drugflow-molstar 0.2.0 → 0.2.2

package/lib/superposition-sifts-mapping.js

@@ -1,159 +1,159 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.alignAndSuperposeWithSIFTSMapping = void 0;
-var int_1 = require("Molstar/mol-data/int");
-var minimize_rmsd_1 = require("Molstar/mol-math/linear-algebra/3d/minimize-rmsd");
-var sifts_mapping_1 = require("./sifts-mapping");
-var element_1 = require("Molstar/mol-model/structure/structure/element");
-function alignAndSuperposeWithSIFTSMapping(structures, options) {
-    var _a, _b;
-    var indexMap = new Map();
-    for (var i = 0; i < structures.length; i++) {
-        var includeResidueTest = (_a = options === null || options === void 0 ? void 0 : options.includeResidueTest) !== null && _a !== void 0 ? _a : _includeAllResidues;
-        if ((options === null || options === void 0 ? void 0 : options.applyTestIndex) && !options.applyTestIndex.includes(i))
-            includeResidueTest = _includeAllResidues;
-        buildIndex(structures[i], indexMap, i, (_b = options === null || options === void 0 ? void 0 : options.traceOnly) !== null && _b !== void 0 ? _b : true, includeResidueTest);
-    }
-    var index = Array.from(indexMap.values());
-    // TODO: support non-first structure pivots
-    var pairs = findPairs(structures.length, index);
-    var zeroOverlapPairs = [];
-    var failedPairs = [];
-    var entries = [];
-    for (var _i = 0, pairs_1 = pairs; _i < pairs_1.length; _i++) {
-        var p = pairs_1[_i];
-        if (p.count === 0) {
-            zeroOverlapPairs.push([p.i, p.j]);
-        }
-        else {
-            var _c = getPositionTables(index, p.i, p.j, p.count), a = _c[0], b = _c[1];
-            var transform = minimize_rmsd_1.MinimizeRmsd.compute({ a: a, b: b });
-            if (Number.isNaN(transform.rmsd)) {
-                failedPairs.push([p.i, p.j]);
-            }
-            else {
-                entries.push({ transform: transform, pivot: p.i, other: p.j });
-            }
-        }
-    }
-    return { entries: entries, zeroOverlapPairs: zeroOverlapPairs, failedPairs: failedPairs };
-}
-exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
-function getPositionTables(index, pivot, other, N) {
-    var xs = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
-    var ys = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
-    var o = 0;
-    for (var _i = 0, index_1 = index; _i < index_1.length; _i++) {
-        var pivots = index_1[_i].pivots;
-        var a = pivots[pivot];
-        var b = pivots[other];
-        if (!a || !b)
-            continue;
-        var l = Math.min(a[2] - a[1], b[2] - b[1]);
-        // 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);
-            xs.y[o] = a[0].conformation.y(eI);
-            xs.z[o] = a[0].conformation.z(eI);
-            eI = (b[1] + i);
-            ys.x[o] = b[0].conformation.x(eI);
-            ys.y[o] = b[0].conformation.y(eI);
-            ys.z[o] = b[0].conformation.z(eI);
-            o++;
-        }
-    }
-    return [xs, ys];
-}
-function findPairs(N, index) {
-    var pairwiseCounts = [];
-    for (var i = 0; i < N; i++) {
-        pairwiseCounts[i] = [];
-        for (var j = 0; j < N; j++)
-            pairwiseCounts[i][j] = 0;
-    }
-    for (var _i = 0, index_2 = index; _i < index_2.length; _i++) {
-        var pivots = index_2[_i].pivots;
-        for (var i = 0; i < N; i++) {
-            if (!pivots[i])
-                continue;
-            var lI = pivots[i][2] - pivots[i][1];
-            for (var j = i + 1; j < N; j++) {
-                if (!pivots[j])
-                    continue;
-                var lJ = pivots[j][2] - pivots[j][1];
-                pairwiseCounts[i][j] = pairwiseCounts[i][j] + Math.min(lI, lJ);
-            }
-        }
-    }
-    var ret = [];
-    for (var j = 1; j < N; j++) {
-        ret[j - 1] = { i: 0, j: j, count: pairwiseCounts[0][j] };
-    }
-    // TODO: support non-first structure pivots
-    // for (let i = 0; i < N - 1; i++) {
-    //     let max = 0, maxJ = i;
-    //     for (let j = i + 1; j < N; j++) {
-    //         if (pairwiseCounts[i][j] > max) {
-    //             maxJ = j;
-    //             max = pairwiseCounts[i][j];
-    //         }
-    //     }
-    //     ret[i] = { i, j: maxJ, count: max };
-    // }
-    return ret;
-}
-function _includeAllResidues() { return true; }
-function buildIndex(structure, index, sI, traceOnly, includeTest) {
-    var _a;
-    var loc = element_1.StructureElement.Location.create(structure);
-    for (var _i = 0, _b = structure.units; _i < _b.length; _i++) {
-        var unit = _b[_i];
-        if (unit.kind !== 0 /* Atomic */)
-            continue;
-        var elements = unit.elements, model = unit.model;
-        loc.unit = unit;
-        var map = sifts_mapping_1.SIFTSMapping.Provider.get(model).value;
-        if (!map)
-            return;
-        var dbName = map.dbName, accession = map.accession, num = map.num;
-        var chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
-        var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
-        var traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
-        while (chainsIt.hasNext) {
-            var chainSegment = chainsIt.move();
-            residuesIt.setSegment(chainSegment);
-            while (residuesIt.hasNext) {
-                var residueSegment = residuesIt.move();
-                var rI = residueSegment.index;
-                if (!dbName[rI])
-                    continue;
-                var traceElement = traceElementIndex[rI];
-                var start = void 0, end = void 0;
-                if (traceOnly) {
-                    start = traceElement;
-                    if (start === -1)
-                        continue;
-                    end = start + 1;
-                }
-                else {
-                    start = elements[residueSegment.start];
-                    end = elements[residueSegment.end - 1] + 1;
-                }
-                loc.element = (traceElement >= 0 ? traceElement : start);
-                if (!includeTest(loc, rI, start, end))
-                    continue;
-                var key = "".concat(dbName[rI], "-").concat(accession[rI].split('-')[0], "-").concat(num[rI]);
-                if (!index.has(key)) {
-                    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, start, end];
-                    }
-                }
-            }
-        }
-    }
-}
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.alignAndSuperposeWithSIFTSMapping = void 0;
+var int_1 = require("Molstar/mol-data/int");
+var minimize_rmsd_1 = require("Molstar/mol-math/linear-algebra/3d/minimize-rmsd");
+var sifts_mapping_1 = require("./sifts-mapping");
+var element_1 = require("Molstar/mol-model/structure/structure/element");
+function alignAndSuperposeWithSIFTSMapping(structures, options) {
+    var _a, _b;
+    var indexMap = new Map();
+    for (var i = 0; i < structures.length; i++) {
+        var includeResidueTest = (_a = options === null || options === void 0 ? void 0 : options.includeResidueTest) !== null && _a !== void 0 ? _a : _includeAllResidues;
+        if ((options === null || options === void 0 ? void 0 : options.applyTestIndex) && !options.applyTestIndex.includes(i))
+            includeResidueTest = _includeAllResidues;
+        buildIndex(structures[i], indexMap, i, (_b = options === null || options === void 0 ? void 0 : options.traceOnly) !== null && _b !== void 0 ? _b : true, includeResidueTest);
+    }
+    var index = Array.from(indexMap.values());
+    // TODO: support non-first structure pivots
+    var pairs = findPairs(structures.length, index);
+    var zeroOverlapPairs = [];
+    var failedPairs = [];
+    var entries = [];
+    for (var _i = 0, pairs_1 = pairs; _i < pairs_1.length; _i++) {
+        var p = pairs_1[_i];
+        if (p.count === 0) {
+            zeroOverlapPairs.push([p.i, p.j]);
+        }
+        else {
+            var _c = getPositionTables(index, p.i, p.j, p.count), a = _c[0], b = _c[1];
+            var transform = minimize_rmsd_1.MinimizeRmsd.compute({ a: a, b: b });
+            if (Number.isNaN(transform.rmsd)) {
+                failedPairs.push([p.i, p.j]);
+            }
+            else {
+                entries.push({ transform: transform, pivot: p.i, other: p.j });
+            }
+        }
+    }
+    return { entries: entries, zeroOverlapPairs: zeroOverlapPairs, failedPairs: failedPairs };
+}
+exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
+function getPositionTables(index, pivot, other, N) {
+    var xs = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
+    var ys = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
+    var o = 0;
+    for (var _i = 0, index_1 = index; _i < index_1.length; _i++) {
+        var pivots = index_1[_i].pivots;
+        var a = pivots[pivot];
+        var b = pivots[other];
+        if (!a || !b)
+            continue;
+        var l = Math.min(a[2] - a[1], b[2] - b[1]);
+        // 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);
+            xs.y[o] = a[0].conformation.y(eI);
+            xs.z[o] = a[0].conformation.z(eI);
+            eI = (b[1] + i);
+            ys.x[o] = b[0].conformation.x(eI);
+            ys.y[o] = b[0].conformation.y(eI);
+            ys.z[o] = b[0].conformation.z(eI);
+            o++;
+        }
+    }
+    return [xs, ys];
+}
+function findPairs(N, index) {
+    var pairwiseCounts = [];
+    for (var i = 0; i < N; i++) {
+        pairwiseCounts[i] = [];
+        for (var j = 0; j < N; j++)
+            pairwiseCounts[i][j] = 0;
+    }
+    for (var _i = 0, index_2 = index; _i < index_2.length; _i++) {
+        var pivots = index_2[_i].pivots;
+        for (var i = 0; i < N; i++) {
+            if (!pivots[i])
+                continue;
+            var lI = pivots[i][2] - pivots[i][1];
+            for (var j = i + 1; j < N; j++) {
+                if (!pivots[j])
+                    continue;
+                var lJ = pivots[j][2] - pivots[j][1];
+                pairwiseCounts[i][j] = pairwiseCounts[i][j] + Math.min(lI, lJ);
+            }
+        }
+    }
+    var ret = [];
+    for (var j = 1; j < N; j++) {
+        ret[j - 1] = { i: 0, j: j, count: pairwiseCounts[0][j] };
+    }
+    // TODO: support non-first structure pivots
+    // for (let i = 0; i < N - 1; i++) {
+    //     let max = 0, maxJ = i;
+    //     for (let j = i + 1; j < N; j++) {
+    //         if (pairwiseCounts[i][j] > max) {
+    //             maxJ = j;
+    //             max = pairwiseCounts[i][j];
+    //         }
+    //     }
+    //     ret[i] = { i, j: maxJ, count: max };
+    // }
+    return ret;
+}
+function _includeAllResidues() { return true; }
+function buildIndex(structure, index, sI, traceOnly, includeTest) {
+    var _a;
+    var loc = element_1.StructureElement.Location.create(structure);
+    for (var _i = 0, _b = structure.units; _i < _b.length; _i++) {
+        var unit = _b[_i];
+        if (unit.kind !== 0 /* Atomic */)
+            continue;
+        var elements = unit.elements, model = unit.model;
+        loc.unit = unit;
+        var map = sifts_mapping_1.SIFTSMapping.Provider.get(model).value;
+        if (!map)
+            return;
+        var dbName = map.dbName, accession = map.accession, num = map.num;
+        var chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+        var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+        var traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
+        while (chainsIt.hasNext) {
+            var chainSegment = chainsIt.move();
+            residuesIt.setSegment(chainSegment);
+            while (residuesIt.hasNext) {
+                var residueSegment = residuesIt.move();
+                var rI = residueSegment.index;
+                if (!dbName[rI])
+                    continue;
+                var traceElement = traceElementIndex[rI];
+                var start = void 0, end = void 0;
+                if (traceOnly) {
+                    start = traceElement;
+                    if (start === -1)
+                        continue;
+                    end = start + 1;
+                }
+                else {
+                    start = elements[residueSegment.start];
+                    end = elements[residueSegment.end - 1] + 1;
+                }
+                loc.element = (traceElement >= 0 ? traceElement : start);
+                if (!includeTest(loc, rI, start, end))
+                    continue;
+                var key = "".concat(dbName[rI], "-").concat(accession[rI].split('-')[0], "-").concat(num[rI]);
+                if (!index.has(key)) {
+                    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, start, end];
+                    }
+                }
+            }
+        }
+    }
+}

package/lib/superposition.d.ts

@@ -1,18 +1,18 @@
-import { Mat4 } from 'Molstar/mol-math/linear-algebra';
-import { PluginContext } from 'Molstar/mol-plugin/context';
-declare type ClusterRec = {
-    pdb_id: string;
-    auth_asym_id: string;
-    struct_asym_id: string;
-    entity_id: string;
-    is_representative: boolean;
-};
-export declare type SuperpositionData = {
-    data: ClusterRec[];
-    matrix: Mat4[];
-};
-export declare function initSuperposition(plugin: PluginContext): Promise<void>;
-export declare function loadAfStructure(plugin: PluginContext): Promise<string | false>;
-export declare function superposeAf(plugin: PluginContext, traceOnly: boolean, segmentIndex?: number): Promise<true | undefined>;
-export declare function renderSuperposition(plugin: PluginContext, segmentIndex: number, entryList: ClusterRec[]): Promise<void>;
-export {};
+import { Mat4 } from 'Molstar/mol-math/linear-algebra';
+import { PluginContext } from 'Molstar/mol-plugin/context';
+declare type ClusterRec = {
+    pdb_id: string;
+    auth_asym_id: string;
+    struct_asym_id: string;
+    entity_id: string;
+    is_representative: boolean;
+};
+export declare type SuperpositionData = {
+    data: ClusterRec[];
+    matrix: Mat4[];
+};
+export declare function initSuperposition(plugin: PluginContext): Promise<void>;
+export declare function loadAfStructure(plugin: PluginContext): Promise<string | false>;
+export declare function superposeAf(plugin: PluginContext, traceOnly: boolean, segmentIndex?: number): Promise<true | undefined>;
+export declare function renderSuperposition(plugin: PluginContext, segmentIndex: number, entryList: ClusterRec[]): Promise<void>;
+export {};