molstar
Version:
A comprehensive macromolecular library.
220 lines (219 loc) • 10.7 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>
*/
import { CifWriter } from '../../../../mol-io/writer/cif';
import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
import { StructureProperties as P } from '../../structure';
var CifField = CifWriter.Field;
var E = CifWriter.Encodings;
function atom_site_label_asym_id(e) {
var l = P.chain.label_asym_id(e);
var suffix = e.unit.conformation.operator.suffix;
if (!suffix)
return l;
return l + suffix;
}
function atom_site_auth_asym_id(e) {
var l = P.chain.auth_asym_id(e);
var suffix = e.unit.conformation.operator.suffix;
if (!suffix)
return l;
return l + suffix;
}
var atom_site_pdbx_label_index = {
shouldInclude: function (s) {
var _a;
return !!((_a = s.atom_site) === null || _a === void 0 ? void 0 : _a.pdbx_label_index.isDefined);
},
value: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_label_index.value(srcIndex);
},
};
var SIFTS = {
shouldInclude: function (s) {
return SIFTSMapping.isAvailable(s.structure.models[0]);
},
pdbx_sifts_xref_db_name: {
value: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_name.value(srcIndex);
},
valueKind: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_name.valueKind(srcIndex);
},
},
pdbx_sifts_xref_db_acc: {
value: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_acc.value(srcIndex);
},
valueKind: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_acc.valueKind(srcIndex);
},
},
pdbx_sifts_xref_db_num: {
value: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_num.value(srcIndex);
},
valueKind: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_num.valueKind(srcIndex);
},
},
pdbx_sifts_xref_db_res: {
value: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_res.value(srcIndex);
},
valueKind: function (e, d) {
var srcIndex = d.sourceIndex.value(e.element);
return d.atom_site.pdbx_sifts_xref_db_res.valueKind(srcIndex);
},
}
};
var atom_site_fields = function () { return CifWriter.fields()
.str('group_PDB', P.residue.group_PDB)
.index('id')
.str('type_symbol', P.atom.type_symbol)
.str('label_atom_id', P.atom.label_atom_id)
.str('label_comp_id', P.atom.label_comp_id)
.int('label_seq_id', P.residue.label_seq_id, {
encoder: E.deltaRLE,
valueKind: function (k, d) {
var m = k.unit.model;
return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[k.element]);
}
})
.str('label_alt_id', P.atom.label_alt_id)
.str('pdbx_PDB_ins_code', P.residue.pdbx_PDB_ins_code)
.str('label_asym_id', atom_site_label_asym_id)
.str('label_entity_id', P.chain.label_entity_id)
.float('Cartn_x', P.atom.x, { digitCount: 3, encoder: E.fixedPoint3 })
.float('Cartn_y', P.atom.y, { digitCount: 3, encoder: E.fixedPoint3 })
.float('Cartn_z', P.atom.z, { digitCount: 3, encoder: E.fixedPoint3 })
.float('occupancy', P.atom.occupancy, { digitCount: 2, encoder: E.fixedPoint2 })
.float('B_iso_or_equiv', P.atom.B_iso_or_equiv, { digitCount: 2, encoder: E.fixedPoint2 })
.int('pdbx_formal_charge', P.atom.pdbx_formal_charge, {
encoder: E.deltaRLE,
valueKind: function (k, d) { return k.unit.model.atomicHierarchy.atoms.pdbx_formal_charge.valueKind(k.element); }
})
.str('auth_atom_id', P.atom.auth_atom_id)
.str('auth_comp_id', P.atom.auth_comp_id)
.int('auth_seq_id', P.residue.auth_seq_id, { encoder: E.deltaRLE })
.str('auth_asym_id', atom_site_auth_asym_id)
.int('pdbx_PDB_model_num', P.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)
// })
.getFields(); };
export var _atom_site = {
name: 'atom_site',
instance: function (_a) {
var structures = _a.structures;
return {
fields: atom_site_fields(),
source: structures.map(function (s) { return ({
data: {
structure: s,
sourceIndex: s.model.atomicHierarchy.atomSourceIndex,
atom_site: MmcifFormat.is(s.model.sourceData) ? s.model.sourceData.data.db.atom_site : void 0
},
rowCount: s.elementCount,
keys: function () { return s.elementLocations(); }
}); })
};
}
};
function prepostfixed(prefix, name) {
if (prefix)
return "".concat(prefix, "_").concat(name);
return name;
}
function prefixedInsCode(prefix) {
if (!prefix)
return 'pdbx_PDB_ins_code';
return "pdbx_".concat(prefix, "_PDB_ins_code");
}
function mappedProp(loc, prop) {
return function (k, d) { return prop(loc(k, d)); };
}
function addModelNum(fields, getLocation, options) {
if (options && options.includeModelNum) {
fields.int('pdbx_PDB_model_num', mappedProp(getLocation, P.unit.model_num));
}
}
export function residueIdFields(getLocation, options) {
var prefix = options && options.prefix;
var ret = CifWriter.fields()
.str(prepostfixed(prefix, "label_comp_id"), mappedProp(getLocation, P.atom.label_comp_id))
.int(prepostfixed(prefix, "label_seq_id"), mappedProp(getLocation, P.residue.label_seq_id), {
encoder: E.deltaRLE,
valueKind: function (k, d) {
var e = getLocation(k, d);
var m = e.unit.model;
return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[e.element]);
}
})
.str(prefixedInsCode(prefix), mappedProp(getLocation, P.residue.pdbx_PDB_ins_code))
.str(prepostfixed(prefix, "label_asym_id"), mappedProp(getLocation, P.chain.label_asym_id))
.str(prepostfixed(prefix, "label_entity_id"), mappedProp(getLocation, P.chain.label_entity_id))
.str(prepostfixed(prefix, "auth_comp_id"), mappedProp(getLocation, P.atom.auth_comp_id))
.int(prepostfixed(prefix, "auth_seq_id"), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE })
.str(prepostfixed(prefix, "auth_asym_id"), mappedProp(getLocation, P.chain.auth_asym_id));
addModelNum(ret, getLocation, options);
return ret.getFields();
}
export function chainIdFields(getLocation, options) {
var prefix = options && options.prefix;
var ret = CifField.build()
.str(prepostfixed(prefix, "label_asym_id"), mappedProp(getLocation, P.chain.label_asym_id))
.str(prepostfixed(prefix, "label_entity_id"), mappedProp(getLocation, P.chain.label_entity_id))
.str(prepostfixed(prefix, "auth_asym_id"), mappedProp(getLocation, P.chain.auth_asym_id));
addModelNum(ret, getLocation, options);
return ret.getFields();
}
export function entityIdFields(getLocation, options) {
var prefix = options && options.prefix;
var ret = CifField.build()
.str(prepostfixed(prefix, "label_entity_id"), mappedProp(getLocation, P.chain.label_entity_id));
addModelNum(ret, getLocation, options);
return ret.getFields();
}
export function atomIdFields(getLocation, options) {
var prefix = options && options.prefix;
var ret = CifWriter.fields()
.str(prepostfixed(prefix, "label_atom_id"), mappedProp(getLocation, P.atom.label_atom_id))
.str(prepostfixed(prefix, "label_comp_id"), mappedProp(getLocation, P.atom.label_comp_id))
.int(prepostfixed(prefix, "label_seq_id"), mappedProp(getLocation, P.residue.label_seq_id), {
encoder: E.deltaRLE,
valueKind: function (k, d) {
var e = getLocation(k, d);
var 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, P.atom.label_alt_id))
.str(prefixedInsCode(prefix), mappedProp(getLocation, P.residue.pdbx_PDB_ins_code))
.str(prepostfixed(prefix, "label_asym_id"), mappedProp(getLocation, P.chain.label_asym_id))
.str(prepostfixed(prefix, "label_entity_id"), mappedProp(getLocation, P.chain.label_entity_id))
.str(prepostfixed(prefix, "auth_atom_id"), mappedProp(getLocation, P.atom.auth_atom_id))
.str(prepostfixed(prefix, "auth_comp_id"), mappedProp(getLocation, P.atom.auth_comp_id))
.int(prepostfixed(prefix, "auth_seq_id"), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE })
.str(prepostfixed(prefix, "auth_asym_id"), mappedProp(getLocation, P.chain.auth_asym_id));
addModelNum(ret, getLocation, options);
return ret.getFields();
}