molstar
Version:
A comprehensive macromolecular library.
231 lines (230 loc) • 12.9 kB
JavaScript
;
/**
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Adam Midlik <midlik@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.wwPDBStructConnExtensionFunctions = void 0;
const mmcif_1 = require("../../../mol-model-formats/structure/mmcif");
const objects_1 = require("../../../mol-plugin-state/objects");
const model_1 = require("../../../mol-plugin-state/transforms/model");
const representation_1 = require("../../../mol-plugin-state/transforms/representation");
const state_1 = require("../../../mol-plugin/behavior/static/state");
const builder_1 = require("../../../mol-script/language/builder");
const names_1 = require("../../../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',
};
/** Parameters for 3D representation of atoms involved in struct_conn (pink bubbles) */
const ATOMS_VISUAL_PARAMS = {
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: names_1.ColorNames.magenta } },
sizeTheme: { name: 'physical', params: {} },
};
/** Parameters for 3D representation of residues involved in struct_conn (normal ball-and-stick) */
const RESIDUES_VISUAL_PARAMS = {
type: { name: 'ball-and-stick', params: { sizeFactor: 0.16 } },
colorTheme: { name: 'element-symbol', params: {} },
sizeTheme: { name: 'physical', params: {} },
};
/** All public functions provided by the StructConn extension */
exports.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, entry) {
var _a;
const structNode = selectStructureNode(plugin, entry);
const structure = (_a = structNode === null || structNode === void 0 ? void 0 : structNode.obj) === null || _a === void 0 ? void 0 : _a.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, entry, structConnId, keepExisting = false) {
var _a, _b;
var _c;
const structNode = selectStructureNode(plugin, entry);
const structure = (_a = structNode === null || structNode === void 0 ? void 0 : structNode.obj) === null || _a === void 0 ? void 0 : _a.data;
if (!structure) {
console.error('Structure not found');
return 0;
}
const conns = (_b = (_c = structure.model._staticPropertyData)['wwpdb-struct-conn-extension-data']) !== null && _b !== void 0 ? _b : (_c['wwpdb-struct-conn-extension-data'] = extractStructConns(structure.model));
const conn = conns[structConnId];
if (!conn) {
console.error(`The structure does not contain struct_conn "${structConnId}"`);
return 0;
}
if (!keepExisting) {
await removeAllStructConnInspections(plugin, structNode);
}
const nSelectedAtoms = await addStructConnInspection(plugin, structNode, conn);
hideSnfgNodes(plugin, structNode);
return nSelectedAtoms;
},
/** Remove anything created by `inspectStructConn` within the structure and
* make visible any carbohydrate SNFG visuals that have been hidden by `inspectStructConn`.
*/
async clearStructConnInspections(plugin, entry) {
const structNode = selectStructureNode(plugin, entry);
if (!structNode)
return;
await removeAllStructConnInspections(plugin, structNode);
unhideSnfgNodes(plugin, structNode);
},
};
/** Return the first structure node belonging to `entry` (e.g. '1tqn'),
* or to the first loaded structure node overall if `entry` is `undefined`.
* Includes only "root" structures, not structure components. */
function selectStructureNode(plugin, entry) {
const structNodes = plugin.state.data
.selectQ(q => q.rootsOfType(objects_1.PluginStateObject.Molecule.Structure));
if (entry) {
const result = structNodes.find(node => node.obj && node.obj.data.model.entry.toLowerCase() === entry.toLowerCase());
if (!result) {
console.warn(`Structure with entry ID "${entry}" was not found. Available structures: ${structNodes.map(node => { var _a; return (_a = node.obj) === null || _a === void 0 ? void 0 : _a.data.model.entry; })}`);
}
return result;
}
else {
if (structNodes.length > 1) {
console.warn(`Structure entry ID was not specified, but there is more than one loaded structure (${structNodes.map(node => { var _a; return (_a = node.obj) === null || _a === void 0 ? void 0 : _a.data.model.entry; })}). Taking the first structure.`);
}
if (structNodes.length === 0) {
console.warn(`There are no loaded structures.`);
}
return structNodes[0];
}
}
/** Return an object with all struct_conn records read from mmCIF.
* Return {} if the model comes from another format than mmCIF.
*/
function extractStructConns(model) {
if (!mmcif_1.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 = {};
for (let i = 0; i < n; i++) {
const conn = {
id: id.value(i),
distance: distance.value(i),
partner1: {
asymId: asym1.value(i),
seqId: seq1.valueKind(i) === 0 /* Column.ValueKinds.Present */ ? seq1.value(i) : undefined,
authSeqId: authSeq1.valueKind(i) === 0 /* 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) === 0 /* Column.ValueKinds.Present */ ? seq2.value(i) : undefined,
authSeqId: authSeq2.valueKind(i) === 0 /* 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, by) {
const { core, struct } = builder_1.MolScriptBuilder;
const partnerExpressions = [];
for (const partner of [conn.partner1, conn.partner2]) {
const propTests = {
'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, structNode, conn) {
var _a, _b, _c, _d;
const expressionByResidues = structConnExpression(conn, 'residues');
const expressionByAtoms = structConnExpression(conn, 'atoms');
const update = plugin.build();
update.to(structNode).apply(model_1.StructureComponent, { label: `${conn.id} (residues)`, type: { name: 'expression', params: expressionByResidues } }, { tags: [TAGS.RESIDUE_SEL] }).apply(representation_1.StructureRepresentation3D, RESIDUES_VISUAL_PARAMS, { tags: [TAGS.RESIDUE_REPR] });
const atomsSelection = update.to(structNode).apply(model_1.StructureComponent, { label: `${conn.id} (atoms)`, type: { name: 'expression', params: expressionByAtoms } }, { tags: [TAGS.ATOM_SEL] });
const atomsVisual = update.to(atomsSelection.ref).apply(representation_1.StructureRepresentation3D, ATOMS_VISUAL_PARAMS, { tags: [TAGS.ATOM_REPR] });
await update.commit();
plugin.managers.camera.focusRenderObjects((_a = atomsVisual.selector.data) === null || _a === void 0 ? void 0 : _a.repr.renderObjects, { extraRadius: EXTRA_RADIUS });
const nSelectedAtoms = (_d = (_c = (_b = atomsSelection.selector.obj) === null || _b === void 0 ? void 0 : _b.data) === null || _c === void 0 ? void 0 : _c.elementCount) !== null && _d !== void 0 ? _d : 0;
return nSelectedAtoms;
}
/** Remove anything created by `addStructConnInspection` */
async function removeAllStructConnInspections(plugin, 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, structNode) {
const snfgNodes = plugin.state.data.selectQ(q => q.byRef(structNode.transform.ref).subtree().withTag('branched-snfg-3d'));
for (const node of snfgNodes) {
(0, state_1.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, structNode) {
const snfgNodes = plugin.state.data.selectQ(q => q.byRef(structNode.transform.ref).subtree().withTag('branched-snfg-3d'));
for (const node of snfgNodes) {
try {
(0, state_1.setSubtreeVisibility)(plugin.state.data, node.transform.ref, false); // false means visible
}
catch (_a) {
// this is OK, the node has been removed
}
}
}