molstar
Version:
A comprehensive macromolecular library.
150 lines (149 loc) • 6.79 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*
* based in part on NGL (https://github.com/arose/ngl)
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.MetalCoordinationProvider = exports.MetalBindingProvider = exports.MetalProvider = exports.MetalCoordinationParams = void 0;
const param_definition_1 = require("../../../mol-util/param-definition");
const features_1 = require("./features");
const util_1 = require("../chemistry/util");
const types_1 = require("../../../mol-model/structure/model/properties/atomic/types");
const common_1 = require("./common");
const types_2 = require("../../../mol-model/structure/model/types");
exports.MetalCoordinationParams = {
distanceMax: param_definition_1.ParamDefinition.Numeric(3.0, { min: 1, max: 5, step: 0.1 }),
};
const IonicTypeMetals = [
types_1.Elements.LI, types_1.Elements.NA, types_1.Elements.K, types_1.Elements.RB, types_1.Elements.CS,
types_1.Elements.MG, types_1.Elements.CA, types_1.Elements.SR, types_1.Elements.BA, types_1.Elements.AL,
types_1.Elements.GA, types_1.Elements.IN, types_1.Elements.TL, types_1.Elements.SC, types_1.Elements.SN,
types_1.Elements.PB, types_1.Elements.BI, types_1.Elements.SB, types_1.Elements.HG
];
function addMetal(structure, unit, builder) {
const { elements } = unit;
const { x, y, z } = unit.model.atomicConformation;
for (let i = 0, il = elements.length; i < il; ++i) {
const element = (0, util_1.typeSymbol)(unit, i);
let type = common_1.FeatureType.None;
if (IonicTypeMetals.includes(element)) {
type = common_1.FeatureType.IonicTypeMetal;
}
else if ((0, types_1.isTransitionMetal)(element) || element === types_1.Elements.ZN || element === types_1.Elements.CD) {
type = common_1.FeatureType.TransitionMetal;
}
if (type) {
builder.add(type, common_1.FeatureGroup.None, x[elements[i]], y[elements[i]], z[elements[i]], i);
}
}
}
function isProteinSidechain(atomname) {
return !types_2.ProteinBackboneAtoms.has(atomname);
}
function isProteinBackbone(atomname) {
return types_2.ProteinBackboneAtoms.has(atomname);
}
function isNucleicBackbone(atomname) {
return types_2.NucleicBackboneAtoms.has(atomname);
}
/**
* Metal binding partners (dative bond or ionic-type interaction)
*/
function addMetalBinding(structure, unit, builder) {
const { elements } = unit;
const { x, y, z } = unit.model.atomicConformation;
for (let i = 0, il = elements.length; i < il; ++i) {
const element = (0, util_1.typeSymbol)(unit, i);
const resname = (0, util_1.compId)(unit, i);
const atomname = (0, util_1.atomId)(unit, i);
let dative = false;
let ionic = false;
const isStandardAminoacid = types_2.AminoAcidNames.has(resname);
const isStandardBase = types_2.BaseNames.has(resname);
if (!isStandardAminoacid && !isStandardBase) {
if ((0, types_1.isHalogen)(element) || element === types_1.Elements.O || element === types_1.Elements.S) {
dative = true;
ionic = true;
}
else if (element === types_1.Elements.N) {
dative = true;
}
}
else if (isStandardAminoacid) {
// main chain oxygen atom or oxygen, nitrogen and sulfur from specific amino acids
if (element === types_1.Elements.O) {
if (['ASP', 'GLU', 'SER', 'THR', 'TYR', 'ASN', 'GLN'].includes(resname) && isProteinSidechain(atomname)) {
dative = true;
ionic = true;
}
else if (isProteinBackbone(atomname)) {
dative = true;
ionic = true;
}
}
else if (element === types_1.Elements.S && (resname === 'CYS' || resname === 'MET')) {
dative = true;
ionic = true;
}
else if (element === types_1.Elements.N) {
if (resname === 'HIS' && isProteinSidechain(atomname)) {
dative = true;
}
}
}
else if (isStandardBase) {
// http://pubs.acs.org/doi/pdf/10.1021/acs.accounts.6b00253
// http://onlinelibrary.wiley.com/doi/10.1002/anie.200900399/full
if (element === types_1.Elements.O && isNucleicBackbone(atomname)) {
dative = true;
ionic = true;
}
else if (['N3', 'N4', 'N7'].includes(atomname)) {
dative = true;
}
else if (['O2', 'O4', 'O6'].includes(atomname)) {
dative = true;
ionic = true;
}
}
if (dative) {
builder.add(common_1.FeatureType.DativeBondPartner, common_1.FeatureGroup.None, x[elements[i]], y[elements[i]], z[elements[i]], i);
}
if (ionic) {
builder.add(common_1.FeatureType.IonicTypePartner, common_1.FeatureGroup.None, x[elements[i]], y[elements[i]], z[elements[i]], i);
}
}
}
function isMetalCoordination(ti, tj) {
if (ti === common_1.FeatureType.TransitionMetal) {
return (tj === common_1.FeatureType.DativeBondPartner ||
tj === common_1.FeatureType.TransitionMetal);
}
else if (ti === common_1.FeatureType.IonicTypeMetal) {
return (tj === common_1.FeatureType.IonicTypePartner);
}
}
function testMetalCoordination(structure, infoA, infoB, distanceSq) {
const typeA = infoA.types[infoA.feature];
const typeB = infoB.types[infoB.feature];
if (!isMetalCoordination(typeA, typeB) && !isMetalCoordination(typeB, typeA))
return;
return common_1.InteractionType.MetalCoordination;
}
//
exports.MetalProvider = features_1.Features.Provider([common_1.FeatureType.IonicTypeMetal, common_1.FeatureType.TransitionMetal], addMetal);
exports.MetalBindingProvider = features_1.Features.Provider([common_1.FeatureType.IonicTypePartner, common_1.FeatureType.DativeBondPartner], addMetalBinding);
exports.MetalCoordinationProvider = {
name: 'metal-coordination',
params: exports.MetalCoordinationParams,
createTester: (props) => {
return {
maxDistance: props.distanceMax,
requiredFeatures: new Set([common_1.FeatureType.IonicTypeMetal, common_1.FeatureType.TransitionMetal, common_1.FeatureType.IonicTypePartner, common_1.FeatureType.DativeBondPartner]),
getType: (structure, infoA, infoB, distanceSq) => testMetalCoordination(structure, infoA, infoB, distanceSq)
};
}
};