molstar
Version:
A comprehensive macromolecular library.
237 lines (236 loc) • 10.8 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2022 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.FeatureGroup = exports.FeatureTypes = exports.FeatureType = exports.InteractionType = exports.InteractionFlag = exports.InteractionsInterContacts = exports.InteractionsIntraContacts = void 0;
exports.interactionTypeLabel = interactionTypeLabel;
exports.featureTypeLabel = featureTypeLabel;
exports.featureGroupLabel = featureGroupLabel;
const inter_unit_graph_1 = require("../../../mol-math/graph/inter-unit-graph");
var InteractionsIntraContacts;
(function (InteractionsIntraContacts) {
/**
* Note: assumes that feature members of a contact are non-overlapping
*/
function createElementsIndex(contacts, features, elementsCount) {
const offsets = new Int32Array(elementsCount + 1);
const bucketFill = new Int32Array(elementsCount);
const bucketSizes = new Int32Array(elementsCount);
const { members, offsets: featureOffsets } = features;
for (let i = 0, il = contacts.edgeCount * 2; i < il; ++i) {
const aI = contacts.a[i];
const bI = contacts.b[i];
if (aI > bI)
continue;
for (let j = featureOffsets[aI], jl = featureOffsets[aI + 1]; j < jl; ++j) {
++bucketSizes[members[j]];
}
for (let j = featureOffsets[bI], jl = featureOffsets[bI + 1]; j < jl; ++j) {
++bucketSizes[members[j]];
}
}
let offset = 0;
for (let i = 0; i < elementsCount; i++) {
offsets[i] = offset;
offset += bucketSizes[i];
}
offsets[elementsCount] = offset;
const indices = new Int32Array(offset);
for (let i = 0, il = contacts.edgeCount * 2; i < il; ++i) {
const aI = contacts.a[i];
const bI = contacts.b[i];
if (aI > bI)
continue;
for (let j = featureOffsets[aI], jl = featureOffsets[aI + 1]; j < jl; ++j) {
const m = members[j];
const om = offsets[m] + bucketFill[m];
indices[om] = i;
++bucketFill[m];
}
for (let j = featureOffsets[bI], jl = featureOffsets[bI + 1]; j < jl; ++j) {
const m = members[j];
const om = offsets[m] + bucketFill[m];
indices[om] = i;
++bucketFill[m];
}
}
return { indices, offsets };
}
InteractionsIntraContacts.createElementsIndex = createElementsIndex;
})(InteractionsIntraContacts || (exports.InteractionsIntraContacts = InteractionsIntraContacts = {}));
class InteractionsInterContacts extends inter_unit_graph_1.InterUnitGraph {
getContactIndicesForElement(index, unit) {
return this.elementKeyIndex.get(this.getElementKey(index, unit.id)) || [];
}
getElementKey(index, unitId) {
return `${index}|${unitId}`;
}
constructor(map, unitsFeatures) {
super(map);
this.elementKeyIndex = new Map();
for (let i = 0, il = this.edges.length; i < il; ++i) {
const { unitA, indexA } = this.edges[i];
const { offsets, members } = unitsFeatures.get(unitA);
for (let j = offsets[indexA], jl = offsets[indexA + 1]; j < jl; ++j) {
const vertexKey = this.getElementKey(members[j], unitA);
const e = this.elementKeyIndex.get(vertexKey);
if (e === undefined) {
this.elementKeyIndex.set(vertexKey, [i]);
}
else {
e.push(i);
}
}
}
}
}
exports.InteractionsInterContacts = InteractionsInterContacts;
var InteractionFlag;
(function (InteractionFlag) {
InteractionFlag[InteractionFlag["None"] = 0] = "None";
InteractionFlag[InteractionFlag["Filtered"] = 1] = "Filtered";
})(InteractionFlag || (exports.InteractionFlag = InteractionFlag = {}));
var InteractionType;
(function (InteractionType) {
InteractionType[InteractionType["Unknown"] = 0] = "Unknown";
InteractionType[InteractionType["Ionic"] = 1] = "Ionic";
InteractionType[InteractionType["CationPi"] = 2] = "CationPi";
InteractionType[InteractionType["PiStacking"] = 3] = "PiStacking";
InteractionType[InteractionType["HydrogenBond"] = 4] = "HydrogenBond";
InteractionType[InteractionType["HalogenBond"] = 5] = "HalogenBond";
InteractionType[InteractionType["Hydrophobic"] = 6] = "Hydrophobic";
InteractionType[InteractionType["MetalCoordination"] = 7] = "MetalCoordination";
InteractionType[InteractionType["WeakHydrogenBond"] = 8] = "WeakHydrogenBond";
})(InteractionType || (exports.InteractionType = InteractionType = {}));
function interactionTypeLabel(type) {
switch (type) {
case InteractionType.HydrogenBond:
return 'Hydrogen Bond';
case InteractionType.Hydrophobic:
return 'Hydrophobic Contact';
case InteractionType.HalogenBond:
return 'Halogen Bond';
case InteractionType.Ionic:
return 'Ionic Interaction';
case InteractionType.MetalCoordination:
return 'Metal Coordination';
case InteractionType.CationPi:
return 'Cation-Pi Interaction';
case InteractionType.PiStacking:
return 'Pi Stacking';
case InteractionType.WeakHydrogenBond:
return 'Weak Hydrogen Bond';
case InteractionType.Unknown:
return 'Unknown Interaction';
}
}
var FeatureType;
(function (FeatureType) {
FeatureType[FeatureType["None"] = 0] = "None";
FeatureType[FeatureType["PositiveCharge"] = 1] = "PositiveCharge";
FeatureType[FeatureType["NegativeCharge"] = 2] = "NegativeCharge";
FeatureType[FeatureType["AromaticRing"] = 3] = "AromaticRing";
FeatureType[FeatureType["HydrogenDonor"] = 4] = "HydrogenDonor";
FeatureType[FeatureType["HydrogenAcceptor"] = 5] = "HydrogenAcceptor";
FeatureType[FeatureType["HalogenDonor"] = 6] = "HalogenDonor";
FeatureType[FeatureType["HalogenAcceptor"] = 7] = "HalogenAcceptor";
FeatureType[FeatureType["HydrophobicAtom"] = 8] = "HydrophobicAtom";
FeatureType[FeatureType["WeakHydrogenDonor"] = 9] = "WeakHydrogenDonor";
FeatureType[FeatureType["IonicTypePartner"] = 10] = "IonicTypePartner";
FeatureType[FeatureType["DativeBondPartner"] = 11] = "DativeBondPartner";
FeatureType[FeatureType["TransitionMetal"] = 12] = "TransitionMetal";
FeatureType[FeatureType["IonicTypeMetal"] = 13] = "IonicTypeMetal";
})(FeatureType || (exports.FeatureType = FeatureType = {}));
// to use with isolatedModules
var FeatureTypes;
(function (FeatureTypes) {
FeatureTypes[FeatureTypes["None"] = 0] = "None";
FeatureTypes[FeatureTypes["PositiveCharge"] = 1] = "PositiveCharge";
FeatureTypes[FeatureTypes["NegativeCharge"] = 2] = "NegativeCharge";
FeatureTypes[FeatureTypes["AromaticRing"] = 3] = "AromaticRing";
FeatureTypes[FeatureTypes["HydrogenDonor"] = 4] = "HydrogenDonor";
FeatureTypes[FeatureTypes["HydrogenAcceptor"] = 5] = "HydrogenAcceptor";
FeatureTypes[FeatureTypes["HalogenDonor"] = 6] = "HalogenDonor";
FeatureTypes[FeatureTypes["HalogenAcceptor"] = 7] = "HalogenAcceptor";
FeatureTypes[FeatureTypes["HydrophobicAtom"] = 8] = "HydrophobicAtom";
FeatureTypes[FeatureTypes["WeakHydrogenDonor"] = 9] = "WeakHydrogenDonor";
FeatureTypes[FeatureTypes["IonicTypePartner"] = 10] = "IonicTypePartner";
FeatureTypes[FeatureTypes["DativeBondPartner"] = 11] = "DativeBondPartner";
FeatureTypes[FeatureTypes["TransitionMetal"] = 12] = "TransitionMetal";
FeatureTypes[FeatureTypes["IonicTypeMetal"] = 13] = "IonicTypeMetal";
})(FeatureTypes || (exports.FeatureTypes = FeatureTypes = {}));
function featureTypeLabel(type) {
switch (type) {
case FeatureType.None:
return 'None';
case FeatureType.PositiveCharge:
return 'Positive Charge';
case FeatureType.NegativeCharge:
return 'Negative Charge';
case FeatureType.AromaticRing:
return 'Aromatic Ring';
case FeatureType.HydrogenDonor:
return 'Hydrogen Donor';
case FeatureType.HydrogenAcceptor:
return 'Hydrogen Acceptor';
case FeatureType.HalogenDonor:
return 'Halogen Donor';
case FeatureType.HalogenAcceptor:
return 'Halogen Acceptor';
case FeatureType.HydrophobicAtom:
return 'HydrophobicAtom';
case FeatureType.WeakHydrogenDonor:
return 'Weak Hydrogen Donor';
case FeatureType.IonicTypePartner:
return 'Ionic Type Partner';
case FeatureType.DativeBondPartner:
return 'Dative Bond Partner';
case FeatureType.TransitionMetal:
return 'Transition Metal';
case FeatureType.IonicTypeMetal:
return 'Ionic Type Metal';
}
}
var FeatureGroup;
(function (FeatureGroup) {
FeatureGroup[FeatureGroup["None"] = 0] = "None";
FeatureGroup[FeatureGroup["QuaternaryAmine"] = 1] = "QuaternaryAmine";
FeatureGroup[FeatureGroup["TertiaryAmine"] = 2] = "TertiaryAmine";
FeatureGroup[FeatureGroup["Sulfonium"] = 3] = "Sulfonium";
FeatureGroup[FeatureGroup["SulfonicAcid"] = 4] = "SulfonicAcid";
FeatureGroup[FeatureGroup["Sulfate"] = 5] = "Sulfate";
FeatureGroup[FeatureGroup["Phosphate"] = 6] = "Phosphate";
FeatureGroup[FeatureGroup["Halocarbon"] = 7] = "Halocarbon";
FeatureGroup[FeatureGroup["Guanidine"] = 8] = "Guanidine";
FeatureGroup[FeatureGroup["Acetamidine"] = 9] = "Acetamidine";
FeatureGroup[FeatureGroup["Carboxylate"] = 10] = "Carboxylate";
})(FeatureGroup || (exports.FeatureGroup = FeatureGroup = {}));
function featureGroupLabel(group) {
switch (group) {
case FeatureGroup.None:
return 'None';
case FeatureGroup.QuaternaryAmine:
return 'Quaternary Amine';
case FeatureGroup.TertiaryAmine:
return 'Tertiary Amine';
case FeatureGroup.Sulfonium:
return 'Sulfonium';
case FeatureGroup.SulfonicAcid:
return 'Sulfonic Acid';
case FeatureGroup.Sulfate:
return 'Sulfate';
case FeatureGroup.Phosphate:
return 'Phosphate';
case FeatureGroup.Halocarbon:
return 'Halocarbon';
case FeatureGroup.Guanidine:
return 'Guanidine';
case FeatureGroup.Acetamidine:
return 'Acetamidine';
case FeatureGroup.Carboxylate:
return 'Carboxylate';
}
}