molstar 3.0.0-dev.7 → 3.0.1

package/lib/mol-io/writer/cif/encoder/binary.js

@@ -170,8 +170,15 @@ function getFieldData(field, arrayCtor, totalCount, data) {
                 allPresent = false;
             }
             else {
-                mask[offset] = 0 /* Present */;
-                array[offset] = getter(key, d, offset);
+                var value = getter(key, d, offset);
+                if (typeof value === 'string' && !value) {
+                    mask[offset] = 1 /* NotPresent */;
+                    allPresent = false;
+                }
+                else {
+                    mask[offset] = 0 /* Present */;
+                }
+                array[offset] = value;
             }
             offset++;
         }

package/lib/mol-math/geometry/gaussian-density/gpu.js

@@ -10,7 +10,7 @@ import { OrderedSet } from '../../../mol-data/int';
 import { Vec3, Tensor, Mat4, Vec2 } from '../../linear-algebra';
 import { ValueCell } from '../../../mol-util';
 import { createComputeRenderable } from '../../../mol-gl/renderable';
-import { decodeFloatRGB } from '../../../mol-util/float-packing';
+import { unpackRGBToInt } from '../../../mol-util/number-packing';
 import { ShaderCode } from '../../../mol-gl/shader-code';
 import { createComputeRenderItem } from '../../../mol-gl/webgl/render-item';
 import { ValueSpec, AttributeSpec, UniformSpec, TextureSpec, DefineSpec } from '../../../mol-gl/renderable/schema';
@@ -371,7 +371,7 @@ function fieldFromTexture2d(ctx, texture, dim, texDim) {
             for (var ix = 0; ix < dx; ++ix) {
                 var idx = 4 * (tmpCol * dx + (iy + tmpRow) * width + ix);
                 data[j] = image[idx + 3] / 255;
-                idData[j] = decodeFloatRGB(image[idx], image[idx + 1], image[idx + 2]);
+                idData[j] = unpackRGBToInt(image[idx], image[idx + 1], image[idx + 2]);
                 j++;
             }
         }

package/lib/mol-math/geometry/symmetry-operator.d.ts

@@ -42,7 +42,7 @@ declare namespace SymmetryOperator {
         hkl?: Vec3;
         spgrOp?: number;
     };
-    function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator;
+    function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator;
     function checkIfRotationAndTranslation(rot: Mat3, offset: Vec3): boolean;
     function ofRotationAndOffset(name: string, rot: Mat3, offset: Vec3, ncsId?: number): SymmetryOperator;
     function lerpFromIdentity(out: Mat4, op: SymmetryOperator, t: number): Mat4;

package/lib/mol-math/geometry/symmetry-operator.js

@@ -19,8 +19,9 @@ var SymmetryOperator;
         var _hkl = hkl ? Vec3.clone(hkl) : Vec3();
         spgrOp = defaults(spgrOp, -1);
         ncsId = ncsId || -1;
-        var suffix = getSuffix(info);
-        if (Mat4.isIdentity(matrix))
+        var isIdentity = Mat4.isIdentity(matrix);
+        var suffix = getSuffix(info, isIdentity);
+        if (isIdentity)
             return { name: name, assembly: assembly, matrix: matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
         if (!Mat4.isRotationAndTranslation(matrix, SymmetryOperator.RotationTranslationEpsilon)) {
             console.warn("Symmetry operator (".concat(name, ") should be a composition of rotation and translation."));
@@ -28,11 +29,16 @@ var SymmetryOperator;
         return { name: name, assembly: assembly, matrix: matrix, inverse: Mat4.invert(Mat4(), matrix), isIdentity: false, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
     }
     SymmetryOperator.create = create;
-    function getSuffix(info) {
+    function isSymmetryOperator(x) {
+        return !!x && !!x.matrix && !!x.inverse && typeof x.name === 'string';
+    }
+    function getSuffix(info, isIdentity) {
         if (!info)
             return '';
         if (info.assembly) {
-            return "_".concat(info.assembly.operId);
+            if (isSymmetryOperator(info))
+                return info.suffix;
+            return isIdentity ? '' : "_".concat(info.assembly.operId);
         }
         if (typeof info.spgrOp !== 'undefined' && typeof info.hkl !== 'undefined' && info.spgrOp !== -1) {
             var _a = info.hkl, i = _a[0], j = _a[1], k = _a[2];

package/lib/mol-model/structure/export/mmcif.d.ts

@@ -28,5 +28,5 @@ declare type encode_mmCIF_categories_Params = {
 };
 /** Doesn't start a data block */
 export declare function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures: Structure | Structure[], params?: encode_mmCIF_categories_Params): void;
-declare function to_mmCIF(name: string, structure: Structure, asBinary?: boolean): string | Uint8Array;
+declare function to_mmCIF(name: string, structure: Structure, asBinary?: boolean, params?: encode_mmCIF_categories_Params): string | Uint8Array;
 export { to_mmCIF };

package/lib/mol-model/structure/export/mmcif.js

@@ -37,6 +37,9 @@ var _entity = {
 function isWithoutSymmetry(structure) {
     return structure.units.every(function (u) { return u.conformation.operator.isIdentity; });
 }
+function isWithoutOperator(structure) {
+    return isWithoutSymmetry(structure) && structure.units.every(function (u) { return !u.conformation.operator.assembly && !u.conformation.operator.suffix; });
+}
 var Categories = [
     // Basics
     copy_mmCif_category('entry'),
@@ -46,9 +49,9 @@ var Categories = [
     copy_mmCif_category('cell', isWithoutSymmetry),
     copy_mmCif_category('symmetry', isWithoutSymmetry),
     // Assemblies
-    copy_mmCif_category('pdbx_struct_assembly', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_oper_list', isWithoutSymmetry),
+    copy_mmCif_category('pdbx_struct_assembly', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_oper_list', isWithoutOperator),
     // Secondary structure
     _struct_conf,
     _struct_sheet_range,
@@ -229,11 +232,11 @@ function encode_mmCIF_categories_copyAll(encoder, ctx, params) {
             encoder.writeCategory(info[0], info[1], info[2]);
     });
 }
-function to_mmCIF(name, structure, asBinary) {
+function to_mmCIF(name, structure, asBinary, params) {
     if (asBinary === void 0) { asBinary = false; }
     var enc = CifWriter.createEncoder({ binary: asBinary });
     enc.startDataBlock(name);
-    encode_mmCIF_categories(enc, structure);
+    encode_mmCIF_categories(enc, structure, params);
     return enc.getData();
 }
 export { to_mmCIF };

package/lib/mol-model/structure/model/properties/coarse/hierarchy.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 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>

package/lib/mol-model/structure/model/properties/coarse/hierarchy.js

@@ -1,11 +1,33 @@
 /**
- * Copyright (c) 2018 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>
  */
+import { Column } from '../../../../../mol-data/db';
+import { Segmentation } from '../../../../../mol-data/int';
+import { SortedRanges } from '../../../../../mol-data/int/sorted-ranges';
+var EmptyCoarseElements = {
+    chainKey: [],
+    entityKey: [],
+    findSequenceKey: function () { return -1; },
+    findChainKey: function () { return -1; },
+    getEntityFromChain: function () { return -1; },
+    count: 0,
+    entity_id: Column.Undefined(0, Column.Schema.str),
+    asym_id: Column.Undefined(0, Column.Schema.str),
+    seq_id_begin: Column.Undefined(0, Column.Schema.int),
+    seq_id_end: Column.Undefined(0, Column.Schema.int),
+    chainElementSegments: Segmentation.create([]),
+    polymerRanges: SortedRanges.ofSortedRanges([]),
+    gapRanges: SortedRanges.ofSortedRanges([]),
+};
 export var CoarseHierarchy;
 (function (CoarseHierarchy) {
-    CoarseHierarchy.Empty = { isDefined: false };
+    CoarseHierarchy.Empty = {
+        isDefined: false,
+        spheres: EmptyCoarseElements,
+        gaussians: EmptyCoarseElements
+    };
 })(CoarseHierarchy || (CoarseHierarchy = {}));
 //# sourceMappingURL=hierarchy.js.map

package/lib/mol-model/structure/model/properties/common.d.ts

@@ -13,7 +13,7 @@ export declare const EntitySubtype: Column.Schema.Aliased<EntitySubtype>;
 export interface Entities {
     data: mmCIF_Database['entity'];
     subtype: Column<EntitySubtype>;
-    prd_id: Column<string>;
+    prd_id?: Column<string>;
     getEntityIndex(id: string): EntityIndex;
 }
 export declare type ChemicalComponent = Table.Row<mmCIF_chemComp_schema>;

package/lib/mol-model/structure/structure/element/stats.js

@@ -49,6 +49,7 @@ export var Stats;
         }
         else if (size === 1) {
             if (Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
+                // handled in `handleUnitChainsSimple`
                 return;
             }
             else {
@@ -174,6 +175,13 @@ export var Stats;
                     Location.set(stats.firstChainLoc, structure, unit, offsets[cI]);
                 }
             }
+            else if (size === 1) {
+                // need to handle here, skipped in `handleElement`
+                stats.elementCount += 1;
+                if (stats.elementCount === 1) {
+                    Location.set(stats.firstElementLoc, structure, unit, eI);
+                }
+            }
         }
     }
     function handleUnitChainsPartitioned(stats, structure, lociElements, start, end) {

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

@@ -87,6 +87,7 @@ declare const StructureProperties: {
         y: StructureElement.Property<number>;
         z: StructureElement.Property<number>;
         asym_id: StructureElement.Property<string>;
+        entity_id: StructureElement.Property<string>;
         seq_id_begin: StructureElement.Property<number>;
         seq_id_end: StructureElement.Property<number>;
         sphere_radius: StructureElement.Property<number>;

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

@@ -111,6 +111,7 @@ var coarse = {
     y: atom.y,
     z: atom.z,
     asym_id: p(function (l) { return !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.asym_id.value(l.element); }),
+    entity_id: p(function (l) { return !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entity_id.value(l.element); }),
     seq_id_begin: p(function (l) { return !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_begin.value(l.element); }),
     seq_id_end: p(function (l) { return !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_end.value(l.element); }),
     sphere_radius: p(function (l) { return !Unit.isSpheres(l.unit) ? notCoarse('spheres') : l.unit.coarseConformation.radius[l.element]; }),
@@ -141,7 +142,7 @@ var entity = {
     pdbx_fragment: p(function (l) { return l.unit.model.entities.data.pdbx_fragment.value(eK(l)); }),
     pdbx_ec: p(function (l) { return l.unit.model.entities.data.pdbx_ec.value(eK(l)); }),
     subtype: p(function (l) { return l.unit.model.entities.subtype.value(eK(l)); }),
-    prd_id: p(function (l) { return l.unit.model.entities.prd_id.value(eK(l)); }),
+    prd_id: p(function (l) { var _a, _b; return (_b = (_a = l.unit.model.entities.prd_id) === null || _a === void 0 ? void 0 : _a.value(eK(l))) !== null && _b !== void 0 ? _b : ''; }),
 };
 var _emptyList = [];
 var unit = {

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

@@ -187,8 +187,6 @@ function getOperatorsForRange(symmetry, ijkMin, ijkMax, modelCenter) {
         ijkMin[2] <= 0 && ijkMax[2] >= 0) {
         operators[0] = Spacegroup.getSymmetryOperator(spacegroup, 0, 0, 0, 0);
     }
-    var toFractional = spacegroup.cell.toFractional;
-    var ref = Vec3.transformMat4(Vec3(), modelCenter, toFractional);
     for (var op = 0; op < spacegroup.operators.length; op++) {
         for (var i = ijkMin[0]; i <= ijkMax[0]; i++) {
             for (var j = ijkMin[1]; j <= ijkMax[1]; j++) {
@@ -196,7 +194,7 @@ function getOperatorsForRange(symmetry, ijkMin, ijkMax, modelCenter) {
                     // check if we have added identity as the 1st operator.
                     if (!ncsCount && op === 0 && i === 0 && j === 0 && k === 0)
                         continue;
-                    operators.push.apply(operators, getOperatorsForIndex(symmetry, op, i, j, k, ref));
+                    operators.push.apply(operators, getOperatorsForIndex(symmetry, op, i, j, k, modelCenter));
                 }
             }
         }

package/lib/mol-model/structure/structure/unit/bonds/common.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>
@@ -17,4 +17,5 @@ export declare const MetalsSet: Set<number>;
 export declare function getElementIdx(e: ElementSymbol): number;
 export declare function getElementPairThreshold(i: number, j: number): number;
 export declare function getElementThreshold(i: number): number;
+export declare function getPairingThreshold(elementIndexA: number, elementIndexB: number, thresholdA: number, thresholdB: number): number;
 export declare function isHydrogen(i: number): boolean;

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

@@ -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>
@@ -99,6 +99,14 @@ export function getElementThreshold(i) {
         return __DefaultBondingRadius;
     return r;
 }
+export 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
+}
 var H_ID = __ElementIndex['H'];
 export function isHydrogen(i) {
     return i === H_ID;

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

@@ -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>
@@ -7,7 +7,7 @@
 import { __assign } from "tslib";
 import { Structure } from '../../structure';
 import { Unit } from '../../unit';
-import { getElementIdx, getElementPairThreshold, getElementThreshold, isHydrogen, MetalsSet, DefaultBondComputationProps } from './common';
+import { getElementIdx, getElementThreshold, isHydrogen, MetalsSet, DefaultBondComputationProps, getPairingThreshold } from './common';
 import { InterUnitBonds } from './data';
 import { SortedArray } from '../../../../../mol-data/int';
 import { Vec3, Mat4 } from '../../../../../mol-math/linear-algebra';
@@ -67,11 +67,26 @@ function findPairBonds(unitA, unitB, props, builder) {
                 var _bI = SortedArray.indexOf(unitB.elements, bI);
                 if (_bI < 0)
                     continue;
-                if (type_symbolA.value(aI) === 'H' && type_symbolB.value(bI) === 'H')
-                    continue;
+                var aeI_1 = getElementIdx(type_symbolA.value(aI));
+                var beI = getElementIdx(type_symbolA.value(bI));
                 var d = distance[i];
                 var dist = getDistance(unitA, aI, unitB, bI);
-                if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
+                var add = false;
+                if (d >= 0) {
+                    add = equalEps(dist, d, 0.3);
+                }
+                else if (maxDistance >= 0) {
+                    add = dist < maxDistance;
+                }
+                else {
+                    var pairingThreshold = getPairingThreshold(aeI_1, beI, getElementThreshold(aeI_1), getElementThreshold(beI));
+                    add = dist < pairingThreshold;
+                    if (isHydrogen(aeI_1) && isHydrogen(beI)) {
+                        // TODO handle molecular hydrogen
+                        add = false;
+                    }
+                }
+                if (add) {
                     builder.add(_aI, _bI, { order: order[i], flag: flag[i] });
                 }
             }
@@ -135,12 +150,7 @@ function findPairBonds(unitA, unitB, props, builder) {
             var dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0)
                 continue;
-            var thresholdAB = getElementPairThreshold(aeI, beI);
-            var pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + getElementThreshold(beI)) / 1.95; // not sure if avg or min but max is too big
+            var pairingThreshold = getPairingThreshold(aeI, beI, thresholdA, getElementThreshold(beI));
             if (dist <= pairingThreshold) {
                 var atomIdB = label_atom_idB.value(bI);
                 var compIdB = label_comp_idB.value(residueIndexB[bI]);

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

@@ -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>
@@ -7,7 +7,7 @@
 import { __assign } from "tslib";
 import { IntraUnitBonds } from './data';
 import { IntAdjacencyGraph } from '../../../../../mol-math/graph';
-import { getElementIdx, MetalsSet, getElementThreshold, isHydrogen, getElementPairThreshold, DefaultBondComputationProps } from './common';
+import { getElementIdx, MetalsSet, getElementThreshold, isHydrogen, DefaultBondComputationProps, getPairingThreshold } from './common';
 import { SortedArray } from '../../../../../mol-data/int';
 import { getIntraBondOrderFromTable } from '../../../model/properties/atomic/bonds';
 import { IndexPairBonds } from '../../../../../mol-model-formats/structure/property/bonds/index-pair';
@@ -50,7 +50,8 @@ 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 = getElementIdx(type_symbol.value(aI));
+        var isHa = isHydrogen(aeI);
         var srcA = sourceIndex.value(aI);
         for (var i = offset[srcA], il = offset[srcA + 1]; i < il; ++i) {
             var bI = invertedIndex[b[i]];
@@ -59,11 +60,25 @@ function findIndexPairBonds(unit) {
             var _bI = SortedArray.indexOf(unit.elements, bI);
             if (_bI < 0)
                 continue;
-            if (isHa && type_symbol.value(bI) === 'H')
-                continue;
+            var beI = getElementIdx(type_symbol.value(bI));
             var d = distance[i];
             var dist = getDistance(unit, aI, bI);
-            if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
+            var add = false;
+            if (d >= 0) {
+                add = equalEps(dist, d, 0.3);
+            }
+            else if (maxDistance >= 0) {
+                add = dist < maxDistance;
+            }
+            else {
+                var pairingThreshold = getPairingThreshold(aeI, beI, getElementThreshold(aeI), getElementThreshold(beI));
+                add = dist < pairingThreshold;
+                if (isHa && isHydrogen(beI)) {
+                    // TODO handle molecular hydrogen
+                    add = false;
+                }
+            }
+            if (add) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;
                 orders[orders.length] = order[i];
@@ -187,12 +202,7 @@ function findBonds(unit, props) {
             var dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0)
                 continue;
-            var thresholdAB = getElementPairThreshold(aeI, beI);
-            var pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + getElementThreshold(beI)) / 1.95; // not sure if avg or min but max is too big
+            var pairingThreshold = getPairingThreshold(aeI, beI, thresholdA, getElementThreshold(beI));
             if (dist <= pairingThreshold) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;

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/volume/volume.d.ts

@@ -48,6 +48,13 @@ export declare namespace Volume {
         function toRelative(value: IsoValue, stats: Grid['stats']): Relative;
         function toString(value: IsoValue): string;
     }
+    function adjustedIsoValue(volume: Volume, value: number, kind: 'absolute' | 'relative'): Readonly<{
+        kind: "absolute";
+        absoluteValue: number;
+    }> | Readonly<{
+        kind: "relative";
+        relativeValue: number;
+    }>;
     function createIsoValueParam(defaultValue: Volume.IsoValue, stats?: Grid['stats']): PD.Conditioned<Readonly<{
         kind: "absolute";
         absoluteValue: number;

package/lib/mol-model/volume/volume.js

@@ -13,6 +13,7 @@ import { equalEps } from '../../mol-math/linear-algebra/3d/common';
 import { CustomProperties } from '../custom-property';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { toPrecision } from '../../mol-util/number';
+import { DscifFormat } from '../../mol-model-formats/volume/density-server';
 export var Volume;
 (function (Volume) {
     function is(x) {
@@ -57,6 +58,23 @@ export var Volume;
         }
         IsoValue.toString = toString;
     })(IsoValue = Volume.IsoValue || (Volume.IsoValue = {}));
+    // Converts iso value to relative if using downsample VolumeServer data
+    function adjustedIsoValue(volume, value, kind) {
+        if (kind === 'relative')
+            return IsoValue.relative(value);
+        var absolute = IsoValue.absolute(value);
+        if (DscifFormat.is(volume.sourceData)) {
+            var stats = {
+                min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
+                max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
+                mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
+                sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
+            };
+            return Volume.IsoValue.toRelative(absolute, stats);
+        }
+        return absolute;
+    }
+    Volume.adjustedIsoValue = adjustedIsoValue;
     var defaultStats = { min: -1, max: 1, mean: 0, sigma: 0.1 };
     function createIsoValueParam(defaultValue, stats) {
         var sts = stats || defaultStats;

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;