diff --git a/src/mol-geo/primitive/pyramid.ts b/src/mol-geo/primitive/pyramid.ts
index 6258cf6c5911ac3e93d5f830beafa612def99fd0..04f9cc0b4538eb10a8469387efe3120a035dd08a 100644
--- a/src/mol-geo/primitive/pyramid.ts
+++ b/src/mol-geo/primitive/pyramid.ts
@@ -54,6 +54,12 @@ export function Pyramid(points: ArrayLike<number>): Primitive {
return builder.getPrimitive()
}
+let triangularPyramid: Primitive
+export function TriangularPyramid() {
+ if (!triangularPyramid) triangularPyramid = Pyramid(polygon(3, true))
+ return triangularPyramid
+}
+
let octagonalPyramid: Primitive
export function OctagonalPyramid() {
if (!octagonalPyramid) octagonalPyramid = Pyramid(polygon(8, true))
diff --git a/src/mol-model-formats/structure/mmcif/atomic.ts b/src/mol-model-formats/structure/mmcif/atomic.ts
index ec4ea2191d133e82a21ff9e939f0c88f920a1a6c..ba23561126f9d8e2207dfbd7eec7284bddbc880f 100644
--- a/src/mol-model-formats/structure/mmcif/atomic.ts
+++ b/src/mol-model-formats/structure/mmcif/atomic.ts
@@ -15,7 +15,6 @@ import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsS
import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
import { ElementSymbol } from '../../../mol-model/structure/model/types';
import { Entities } from '../../../mol-model/structure/model/properties/common';
-import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
import { FormatData } from './parser';
@@ -100,7 +99,6 @@ export function getAtomicHierarchyAndConformation(atom_site: AtomSite, sourceInd
const index = getAtomicIndex(hierarchyData, entities, hierarchySegments);
const derived = getAtomicDerivedData(hierarchyData, index, formatData.chemicalComponentMap);
- const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, conformation, index, derived.residue.moleculeType);
- const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, ...hierarchyRanges, index, derived };
+ const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, index, derived };
return { sameAsPrevious: false, hierarchy, conformation };
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 7a35b55203149878a443912a8c3c12e9b744f885..d4827cb4198352f86de1fa87db2e88007fca29aa 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -30,6 +30,7 @@ import mmCIF_Format = ModelFormat.mmCIF
import { memoize1 } from '../../../mol-util/memoize';
import { ElementIndex, EntityIndex } from '../../../mol-model/structure/model';
import { AtomSiteAnisotrop } from './anisotropic';
+import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
export async function _parse_mmCif(format: mmCIF_Format, ctx: RuntimeContext) {
const formatData = getFormatData(format)
@@ -224,6 +225,9 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
}
const coarse = EmptyIHMCoarse;
+ const sequence = getSequence(format.data, entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId)
+ const atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence)
+
const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
? format.data.entry.id.value(0)
: format.data._name;
@@ -241,9 +245,10 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
modelNum,
entities,
symmetry: getSymmetry(format),
- sequence: getSequence(format.data, entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId),
+ sequence,
atomicHierarchy: atomic.hierarchy,
atomicConformation: atomic.conformation,
+ atomicRanges,
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
@@ -259,6 +264,9 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatData): Model {
const atomic = getAtomicHierarchyAndConformation(data.atom_site, data.atom_site_sourceIndex, data.entities, formatData);
const coarse = getIHMCoarse(data, formatData);
+ const sequence = getSequence(format.data, data.entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId)
+ const atomicRanges = getAtomicRanges(atomic.hierarchy, data.entities, atomic.conformation, sequence)
+
const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
? format.data.entry.id.value(0)
: format.data._name;
@@ -278,9 +286,10 @@ function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatD
modelNum: data.model_id,
entities: data.entities,
symmetry: getSymmetry(format),
- sequence: getSequence(format.data, data.entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId),
+ sequence,
atomicHierarchy: atomic.hierarchy,
atomicConformation: atomic.conformation,
+ atomicRanges,
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 5c2a45a64744a1bea3489673a199f20b4d9a6f47..3b0be2a6eb49553bc0ac8c8b640ecdb235b9901c 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -7,7 +7,7 @@
import UUID from '../../../mol-util/uuid';
import StructureSequence from './properties/sequence';
-import { AtomicHierarchy, AtomicConformation } from './properties/atomic';
+import { AtomicHierarchy, AtomicConformation, AtomicRanges } from './properties/atomic';
import { ModelSymmetry } from './properties/symmetry';
import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
import { Entities, ChemicalComponentMap, MissingResidues } from './properties/common';
@@ -42,6 +42,7 @@ export interface Model extends Readonly<{
atomicHierarchy: AtomicHierarchy,
atomicConformation: AtomicConformation,
+ atomicRanges: AtomicRanges,
properties: {
/** secondary structure provided by the input file */
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index 12bac4737e68a5039305568b164b4c7aff5e20f0..ae7337b34afe2b8bba8985620b833eb2e356fff6 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -222,7 +222,7 @@ export interface AtomicRanges {
cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
}
-type _Hierarchy = AtomicData & AtomicSegments & AtomicRanges
+type _Hierarchy = AtomicData & AtomicSegments
export interface AtomicHierarchy extends _Hierarchy {
index: AtomicIndex
derived: AtomicDerivedData
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 ab38a48e28231ebbff787985b9e7cb9a74739901..0c098a917acc02166b529be9c00122efcd57568a 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
@@ -1,11 +1,10 @@
/**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { AtomicSegments } from '../atomic';
-import { AtomicData, AtomicRanges, AtomicIndex } from '../atomic/hierarchy';
+import { AtomicRanges, AtomicIndex, AtomicHierarchy } from '../atomic/hierarchy';
import { Segmentation, Interval } from '../../../../../mol-data/int';
import SortedRanges from '../../../../../mol-data/int/sorted-ranges';
import { MoleculeType, isPolymer } from '../../types';
@@ -13,10 +12,10 @@ import { ElementIndex, ResidueIndex } from '../../indexing';
import { getAtomIdForAtomRole } from '../../../util';
import { AtomicConformation } from '../atomic/conformation';
import { Vec3 } from '../../../../../mol-math/linear-algebra';
+import { Entities } from '../common';
+import StructureSequence from '../sequence';
-// TODO add gaps at the ends of the chains by comparing to the polymer sequence data
-
-function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, index: AtomicIndex, moleculeType: ArrayLike<MoleculeType>) {
+function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, conformation: AtomicConformation, index: AtomicIndex, moleculeType: ArrayLike<MoleculeType>) {
const mtStart = moleculeType[riStart]
const mtEnd = moleculeType[riEnd]
if (!isPolymer(mtStart) || !isPolymer(mtEnd)) return false
@@ -35,13 +34,16 @@ function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data:
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, index: AtomicIndex, moleculeType: ArrayLike<MoleculeType>): AtomicRanges {
+export function getAtomicRanges(hierarchy: AtomicHierarchy, entities: Entities, conformation: AtomicConformation, sequence: StructureSequence): 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 } = data.residues
+ const chainIt = Segmentation.transientSegments(hierarchy.chainAtomSegments, Interval.ofBounds(0, hierarchy.atoms._rowCount))
+ const residueIt = Segmentation.transientSegments(hierarchy.residueAtomSegments, Interval.ofBounds(0, hierarchy.atoms._rowCount))
+ const { index, derived } = hierarchy
+ const { label_seq_id } = hierarchy.residues
+ // const { label_entity_id } = hierarchy.chains
+ const { moleculeType, traceElementIndex } = derived.residue
let prevSeqId: number
let prevStart: number
@@ -56,18 +58,24 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
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, index, moleculeType)) {
+ const riStart = hierarchy.residueAtomSegments.index[chainSegment.start]
+ const riEnd = hierarchy.residueAtomSegments.index[chainSegment.end - 1]
+ if (areBackboneConnected(riStart, riEnd, conformation, index, moleculeType)) {
cyclicPolymerMap.set(riStart, riEnd)
cyclicPolymerMap.set(riEnd, riStart)
}
+ // TODO
+ // const eI = entities.getEntityIndex(label_entity_id.value(chainSegment.index))
+ // const seq = sequence.byEntityKey[eI]
+ // const maxSeqId = seq ? seq.sequence.seqId.value(seq.sequence.seqId.rowCount - 1) : -1
+
while (residueIt.hasNext) {
const residueSegment = residueIt.move();
const residueIndex = residueSegment.index
const seqId = label_seq_id.value(residueIndex)
- if (isPolymer(moleculeType[residueIndex])) {
+ // treat polymers residues that don't have a trace element resolved as gaps
+ if (isPolymer(moleculeType[residueIndex]) && traceElementIndex[residueIndex] !== -1) {
if (startIndex !== -1) {
if (seqId !== prevSeqId + 1) {
polymerRanges.push(startIndex, prevEnd - 1)
@@ -75,16 +83,24 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
startIndex = residueSegment.start
} else if (!residueIt.hasNext) {
polymerRanges.push(startIndex, residueSegment.end - 1)
+ // TODO
+ // if (seqId !== maxSeqId) {
+ // gapRanges.push(residueSegment.end - 1, residueSegment.end - 1)
+ // }
} else {
- const riStart = segments.residueAtomSegments.index[residueSegment.start]
- const riEnd = segments.residueAtomSegments.index[prevEnd - 1]
- if (!areBackboneConnected(riStart, riEnd, data, segments, conformation, index, moleculeType)) {
+ const riStart = hierarchy.residueAtomSegments.index[residueSegment.start]
+ const riEnd = hierarchy.residueAtomSegments.index[prevEnd - 1]
+ if (!areBackboneConnected(riStart, riEnd, conformation, hierarchy.index, moleculeType)) {
polymerRanges.push(startIndex, prevEnd - 1)
startIndex = residueSegment.start
}
}
} else {
startIndex = residueSegment.start // start polymer
+ // TODO
+ // if (seqId !== 1) {
+ // gapRanges.push(residueSegment.start, residueSegment.start)
+ // }
}
} else {
if (startIndex !== -1) {
diff --git a/src/mol-model/structure/structure/util/polymer.ts b/src/mol-model/structure/structure/util/polymer.ts
index 261cd942d56606756df7e2d354a58471f4e44415..02ca015b771978b4ee16f9d4a7d063bfc6ff00d1 100644
--- a/src/mol-model/structure/structure/util/polymer.ts
+++ b/src/mol-model/structure/structure/util/polymer.ts
@@ -14,7 +14,7 @@ export function getAtomicPolymerElements(unit: Unit.Atomic) {
const { elements, model } = unit
const { residueAtomSegments } = unit.model.atomicHierarchy
const { traceElementIndex } = model.atomicHierarchy.derived.residue
- const polymerIt = SortedRanges.transientSegments(unit.model.atomicHierarchy.polymerRanges, elements)
+ const polymerIt = SortedRanges.transientSegments(unit.model.atomicRanges.polymerRanges, elements)
const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
while (polymerIt.hasNext) {
const polymerSegment = polymerIt.move()
@@ -51,7 +51,7 @@ export function getAtomicGapElements(unit: Unit.Atomic) {
const { elements, model, residueIndex } = unit
const { residueAtomSegments } = unit.model.atomicHierarchy
const { traceElementIndex } = model.atomicHierarchy.derived.residue
- const gapIt = SortedRanges.transientSegments(unit.model.atomicHierarchy.gapRanges, unit.elements);
+ const gapIt = SortedRanges.transientSegments(unit.model.atomicRanges.gapRanges, unit.elements);
while (gapIt.hasNext) {
const gapSegment = gapIt.move();
const indexStart = residueIndex[elements[gapSegment.start]]
diff --git a/src/mol-repr/structure/visual/polymer-gap-cylinder.ts b/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
index 5c662460e7a27b0f9ca99955253ccf1f9f41e38b..160010b4a97a8389434431b9bd824812c61da79f 100644
--- a/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
@@ -1,5 +1,5 @@
/**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -13,11 +13,11 @@ import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { CylinderProps } from '../../../mol-geo/primitive/cylinder';
import { PolymerGapIterator, PolymerGapLocationIterator, getPolymerGapElementLoci, eachPolymerGapElement } from './util/polymer';
-import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
import { addFixedCountDashedCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
import { LinkCylinderParams } from './util/link';
import { VisualUpdateState } from '../../util';
+// import { TriangularPyramid } from '../../../mol-geo/primitive/pyramid';
const segmentCount = 10
@@ -28,6 +28,10 @@ export const PolymerGapCylinderParams = {
export const DefaultPolymerGapCylinderProps = PD.getDefaultValues(PolymerGapCylinderParams)
export type PolymerGapCylinderProps = typeof DefaultPolymerGapCylinderProps
+// const triangularPyramid = TriangularPyramid()
+// const t = Mat4.identity()
+// const pd = Vec3.zero()
+
function createPolymerGapCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerGapCylinderProps, mesh?: Mesh) {
const polymerGapCount = unit.gapElements.length
if (!polymerGapCount) return Mesh.createEmpty(mesh)
@@ -49,9 +53,14 @@ function createPolymerGapCylinderMesh(ctx: VisualContext, unit: Unit, structure:
while (polymerGapIt.hasNext) {
const { centerA, centerB } = polymerGapIt.move()
if (centerA.element === centerB.element) {
- builderState.currentGroup = i
- pos(centerA.element, pA)
- addSphere(builderState, pA, 0.6, 0)
+ // TODO
+ // builderState.currentGroup = i
+ // pos(centerA.element, pA)
+ // Vec3.add(pd, pA, Vec3.create(1, 0, 0))
+ // Mat4.targetTo(t, pA, pd, Vec3.create(0, 1, 0))
+ // Mat4.setTranslation(t, pA)
+ // Mat4.scale(t, t, Vec3.create(0.7, 0.7, 2.5))
+ // MeshBuilder.addPrimitive(builderState, t, triangularPyramid)
} else {
pos(centerA.element, pA)
pos(centerB.element, pB)
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index 5fac3e83b765cb38e0a351b4ebcb70c707ba4a14..e929e844b1e545597da539d7171422c75abfaaaa 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.ts
@@ -26,7 +26,7 @@ export const OverhangFactor = 2
export function getPolymerRanges(unit: Unit): SortedRanges<ElementIndex> {
switch (unit.kind) {
- case Unit.Kind.Atomic: return unit.model.atomicHierarchy.polymerRanges
+ case Unit.Kind.Atomic: return unit.model.atomicRanges.polymerRanges
case Unit.Kind.Spheres: return unit.model.coarseHierarchy.spheres.polymerRanges
case Unit.Kind.Gaussians: return unit.model.coarseHierarchy.gaussians.polymerRanges
}
@@ -34,7 +34,7 @@ export function getPolymerRanges(unit: Unit): SortedRanges<ElementIndex> {
export function getGapRanges(unit: Unit): SortedRanges<ElementIndex> {
switch (unit.kind) {
- case Unit.Kind.Atomic: return unit.model.atomicHierarchy.gapRanges
+ case Unit.Kind.Atomic: return unit.model.atomicRanges.gapRanges
case Unit.Kind.Spheres: return unit.model.coarseHierarchy.spheres.gapRanges
case Unit.Kind.Gaussians: return unit.model.coarseHierarchy.gaussians.gapRanges
}
diff --git a/src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts b/src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts
index 42db2945f5522c3f781c3b81613711d0fbdbd0c4..82155734d9d95f0cbe9ab739ddd7989e4a50a83a 100644
--- a/src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts
@@ -61,7 +61,7 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
this.value.centerA.element = this.value.centerB.element
this.value.centerB.element = this.traceElementIndex[this.residueSegment.index]
if (!this.residueIt.hasNext) {
- if (this.unit.model.atomicHierarchy.cyclicPolymerMap.has(this.residueSegment.index)) {
+ if (this.unit.model.atomicRanges.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)
@@ -69,7 +69,7 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
}
}
} else if (this.state === AtomicPolymerBackboneIteratorState.cycle) {
- const { cyclicPolymerMap } = this.unit.model.atomicHierarchy
+ const { cyclicPolymerMap } = this.unit.model.atomicRanges
this.value.centerA.element = this.value.centerB.element
this.value.centerB.element = this.traceElementIndex[cyclicPolymerMap.get(this.residueSegment.index)!]
// TODO need to advance to a polymer that has two or more residues (can't assume it has)
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 889c57ab7f373a439e97868d032c1c3f5ab6fa1c..d8964ad78ab6b28e2e627b9ebdb39d522c45a61f 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -296,12 +296,12 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
constructor(private unit: Unit.Atomic, structure: Structure) {
this.atomicConformation = unit.model.atomicConformation
this.residueAtomSegments = unit.model.atomicHierarchy.residueAtomSegments
- this.polymerRanges = unit.model.atomicHierarchy.polymerRanges
+ this.polymerRanges = unit.model.atomicRanges.polymerRanges
this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex> // can assume it won't be -1 for polymer residues
this.directionFromElementIndex = unit.model.atomicHierarchy.derived.residue.directionFromElementIndex
this.directionToElementIndex = unit.model.atomicHierarchy.derived.residue.directionToElementIndex
this.moleculeType = unit.model.atomicHierarchy.derived.residue.moleculeType
- this.cyclicPolymerMap = unit.model.atomicHierarchy.cyclicPolymerMap
+ this.cyclicPolymerMap = unit.model.atomicRanges.cyclicPolymerMap
this.polymerIt = SortedRanges.transientSegments(this.polymerRanges, unit.elements)
this.residueIt = Segmentation.transientSegments(this.residueAtomSegments, unit.elements);
this.value = createPolymerTraceElement(unit)