molstar
Version:
A comprehensive macromolecular library.
104 lines (103 loc) • 5.21 kB
JavaScript
;
/**
* Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.SecondaryStructureProvider = exports.SecondaryStructureParams = void 0;
const dssp_1 = require("./secondary-structure/dssp");
const param_definition_1 = require("../../mol-util/param-definition");
const structure_1 = require("../../mol-model/structure/structure");
const custom_structure_property_1 = require("../common/custom-structure-property");
const secondary_structure_1 = require("../../mol-model-formats/structure/property/secondary-structure");
const custom_property_1 = require("../../mol-model/custom-property");
const model_1 = require("../../mol-model/structure/model");
const zhang_skolnik_1 = require("./secondary-structure/zhang-skolnik");
function getSecondaryStructureParams(_data) {
return {
type: param_definition_1.ParamDefinition.MappedStatic('auto', {
'auto': param_definition_1.ParamDefinition.EmptyGroup({ label: 'Automatic' }),
'model': param_definition_1.ParamDefinition.EmptyGroup({ label: 'Model' }),
'dssp': param_definition_1.ParamDefinition.Group(dssp_1.DSSPComputationParams, { label: 'DSSP', isFlat: true }),
'zhang-skolnick': param_definition_1.ParamDefinition.EmptyGroup({ label: 'Zhang-Skolnick' }),
}, { options: [['auto', 'Automatic'], ['model', 'Model'], ['dssp', 'DSSP'], ['zhang-skolnick', 'Zhang-Skolnick']] })
};
}
exports.SecondaryStructureParams = getSecondaryStructureParams();
exports.SecondaryStructureProvider = custom_structure_property_1.CustomStructureProperty.createProvider({
label: 'Secondary Structure',
descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
name: 'molstar_computed_secondary_structure',
// TODO `cifExport` and `symbol`
}),
type: 'root',
defaultParams: exports.SecondaryStructureParams,
getParams: getSecondaryStructureParams,
isApplicable: (data) => true,
obtain: async (ctx, data, props) => {
const p = { ...param_definition_1.ParamDefinition.getDefaultValues(exports.SecondaryStructureParams), ...props };
switch (p.type.name) {
case 'auto': return { value: await computeAuto(data) };
case 'dssp': return { value: await computeDssp(data, p.type.params) };
case 'model': return { value: await computeModel(data) };
case 'zhang-skolnick': return { value: await computeZhangSkolnik(data) };
}
}
});
async function computeAuto(structure) {
const map = new Map();
for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
const u = structure.unitSymmetryGroups[i].units[0];
const m = u.model;
if ((model_1.Model.isFromPdbArchive(m) && model_1.Model.isExperimental(m) && !model_1.Model.isCoarseGrained(m)) || model_1.Model.hasSecondaryStructure(m)) {
const secondaryStructure = secondary_structure_1.ModelSecondaryStructure.Provider.get(m);
if (secondaryStructure)
map.set(u.invariantId, secondaryStructure);
}
else if (structure_1.Unit.isAtomic(u) && !model_1.Model.isCoarseGrained(m)) {
const secondaryStructure = await (0, dssp_1.computeUnitDSSP)(u, dssp_1.DefaultDSSPComputationProps);
map.set(u.invariantId, secondaryStructure);
}
else if (structure_1.Unit.isAtomic(u)) {
const secondaryStructure = await (0, zhang_skolnik_1.computeUnitZhangSkolnik)(u);
map.set(u.invariantId, secondaryStructure);
}
}
return map;
}
async function computeDssp(structure, props) {
// TODO take inter-unit hbonds into account for bridge, ladder, sheet assignment
const map = new Map();
for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
const u = structure.unitSymmetryGroups[i].units[0];
if (structure_1.Unit.isAtomic(u) && !model_1.Model.isCoarseGrained(u.model)) {
const secondaryStructure = await (0, dssp_1.computeUnitDSSP)(u, props);
map.set(u.invariantId, secondaryStructure);
}
}
return map;
}
async function computeZhangSkolnik(structure) {
const map = new Map();
for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
const u = structure.unitSymmetryGroups[i].units[0];
if (structure_1.Unit.isAtomic(u)) {
const secondaryStructure = await (0, zhang_skolnik_1.computeUnitZhangSkolnik)(u);
map.set(u.invariantId, secondaryStructure);
}
}
return map;
}
async function computeModel(structure) {
const map = new Map();
for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
const u = structure.unitSymmetryGroups[i].units[0];
if (structure_1.Unit.isAtomic(u)) {
const secondaryStructure = secondary_structure_1.ModelSecondaryStructure.Provider.get(u.model);
if (secondaryStructure)
map.set(u.invariantId, secondaryStructure);
}
}
return map;
}