diff --git a/src/mol-model-formats/structure/mmcif/atomic.ts b/src/mol-model-formats/structure/mmcif/atomic.ts
index 422d45776d1fdd1f8b89378a0f7f4e902c8de3f5..b43be7fe712175330a35626d2840383eda44e77b 100644
--- a/src/mol-model-formats/structure/mmcif/atomic.ts
+++ b/src/mol-model-formats/structure/mmcif/atomic.ts
@@ -101,7 +101,7 @@ export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_sit
const index = getAtomicIndex(hierarchyData, entities, hierarchySegments);
const derived = getAtomicDerivedData(hierarchyData, index, formatData.chemicalComponentMap);
- const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, conformation, derived.residue.moleculeType);
+ const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, conformation, index, derived.residue.moleculeType);
const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, ...hierarchyRanges, index, derived };
return { sameAsPrevious: false, hierarchy, conformation };
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index 02bde17f01248af5c255b69f53de721f609d3a3d..33c5993245ff39f69f73a5baf4a1e8dbb3a08c45 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -145,7 +145,7 @@ export interface AtomicIndex {
/**
* Index of the 1st occurence of this residue.
* auth_seq_id is used because label_seq_id is undefined for "ligands" in mmCIF.
- * @param pdbx_PDB_ins_code Empty string for undefined
+ * @param key.pdbx_PDB_ins_code Empty string for undefined
* @returns index or -1 if not present.
*/
findResidue(key: AtomicIndex.ResidueKey): ResidueIndex,
@@ -153,7 +153,7 @@ export interface AtomicIndex {
/**
* Index of the 1st occurence of this residue.
- * @param pdbx_PDB_ins_code Empty string for undefined
+ * @param key.pdbx_PDB_ins_code Empty string for undefined
* @returns index or -1 if not present.
*/
findResidueAuth(key: AtomicIndex.ResidueAuthKey): ResidueIndex,
@@ -161,7 +161,7 @@ export interface AtomicIndex {
/**
* Find the residue index where the spefied residue should be inserted to maintain the ordering (entity_id, asym_id, seq_id, ins_code).
* Useful for determining ranges for sequence-level annotations.
- * @param pdbx_PDB_ins_code Empty string for undefined
+ * @param key.pdbx_PDB_ins_code Use empty string for undefined
*/
findResidueInsertion(key: AtomicIndex.ResidueLabelKey): ResidueIndex,
@@ -181,11 +181,16 @@ export interface AtomicIndex {
/**
* Find element index of an atom on a given residue.
- * @param key
* @returns index or -1 if the atom is not present.
*/
findAtomOnResidue(residueIndex: ResidueIndex, label_atom_id: string, label_alt_id?: string): ElementIndex
+ /**
+ * Find element index of any given atom on a given residue.
+ * @returns first found index or -1 if none of the given atoms are present.
+ */
+ findAtomsOnResidue(residueIndex: ResidueIndex, label_atom_ids: Set<string>): ElementIndex
+
// TODO: add indices that support comp_id?
}
diff --git a/src/mol-model/structure/model/properties/utils/atomic-derived.ts b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
index 47daf9dffaf6bdbc92539ad263f72de68f77fb2c..80c1d10e59e9bbf13e9cfac3ecb3854dcda7cf6a 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-derived.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
@@ -37,10 +37,15 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
moleculeType[i] = molType
const traceAtomId = getAtomIdForAtomRole(molType, 'trace')
- traceElementIndex[i] = index.findAtomOnResidue(i as ResidueIndex, traceAtomId)
+ let traceIndex = index.findAtomsOnResidue(i as ResidueIndex, traceAtomId)
+ if (traceIndex === -1) {
+ const coarseAtomId = getAtomIdForAtomRole(molType, 'coarseBackbone')
+ traceIndex = index.findAtomsOnResidue(i as ResidueIndex, coarseAtomId)
+ }
+ traceElementIndex[i] = traceIndex
const directionAtomId = getAtomIdForAtomRole(molType, 'direction')
- directionElementIndex[i] = index.findAtomOnResidue(i as ResidueIndex, directionAtomId)
+ directionElementIndex[i] = index.findAtomsOnResidue(i as ResidueIndex, directionAtomId)
}
return {
diff --git a/src/mol-model/structure/model/properties/utils/atomic-index.ts b/src/mol-model/structure/model/properties/utils/atomic-index.ts
index 9460ed19474e0daf1308069ab345a115bd4042de..17bc9dc6426fd67b758304a87b7930bee0a0dd4f 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-index.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-index.ts
@@ -158,6 +158,10 @@ class Index implements AtomicIndex {
return findAtomByNameAndAltLoc(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, this.map.label_alt_id, label_atom_id, label_alt_id);
}
+ findAtomsOnResidue(rI: ResidueIndex, label_atom_ids: Set<string>) {
+ return findAtomByNames(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, label_atom_ids)
+ }
+
constructor(private map: Mapping) {
this.entityIndex = map.entities.getEntityIndex;
this.residueOffsets = this.map.segments.residueAtomSegments.offsets;
@@ -171,6 +175,13 @@ function findAtomByName(start: ElementIndex, end: ElementIndex, data: Column<str
return -1 as ElementIndex;
}
+function findAtomByNames(start: ElementIndex, end: ElementIndex, data: Column<string>, atomNames: Set<string>): ElementIndex {
+ for (let i = start; i < end; i++) {
+ if (atomNames.has(data.value(i))) return i;
+ }
+ return -1 as ElementIndex;
+}
+
function findAtomByNameAndAltLoc(start: ElementIndex, end: ElementIndex, nameData: Column<string>, altLocData: Column<string>,
atomName: string, altLoc: string): ElementIndex {
for (let i = start; i < end; i++) {
diff --git a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
index ed6816364115f26aa64dbf6a981bf35b3a8c751d..86ddca7d17eed50bf2166f989a6cd4e6c681a429 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
@@ -5,7 +5,7 @@
*/
import { AtomicSegments } from '../atomic';
-import { AtomicData, AtomicRanges } from '../atomic/hierarchy';
+import { AtomicData, AtomicRanges, AtomicIndex } from '../atomic/hierarchy';
import { Segmentation, Interval } from 'mol-data/int';
import SortedRanges from 'mol-data/int/sorted-ranges';
import { MoleculeType, isPolymer } from '../../types';
@@ -16,33 +16,26 @@ import { Vec3 } from 'mol-math/linear-algebra';
// TODO add gaps at the ends of the chains by comparing to the polymer sequence data
-function getElementIndexForAtomId(rI: ResidueIndex, atomId: string, data: AtomicData, segments: AtomicSegments): ElementIndex {
- const { offsets } = segments.residueAtomSegments
- const { label_atom_id } = data.atoms
- for (let j = offsets[rI], _j = offsets[rI + 1]; j < _j; j++) {
- if (label_atom_id.value(j) === atomId) return j
- }
- return offsets[rI]
-}
-
-function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, moleculeType: ArrayLike<MoleculeType>) {
+function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, index: AtomicIndex, moleculeType: ArrayLike<MoleculeType>) {
const mtStart = moleculeType[riStart]
const mtEnd = moleculeType[riEnd]
if (!isPolymer(mtStart) || !isPolymer(mtEnd)) return false
- const startId = getAtomIdForAtomRole(mtStart, 'backboneStart')
- const endId = getAtomIdForAtomRole(mtEnd, 'backboneEnd')
+ let eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(mtStart, 'backboneStart'))
+ let eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(mtEnd, 'backboneEnd'))
- const eiStart = getElementIndexForAtomId(riStart, startId, data, segments)
- const eiEnd = getElementIndexForAtomId(riEnd, endId, data, segments)
+ if (eiStart === -1 || eiEnd === -1) {
+ eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(mtStart, 'coarseBackbone'))
+ eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(mtEnd, 'coarseBackbone'))
+ }
const { x, y, z } = conformation
const pStart = Vec3.create(x[eiStart], y[eiStart], z[eiStart])
const pEnd = Vec3.create(x[eiEnd], y[eiEnd], z[eiEnd])
- return Vec3.distance(pStart, pEnd) < 10
+ return Vec3.distance(pStart, pEnd) < 10 // TODO better distance check, take into account if protein/nucleic and if coarse
}
-export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, moleculeType: ArrayLike<MoleculeType>): AtomicRanges {
+export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, index: AtomicIndex, moleculeType: ArrayLike<MoleculeType>): AtomicRanges {
const polymerRanges: number[] = []
const gapRanges: number[] = []
const cyclicPolymerMap = new Map<ResidueIndex, ResidueIndex>()
@@ -65,7 +58,7 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
const riStart = segments.residueAtomSegments.index[chainSegment.start]
const riEnd = segments.residueAtomSegments.index[chainSegment.end - 1]
- if (areBackboneConnected(riStart, riEnd, data, segments, conformation, moleculeType)) {
+ if (areBackboneConnected(riStart, riEnd, data, segments, conformation, index, moleculeType)) {
cyclicPolymerMap.set(riStart, riEnd)
cyclicPolymerMap.set(riEnd, riStart)
}
@@ -85,7 +78,7 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
} else {
const riStart = segments.residueAtomSegments.index[residueSegment.start]
const riEnd = segments.residueAtomSegments.index[prevEnd - 1]
- if (!areBackboneConnected(riStart, riEnd, data, segments, conformation, moleculeType)) {
+ if (!areBackboneConnected(riStart, riEnd, data, segments, conformation, index, moleculeType)) {
polymerRanges.push(startIndex, prevEnd - 1)
startIndex = residueSegment.start
}
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index a550f8f32516575bf3c926ed5a2728e759829e8c..2031a00c06ce8c830154c9224ea42aa362593f79 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -59,32 +59,36 @@ export const enum MoleculeType {
saccharide
}
-export type AtomRole = 'trace' | 'direction' | 'backboneStart' | 'backboneEnd'
+export type AtomRole = 'trace' | 'direction' | 'backboneStart' | 'backboneEnd' | 'coarseBackbone'
-export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: string } } = {
+export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<string> } } = {
[MoleculeType.protein]: {
- trace: 'CA', // TODO 'BB'
- direction: 'O', // TODO 'OC1', 'O1', 'OX1', 'OXT'
- backboneStart: 'N',
- backboneEnd: 'C'
+ trace: new Set(['CA']),
+ direction: new Set(['O', 'OC1', 'O1', 'OX1', 'OXT']),
+ backboneStart: new Set(['N']),
+ backboneEnd: new Set(['C']),
+ coarseBackbone: new Set(['CA', 'BB'])
},
[MoleculeType.RNA]: {
- trace: 'C4\'', // TODO 'C4*'
- direction: 'C3\'', // 'C3*'
- backboneStart: 'P',
- backboneEnd: 'O3\'' // TODO 'O3*'
+ trace: new Set(['C4\'', 'C4*']),
+ direction: new Set(['C3\'', 'C3*']),
+ backboneStart: new Set(['P']),
+ backboneEnd: new Set(['O3\'', 'O3*']),
+ coarseBackbone: new Set(['P'])
},
[MoleculeType.DNA]: {
- trace: 'C3\'', // TODO 'C3*'
- direction: 'C1\'', // TODO 'C1*'
- backboneStart: 'P',
- backboneEnd: 'O3\'' // TODO 'O3*'
+ trace: new Set(['C3\'', 'C3*']),
+ direction: new Set(['C1\'', 'C1*']),
+ backboneStart: new Set(['P']),
+ backboneEnd: new Set(['O3\'', 'O3*']),
+ coarseBackbone: new Set(['P'])
},
[MoleculeType.PNA]: {
- trace: 'N4\'', // TODO 'N4*'
- direction: 'C7\'', // TODO 'C7*'
- backboneStart: 'N1\'', // TODO 'N1*'
- backboneEnd: 'C1\'' // TODO 'C1*'
+ trace: new Set(['N4\'', 'N4*']),
+ direction: new Set(['C7\'', 'C7*']),
+ backboneStart: new Set(['N1\'', 'N1*']),
+ backboneEnd: new Set(['C1\'', 'C1*']),
+ coarseBackbone: new Set(['P'])
}
}
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index 3f65f5f16755cb2ce569e0940f73e07d07dc4c7a..87e34b6e024c77874205055fa2b9448981dce467 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -35,13 +35,14 @@ export function getAtomicMoleculeType(model: Model, rI: ResidueIndex): MoleculeT
return model.atomicHierarchy.derived.residue.moleculeType[rI]
}
+const EmptyAtomIds = new Set<string>()
export function getAtomIdForAtomRole(moleculeType: MoleculeType, atomRole: AtomRole) {
const m = MoleculeTypeAtomRoleId[moleculeType]
if (m !== undefined) {
const a = m[atomRole]
if (a !== undefined) return a
}
- return ''
+ return EmptyAtomIds
}
export function residueLabel(model: Model, rI: number) {
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index 1da10764176ca24e053608db0e38aa325d3be4db..11ef2c8a6428d177d247ee2053fcf2e0ef7f750d 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -72,11 +72,11 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
addSheet(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, w1, h1, arrowHeight, v.secStrucFirst, v.secStrucLast)
} else {
let h0: number, h1: number, h2: number
- if (isHelix) {
+ if (isHelix && !v.isCoarseBackbone) {
h0 = w0 * aspectRatio
h1 = w1 * aspectRatio
h2 = w2 * aspectRatio
- } else if (isNucleicType) {
+ } else if (isNucleicType && !v.isCoarseBackbone) {
h0 = w0 * aspectRatio;
[w0, h0] = [h0, w0]
h1 = w1 * aspectRatio;
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index 5332a697035c9b1f42f7ed175fb709af5280caa0..9099462cd9e394ea32546b6a35386930c056198c 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -35,6 +35,7 @@ interface PolymerTraceElement {
secStrucFirst: boolean, secStrucLast: boolean
secStrucType: SecondaryStructureType
moleculeType: MoleculeType
+ isCoarseBackbone: boolean
p0: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, p4: Vec3
d12: Vec3, d23: Vec3
@@ -51,6 +52,7 @@ function createPolymerTraceElement (unit: Unit): PolymerTraceElement {
secStrucFirst: false, secStrucLast: false,
secStrucType: SecStrucTypeNA,
moleculeType: MoleculeType.unknown,
+ isCoarseBackbone: false,
p0: Vec3.zero(), p1: Vec3.zero(), p2: Vec3.zero(), p3: Vec3.zero(), p4: Vec3.zero(),
d12: Vec3.create(1, 0, 0), d23: Vec3.create(1, 0, 0),
}
@@ -199,6 +201,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
value.centerNext.element = this.traceElementIndex[residueIndexNext1]
this.pos(this.p6, this.traceElementIndex[residueIndexNext3])
this.pos(this.v23, this.directionElementIndex[residueIndex])
+ value.isCoarseBackbone = this.directionElementIndex[residueIndex] === -1
this.setControlPoint(value.p0, this.p0, this.p1, this.p2, residueIndexPrev2)
this.setControlPoint(value.p1, this.p1, this.p2, this.p3, residueIndexPrev1)