@rcsb/rcsb-saguaro-3d
Version:
RCSB Molstar/Saguaro Web App
299 lines • 15.1 kB
JavaScript
import { __awaiter } from "tslib";
import { StructureElement, StructureSelection } from "molstar/lib/mol-model/structure";
import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
import { Script } from "molstar/lib/mol-script/script";
export var LoadMethod;
(function (LoadMethod) {
LoadMethod["loadPdbId"] = "loadPdbId";
LoadMethod["loadStructureFromUrl"] = "loadStructureFromUrl";
LoadMethod["loadSnapshotFromUrl"] = "loadSnapshotFromUrl";
LoadMethod["loadStructureFromData"] = "loadStructureFromData";
})(LoadMethod || (LoadMethod = {}));
export class MolstarActionManager {
constructor(config) {
this.viewer = config.viewer;
this.modelMapManager = config.modelMapManager;
this.innerSelectionFlag = config.innerSelectionFlag;
this.innerReprChangeFlag = config.innerReprChangeFlag;
this.loadingFlag = config.loadingFlag;
}
load(loadConfig) {
return __awaiter(this, void 0, void 0, function* () {
this.loadingFlag.set(true);
const out = [];
for (const lC of (Array.isArray(loadConfig) ? loadConfig : [loadConfig])) {
if (checkLoadData(lC)) {
if (lC.loadMethod == LoadMethod.loadPdbId) {
const config = lC.loadParams;
out.push(yield this.viewer.loadPdbId(config.entryId, { props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params }));
}
else if (lC.loadMethod == LoadMethod.loadStructureFromUrl) {
const config = lC.loadParams;
out.push(yield this.viewer.loadStructureFromUrl(config.url, config.format, config.isBinary, { props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params }));
}
else if (lC.loadMethod == LoadMethod.loadSnapshotFromUrl) {
const config = lC.loadParams;
yield this.viewer.loadSnapshotFromUrl(config.url, config.type);
}
else if (lC.loadMethod == LoadMethod.loadStructureFromData) {
const config = lC.loadParams;
out.push(yield this.viewer.loadStructureFromData(config.data, config.format, config.isBinary, { props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params }));
}
const trajectory = out[out.length - 1];
if (trajectory)
this.modelMapManager.add(lC, trajectory);
}
}
this.loadingFlag.set(false);
return out.length == 1 ? out[0] : out;
});
}
removeStructure(loadConfig) {
return __awaiter(this, void 0, void 0, function* () {
loadConfig = Array.isArray(loadConfig) ? loadConfig : [loadConfig];
loadConfig.forEach(lC => {
(Array.isArray(lC.loadParams) ? lC.loadParams : [lC.loadParams]).forEach(loadParams => {
if (typeof loadParams.id === "string") {
const pdbStr = this.viewer.plugin.managers.structure.hierarchy.current.structures.find(s => { var _a, _b, _c, _d, _e, _f; return ((_f = (_e = (_d = (_c = (_b = (_a = s.properties) === null || _a === void 0 ? void 0 : _a.cell) === null || _b === void 0 ? void 0 : _b.obj) === null || _c === void 0 ? void 0 : _c.data) === null || _d === void 0 ? void 0 : _d.units[0]) === null || _e === void 0 ? void 0 : _e.model) === null || _f === void 0 ? void 0 : _f.id) == this.modelMapManager.getModelId(loadParams.id); });
if (pdbStr) {
this.viewer.plugin.managers.structure.hierarchy.remove([pdbStr]);
}
}
});
});
});
}
select(...args) {
if (args[5] != undefined) {
this.selectRange(args[0], args[1], args[2], args[3], args[4], args[5], args[6]);
}
else if (Array.isArray(args[0]) && args[0].length > 0 && typeof args[0][0].position === 'number') {
this.selectSet(args[0], args[1], args[2]);
}
else if (Array.isArray(args[0]) && args[0].length > 0 && typeof args[0][0].begin === 'number') {
this.selectMultipleRanges(args[0], args[1], args[2]);
}
}
selectRange(modelId, labelAsymId, begin, end, mode, operation, operatorName) {
if (mode == null || mode === 'select') {
this.innerSelectionFlag.set(true);
}
this.viewer.select({ modelId: this.modelMapManager.getModelId(modelId), labelAsymId: labelAsymId, labelSeqRange: { beg: begin, end: end }, operatorName: operatorName }, mode, operation);
this.innerSelectionFlag.set(false);
}
selectSet(selection, mode, operation) {
if (mode == null || mode === 'select') {
this.innerSelectionFlag.set(true);
}
this.viewer.select(selection.map(r => ({ modelId: this.modelMapManager.getModelId(r.modelId), labelSeqId: r.position, labelAsymId: r.labelAsymId, operatorName: r.operatorName })), mode, operation);
this.innerSelectionFlag.set(false);
}
selectMultipleRanges(selection, mode, operation) {
if (mode == null || mode === 'select') {
this.innerSelectionFlag.set(true);
}
this.viewer.select(selection.map(r => ({ modelId: this.modelMapManager.getModelId(r.modelId), labelAsymId: r.labelAsymId, labelSeqRange: { beg: r.begin, end: r.end }, operatorName: r.operatorName })), mode, operation);
this.innerSelectionFlag.set(false);
}
clear() {
return __awaiter(this, void 0, void 0, function* () {
yield this.viewer.clear();
});
}
clearSelection(mode, option) {
if (mode === 'select') {
this.viewer.clearFocus();
this.innerSelectionFlag.set(true);
}
if (option != null)
this.viewer.clearSelection(mode, Object.assign(Object.assign({}, option), { modelId: this.modelMapManager.getModelId(option.modelId) }));
else
this.viewer.clearSelection(mode);
this.innerSelectionFlag.set(false);
}
setFocus(modelId, labelAsymId, begin, end, operatorName) {
this.viewer.setFocus({ modelId: this.modelMapManager.getModelId(modelId), labelAsymId: labelAsymId, labelSeqRange: { beg: begin, end: end }, operatorName: operatorName });
}
clearFocus() {
this.viewer.clearFocus();
}
cameraFocus(...args) {
if (Array.isArray(args[2])) {
this.focusPositions(args[0], args[1], args[2], args[3]);
}
else {
this.focusRange(args[0], args[1], args[2], args[3], args[4]);
}
}
focusRange(modelId, labelAsymId, begin, end, operatorName) {
const seqIds = new Array();
for (let n = begin; n <= end; n++) {
seqIds.push(n);
}
this.focusPositions(modelId, labelAsymId, seqIds, operatorName);
}
focusPositions(modelId, labelAsymId, positions, operatorName) {
const structure = getStructureWithModelId(this.viewer.plugin.managers.structure.hierarchy.current.structures, this.modelMapManager.getModelId(modelId));
if (structure == null)
return;
const chainTests = [MS.core.rel.eq([MS.ammp('label_asym_id'), labelAsymId])];
if (operatorName)
chainTests.push(MS.core.rel.eq([operatorName, MS.acp('operatorName')]));
const sel = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
'chain-test': Q.core.logic.and(chainTests),
'residue-test': Q.core.logic.or(Array.from(new Set(positions)).map(p => MS.struct.atomProperty.ihm.hasSeqId([p])))
}), structure);
const loci = StructureSelection.toLociWithSourceUnits(sel);
if (!StructureElement.Loci.isEmpty(loci)) {
this.viewer.plugin.managers.camera.focusLoci(loci);
}
else {
this.resetCamera();
}
}
createComponent(...args) {
return __awaiter(this, void 0, void 0, function* () {
this.innerReprChangeFlag.set(true);
yield this.removeComponent(args[0]);
if (Array.isArray(args[1])) {
if (args[1].length > 0) {
if (typeof args[1][0].position === "number") {
yield this.viewer.createComponent(args[0], args[1].map(r => ({ modelId: this.modelMapManager.getModelId(r.modelId), labelAsymId: r.labelAsymId, labelSeqId: r.position, operatorName: r.operatorName })), args[2]);
}
else {
yield this.viewer.createComponent(args[0], args[1].map(r => ({ modelId: this.modelMapManager.getModelId(r.modelId), labelAsymId: r.labelAsymId, labelSeqRange: { beg: r.begin, end: r.end }, operatorName: r.operatorName })), args[2]);
}
}
}
else if (args[5] != undefined) {
yield this.viewer.createComponent(args[0], { modelId: this.modelMapManager.getModelId(args[1]), labelAsymId: args[2], labelSeqRange: { beg: args[3], end: args[4] }, operatorName: args[6] }, args[5]);
}
else {
yield this.viewer.createComponent(args[0], { modelId: this.modelMapManager.getModelId(args[1]), labelAsymId: args[2], operatorName: args[4] }, args[3]);
}
this.innerReprChangeFlag.set(false);
});
}
isComponent(componentLabel) {
var _a;
for (const c of this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups) {
for (const comp of c) {
if (((_a = comp.cell.obj) === null || _a === void 0 ? void 0 : _a.label) === componentLabel) {
return true;
}
}
}
return false;
}
colorComponent(componentLabel, color) {
return __awaiter(this, void 0, void 0, function* () {
var _a;
for (const c of this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups) {
for (const comp of c) {
if (((_a = comp.cell.obj) === null || _a === void 0 ? void 0 : _a.label) === componentLabel) {
yield this.viewer.plugin.managers.structure.component.updateRepresentationsTheme([comp], { color: color });
return;
}
}
}
});
}
getComponentSet() {
const out = new Set();
this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups.forEach((c) => {
var _a, _b, _c, _d;
for (const comp of c) {
if (((_a = comp.cell.obj) === null || _a === void 0 ? void 0 : _a.label) != null && out.has((_b = comp.cell.obj) === null || _b === void 0 ? void 0 : _b.label)) {
break;
}
else if (((_c = comp.cell.obj) === null || _c === void 0 ? void 0 : _c.label) != null) {
out.add((_d = comp.cell.obj) === null || _d === void 0 ? void 0 : _d.label);
}
}
});
return out;
}
removeComponent(componentLabel) {
return __awaiter(this, void 0, void 0, function* () {
if (componentLabel == null) {
this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups.forEach(c => this.viewer.plugin.managers.structure.hierarchy.remove(c));
}
else {
yield this.viewer.removeComponent(componentLabel);
}
});
}
displayComponent(componentLabel, visibilityFlag) {
if (typeof visibilityFlag === 'boolean')
return this.changeComponentDisplay(componentLabel, visibilityFlag);
else
return this.getComponentDisplay(componentLabel);
}
changeComponentDisplay(componentLabel, visibilityFlag) {
var _a;
this.innerReprChangeFlag.set(true);
for (const c of this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups) {
for (const comp of c) {
if (((_a = comp.cell.obj) === null || _a === void 0 ? void 0 : _a.label) === componentLabel) {
if (!comp.cell.state.isHidden != visibilityFlag) {
this.viewer.plugin.managers.structure.component.toggleVisibility(c);
return void 0;
}
}
}
}
this.innerReprChangeFlag.set(false);
}
getComponentDisplay(componentLabel) {
var _a;
for (const c of this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups) {
for (const comp of c) {
if (((_a = comp.cell.obj) === null || _a === void 0 ? void 0 : _a.label) === componentLabel) {
return !comp.cell.state.isHidden;
}
}
}
return false;
}
resetCamera() {
this.viewer.plugin.managers.camera.reset();
}
exportLoadedStructures() {
return __awaiter(this, void 0, void 0, function* () {
yield this.viewer.exportLoadedStructures();
});
}
}
function getStructureWithModelId(structures, modelId) {
var _a, _b, _c;
for (const structure of structures) {
if (!((_c = (_b = (_a = structure.cell) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data) === null || _c === void 0 ? void 0 : _c.units))
continue;
const unit = structure.cell.obj.data.units[0];
const id = unit.model.id;
if (id === modelId)
return structure.cell.obj.data;
}
}
function checkLoadData(loadConfig) {
const method = loadConfig.loadMethod;
const params = loadConfig.loadParams;
if (method == LoadMethod.loadPdbId) {
if (params instanceof Array || params.entryId == null)
throw loadConfig.loadMethod + ": missing pdbId";
}
else if (method == LoadMethod.loadStructureFromUrl) {
if (params instanceof Array || params.url == null || params.isBinary == null || params.format == null)
throw loadConfig.loadMethod + ": arguments needed url, format, isBinary";
}
else if (method == LoadMethod.loadSnapshotFromUrl) {
if (params instanceof Array || params.url == null || params.type == null)
throw loadConfig.loadMethod + ": arguments needed url, type";
}
else if (method == LoadMethod.loadStructureFromData) {
if (params instanceof Array || params.data == null || params.format == null || params.isBinary == null)
throw loadConfig.loadMethod + ": arguments needed data, format, isBinary";
}
return true;
}
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