molstar
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A comprehensive macromolecular library.
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JavaScript
/**
* Copyright (c) 2017-2021 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 { Column } from '../../../../../mol-data/db';
import { mmCIF_Schema as mmCIF } from '../../../../../mol-io/reader/cif/schema/mmcif';
export const AtomsSchema = {
/**
* The chemical element of this atom site.
* For mmCIF files, this points to atom_type.symbol in the ATOM_TYPE category.
*/
type_symbol: Column.Schema.Aliased(mmCIF.atom_site.type_symbol),
/**
* A component of the identifier for this atom site.
* This is a standardized name for the atom within its residue.
* For mmCIF files, this points to chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
*/
label_atom_id: mmCIF.atom_site.label_atom_id,
/**
* An alternative identifier for label_atom_id that may be provided by an author
* in order to match the identification used in the publication that describes the structure.
*/
auth_atom_id: mmCIF.atom_site.auth_atom_id,
/**
* A component of the identifier for this atom site.
* Identifies an alternative conformation for this atom site.
*/
label_alt_id: mmCIF.atom_site.label_alt_id,
/**
* A component of the identifier for this atom site.
* For mmCIF files, this points to chem_comp.id in the CHEM_COMP category.
*/
label_comp_id: mmCIF.atom_site.label_comp_id,
/**
* An alternative identifier for atom_site.label_comp_id that may be provided by an author
* in order to match the identification used in the publication that describes the structure.
*/
auth_comp_id: mmCIF.atom_site.auth_comp_id,
/**
* The net integer charge assigned to this atom.
* This is the formal charge assignment normally found in chemical diagrams.
*/
pdbx_formal_charge: mmCIF.atom_site.pdbx_formal_charge,
// id, occupancy and B_iso_or_equiv are part of conformation
};
export const ResiduesSchema = {
/**
* The group of atoms to which the atom site belongs. This data item is provided for
* compatibility with the original Protein Data Bank format, and only for that purpose.
*/
group_PDB: mmCIF.atom_site.group_PDB,
/**
* For mmCIF files, this points to entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
label_seq_id: mmCIF.atom_site.label_seq_id,
/**
* An alternative identifier for atom_site.label_seq_id that may be provided by an author
* in order to match the identification used in the publication that describes the structure.
*/
auth_seq_id: mmCIF.atom_site.auth_seq_id,
/**
* PDB insertion code.
*/
pdbx_PDB_ins_code: mmCIF.atom_site.pdbx_PDB_ins_code,
// comp_id is part of atoms because of microheterogeneity
};
export const ChainsSchema = {
/**
* A component of the identifier for this atom site.
* For mmCIF files, this points to struct_asym.id in the STRUCT_ASYM category.
*/
label_asym_id: mmCIF.atom_site.label_asym_id,
/**
* An alternative identifier for atomsite.label_asym_id that may be provided by an author
* in order to match the identification used in the publication that describes the structure.
*/
auth_asym_id: mmCIF.atom_site.auth_asym_id,
/**
* For mmCIF files, this points to _entity.id in the ENTITY category.
*/
label_entity_id: mmCIF.atom_site.label_entity_id
};
export var AtomicIndex;
(function (AtomicIndex) {
function EmptyResidueKey() { return { label_entity_id: '', label_asym_id: '', auth_seq_id: 0, pdbx_PDB_ins_code: void 0 }; }
AtomicIndex.EmptyResidueKey = EmptyResidueKey;
})(AtomicIndex || (AtomicIndex = {}));
export var AtomicHierarchy;
(function (AtomicHierarchy) {
/** Start residue inclusive */
function chainStartResidueIndex(segs, cI) {
return segs.residueAtomSegments.index[segs.chainAtomSegments.offsets[cI]];
}
AtomicHierarchy.chainStartResidueIndex = chainStartResidueIndex;
/** End residue exclusive */
function chainEndResidueIndexExcl(segs, cI) {
return segs.residueAtomSegments.index[segs.chainAtomSegments.offsets[cI + 1] - 1] + 1;
}
AtomicHierarchy.chainEndResidueIndexExcl = chainEndResidueIndexExcl;
function chainResidueCount(segs, cI) {
return chainEndResidueIndexExcl(segs, cI) - chainStartResidueIndex(segs, cI);
}
AtomicHierarchy.chainResidueCount = chainResidueCount;
function residueFirstAtomIndex(hierarchy, rI) {
return hierarchy.residueAtomSegments.offsets[rI];
}
AtomicHierarchy.residueFirstAtomIndex = residueFirstAtomIndex;
function atomChainIndex(hierarchy, eI) {
return hierarchy.chainAtomSegments.index[eI];
}
AtomicHierarchy.atomChainIndex = atomChainIndex;
function residueChainIndex(hierarchy, rI) {
return hierarchy.chainAtomSegments.index[hierarchy.residueAtomSegments.offsets[rI]];
}
AtomicHierarchy.residueChainIndex = residueChainIndex;
})(AtomicHierarchy || (AtomicHierarchy = {}));