diff --git a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
index 790a51a9ed04e4d02d90748d8872fc9bb0f40a98..69fe8db7a0e47b3d9847764f367b94df952a2557 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -25,8 +25,7 @@ import { getElementLoci, markElement } from './util/element';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Segmentation, SortedArray } from 'mol-data/int';
import { MoleculeType, isNucleic, isPurinBase, isPyrimidineBase } from 'mol-model/structure/model/types';
-import { getElementIndexForAtomId } from 'mol-model/structure/util';
-import { getElementIndexForResidueTypeAtomId } from './util/polymer';
+import { getElementIndexForAtomId, getElementIndexForAtomRole } from 'mol-model/structure/util';
async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
@@ -77,7 +76,7 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?:
idx3 = getElementIndexForAtomId(model, residueIndex, 'C6')
idx4 = getElementIndexForAtomId(model, residueIndex, 'C2')
idx5 = getElementIndexForAtomId(model, residueIndex, 'N9')
- idx6 = getElementIndexForResidueTypeAtomId(model, residueIndex, 'trace')
+ idx6 = getElementIndexForAtomRole(model, residueIndex, 'trace')
} else if (isPyrimidineBase(compId)) {
height = 3.0
idx1 = getElementIndexForAtomId(model, residueIndex, 'N3')
@@ -85,7 +84,7 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?:
idx3 = getElementIndexForAtomId(model, residueIndex, 'C4')
idx4 = getElementIndexForAtomId(model, residueIndex, 'C2')
idx5 = getElementIndexForAtomId(model, residueIndex, 'N1')
- idx6 = getElementIndexForResidueTypeAtomId(model, residueIndex, 'trace')
+ idx6 = getElementIndexForAtomRole(model, residueIndex, 'trace')
}
if (idx1 !== -1 && idx2 !== -1 && idx3 !== -1 && idx4 !== -1 && idx5 !== -1 && idx6 !== -1) {
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 18186967701321c19269be43fb7e32b72973c379..6b664c894c4b608357025c2efc60ca2eb98562c8 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -4,14 +4,14 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureElement, Model, ElementIndex, ResidueIndex } from 'mol-model/structure';
+import { Unit, StructureElement, ElementIndex, ResidueIndex } from 'mol-model/structure';
import { Segmentation, OrderedSet, Interval, SortedArray } from 'mol-data/int';
-import { MoleculeType, SecondaryStructureType } from 'mol-model/structure/model/types';
+import { MoleculeType, SecondaryStructureType, AtomRole } from 'mol-model/structure/model/types';
import Iterator from 'mol-data/iterator';
import { Vec3 } from 'mol-math/linear-algebra';
import SortedRanges from 'mol-data/int/sorted-ranges';
import { CoarseSphereConformation, CoarseGaussianConformation } from 'mol-model/structure/model/properties/coarse';
-import { getElementIndexForAtomId, getMoleculeType } from 'mol-model/structure/util';
+import { getMoleculeType, getElementIndexForAtomRole } from 'mol-model/structure/util';
export function getPolymerRanges(unit: Unit): SortedRanges<ElementIndex> {
switch (unit.kind) {
@@ -68,34 +68,7 @@ export function getPolymerGapCount(unit: Unit) {
return count
}
-export function getResidueTypeAtomId(moleculeType: MoleculeType, atomType: 'trace' | 'direction') {
- switch (moleculeType) {
- case MoleculeType.protein:
- switch (atomType) {
- case 'trace': return 'CA'
- case 'direction': return 'O'
- }
- break
- case MoleculeType.RNA:
- switch (atomType) {
- case 'trace': return 'C4\''
- case 'direction': return 'C3\''
- }
- break
- case MoleculeType.DNA:
- switch (atomType) {
- case 'trace': return 'C3\''
- case 'direction': return 'C1\''
- }
- break
- }
- return ''
-}
-export function getElementIndexForResidueTypeAtomId(model: Model, rI: ResidueIndex, atomType: 'trace' | 'direction') {
- const atomId = getResidueTypeAtomId(getMoleculeType(model, rI), atomType)
- return getElementIndexForAtomId(model, rI, atomId)
-}
/** Iterates over consecutive pairs of residues/coarse elements in polymers */
export function PolymerBackboneIterator(unit: Unit): Iterator<PolymerBackbonePair> {
@@ -119,21 +92,22 @@ function createPolymerBackbonePair (unit: Unit) {
}
}
-const enum AtomicPolymerBackboneIteratorState { nextPolymer, firstResidue, nextResidue }
+const enum AtomicPolymerBackboneIteratorState { nextPolymer, firstResidue, nextResidue, cycle }
export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePair> {
private value: PolymerBackbonePair
private polymerIt: SortedRanges.Iterator<ElementIndex, ResidueIndex>
private residueIt: Segmentation.SegmentIterator<ResidueIndex>
private state: AtomicPolymerBackboneIteratorState = AtomicPolymerBackboneIteratorState.nextPolymer
+ private residueSegment: Segmentation.Segment<ResidueIndex>
hasNext: boolean = false;
- private getElementIndex(residueIndex: ResidueIndex, atomType: 'trace' | 'direction') {
- const index = getElementIndexForResidueTypeAtomId(this.unit.model, residueIndex, atomType)
+ private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
+ const index = getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
// TODO handle case when it returns -1
const elementIndex = SortedArray.indexOf(this.unit.elements, index) as ElementIndex
if (elementIndex === -1) {
- console.log('-1', residueIndex, atomType, index)
+ console.log('-1', residueIndex, atomRole, index)
}
return elementIndex === -1 ? 0 as ElementIndex : elementIndex
}
@@ -141,10 +115,10 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
move() {
if (this.state === AtomicPolymerBackboneIteratorState.nextPolymer) {
while (this.polymerIt.hasNext) {
- const residueSegment = this.polymerIt.move()
- this.residueIt.setSegment(residueSegment);
+ this.residueIt.setSegment(this.polymerIt.move());
if (this.residueIt.hasNext) {
- this.value.centerB.element = this.getElementIndex(this.residueIt.move().index, 'trace')
+ this.residueSegment = this.residueIt.move()
+ this.value.centerB.element = this.getElementIndex(this.residueSegment.index, 'trace')
this.state = AtomicPolymerBackboneIteratorState.nextResidue
break
}
@@ -152,15 +126,26 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
}
if (this.state === AtomicPolymerBackboneIteratorState.nextResidue) {
+ this.residueSegment = this.residueIt.move()
this.value.centerA.element = this.value.centerB.element
- this.value.centerB.element = this.getElementIndex(this.residueIt.move().index, 'trace')
+ this.value.centerB.element = this.getElementIndex(this.residueSegment.index, 'trace')
if (!this.residueIt.hasNext) {
- // TODO need to advance to a polymer that has two or more residues (can't assume it has)
- this.state = AtomicPolymerBackboneIteratorState.nextPolymer
+ if (this.unit.model.atomicHierarchy.cyclicPolymerMap.has(this.residueSegment.index)) {
+ this.state = AtomicPolymerBackboneIteratorState.cycle
+ } else {
+ // TODO need to advance to a polymer that has two or more residues (can't assume it has)
+ this.state = AtomicPolymerBackboneIteratorState.nextPolymer
+ }
}
+ } else if (this.state === AtomicPolymerBackboneIteratorState.cycle) {
+ const { cyclicPolymerMap } = this.unit.model.atomicHierarchy
+ this.value.centerA.element = this.value.centerB.element
+ this.value.centerB.element = this.getElementIndex(cyclicPolymerMap.get(this.residueSegment.index)!, 'trace')
+ // TODO need to advance to a polymer that has two or more residues (can't assume it has)
+ this.state = AtomicPolymerBackboneIteratorState.nextPolymer
}
- this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext
+ this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext || this.state === AtomicPolymerBackboneIteratorState.cycle
return this.value;
}
@@ -243,12 +228,12 @@ export class AtomicPolymerGapIterator implements Iterator<PolymerGapPair> {
private gapIt: SortedRanges.Iterator<ElementIndex, ResidueIndex>
hasNext: boolean = false;
- private getElementIndex(residueIndex: ResidueIndex, atomType: 'trace' | 'direction') {
- const index = getElementIndexForResidueTypeAtomId(this.unit.model, residueIndex, atomType)
+ private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
+ const index = getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
// TODO handle case when it returns -1
const elementIndex = SortedArray.indexOf(this.unit.elements, index) as ElementIndex
if (elementIndex === -1) {
- console.log('-1', residueIndex, atomType, index)
+ console.log('-1', residueIndex, atomRole, index)
}
return elementIndex === -1 ? 0 as ElementIndex : elementIndex
}
@@ -363,22 +348,38 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.residueSegmentMax = index[this.unit.elements[polymerSegment.end - 1]]
}
- private getAtomIndex(residueIndex: number, atomType: 'trace' | 'direction') {
- const index = Math.min(Math.max(this.residueSegmentMin, residueIndex), this.residueSegmentMax)
- return getElementIndexForResidueTypeAtomId(this.unit.model, index as ResidueIndex, atomType)
+ private getAtomIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
+ const { cyclicPolymerMap } = this.unit.model.atomicHierarchy
+ if (residueIndex < this.residueSegmentMin) {
+ const cyclicIndex = cyclicPolymerMap.get(this.residueSegmentMin)
+ if (cyclicIndex !== undefined) {
+
+ residueIndex = cyclicIndex - (this.residueSegmentMin - residueIndex - 1) as ResidueIndex
+ } else {
+ residueIndex = this.residueSegmentMin
+ }
+ } else if (residueIndex > this.residueSegmentMax) {
+ const cyclicIndex = cyclicPolymerMap.get(this.residueSegmentMax)
+ if (cyclicIndex !== undefined) {
+ residueIndex = cyclicIndex + (residueIndex - this.residueSegmentMax - 1) as ResidueIndex
+ } else {
+ residueIndex = this.residueSegmentMax
+ }
+ }
+ return getElementIndexForAtomRole(this.unit.model, residueIndex as ResidueIndex, atomRole)
}
- private getElementIndex(residueIndex: number, atomType: 'trace' | 'direction') {
- const index = this.getAtomIndex(residueIndex, atomType)
+ private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
+ const index = this.getAtomIndex(residueIndex, atomRole)
// TODO handle case when it returns -1
const elementIndex = SortedArray.indexOf(this.unit.elements, index) as ElementIndex
if (elementIndex === -1) {
- console.log('-1', residueIndex, atomType, index)
+ console.log('-1', residueIndex, atomRole, index)
}
return elementIndex === -1 ? 0 as ElementIndex : elementIndex
}
- private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: number) {
+ private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: ResidueIndex) {
const ss = this.unit.model.properties.secondaryStructure.type[residueIndex]
if (SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Beta)) {
Vec3.scale(out, Vec3.add(out, p1, Vec3.add(out, p3, Vec3.add(out, p2, p2))), 1/4)
@@ -387,15 +388,6 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
}
}
- // private setDirectionVector(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: number) {
- // const ss = this.unit.model.properties.secondaryStructure.type[residueIndex]
- // if (SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Beta)) {
- // Vec3.scale(out, Vec3.add(out, p1, Vec3.add(out, p2, p3)), 1/3)
- // } else {
- // Vec3.copy(out, p2)
- // }
- // }
-
move() {
const { residueIt, polymerIt, value } = this
@@ -415,29 +407,27 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
const { index: residueIndex } = residueIt.move();
value.center.element = this.getElementIndex(residueIndex, 'trace')
- this.pos(this.p0, this.getAtomIndex(residueIndex - 3, 'trace'))
- this.pos(this.p1, this.getAtomIndex(residueIndex - 2, 'trace'))
- this.pos(this.p2, this.getAtomIndex(residueIndex - 1, 'trace'))
+ this.pos(this.p0, this.getAtomIndex(residueIndex - 3 as ResidueIndex, 'trace'))
+ this.pos(this.p1, this.getAtomIndex(residueIndex - 2 as ResidueIndex, 'trace'))
+ this.pos(this.p2, this.getAtomIndex(residueIndex - 1 as ResidueIndex, 'trace'))
this.pos(this.p3, this.getAtomIndex(residueIndex, 'trace'))
- this.pos(this.p4, this.getAtomIndex(residueIndex + 1, 'trace'))
- this.pos(this.p5, this.getAtomIndex(residueIndex + 2, 'trace'))
- this.pos(this.p6, this.getAtomIndex(residueIndex + 3, 'trace'))
+ this.pos(this.p4, this.getAtomIndex(residueIndex + 1 as ResidueIndex, 'trace'))
+ this.pos(this.p5, this.getAtomIndex(residueIndex + 2 as ResidueIndex, 'trace'))
+ this.pos(this.p6, this.getAtomIndex(residueIndex + 3 as ResidueIndex, 'trace'))
- // this.pos(this.v01, this.getAtomIndex(residueIndex - 2, 'direction'))
- this.pos(this.v12, this.getAtomIndex(residueIndex - 1, 'direction'))
+ // this.pos(this.v01, this.getAtomIndex(residueIndex - 2 as ResidueIndex, 'direction'))
+ this.pos(this.v12, this.getAtomIndex(residueIndex - 1 as ResidueIndex, 'direction'))
this.pos(this.v23, this.getAtomIndex(residueIndex, 'direction'))
- // this.pos(this.v34, this.getAtomIndex(residueIndex + 1, 'direction'))
+ // this.pos(this.v34, this.getAtomIndex(residueIndex + 1 as ResidueIndex, 'direction'))
this.value.secStrucType = this.unit.model.properties.secondaryStructure.type[residueIndex]
- this.setControlPoint(value.t0, this.p0, this.p1, this.p2, residueIndex - 2)
- this.setControlPoint(value.t1, this.p1, this.p2, this.p3, residueIndex - 1)
+ this.setControlPoint(value.t0, this.p0, this.p1, this.p2, residueIndex - 2 as ResidueIndex)
+ this.setControlPoint(value.t1, this.p1, this.p2, this.p3, residueIndex - 1 as ResidueIndex)
this.setControlPoint(value.t2, this.p2, this.p3, this.p4, residueIndex)
- this.setControlPoint(value.t3, this.p3, this.p4, this.p5, residueIndex + 1)
- this.setControlPoint(value.t4, this.p4, this.p5, this.p6, residueIndex + 2)
+ this.setControlPoint(value.t3, this.p3, this.p4, this.p5, residueIndex + 1 as ResidueIndex)
+ this.setControlPoint(value.t4, this.p4, this.p5, this.p6, residueIndex + 2 as ResidueIndex)
- // this.setDirectionVector(value.d12, this.v01, this.v12, this.v23, residueIndex)
- // this.setDirectionVector(value.d23, this.v12, this.v23, this.v34, residueIndex + 1)
Vec3.copy(value.d12, this.v12)
Vec3.copy(value.d23, this.v23)
diff --git a/src/mol-model/structure/model/formats/mmcif/atomic.ts b/src/mol-model/structure/model/formats/mmcif/atomic.ts
index db05907fcb8ee28852f7d1abbf93e883ea11c8e9..005dfc7ff933d59a48d29b6a075e33fa417ecbf8 100644
--- a/src/mol-model/structure/model/formats/mmcif/atomic.ts
+++ b/src/mol-model/structure/model/formats/mmcif/atomic.ts
@@ -91,17 +91,15 @@ export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_sit
};
}
+ const conformation = getConformation(atom_site)
+
const hierarchySegments: AtomicSegments = {
residueAtomSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, Interval.ofBounds(0, atom_site._rowCount)),
chainAtomSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, Interval.ofBounds(0, atom_site._rowCount)),
}
const hierarchyKeys = getAtomicKeys(hierarchyData, entities, hierarchySegments);
- const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, formatData.chemicalComponentMap);
+ const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, conformation, formatData.chemicalComponentMap);
const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments, ...hierarchyRanges };
- return {
- sameAsPrevious: false,
- hierarchy,
- conformation: getConformation(atom_site)
- };
+ 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 33d98c72d09a399e19d76f9810b13f1d5ebc6731..d4db8be333386f1306dbbc422011262412819842 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -83,6 +83,7 @@ export interface AtomicKeys {
export interface AtomicRanges {
polymerRanges: SortedRanges<ElementIndex>
gapRanges: SortedRanges<ElementIndex>
+ cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
}
type _Hierarchy = AtomicData & AtomicSegments & AtomicKeys & AtomicRanges
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 cef6e3c7a42a457f9f4460cc5842d93dfe4f9f9c..52db07fc11d0cb33654db16bef3e6ddb83b52713 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
@@ -8,15 +8,51 @@ import { AtomicSegments } from '../atomic';
import { AtomicData, AtomicRanges } from '../atomic/hierarchy';
import { Segmentation, Interval } from 'mol-data/int';
import SortedRanges from 'mol-data/int/sorted-ranges';
-import { ChemicalComponent } from '../chemical-component';
+import { ChemicalComponentMap } from '../chemical-component';
import { MoleculeType, isPolymer } from '../../types';
-import { ElementIndex } from '../../indexing';
+import { ElementIndex, ResidueIndex } from '../../indexing';
+import { getAtomIdForAtomRole } from '../../../util';
+import { AtomicConformation } from '../atomic/conformation';
+import { Vec3 } from 'mol-math/linear-algebra';
// TODO add gaps at the ends of the chains by comparing to the polymer sequence data
-export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, chemicalComponentMap: Map<string, ChemicalComponent>): AtomicRanges {
+function getMoleculeType(compId: string, chemicalComponentMap: ChemicalComponentMap) {
+ const cc = chemicalComponentMap.get(compId)
+ return cc ? cc.moleculeType : MoleculeType.unknown
+}
+
+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 as ElementIndex
+ }
+ return offsets[rI] as ElementIndex
+}
+
+function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, chemicalComponentMap: ChemicalComponentMap) {
+ const { label_comp_id } = data.residues
+ const mtStart = getMoleculeType(label_comp_id.value(riStart), chemicalComponentMap)
+ const mtEnd = getMoleculeType(label_comp_id.value(riEnd), chemicalComponentMap)
+ if (!isPolymer(mtStart) || !isPolymer(mtEnd)) return false
+
+ const startId = getAtomIdForAtomRole(mtStart, 'backboneStart')
+ const endId = getAtomIdForAtomRole(mtEnd, 'backboneEnd')
+
+ const eiStart = getElementIndexForAtomId(riStart, startId, data, segments)
+ const eiEnd = getElementIndexForAtomId(riEnd, endId, data, segments)
+
+ 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) < 2
+}
+
+export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, chemicalComponentMap: ChemicalComponentMap): AtomicRanges {
const polymerRanges: number[] = []
const gapRanges: number[] = []
+ const cyclicPolymerMap = new Map<ResidueIndex, ResidueIndex>()
const chainIt = Segmentation.transientSegments(segments.chainAtomSegments, Interval.ofBounds(0, data.atoms._rowCount))
const residueIt = Segmentation.transientSegments(segments.residueAtomSegments, Interval.ofBounds(0, data.atoms._rowCount))
const { label_seq_id, label_comp_id } = data.residues
@@ -34,11 +70,17 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, chem
prevEnd = -1
startIndex = -1
+ const riStart = segments.residueAtomSegments.index[chainSegment.start]
+ const riEnd = segments.residueAtomSegments.index[chainSegment.end - 1]
+ if (areBackboneConnected(riStart, riEnd, data, segments, conformation, chemicalComponentMap)) {
+ cyclicPolymerMap.set(riStart, riEnd)
+ cyclicPolymerMap.set(riEnd, riStart)
+ }
+
while (residueIt.hasNext) {
const residueSegment = residueIt.move();
const residueIndex = residueSegment.index
- const cc = chemicalComponentMap.get(label_comp_id.value(residueIndex))
- const moleculeType = cc ? cc.moleculeType : MoleculeType.unknown
+ const moleculeType = getMoleculeType(label_comp_id.value(residueIndex), chemicalComponentMap)
const seqId = label_seq_id.value(residueIndex)
if (isPolymer(moleculeType)) {
if (startIndex !== -1) {
@@ -67,6 +109,7 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, chem
return {
polymerRanges: SortedRanges.ofSortedRanges(polymerRanges as ElementIndex[]),
- gapRanges: SortedRanges.ofSortedRanges(gapRanges as ElementIndex[])
+ gapRanges: SortedRanges.ofSortedRanges(gapRanges as ElementIndex[]),
+ cyclicPolymerMap
}
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index cced8c8808d71d137ffbd8b352fd3f2b42a09d7e..1492b2e05ada7a7fe0ab10b648719305e48736d7 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -54,6 +54,45 @@ export const enum MoleculeType {
saccharide
}
+const AtomRole = {
+ trace: '', direction: '', backboneStart: '', backboneEnd: ''
+}
+export type AtomRole = keyof typeof AtomRole
+
+export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: string } } = {
+ [MoleculeType.protein]: {
+ trace: 'CA', // TODO 'BB'
+ direction: 'O', // TODO 'OC1', 'O1', 'OX1', 'OXT'
+ backboneStart: 'N',
+ backboneEnd: 'C'
+ },
+ [MoleculeType.RNA]: {
+ trace: 'C4\'', // TODO 'C4*'
+ direction: 'C3\'', // 'C3*'
+ backboneStart: 'P',
+ backboneEnd: 'O3\'' // TODO 'O3*'
+ },
+ [MoleculeType.DNA]: {
+ trace: 'C3\'', // TODO 'C3*'
+ direction: 'C1\'', // TODO 'C1*'
+ backboneStart: 'P',
+ backboneEnd: 'O3\'' // TODO 'O3*'
+ }
+}
+
+export const ProteinBackboneAtoms = [
+ 'CA', 'C', 'N', 'O',
+ 'O1', 'O2', 'OC1', 'OC2', 'OX1', 'OXT',
+ 'H', 'H1', 'H2', 'H3', 'HA', 'HN',
+ 'BB'
+]
+
+export const NucleicBackboneAtoms = [
+ 'P', 'OP1', 'OP2',
+ 'O2\'', 'O3\'', 'O4\'', 'O5\'', 'C1\'', 'C2\'', 'C3\'', 'C4\'', 'C5\'',
+ 'O2*', 'O3*', 'O4*', 'O5*', 'C1*', 'C2*', 'C3*', 'C4*', 'C5*'
+]
+
/** Chemical component types as defined in the mmCIF CCD */
export enum ComponentType {
// protein
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index eab551c3f9cb9d71e15c42d8e3c05a1b48a15d31..fbe525649c4e876ffe7eb21d39c805d030e33af7 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -5,7 +5,7 @@
*/
import { Model, ResidueIndex, ElementIndex } from './model';
-import { MoleculeType } from './model/types';
+import { MoleculeType, AtomRole, MoleculeTypeAtomRoleId } from './model/types';
export function getMoleculeType(model: Model, rI: ResidueIndex) {
const compId = model.atomicHierarchy.residues.label_comp_id.value(rI)
@@ -14,6 +14,15 @@ export function getMoleculeType(model: Model, rI: ResidueIndex) {
return cc ? cc.moleculeType : MoleculeType.unknown
}
+export function getAtomIdForAtomRole(moleculeType: MoleculeType, atomRole: AtomRole) {
+ const m = MoleculeTypeAtomRoleId[moleculeType]
+ if (m !== undefined) {
+ const a = m[atomRole]
+ if (a !== undefined) return a
+ }
+ return ''
+}
+
export function getElementIndexForAtomId(model: Model, rI: ResidueIndex, atomId: string): ElementIndex {
const { offsets } = model.atomicHierarchy.residueAtomSegments
const { label_atom_id } = model.atomicHierarchy.atoms
@@ -23,6 +32,11 @@ export function getElementIndexForAtomId(model: Model, rI: ResidueIndex, atomId:
return offsets[rI] as ElementIndex
}
+export function getElementIndexForAtomRole(model: Model, rI: ResidueIndex, atomRole: AtomRole) {
+ const atomId = getAtomIdForAtomRole(getMoleculeType(model, rI), atomRole)
+ return getElementIndexForAtomId(model, rI, atomId)
+}
+
export function residueLabel(model: Model, rI: number) {
const { residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy
const { label_comp_id, label_seq_id } = residues
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index ddd499c4b2d34ae291c606beacb9f196791a6b25..992773ebbcb7ebabebc69f38c9621482cd026112 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -83,7 +83,7 @@ export class Stage {
// this.loadPdbid('2np2') // dna
// this.loadPdbid('1d66') // dna
// this.loadPdbid('9dna') // A form dna
- this.loadPdbid('1bna') // B form dna
+ // this.loadPdbid('1bna') // B form dna
// this.loadPdbid('199d') // C form dna
// this.loadPdbid('4lb6') // Z form dna
// this.loadPdbid('1egk') // 4-way dna-rna junction
@@ -91,7 +91,7 @@ export class Stage {
// this.loadPdbid('1xv6') // rna, modified nucleotides
// this.loadPdbid('3bbm') // rna with linker
// this.loadPdbid('1gfl') // GFP, flourophore has carbonyl oxygen removed
- // this.loadPdbid('1sfi') // contains cyclic peptid
+ this.loadPdbid('1sfi') // contains cyclic peptid
// this.loadPdbid('3sn6') // discontinuous chains
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../examples/1cbs_updated.cif`)