molstar 3.0.0-dev.6 → 3.0.0

package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.js

@@ -1,12 +1,12 @@
 "use strict";
 /**
- * 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isHydrogen = exports.getElementThreshold = exports.getElementPairThreshold = exports.getElementIdx = exports.MetalsSet = exports.DefaultBondComputationProps = exports.DefaultBondMaxRadius = void 0;
+exports.isHydrogen = exports.getPairingThreshold = exports.getElementThreshold = exports.getElementPairThreshold = exports.getElementIdx = exports.MetalsSet = exports.DefaultBondComputationProps = exports.DefaultBondMaxRadius = void 0;
 /** Default for atomic bonds */
 exports.DefaultBondMaxRadius = 4;
 exports.DefaultBondComputationProps = {
@@ -105,6 +105,15 @@ function getElementThreshold(i) {
     return r;
 }
 exports.getElementThreshold = getElementThreshold;
+function getPairingThreshold(elementIndexA, elementIndexB, thresholdA, thresholdB) {
+    var thresholdAB = getElementPairThreshold(elementIndexA, elementIndexB);
+    return thresholdAB > 0
+        ? thresholdAB
+        : elementIndexB < 0
+            ? thresholdA
+            : (thresholdA + thresholdB) / 1.95; // not sure if avg or min but max is too big
+}
+exports.getPairingThreshold = getPairingThreshold;
 var H_ID = __ElementIndex['H'];
 function isHydrogen(i) {
     return i === H_ID;

package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.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>

package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -70,11 +70,26 @@ function findPairBonds(unitA, unitB, props, builder) {
                 var _bI = int_1.SortedArray.indexOf(unitB.elements, bI);
                 if (_bI < 0)
                     continue;
-                if (type_symbolA.value(aI) === 'H' && type_symbolB.value(bI) === 'H')
-                    continue;
+                var aeI_1 = (0, common_1.getElementIdx)(type_symbolA.value(aI));
+                var beI = (0, common_1.getElementIdx)(type_symbolA.value(bI));
                 var d = distance[i];
                 var dist = getDistance(unitA, aI, unitB, bI);
-                if ((d !== -1 && (0, common_2.equalEps)(dist, d, 0.5)) || dist < maxDistance) {
+                var add = false;
+                if (d >= 0) {
+                    add = (0, common_2.equalEps)(dist, d, 0.3);
+                }
+                else if (maxDistance >= 0) {
+                    add = dist < maxDistance;
+                }
+                else {
+                    var pairingThreshold = (0, common_1.getPairingThreshold)(aeI_1, beI, (0, common_1.getElementThreshold)(aeI_1), (0, common_1.getElementThreshold)(beI));
+                    add = dist < pairingThreshold;
+                    if ((0, common_1.isHydrogen)(aeI_1) && (0, common_1.isHydrogen)(beI)) {
+                        // TODO handle molecular hydrogen
+                        add = false;
+                    }
+                }
+                if (add) {
                     builder.add(_aI, _bI, { order: order[i], flag: flag[i] });
                 }
             }
@@ -138,12 +153,7 @@ function findPairBonds(unitA, unitB, props, builder) {
             var dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0)
                 continue;
-            var thresholdAB = (0, common_1.getElementPairThreshold)(aeI, beI);
-            var pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + (0, common_1.getElementThreshold)(beI)) / 1.95; // not sure if avg or min but max is too big
+            var pairingThreshold = (0, common_1.getPairingThreshold)(aeI, beI, thresholdA, (0, common_1.getElementThreshold)(beI));
             if (dist <= pairingThreshold) {
                 var atomIdB = label_atom_idB.value(bI);
                 var compIdB = label_comp_idB.value(residueIndexB[bI]);

package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.d.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>

package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -53,7 +53,8 @@ function findIndexPairBonds(unit) {
     var orders = [];
     for (var _aI = 0; _aI < atomCount; _aI++) {
         var aI = atoms[_aI];
-        var isHa = type_symbol.value(aI) === 'H';
+        var aeI = (0, common_1.getElementIdx)(type_symbol.value(aI));
+        var isHa = (0, common_1.isHydrogen)(aeI);
         var srcA = sourceIndex.value(aI);
         for (var i = offset[srcA], il = offset[srcA + 1]; i < il; ++i) {
             var bI = invertedIndex[b[i]];
@@ -62,11 +63,25 @@ function findIndexPairBonds(unit) {
             var _bI = int_1.SortedArray.indexOf(unit.elements, bI);
             if (_bI < 0)
                 continue;
-            if (isHa && type_symbol.value(bI) === 'H')
-                continue;
+            var beI = (0, common_1.getElementIdx)(type_symbol.value(bI));
             var d = distance[i];
             var dist = getDistance(unit, aI, bI);
-            if ((d !== -1 && (0, common_2.equalEps)(dist, d, 0.5)) || dist < maxDistance) {
+            var add = false;
+            if (d >= 0) {
+                add = (0, common_2.equalEps)(dist, d, 0.3);
+            }
+            else if (maxDistance >= 0) {
+                add = dist < maxDistance;
+            }
+            else {
+                var pairingThreshold = (0, common_1.getPairingThreshold)(aeI, beI, (0, common_1.getElementThreshold)(aeI), (0, common_1.getElementThreshold)(beI));
+                add = dist < pairingThreshold;
+                if (isHa && (0, common_1.isHydrogen)(beI)) {
+                    // TODO handle molecular hydrogen
+                    add = false;
+                }
+            }
+            if (add) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;
                 orders[orders.length] = order[i];
@@ -190,12 +205,7 @@ function findBonds(unit, props) {
             var dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0)
                 continue;
-            var thresholdAB = (0, common_1.getElementPairThreshold)(aeI, beI);
-            var pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + (0, common_1.getElementThreshold)(beI)) / 1.95; // not sure if avg or min but max is too big
+            var pairingThreshold = (0, common_1.getPairingThreshold)(aeI, beI, thresholdA, (0, common_1.getElementThreshold)(beI));
             if (dist <= pairingThreshold) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;

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

@@ -7,6 +7,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.alignAndSuperposeWithBestDatabaseMapping = void 0;
 var int_1 = require("../../../../mol-data/int");
+var linear_algebra_1 = require("../../../../mol-math/linear-algebra");
 var minimize_rmsd_1 = require("../../../../mol-math/linear-algebra/3d/minimize-rmsd");
 var best_database_mapping_1 = require("../../../../mol-model-props/sequence/best-database-mapping");
 function alignAndSuperposeWithBestDatabaseMapping(structures) {
@@ -22,6 +23,7 @@ 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 = minimize_rmsd_1.MinimizeRmsd.compute({ a: a, b: b });
+        console.log(linear_algebra_1.Mat4.makeTable(transform.bTransform), transform.rmsd);
         ret.push({ transform: transform, pivot: p.i, other: p.j });
     }
     return ret;
@@ -38,6 +40,8 @@ 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);
@@ -97,7 +101,6 @@ 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 = best_database_mapping_1.BestDatabaseSequenceMapping.Provider.get(model).value;
         if (!map)
             return;
@@ -109,22 +112,24 @@ 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/commonjs/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/commonjs/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/commonjs/mol-model-formats/structure/basic/atomic.js

@@ -10,16 +10,16 @@ exports.getAtomicHierarchyAndConformation = void 0;
 var tslib_1 = require("tslib");
 var db_1 = require("../../../mol-data/db");
 var int_1 = require("../../../mol-data/int");
-var uuid_1 = require("../../../mol-util/uuid");
+var schema_1 = require("../../../mol-io/reader/cif/schema");
+var geometry_1 = require("../../../mol-math/geometry");
+var linear_algebra_1 = require("../../../mol-math/linear-algebra");
+var atom_site_operator_mapping_1 = require("../../../mol-model/structure/export/categories/atom_site_operator_mapping");
 var atomic_1 = require("../../../mol-model/structure/model/properties/atomic");
+var atomic_derived_1 = require("../../../mol-model/structure/model/properties/utils/atomic-derived");
 var atomic_index_1 = require("../../../mol-model/structure/model/properties/utils/atomic-index");
 var types_1 = require("../../../mol-model/structure/model/types");
-var atomic_derived_1 = require("../../../mol-model/structure/model/properties/utils/atomic-derived");
-var geometry_1 = require("../../../mol-math/geometry");
+var uuid_1 = require("../../../mol-util/uuid");
 var mmcif_1 = require("../mmcif");
-var atom_site_operator_mapping_1 = require("../../../mol-model/structure/export/categories/atom_site_operator_mapping");
-var schema_1 = require("../../../mol-io/reader/cif/schema");
-var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 function findHierarchyOffsets(atom_site) {
     if (atom_site._rowCount === 0)
         return { residues: [], chains: [] };

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

@@ -16,18 +16,18 @@ var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var coarse_ranges_1 = require("../../../mol-model/structure/model/properties/utils/coarse-ranges");
 var schema_1 = require("./schema");
 exports.EmptyCoarse = { hierarchy: coarse_1.CoarseHierarchy.Empty, conformation: void 0 };
-function getCoarse(data, properties) {
+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 exports.EmptyCoarse;
     var sphereData = getData(ihm_sphere_obj_site);
     var sphereConformation = getSphereConformation(ihm_sphere_obj_site);
     var sphereKeys = (0, coarse_keys_1.getCoarseKeys)(sphereData, data.entities);
-    var sphereRanges = (0, coarse_ranges_1.getCoarseRanges)(sphereData, properties.chemicalComponentMap);
+    var sphereRanges = (0, coarse_ranges_1.getCoarseRanges)(sphereData, chemicalComponentMap);
     var gaussianData = getData(ihm_gaussian_obj_site);
     var gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
     var gaussianKeys = (0, coarse_keys_1.getCoarseKeys)(gaussianData, data.entities);
-    var gaussianRanges = (0, coarse_ranges_1.getCoarseRanges)(gaussianData, properties.chemicalComponentMap);
+    var gaussianRanges = (0, coarse_ranges_1.getCoarseRanges)(gaussianData, chemicalComponentMap);
     return {
         hierarchy: {
             isDefined: true,

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

@@ -6,19 +6,19 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getEntities = void 0;
+exports.getEntitiesWithPRD = exports.getEntityData = void 0;
+var tslib_1 = require("tslib");
 var db_1 = require("../../../mol-data/db");
 var common_1 = require("../../../mol-model/structure/model/properties/common");
 var types_1 = require("../../../mol-model/structure/model/types");
 var schema_1 = require("./schema");
-function getEntities(data, properties) {
-    var _a;
+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)) {
@@ -60,7 +60,7 @@ 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);
@@ -71,7 +71,7 @@ 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);
@@ -88,13 +88,13 @@ 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)) {
@@ -108,26 +108,30 @@ function getEntities(data, properties) {
         // TODO how to handle coarse?
     }
     var subtypeColumn = db_1.Column.ofArray({ array: subtypes, schema: common_1.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 = db_1.Column.ofArray({ array: prdIds, schema: db_1.Column.Schema.str });
     return {
         data: entityData,
         subtype: subtypeColumn,
-        prd_id: prdIdColumn,
         getEntityIndex: getEntityIndex
     };
 }
-exports.getEntities = getEntities;
+exports.getEntityData = getEntityData;
+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 = db_1.Column.ofArray({ array: prdIds, schema: db_1.Column.Schema.str });
+    return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, entities), { prd_id: prdIdColumn });
+}
+exports.getEntitiesWithPRD = getEntitiesWithPRD;
 //# sourceMappingURL=entities.js.map

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

@@ -27,7 +27,7 @@ function createModels(data, format, ctx) {
         return (0, tslib_1.__generator)(this, function (_b) {
             switch (_b.label) {
                 case 0:
-                    properties = (0, properties_1.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:
@@ -48,6 +48,13 @@ function createModels(data, format, ctx) {
     });
 }
 exports.createModels = createModels;
+function getCommonProperties(data, format) {
+    return {
+        missingResidues: (0, properties_1.getMissingResidues)(data),
+        chemicalComponentMap: (0, properties_1.getChemicalComponentMap)(data),
+        saccharideComponentMap: (0, properties_1.getSaccharideComponentMap)(data)
+    };
+}
 /** Standard atomic model */
 function createStandardModel(data, atom_site, sourceIndex, entities, properties, format, previous) {
     var atomic = (0, atomic_1.getAtomicHierarchyAndConformation)(atom_site, sourceIndex, entities, properties.chemicalComponentMap, format, previous);
@@ -58,6 +65,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
     var coarse = coarse_1.EmptyCoarse;
     var sequence = (0, sequence_1.getSequence)(data, entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = (0, atomic_ranges_1.getAtomicRanges)(atomic.hierarchy, entities, atomic.conformation, sequence);
+    var structAsymMap = (0, properties_1.getStructAsymMap)(atomic.hierarchy);
     var entry = data.entry.id.valueKind(0) === 0 /* Present */
         ? data.entry.id.value(0) : format.name;
     var label = [];
@@ -73,7 +81,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
         sourceData: format,
         modelNum: modelNum,
         parent: undefined,
-        entities: entities,
+        entities: (0, entities_1.getEntitiesWithPRD)(data, entities, structAsymMap),
         sequence: sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
@@ -81,7 +89,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: properties,
+        properties: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new custom_property_1.CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -90,7 +98,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
 /** Integrative model with atomic/coarse parts */
 function createIntegrativeModel(data, ihm, properties, format) {
     var atomic = (0, atomic_1.getAtomicHierarchyAndConformation)(ihm.atom_site, ihm.atom_site_sourceIndex, ihm.entities, properties.chemicalComponentMap, format);
-    var coarse = (0, coarse_1.getCoarse)(ihm, properties);
+    var coarse = (0, coarse_1.getCoarse)(ihm, properties.chemicalComponentMap);
     var sequence = (0, sequence_1.getSequence)(data, ihm.entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = (0, atomic_ranges_1.getAtomicRanges)(atomic.hierarchy, ihm.entities, atomic.conformation, sequence);
     var entry = data.entry.id.valueKind(0) === 0 /* Present */
@@ -104,6 +112,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         label.push(ihm.model_name);
     if (ihm.model_group_name)
         label.push(ihm.model_group_name);
+    var structAsymMap = (0, properties_1.getStructAsymMap)(atomic.hierarchy, data);
     return {
         id: uuid_1.UUID.create22(),
         entryId: entry,
@@ -112,7 +121,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         sourceData: format,
         modelNum: ihm.model_id,
         parent: undefined,
-        entities: ihm.entities,
+        entities: (0, entities_1.getEntitiesWithPRD)(data, ihm.entities, structAsymMap),
         sequence: sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
@@ -120,7 +129,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: properties,
+        properties: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new custom_property_1.CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -144,7 +153,7 @@ function readStandard(ctx, data, properties, format) {
                     models = [];
                     if (!data.atom_site) return [3 /*break*/, 3];
                     atomCount = data.atom_site.id.rowCount;
-                    entities = (0, entities_1.getEntities)(data, properties);
+                    entities = (0, entities_1.getEntityData)(data);
                     modelStart = 0;
                     _b.label = 1;
                 case 1:
@@ -184,7 +193,7 @@ function readIntegrative(ctx, data, properties, format) {
         return (0, tslib_1.__generator)(this, function (_c) {
             switch (_c.label) {
                 case 0:
-                    entities = (0, entities_1.getEntities)(data, properties);
+                    entities = (0, entities_1.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/commonjs/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/commonjs/mol-model-formats/structure/basic/properties.js

@@ -6,11 +6,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getProperties = void 0;
+exports.getStructAsymMap = exports.getSaccharideComponentMap = exports.getChemicalComponentMap = exports.getMissingResidues = void 0;
+var db_1 = require("../../../mol-data/db");
 var types_1 = require("../../../mol-model/structure/model/types");
 var constants_1 = require("../../../mol-model/structure/structure/carbohydrates/constants");
 var memoize_1 = require("../../../mol-util/memoize");
-var db_1 = require("../../../mol-data/db");
 function getMissingResidues(data) {
     var map = new Map();
     var getKey = function (model_num, asym_id, seq_id) {
@@ -31,6 +31,7 @@ function getMissingResidues(data) {
         size: map.size
     };
 }
+exports.getMissingResidues = getMissingResidues;
 function getChemicalComponentMap(data) {
     var map = new Map();
     if (data.chem_comp._rowCount > 0) {
@@ -47,6 +48,7 @@ function getChemicalComponentMap(data) {
     }
     return map;
 }
+exports.getChemicalComponentMap = getChemicalComponentMap;
 function getSaccharideComponentMap(data) {
     var map = new Map();
     if (data.pdbx_chem_comp_identifier._rowCount > 0) {
@@ -93,6 +95,7 @@ function getSaccharideComponentMap(data) {
     }
     return map;
 }
+exports.getSaccharideComponentMap = getSaccharideComponentMap;
 var getUniqueComponentNames = (0, memoize_1.memoize1)(function (data) {
     var uniqueNames = new Set();
     var _a = data.atom_site, label_comp_id = _a.label_comp_id, auth_comp_id = _a.auth_comp_id;
@@ -102,20 +105,15 @@ var getUniqueComponentNames = (0, memoize_1.memoize1)(function (data) {
     }
     return uniqueNames;
 });
-function getStructAsymMap(data) {
+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);
@@ -130,13 +128,5 @@ function getStructAsymMap(data) {
     }
     return map;
 }
-function getProperties(data) {
-    return {
-        missingResidues: getMissingResidues(data),
-        chemicalComponentMap: getChemicalComponentMap(data),
-        saccharideComponentMap: getSaccharideComponentMap(data),
-        structAsymMap: getStructAsymMap(data)
-    };
-}
-exports.getProperties = getProperties;
+exports.getStructAsymMap = getStructAsymMap;
 //# sourceMappingURL=properties.js.map

package/lib/commonjs/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';