molstar
Version:
A comprehensive macromolecular library.
235 lines (234 loc) • 12.3 kB
JavaScript
;
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports._atom_site = void 0;
exports.residueIdFields = residueIdFields;
exports.chainIdFields = chainIdFields;
exports.entityIdFields = entityIdFields;
exports.atomIdFields = atomIdFields;
const cif_1 = require("../../../../mol-io/writer/cif");
const mmcif_1 = require("../../../../mol-model-formats/structure/mmcif");
const sifts_mapping_1 = require("../../../../mol-model-props/sequence/sifts-mapping");
const structure_1 = require("../../structure");
var CifField = cif_1.CifWriter.Field;
var E = cif_1.CifWriter.Encodings;
function atom_site_label_asym_id(e) {
const l = structure_1.StructureProperties.chain.label_asym_id(e);
const suffix = e.unit.conformation.operator.suffix;
if (!suffix)
return l;
return l + suffix;
}
function atom_site_auth_asym_id(e) {
const l = structure_1.StructureProperties.chain.auth_asym_id(e);
const suffix = e.unit.conformation.operator.suffix;
if (!suffix)
return l;
return l + suffix;
}
const atom_site_pdbx_label_index = {
shouldInclude(s) {
var _a;
return !!((_a = s.atom_site) === null || _a === void 0 ? void 0 : _a.pdbx_label_index.isDefined);
},
value(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_label_index.value(srcIndex);
},
};
const SIFTS = {
shouldInclude(s) {
return sifts_mapping_1.SIFTSMapping.isAvailable(s.structure.models[0]);
},
pdbx_sifts_xref_db_name: {
value(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_name.value(srcIndex);
},
valueKind(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_name.valueKind(srcIndex);
},
},
pdbx_sifts_xref_db_acc: {
value(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_acc.value(srcIndex);
},
valueKind(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_acc.valueKind(srcIndex);
},
},
pdbx_sifts_xref_db_num: {
value(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_num.value(srcIndex);
},
valueKind(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_num.valueKind(srcIndex);
},
},
pdbx_sifts_xref_db_res: {
value(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_res.value(srcIndex);
},
valueKind(e, d) {
const srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_res.valueKind(srcIndex);
},
}
};
const atom_site_fields = (keepId) => {
const fields = cif_1.CifWriter.fields();
fields.str('group_PDB', structure_1.StructureProperties.residue.group_PDB);
if (keepId) {
fields.int('id', structure_1.StructureProperties.atom.id);
}
else {
fields.index('id');
}
fields
.str('type_symbol', structure_1.StructureProperties.atom.type_symbol)
.str('label_atom_id', structure_1.StructureProperties.atom.label_atom_id)
.str('label_comp_id', structure_1.StructureProperties.atom.label_comp_id)
.int('label_seq_id', structure_1.StructureProperties.residue.label_seq_id, {
encoder: E.deltaRLE,
valueKind: (k, d) => {
const m = k.unit.model;
return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[k.element]);
}
})
.str('label_alt_id', structure_1.StructureProperties.atom.label_alt_id)
.str('pdbx_PDB_ins_code', structure_1.StructureProperties.residue.pdbx_PDB_ins_code)
.str('label_asym_id', atom_site_label_asym_id)
.str('label_entity_id', structure_1.StructureProperties.chain.label_entity_id)
.float('Cartn_x', structure_1.StructureProperties.atom.x, { digitCount: 3, encoder: E.fixedPoint3 })
.float('Cartn_y', structure_1.StructureProperties.atom.y, { digitCount: 3, encoder: E.fixedPoint3 })
.float('Cartn_z', structure_1.StructureProperties.atom.z, { digitCount: 3, encoder: E.fixedPoint3 })
.float('occupancy', structure_1.StructureProperties.atom.occupancy, { digitCount: 2, encoder: E.fixedPoint2 })
.float('B_iso_or_equiv', structure_1.StructureProperties.atom.B_iso_or_equiv, { digitCount: 2, encoder: E.fixedPoint2 })
.int('pdbx_formal_charge', structure_1.StructureProperties.atom.pdbx_formal_charge, {
encoder: E.deltaRLE,
valueKind: (k, d) => k.unit.model.atomicHierarchy.atoms.pdbx_formal_charge.valueKind(k.element)
})
.str('auth_atom_id', structure_1.StructureProperties.atom.auth_atom_id)
.str('auth_comp_id', structure_1.StructureProperties.atom.auth_comp_id)
.int('auth_seq_id', structure_1.StructureProperties.residue.auth_seq_id, { encoder: E.deltaRLE })
.str('auth_asym_id', atom_site_auth_asym_id)
.int('pdbx_PDB_model_num', structure_1.StructureProperties.unit.model_num, { encoder: E.deltaRLE })
.int('pdbx_label_index', atom_site_pdbx_label_index.value, { shouldInclude: atom_site_pdbx_label_index.shouldInclude })
// SIFTS
.str('pdbx_sifts_xref_db_name', SIFTS.pdbx_sifts_xref_db_name.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_name.valueKind })
.str('pdbx_sifts_xref_db_acc', SIFTS.pdbx_sifts_xref_db_acc.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_acc.valueKind })
.str('pdbx_sifts_xref_db_num', SIFTS.pdbx_sifts_xref_db_num.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_num.valueKind })
.str('pdbx_sifts_xref_db_res', SIFTS.pdbx_sifts_xref_db_res.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_res.valueKind });
// .str('operator_name', P.unit.operator_name, {
// shouldInclude: structure => structure.units.some(u => !u.conformation.operator.isIdentity)
// })
return fields.getFields();
};
const _atom_site = (options) => ({
name: 'atom_site',
instance({ structures }) {
return {
fields: atom_site_fields(options === null || options === void 0 ? void 0 : options.keepId),
source: structures.map(s => ({
data: {
structure: s,
sourceIndex: s.model.atomicHierarchy.atomSourceIndex,
atom_site: mmcif_1.MmcifFormat.is(s.model.sourceData) ? s.model.sourceData.data.db.atom_site : void 0
},
rowCount: s.elementCount,
keys: () => s.elementLocations()
}))
};
}
});
exports._atom_site = _atom_site;
function prepostfixed(prefix, name) {
if (prefix)
return `${prefix}_${name}`;
return name;
}
function prefixedInsCode(prefix) {
if (!prefix)
return 'pdbx_PDB_ins_code';
return `pdbx_${prefix}_PDB_ins_code`;
}
function mappedProp(loc, prop) {
return (k, d) => prop(loc(k, d));
}
function addModelNum(fields, getLocation, options) {
if (options && options.includeModelNum) {
fields.int('pdbx_PDB_model_num', mappedProp(getLocation, structure_1.StructureProperties.unit.model_num));
}
}
function residueIdFields(getLocation, options) {
const prefix = options && options.prefix;
const ret = cif_1.CifWriter.fields()
.str(prepostfixed(prefix, `label_comp_id`), mappedProp(getLocation, structure_1.StructureProperties.atom.label_comp_id))
.int(prepostfixed(prefix, `label_seq_id`), mappedProp(getLocation, structure_1.StructureProperties.residue.label_seq_id), {
encoder: E.deltaRLE,
valueKind: (k, d) => {
const e = getLocation(k, d);
const m = e.unit.model;
return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[e.element]);
}
})
.str(prefixedInsCode(prefix), mappedProp(getLocation, structure_1.StructureProperties.residue.pdbx_PDB_ins_code))
.str(prepostfixed(prefix, `label_asym_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.label_asym_id))
.str(prepostfixed(prefix, `label_entity_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.label_entity_id))
.str(prepostfixed(prefix, `auth_comp_id`), mappedProp(getLocation, structure_1.StructureProperties.atom.auth_comp_id))
.int(prepostfixed(prefix, `auth_seq_id`), mappedProp(getLocation, structure_1.StructureProperties.residue.auth_seq_id), { encoder: E.deltaRLE })
.str(prepostfixed(prefix, `auth_asym_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.auth_asym_id));
addModelNum(ret, getLocation, options);
return ret.getFields();
}
function chainIdFields(getLocation, options) {
const prefix = options && options.prefix;
const ret = CifField.build()
.str(prepostfixed(prefix, `label_asym_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.label_asym_id))
.str(prepostfixed(prefix, `label_entity_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.label_entity_id))
.str(prepostfixed(prefix, `auth_asym_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.auth_asym_id));
addModelNum(ret, getLocation, options);
return ret.getFields();
}
function entityIdFields(getLocation, options) {
const prefix = options && options.prefix;
const ret = CifField.build()
.str(prepostfixed(prefix, `label_entity_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.label_entity_id));
addModelNum(ret, getLocation, options);
return ret.getFields();
}
function atomIdFields(getLocation, options) {
const prefix = options && options.prefix;
const ret = cif_1.CifWriter.fields()
.str(prepostfixed(prefix, `label_atom_id`), mappedProp(getLocation, structure_1.StructureProperties.atom.label_atom_id))
.str(prepostfixed(prefix, `label_comp_id`), mappedProp(getLocation, structure_1.StructureProperties.atom.label_comp_id))
.int(prepostfixed(prefix, `label_seq_id`), mappedProp(getLocation, structure_1.StructureProperties.residue.label_seq_id), {
encoder: E.deltaRLE,
valueKind: (k, d) => {
const e = getLocation(k, d);
const m = e.unit.model;
return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[e.element]);
}
})
.str(prepostfixed(prefix, `label_alt_id`), mappedProp(getLocation, structure_1.StructureProperties.atom.label_alt_id))
.str(prefixedInsCode(prefix), mappedProp(getLocation, structure_1.StructureProperties.residue.pdbx_PDB_ins_code))
.str(prepostfixed(prefix, `label_asym_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.label_asym_id))
.str(prepostfixed(prefix, `label_entity_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.label_entity_id))
.str(prepostfixed(prefix, `auth_atom_id`), mappedProp(getLocation, structure_1.StructureProperties.atom.auth_atom_id))
.str(prepostfixed(prefix, `auth_comp_id`), mappedProp(getLocation, structure_1.StructureProperties.atom.auth_comp_id))
.int(prepostfixed(prefix, `auth_seq_id`), mappedProp(getLocation, structure_1.StructureProperties.residue.auth_seq_id), { encoder: E.deltaRLE })
.str(prepostfixed(prefix, `auth_asym_id`), mappedProp(getLocation, structure_1.StructureProperties.chain.auth_asym_id));
addModelNum(ret, getLocation, options);
return ret.getFields();
}