drugflow-molstar
Version:
Molstar implementation for DrugFlow
777 lines • 50.7 kB
JavaScript
"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.renderSuperposition = exports.superposeAf = exports.loadAfStructure = exports.initSuperposition = void 0;
var tslib_1 = require("tslib");
var linear_algebra_1 = require("Molstar/mol-math/linear-algebra");
var builder_1 = require("Molstar/mol-script/language/builder");
var mol_state_1 = require("Molstar/mol-state");
var transforms_1 = require("Molstar/mol-plugin-state/transforms");
var assets_1 = require("Molstar/mol-util/assets");
var helpers_1 = require("./helpers");
var lists_1 = require("Molstar/mol-util/color/lists");
var color_1 = require("Molstar/mol-util/color/color");
var script_1 = require("Molstar/mol-script/script");
var mol_task_1 = require("Molstar/mol-task");
var superposition_sifts_mapping_1 = require("./superposition-sifts-mapping");
var alphafold_transparency_1 = require("./alphafold-transparency");
var structure_1 = require("Molstar/mol-model/structure");
function getRandomColor(plugin, segmentIndex) {
var clList = lists_1.ColorLists;
var spState = plugin.customState.superpositionState;
var palleteIndex = spState.colorState[segmentIndex].palleteIndex;
var colorIndex = spState.colorState[segmentIndex].colorIndex;
if (clList[spState.colorPalette[palleteIndex]].list[colorIndex + 1]) {
colorIndex += 1;
}
else {
colorIndex = 0;
palleteIndex = spState.colorPalette[palleteIndex + 1] ? palleteIndex + 1 : 0;
}
var palleteName = spState.colorPalette[palleteIndex];
plugin.customState.superpositionState.colorState[segmentIndex].palleteIndex = palleteIndex;
plugin.customState.superpositionState.colorState[segmentIndex].colorIndex = colorIndex;
return clList[palleteName].list[colorIndex];
}
function initSuperposition(plugin) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var customState, superpositionParams, segmentData, afStrUrls, segmentIndex, clusterIndexs, entryList, clusters;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, plugin.clear()];
case 1:
_a.sent();
customState = plugin.customState;
superpositionParams = customState.initParams.superpositionParams;
plugin.customState.superpositionState = {
models: {},
entries: {},
refMaps: {},
segmentData: void 0,
matrixData: {},
activeSegment: 0,
loadedStructs: [],
visibleRefs: [],
invalidStruct: [],
noMatrixStruct: [],
hets: {},
colorPalette: ['dark-2', 'red-yellow-green', 'paired', 'set-1', 'accent', 'set-2', 'rainbow'],
colorState: [],
alphafold: {
apiData: {
cif: '',
pae: '',
length: 0
},
length: 0,
ref: '',
traceOnly: true,
visibility: [],
transforms: [],
rmsds: [],
coordinateSystems: []
}
};
// Get segment and cluster information for the given uniprot accession
return [4 /*yield*/, getSegmentData(plugin)];
case 2:
// Get segment and cluster information for the given uniprot accession
_a.sent();
segmentData = plugin.customState.superpositionState.segmentData;
if (!segmentData)
return [2 /*return*/];
// Load Matrix Data
return [4 /*yield*/, getMatrixData(plugin)];
case 3:
// Load Matrix Data
_a.sent();
if (!plugin.customState.superpositionState.segmentData)
return [2 /*return*/];
return [4 /*yield*/, getAfUrl(plugin, customState.initParams.moleculeId)];
case 4:
afStrUrls = _a.sent();
if (afStrUrls)
customState.superpositionState.alphafold.apiData = afStrUrls;
segmentData.forEach(function () {
plugin.customState.superpositionState.loadedStructs.push([]);
plugin.customState.superpositionState.visibleRefs.push([]);
plugin.customState.superpositionState.colorState.push({ palleteIndex: 0, colorIndex: -1 });
});
segmentIndex = (superpositionParams && superpositionParams.segment) ? superpositionParams.segment - 1 : 0;
plugin.customState.superpositionState.activeSegment = segmentIndex + 1;
clusterIndexs = (superpositionParams && superpositionParams.cluster) ? superpositionParams.cluster : void 0;
// Emit segment API data load event
plugin.customState.events.superpositionInit.next(true);
entryList = [];
clusters = segmentData[segmentIndex].clusters;
clusters.forEach(function (cluster, clusterIndex) {
// Validate for cluster index if provided in superPositionParams
if (clusterIndexs && clusterIndexs.indexOf(clusterIndex) === -1)
return;
// Add respresentative structure to the list
if (superpositionParams && superpositionParams.superposeAll) {
entryList = entryList.concat(cluster);
}
else {
entryList.push(cluster[0]);
}
});
return [4 /*yield*/, renderSuperposition(plugin, segmentIndex, entryList)];
case 5:
_a.sent();
return [2 /*return*/];
}
});
});
}
exports.initSuperposition = initSuperposition;
function createCarbVisLabel(carbLigNamesAndCount) {
var compList = [];
for (var carbCompId in carbLigNamesAndCount) {
compList.push("".concat(carbCompId, " (").concat(carbLigNamesAndCount[carbCompId], ")"));
}
return compList.join(', ');
}
function getAfUrl(plugin, accession) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var apiResponse, apiData;
var _this = this;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Get AlphaFold URL', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var e_1;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
_a.trys.push([0, 2, , 3]);
return [4 /*yield*/, plugin.fetch({ url: "https://alphafold.ebi.ac.uk/api/prediction/".concat(accession), type: 'json' }).runInContext(ctx)];
case 1:
apiResponse = _a.sent();
if (apiResponse && (apiResponse === null || apiResponse === void 0 ? void 0 : apiResponse[0].bcifUrl)) {
apiData = {
cif: apiResponse === null || apiResponse === void 0 ? void 0 : apiResponse[0].cifUrl,
pae: apiResponse === null || apiResponse === void 0 ? void 0 : apiResponse[0].paeImageUrl,
length: apiResponse === null || apiResponse === void 0 ? void 0 : apiResponse[0].uniprotEnd
};
}
return [3 /*break*/, 3];
case 2:
e_1 = _a.sent();
return [3 /*break*/, 3];
case 3: return [2 /*return*/];
}
});
}); }))];
case 1:
_a.sent();
return [2 /*return*/, apiData];
}
});
});
}
function loadAfStructure(plugin) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var customState, structure, strInstance, spState, chainSel;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
customState = plugin.customState;
return [4 /*yield*/, loadStructure(plugin, customState.superpositionState.alphafold.apiData.cif, 'mmcif', false)];
case 1:
structure = (_a.sent()).structure;
strInstance = structure;
if (!strInstance)
return [2 /*return*/, false];
spState = plugin.customState.superpositionState;
spState.alphafold.ref = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
spState.models["AF-".concat(customState.initParams.moleculeId)] = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
return [4 /*yield*/, plugin.builders.structure.tryCreateComponentStatic(strInstance, 'polymer', { label: "AlphaFold Structure", tags: ["alphafold-chain", "superposition-sel"] })];
case 2:
chainSel = _a.sent();
if (!chainSel) return [3 /*break*/, 4];
return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'plddt-confidence', size: 'uniform', sizeParams: { value: 1.5 } }, { tag: "af-superposition-visual" })];
case 3:
_a.sent();
return [2 /*return*/, strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref];
case 4: return [2 /*return*/, false];
}
});
});
}
exports.loadAfStructure = loadAfStructure;
function superposeAf(plugin, traceOnly, segmentIndex) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var customState, spState, afStrRef, _a, afStr, segmentNum, mappingResult_1, coordinateSystems_1, failedPairsResult_1, zeroOverlapPairsResult_1, minRmsd_1, minIndex_1, rmsdList_1, segmentClusters;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
customState = plugin.customState;
if (!customState.superpositionState || !customState.superpositionState.segmentData)
return [2 /*return*/];
spState = customState.superpositionState;
_a = spState.alphafold.ref;
if (_a) return [3 /*break*/, 2];
return [4 /*yield*/, loadAfStructure(plugin)];
case 1:
_a = (_b.sent());
_b.label = 2;
case 2:
afStrRef = _a;
if (!afStrRef)
return [2 /*return*/];
afStr = plugin.managers.structure.hierarchy.current.refs.get(afStrRef);
segmentNum = segmentIndex ? segmentIndex : spState.activeSegment - 1;
if (!spState.alphafold.transforms[segmentNum]) {
mappingResult_1 = [];
coordinateSystems_1 = [];
failedPairsResult_1 = [];
zeroOverlapPairsResult_1 = [];
minRmsd_1 = 0;
minIndex_1 = 0;
rmsdList_1 = [];
segmentClusters = spState.segmentData[segmentNum].clusters;
segmentClusters.forEach(function (cluster) {
var _a, _b, _c;
var modelRef = spState.models["".concat(cluster[0].pdb_id, "_").concat(cluster[0].struct_asym_id)];
if (modelRef) {
var structHierarchy = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
if (structHierarchy) {
var input = [structHierarchy.components[0], afStr];
var structures = input.map(function (s) { var _a; return (_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data; });
var _d = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, { traceOnly: traceOnly, includeResidueTest: function (loc) { return structure_1.StructureProperties.atom.B_iso_or_equiv(loc) > 70; },
applyTestIndex: [1] }), entries = _d.entries, failedPairs = _d.failedPairs, zeroOverlapPairs = _d.zeroOverlapPairs;
if (entries.length === 0 || (entries && entries[0] && entries[0].transform.rmsd.toFixed(1) === '0.0')) {
var alignWithoutPlddt = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, { traceOnly: traceOnly });
entries = alignWithoutPlddt.entries;
}
if (entries && entries[0]) {
mappingResult_1.push(entries[0]);
coordinateSystems_1.push((_c = (_b = (_a = input[0]) === null || _a === void 0 ? void 0 : _a.transform) === null || _b === void 0 ? void 0 : _b.cell.obj) === null || _c === void 0 ? void 0 : _c.data.coordinateSystem);
var totalMappings = mappingResult_1.length;
if (totalMappings === 1 || entries[0].transform.rmsd < minRmsd_1) {
minRmsd_1 = entries[0].transform.rmsd;
minIndex_1 = totalMappings === 1 ? 0 : mappingResult_1.length - 1;
}
rmsdList_1.push("".concat(cluster[0].pdb_id, " chain ").concat(cluster[0].struct_asym_id, ":").concat(entries[0].transform.rmsd.toFixed(2)));
}
else {
if (failedPairs.length > 0)
failedPairsResult_1.push(failedPairs);
if (zeroOverlapPairs.length > 0)
zeroOverlapPairsResult_1.push(zeroOverlapPairs);
// rmsdList.push(`${cluster[0].pdb_id} ${cluster[0].struct_asym_id}:-`)
}
}
}
});
// console.log(failedPairsResult);
// console.log(zeroOverlapPairsResult);
if (mappingResult_1.length > 0) {
spState.alphafold.visibility[segmentNum] = true;
spState.alphafold.transforms[segmentNum] = mappingResult_1[minIndex_1].transform.bTransform;
spState.alphafold.coordinateSystems[segmentNum] = coordinateSystems_1[minIndex_1];
spState.alphafold.rmsds[segmentNum] = rmsdList_1.sort(function (a, b) { return parseFloat(a.split(':')[1]) - parseFloat(b.split(':')[1]); });
}
}
return [4 /*yield*/, afTransform(plugin, afStr.cell, spState.alphafold.transforms[segmentNum], spState.alphafold.coordinateSystems[segmentNum])];
case 3:
_b.sent();
(0, alphafold_transparency_1.applyAFTransparency)(plugin, afStr, 0.8, 70);
return [2 /*return*/, true];
}
});
});
}
exports.superposeAf = superposeAf;
function renderSuperposition(plugin, segmentIndex, entryList) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var customState, superpositionParams, busyFlagOn;
var _this = this;
return tslib_1.__generator(this, function (_a) {
customState = plugin.customState;
superpositionParams = customState.initParams.superpositionParams;
busyFlagOn = false;
if (entryList.length > 1) {
busyFlagOn = true;
customState.events.isBusy.next(true);
}
// Load Coordinates and render respresentations
return [2 /*return*/, plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var spState, entryList_1, entryList_1_1, s, strUrl, strInstance, modelRef, clearOnFail, polymerInstance, modelInstance, isBinary, _a, model, structure, matrix, chainSel, uniformColor1, uniformColor2, invalidStruct, state, hetInfo, hets, hets_1, hets_1_1, het, ligand, labelTagParams, hetColor, _b, r, g, b, ligandExp, e_2_1, carbEntityCount, allCarbPolymers, polymerChainWithSurroundings, i, _i, _c, carbEntityChainId, carbEntityChain, carbEntityChainInVicinity, data, carbChainSel, carbLigands, carbLigNamesAndCount, carbLigList, _d, _e, carbLigs, ligResDetails, carbVisLabel, branchedEntity, labelTagParams, ligandExp, loadedStructIndex, e_3_1;
var e_3, _f, e_2, _g;
return tslib_1.__generator(this, function (_h) {
switch (_h.label) {
case 0:
spState = plugin.customState.superpositionState;
_h.label = 1;
case 1:
_h.trys.push([1, 41, 42, 47]);
entryList_1 = tslib_1.__asyncValues(entryList);
_h.label = 2;
case 2: return [4 /*yield*/, entryList_1.next()];
case 3:
if (!(entryList_1_1 = _h.sent(), !entryList_1_1.done)) return [3 /*break*/, 40];
s = entryList_1_1.value;
// validate matrix availability
if (!spState.matrixData["".concat(s.pdb_id, "_").concat(s.auth_asym_id)]) {
spState.noMatrixStruct.push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
spState.invalidStruct.push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
return [3 /*break*/, 39];
}
spState.loadedStructs[segmentIndex].push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
strUrl = "".concat(customState.initParams.pdbeUrl, "model-server/v1/").concat(s.pdb_id, "/atoms?auth_asym_id=").concat(s.auth_asym_id, "&encoding=").concat(customState.initParams.encoding);
if (superpositionParams && superpositionParams.ligandView)
strUrl = "https://www.ebi.ac.uk/pdbe/entry-files/download/".concat(s.pdb_id, ".bcif");
strInstance = void 0;
modelRef = void 0;
clearOnFail = true;
if (!(superpositionParams && superpositionParams.ligandView && spState.entries[s.pdb_id])) return [3 /*break*/, 5];
polymerInstance = plugin.state.data.select(spState.entries[s.pdb_id])[0];
modelRef = polymerInstance.transform.parent;
modelInstance = plugin.state.data.select(modelRef)[0];
return [4 /*yield*/, plugin.builders.structure.createStructure(modelInstance, { name: 'model', params: {} })];
case 4:
strInstance = _h.sent();
clearOnFail = false;
return [3 /*break*/, 7];
case 5:
isBinary = customState.initParams.encoding === 'bcif' ? true : false;
return [4 /*yield*/, loadStructure(plugin, strUrl, 'mmcif', isBinary)];
case 6:
_a = _h.sent(), model = _a.model, structure = _a.structure;
strInstance = structure;
modelRef = model.ref;
_h.label = 7;
case 7:
if (!strInstance)
return [3 /*break*/, 39];
// Store Refs in state
if (!spState.models["".concat(s.pdb_id, "_").concat(s.struct_asym_id)])
spState.models["".concat(s.pdb_id, "_").concat(s.struct_asym_id)] = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
if (superpositionParams && superpositionParams.ligandView && !spState.entries[s.pdb_id])
spState.entries[s.pdb_id] = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
matrix = linear_algebra_1.Mat4.ofRows(plugin.customState.superpositionState.matrixData["".concat(s.pdb_id, "_").concat(s.auth_asym_id)].matrix);
return [4 /*yield*/, transform(plugin, strInstance, matrix)];
case 8:
_h.sent();
chainSel = void 0;
if (!((superpositionParams && superpositionParams.ligandView) && s.is_representative)) return [3 /*break*/, 12];
uniformColor1 = getRandomColor(plugin, segmentIndex);
return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, chainSelection(s.struct_asym_id), "Chain-".concat(segmentIndex), { label: "Chain", tags: ["superposition-sel"] })];
case 9:
chainSel = _h.sent();
if (!chainSel) return [3 /*break*/, 11];
return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor1 }, size: 'uniform' }, { tag: "superposition-visual" })];
case 10:
_h.sent();
spState.refMaps[chainSel.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
_h.label = 11;
case 11: return [3 /*break*/, 16];
case 12:
if (!((superpositionParams && superpositionParams.ligandView) && !s.is_representative)) return [3 /*break*/, 13];
return [3 /*break*/, 16];
case 13:
uniformColor2 = getRandomColor(plugin, segmentIndex);
return [4 /*yield*/, plugin.builders.structure.tryCreateComponentStatic(strInstance, 'polymer', { label: "Chain", tags: ["Chain-".concat(segmentIndex), "superposition-sel"] })];
case 14:
chainSel = _h.sent();
if (!chainSel) return [3 /*break*/, 16];
return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor2 }, size: 'uniform' }, { tag: "superposition-visual" })];
case 15:
_h.sent();
spState.refMaps[chainSel.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
_h.label = 16;
case 16:
invalidStruct = chainSel ? false : true;
if (!(superpositionParams && superpositionParams.ligandView)) return [3 /*break*/, 39];
state = plugin.state.data;
return [4 /*yield*/, getLigandNamesFromModelData(plugin, state, modelRef)];
case 17:
hetInfo = _h.sent();
hets = hetInfo ? hetInfo.hetNames : [];
if (!(hets && hets.length > 0)) return [3 /*break*/, 31];
_h.label = 18;
case 18:
_h.trys.push([18, 25, 26, 31]);
hets_1 = (e_2 = void 0, tslib_1.__asyncValues(hets));
_h.label = 19;
case 19: return [4 /*yield*/, hets_1.next()];
case 20:
if (!(hets_1_1 = _h.sent(), !hets_1_1.done)) return [3 /*break*/, 24];
het = hets_1_1.value;
ligand = builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), s.auth_asym_id]),
'residue-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.label_comp_id(), het]),
'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
});
labelTagParams = { label: "".concat(het), tags: ["superposition-ligand-sel"] };
hetColor = color_1.Color.fromRgb(253, 3, 253);
if (superpositionParams && superpositionParams.ligandColor) {
_b = superpositionParams.ligandColor, r = _b.r, g = _b.g, b = _b.b;
hetColor = color_1.Color.fromRgb(r, g, b);
}
return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, ligand, "".concat(het, "-").concat(segmentIndex), labelTagParams)];
case 21:
ligandExp = _h.sent();
if (!ligandExp) return [3 /*break*/, 23];
return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(ligandExp, { type: 'ball-and-stick', color: 'uniform', colorParams: { value: hetColor } }, { tag: "superposition-ligand-visual" })];
case 22:
_h.sent();
spState.refMaps[ligandExp.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
invalidStruct = false;
_h.label = 23;
case 23: return [3 /*break*/, 19];
case 24: return [3 /*break*/, 31];
case 25:
e_2_1 = _h.sent();
e_2 = { error: e_2_1 };
return [3 /*break*/, 31];
case 26:
_h.trys.push([26, , 29, 30]);
if (!(hets_1_1 && !hets_1_1.done && (_g = hets_1.return))) return [3 /*break*/, 28];
return [4 /*yield*/, _g.call(hets_1)];
case 27:
_h.sent();
_h.label = 28;
case 28: return [3 /*break*/, 30];
case 29:
if (e_2) throw e_2.error;
return [7 /*endfinally*/];
case 30: return [7 /*endfinally*/];
case 31:
carbEntityCount = hetInfo ? hetInfo.carbEntityCount : 0;
if (!(carbEntityCount > 0)) return [3 /*break*/, 38];
return [4 /*yield*/, getCarbPolymerDetailsFromApi(plugin, s.pdb_id)];
case 32:
allCarbPolymers = _h.sent();
polymerChainWithSurroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
0: builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), s.auth_asym_id]),
'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
}),
radius: 5,
'as-whole-residues': true
});
i = 0;
_i = 0, _c = allCarbPolymers.branchedChains;
_h.label = 33;
case 33:
if (!(_i < _c.length)) return [3 /*break*/, 38];
carbEntityChainId = _c[_i];
carbEntityChain = builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'branched']),
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), carbEntityChainId]),
'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
});
carbEntityChainInVicinity = builder_1.MolScriptBuilder.struct.filter.intersectedBy({
0: polymerChainWithSurroundings,
by: carbEntityChain
});
data = (plugin.state.data.select(strInstance.ref)[0].obj).data;
carbChainSel = script_1.Script.getStructureSelection(carbEntityChainInVicinity, data);
if (!(carbChainSel && carbChainSel.kind === 'sequence')) return [3 /*break*/, 36];
carbLigands = [];
carbLigNamesAndCount = {};
carbLigList = [];
for (_d = 0, _e = allCarbPolymers.branchedLigands[i]; _d < _e.length; _d++) {
carbLigs = _e[_d];
ligResDetails = carbLigs.split('-');
carbLigands.push(builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_seq_id(), +ligResDetails[1]]));
if (carbLigNamesAndCount[ligResDetails[0]]) {
carbLigNamesAndCount[ligResDetails[0]]++;
}
else {
carbLigNamesAndCount[ligResDetails[0]] = 1;
}
carbLigList.push(ligResDetails[0]);
}
carbVisLabel = createCarbVisLabel(carbLigNamesAndCount);
branchedEntity = builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'branched']),
'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()]),
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), carbEntityChainId]),
'residue-test': builder_1.MolScriptBuilder.core.logic.or(carbLigands)
});
labelTagParams = { label: "".concat(carbVisLabel), tags: ["superposition-carb-sel"] };
return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(strInstance, branchedEntity, "".concat(carbLigList.join('-'), "-").concat(segmentIndex), labelTagParams)];
case 34:
ligandExp = _h.sent();
if (!ligandExp) return [3 /*break*/, 36];
return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(ligandExp, { type: 'carbohydrate' }, { tag: "superposition-carb-visual" })];
case 35:
_h.sent();
spState.refMaps[ligandExp.ref] = "".concat(s.pdb_id, "_").concat(s.struct_asym_id);
invalidStruct = false;
_h.label = 36;
case 36:
i++;
_h.label = 37;
case 37:
_i++;
return [3 /*break*/, 33];
case 38:
if (invalidStruct) {
spState.invalidStruct.push("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
loadedStructIndex = spState.loadedStructs[segmentIndex].indexOf("".concat(s.pdb_id, "_").concat(s.struct_asym_id));
if (loadedStructIndex > -1)
spState.loadedStructs[segmentIndex].splice(loadedStructIndex, 1);
// remove downloaded data
if (clearOnFail) {
// const m = plugin.state.data.select(modelRef)[0];
// const t = plugin.state.data.select(m.transform.parent)[0];
// const d = plugin.state.data.select(t.transform.parent)[0];
// PluginCommands.State.RemoveObject(plugin, { state: d.parent!, ref: d.transform.parent, removeParentGhosts: true });
}
}
else {
// if(interactingHets.length > 0) spState.hets[`${s.pdb_id}_${s.struct_asym_id}`] = interactingHets;
}
_h.label = 39;
case 39: return [3 /*break*/, 2];
case 40: return [3 /*break*/, 47];
case 41:
e_3_1 = _h.sent();
e_3 = { error: e_3_1 };
return [3 /*break*/, 47];
case 42:
_h.trys.push([42, , 45, 46]);
if (!(entryList_1_1 && !entryList_1_1.done && (_f = entryList_1.return))) return [3 /*break*/, 44];
return [4 /*yield*/, _f.call(entryList_1)];
case 43:
_h.sent();
_h.label = 44;
case 44: return [3 /*break*/, 46];
case 45:
if (e_3) throw e_3.error;
return [7 /*endfinally*/];
case 46: return [7 /*endfinally*/];
case 47:
if (busyFlagOn) {
busyFlagOn = false;
customState.events.isBusy.next(false);
}
return [2 /*return*/];
}
});
}); })];
});
});
}
exports.renderSuperposition = renderSuperposition;
function getLigandNamesFromModelData(plugin, state, modelRef) {
var _a;
return tslib_1.__awaiter(this, void 0, void 0, function () {
var cell, model, structures, _i, _b, s, structure, info;
return tslib_1.__generator(this, function (_c) {
switch (_c.label) {
case 0:
cell = state.select(modelRef)[0];
if (!cell || !cell.obj)
return [2 /*return*/, void 0];
model = cell.obj.data;
if (!model)
return [2 /*return*/];
structures = [];
for (_i = 0, _b = plugin.managers.structure.hierarchy.selection.structures; _i < _b.length; _i++) {
s = _b[_i];
structure = (_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data;
if (structure)
structures.push(structure);
}
return [4 /*yield*/, helpers_1.ModelInfo.get(model, structures)];
case 1:
info = _c.sent();
return [2 /*return*/, info];
}
});
});
}
function loadStructure(plugin, url, format, isBinary) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var data, trajectory, model, modelProperties, structure, e_4;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
_a.trys.push([0, 7, , 8]);
return [4 /*yield*/, plugin.builders.data.download({ url: assets_1.Asset.Url(url), isBinary: isBinary })];
case 1:
data = _a.sent();
return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, format)];
case 2:
trajectory = _a.sent();
return [4 /*yield*/, plugin.builders.structure.createModel(trajectory)];
case 3:
model = _a.sent();
return [4 /*yield*/, plugin.builders.structure.insertModelProperties(model)];
case 4:
modelProperties = _a.sent();
return [4 /*yield*/, plugin.builders.structure.createStructure(modelProperties || model, { name: 'model', params: {} })];
case 5:
structure = _a.sent();
return [4 /*yield*/, plugin.builders.structure.insertStructureProperties(structure)];
case 6:
_a.sent();
return [2 /*return*/, { data: data, trajectory: trajectory, model: model, structure: structure }];
case 7:
e_4 = _a.sent();
return [2 /*return*/, { structure: void 0 }];
case 8: return [2 /*return*/];
}
});
});
}
function chainSelection(struct_asym_id) {
return builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.label_asym_id(), struct_asym_id])
});
}
function transform(plugin, s, matrix) {
var b = plugin.state.data.build().to(s)
.insert(transforms_1.StateTransforms.Model.TransformStructureConformation, { transform: { name: 'matrix', params: { data: matrix, transpose: false } } });
return plugin.runTask(plugin.state.data.updateTree(b));
}
function afTransform(plugin, s, matrix, coordinateSystem) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var r, o, transform, params, b;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
r = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, s);
if (!r)
return [2 /*return*/];
o = plugin.state.data.selectQ(function (q) { return q.byRef(r.transform.ref).subtree().withTransformer(transforms_1.StateTransforms.Model.TransformStructureConformation); })[0];
transform = coordinateSystem && !linear_algebra_1.Mat4.isIdentity(coordinateSystem.matrix)
? linear_algebra_1.Mat4.mul((0, linear_algebra_1.Mat4)(), coordinateSystem.matrix, matrix)
: matrix;
params = {
transform: {
name: 'matrix',
params: { data: transform, transpose: false }
}
};
b = o
? plugin.state.data.build().to(o).update(params)
: plugin.state.data.build().to(s)
.insert(transforms_1.StateTransforms.Model.TransformStructureConformation, params, { tags: 'SuperpositionTransform' });
return [4 /*yield*/, plugin.runTask(plugin.state.data.updateTree(b))];
case 1:
_a.sent();
return [2 /*return*/];
}
});
});
}
function getMatrixData(plugin) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var customState, matrixAccession, clusterRecUrlStr, assetManager, clusterRecUrl, clusterRecData, e_5;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
customState = plugin.customState;
matrixAccession = customState.initParams.superpositionParams.matrixAccession ? customState.initParams.superpositionParams.matrixAccession : customState.initParams.moleculeId;
clusterRecUrlStr = "".concat(customState.initParams.pdbeUrl, "static/superpose/matrices/").concat(matrixAccession);
assetManager = plugin.managers.asset;
clusterRecUrl = assets_1.Asset.getUrlAsset(assetManager, clusterRecUrlStr);
_a.label = 1;
case 1:
_a.trys.push([1, 3, , 4]);
return [4 /*yield*/, plugin.runTask(assetManager.resolve(clusterRecUrl, 'json', false))];
case 2:
clusterRecData = _a.sent();
if (clusterRecData && clusterRecData.data) {
plugin.customState.superpositionState.matrixData = clusterRecData.data;
}
return [3 /*break*/, 4];
case 3:
e_5 = _a.sent();
customState['superpositionError'] = "Matrix data not available for ".concat(matrixAccession);
plugin.customState.events.superpositionInit.next(true); // Emit segment API data load event
return [3 /*break*/, 4];
case 4: return [2 /*return*/];
}
});
});
}
function getSegmentData(plugin) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var customState, segmentsUrl, assetManager, url, result, e_6;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
customState = plugin.customState;
segmentsUrl = "".concat(customState.initParams.pdbeUrl, "graph-api/uniprot/superposition/").concat(customState.initParams.moleculeId);
assetManager = plugin.managers.asset;
url = assets_1.Asset.getUrlAsset(assetManager, segmentsUrl);
_a.label = 1;
case 1:
_a.trys.push([1, 3, , 4]);
return [4 /*yield*/, plugin.runTask(assetManager.resolve(url, 'json', false))];
case 2:
result = _a.sent();
if (result && result.data) {
customState.superpositionState.segmentData = result.data[customState.initParams.moleculeId];
}
return [3 /*break*/, 4];
case 3:
e_6 = _a.sent();
customState['superpositionError'] = "Superposition data not available for ".concat(customState.initParams.moleculeId);
plugin.customState.events.superpositionInit.next(true); // Emit segment API data load event
return [3 /*break*/, 4];
case 4: return [2 /*return*/];
}
});
});
}
function getChainLigands(carbEntity) {
var ligandChain = [];
var ligandLabels = [];
var ligands = [];
var labelValueArr = [];
var ligNameStr = '';
for (var _i = 0, _a = carbEntity.chem_comp_list; _i < _a.length; _i++) {
var chemComp = _a[_i];
labelValueArr.push("".concat(chemComp.chem_comp_id, " (").concat(chemComp.count, ")"));
}
ligNameStr = labelValueArr.join(', ');
for (var _b = 0, _c = carbEntity.chains; _b < _c.length; _b++) {
var chain = _c[_b];
ligandChain.push(chain.chain_id);
ligandLabels.push(ligNameStr);
var chainLigands = [];
for (var _d = 0, _e = chain.residues; _d < _e.length; _d++) {
var residue = _e[_d];
chainLigands.push(residue.chem_comp_id + '-' + residue.residue_number);
}
ligands.push(chainLigands);
}
return {
ligands: ligands,
ligandChain: ligandChain,
ligandLabels: ligandLabels
};
}
function getCarbPolymerDetailsFromApi(plugin, pdb_id) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var customState, apiUrl, assetManager, url, branchedLigands, branchedChains, branchedlabels, result, carbEntities, _i, carbEntities_1, carbEntity, carbLigData, e_7;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
customState = plugin.customState;
apiUrl = "".concat(customState.initParams.pdbeUrl, "api/pdb/entry/carbohydrate_polymer/").concat(pdb_id);
assetManager = plugin.managers.asset;
url = assets_1.Asset.getUrlAsset(assetManager, apiUrl);
branchedLigands = [];
branchedChains = [];
branchedlabels = [];
_a.label = 1;
case 1:
_a.trys.push([1, 3, , 4]);
return [4 /*yield*/, plugin.runTask(assetManager.resolve(url, 'json', false))];
case 2:
result = _a.sent();
if (result && result.data) {
carbEntities = result.data[pdb_id];
for (_i = 0, carbEntities_1 = carbEntities; _i < carbEntities_1.length; _i++) {
carbEntity = carbEntities_1[_i];
carbLigData = getChainLigands(carbEntity);
branchedLigands = branchedLig