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 03a2eeb9443c3582cf42ae8a653ed7c7bbfe89fb..8591ca379aca4372f51ec30ea854281c09c2a039 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -9,14 +9,15 @@ import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
import { MeshBuilder } from '../../../mesh/mesh-builder';
-import { getElementLoci, markElement, StructureElementIterator } from './util/element';
+import { getElementLoci, markElement } from './util/element';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
-import { Segmentation, SortedArray } from 'mol-data/int';
+import { Segmentation } from 'mol-data/int';
import { MoleculeType, isNucleic, isPurinBase, isPyrimidineBase } from 'mol-model/structure/model/types';
import { getElementIndexForAtomId, getElementIndexForAtomRole } from 'mol-model/structure/util';
import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
import { addCylinder } from '../../../mesh/builder/cylinder';
import { Box } from '../../../primitive/box';
+import { NucleotideLocationIterator } from './util/nucleotide';
const p1 = Vec3.zero()
const p2 = Vec3.zero()
@@ -84,7 +85,7 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props:
if (idx5 !== -1 && idx6 !== -1) {
pos(idx5, p5); pos(idx6, p6)
- builder.setGroup(SortedArray.findPredecessorIndex(elements, idx6))
+ builder.setGroup(i)
addCylinder(builder, p5, p6, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
if (idx1 !== -1 && idx2 !== -1 && idx3 !== -1 && idx4 !== -1) {
pos(idx1, p1); pos(idx2, p2); pos(idx3, p3); pos(idx4, p4);
@@ -98,12 +99,12 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props:
builder.add(t, box)
}
}
- }
- if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Nucleotide block mesh', current: i });
+ if (i % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Nucleotide block mesh', current: i });
+ }
+ ++i
}
- ++i
}
}
@@ -119,7 +120,7 @@ export function NucleotideBlockVisual(): UnitsVisual<NucleotideBlockProps> {
return UnitsMeshVisual<NucleotideBlockProps>({
defaultProps: DefaultNucleotideBlockProps,
createMesh: createNucleotideBlockMesh,
- createLocationIterator: StructureElementIterator.fromGroup,
+ createLocationIterator: NucleotideLocationIterator.fromGroup,
getLoci: getElementLoci,
mark: markElement,
setUpdateState: () => {}
diff --git a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
index 6ad043eba547f99896cfbc6e620c709b76dfcc7d..da3d7513ccee7ab5ec10f911074b15c10e76e4e1 100644
--- a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
@@ -7,15 +7,14 @@
import { Unit } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { markElement, getElementLoci, StructureElementIterator } from './util/element';
+import { markElement, getElementLoci } from './util/element';
import { Mesh } from '../../../mesh/mesh';
import { MeshBuilder } from '../../../mesh/mesh-builder';
-import { getPolymerElementCount, PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment } from './util/polymer';
+import { getPolymerElementCount, PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator } from './util/polymer';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/types';
import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
-import { OrderedSet } from 'mol-data/int';
import { Wedge } from '../../../primitive/wedge';
const t = Mat4.identity()
@@ -51,7 +50,7 @@ async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit,
const polymerTraceIt = PolymerTraceIterator(unit)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
- builder.setGroup(OrderedSet.findPredecessorIndex(unit.elements, v.center.element))
+ builder.setGroup(i)
const isNucleic = v.moleculeType === MoleculeType.DNA || v.moleculeType === MoleculeType.RNA
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
@@ -95,7 +94,7 @@ export function PolymerDirectionVisual(): UnitsVisual<PolymerDirectionProps> {
return UnitsMeshVisual<PolymerDirectionProps>({
defaultProps: DefaultPolymerDirectionProps,
createMesh: createPolymerDirectionWedgeMesh,
- createLocationIterator: StructureElementIterator.fromGroup,
+ createLocationIterator: PolymerLocationIterator.fromGroup,
getLoci: getElementLoci,
mark: markElement,
setUpdateState: () => {}
diff --git a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
index 047850c67aae193be0cb0035aed18925e054bfcd..883e2f9e6f84ff4f83af93dfa5ed07df2f5b48b3 100644
--- a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
@@ -9,8 +9,8 @@ import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
import { MeshBuilder } from '../../../mesh/mesh-builder';
-import { getPolymerGapCount, PolymerGapIterator } from './util/polymer';
-import { getElementLoci, markElement, StructureElementIterator } from './util/element';
+import { getPolymerGapCount, PolymerGapIterator, PolymerGapLocationIterator } from './util/polymer';
+import { getElementLoci, markElement } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
@@ -35,11 +35,9 @@ async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, pro
const vertexCountEstimate = segmentCount * radialSegments * 2 * polymerGapCount * 2
const builder = MeshBuilder.create(vertexCountEstimate, vertexCountEstimate / 10, mesh)
- const { elements } = unit
const pos = unit.conformation.invariantPosition
const pA = Vec3.zero()
const pB = Vec3.zero()
- const l = StructureElement.create(unit)
const cylinderProps: CylinderProps = {
radiusTop: 1, radiusBottom: 1, topCap: true, bottomCap: true, radialSegments
}
@@ -49,30 +47,26 @@ async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, pro
while (polymerGapIt.hasNext) {
const { centerA, centerB } = polymerGapIt.move()
if (centerA.element === centerB.element) {
- builder.setGroup(centerA.element)
- pos(elements[centerA.element], pA)
+ builder.setGroup(i)
+ pos(centerA.element, pA)
addSphere(builder, pA, 0.6, 0)
} else {
- const elmA = elements[centerA.element]
- const elmB = elements[centerB.element]
- pos(elmA, pA)
- pos(elmB, pB)
+ pos(centerA.element, pA)
+ pos(centerB.element, pB)
- l.element = elmA
- cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(l)
- builder.setGroup(centerA.element)
+ cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(centerA)
+ builder.setGroup(i)
addFixedCountDashedCylinder(builder, pA, pB, 0.5, segmentCount, cylinderProps)
- l.element = elmB
- cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(l)
- builder.setGroup(centerB.element)
+ cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(centerB)
+ builder.setGroup(i + 1)
addFixedCountDashedCylinder(builder, pB, pA, 0.5, segmentCount, cylinderProps)
}
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'Gap mesh', current: i, max: polymerGapCount });
}
- ++i
+ i += 2
}
return builder.getMesh()
@@ -88,7 +82,7 @@ export function PolymerGapVisual(): UnitsVisual<PolymerGapProps> {
return UnitsMeshVisual<PolymerGapProps>({
defaultProps: DefaultPolymerGapProps,
createMesh: createPolymerGapCylinderMesh,
- createLocationIterator: StructureElementIterator.fromGroup,
+ createLocationIterator: PolymerGapLocationIterator.fromGroup,
getLoci: getElementLoci,
mark: markElement,
setUpdateState: () => {}
diff --git a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
index f65c7fb9cb36488df559bbe8a412d1ee03bd81f6..f5fa0efd09789fcd4a264c561273e9e59c63ddce 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -7,14 +7,13 @@
import { Unit } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { markElement, getElementLoci, StructureElementIterator } from './util/element';
+import { markElement, getElementLoci } from './util/element';
import { Mesh } from '../../../mesh/mesh';
import { MeshBuilder } from '../../../mesh/mesh-builder';
-import { getPolymerElementCount, PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment } from './util/polymer';
+import { getPolymerElementCount, PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator } from './util/polymer';
import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
-import { OrderedSet } from 'mol-data/int';
import { addSheet } from '../../../mesh/builder/sheet';
import { addTube } from '../../../mesh/builder/tube';
@@ -45,7 +44,7 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, props: Po
const polymerTraceIt = PolymerTraceIterator(unit)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
- builder.setGroup(OrderedSet.findPredecessorIndex(unit.elements, v.center.element))
+ builder.setGroup(i)
const isNucleicType = isNucleic(v.moleculeType)
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
@@ -95,7 +94,7 @@ export function PolymerTraceVisual(): UnitsVisual<PolymerTraceProps> {
return UnitsMeshVisual<PolymerTraceProps>({
defaultProps: DefaultPolymerTraceProps,
createMesh: createPolymerTraceMesh,
- createLocationIterator: StructureElementIterator.fromGroup,
+ createLocationIterator: PolymerLocationIterator.fromGroup,
getLoci: getElementLoci,
mark: markElement,
setUpdateState: (state: MeshUpdateState, newProps: PolymerTraceProps, currentProps: PolymerTraceProps) => {
diff --git a/src/mol-geo/representation/structure/visual/util/nucleotide.ts b/src/mol-geo/representation/structure/visual/util/nucleotide.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2243e8a6bb32f1719b5f68f16b268c18bae6d49b
--- /dev/null
+++ b/src/mol-geo/representation/structure/visual/util/nucleotide.ts
@@ -0,0 +1,51 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Unit, ElementIndex, StructureElement } from 'mol-model/structure';
+import { LocationIterator } from '../../../../util/location-iterator';
+import { Segmentation } from 'mol-data/int';
+import { isNucleic, MoleculeType } from 'mol-model/structure/model/types';
+import { getElementIndexForAtomRole } from 'mol-model/structure/util';
+
+export function getNucleotideElementIndices(unit: Unit) {
+ const indices: ElementIndex[] = []
+ const { elements, model } = unit
+ const { chemicalComponentMap } = model.properties
+ const { chainAtomSegments, residueAtomSegments, residues } = model.atomicHierarchy
+ const { label_comp_id } = residues
+ const chainIt = Segmentation.transientSegments(chainAtomSegments, elements)
+ const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
+ while (chainIt.hasNext) {
+ residueIt.setSegment(chainIt.move());
+
+ while (residueIt.hasNext) {
+ const { index } = residueIt.move();
+ const cc = chemicalComponentMap.get(label_comp_id.value(index))
+ const moleculeType = cc ? cc.moleculeType : MoleculeType.unknown
+
+ if (isNucleic(moleculeType)) {
+ const elementIndex = getElementIndexForAtomRole(model, index, 'trace')
+ indices.push(elementIndex === -1 ? residueAtomSegments.offsets[index] : elementIndex)
+ }
+ }
+ }
+ return indices
+}
+
+export namespace NucleotideLocationIterator {
+ export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
+ const nucleotideElementIndices = getNucleotideElementIndices(group.units[0])
+ const groupCount = nucleotideElementIndices.length
+ const instanceCount = group.units.length
+ const location = StructureElement.create()
+ const getLocation = (groupIndex: number, instanceIndex: number) => {
+ const unit = group.units[instanceIndex]
+ location.unit = unit
+ location.element = nucleotideElementIndices[groupIndex]
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation)
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 24d9b7e937e2953c1e1acb3c958a6f69de6b264c..22972c0bbc454cd188d365921c5203a0b0c62337 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -4,9 +4,12 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, ElementIndex } from 'mol-model/structure';
+import { Unit, ElementIndex, StructureElement } from 'mol-model/structure';
import { Segmentation, OrderedSet, Interval } from 'mol-data/int';
import SortedRanges from 'mol-data/int/sorted-ranges';
+import { LocationIterator } from '../../../../util/location-iterator';
+import { getElementIndexForAtomRole } from 'mol-model/structure/util';
+import { PolymerGapIterator } from './polymer/gap-iterator';
export * from './polymer/backbone-iterator'
export * from './polymer/gap-iterator'
@@ -57,6 +60,54 @@ export function getPolymerElementCount(unit: Unit) {
return count
}
+export function getPolymerElementIndices(unit: Unit) {
+ const indices: ElementIndex[] = []
+ const { elements, model } = unit
+ const { residueAtomSegments } = unit.model.atomicHierarchy
+ const polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), elements)
+ switch (unit.kind) {
+ case Unit.Kind.Atomic:
+ const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
+ while (polymerIt.hasNext) {
+ const polymerSegment = polymerIt.move()
+ residueIt.setSegment(polymerSegment)
+ while (residueIt.hasNext) {
+ const residueSegment = residueIt.move()
+ const { start, end, index } = residueSegment
+ if (OrderedSet.areIntersecting(Interval.ofBounds(elements[start], elements[end - 1]), elements)) {
+ const elementIndex = getElementIndexForAtomRole(model, index, 'trace')
+ indices.push(elementIndex === -1 ? residueAtomSegments.offsets[index] : elementIndex)
+ }
+ }
+ }
+ break
+ case Unit.Kind.Spheres:
+ case Unit.Kind.Gaussians:
+ while (polymerIt.hasNext) {
+ const { start, end } = polymerIt.move()
+ for (let i = start; i < end; ++i) { indices.push(elements[i]) }
+ }
+ break
+ }
+ return indices
+}
+
+export namespace PolymerLocationIterator {
+ export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
+ const polymerElementIndices = getPolymerElementIndices(group.units[0])
+ const groupCount = polymerElementIndices.length
+ const instanceCount = group.units.length
+ const location = StructureElement.create()
+ const getLocation = (groupIndex: number, instanceIndex: number) => {
+ const unit = group.units[instanceIndex]
+ location.unit = unit
+ location.element = polymerElementIndices[groupIndex]
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation)
+ }
+}
+
export function getPolymerGapCount(unit: Unit) {
let count = 0
const { elements } = unit
@@ -67,3 +118,29 @@ export function getPolymerGapCount(unit: Unit) {
}
return count
}
+
+export function getPolymerGapElementIndices(unit: Unit) {
+ const indices: ElementIndex[] = []
+ const polymerGapIt = PolymerGapIterator(unit)
+ while (polymerGapIt.hasNext) {
+ const { centerA, centerB } = polymerGapIt.move()
+ indices.push(centerA.element, centerB.element)
+ }
+ return indices
+}
+
+export namespace PolymerGapLocationIterator {
+ export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
+ const polymerGapElementIndices = getPolymerGapElementIndices(group.units[0])
+ const groupCount = polymerGapElementIndices.length
+ const instanceCount = group.units.length
+ const location = StructureElement.create()
+ const getLocation = (groupIndex: number, instanceIndex: number) => {
+ const unit = group.units[instanceIndex]
+ location.unit = unit
+ location.element = polymerGapElementIndices[groupIndex]
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation)
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/util/polymer/gap-iterator.ts b/src/mol-geo/representation/structure/visual/util/polymer/gap-iterator.ts
index 9b91f2894e01ebd89546cee4fafa59514248ee4d..663f10162596a611ff62efc0c4811a5508e99255 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer/gap-iterator.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer/gap-iterator.ts
@@ -5,7 +5,6 @@
*/
import { Unit, StructureElement, ElementIndex, ResidueIndex } from 'mol-model/structure';
-import { SortedArray } from 'mol-data/int';
import { AtomRole } from 'mol-model/structure/model/types';
import Iterator from 'mol-data/iterator';
import SortedRanges from 'mol-data/int/sorted-ranges';
@@ -40,13 +39,8 @@ export class AtomicPolymerGapIterator implements Iterator<PolymerGapPair> {
hasNext: boolean = false;
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, atomRole, index)
- }
- return elementIndex === -1 ? 0 as ElementIndex : elementIndex
+ const elementIndex = getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
+ return elementIndex === -1 ? this.unit.model.atomicHierarchy.residueAtomSegments.offsets[residueIndex] : elementIndex
}
move() {
diff --git a/src/mol-geo/util/color-data.ts b/src/mol-geo/util/color-data.ts
index e8712bd66db5bceb72554790324f7b6f201222a1..87ea59ccd7dd922f2b0bacb36cf4256e1f2f47c9 100644
--- a/src/mol-geo/util/color-data.ts
+++ b/src/mol-geo/util/color-data.ts
@@ -96,9 +96,7 @@ export function createGroupColor(locationIt: LocationIterator, color: LocationCo
export function createGroupInstanceColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
const { groupCount, instanceCount } = locationIt
const count = instanceCount * groupCount
- console.log(count, instanceCount, groupCount)
const colors = colorData && colorData.tColor.ref.value.array.length >= count * 3 ? colorData.tColor.ref.value : createTextureImage(count, 3)
- console.log(colors.array.length / 3, count)
while (locationIt.hasNext) {
const { location, isSecondary, index } = locationIt.move()
Color.toArray(color(location, isSecondary), colors.array, index * 3)
diff --git a/src/mol-view/theme/color/unit-index.ts b/src/mol-view/theme/color/unit-index.ts
index f59d371d8a91d91684e9c88c8c007c6a19ca2dde..2b0231e0d838b92e973cff0f66693bf7bfe67266 100644
--- a/src/mol-view/theme/color/unit-index.ts
+++ b/src/mol-view/theme/color/unit-index.ts
@@ -20,7 +20,6 @@ export function UnitIndexColorTheme(props: ColorThemeProps): ColorTheme {
color = (location: Location): Color => {
if (StructureElement.isLocation(location)) {
- // console.log(location.unit.id, Unit.findUnitById(location.unit.id, units), units.length, units)
return scale.color(Unit.findUnitById(location.unit.id, units))
} else if (Link.isLocation(location)) {
return scale.color(Unit.findUnitById(location.aUnit.id, units))