managers.structure.component.state.options, ignoreLight: true });
+
+        if (this.plugin.canvas3d) {
+            const pp = this.plugin.canvas3d.props.postprocessing;
+            this.plugin.canvas3d.setProps({
+                postprocessing: {
+                    outline: {
+                        name: 'on',
+                        params: pp.outline.name === 'on'
+                            ? pp.outline.params
+                            : { scale: 1, color: Color(0x000000), threshold: 0.33 }
+                    },
+                    occlusion: {
+                        name: 'on',
+                        params: pp.occlusion.name === 'on'
+                            ? pp.occlusion.params
+                            : { bias: 0.8, blurKernelSize: 15, radius: 5, samples: 32, resolutionScale: 1 }
+                    },
+                }
+            });
+        }
+    }
+
+    render() {
+        return <div className='msp-flex-row'>
+            <Button noOverflow title='Applies default representation preset. Set outline and occlusion effects to defaults.' onClick={() => this.default()} style={{ width: 'auto' }}>
+                Default
+            </Button>
+            <Button noOverflow title='Applies no representation preset. Enables outline and occlusion effects. Enables ignore-light representation parameter.' onClick={() => this.stylized()} style={{ width: 'auto' }}>
+                Stylized
+            </Button>
+            <Button noOverflow title='Applies illustrative representation preset. Enables outline and occlusion effects. Enables ignore-light parameter.' onClick={() => this.illustrative()} style={{ width: 'auto' }}>
+                Illustrative
+            </Button>
+        </div>;
+    }
+}

src/mol-plugin-ui/structure/superposition.tsx

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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 { CollapsableControls, PurePluginUIComponent } from '../base';
@@ -20,9 +21,9 @@ import { ParameterControls } from '../controls/parameters';
 import { stripTags } from '../../mol-util/string';
 import { StructureSelectionHistoryEntry } from '../../mol-plugin-state/manager/structure/selection';
 import { ToggleSelectionModeButton } from './selection';
-import { alignAndSuperposeWithBestDatabaseMapping } from '../../mol-model/structure/structure/util/superposition-db-mapping';
+import { alignAndSuperposeWithSIFTSMapping } from '../../mol-model/structure/structure/util/superposition-sifts-mapping';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { BestDatabaseSequenceMapping } from '../../mol-model-props/sequence/best-database-mapping';
+import { SIFTSMapping } from '../../mol-model-props/sequence/sifts-mapping';
 
 export class StructureSuperpositionControls extends CollapsableControls {
     defaultState() {
@@ -48,7 +49,8 @@ export class StructureSuperpositionControls extends CollapsableControls {
 }
 
 export const StructureSuperpositionParams = {
-    alignSequences: PD.Boolean(true, { isEssential: true, description: 'Perform a sequence alignment and use the aligned residue pairs to guide the 3D superposition.' }),
+    alignSequences: PD.Boolean(true, { isEssential: true, description: 'For Chain-based 3D superposition, perform a sequence alignment and use the aligned residue pairs to guide the 3D superposition.' }),
+    traceOnly: PD.Boolean(true, { description: 'For Chain- and Uniprot-based 3D superposition, base superposition only on CA (and equivalent) atoms.' })
 };
 const DefaultStructureSuperpositionOptions = PD.getDefaultValues(StructureSuperpositionParams);
 export type StructureSuperpositionOptions = PD.ValuesFor<typeof StructureSuperpositionParams>
@@ -94,7 +96,7 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
         });
 
         this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, sel => {
-            this.setState({ canUseDb: sel.structures.every(s => !!s.cell.obj?.data && s.cell.obj.data.models.some(m => BestDatabaseSequenceMapping.Provider.isApplicable(m))) });
+            this.setState({ canUseDb: sel.structures.every(s => !!s.cell.obj?.data && s.cell.obj.data.models.some(m => SIFTSMapping.Provider.isApplicable(m))) });
         });
     }
 
@@ -123,10 +125,10 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
     }
 
     superposeChains = async () => {
-        const { query } = StructureSelectionQueries.trace;
+        const { query } = this.state.options.traceOnly ? StructureSelectionQueries.trace : StructureSelectionQueries.polymer;
         const entries = this.chainEntries;
 
-        const traceLocis = entries.map((e, i) => {
+        const locis = entries.map((e, i) => {
             const s = StructureElement.Loci.toStructure(e.loci);
             const loci = StructureSelection.toLociWithSourceUnits(query(new QueryContext(s)));
             return StructureElement.Loci.remap(loci, i === 0
@@ -136,11 +138,11 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
         });
 
         const transforms = this.state.options.alignSequences
-            ? alignAndSuperpose(traceLocis)
-            : superpose(traceLocis);
+            ? alignAndSuperpose(locis)
+            : superpose(locis);
 
         const eA = entries[0];
-        for (let i = 1, il = traceLocis.length; i < il; ++i) {
+        for (let i = 1, il = locis.length; i < il; ++i) {
             const eB = entries[i];
             const { bTransform, rmsd } = transforms[i - 1];
             await this.transform(eB.cell, bTransform);
@@ -148,6 +150,7 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
             const labelB = stripTags(eB.label);
             this.plugin.log.info(`Superposed [${labelA}] and [${labelB}] with RMSD ${rmsd.toFixed(2)}.`);
         }
+        await this.cameraReset();
     };
 
     superposeAtoms = async () => {
@@ -171,26 +174,47 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
             const count = entries[i].atoms.length;
             this.plugin.log.info(`Superposed ${count} ${count === 1 ? 'atom' : 'atoms'} of [${labelA}] and [${labelB}] with RMSD ${rmsd.toFixed(2)}.`);
         }
+        await this.cameraReset();
     };
 
     superposeDb = async () => {
         const input = this.plugin.managers.structure.hierarchy.behaviors.selection.value.structures;
+        const traceOnly = this.state.options.traceOnly;
 
-        const transforms = alignAndSuperposeWithBestDatabaseMapping(input.map(s => s.cell.obj?.data!));
+        const structures = input.map(s => s.cell.obj?.data!);
+        const { entries, failedPairs, zeroOverlapPairs } = alignAndSuperposeWithSIFTSMapping(structures, { traceOnly });
 
         let rmsd = 0;
 
-        for (const xform of transforms) {
+        for (const xform of entries) {
             await this.transform(input[xform.other].cell, xform.transform.bTransform);
             rmsd += xform.transform.rmsd;
         }
 
-        rmsd /= Math.max(transforms.length - 1, 1);
+        rmsd /= Math.max(entries.length - 1, 1);
 
-        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)} Å.`);
+        const formatPairs = (pairs: [number, number][]) => {
+            return `[${pairs.map(([i, j]) => `(${structures[i].models[0].entryId}, ${structures[j].models[0].entryId})`).join(', ')}]`;
+        };
+
+        if (zeroOverlapPairs.length) {
+            this.plugin.log.warn(`Superposition: No UNIPROT mapping overlap between structures ${formatPairs(zeroOverlapPairs)}.`);
+        }
+
+        if (failedPairs.length) {
+            this.plugin.log.error(`Superposition: Failed to superpose structures ${formatPairs(failedPairs)}.`);
+        }
+
+        if (entries.length) {
+            this.plugin.log.info(`Superposed ${entries.length + 1} structures with avg. RMSD ${rmsd.toFixed(2)} Å.`);
+            await this.cameraReset();
+        }
+    };
+
+    async cameraReset() {
         await new Promise(res => requestAnimationFrame(res));
         PluginCommands.Camera.Reset(this.plugin);
-    };
+    }
 
     toggleByChains = () => this.setState({ action: this.state.action === 'byChains' ? void 0 : 'byChains' });
     toggleByAtoms = () => this.setState({ action: this.state.action === 'byAtoms' ? void 0 : 'byAtoms' });
@@ -323,8 +347,8 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
 
     superposeByDbMapping() {
         return <>
-            <Button icon={SuperposeChainsSvg} title='Superpose structures using database mapping.' className='msp-btn msp-btn-block' onClick={this.superposeDb} style={{ marginTop: '1px' }} disabled={this.state.isBusy}>
-                DB
+            <Button icon={SuperposeChainsSvg} title='Superpose structures using intersection of residues from SIFTS UNIPROT mapping.' className='msp-btn msp-btn-block' onClick={this.superposeDb} style={{ marginTop: '1px' }} disabled={this.state.isBusy}>
+                Uniprot
             </Button>
         </>;
     }

src/mol-plugin-ui/structure/volume.tsx

@@ -77,9 +77,9 @@ export class VolumeStreamingControls extends CollapsableControls<{}, VolumeStrea
         const rootCell = root && pivot.cell.parent.cells.get(root);
 
         const simpleApply = rootCell && rootCell.status === 'error'
-            ? { header: 'Error enabling', icon: ErrorSvg, title: rootCell.errorText }
+            ? { header: !!rootCell.errorText && rootCell.errorText?.includes('404') ? 'No Density Data Available' : 'Error Enabling', icon: ErrorSvg, title: rootCell.errorText }
             : rootCell && rootCell.obj?.data.entries.length === 0
-                ? { header: 'Error enabling', icon: ErrorSvg, title: 'No entry for streaming found' }
+                ? { header: 'Error Enabling', icon: ErrorSvg, title: 'No Entry for Streaming Found' }
                 : { header: 'Enable', icon: CheckSvg, title: 'Enable' };
 
         return <ApplyActionControl state={pivot.cell.parent} action={InitVolumeStreaming} initiallyCollapsed={true} nodeRef={pivot.cell.transform.ref} simpleApply={simpleApply} />;

src/mol-plugin/behavior/dynamic/custom-props.ts

@@ -11,6 +11,6 @@ export { AccessibleSurfaceArea } from './custom-props/computed/accessible-surfac
 export { Interactions } from './custom-props/computed/interactions';
 export { SecondaryStructure } from './custom-props/computed/secondary-structure';
 export { ValenceModel } from './custom-props/computed/valence-model';
-export { BestDatabaseSequenceMapping } from './custom-props/sequence/best-database-mapping';
+export { SIFTSMapping as BestDatabaseSequenceMapping } from './custom-props/sequence/sifts-mapping';
 
 export { CrossLinkRestraint } from './custom-props/integrative/cross-link-restraint';

src/mol-plugin/behavior/dynamic/custom-props/sequence/sifts-mapping.ts

@@ -5,17 +5,17 @@
  */
 
 import { OrderedSet } from '../../../../../mol-data/int';
-import { BestDatabaseSequenceMapping as BestDatabaseSequenceMappingProp } from '../../../../../mol-model-props/sequence/best-database-mapping';
-import { BestDatabaseSequenceMappingColorThemeProvider } from '../../../../../mol-model-props/sequence/themes/best-database-mapping';
+import { SIFTSMapping as BestDatabaseSequenceMappingProp } from '../../../../../mol-model-props/sequence/sifts-mapping';
+import { SIFTSMappingColorThemeProvider } from '../../../../../mol-model-props/sequence/themes/sifts-mapping';
 import { Loci } from '../../../../../mol-model/loci';
 import { StructureElement } from '../../../../../mol-model/structure';
 import { ParamDefinition as PD } from '../../../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../behavior';
 
-export const BestDatabaseSequenceMapping = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
-    name: 'best-sequence-database-mapping-prop',
+export const SIFTSMapping = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'sifts-mapping-prop',
     category: 'custom-props',
-    display: { name: 'Best Database Sequence Mapping' },
+    display: { name: 'SIFTS Mapping' },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
         private provider = BestDatabaseSequenceMappingProp.Provider;
 
@@ -39,13 +39,13 @@ export const BestDatabaseSequenceMapping = PluginBehavior.create<{ autoAttach: b
 
         register(): void {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(BestDatabaseSequenceMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.addProvider(this.labelProvider);
         }
 
         unregister() {
             this.ctx.customModelProperties.unregister(this.provider.descriptor.name);
-            this.ctx.representation.structure.themes.colorThemeRegistry.remove(BestDatabaseSequenceMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
         }
     },

src/mol-plugin/behavior/dynamic/representation.ts

@@ -43,9 +43,9 @@ export const HighlightLoci = PluginBehavior.create({
     name: 'representation-highlight-loci',
     category: 'interaction',
     ctor: class extends PluginBehavior.Handler<HighlightLociProps> {
-        private lociMarkProvider = (interactionLoci: Representation.Loci, action: MarkerAction, noRender?: boolean) => {
+        private lociMarkProvider = (interactionLoci: Representation.Loci, action: MarkerAction) => {
             if (!this.ctx.canvas3d || !this.params.mark) return;
-            this.ctx.canvas3d.mark(interactionLoci, action, noRender);
+            this.ctx.canvas3d.mark(interactionLoci, action);
         };
         private getLoci(loci: Loci) {
             return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
@@ -113,9 +113,9 @@ export const SelectLoci = PluginBehavior.create({
     category: 'interaction',
     ctor: class extends PluginBehavior.Handler<SelectLociProps> {
         private spine: StateTreeSpine.Impl;
-        private lociMarkProvider = (reprLoci: Representation.Loci, action: MarkerAction, noRender?: boolean) => {
+        private lociMarkProvider = (reprLoci: Representation.Loci, action: MarkerAction) => {
             if (!this.ctx.canvas3d || !this.params.mark) return;
-            this.ctx.canvas3d.mark({ loci: reprLoci.loci }, action, noRender);
+            this.ctx.canvas3d.mark({ loci: reprLoci.loci }, action);
         };
         private getLoci(loci: Loci) {
             return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2

src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 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>
@@ -27,11 +27,19 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
         expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
         targetParams: PD.Group(reprParams, {
             label: 'Target',
-            customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51, adjustCylinderLength: true } })
+            customDefault: createStructureRepresentationParams(plugin, void 0, {
+                type: 'ball-and-stick',
+                size: 'physical',
+                typeParams: { sizeFactor: 0.22, sizeAspectRatio: 0.73, adjustCylinderLength: true, xrayShaded: true, aromaticBonds: false, multipleBonds: 'off', excludeTypes: ['hydrogen-bond', 'metal-coordination'] },
+            })
         }),
         surroundingsParams: PD.Group(reprParams, {
             label: 'Surroundings',
-            customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.16 } })
+            customDefault: createStructureRepresentationParams(plugin, void 0, {
+                type: 'ball-and-stick',
+                size: 'physical',
+                typeParams: { sizeFactor: 0.16, excludeTypes: ['hydrogen-bond', 'metal-coordination'] }
+            })
         }),
         nciParams: PD.Group(reprParams, {
             label: 'Non-covalent Int.',
@@ -44,6 +52,7 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
         components: PD.MultiSelect(FocusComponents, PD.arrayToOptions(FocusComponents)),
         excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
         ignoreHydrogens: PD.Boolean(false),
+        ignoreLight: PD.Boolean(false),
         material: Material.getParam(),
         clip: PD.Group(Clip.Params),
     };
@@ -68,10 +77,10 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
 
     private getReprParams(reprParams: PD.Values<PD.Params>) {
         return {
-            ...this.params.targetParams,
+            ...reprParams,
             type: {
                 name: reprParams.type.name,
-                params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material, clip: this.params.clip }
+                params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip }
             }
         };
     }
@@ -114,7 +123,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
         if (components.indexOf('interactions') >= 0 && !refs[StructureFocusRepresentationTags.SurrNciRepr] && cell.obj && InteractionsRepresentationProvider.isApplicable(cell.obj?.data)) {
             refs[StructureFocusRepresentationTags.SurrNciRepr] = builder
                 .to(refs[StructureFocusRepresentationTags.SurrSel]!)
-                .apply(StateTransforms.Representation.StructureRepresentation3D, this.params.nciParams, { tags: StructureFocusRepresentationTags.SurrNciRepr }).ref;
+                .apply(StateTransforms.Representation.StructureRepresentation3D, this.getReprParams(this.params.nciParams), { tags: StructureFocusRepresentationTags.SurrNciRepr }).ref;
         }
 
         return { state, builder, refs };
@@ -216,7 +225,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
         hasComponent = components.indexOf('interactions') >= 0;
         for (const repr of state.select(all.withTag(StructureFocusRepresentationTags.SurrNciRepr))) {
             if (!hasComponent) builder.delete(repr.transform.ref);
-            else builder.to(repr).update(this.params.nciParams);
+            else builder.to(repr).update(this.getReprParams(this.params.nciParams));
         }
 
         await PluginCommands.State.Update(this.plugin, { state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });

src/mol-plugin/behavior/dynamic/volume-streaming/util.ts

@@ -69,8 +69,16 @@ export async function getContourLevel(provider: 'emdb' | 'pdbe', plugin: PluginC
 export async function getContourLevelEmdb(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
     const emdbHeaderServer = plugin.config.get(PluginConfig.VolumeStreaming.EmdbHeaderServer);
     const header = await plugin.fetch({ url: `${emdbHeaderServer}/${emdbId.toUpperCase()}/header/${emdbId.toLowerCase()}.xml`, type: 'xml' }).runInContext(taskCtx);
-    const map = header.getElementsByTagName('map')[0];
-    const contourLevel = parseFloat(map.getElementsByTagName('contourLevel')[0].textContent!);
+    const contours = header.getElementsByTagName('contour');
+
+    let primaryContour = contours[0];
+    for (let i = 1; i < contours.length; i++) {
+        if (contours[i].getAttribute('primary') === 'true') {
+            primaryContour = contours[i];
+            break;
+        }
+    }
+    const contourLevel = parseFloat(primaryContour.getElementsByTagName('level')[0].textContent!);
 
     return contourLevel;
 }

src/mol-plugin/util/viewport-screenshot.ts

@@ -119,7 +119,7 @@ class ViewportScreenshotHelper extends PluginComponent {
             postprocessing: {
                 ...c.props.postprocessing,
                 occlusion: aoProps.name === 'on'
-                    ? { name: 'on', params: { ...aoProps.params, samples: 128 } }
+                    ? { name: 'on', params: { ...aoProps.params, samples: 128, resolutionScale: 1 } }
                     : aoProps
             },
             marking: { ...c.props.marking }
@@ -143,7 +143,7 @@ class ViewportScreenshotHelper extends PluginComponent {
                 postprocessing: {
                     ...c.props.postprocessing,
                     occlusion: aoProps.name === 'on'
-                        ? { name: 'on', params: { ...aoProps.params, samples: 128 } }
+                        ? { name: 'on', params: { ...aoProps.params, samples: 128, resolutionScale: 1 } }
                         : aoProps
                 },
                 marking: { ...c.props.marking }

src/mol-repr/structure/representation/cartoon.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -35,7 +35,7 @@ export const CartoonParams = {
     ...NucleotideRingParams,
     ...PolymerDirectionParams,
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
-    visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], PD.objectToOptions(CartoonVisuals)),
+    visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-ring'], PD.objectToOptions(CartoonVisuals)),
     bumpFrequency: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
 };
 
@@ -49,7 +49,7 @@ export function getCartoonParams(ctx: ThemeRegistryContext, structure: Structure
         if (!hasGaps && u.gapElements.length) hasGaps = true;
     });
     params.visuals.defaultValue = ['polymer-trace'];
-    if (hasNucleotides) params.visuals.defaultValue.push('nucleotide-block');
+    if (hasNucleotides) params.visuals.defaultValue.push('nucleotide-ring');
     if (hasGaps) params.visuals.defaultValue.push('polymer-gap');
     return params;
 }

src/mol-repr/structure/representation/line.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -31,7 +31,7 @@ export const LineParams = {
     ...ElementCrossParams,
     multipleBonds: PD.Select('offset', PD.arrayToOptions(['off', 'symmetric', 'offset'] as const)),
     includeParent: PD.Boolean(false),
-    sizeFactor: PD.Numeric(3, { min: 0.01, max: 10, step: 0.01 }),
+    sizeFactor: PD.Numeric(2, { min: 0.01, max: 10, step: 0.01 }),
     unitKinds: getUnitKindsParam(['atomic']),
     visuals: PD.MultiSelect(['intra-bond', 'inter-bond', 'element-point', 'element-cross'], PD.objectToOptions(LineVisuals))
 };

src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -79,12 +79,16 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
     };
 
     const { elementRingIndices, elementAromaticRingIndices } = unit.rings;
+    const deloTriplets = aromaticBonds ? unit.resonance.delocalizedTriplets : undefined;
 
     return {
         linkCount: edgeCount * 2,
         referencePosition: (edgeIndex: number) => {
             let aI = a[edgeIndex], bI = b[edgeIndex];
 
+            const rI = deloTriplets?.getThirdElement(aI, bI);
+            if (rI !== undefined) return pos(elements[rI], vRef);
+
             if (aI > bI) [aI, bI] = [bI, aI];
             if (offset[aI + 1] - offset[aI] === 1) [aI, bI] = [bI, aI];
 
@@ -145,8 +149,10 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
                 if (isBondType(f, BondType.Flag.Aromatic) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
                         return LinkStyle.MirroredAromatic;
-                    } else {
+                    } else if (arCount === 1 || deloTriplets?.getThirdElement(aI, bI)) {
                         return LinkStyle.Aromatic;
+                    } else {
+                        // case for bonds between two aromatic rings
                     }
                 }
             }

src/mol-repr/structure/visual/bond-intra-unit-line.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -52,12 +52,16 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
     const pos = unit.conformation.invariantPosition;
 
     const { elementRingIndices, elementAromaticRingIndices } = unit.rings;
+    const deloTriplets = aromaticBonds ? unit.resonance.delocalizedTriplets : undefined;
 
     const builderProps: LinkBuilderProps = {
         linkCount: edgeCount * 2,
         referencePosition: (edgeIndex: number) => {
             let aI = a[edgeIndex], bI = b[edgeIndex];
 
+            const rI = deloTriplets?.getThirdElement(aI, bI);
+            if (rI !== undefined) return pos(elements[rI], vRef);
+
             if (aI > bI) [aI, bI] = [bI, aI];
             if (offset[aI + 1] - offset[aI] === 1) [aI, bI] = [bI, aI];
 
@@ -106,8 +110,10 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
                 if (isBondType(f, BondType.Flag.Aromatic) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
                         return LinkStyle.MirroredAromatic;
-                    } else {
+                    } else if (arCount === 1 || deloTriplets?.getThirdElement(aI, bI)) {
                         return LinkStyle.Aromatic;
+                    } else {
+                        // case for bonds between two aromatic rings
                     }
                 }
             }

src/mol-repr/structure/visual/util/bond.ts

@@ -264,4 +264,4 @@ export function eachInterBond(loci: Loci, structure: Structure, apply: (interval
         __unitMap.clear();
     }
     return changed;
-}
+}

src/mol-repr/structure/visual/util/element.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -22,9 +22,6 @@ import { SpheresBuilder } from '../../../../mol-geo/geometry/spheres/spheres-bui
 import { isTrace, isH, StructureGroup } from './common';
 import { Sphere3D } from '../../../../mol-math/geometry';
 
-// avoiding namespace lookup improved performance in Chrome (Aug 2020)
-const v3add = Vec3.add;
-
 type ElementProps = {
     ignoreHydrogens: boolean,
     traceOnly: boolean,
@@ -73,17 +70,13 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
     const ignore = makeElementIgnoreTest(structure, unit, props);
     const l = StructureElement.Location.create(structure, unit);
     const themeSize = theme.size.size;
-    const center = Vec3();
     let maxSize = 0;
-    let count = 0;
 
     for (let i = 0; i < elementCount; i++) {
         if (ignore && ignore(elements[i])) continue;
 
         l.element = elements[i];
         pos(elements[i], v);
-        v3add(center, center, v);
-        count += 1;
 
         builderState.currentGroup = i;
         const size = themeSize(l);
@@ -92,17 +85,8 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
         addSphere(builderState, v, size * sizeFactor, detail);
     }
 
-    // re-use boundingSphere if it has not changed much
-    let boundingSphere: Sphere3D;
-    Vec3.scale(center, center, 1 / count);
-    if (mesh && Vec3.distance(center, mesh.boundingSphere.center) / mesh.boundingSphere.radius < 1.0) {
-        boundingSphere = Sphere3D.clone(mesh.boundingSphere);
-    } else {
-        boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * sizeFactor + 0.05);
-    }
-
     const m = MeshBuilder.getMesh(builderState);
-    m.setBoundingSphere(boundingSphere);
+    m.setBoundingSphere(Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * sizeFactor + 0.05));
 
     return m;
 }
@@ -126,34 +110,21 @@ export function createElementSphereImpostor(ctx: VisualContext, unit: Unit, stru
 
     const l = StructureElement.Location.create(structure, unit);
     const themeSize = theme.size.size;
-    const center = Vec3();
     let maxSize = 0;
-    let count = 0;
 
     for (let i = 0; i < elementCount; i++) {
         if (ignore?.(elements[i])) continue;
 
         pos(elements[i], v);
         builder.add(v[0], v[1], v[2], i);
-        v3add(center, center, v);
-        count += 1;
 
         l.element = elements[i];
         const size = themeSize(l);
         if (size > maxSize) maxSize = size;
     }
 
-    // re-use boundingSphere if it has not changed much
-    let boundingSphere: Sphere3D;
-    Vec3.scale(center, center, 1 / count);
-    if (spheres && Vec3.distance(center, spheres.boundingSphere.center) / spheres.boundingSphere.radius < 1.0) {
-        boundingSphere = Sphere3D.clone(spheres.boundingSphere);
-    } else {
-        boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * props.sizeFactor + 0.05);
-    }
-
     const s = builder.getSpheres();
-    s.setBoundingSphere(boundingSphere);
+    s.setBoundingSphere(Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * props.sizeFactor + 0.05));
 
     return s;
 }

tsconfig.commonjs.json

@@ -5,7 +5,7 @@
         "alwaysStrict": true,
         "noImplicitAny": true,
         "noImplicitThis": true,
-        "sourceMap": true,
+        "sourceMap": false,
         "noUnusedLocals": true,
         "strictNullChecks": true,
         "strictFunctionTypes": true,

tsconfig.json

@@ -5,7 +5,7 @@
         "alwaysStrict": true,
         "noImplicitAny": true,
         "noImplicitThis": true,
-        "sourceMap": true,
+        "sourceMap": false,
         "noUnusedLocals": true,
         "strictNullChecks": true,
         "strictFunctionTypes": true,