molstar
Version:
A comprehensive macromolecular library.
93 lines • 3.1 kB
JavaScript
;
/**
* Copyright (c) 2019 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.getInterBondOrderFromTable = exports.getIntraBondOrderFromTable = void 0;
var types_1 = require("../../types");
/**
* Map of intra component bond orders in aminoacids and nucleotides assuming standard IUPAC naming.
* The key is constructed as `${compId}|${atomId1}|${atomId2}` with `atomId1 < atomId2`.
*/
var IntraBondOrderTable = new Map([
['HIS|CD2|CG', 2],
['HIS|CE1|ND1', 2],
['ARG|CZ|NH2', 2],
['PHE|CE1|CZ', 2],
['PHE|CD2|CE2', 2],
['PHE|CD1|CG', 2],
['TRP|CD1|CG', 2],
['TRP|CD2|CE2', 2],
['TRP|CE3|CZ3', 2],
['TRP|CH2|CZ2', 2],
['ASN|CG|OD1', 2],
['GLN|CD|OE1', 2],
['TYR|CD1|CG', 2],
['TYR|CD2|CE2', 2],
['TYR|CE1|CZ', 2],
['ASP|CG|OD1', 2],
['GLU|CD|OE1', 2],
['G|C8|N7', 2],
['G|C4|C5', 2],
['G|C2|N3', 2],
['G|C6|O6', 2],
['C|C4|N3', 2],
['C|C5|C6', 2],
['C|C2|O2', 2],
['A|C2|N3', 2],
['A|C6|N1', 2],
['A|C4|C5', 2],
['A|C8|N7', 2],
['U|C5|C6', 2],
['U|C2|O2', 2],
['U|C4|O4', 2],
['DG|C8|N7', 2],
['DG|C4|C5', 2],
['DG|C2|N3', 2],
['DG|C6|O6', 2],
['DC|C4|N3', 2],
['DC|C5|C6', 2],
['DC|C2|O2', 2],
['DA|C2|N3', 2],
['DA|C6|N1', 2],
['DA|C4|C5', 2],
['DA|C8|N7', 2],
['DT|C5|C6', 2],
['DT|C2|O2', 2],
['DT|C4|O4', 2]
]);
/**
* Get order for bonds in aminoacids and nucleotides assuming standard IUPAC naming
*/
function getIntraBondOrderFromTable(compId, atomId1, atomId2) {
var _a;
_a = atomId1 < atomId2 ? [atomId1, atomId2] : [atomId2, atomId1], atomId1 = _a[0], atomId2 = _a[1];
if (types_1.AminoAcidNames.has(compId) && atomId1 === 'C' && atomId2 === 'O')
return 2;
if (types_1.BaseNames.has(compId) && atomId1 === 'OP1' && atomId2 === 'P')
return 2;
return IntraBondOrderTable.get(compId + "|" + atomId1 + "|" + atomId2) || 1;
}
exports.getIntraBondOrderFromTable = getIntraBondOrderFromTable;
/**
* Map of inter component bond orders assuming PDBx/mmCIF naming.
* The key is constructed as `${compId1}|${compId2}|${atomId1}|${atomId2}` with `compId1 < compId2`.
*/
var InterBondOrderTable = new Map([
['LYS|NZ|RET|C15', 2] // Schiff base in Rhodopsin and Bacteriorhodopsin
]);
/**
* Get order for bonds between component assuming PDBx/mmCIF naming.
*/
function getInterBondOrderFromTable(compId1, atomId1, compId2, atomId2) {
var _a, _b;
if (compId1 > compId2) {
_a = [compId2, compId1], compId1 = _a[0], compId2 = _a[1];
_b = [atomId2, atomId1], atomId1 = _b[0], atomId2 = _b[1];
}
return InterBondOrderTable.get(compId1 + "|" + atomId1 + "|" + compId2 + "|" + atomId2) || 1;
}
exports.getInterBondOrderFromTable = getInterBondOrderFromTable;
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