diff --git a/src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts b/src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts
index 6930ff97c4226f37b297e587406ede6f383f3b76..de81e58df39a4d2da5573d99895442b6b651fbca 100644
--- a/src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts
@@ -29,15 +29,15 @@ async function createCrossLinkRestraintCylinderMesh(ctx: RuntimeContext, structu
const builderProps = {
linkCount: crossLinks.count,
- referencePosition: (edgeIndex: number) => null,
+ referencePosition: () => null,
position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
const b = crossLinks.pairs[edgeIndex]
const uA = b.unitA, uB = b.unitB
uA.conformation.position(uA.elements[b.indexA], posA)
uB.conformation.position(uB.elements[b.indexB], posB)
},
- order: (edgeIndex: number) => 1,
- flags: (edgeIndex: number) => BitFlags.create(LinkType.Flag.None),
+ order: () => 1,
+ flags: () => BitFlags.create(LinkType.Flag.None),
radius: (edgeIndex: number) => {
const b = crossLinks.pairs[edgeIndex]
location.unit = b.unitA
@@ -76,7 +76,7 @@ function CrossLinkRestraintIterator(structure: Structure): LocationIterator {
const elementCount = pairs.length
const instanceCount = 1
const location = Link.Location()
- const getLocation = (elementIndex: number, instanceIndex: number) => {
+ const getLocation = (elementIndex: number) => {
const pair = pairs[elementIndex]
location.aUnit = pair.unitA
location.aIndex = pair.indexA
@@ -92,12 +92,7 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
if (id === objectId) {
const pair = structure.crossLinkRestraints.pairs[elementId]
if (pair) {
- return Link.Loci([
- Link.Location(
- pair.unitA, pair.indexA as StructureElement.UnitIndex,
- pair.unitB, pair.indexB as StructureElement.UnitIndex
- )
- ])
+ return Link.Loci([ Link.Location(pair.unitA, pair.indexA, pair.unitB, pair.indexB) ])
}
}
return EmptyLoci
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 233d73f9821d364a742c10199e5c3240ee22c036..edc6447f0a1447cd06ccd8f4a0e7a4870468f926 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -15,7 +15,7 @@ import { StructureLookup3D } from './util/lookup3d';
import { CoarseElements } from '../model/properties/coarse';
import { StructureSubsetBuilder } from './util/subset-builder';
import { InterUnitBonds, computeInterUnitBonds } from './unit/links';
-import { CrossLinkRestraints, extractCrossLinkRestraints } from './unit/pair-restraints';
+import { PairRestraints, CrossLinkRestraint, extractCrossLinkRestraints } from './unit/pair-restraints';
import StructureSymmetry from './symmetry';
import StructureProperties from './properties';
import { ResidueIndex } from '../model/indexing';
@@ -29,7 +29,7 @@ class Structure {
private _props: {
lookup3d?: StructureLookup3D,
links?: InterUnitBonds,
- crossLinkRestraints?: CrossLinkRestraints,
+ crossLinkRestraints?: PairRestraints<CrossLinkRestraint>,
unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup>,
carbohydrates?: Carbohydrates,
models?: ReadonlyArray<Model>,
diff --git a/src/mol-model/structure/structure/unit/pair-restraints.ts b/src/mol-model/structure/structure/unit/pair-restraints.ts
index 6d0d0bd78e446cc9141a4f4b20b2cc8d61332f68..890fb6b03666a40e5157d80430f0b098d2db98ad 100644
--- a/src/mol-model/structure/structure/unit/pair-restraints.ts
+++ b/src/mol-model/structure/structure/unit/pair-restraints.ts
@@ -6,4 +6,5 @@
export * from './pair-restraints/data'
export * from './pair-restraints/extract-cross-links'
-// export * from './pair-restraints/extract-predicted_contacts'
+// export * from './pair-restraints/extract-predicted-contacts'
+// export * from './pair-restraints/extract-distance-restraints'
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/data.ts b/src/mol-model/structure/structure/unit/pair-restraints/data.ts
index 7b0d01e86e2d65de009fe9ed27be05ba197cb04c..f402aab8e991b6fbc7a03e4bdc4fb38fbb9ef622 100644
--- a/src/mol-model/structure/structure/unit/pair-restraints/data.ts
+++ b/src/mol-model/structure/structure/unit/pair-restraints/data.ts
@@ -9,26 +9,37 @@ import { StructureElement } from '../../../structure';
const emptyArray: number[] = []
-class CrossLinkRestraints {
+interface PairRestraint {
+ readonly unitA: Unit,
+ readonly unitB: Unit,
+ readonly indexA: StructureElement.UnitIndex,
+ readonly indexB: StructureElement.UnitIndex,
+}
+
+function getPairKey(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit) {
+ return `${indexA}|${unitA.id}|${indexB}|${unitB.id}`
+}
+
+export class PairRestraints<T extends PairRestraint> {
readonly count: number
private readonly pairKeyIndices: Map<string, number[]>
/** Indices into this.pairs */
getPairIndices(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): ReadonlyArray<number> {
- const key = CrossLinkRestraints.getPairKey(indexA, unitA, indexB, unitB)
+ const key = getPairKey(indexA, unitA, indexB, unitB)
const indices = this.pairKeyIndices.get(key)
return indices !== undefined ? indices : emptyArray
}
- getPairs(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): CrossLinkRestraints.Pair[] | undefined {
+ getPairs(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): T[] | undefined {
const indices = this.getPairIndices(indexA, unitA, indexB, unitB)
return indices.length ? indices.map(idx => this.pairs[idx]) : undefined
}
- constructor(public pairs: ReadonlyArray<CrossLinkRestraints.Pair>) {
+ constructor(public pairs: ReadonlyArray<T>) {
const pairKeyIndices = new Map<string, number[]>()
this.pairs.forEach((p, i) => {
- const key = CrossLinkRestraints.getPairKey(p.indexA, p.unitA, p.indexB, p.unitB)
+ const key = getPairKey(p.indexA, p.unitA, p.indexB, p.unitB)
const indices = pairKeyIndices.get(key)
if (indices) indices.push(i)
else pairKeyIndices.set(key, [i])
@@ -39,23 +50,28 @@ class CrossLinkRestraints {
}
}
-namespace CrossLinkRestraints {
- export interface Pair {
- readonly unitA: Unit,
- readonly unitB: Unit,
- readonly indexA: StructureElement.UnitIndex,
- readonly indexB: StructureElement.UnitIndex,
-
- readonly restraintType: 'harmonic' | 'upper bound' | 'lower bound',
- readonly distanceThreshold: number,
- readonly psi: number,
- readonly sigma1: number,
- readonly sigma2: number,
- }
+export interface CrossLinkRestraint extends PairRestraint {
+ readonly restraintType: 'harmonic' | 'upper bound' | 'lower bound'
+ readonly distanceThreshold: number
+ readonly psi: number
+ readonly sigma1: number
+ readonly sigma2: number
+}
- export function getPairKey(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit) {
- return `${indexA}|${unitA.id}|${indexB}|${unitB.id}`
- }
+export interface PredictedContactRestraint extends PairRestraint {
+ readonly distance_lower_limit: number
+ readonly distance_upper_limit: number
+ readonly probability: number
+ readonly restraint_type: 'lower bound' | 'upper bound' | 'lower and upper bound'
+ readonly model_granularity: 'by-residue' | 'by-feature' | 'by-atom'
}
-export { CrossLinkRestraints }
\ No newline at end of file
+export interface DistanceRestraint extends PairRestraint {
+ readonly upper_limit: number
+ readonly upper_limit_esd: number
+ readonly lower_limit: number
+ readonly lower_limit_esd: number
+ readonly probability: number
+ readonly restraint_type: 'lower bound' | 'upper bound' | 'lower and upper bound'
+ readonly granularity: 'by-residue' | 'by-atom'
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts b/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
index cfe6aaa2326f812e380adcea1b1add4a10dd8645..28ae9d1be1bb2d38ac20cd7a50206415f6acfd88 100644
--- a/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
+++ b/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
@@ -7,7 +7,7 @@
import Unit from '../../unit';
import Structure from '../../structure';
import { IHMCrossLinkRestraint } from '../../../model/formats/mmcif/pair-restraint';
-import { CrossLinkRestraints } from './data';
+import { PairRestraints, CrossLinkRestraint } from './data';
import { StructureElement } from '../../../structure';
function _addRestraints(map: Map<number, number>, unit: Unit, restraints: IHMCrossLinkRestraint) {
@@ -21,7 +21,7 @@ function _addRestraints(map: Map<number, number>, unit: Unit, restraints: IHMCro
}
}
-function extractInter(pairs: CrossLinkRestraints.Pair[], unitA: Unit, unitB: Unit) {
+function extractInter(pairs: CrossLinkRestraint[], unitA: Unit, unitB: Unit) {
if (unitA.model !== unitB.model) return
if (unitA.model.sourceData.kind !== 'mmCIF') return
@@ -44,7 +44,7 @@ function extractInter(pairs: CrossLinkRestraints.Pair[], unitA: Unit, unitB: Uni
})
}
-function extractIntra(pairs: CrossLinkRestraints.Pair[], unit: Unit) {
+function extractIntra(pairs: CrossLinkRestraint[], unit: Unit) {
if (unit.model.sourceData.kind !== 'mmCIF') return
const restraints = IHMCrossLinkRestraint.fromModel(unit.model)
@@ -75,7 +75,7 @@ function extractIntra(pairs: CrossLinkRestraints.Pair[], unit: Unit) {
})
}
-function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitIndex, unitB: Unit, indexB: StructureElement.UnitIndex, restraints: IHMCrossLinkRestraint, row: number): CrossLinkRestraints.Pair {
+function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitIndex, unitB: Unit, indexB: StructureElement.UnitIndex, restraints: IHMCrossLinkRestraint, row: number): CrossLinkRestraint {
return {
unitA, indexA, unitB, indexB,
@@ -87,8 +87,8 @@ function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitInde
}
}
-function extractCrossLinkRestraints(structure: Structure): CrossLinkRestraints {
- const pairs: CrossLinkRestraints.Pair[] = []
+function extractCrossLinkRestraints(structure: Structure): PairRestraints<CrossLinkRestraint> {
+ const pairs: CrossLinkRestraint[] = []
const n = structure.units.length
for (let i = 0; i < n; ++i) {
@@ -100,7 +100,7 @@ function extractCrossLinkRestraints(structure: Structure): CrossLinkRestraints {
}
}
- return new CrossLinkRestraints(pairs)
+ return new PairRestraints(pairs)
}
export { extractCrossLinkRestraints };
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/extract-distance-restraints.ts b/src/mol-model/structure/structure/unit/pair-restraints/extract-distance-restraints.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f19797cb6a8dc5eed5dacaaf0201d24d458fba44
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/pair-restraints/extract-distance-restraints.ts
@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+// TODO extract from `_ma_distance_restraints`
\ No newline at end of file
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 3c21cce9fc41f1f8e750ef17b3ddd154372720a5..e13d439a542d27d850c7b19018d7904924228e36 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -30,7 +30,6 @@ const ballAndStickProps: Partial<BallAndStickProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
sizeTheme: { name: 'uniform', value: 0.15 },
- linkRadius: 0.15,
quality: 'auto',
useFog: false
}
@@ -38,7 +37,7 @@ const ballAndStickProps: Partial<BallAndStickProps> = {
const distanceRestraintProps: Partial<DistanceRestraintProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
- linkRadius: 0.5,
+ sizeTheme: { name: 'uniform', value: 0.6 },
quality: 'auto',
useFog: false
}
@@ -132,11 +131,16 @@ export class Stage {
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000006.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000007.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000008.cif`) // ok
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000009.cif`) // TODO sequence related error
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000010.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000011.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000012.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000014.cif`) // ok
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000015.cif`) // TODO sequence related error
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000016.cif`) // ok
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000017.cif`) // ok
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000020.cif`) // ok
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000021.cif`) // ok
}
async loadMmcifUrl (url: string) {
@@ -146,7 +150,7 @@ export class Stage {
StructureToBallAndStick.apply(this.ctx, structureEntity, { ...ballAndStickProps, visible: true })
StructureToSpacefill.apply(this.ctx, structureEntity, { ...spacefillProps, visible: false })
- StructureToDistanceRestraint.apply(this.ctx, structureEntity, { ...distanceRestraintProps, visible: false })
+ StructureToDistanceRestraint.apply(this.ctx, structureEntity, { ...distanceRestraintProps, visible: true })
StructureToBackbone.apply(this.ctx, structureEntity, { ...backboneProps, visible: false })
StructureToCartoon.apply(this.ctx, structureEntity, { ...cartoonProps, visible: true })
StructureToCarbohydrate.apply(this.ctx, structureEntity, { ...carbohydrateProps, visible: true })