diff --git a/.vscode/settings.json b/.vscode/settings.json
index 9f20238be3337de52d4b5264853a36f5bdf719b8..1fcd8d6e6dfa22aacc0161cadd9eddcd5c007499 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -6,4 +6,7 @@
"*.vert.ts": "glsl",
"*.gql.ts": "graphql"
},
+ "eslint.options": {
+ "ignorePattern": ["webpack.config.js", "scripts/*"],
+ }
}
\ No newline at end of file
diff --git a/src/mol-model-props/computed/interactions/charged.ts b/src/mol-model-props/computed/interactions/charged.ts
index 75979f75ebf27a6226a6f1511b8d9366a1bc3dbe..7f22026d8e1141fb143b8dfbf0dd592b8063d923 100644
--- a/src/mol-model-props/computed/interactions/charged.ts
+++ b/src/mol-model-props/computed/interactions/charged.ts
@@ -240,22 +240,18 @@ const tmpVecD = Vec3()
function getNormal(out: Vec3, info: Features.Info) {
const { unit, feature, offsets, members } = info
const { elements } = unit
- const { x, y, z } = unit.model.atomicConformation
const i = offsets[feature]
- const aI = elements[members[i]]
- const bI = elements[members[i + 1]]
- const cI = elements[members[i + 2]]
- Vec3.set(tmpVecA, x[aI], y[aI], z[aI])
- Vec3.set(tmpVecB, x[bI], y[bI], z[bI])
- Vec3.set(tmpVecC, x[cI], y[cI], z[cI])
+ info.unit.conformation.position(elements[members[i]], tmpVecA)
+ info.unit.conformation.position(elements[members[i + 1]], tmpVecB)
+ info.unit.conformation.position(elements[members[i + 2]], tmpVecC)
return Vec3.triangleNormal(out, tmpVecA, tmpVecB, tmpVecC)
}
const getOffset = function (infoA: Features.Info, infoB: Features.Info, normal: Vec3) {
- Vec3.set(tmpVecA, infoA.x[infoA.feature], infoA.y[infoA.feature], infoA.z[infoA.feature])
- Vec3.set(tmpVecB, infoB.x[infoB.feature], infoB.y[infoB.feature], infoB.z[infoB.feature])
+ Features.position(tmpVecA, infoA)
+ Features.position(tmpVecB, infoB)
Vec3.sub(tmpVecC, tmpVecA, tmpVecB)
diff --git a/src/mol-model-props/computed/interactions/contacts.ts b/src/mol-model-props/computed/interactions/contacts.ts
index 9c85398e1d6058d1d80a4361454d465462c5a1bf..57967b0c19e8210b4ed905fa52162ad76a6d7287 100644
--- a/src/mol-model-props/computed/interactions/contacts.ts
+++ b/src/mol-model-props/computed/interactions/contacts.ts
@@ -65,12 +65,6 @@ function isMember(element: StructureElement.UnitIndex, info: Features.Info) {
return false
}
-function setPosition(out: Vec3, info: Features.Info) {
- Vec3.set(out, info.x[info.feature], info.y[info.feature], info.z[info.feature])
- Vec3.transformMat4(out, out, info.unit.conformation.operator.matrix)
- return out
-}
-
const tmpVec = Vec3()
const tmpVecA = Vec3()
const tmpVecB = Vec3()
@@ -81,8 +75,8 @@ function checkLineOfSight(structure: Structure, infoA: Features.Info, infoB: Fea
const indexA = infoA.members[infoA.offsets[featureA]]
const indexB = infoB.members[infoB.offsets[featureB]]
- setPosition(tmpVecA, infoA)
- setPosition(tmpVecB, infoB)
+ Features.position(tmpVecA, infoA)
+ Features.position(tmpVecB, infoB)
Vec3.scale(tmpVec, Vec3.add(tmpVec, tmpVecA, tmpVecB), 0.5)
const distMax = distFactor * MAX_LINE_OF_SIGHT_DISTANCE
diff --git a/src/mol-model-props/computed/interactions/features.ts b/src/mol-model-props/computed/interactions/features.ts
index 9bf69761a79ab977636238509c77ba0a44e8cfa9..e7763a2e6679fb272309951ac9e8d4fe85d9ad4d 100644
--- a/src/mol-model-props/computed/interactions/features.ts
+++ b/src/mol-model-props/computed/interactions/features.ts
@@ -161,6 +161,22 @@ namespace Features {
}
}
+ export function position(out: Vec3, info: Info) {
+ Vec3.set(out, info.x[info.feature], info.y[info.feature], info.z[info.feature])
+ Vec3.transformMat4(out, out, info.unit.conformation.operator.matrix)
+ return out
+ }
+
+ const tmpVecA = Vec3()
+ const tmpVecB = Vec3()
+ export function distance(infoA: Info, infoB: Info) {
+ const elementA = infoA.members[infoA.offsets[infoA.feature]]
+ const elementB = infoB.members[infoB.offsets[infoB.feature]]
+ infoA.unit.conformation.position(infoA.unit.elements[elementA], tmpVecA)
+ infoB.unit.conformation.position(infoB.unit.elements[elementB], tmpVecB)
+ return Vec3.distance(tmpVecA, tmpVecB)
+ }
+
export interface Provider {
types: Set<FeatureType>
add: (structure: Structure, unit: Unit.Atomic, featuresBuilder: FeaturesBuilder) => void
diff --git a/src/mol-model-props/computed/interactions/hydrogen-bonds.ts b/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
index f6021978c047171c53ed3df3a15e61c76a25db18..37bc77ffc86f158c637861023661a5a4ba680b32 100644
--- a/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
+++ b/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
@@ -68,8 +68,11 @@ function addUnitHydrogenDonors(structure: Structure, unit: Unit.Atomic, builder:
const { totalH } = getUnitValenceModel(structure, unit)
const { elements } = unit
const { x, y, z } = unit.model.atomicConformation
+ const { elementAromaticRingIndices } = unit.rings
for (let i = 0 as StructureElement.UnitIndex, il = elements.length; i < il; ++i) {
+ if (elementAromaticRingIndices.has(i)) continue;
+
const element = typeSymbol(unit, i)
if ((
// include both nitrogen atoms in histidine due to
@@ -99,7 +102,7 @@ function addUnitWeakHydrogenDonors(structure: Structure, unit: Unit.Atomic, buil
(
bondToElementCount(structure, unit, i, Elements.N) > 0 ||
bondToElementCount(structure, unit, i, Elements.O) > 0 ||
- inAromaticRingWithElectronNegativeElement(structure, unit, i)
+ inAromaticRingWithElectronNegativeElement(unit, i)
)
) {
builder.add(FeatureType.WeakHydrogenDonor, FeatureGroup.None, x[elements[i]], y[elements[i]], z[elements[i]], i)
@@ -107,27 +110,21 @@ function addUnitWeakHydrogenDonors(structure: Structure, unit: Unit.Atomic, buil
}
}
-function inAromaticRingWithElectronNegativeElement(structure: Structure, unit: Unit.Atomic, index: StructureElement.UnitIndex) {
- return false // TODO
- // if (!a.isAromatic()) return false
-
- // const ringData = a.residueType.getRings()
- // if (!ringData) return false
-
- // let hasElement = false
- // const rings = ringData.rings
- // rings.forEach(ring => {
- // if (hasElement) return // already found one
- // if (ring.some(idx => (a.index - a.residueAtomOffset) === idx)) { // in ring
- // hasElement = ring.some(idx => {
- // const atomTypeId = a.residueType.atomTypeIdList[ idx ]
- // const number = a.atomMap.get(atomTypeId).number
- // return number === Elements.N || number === Elements.O
- // })
- // }
- // })
-
- // return hasElement
+function inAromaticRingWithElectronNegativeElement(unit: Unit.Atomic, index: StructureElement.UnitIndex) {
+ const { elementAromaticRingIndices, all } = unit.rings
+ const ringIndices = elementAromaticRingIndices.get(index)
+ if (ringIndices === undefined) return false
+
+ for (let i = 0, il = ringIndices.length; i < il; ++i) {
+ const ring = all[ringIndices[i]]
+ for (let j = 0, jl = ring.length; j < jl; ++j) {
+ const element = typeSymbol(unit, ring[j])
+ if (element === Elements.N || element === Elements.O) {
+ return true
+ }
+ }
+ }
+ return false
}
/**
@@ -137,12 +134,15 @@ function addUnitHydrogenAcceptors(structure: Structure, unit: Unit.Atomic, build
const { charge, implicitH, idealGeometry } = getUnitValenceModel(structure, unit)
const { elements } = unit
const { x, y, z } = unit.model.atomicConformation
+ const { elementAromaticRingIndices } = unit.rings
const add = (i: StructureElement.UnitIndex) => {
builder.add(FeatureType.HydrogenAcceptor, FeatureGroup.None, x[elements[i]], y[elements[i]], z[elements[i]], i)
}
for (let i = 0 as StructureElement.UnitIndex, il = elements.length; i < il; ++i) {
+ if (elementAromaticRingIndices.has(i)) continue;
+
const element = typeSymbol(unit, i)
if (element === Elements.O) {
// Basically assume all oxygen atoms are acceptors!
diff --git a/src/mol-model-props/computed/interactions/refine.ts b/src/mol-model-props/computed/interactions/refine.ts
index 4e1dacbf8ef88a2660195421abd141c6dd2ff71b..2bda57a2279625f5a044a14b0c9b103b90f15378 100644
--- a/src/mol-model-props/computed/interactions/refine.ts
+++ b/src/mol-model-props/computed/interactions/refine.ts
@@ -8,7 +8,6 @@
import { Interactions } from './interactions';
import { InteractionType, InteractionFlag, InteractionsIntraContacts, FeatureType, InteractionsInterContacts } from './common';
-import { Vec3 } from '../../../mol-math/linear-algebra';
import { Unit, Structure } from '../../../mol-model/structure';
import { Features } from './features';
@@ -91,22 +90,17 @@ function hydrophobicRefiner(structure: Structure, interactions: Interactions): C
}
}
- const pA = Vec3()
- const pB = Vec3()
-
function handleEdge(edge: number, infoA: Features.Info, infoB: Features.Info, map: Map<string, [number, number]>, set: (i: number) => void) {
const elementA = infoA.members[infoA.offsets[infoA.feature]]
const elementB = infoB.members[infoB.offsets[infoB.feature]]
const residueA = infoA.unit.getResidueIndex(elementA)
const residueB = infoB.unit.getResidueIndex(elementB)
- infoA.unit.conformation.position(infoA.unit.elements[elementA], pA)
- infoB.unit.conformation.position(infoB.unit.elements[elementB], pB)
- const dist = Vec3.distance(pA, pB)
-
const keyA = `${elementA}|${infoA.unit.id}|${residueB}|${infoB.unit.id}|A`
const keyB = `${elementB}|${infoB.unit.id}|${residueA}|${infoA.unit.id}|B`
+ const dist = Features.distance(infoA, infoB)
+
handleResidueContact(dist, edge, keyA, map, set)
handleResidueContact(dist, edge, keyB, map, set)
}
diff --git a/src/mol-model/structure/structure/unit/rings.ts b/src/mol-model/structure/structure/unit/rings.ts
index d9f1024ef8a600fa073247726020ada8b9ccff16..40296716a076b33880557c844ed2193dadeb3192 100644
--- a/src/mol-model/structure/structure/unit/rings.ts
+++ b/src/mol-model/structure/structure/unit/rings.ts
@@ -25,6 +25,7 @@ class UnitRings {
private _byFingerprint?: ReadonlyMap<UnitRing.Fingerprint, ReadonlyArray<UnitRings.Index>>;
private _index?: {
readonly elementRingIndices: ReadonlyMap<StructureElement.UnitIndex, UnitRings.Index[]>,
+ readonly elementAromaticRingIndices: ReadonlyMap<StructureElement.UnitIndex, UnitRings.Index[]>,
readonly ringComponentIndex: ReadonlyArray<UnitRings.ComponentIndex>,
readonly ringComponents: ReadonlyArray<ReadonlyArray<UnitRings.Index>>
};
@@ -32,7 +33,7 @@ class UnitRings {
private get index() {
if (this._index) return this._index;
- this._index = createIndex(this.all);
+ this._index = createIndex(this.all, this.aromaticRings);
return this._index;
}
@@ -42,11 +43,15 @@ class UnitRings {
return this._byFingerprint;
}
- /** Maps atom index inside a Unit to the smallest ring index (an atom can be part of more than one ring) */
+ /** Maps atom index inside a Unit to ring indices (an atom can be part of more than one ring) */
get elementRingIndices() {
return this.index.elementRingIndices;
}
+ get elementAromaticRingIndices() {
+ return this.index.elementAromaticRingIndices;
+ }
+
/** Maps UnitRings.Index to index to ringComponents */
get ringComponentIndex() {
return this.index.ringComponentIndex;
diff --git a/src/mol-model/structure/structure/unit/rings/compute.ts b/src/mol-model/structure/structure/unit/rings/compute.ts
index 177ed65a17098855d5f90be8badd07af9af55a15..db31f0f6900e95aeeb729f0c9e3cafbe9eaaa205 100644
--- a/src/mol-model/structure/structure/unit/rings/compute.ts
+++ b/src/mol-model/structure/structure/unit/rings/compute.ts
@@ -253,8 +253,9 @@ function buildFinderprint(elements: string[], offset: number) {
type RingIndex = import('../rings').UnitRings.Index
type RingComponentIndex = import('../rings').UnitRings.ComponentIndex
-export function createIndex(rings: ArrayLike<SortedArray<StructureElement.UnitIndex>>) {
+export function createIndex(rings: ArrayLike<SortedArray<StructureElement.UnitIndex>>, aromaticRings: ReadonlyArray<RingIndex>) {
const elementRingIndices: Map<StructureElement.UnitIndex, RingIndex[]> = new Map();
+ const elementAromaticRingIndices: Map<StructureElement.UnitIndex, RingIndex[]> = new Map();
// for each ring atom, assign all rings that it is present in
for (let rI = 0 as RingIndex, _rI = rings.length; rI < _rI; rI++) {
@@ -266,6 +267,17 @@ export function createIndex(rings: ArrayLike<SortedArray<StructureElement.UnitIn
}
}
+ // for each ring atom, assign all aromatic rings that it is present in
+ for (let aI = 0, _aI = aromaticRings.length; aI < _aI; aI++) {
+ const rI = aromaticRings[aI]
+ const r = rings[rI];
+ for (let i = 0, _i = r.length; i < _i; i++) {
+ const e = r[i];
+ if (elementAromaticRingIndices.has(e)) elementAromaticRingIndices.get(e)!.push(rI);
+ else elementAromaticRingIndices.set(e, [rI]);
+ }
+ }
+
// create a graph where vertices are rings, edge if two rings share at least one atom
const graph = new IntAdjacencyGraph.UniqueEdgeBuilder(rings.length);
for (let rI = 0 as RingIndex, _rI = rings.length; rI < _rI; rI++) {
@@ -296,5 +308,5 @@ export function createIndex(rings: ArrayLike<SortedArray<StructureElement.UnitIn
ringComponents[ringComponentIndex[rI]].push(rI);
}
- return { elementRingIndices, ringComponentIndex, ringComponents };
+ return { elementRingIndices, elementAromaticRingIndices, ringComponentIndex, ringComponents };
}
\ No newline at end of file