molstar 3.0.0-dev.6 → 3.0.0

package/lib/mol-model/structure/structure/util/superposition-db-mapping.js

@@ -4,6 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 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';
 export function alignAndSuperposeWithBestDatabaseMapping(structures) {
@@ -19,6 +20,7 @@ export function alignAndSuperposeWithBestDatabaseMapping(structures) {
         var p = pairs_1[_i];
         var _a = getPositionTables(index, p.i, p.j, p.count), a = _a[0], b = _a[1];
         var transform = MinimizeRmsd.compute({ a: a, b: b });
+        console.log(Mat4.makeTable(transform.bTransform), transform.rmsd);
         ret.push({ transform: transform, pivot: p.i, other: p.j });
     }
     return ret;
@@ -34,6 +36,8 @@ function getPositionTables(index, pivot, other, N) {
         if (!a || !b)
             continue;
         var 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 (var i = 0; i < l; i++) {
             var eI = (a[1] + i);
             xs.x[o] = a[0].conformation.x(eI);
@@ -93,7 +97,6 @@ function buildIndex(structure, index, sI) {
         if (unit.kind !== 0 /* Atomic */)
             continue;
         var elements = unit.elements, model = unit.model;
-        var residueOffset = model.atomicHierarchy.residueAtomSegments.offsets;
         var map = BestDatabaseSequenceMapping.Provider.get(model).value;
         if (!map)
             return;
@@ -105,22 +108,24 @@ function buildIndex(structure, index, sI) {
             residuesIt.setSegment(chainSegment);
             while (residuesIt.hasNext) {
                 var residueSegment = residuesIt.move();
-                var eI = elements[residueSegment.start];
-                var rI = residueOffset[eI];
+                var rI = residueSegment.index;
                 if (!dbName[rI])
                     continue;
+                var start = elements[residueSegment.start];
+                var end = elements[residueSegment.end - 1] + 1;
                 var key = "".concat(dbName[rI], "-").concat(accession[rI], "-").concat(num[rI]);
                 if (!index.has(key)) {
-                    index.set(key, { key: key, pivots: (_a = {}, _a[sI] = [unit, eI, elements[residueSegment.end]], _a) });
+                    index.set(key, { key: key, pivots: (_a = {}, _a[sI] = [unit, start, end], _a) });
                 }
                 else {
                     var entry = index.get(key);
                     if (!entry.pivots[sI]) {
-                        entry.pivots[sI] = [unit, eI, elements[residueSegment.end]];
+                        entry.pivots[sI] = [unit, start, end];
                     }
                 }
             }
         }
     }
+    console.log(index);
 }
 //# sourceMappingURL=superposition-db-mapping.js.map

package/lib/mol-model-formats/shape/ply.d.ts

@@ -39,6 +39,16 @@ export declare const PlyShapeParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type PlyShapeParams = typeof PlyShapeParams;
 export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapeProvider<PlyFile, Mesh, {
@@ -70,4 +80,14 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }>>;

package/lib/mol-model-formats/structure/basic/atomic.d.ts

@@ -5,13 +5,13 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Column } from '../../../mol-data/db';
+import { SymmetryOperator } from '../../../mol-math/geometry';
 import { ChainIndex } from '../../../mol-model/structure';
 import { Model } from '../../../mol-model/structure/model/model';
 import { AtomicConformation, AtomicHierarchy } from '../../../mol-model/structure/model/properties/atomic';
 import { Entities } from '../../../mol-model/structure/model/properties/common';
-import { AtomSite } from './schema';
 import { ModelFormat } from '../../format';
-import { SymmetryOperator } from '../../../mol-math/geometry';
+import { AtomSite } from './schema';
 export declare function getAtomicHierarchyAndConformation(atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, chemicalComponentMap: Model['properties']['chemicalComponentMap'], format: ModelFormat, previous?: Model): {
     sameAsPrevious: boolean;
     hierarchy: AtomicHierarchy;

package/lib/mol-model-formats/structure/basic/atomic.js

@@ -7,16 +7,16 @@
 import { __assign } from "tslib";
 import { Column, Table } from '../../../mol-data/db';
 import { Interval, Segmentation } from '../../../mol-data/int';
-import { UUID } from '../../../mol-util/uuid';
+import { toDatabase } from '../../../mol-io/reader/cif/schema';
+import { SymmetryOperator } from '../../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
 import { AtomsSchema, ChainsSchema, ResiduesSchema } from '../../../mol-model/structure/model/properties/atomic';
+import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
 import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
 import { ElementSymbol } from '../../../mol-model/structure/model/types';
-import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
-import { SymmetryOperator } from '../../../mol-math/geometry';
+import { UUID } from '../../../mol-util/uuid';
 import { MmcifFormat } from '../mmcif';
-import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
-import { toDatabase } from '../../../mol-io/reader/cif/schema';
-import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
 function findHierarchyOffsets(atom_site) {
     if (atom_site._rowCount === 0)
         return { residues: [], chains: [] };

package/lib/mol-model-formats/structure/basic/coarse.d.ts

@@ -23,7 +23,7 @@ export declare const EmptyCoarse: {
     hierarchy: CoarseHierarchy;
     conformation: any;
 };
-export declare function getCoarse(data: CoarseData, properties: Model['properties']): {
+export declare function getCoarse(data: CoarseData, chemicalComponentMap: Model['properties']['chemicalComponentMap']): {
     hierarchy: CoarseHierarchy;
     conformation: CoarseConformation;
 };

package/lib/mol-model-formats/structure/basic/coarse.js

@@ -13,18 +13,18 @@ import { Mat3, Tensor } from '../../../mol-math/linear-algebra';
 import { getCoarseRanges } from '../../../mol-model/structure/model/properties/utils/coarse-ranges';
 import { BasicSchema } from './schema';
 export var EmptyCoarse = { hierarchy: CoarseHierarchy.Empty, conformation: void 0 };
-export function getCoarse(data, properties) {
+export function getCoarse(data, chemicalComponentMap) {
     var ihm_sphere_obj_site = data.ihm_sphere_obj_site, ihm_gaussian_obj_site = data.ihm_gaussian_obj_site;
     if (ihm_sphere_obj_site._rowCount === 0 && ihm_gaussian_obj_site._rowCount === 0)
         return EmptyCoarse;
     var sphereData = getData(ihm_sphere_obj_site);
     var sphereConformation = getSphereConformation(ihm_sphere_obj_site);
     var sphereKeys = getCoarseKeys(sphereData, data.entities);
-    var sphereRanges = getCoarseRanges(sphereData, properties.chemicalComponentMap);
+    var sphereRanges = getCoarseRanges(sphereData, chemicalComponentMap);
     var gaussianData = getData(ihm_gaussian_obj_site);
     var gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
     var gaussianKeys = getCoarseKeys(gaussianData, data.entities);
-    var gaussianRanges = getCoarseRanges(gaussianData, properties.chemicalComponentMap);
+    var gaussianRanges = getCoarseRanges(gaussianData, chemicalComponentMap);
     return {
         hierarchy: {
             isDefined: true,

package/lib/mol-model-formats/structure/basic/entities.d.ts

@@ -7,4 +7,5 @@
 import { Entities } from '../../../mol-model/structure/model/properties/common';
 import { Model } from '../../../mol-model/structure/model';
 import { BasicData } from './schema';
-export declare function getEntities(data: BasicData, properties: Model['properties']): Entities;
+export declare function getEntityData(data: BasicData): Entities;
+export declare function getEntitiesWithPRD(data: BasicData, entities: Entities, structAsymMap: Model['properties']['structAsymMap']): Entities;

package/lib/mol-model-formats/structure/basic/entities.js

@@ -4,18 +4,18 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
+import { __assign } from "tslib";
 import { Column, Table } from '../../../mol-data/db';
 import { EntitySubtype } from '../../../mol-model/structure/model/properties/common';
 import { getEntityType, getEntitySubtype } from '../../../mol-model/structure/model/types';
 import { BasicSchema } from './schema';
-export function getEntities(data, properties) {
-    var _a;
+export function getEntityData(data) {
     var entityData;
     if (!data.entity.id.isDefined) {
         var entityIds_1 = new Set();
         var ids = [];
         var types = [];
-        var _b = data.atom_site, label_entity_id = _b.label_entity_id, label_comp_id = _b.label_comp_id;
+        var _a = data.atom_site, label_entity_id = _a.label_entity_id, label_comp_id = _a.label_comp_id;
         for (var i = 0, il = data.atom_site._rowCount; i < il; i++) {
             var entityId = label_entity_id.value(i);
             if (!entityIds_1.has(entityId)) {
@@ -57,7 +57,7 @@ export function getEntities(data, properties) {
     var entityIds = new Set();
     var assignSubtype = false;
     if (data.entity_poly && data.entity_poly.type.isDefined) {
-        var _c = data.entity_poly, entity_id = _c.entity_id, type = _c.type, _rowCount = _c._rowCount;
+        var _b = data.entity_poly, entity_id = _b.entity_id, type = _b.type, _rowCount = _b._rowCount;
         for (var i = 0; i < _rowCount; ++i) {
             var entityId = entity_id.value(i);
             subtypes[getEntityIndex(entityId)] = type.value(i);
@@ -68,7 +68,7 @@ export function getEntities(data, properties) {
         assignSubtype = true;
     }
     if (data.pdbx_entity_branch && data.pdbx_entity_branch.entity_id.isDefined) {
-        var _d = data.pdbx_entity_branch, entity_id = _d.entity_id, type = _d.type, _rowCount = _d._rowCount;
+        var _c = data.pdbx_entity_branch, entity_id = _c.entity_id, type = _c.type, _rowCount = _c._rowCount;
         for (var i = 0; i < _rowCount; ++i) {
             var entityId = entity_id.value(i);
             subtypes[getEntityIndex(entityId)] = type.value(i);
@@ -85,13 +85,13 @@ export function getEntities(data, properties) {
     if (assignSubtype) {
         var chemCompType = new Map();
         if (data.chem_comp) {
-            var _e = data.chem_comp, id = _e.id, type = _e.type;
+            var _d = data.chem_comp, id = _d.id, type = _d.type;
             for (var i = 0, il = data.chem_comp._rowCount; i < il; i++) {
                 chemCompType.set(id.value(i), type.value(i));
             }
         }
         if (data.atom_site) {
-            var _f = data.atom_site, label_entity_id = _f.label_entity_id, label_comp_id = _f.label_comp_id;
+            var _e = data.atom_site, label_entity_id = _e.label_entity_id, label_comp_id = _e.label_comp_id;
             for (var i = 0, il = data.atom_site._rowCount; i < il; i++) {
                 var entityId = label_entity_id.value(i);
                 if (!entityIds.has(entityId)) {
@@ -105,25 +105,28 @@ export function getEntities(data, properties) {
         // TODO how to handle coarse?
     }
     var subtypeColumn = Column.ofArray({ array: subtypes, schema: EntitySubtype });
-    //
-    var prdIds = new Array(entityData._rowCount);
-    prdIds.fill('');
-    if (data.pdbx_molecule && data.pdbx_molecule.prd_id.isDefined) {
-        var _g = data.pdbx_molecule, asym_id = _g.asym_id, prd_id = _g.prd_id, _rowCount = _g._rowCount;
-        for (var i = 0; i < _rowCount; ++i) {
-            var asymId = asym_id.value(i);
-            var entityId = (_a = properties.structAsymMap.get(asymId)) === null || _a === void 0 ? void 0 : _a.entity_id;
-            if (entityId !== undefined) {
-                prdIds[getEntityIndex(entityId)] = prd_id.value(i);
-            }
-        }
-    }
-    var prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
     return {
         data: entityData,
         subtype: subtypeColumn,
-        prd_id: prdIdColumn,
         getEntityIndex: getEntityIndex
     };
 }
+export function getEntitiesWithPRD(data, entities, structAsymMap) {
+    var _a;
+    if (!data.pdbx_molecule || !data.pdbx_molecule.prd_id.isDefined) {
+        return entities;
+    }
+    var prdIds = new Array(entities.data._rowCount);
+    prdIds.fill('');
+    var _b = data.pdbx_molecule, asym_id = _b.asym_id, prd_id = _b.prd_id, _rowCount = _b._rowCount;
+    for (var i = 0; i < _rowCount; ++i) {
+        var asymId = asym_id.value(i);
+        var entityId = (_a = structAsymMap.get(asymId)) === null || _a === void 0 ? void 0 : _a.entity_id;
+        if (entityId !== undefined) {
+            prdIds[entities.getEntityIndex(entityId)] = prd_id.value(i);
+        }
+    }
+    var prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
+    return __assign(__assign({}, entities), { prd_id: prdIdColumn });
+}
 //# sourceMappingURL=entities.js.map

package/lib/mol-model-formats/structure/basic/parser.js

@@ -14,8 +14,8 @@ import { getCoarse, EmptyCoarse } from './coarse';
 import { getSequence } from './sequence';
 import { sortAtomSite } from './sort';
 import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
-import { getProperties } from './properties';
-import { getEntities } from './entities';
+import { getChemicalComponentMap, getMissingResidues, getSaccharideComponentMap, getStructAsymMap } from './properties';
+import { getEntitiesWithPRD, getEntityData } from './entities';
 import { getModelGroupName } from './util';
 import { ArrayTrajectory } from '../../../mol-model/structure/trajectory';
 export function createModels(data, format, ctx) {
@@ -24,7 +24,7 @@ export function createModels(data, format, ctx) {
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
-                    properties = getProperties(data);
+                    properties = getCommonProperties(data, format);
                     if (!(data.ihm_model_list._rowCount > 0)) return [3 /*break*/, 2];
                     return [4 /*yield*/, readIntegrative(ctx, data, properties, format)];
                 case 1:
@@ -44,6 +44,13 @@ export function createModels(data, format, ctx) {
         });
     });
 }
+function getCommonProperties(data, format) {
+    return {
+        missingResidues: getMissingResidues(data),
+        chemicalComponentMap: getChemicalComponentMap(data),
+        saccharideComponentMap: getSaccharideComponentMap(data)
+    };
+}
 /** Standard atomic model */
 function createStandardModel(data, atom_site, sourceIndex, entities, properties, format, previous) {
     var atomic = getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, properties.chemicalComponentMap, format, previous);
@@ -54,6 +61,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
     var coarse = EmptyCoarse;
     var sequence = getSequence(data, entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence);
+    var structAsymMap = getStructAsymMap(atomic.hierarchy);
     var entry = data.entry.id.valueKind(0) === 0 /* Present */
         ? data.entry.id.value(0) : format.name;
     var label = [];
@@ -69,7 +77,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
         sourceData: format,
         modelNum: modelNum,
         parent: undefined,
-        entities: entities,
+        entities: getEntitiesWithPRD(data, entities, structAsymMap),
         sequence: sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
@@ -77,7 +85,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: properties,
+        properties: __assign(__assign({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -86,7 +94,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
 /** Integrative model with atomic/coarse parts */
 function createIntegrativeModel(data, ihm, properties, format) {
     var atomic = getAtomicHierarchyAndConformation(ihm.atom_site, ihm.atom_site_sourceIndex, ihm.entities, properties.chemicalComponentMap, format);
-    var coarse = getCoarse(ihm, properties);
+    var coarse = getCoarse(ihm, properties.chemicalComponentMap);
     var sequence = getSequence(data, ihm.entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = getAtomicRanges(atomic.hierarchy, ihm.entities, atomic.conformation, sequence);
     var entry = data.entry.id.valueKind(0) === 0 /* Present */
@@ -100,6 +108,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         label.push(ihm.model_name);
     if (ihm.model_group_name)
         label.push(ihm.model_group_name);
+    var structAsymMap = getStructAsymMap(atomic.hierarchy, data);
     return {
         id: UUID.create22(),
         entryId: entry,
@@ -108,7 +117,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         sourceData: format,
         modelNum: ihm.model_id,
         parent: undefined,
-        entities: ihm.entities,
+        entities: getEntitiesWithPRD(data, ihm.entities, structAsymMap),
         sequence: sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
@@ -116,7 +125,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: properties,
+        properties: __assign(__assign({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -140,7 +149,7 @@ function readStandard(ctx, data, properties, format) {
                     models = [];
                     if (!data.atom_site) return [3 /*break*/, 3];
                     atomCount = data.atom_site.id.rowCount;
-                    entities = getEntities(data, properties);
+                    entities = getEntityData(data);
                     modelStart = 0;
                     _b.label = 1;
                 case 1:
@@ -180,7 +189,7 @@ function readIntegrative(ctx, data, properties, format) {
         return __generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
-                    entities = getEntities(data, properties);
+                    entities = getEntityData(data);
                     atom_sites_modelColumn = data.atom_site.ihm_model_id.isDefined
                         ? data.atom_site.ihm_model_id : data.atom_site.pdbx_PDB_model_num;
                     atom_sites = splitTable(data.atom_site, atom_sites_modelColumn);

package/lib/mol-model-formats/structure/basic/properties.d.ts

@@ -5,5 +5,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Model } from '../../../mol-model/structure/model/model';
+import { AtomicHierarchy } from '../../../mol-model/structure/model/properties/atomic';
+import { SaccharideComponentMap } from '../../../mol-model/structure/structure/carbohydrates/constants';
 import { BasicData } from './schema';
-export declare function getProperties(data: BasicData): Model['properties'];
+export declare function getMissingResidues(data: BasicData): Model['properties']['missingResidues'];
+export declare function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'];
+export declare function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap;
+export declare function getStructAsymMap(atomic: AtomicHierarchy, data?: BasicData): Model['properties']['structAsymMap'];

package/lib/mol-model-formats/structure/basic/properties.js

@@ -4,11 +4,11 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-import { getMoleculeType, getDefaultChemicalComponent } from '../../../mol-model/structure/model/types';
-import { SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
-import { memoize1 } from '../../../mol-util/memoize';
 import { Table } from '../../../mol-data/db';
-function getMissingResidues(data) {
+import { getDefaultChemicalComponent, getMoleculeType } from '../../../mol-model/structure/model/types';
+import { SaccharideCompIdMap, SaccharidesSnfgMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
+import { memoize1 } from '../../../mol-util/memoize';
+export function getMissingResidues(data) {
     var map = new Map();
     var getKey = function (model_num, asym_id, seq_id) {
         return "".concat(model_num, "|").concat(asym_id, "|").concat(seq_id);
@@ -28,7 +28,7 @@ function getMissingResidues(data) {
         size: map.size
     };
 }
-function getChemicalComponentMap(data) {
+export function getChemicalComponentMap(data) {
     var map = new Map();
     if (data.chem_comp._rowCount > 0) {
         var id = data.chem_comp.id;
@@ -44,7 +44,7 @@ function getChemicalComponentMap(data) {
     }
     return map;
 }
-function getSaccharideComponentMap(data) {
+export function getSaccharideComponentMap(data) {
     var map = new Map();
     if (data.pdbx_chem_comp_identifier._rowCount > 0) {
         // note that `pdbx_chem_comp_identifier` does not contain
@@ -99,20 +99,15 @@ var getUniqueComponentNames = memoize1(function (data) {
     }
     return uniqueNames;
 });
-function getStructAsymMap(data) {
+export function getStructAsymMap(atomic, data) {
     var map = new Map();
-    var _a = data.atom_site, label_asym_id = _a.label_asym_id, auth_asym_id = _a.auth_asym_id, label_entity_id = _a.label_entity_id;
-    for (var i = 0, il = label_asym_id.rowCount; i < il; ++i) {
+    var _a = atomic.chains, auth_asym_id = _a.auth_asym_id, label_asym_id = _a.label_asym_id, label_entity_id = _a.label_entity_id;
+    for (var i = 0, _i = atomic.chains._rowCount; i < _i; i++) {
         var id = label_asym_id.value(i);
-        if (!map.has(id)) {
-            map.set(id, {
-                id: id,
-                auth_id: auth_asym_id.value(i),
-                entity_id: label_entity_id.value(i)
-            });
-        }
+        map.set(id, { id: id, auth_id: auth_asym_id.value(i), entity_id: label_entity_id.value(i) });
     }
-    if (data.struct_asym._rowCount > 0) {
+    // to get asym mapping for coarse/ihm data
+    if (data === null || data === void 0 ? void 0 : data.struct_asym._rowCount) {
         var _b = data.struct_asym, id = _b.id, entity_id = _b.entity_id;
         for (var i = 0, il = id.rowCount; i < il; ++i) {
             var _id = id.value(i);
@@ -127,12 +122,4 @@ function getStructAsymMap(data) {
     }
     return map;
 }
-export function getProperties(data) {
-    return {
-        missingResidues: getMissingResidues(data),
-        chemicalComponentMap: getChemicalComponentMap(data),
-        saccharideComponentMap: getSaccharideComponentMap(data),
-        structAsymMap: getStructAsymMap(data)
-    };
-}
 //# sourceMappingURL=properties.js.map

package/lib/mol-model-formats/structure/mol.d.ts

@@ -1,8 +1,9 @@
 /**
- * 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { MolFile } from '../../mol-io/reader/mol/parser';
 import { RuntimeContext, Task } from '../../mol-task';

package/lib/mol-model-formats/structure/mol.js

@@ -1,11 +1,13 @@
 /**
- * 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { __awaiter, __generator } from "tslib";
 import { Column, Table } from '../../mol-data/db';
+import { formalChargeMapper } from '../../mol-io/reader/mol/parser';
 import { Task } from '../../mol-task';
 import { createModels } from './basic/parser';
 import { BasicSchema, createBasic } from './basic/schema';
@@ -14,15 +16,26 @@ import { EntityBuilder } from './common/entity';
 import { IndexPairBonds } from './property/bonds/index-pair';
 export function getMolModels(mol, format, ctx) {
     return __awaiter(this, void 0, void 0, function () {
-        var atoms, bonds, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
+        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    atoms = mol.atoms, bonds = mol.bonds;
+                    atoms = mol.atoms, bonds = mol.bonds, formalCharges = mol.formalCharges;
                     MOL = Column.ofConst('MOL', mol.atoms.count, Column.Schema.str);
                     A = Column.ofConst('A', mol.atoms.count, Column.Schema.str);
                     type_symbol = Column.asArrayColumn(atoms.type_symbol);
                     seq_id = Column.ofConst(1, atoms.count, Column.Schema.int);
+                    computedFormalCharges = new Int32Array(mol.atoms.count);
+                    if (formalCharges.atomIdx.rowCount > 0) {
+                        for (i = 0; i < formalCharges.atomIdx.rowCount; i++) {
+                            computedFormalCharges[formalCharges.atomIdx.value(i) - 1] = formalCharges.charge.value(i);
+                        }
+                    }
+                    else {
+                        for (i = 0; i < mol.atoms.count; i++) {
+                            computedFormalCharges[i] = formalChargeMapper(atoms.formal_charge.value(i));
+                        }
+                    }
                     atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
                         auth_asym_id: A,
                         auth_atom_id: type_symbol,
@@ -40,6 +53,7 @@ export function getMolModels(mol, format, ctx) {
                         occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
                         type_symbol: type_symbol,
                         pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
+                        pdbx_formal_charge: Column.ofIntArray(computedFormalCharges)
                     }, atoms.count);
                     entityBuilder = new EntityBuilder();
                     entityBuilder.setNames([['MOL', 'Unknown Entity']]);

package/lib/mol-model-formats/structure/mol2.d.ts

@@ -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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-model-formats/structure/mol2.js

@@ -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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,9 +14,12 @@ import { IndexPairBonds } from './property/bonds/index-pair';
 import { AtomPartialCharge } from './property/partial-charge';
 import { ArrayTrajectory } from '../../mol-model/structure';
 import { guessElementSymbolString } from './util';
+import { ModelSymmetry } from './property/symmetry';
+import { Spacegroup, SpacegroupCell } from '../../mol-math/geometry';
+import { Vec3 } from '../../mol-math/linear-algebra';
 function getModels(mol2, ctx) {
     return __awaiter(this, void 0, void 0, function () {
-        var models, i, il, _a, atoms, bonds, molecule, A, type_symbol, i_1, atom_site, entityBuilder, componentBuilder, i_2, il_1, basics, _models, indexA, indexB, order, flag, pairBonds, first;
+        var models, i, il, _a, molecule, atoms, bonds, crysin, A, type_symbol, hasAtomType, i_1, i_2, atom_site, entityBuilder, componentBuilder, i_3, il_1, basics, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
@@ -25,11 +28,20 @@ function getModels(mol2, ctx) {
                     _b.label = 1;
                 case 1:
                     if (!(i < il)) return [3 /*break*/, 4];
-                    _a = mol2.structures[i], atoms = _a.atoms, bonds = _a.bonds, molecule = _a.molecule;
+                    _a = mol2.structures[i], molecule = _a.molecule, atoms = _a.atoms, bonds = _a.bonds, crysin = _a.crysin;
                     A = Column.ofConst('A', atoms.count, Column.Schema.str);
                     type_symbol = new Array(atoms.count);
+                    hasAtomType = false;
                     for (i_1 = 0; i_1 < atoms.count; ++i_1) {
-                        type_symbol[i_1] = guessElementSymbolString(atoms.atom_name.value(i_1));
+                        if (atoms.atom_type.value(i_1).includes('.')) {
+                            hasAtomType = true;
+                            break;
+                        }
+                    }
+                    for (i_2 = 0; i_2 < atoms.count; ++i_2) {
+                        type_symbol[i_2] = hasAtomType
+                            ? atoms.atom_type.value(i_2).split('.')[0].toUpperCase()
+                            : guessElementSymbolString(atoms.atom_name.value(i_2));
                     }
                     atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
                         auth_asym_id: A,
@@ -53,8 +65,8 @@ function getModels(mol2, ctx) {
                     entityBuilder.setNames([['MOL', molecule.mol_name || 'Unknown Entity']]);
                     entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
                     componentBuilder = new ComponentBuilder(atoms.subst_id, atoms.atom_name);
-                    for (i_2 = 0, il_1 = atoms.subst_name.rowCount; i_2 < il_1; ++i_2) {
-                        componentBuilder.add(atoms.subst_name.value(i_2), i_2);
+                    for (i_3 = 0, il_1 = atoms.subst_name.rowCount; i_3 < il_1; ++i_3) {
+                        componentBuilder.add(atoms.subst_name.value(i_3), i_3);
                     }
                     basics = createBasic({
                         entity: entityBuilder.getEntityTable(),
@@ -67,6 +79,7 @@ function getModels(mol2, ctx) {
                     if (_models.frameCount > 0) {
                         indexA = Column.ofIntArray(Column.mapToArray(bonds.origin_atom_id, function (x) { return x - 1; }, Int32Array));
                         indexB = Column.ofIntArray(Column.mapToArray(bonds.target_atom_id, function (x) { return x - 1; }, Int32Array));
+                        key = bonds.bond_id;
                         order = Column.ofIntArray(Column.mapToArray(bonds.bond_type, function (x) {
                             switch (x) {
                                 case 'ar': // aromatic
@@ -93,13 +106,18 @@ function getModels(mol2, ctx) {
                                     return 1 /* Covalent */;
                             }
                         }, Int8Array));
-                        pairBonds = IndexPairBonds.fromData({ pairs: { indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count });
+                        pairBonds = IndexPairBonds.fromData({ pairs: { key: key, indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count });
                         first = _models.representative;
                         IndexPairBonds.Provider.set(first, pairBonds);
                         AtomPartialCharge.Provider.set(first, {
                             data: atoms.charge,
                             type: molecule.charge_type
                         });
+                        if (crysin) {
+                            symmetry = getSymmetry(crysin);
+                            if (symmetry)
+                                ModelSymmetry.Provider.set(first, symmetry);
+                        }
                         models.push(first);
                     }
                     _b.label = 3;
@@ -111,6 +129,18 @@ function getModels(mol2, ctx) {
         });
     });
 }
+function getSymmetry(crysin) {
+    // TODO handle `crysin.setting`
+    if (crysin.setting !== 1)
+        return;
+    var spaceCell = SpacegroupCell.create(crysin.spaceGroup, Vec3.create(crysin.a, crysin.b, crysin.c), Vec3.scale(Vec3(), Vec3.create(crysin.alpha, crysin.beta, crysin.gamma), Math.PI / 180));
+    return {
+        spacegroup: Spacegroup.create(spaceCell),
+        assemblies: [],
+        isNonStandardCrystalFrame: false,
+        ncsOperators: []
+    };
+}
 //
 export { Mol2Format };
 var Mol2Format;