molstar
Version:
A comprehensive macromolecular library.
148 lines • 5.9 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.assignRadiusForHeavyAtoms = void 0;
var common_1 = require("./common");
var common_2 = require("../../../../mol-model/structure/structure/unit/bonds/common");
var types_1 = require("../../../../mol-model/structure/model/types");
var atomic_1 = require("../../../../mol-model/structure/model/properties/atomic");
var structure_1 = require("../../../../mol-model/structure/structure");
var util_1 = require("../../../../mol-model/structure/util");
function assignRadiusForHeavyAtoms(ctx) {
var key = structure_1.StructureProperties.residue.key;
var _a = structure_1.StructureProperties.atom, type_symbol = _a.type_symbol, label_atom_id = _a.label_atom_id, label_comp_id = _a.label_comp_id;
var structure = ctx.structure, atomRadiusType = ctx.atomRadiusType, serialResidueIndex = ctx.serialResidueIndex;
var l = structure_1.StructureElement.Location.create(structure);
var prevResidueIdx = 0;
var residueIdx = 0;
var serialResidueIdx = -1;
l.structure = structure;
for (var i = 0, m = 0, il = structure.units.length; i < il; ++i) {
var unit = structure.units[i];
var elements = unit.elements;
l.unit = unit;
prevResidueIdx = -1;
for (var j = 0, jl = elements.length; j < jl; ++j) {
var eI = elements[j];
var mj = m + j;
l.element = eI;
residueIdx = key(l);
if (prevResidueIdx !== residueIdx)
++serialResidueIdx;
prevResidueIdx = residueIdx;
var element = type_symbol(l);
var elementIdx = (0, common_2.getElementIdx)(element);
// skip hydrogen atoms
if ((0, common_2.isHydrogen)(elementIdx)) {
atomRadiusType[mj] = 0;
serialResidueIndex[mj] = -1;
continue;
}
var atomId = label_atom_id(l);
var moleculeType = (0, util_1.getElementMoleculeType)(unit, eI);
// skip water and optionally non-polymer groups
if (moleculeType === 2 /* Water */ || (!ctx.nonPolymer && !(0, types_1.isPolymer)(moleculeType))) {
atomRadiusType[mj] = 0;
serialResidueIndex[mj] = -1;
continue;
}
var compId = label_comp_id(l);
if (ctx.traceOnly && ((atomId !== 'CA' && atomId !== 'BB') || !common_1.MaxAsa[compId])) {
atomRadiusType[mj] = 0;
serialResidueIndex[mj] = serialResidueIdx;
continue;
}
if ((0, types_1.isNucleic)(moleculeType)) {
atomRadiusType[mj] = determineRadiusNucl(atomId, element, compId);
}
else if (moleculeType === 5 /* Protein */) {
atomRadiusType[mj] = determineRadiusAmino(atomId, element, compId);
}
else {
atomRadiusType[mj] = handleNonStandardCase(element);
}
serialResidueIndex[mj] = serialResidueIdx;
}
m += elements.length;
}
}
exports.assignRadiusForHeavyAtoms = assignRadiusForHeavyAtoms;
/**
* Gets the van der Waals radius of the given atom following the values defined by Chothia (1976)
* J.Mol.Biol.105,1-14. NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly
* the heavy atoms to account for Hydrogens.
*/
function determineRadiusAmino(atomId, element, compId) {
switch (element) {
case 'O':
return 5;
case 'S':
return 6;
case 'N':
return atomId === 'NZ' ? 4 : 3;
case 'C':
switch (atomId) {
case 'C':
case 'CE1':
case 'CE2':
case 'CE3':
case 'CH2':
case 'CZ':
case 'CZ2':
case 'CZ3':
return 1;
case 'CA':
case 'CB':
case 'CE':
case 'CG1':
case 'CG2':
return 2;
default:
switch (compId) {
case 'PHE':
case 'TRP':
case 'TYR':
case 'HIS':
case 'ASP':
case 'ASN':
return 1;
case 'PRO':
case 'LYS':
case 'ARG':
case 'MET':
case 'ILE':
case 'LEU':
return 2;
case 'GLU':
case 'GLN':
return atomId === 'CD' ? 1 : 2;
}
}
}
return handleNonStandardCase(element);
}
function determineRadiusNucl(atomId, element, compId) {
switch (element) {
case 'C': return 7;
case 'N': return 8;
case 'P': return 9;
case 'O': return 5;
}
return handleNonStandardCase(element);
}
function handleNonStandardCase(element) {
var radius = (0, atomic_1.VdwRadius)(element);
var index = common_1.VdWLookup.indexOf(radius);
if (index === -1) {
// add novel value to lookup array
index = common_1.VdWLookup.length;
common_1.VdWLookup[index] = radius;
}
return index;
}
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