|
|
@@ -0,0 +1,301 @@
|
|
|
+/**
|
|
|
+ * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
|
+ *
|
|
|
+ * @author Adam Midlik <midlik@gmail.com>
|
|
|
+ */
|
|
|
+
|
|
|
+import { Column } from '../../../mol-data/db';
|
|
|
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
|
|
|
+import { Model } from '../../../mol-model/structure';
|
|
|
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
|
|
|
+import { StructureComponent } from '../../../mol-plugin-state/transforms/model';
|
|
|
+import { StructureRepresentation3D } from '../../../mol-plugin-state/transforms/representation';
|
|
|
+import { setSubtreeVisibility } from '../../../mol-plugin/behavior/static/state';
|
|
|
+import { PluginContext } from '../../../mol-plugin/context';
|
|
|
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
|
|
|
+import { ColorNames } from '../../../mol-util/color/names';
|
|
|
+
|
|
|
+
|
|
|
+/** Amount by which to expand the camera radius when zooming to atoms involved in struct_conn (angstroms) */
|
|
|
+const EXTRA_RADIUS = 4;
|
|
|
+
|
|
|
+/** Tags for state tree nodes managed by this extension */
|
|
|
+const TAGS = {
|
|
|
+ RESIDUE_SEL: 'structconn-focus-residue-sel',
|
|
|
+ ATOM_SEL: 'structconn-focus-atom-sel',
|
|
|
+ RESIDUE_REPR: 'structconn-focus-residue-repr',
|
|
|
+ RESIDUE_NCI_REPR: 'structconn-focus-residue-nci-repr',
|
|
|
+ ATOM_REPR: 'structconn-focus-atom-repr',
|
|
|
+} as const;
|
|
|
+
|
|
|
+type VisualParams = ReturnType<typeof StructureRepresentation3D.createDefaultParams>
|
|
|
+
|
|
|
+/** Parameters for 3D representation of atoms involved in struct_conn (pink bubbles) */
|
|
|
+const ATOMS_VISUAL_PARAMS: VisualParams = {
|
|
|
+ type: { name: 'ball-and-stick', params: { sizeFactor: 0.25, sizeAspectRatio: 0.73, adjustCylinderLength: true, xrayShaded: true, aromaticBonds: false, multipleBonds: 'off', dashCount: 1, dashCap: false } },
|
|
|
+ colorTheme: { name: 'uniform', params: { value: ColorNames.magenta } },
|
|
|
+ sizeTheme: { name: 'physical', params: {} },
|
|
|
+} as const;
|
|
|
+
|
|
|
+/** Parameters for 3D representation of residues involved in struct_conn (normal ball-and-stick) */
|
|
|
+const RESIDUES_VISUAL_PARAMS: VisualParams = {
|
|
|
+ type: { name: 'ball-and-stick', params: { sizeFactor: 0.16 } },
|
|
|
+ colorTheme: { name: 'element-symbol', params: {} },
|
|
|
+ sizeTheme: { name: 'physical', params: {} },
|
|
|
+} as const;
|
|
|
+
|
|
|
+
|
|
|
+/** All public functions provided by the StructConn extension */
|
|
|
+export const wwPDBStructConnExtensionFunctions = {
|
|
|
+ /** Return an object with all struct_conn records for a loaded structure.
|
|
|
+ * Applies to the first structure belonging to `entry` (e.g. '1tqn'),
|
|
|
+ * or to the first loaded structure overall if `entry` is `undefined`.
|
|
|
+ */
|
|
|
+ getStructConns(plugin: PluginContext, entry: string | undefined): { [id: string]: StructConnRecord } {
|
|
|
+ const structNode = selectStructureNode(plugin, entry);
|
|
|
+ const structure = structNode?.obj?.data;
|
|
|
+ if (structure) return extractStructConns(structure.model);
|
|
|
+ else return {};
|
|
|
+ },
|
|
|
+
|
|
|
+ /** Create visuals for residues and atoms involved in a struct_conn with ID `structConnId`
|
|
|
+ * and zoom on them. If `keepExisting` is false (default), remove any such visuals created by previous calls to this function.
|
|
|
+ * Also hide all carbohydrate SNFG visuals within the structure (as they would occlude our residues of interest).
|
|
|
+ * Return a promise that resolves to the number of involved atoms which were successfully selected (2, 1, or 0).
|
|
|
+ */
|
|
|
+ async inspectStructConn(plugin: PluginContext, entry: string | undefined, structConnId: string, keepExisting: boolean = false): Promise<number> {
|
|
|
+ const structNode = selectStructureNode(plugin, entry);
|
|
|
+ const structure = structNode?.obj?.data;
|
|
|
+ if (!structure) {
|
|
|
+ console.error('Structure not found');
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ const conns: { [id: string]: StructConnRecord } = structure.model._staticPropertyData['wwpdb-struct-conn-extension-data'] ??= extractStructConns(structure.model);
|
|
|
+ const conn = conns[structConnId];
|
|
|
+ if (!conn) {
|
|
|
+ console.error(`The structure does not contain struct_conn "${structConnId}"`);
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ if (!keepExisting) {
|
|
|
+ await removeAllStructConnInspections(plugin, structNode);
|
|
|
+ }
|
|
|
+ const nSelectedAtoms = await addStructConnInspection(plugin, structNode, conn);
|
|
|
+ hideSnfgNodes(plugin, structNode);
|
|
|
+ return nSelectedAtoms;
|
|
|
+ },
|
|
|
+
|
|
|
+ /** Remove anything created by `inspectStructConn` within the structure and
|
|
|
+ * make visible any carbohydrate SNFG visuals that have been hidden by `inspectStructConn`.
|
|
|
+ */
|
|
|
+ async clearStructConnInspections(plugin: PluginContext, entry: string | undefined) {
|
|
|
+ const structNode = selectStructureNode(plugin, entry);
|
|
|
+ if (!structNode) return;
|
|
|
+ await removeAllStructConnInspections(plugin, structNode);
|
|
|
+ unhideSnfgNodes(plugin, structNode);
|
|
|
+ },
|
|
|
+};
|
|
|
+
|
|
|
+
|
|
|
+type StructNode = Exclude<ReturnType<typeof selectStructureNode>, undefined>
|
|
|
+
|
|
|
+/** Return the first structure node belonging to `entry` (e.g. '1tqn'),
|
|
|
+ * or to the first loaded structure node overall if `entry` is `undefined`.
|
|
|
+ * Includes only "root" structures, not structure components. */
|
|
|
+function selectStructureNode(plugin: PluginContext, entry: string | undefined) {
|
|
|
+ const structNodes = plugin.state.data
|
|
|
+ .selectQ(q => q.rootsOfType(PluginStateObject.Molecule.Structure));
|
|
|
+ if (entry) {
|
|
|
+ const result = structNodes.find(node => node.obj && node.obj.data.model.entry.toLowerCase() === entry.toLowerCase());
|
|
|
+ if (!result) {
|
|
|
+ console.warn(`Structure with entry ID "${entry}" was not found. Available structures: ${structNodes.map(node => node.obj?.data.model.entry)}`);
|
|
|
+ }
|
|
|
+ return result;
|
|
|
+ } else {
|
|
|
+ if (structNodes.length > 1) {
|
|
|
+ console.warn(`Structure entry ID was not specified, but there is more than one loaded structure (${structNodes.map(node => node.obj?.data.model.entry)}). Taking the first structure.`);
|
|
|
+ }
|
|
|
+ if (structNodes.length === 0) {
|
|
|
+ console.warn(`There are no loaded structures.`);
|
|
|
+ }
|
|
|
+ return structNodes[0];
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/** Represents one partner (i.e. atom) of a struct_conn */
|
|
|
+interface StructConnPartner {
|
|
|
+ asymId: string,
|
|
|
+ seqId: number | undefined,
|
|
|
+ authSeqId: number | undefined,
|
|
|
+ insCode: string,
|
|
|
+ compId: string,
|
|
|
+ atomId: string,
|
|
|
+ /** Alternative location (use empty string if not given) */
|
|
|
+ altId: string,
|
|
|
+}
|
|
|
+
|
|
|
+/** Represents a struct_conn (interaction between two partners) */
|
|
|
+export interface StructConnRecord {
|
|
|
+ id: string,
|
|
|
+ distance: number,
|
|
|
+ partner1: StructConnPartner,
|
|
|
+ partner2: StructConnPartner,
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/** Return an object with all struct_conn records read from mmCIF.
|
|
|
+ * Return {} if the model comes from another format than mmCIF.
|
|
|
+ */
|
|
|
+function extractStructConns(model: Model): { [id: string]: StructConnRecord } {
|
|
|
+ if (!MmcifFormat.is(model.sourceData)) {
|
|
|
+ console.error('Cannot get struct_conn because source data are not mmCIF.');
|
|
|
+ return {};
|
|
|
+ }
|
|
|
+ const mmcifData = model.sourceData.data;
|
|
|
+ const {
|
|
|
+ id,
|
|
|
+ ptnr1_label_asym_id: asym1,
|
|
|
+ ptnr1_label_seq_id: seq1,
|
|
|
+ ptnr1_auth_seq_id: authSeq1,
|
|
|
+ pdbx_ptnr1_PDB_ins_code: authInsCode1,
|
|
|
+ ptnr1_label_comp_id: comp1,
|
|
|
+ ptnr1_label_atom_id: atom1,
|
|
|
+ pdbx_ptnr1_label_alt_id: alt1,
|
|
|
+ ptnr2_label_asym_id: asym2,
|
|
|
+ ptnr2_label_seq_id: seq2,
|
|
|
+ ptnr2_auth_seq_id: authSeq2,
|
|
|
+ pdbx_ptnr2_PDB_ins_code: authInsCode2,
|
|
|
+ ptnr2_label_comp_id: comp2,
|
|
|
+ ptnr2_label_atom_id: atom2,
|
|
|
+ pdbx_ptnr2_label_alt_id: alt2,
|
|
|
+ pdbx_dist_value: distance } = mmcifData.db.struct_conn;
|
|
|
+ const n = id.rowCount;
|
|
|
+ const result: { [id: string]: StructConnRecord } = {};
|
|
|
+ for (let i = 0; i < n; i++) {
|
|
|
+ const conn: StructConnRecord = {
|
|
|
+ id: id.value(i),
|
|
|
+ distance: distance.value(i),
|
|
|
+ partner1: {
|
|
|
+ asymId: asym1.value(i),
|
|
|
+ seqId: seq1.valueKind(i) === Column.ValueKinds.Present ? seq1.value(i) : undefined,
|
|
|
+ authSeqId: authSeq1.valueKind(i) === Column.ValueKinds.Present ? authSeq1.value(i) : undefined,
|
|
|
+ insCode: authInsCode1.value(i),
|
|
|
+ compId: comp1.value(i),
|
|
|
+ atomId: atom1.value(i),
|
|
|
+ altId: alt1.value(i),
|
|
|
+ },
|
|
|
+ partner2: {
|
|
|
+ asymId: asym2.value(i),
|
|
|
+ seqId: seq2.valueKind(i) === Column.ValueKinds.Present ? seq2.value(i) : undefined,
|
|
|
+ authSeqId: authSeq2.valueKind(i) === Column.ValueKinds.Present ? authSeq2.value(i) : undefined,
|
|
|
+ insCode: authInsCode2.value(i),
|
|
|
+ compId: comp2.value(i),
|
|
|
+ atomId: atom2.value(i),
|
|
|
+ altId: alt2.value(i),
|
|
|
+ },
|
|
|
+ };
|
|
|
+ result[conn.id] = conn;
|
|
|
+ }
|
|
|
+ return result;
|
|
|
+}
|
|
|
+
|
|
|
+/** Return MolScript expression for atoms or residues involved in a struct_conn */
|
|
|
+function structConnExpression(conn: StructConnRecord, by: 'atoms' | 'residues') {
|
|
|
+ const { core, struct } = MolScriptBuilder;
|
|
|
+ const partnerExpressions = [];
|
|
|
+ for (const partner of [conn.partner1, conn.partner2]) {
|
|
|
+ const propTests: Parameters<typeof struct.generator.atomGroups>[0] = {
|
|
|
+ 'chain-test': core.rel.eq([struct.atomProperty.macromolecular.label_asym_id(), partner.asymId]),
|
|
|
+ 'group-by': struct.atomProperty.core.operatorName(),
|
|
|
+ };
|
|
|
+ if (partner.seqId !== undefined) {
|
|
|
+ propTests['residue-test'] = core.rel.eq([struct.atomProperty.macromolecular.label_seq_id(), partner.seqId]);
|
|
|
+ } else if (partner.authSeqId !== undefined) { // for the case of water and carbohydrates (see 5elb, covale3 vs covale5)
|
|
|
+ propTests['residue-test'] = core.logic.and([
|
|
|
+ core.rel.eq([struct.atomProperty.macromolecular.auth_seq_id(), partner.authSeqId]),
|
|
|
+ core.rel.eq([struct.atomProperty.macromolecular.pdbx_PDB_ins_code(), partner.insCode]),
|
|
|
+ ]);
|
|
|
+ }
|
|
|
+ if (by === 'residues' && partner.altId !== '') {
|
|
|
+ propTests['atom-test'] = core.rel.eq([struct.atomProperty.macromolecular.label_alt_id(), partner.altId]);
|
|
|
+ }
|
|
|
+ if (by === 'atoms') {
|
|
|
+ propTests['atom-test'] = core.logic.and([
|
|
|
+ core.rel.eq([struct.atomProperty.macromolecular.label_atom_id(), partner.atomId]),
|
|
|
+ core.rel.eq([struct.atomProperty.macromolecular.label_alt_id(), partner.altId]),
|
|
|
+ ]);
|
|
|
+ }
|
|
|
+ partnerExpressions.push(struct.filter.first([struct.generator.atomGroups(propTests)]));
|
|
|
+ }
|
|
|
+ return struct.combinator.merge(partnerExpressions.map(e => struct.modifier.union([e])));
|
|
|
+}
|
|
|
+
|
|
|
+/** Create visuals for residues and atoms involved in a struct_conn and zoom on them.
|
|
|
+ * Return a promise that resolves to the number of involved atoms which were successfully selected (2, 1, or 0).
|
|
|
+ */
|
|
|
+async function addStructConnInspection(plugin: PluginContext, structNode: StructNode, conn: StructConnRecord): Promise<number> {
|
|
|
+ const expressionByResidues = structConnExpression(conn, 'residues');
|
|
|
+ const expressionByAtoms = structConnExpression(conn, 'atoms');
|
|
|
+
|
|
|
+ const update = plugin.build();
|
|
|
+ update.to(structNode).apply(
|
|
|
+ StructureComponent,
|
|
|
+ { label: `${conn.id} (residues)`, type: { name: 'expression', params: expressionByResidues } },
|
|
|
+ { tags: [TAGS.RESIDUE_SEL] }
|
|
|
+ ).apply(
|
|
|
+ StructureRepresentation3D,
|
|
|
+ RESIDUES_VISUAL_PARAMS,
|
|
|
+ { tags: [TAGS.RESIDUE_REPR] }
|
|
|
+ );
|
|
|
+
|
|
|
+ const atomsSelection = update.to(structNode).apply(
|
|
|
+ StructureComponent,
|
|
|
+ { label: `${conn.id} (atoms)`, type: { name: 'expression', params: expressionByAtoms } },
|
|
|
+ { tags: [TAGS.ATOM_SEL] }
|
|
|
+ );
|
|
|
+ const atomsVisual = update.to(atomsSelection.ref).apply(
|
|
|
+ StructureRepresentation3D,
|
|
|
+ ATOMS_VISUAL_PARAMS,
|
|
|
+ { tags: [TAGS.ATOM_REPR] }
|
|
|
+ );
|
|
|
+ await update.commit();
|
|
|
+
|
|
|
+ plugin.managers.camera.focusRenderObjects(atomsVisual.selector.data?.repr.renderObjects, { extraRadius: EXTRA_RADIUS });
|
|
|
+ const nSelectedAtoms = atomsSelection.selector.obj?.data?.elementCount ?? 0;
|
|
|
+ return nSelectedAtoms;
|
|
|
+}
|
|
|
+
|
|
|
+/** Remove anything created by `addStructConnInspection` */
|
|
|
+async function removeAllStructConnInspections(plugin: PluginContext, structNode: StructNode) {
|
|
|
+ const selNodes = [
|
|
|
+ ...plugin.state.data.selectQ(q => q.byRef(structNode.transform.ref).subtree().withTag(TAGS.RESIDUE_SEL)),
|
|
|
+ ...plugin.state.data.selectQ(q => q.byRef(structNode.transform.ref).subtree().withTag(TAGS.ATOM_SEL)),
|
|
|
+ ];
|
|
|
+ const update = plugin.build();
|
|
|
+ for (const node of selNodes) {
|
|
|
+ update.delete(node);
|
|
|
+ }
|
|
|
+ await update.commit();
|
|
|
+}
|
|
|
+
|
|
|
+/** Hide all carbohydrate SNFG visuals */
|
|
|
+function hideSnfgNodes(plugin: PluginContext, structNode: StructNode) {
|
|
|
+ const snfgNodes = plugin.state.data.selectQ(q => q.byRef(structNode.transform.ref).subtree().withTag('branched-snfg-3d'));
|
|
|
+ for (const node of snfgNodes) {
|
|
|
+ setSubtreeVisibility(plugin.state.data, node.transform.ref, true); // true means hidden
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/** Make visible all carbohydrate SNFG visuals that have been hidden by `hideSnfgNodes` */
|
|
|
+function unhideSnfgNodes(plugin: PluginContext, structNode: StructNode) {
|
|
|
+ const snfgNodes = plugin.state.data.selectQ(q => q.byRef(structNode.transform.ref).subtree().withTag('branched-snfg-3d'));
|
|
|
+ for (const node of snfgNodes) {
|
|
|
+ try {
|
|
|
+ setSubtreeVisibility(plugin.state.data, node.transform.ref, false); // false means visible
|
|
|
+ } catch {
|
|
|
+ // this is OK, the node has been removed
|
|
|
+ }
|
|
|
+ }
|
|
|
+}
|
midlik