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decouple water bridges from hbond detection

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Sebastian
2026-05-26 16:35:38 +02:00
parent 340806d774
commit 2601d2ba63
2 changed files with 38 additions and 13 deletions
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45
src/mol-model-props/computed/interactions/interactions.ts
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@@ -15,7 +15,7 @@ import { IntMap } from '../../../mol-data/int';
import { addUnitContacts, ContactTester, addStructureContacts, ContactsParams, ContactsProps } from './contacts';
import { HalogenDonorProvider, HalogenAcceptorProvider, HalogenBondsProvider } from './halogen-bonds';
import { HydrogenDonorProvider, WeakHydrogenDonorProvider, HydrogenAcceptorProvider, HydrogenBondsProvider, WeakHydrogenBondsProvider } from './hydrogen-bonds';
import { findWaterBridgeContacts, WaterBridgesParams, WaterBridgeContact } from './water-bridges';
import { WaterBridgesProvider, WaterBridgeContact } from './water-bridges';
import { NegativChargeProvider, PositiveChargeProvider, AromaticRingProvider, IonicProvider, PiStackingProvider, CationPiProvider } from './charged';
import { HydrophobicAtomProvider, HydrophobicProvider } from './hydrophobic';
import { SetUtils } from '../../../mol-util/set';
@@ -181,16 +181,30 @@ export const ContactProviderParams = getProvidersParams([
// 'weak-hydrogen-bonds',
]);
export const WaterBridgesToggleParams = {
'water-bridges': PD.MappedStatic('off', {
on: PD.Group(WaterBridgesParams),
off: PD.Group({})
}, { cycle: true }),
const BridgeProviders = {
'water-bridges': WaterBridgesProvider,
};
type BridgeProviders = typeof BridgeProviders
function getBridgeProviderParams(defaultOn: string[] = []) {
const params: { [k in keyof BridgeProviders]: PD.Mapped<PD.NamedParamUnion<{
on: PD.Group<BridgeProviders[k]['params']>
off: PD.Group<{}>
}>> } = Object.create(null);
Object.keys(BridgeProviders).forEach(k => {
(params as any)[k] = PD.MappedStatic(defaultOn.includes(k) ? 'on' : 'off', {
on: PD.Group(BridgeProviders[k as keyof BridgeProviders].params),
off: PD.Group({})
}, { cycle: true });
});
return params;
}
export const BridgeProviderParams = getBridgeProviderParams([]);
export const InteractionsParams = {
providers: PD.Group(ContactProviderParams, { isFlat: true }),
waterBridges: PD.Group(WaterBridgesToggleParams, { isFlat: true }),
bridges: PD.Group(BridgeProviderParams, { isFlat: true }),
contacts: PD.Group(ContactsParams, { label: 'Advanced Options' }),
};
export type InteractionsParams = typeof InteractionsParams
@@ -217,6 +231,9 @@ export async function computeInteractions(ctx: CustomProperty.Context, structure
const requiredFeatures = new Set<FeatureType>();
contactTesters.forEach(l => SetUtils.add(requiredFeatures, l.requiredFeatures));
ObjectKeys(BridgeProviders).forEach(k => {
if (p.bridges[k].name === 'on') SetUtils.add(requiredFeatures, BridgeProviders[k].requiredFeatures);
});
const featureProviders = FeatureProviders.filter(f => SetUtils.areIntersecting(requiredFeatures, f.types));
const unitsFeatures = IntMap.Mutable<Features>();
@@ -243,7 +260,7 @@ export async function computeInteractions(ctx: CustomProperty.Context, structure
}
const contacts = findInterUnitContacts(structure, unitsFeatures, contactTesters, p.contacts, options);
const bridges = findBridges(structure, unitsFeatures, p.waterBridges);
const bridges = findBridges(structure, unitsFeatures, p.bridges);
const interactions = { unitsFeatures, unitsContacts, contacts, bridges };
refineInteractions(structure, interactions);
@@ -276,13 +293,15 @@ function findIntraUnitContacts(structure: Structure, unit: Unit, features: Featu
return builder.getContacts();
}
function findBridges(structure: Structure, unitsFeatures: IntMap<Features>, props: PD.Values<typeof WaterBridgesToggleParams>): BridgeContacts {
function findBridges(structure: Structure, unitsFeatures: IntMap<Features>, props: PD.Values<typeof BridgeProviderParams>): BridgeContacts {
const bridges: BridgeContact[] = [];
const wb = props['water-bridges'];
if (wb.name === 'on') {
for (const b of findWaterBridgeContacts(structure, unitsFeatures, wb.params)) bridges.push(b);
}
ObjectKeys(BridgeProviders).forEach(k => {
const { name, params } = props[k];
if (name === 'on') {
for (const b of BridgeProviders[k].find(structure, unitsFeatures, params as any)) bridges.push(b);
}
});
return bridges;
}

6
src/mol-model-props/computed/interactions/water-bridges.ts
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@@ -58,6 +58,12 @@ export const WaterBridgesParams = {
export type WaterBridgesParams = typeof WaterBridgesParams;
export type WaterBridgesProps = PD.Values<WaterBridgesParams>;
export const WaterBridgesProvider = {
requiredFeatures: new Set([FeatureType.HydrogenDonor, FeatureType.HydrogenAcceptor]),
params: WaterBridgesParams,
find: findWaterBridgeContacts,
};
function isWater(unit: Unit.Atomic, index: StructureElement.UnitIndex): boolean {
return unit.model.atomicHierarchy.derived.residue.moleculeType[
unit.residueIndex[unit.elements[index]]