From b863aaedb364b53ecbdce671719fa142706f7ae4 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 10 Jan 2020 15:33:06 -0800
Subject: [PATCH] general support for aromatic rings
- containing annotated aromatic bonds
- being flat with certain elements
---
.../computed/interactions/charged.ts | 38 ++---------
.../structure/query/queries/generators.ts | 13 +++-
.../structure/structure/unit/rings.ts | 64 ++++++++++++++++++-
src/mol-plugin-ui/structure/selection.tsx | 3 +-
.../util/structure-selection-helper.ts | 5 ++
.../language/symbol-table/structure-query.ts | 5 +-
src/mol-script/runtime/query/table.ts | 2 +-
7 files changed, 89 insertions(+), 41 deletions(-)
diff --git a/src/mol-model-props/computed/interactions/charged.ts b/src/mol-model-props/computed/interactions/charged.ts
index 8db9c4805..b12631f00 100644
--- a/src/mol-model-props/computed/interactions/charged.ts
+++ b/src/mol-model-props/computed/interactions/charged.ts
@@ -10,17 +10,15 @@
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Structure, Unit, StructureElement } from '../../../mol-model/structure';
import { FeaturesBuilder, Features } from './features';
-import { ProteinBackboneAtoms, PolymerNames, BaseNames, ElementSymbol } from '../../../mol-model/structure/model/types';
-import { typeSymbol, atomId, eachBondedAtom, compId } from '../chemistry/util';
+import { ProteinBackboneAtoms, PolymerNames, BaseNames } from '../../../mol-model/structure/model/types';
+import { typeSymbol, atomId, eachBondedAtom } from '../chemistry/util';
import { Elements } from '../../../mol-model/structure/model/properties/atomic/types';
import { ValenceModelProvider } from '../valence-model';
import { degToRad } from '../../../mol-math/misc';
import { FeatureType, FeatureGroup, InteractionType } from './common';
import { ContactProvider } from './contacts';
-import { Segmentation, SortedArray } from '../../../mol-data/int';
+import { Segmentation } from '../../../mol-data/int';
import { isGuanidine, isAcetamidine, isPhosphate, isSulfonicAcid, isSulfate, isCarboxylate } from '../chemistry/functional-group';
-import { PrincipalAxes } from '../../../mol-math/linear-algebra/matrix/principal-axes';
-import { getPositions } from '../../../mol-model/structure/util';
import { Vec3 } from '../../../mol-math/linear-algebra';
const IonicParams = {
@@ -189,38 +187,12 @@ function addUnitNegativeCharges(structure: Structure, unit: Unit.Atomic, builder
}
}
-const AromaticRingElements = [
- Elements.B, Elements.C, Elements.N, Elements.O,
- Elements.SI, Elements.P, Elements.S,
- Elements.GE, Elements.AS,
- Elements.SN, Elements.SB,
- Elements.BI
-] as ElementSymbol[]
-const AromaticRingPlanarityThreshold = 0.05
-
-function isRingAromatic(unit: Unit.Atomic, ring: SortedArray<StructureElement.UnitIndex>) {
- // ignore Proline (can be flat because of bad geometry)
- if (compId(unit, ring[0]) === 'PRO') return
- // TODO also check `chem_comp_bond.pdbx_aromatic_flag`
- let hasAromaticRingElement = false
- for (let i = 0, il = ring.length; i < il; ++i) {
- if (AromaticRingElements.includes(typeSymbol(unit, ring[i]))) {
- hasAromaticRingElement = true
- break
- }
- }
- if (!hasAromaticRingElement) return
-
- const ma = PrincipalAxes.calculateMomentsAxes(getPositions(unit, ring))
- return Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold
-}
-
function addUnitAromaticRings(structure: Structure, unit: Unit.Atomic, builder: FeaturesBuilder) {
const { elements } = unit
const { x, y, z } = unit.model.atomicConformation
- for (const ring of unit.rings.all) {
- if (!isRingAromatic(unit, ring)) continue
+ for (const ringIndex of unit.rings.aromaticRings) {
+ const ring = unit.rings.all[ringIndex]
builder.startState()
for (let i = 0, il = ring.length; i < il; ++i) {
const j = ring[i]
diff --git a/src/mol-model/structure/query/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index 906d70c6b..646f67dfc 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -223,7 +223,7 @@ function getRingStructure(unit: Unit.Atomic, ring: UnitRing, inputStructure: Str
return Structure.create([unit.getChild(SortedArray.ofSortedArray(elements))], { parent: inputStructure });
}
-export function rings(fingerprints?: ArrayLike<UnitRing.Fingerprint>): StructureQuery {
+export function rings(fingerprints?: ArrayLike<UnitRing.Fingerprint>, onlyAromatic?: boolean): StructureQuery {
return function query_rings(ctx) {
const { units } = ctx.inputStructure;
const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
@@ -232,8 +232,14 @@ export function rings(fingerprints?: ArrayLike<UnitRing.Fingerprint>): Structure
for (const u of units) {
if (!Unit.isAtomic(u)) continue;
- for (const r of u.rings.all) {
- ret.add(getRingStructure(u, r, ctx.inputStructure));
+ if (onlyAromatic) {
+ for (const r of u.rings.aromaticRings) {
+ ret.add(getRingStructure(u, u.rings.all[r], ctx.inputStructure));
+ }
+ } else {
+ for (const r of u.rings.all) {
+ ret.add(getRingStructure(u, r, ctx.inputStructure));
+ }
}
}
} else {
@@ -247,6 +253,7 @@ export function rings(fingerprints?: ArrayLike<UnitRing.Fingerprint>): Structure
for (const fp of uniqueFps.array) {
if (!rings.byFingerprint.has(fp)) continue;
for (const r of rings.byFingerprint.get(fp)!) {
+ if (onlyAromatic && !rings.aromaticRings.includes(r)) continue;
ret.add(getRingStructure(u, rings.all[r], ctx.inputStructure));
}
}
diff --git a/src/mol-model/structure/structure/unit/rings.ts b/src/mol-model/structure/structure/unit/rings.ts
index bb3f50d3c..d9f1024ef 100644
--- a/src/mol-model/structure/structure/unit/rings.ts
+++ b/src/mol-model/structure/structure/unit/rings.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { computeRings, getFingerprint, createIndex } from './rings/compute'
@@ -9,7 +10,11 @@ import Unit from '../unit';
import StructureElement from '../element';
import { SortedArray } from '../../../../mol-data/int';
import { ResidueIndex } from '../../model';
-import { ElementSymbol } from '../../model/types';
+import { ElementSymbol, BondType } from '../../model/types';
+import { Elements } from '../../model/properties/atomic/types';
+import { getPositions } from '../../util';
+import { PrincipalAxes } from '../../../../mol-math/linear-algebra/matrix/principal-axes';
+import { Vec3 } from '../../../../mol-math/linear-algebra';
type UnitRing = SortedArray<StructureElement.UnitIndex>
@@ -23,6 +28,7 @@ class UnitRings {
readonly ringComponentIndex: ReadonlyArray<UnitRings.ComponentIndex>,
readonly ringComponents: ReadonlyArray<ReadonlyArray<UnitRings.Index>>
};
+ private _aromaticRings?: ReadonlyArray<UnitRings.Index>
private get index() {
if (this._index) return this._index;
@@ -50,6 +56,12 @@ class UnitRings {
return this.index.ringComponents;
}
+ get aromaticRings() {
+ if (this._aromaticRings) return this._aromaticRings;
+ this._aromaticRings = getAromaticRings(this.unit, this.all);
+ return this._aromaticRings;
+ }
+
constructor(all: ReadonlyArray<UnitRing>, public unit: Unit.Atomic) {
this.all = all;
}
@@ -70,6 +82,47 @@ namespace UnitRing {
export function elementFingerprint(elements: ArrayLike<ElementSymbol>) {
return getFingerprint(elements as ArrayLike<string> as string[]) as Fingerprint;
}
+
+ const AromaticRingElements = new Set([
+ Elements.B, Elements.C, Elements.N, Elements.O,
+ Elements.SI, Elements.P, Elements.S,
+ Elements.GE, Elements.AS,
+ Elements.SN, Elements.SB,
+ Elements.BI
+ ] as ElementSymbol[])
+ const AromaticRingPlanarityThreshold = 0.05
+
+ export function isAromatic(unit: Unit.Atomic, ring: SortedArray<StructureElement.UnitIndex>): boolean {
+ const { elements, bonds: { b, offset, edgeProps: { flags } } } = unit;
+ const { type_symbol } = unit.model.atomicHierarchy.atoms;
+ const { label_comp_id } = unit.model.atomicHierarchy.residues;
+
+ // ignore Proline (can be flat because of bad geometry)
+ if (label_comp_id.value(unit.getResidueIndex(ring[0])) === 'PRO') return false
+
+ let aromaticBondCount = 0
+ let hasAromaticRingElement = false
+
+ for (let i = 0, il = ring.length; i < il; ++i) {
+ const aI = ring[i]
+ if (!hasAromaticRingElement && AromaticRingElements.has(type_symbol.value(elements[aI]))) {
+ hasAromaticRingElement = true
+ }
+
+ for (let j = offset[aI], jl = offset[aI + 1]; j < jl; ++j) {
+ // comes e.g. from `chem_comp_bond.pdbx_aromatic_flag`
+ if (BondType.is(BondType.Flag.Aromatic, flags[j])) {
+ if (SortedArray.has(ring, b[j])) aromaticBondCount += 1
+
+ }
+ }
+ }
+ if (aromaticBondCount === 2 * ring.length) return true
+ if (!hasAromaticRingElement) return false
+
+ const ma = PrincipalAxes.calculateMomentsAxes(getPositions(unit, ring))
+ return Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold
+ }
}
namespace UnitRings {
@@ -126,5 +179,12 @@ function addSingleResidueRings(rings: UnitRings, fp: UnitRing.Fingerprint, map:
}
}
+function getAromaticRings(unit: Unit.Atomic, rings: ReadonlyArray<UnitRing>): ReadonlyArray<UnitRings.Index> {
+ const aromaticRings: UnitRings.Index[] = []
+ for (let i = 0 as UnitRings.Index, il = rings.length; i < il; ++i) {
+ if (UnitRing.isAromatic(unit, rings[i])) aromaticRings.push(i)
+ }
+ return aromaticRings
+}
export { UnitRing, UnitRings }
\ No newline at end of file
diff --git a/src/mol-plugin-ui/structure/selection.tsx b/src/mol-plugin-ui/structure/selection.tsx
index ea6d6b1a3..aa1000edb 100644
--- a/src/mol-plugin-ui/structure/selection.tsx
+++ b/src/mol-plugin-ui/structure/selection.tsx
@@ -19,7 +19,8 @@ const SSQ = StructureSelectionQueries
const DefaultQueries: (keyof typeof SSQ)[] = [
'all', 'polymer', 'trace', 'backbone', 'protein', 'nucleic',
'helix', 'beta',
- 'water', 'branched', 'ligand', 'nonStandardPolymer', 'ring',
+ 'water', 'branched', 'ligand', 'nonStandardPolymer',
+ 'ring', 'aromaticRing',
'surroundings', 'complement', 'bonded'
]
diff --git a/src/mol-plugin/util/structure-selection-helper.ts b/src/mol-plugin/util/structure-selection-helper.ts
index a24f03399..0c8f3916a 100644
--- a/src/mol-plugin/util/structure-selection-helper.ts
+++ b/src/mol-plugin/util/structure-selection-helper.ts
@@ -298,6 +298,10 @@ const ring = StructureSelectionQuery('Rings in Residues', MS.struct.modifier.uni
MS.struct.generator.rings()
]))
+const aromaticRing = StructureSelectionQuery('Aromatic Rings in Residues', MS.struct.modifier.union([
+ MS.struct.generator.rings({ 'only-aromatic': true })
+]))
+
const surroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of Selection', MS.struct.modifier.union([
MS.struct.modifier.exceptBy({
0: MS.struct.modifier.includeSurroundings({
@@ -345,6 +349,7 @@ export const StructureSelectionQueries = {
nonStandardPolymer,
coarse,
ring,
+ aromaticRing,
surroundings,
complement,
bonded,
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index 2e1657038..d76329a1f 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -99,7 +99,10 @@ const generator = {
// 'group-by': Argument(Type.Any, { isOptional: true, defaultValue: ``, description: 'Group the bonds using the privided value' }),
}), Types.ElementSelectionQuery, 'Return all pairs of atoms for which the test is satisfied.'),
- rings: symbol(Arguments.List(Types.RingFingerprint), Types.ElementSelectionQuery, 'Return rings with the specified fingerprint(s). If no fingerprints are given, return all rings.'),
+ rings: symbol(Arguments.Dictionary({
+ 'fingerprint': Argument(Types.RingFingerprint, { isOptional: true }),
+ 'only-aromatic': Argument(Type.Bool, { isOptional: true, defaultValue: false }),
+ }), Types.ElementSelectionQuery, 'Return all rings or those with the specified fingerprint and/or only aromatic rings.'),
queryInSelection: symbol(Arguments.Dictionary({
0: Argument(Types.ElementSelectionQuery),
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index 4eaa59ebc..75a9104a8 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -239,7 +239,7 @@ const symbols = [
D(MolScript.structureQuery.generator.all, function structureQuery_generator_all(ctx) { return Queries.generators.all(ctx) }),
D(MolScript.structureQuery.generator.empty, function structureQuery_generator_empty(ctx) { return Queries.generators.none(ctx) }),
D(MolScript.structureQuery.generator.bondedAtomicPairs, function structureQuery_generator_bondedAtomicPairs(ctx, xs) { return Queries.generators.bondedAtomicPairs(xs && xs[0])(ctx) }),
- D(MolScript.structureQuery.generator.rings, function structureQuery_generator_rings(ctx, xs) { return Queries.generators.rings(getArray(ctx, xs))(ctx) }),
+ D(MolScript.structureQuery.generator.rings, function structureQuery_generator_rings(ctx, xs) { return Queries.generators.rings(xs?.['fingerprint']?.(ctx) as any, xs?.['only-aromatic']?.(ctx))(ctx) }),
// ============= MODIFIERS ================
--
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