molstar
Version:
A comprehensive macromolecular library.
170 lines (169 loc) • 7.11 kB
JavaScript
/**
* Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __extends } from "tslib";
import { InterUnitGraph } from '../../../mol-math/graph/inter-unit-graph';
export { InteractionsIntraContacts };
var InteractionsIntraContacts;
(function (InteractionsIntraContacts) {
/**
* Note: assumes that feature members of a contact are non-overlapping
*/
function createElementsIndex(contacts, features, elementsCount) {
var offsets = new Int32Array(elementsCount + 1);
var bucketFill = new Int32Array(elementsCount);
var bucketSizes = new Int32Array(elementsCount);
var members = features.members, featureOffsets = features.offsets;
for (var i = 0, il = contacts.edgeCount * 2; i < il; ++i) {
var aI = contacts.a[i];
var bI = contacts.b[i];
if (aI > bI)
continue;
for (var j = featureOffsets[aI], jl = featureOffsets[aI + 1]; j < jl; ++j) {
++bucketSizes[members[j]];
}
for (var j = featureOffsets[bI], jl = featureOffsets[bI + 1]; j < jl; ++j) {
++bucketSizes[members[j]];
}
}
var offset = 0;
for (var i = 0; i < elementsCount; i++) {
offsets[i] = offset;
offset += bucketSizes[i];
}
offsets[elementsCount] = offset;
var indices = new Int32Array(offset);
for (var i = 0, il = contacts.edgeCount * 2; i < il; ++i) {
var aI = contacts.a[i];
var bI = contacts.b[i];
if (aI > bI)
continue;
for (var j = featureOffsets[aI], jl = featureOffsets[aI + 1]; j < jl; ++j) {
var m = members[j];
var om = offsets[m] + bucketFill[m];
indices[om] = i;
++bucketFill[m];
}
for (var j = featureOffsets[bI], jl = featureOffsets[bI + 1]; j < jl; ++j) {
var m = members[j];
var om = offsets[m] + bucketFill[m];
indices[om] = i;
++bucketFill[m];
}
}
return { indices: indices, offsets: offsets };
}
InteractionsIntraContacts.createElementsIndex = createElementsIndex;
})(InteractionsIntraContacts || (InteractionsIntraContacts = {}));
export { InteractionsInterContacts };
var InteractionsInterContacts = /** @class */ (function (_super) {
__extends(InteractionsInterContacts, _super);
function InteractionsInterContacts(map, unitsFeatures) {
var _this = _super.call(this, map) || this;
_this.elementKeyIndex = new Map();
for (var i = 0, il = _this.edges.length; i < il; ++i) {
var _a = _this.edges[i], unitA = _a.unitA, indexA = _a.indexA;
var _b = unitsFeatures.get(unitA), offsets = _b.offsets, members = _b.members;
for (var j = offsets[indexA], jl = offsets[indexA + 1]; j < jl; ++j) {
var vertexKey = _this.getElementKey(members[j], unitA);
var e = _this.elementKeyIndex.get(vertexKey);
if (e === undefined) {
_this.elementKeyIndex.set(vertexKey, [i]);
}
else {
e.push(i);
}
}
}
return _this;
}
InteractionsInterContacts.prototype.getContactIndicesForElement = function (index, unit) {
return this.elementKeyIndex.get(this.getElementKey(index, unit.id)) || [];
};
InteractionsInterContacts.prototype.getElementKey = function (index, unitId) {
return "".concat(index, "|").concat(unitId);
};
return InteractionsInterContacts;
}(InterUnitGraph));
export function interactionTypeLabel(type) {
switch (type) {
case 4 /* InteractionType.HydrogenBond */:
return 'Hydrogen Bond';
case 6 /* InteractionType.Hydrophobic */:
return 'Hydrophobic Contact';
case 5 /* InteractionType.HalogenBond */:
return 'Halogen Bond';
case 1 /* InteractionType.Ionic */:
return 'Ionic Interaction';
case 7 /* InteractionType.MetalCoordination */:
return 'Metal Coordination';
case 2 /* InteractionType.CationPi */:
return 'Cation-Pi Interaction';
case 3 /* InteractionType.PiStacking */:
return 'Pi Stacking';
case 8 /* InteractionType.WeakHydrogenBond */:
return 'Weak Hydrogen Bond';
case 0 /* InteractionType.Unknown */:
return 'Unknown Interaction';
}
}
export function featureTypeLabel(type) {
switch (type) {
case 0 /* FeatureType.None */:
return 'None';
case 1 /* FeatureType.PositiveCharge */:
return 'Positive Charge';
case 2 /* FeatureType.NegativeCharge */:
return 'Negative Charge';
case 3 /* FeatureType.AromaticRing */:
return 'Aromatic Ring';
case 4 /* FeatureType.HydrogenDonor */:
return 'Hydrogen Donor';
case 5 /* FeatureType.HydrogenAcceptor */:
return 'Hydrogen Acceptor';
case 6 /* FeatureType.HalogenDonor */:
return 'Halogen Donor';
case 7 /* FeatureType.HalogenAcceptor */:
return 'Halogen Acceptor';
case 8 /* FeatureType.HydrophobicAtom */:
return 'HydrophobicAtom';
case 9 /* FeatureType.WeakHydrogenDonor */:
return 'Weak Hydrogen Donor';
case 10 /* FeatureType.IonicTypePartner */:
return 'Ionic Type Partner';
case 11 /* FeatureType.DativeBondPartner */:
return 'Dative Bond Partner';
case 12 /* FeatureType.TransitionMetal */:
return 'Transition Metal';
case 13 /* FeatureType.IonicTypeMetal */:
return 'Ionic Type Metal';
}
}
export function featureGroupLabel(group) {
switch (group) {
case 0 /* FeatureGroup.None */:
return 'None';
case 1 /* FeatureGroup.QuaternaryAmine */:
return 'Quaternary Amine';
case 2 /* FeatureGroup.TertiaryAmine */:
return 'Tertiary Amine';
case 3 /* FeatureGroup.Sulfonium */:
return 'Sulfonium';
case 4 /* FeatureGroup.SulfonicAcid */:
return 'Sulfonic Acid';
case 5 /* FeatureGroup.Sulfate */:
return 'Sulfate';
case 6 /* FeatureGroup.Phosphate */:
return 'Phosphate';
case 7 /* FeatureGroup.Halocarbon */:
return 'Halocarbon';
case 8 /* FeatureGroup.Guanidine */:
return 'Guanidine';
case 9 /* FeatureGroup.Acetamidine */:
return 'Acetamidine';
case 10 /* FeatureGroup.Carboxylate */:
return 'Carboxylate';
}
}