diff --git a/src/mol-data/int/impl/interval.ts b/src/mol-data/int/impl/interval.ts
index f7568480900db112b77c934e7e4d856a923062b8..fe293e0a0c013897a68b07321349a5e8277ee6e9 100644
--- a/src/mol-data/int/impl/interval.ts
+++ b/src/mol-data/int/impl/interval.ts
@@ -19,6 +19,7 @@ export function size(i: Tuple) { return Tuple.snd(i) - Tuple.fst(i); }
export const hashCode = Tuple.hashCode;
export function has(int: Tuple, v: number) { return Tuple.fst(int) <= v && v < Tuple.snd(int); }
+/** Returns the index of `x` in `set` or -1 if not found. */
export function indexOf(int: Tuple, x: number) { const m = start(int); return x >= m && x < end(int) ? x - m : -1; }
export function getAt(int: Tuple, i: number) { return Tuple.fst(int) + i; }
diff --git a/src/mol-data/int/impl/ordered-set.ts b/src/mol-data/int/impl/ordered-set.ts
index 27ee1f1db798f09ebc789a2043520656c63ebec3..33794046c652e26bba6469695c510d928ad46977 100644
--- a/src/mol-data/int/impl/ordered-set.ts
+++ b/src/mol-data/int/impl/ordered-set.ts
@@ -25,6 +25,7 @@ export function ofSortedArray(xs: Nums): OrderedSetImpl {
export function size(set: OrderedSetImpl) { return I.is(set) ? I.size(set) : S.size(set); }
export function has(set: OrderedSetImpl, x: number) { return I.is(set) ? I.has(set, x) : S.has(set, x); }
+/** Returns the index of `x` in `set` or -1 if not found. */
export function indexOf(set: OrderedSetImpl, x: number) { return I.is(set) ? I.indexOf(set, x) : S.indexOf(set, x); }
export function getAt(set: OrderedSetImpl, i: number) { return I.is(set) ? I.getAt(set, i) : set[i]; }
export function min(set: OrderedSetImpl) { return I.is(set) ? I.min(set) : S.min(set); }
diff --git a/src/mol-data/int/impl/sorted-array.ts b/src/mol-data/int/impl/sorted-array.ts
index 2d441bc3fdf4304e7808e9a417d64a98060441a6..6fff1aa007c47f26cc99d19e8ed790e0e57c4398 100644
--- a/src/mol-data/int/impl/sorted-array.ts
+++ b/src/mol-data/int/impl/sorted-array.ts
@@ -36,6 +36,7 @@ export function hashCode(xs: Nums) {
return hash3(s, xs[0], xs[s - 1]);
}
+/** Returns the index of `x` in `set` or -1 if not found. */
export function indexOf(xs: Nums, v: number) {
const l = xs.length;
return l === 0 ? -1 : xs[0] <= v && v <= xs[l - 1] ? binarySearchRange(xs, v, 0, l) : -1;
diff --git a/src/mol-data/int/interval.ts b/src/mol-data/int/interval.ts
index b2ab7fb8350624c57d88f4d39960e6f41465abe7..ef72450b05865a03ecbffc4562e06c81ada34f49 100644
--- a/src/mol-data/int/interval.ts
+++ b/src/mol-data/int/interval.ts
@@ -18,6 +18,7 @@ namespace Interval {
/** Test if a value is within the bounds of the interval */
export const has: <T extends number = number>(interval: Interval<T>, x: T) => boolean = Impl.has as any;
+ /** Returns the index of `x` in `set` or -1 if not found. */
export const indexOf: <T extends number = number>(interval: Interval<T>, x: T) => number = Impl.indexOf as any;
export const getAt: <T extends number = number>(interval: Interval<T>, i: number) => T = Impl.getAt as any;
diff --git a/src/mol-data/int/ordered-set.ts b/src/mol-data/int/ordered-set.ts
index d18e61446d77582a7c5e8d6af78c586db838f875..046c1b6ab94b3acf93b5b5d232eb711c8b054402 100644
--- a/src/mol-data/int/ordered-set.ts
+++ b/src/mol-data/int/ordered-set.ts
@@ -18,6 +18,7 @@ namespace OrderedSet {
export const ofSortedArray: <T extends number = number>(xs: ArrayLike<T>) => OrderedSet<T> = Base.ofSortedArray as any;
export const has: <T extends number = number>(set: OrderedSet<T>, x: T) => boolean = Base.has as any;
+ /** Returns the index of `x` in `set` or -1 if not found. */
export const indexOf: <T extends number = number>(set: OrderedSet<T>, x: T) => number = Base.indexOf as any;
export const getAt: <T extends number = number>(set: OrderedSet<T>, i: number) => T = Base.getAt as any;
diff --git a/src/mol-data/int/sorted-array.ts b/src/mol-data/int/sorted-array.ts
index c0f1248db3f25e3c7764c67164412d1baafb0c7a..cf0f5d11e09470a4b520cb00707faf4e7f034ea3 100644
--- a/src/mol-data/int/sorted-array.ts
+++ b/src/mol-data/int/sorted-array.ts
@@ -19,6 +19,7 @@ namespace SortedArray {
export const is: <T extends number = number>(v: any) => v is SortedArray<T> = Impl.is as any;
export const has: <T extends number = number>(array: SortedArray<T>, x: T) => boolean = Impl.has as any;
+ /** Returns the index of `x` in `set` or -1 if not found. */
export const indexOf: <T extends number = number>(array: SortedArray<T>, x: T) => number = Impl.indexOf as any;
export const indexOfInInterval: <T extends number = number>(array: SortedArray<T>, x: number, bounds: Interval) => number = Impl.indexOfInInterval as any;
diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
index dca53ec6fe4b9beab83016395e6139a1a2623bc0..185835c629e4bcca92a85f02008992f9466199df 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
@@ -92,8 +92,8 @@ function CarbohydrateLinkIterator(structure: Structure): LocationIterator {
const link = links[groupIndex]
const carbA = elements[link.carbohydrateIndexA]
const carbB = elements[link.carbohydrateIndexB]
- const indexA = OrderedSet.findPredecessorIndex(carbA.unit.elements, carbA.anomericCarbon)
- const indexB = OrderedSet.findPredecessorIndex(carbB.unit.elements, carbB.anomericCarbon)
+ const indexA = OrderedSet.indexOf(carbA.unit.elements, carbA.anomericCarbon)
+ const indexB = OrderedSet.indexOf(carbB.unit.elements, carbB.anomericCarbon)
location.aUnit = carbA.unit
location.aIndex = indexA as StructureElement.UnitIndex
location.bUnit = carbB.unit
@@ -110,14 +110,16 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
const l = links[groupId]
const carbA = elements[l.carbohydrateIndexA]
const carbB = elements[l.carbohydrateIndexB]
- const indexA = OrderedSet.findPredecessorIndex(carbA.unit.elements, carbA.anomericCarbon)
- const indexB = OrderedSet.findPredecessorIndex(carbB.unit.elements, carbB.anomericCarbon)
- return Link.Loci([
- Link.Location(
- carbA.unit, indexA as StructureElement.UnitIndex,
- carbB.unit, indexB as StructureElement.UnitIndex
- )
- ])
+ const indexA = OrderedSet.indexOf(carbA.unit.elements, carbA.anomericCarbon)
+ const indexB = OrderedSet.indexOf(carbB.unit.elements, carbB.anomericCarbon)
+ if (indexA !== -1 && indexB !== -1) {
+ return Link.Loci([
+ Link.Location(
+ carbA.unit, indexA as StructureElement.UnitIndex,
+ carbB.unit, indexB as StructureElement.UnitIndex
+ )
+ ])
+ }
}
return EmptyLoci
}
diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
index 309319c00520fff4fbe60e499c787db5a19e717c..13d568ccb73cd097c659a36a8281c9e600b4aa85 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -182,9 +182,11 @@ function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: num
if (id === objectId) {
const carb = structure.carbohydrates.elements[Math.floor(groupId / 2)]
const { unit } = carb
- const index = OrderedSet.findPredecessorIndex(unit.elements, carb.anomericCarbon)
- const indices = OrderedSet.ofSingleton(index as StructureElement.UnitIndex)
- return StructureElement.Loci([{ unit, indices }])
+ const index = OrderedSet.indexOf(unit.elements, carb.anomericCarbon)
+ if (index !== -1) {
+ const indices = OrderedSet.ofSingleton(index as StructureElement.UnitIndex)
+ return StructureElement.Loci([{ unit, indices }])
+ }
}
return EmptyLoci
}
diff --git a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
index f7d82a34a3de4967a425a480c6355dea118ee598..9b9452a4191d579a07837137b34ccb22082261ae 100644
--- a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
@@ -102,12 +102,13 @@ function markLink(loci: Loci, group: Unit.SymmetryGroup, apply: (interval: Inter
let changed = false
if (Unit.isAtomic(unit) && Link.isLoci(loci)) {
+ const groupCount = unit.links.edgeCount * 2
for (const b of loci.links) {
const unitIdx = group.unitIndexMap.get(b.aUnit.id)
if (unitIdx !== undefined) {
const idx = unit.links.getDirectedEdgeIndex(b.aIndex, b.bIndex)
if (idx !== -1) {
- if (apply(Interval.ofSingleton(idx))) changed = true
+ if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
}
}
}
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 8591ca379aca4372f51ec30ea854281c09c2a039..8b5d893ef85dc1b6ae8b18ea8a651c3427e8872d 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -9,7 +9,6 @@ import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
import { MeshBuilder } from '../../../mesh/mesh-builder';
-import { getElementLoci, markElement } from './util/element';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Segmentation } from 'mol-data/int';
import { MoleculeType, isNucleic, isPurinBase, isPyrimidineBase } from 'mol-model/structure/model/types';
@@ -17,7 +16,7 @@ import { getElementIndexForAtomId, getElementIndexForAtomRole } from 'mol-model/
import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
import { addCylinder } from '../../../mesh/builder/cylinder';
import { Box } from '../../../primitive/box';
-import { NucleotideLocationIterator } from './util/nucleotide';
+import { NucleotideLocationIterator, markNucleotideElement, getNucleotideElementLoci } from './util/nucleotide';
const p1 = Vec3.zero()
const p2 = Vec3.zero()
@@ -121,8 +120,8 @@ export function NucleotideBlockVisual(): UnitsVisual<NucleotideBlockProps> {
defaultProps: DefaultNucleotideBlockProps,
createMesh: createNucleotideBlockMesh,
createLocationIterator: NucleotideLocationIterator.fromGroup,
- getLoci: getElementLoci,
- mark: markElement,
+ getLoci: getNucleotideElementLoci,
+ mark: markNucleotideElement,
setUpdateState: () => {}
})
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
index dd277116de925dbc3d0d210626d797167e536e9d..d975ae940228601a3fd1a833979d28dc2c0dc96e 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -47,11 +47,11 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
pos(centerB.element, pB)
cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(centerA)
- builder.setGroup(OrderedSet.findPredecessorIndex(elements, centerA.element))
+ builder.setGroup(OrderedSet.indexOf(elements, centerA.element))
addCylinder(builder, pA, pB, 0.5, cylinderProps)
cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(centerB)
- builder.setGroup(OrderedSet.findPredecessorIndex(elements, centerB.element))
+ builder.setGroup(OrderedSet.indexOf(elements, centerB.element))
addCylinder(builder, pB, pA, 0.5, cylinderProps)
if (i % 10000 === 0 && ctx.shouldUpdate) {
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 e5a319c08e9e83a8c760145664228697696cc6bf..24038dfc3182746c74d2ae0336a5556ff00cfcde 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 +9,7 @@ import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
import { MeshBuilder } from '../../../mesh/mesh-builder';
-import { PolymerGapIterator, PolymerGapLocationIterator } from './util/polymer';
-import { getElementLoci, markElement } from './util/element';
+import { PolymerGapIterator, PolymerGapLocationIterator, markPolymerGapElement, getPolymerGapElementLoci } from './util/polymer';
import { Vec3 } from 'mol-math/linear-algebra';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
@@ -83,8 +82,8 @@ export function PolymerGapVisual(): UnitsVisual<PolymerGapProps> {
defaultProps: DefaultPolymerGapProps,
createMesh: createPolymerGapCylinderMesh,
createLocationIterator: PolymerGapLocationIterator.fromGroup,
- getLoci: getElementLoci,
- mark: markElement,
+ getLoci: getPolymerGapElementLoci,
+ mark: markPolymerGapElement,
setUpdateState: (state: MeshUpdateState, newProps: PolymerGapProps, currentProps: PolymerGapProps) => {
state.createMesh = newProps.radialSegments !== currentProps.radialSegments
}
diff --git a/src/mol-geo/representation/structure/visual/util/nucleotide.ts b/src/mol-geo/representation/structure/visual/util/nucleotide.ts
index 2243e8a6bb32f1719b5f68f16b268c18bae6d49b..ab334d1d0d156d8043f129a9a20999fd14349192 100644
--- a/src/mol-geo/representation/structure/visual/util/nucleotide.ts
+++ b/src/mol-geo/representation/structure/visual/util/nucleotide.ts
@@ -3,40 +3,18 @@
*
* @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
-}
+import { Unit, StructureElement } from 'mol-model/structure';
+import { LocationIterator } from '../../../../util/location-iterator';
+import { getNucleotideElements } from 'mol-model/structure/structure/util/nucleotide';
+import { PickingId } from '../../../../util/picking';
+import { Loci, EmptyLoci } from 'mol-model/loci';
+import { OrderedSet, Interval } from 'mol-data/int';
export namespace NucleotideLocationIterator {
export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
- const nucleotideElementIndices = getNucleotideElementIndices(group.units[0])
+ const u = group.units[0]
+ const nucleotideElementIndices = Unit.isAtomic(u) ? getNucleotideElements(u) : []
const groupCount = nucleotideElementIndices.length
const instanceCount = group.units.length
const location = StructureElement.create()
@@ -48,4 +26,47 @@ export namespace NucleotideLocationIterator {
}
return LocationIterator(groupCount, instanceCount, getLocation)
}
+}
+
+export function getNucleotideElementLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number) {
+ const { objectId, instanceId, groupId } = pickingId
+ if (id === objectId) {
+ const unit = group.units[instanceId]
+ if (Unit.isAtomic(unit)) {
+ const unitIndex = OrderedSet.indexOf(unit.elements, unit.nucleotideElements[groupId]) as StructureElement.UnitIndex
+ if (unitIndex !== -1) {
+ const indices = OrderedSet.ofSingleton(unitIndex)
+ return StructureElement.Loci([{ unit, indices }])
+ }
+ }
+ }
+ return EmptyLoci
+}
+
+export function markNucleotideElement(loci: Loci, group: Unit.SymmetryGroup, apply: (interval: Interval) => boolean) {
+ let changed = false
+ const u = group.units[0]
+ if (StructureElement.isLoci(loci) && Unit.isAtomic(u)) {
+ const groupCount = u.nucleotideElements.length
+ for (const e of loci.elements) {
+ const unitIdx = group.unitIndexMap.get(e.unit.id)
+ if (unitIdx !== undefined && Unit.isAtomic(e.unit)) {
+ if (Interval.is(e.indices)) {
+ const min = unitIdx * groupCount + OrderedSet.indexOf(e.unit.nucleotideElements, e.unit.elements[Interval.min(e.indices)])
+ const max = unitIdx * groupCount + OrderedSet.indexOf(e.unit.nucleotideElements, e.unit.elements[Interval.max(e.indices)])
+ if (min !== -1 && max !== -1) {
+ if (apply(Interval.ofRange(unitIdx * groupCount + min, unitIdx * groupCount + max))) changed = true
+ }
+ } else {
+ for (let i = 0, _i = e.indices.length; i < _i; i++) {
+ const idx = OrderedSet.indexOf(e.unit.nucleotideElements, e.unit.elements[e.indices[i]])
+ if (idx !== -1) {
+ if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
+ }
+ }
+ }
+ }
+ }
+ }
+ return changed
}
\ 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 41458be2e366e10e957d6bc7af871694b9806f09..8586b9e50ad5188b6ab1d7a0b37e3d70944a112d 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, ElementIndex, StructureElement } from 'mol-model/structure';
+import { Unit, ElementIndex, StructureElement, Link } from 'mol-model/structure';
import SortedRanges from 'mol-data/int/sorted-ranges';
import { LocationIterator } from '../../../../util/location-iterator';
import { PickingId } from '../../../../util/picking';
@@ -68,9 +68,11 @@ export function getPolymerElementLoci(pickingId: PickingId, group: Unit.Symmetry
const { objectId, instanceId, groupId } = pickingId
if (id === objectId) {
const unit = group.units[instanceId]
- const unitIndex = OrderedSet.findPredecessorIndex(unit.elements, unit.polymerElements[groupId]) as StructureElement.UnitIndex
- const indices = OrderedSet.ofSingleton(unitIndex);
- return StructureElement.Loci([{ unit, indices }])
+ const unitIndex = OrderedSet.indexOf(unit.elements, unit.polymerElements[groupId]) as StructureElement.UnitIndex
+ if (unitIndex !== -1) {
+ const indices = OrderedSet.ofSingleton(unitIndex)
+ return StructureElement.Loci([{ unit, indices }])
+ }
}
return EmptyLoci
}
@@ -84,17 +86,52 @@ export function markPolymerElement(loci: Loci, group: Unit.SymmetryGroup, apply:
const unitIdx = group.unitIndexMap.get(e.unit.id)
if (unitIdx !== undefined) {
if (Interval.is(e.indices)) {
- const start = unitIdx * groupCount + OrderedSet.findPredecessorIndex(e.unit.polymerElements, e.unit.elements[Interval.start(e.indices)])
- const end = unitIdx * groupCount + OrderedSet.findPredecessorIndex(e.unit.polymerElements, e.unit.elements[Interval.end(e.indices)])
- if (apply(Interval.ofBounds(start, end))) changed = true
+ const min = + OrderedSet.indexOf(e.unit.polymerElements, e.unit.elements[Interval.min(e.indices)])
+ const max = OrderedSet.indexOf(e.unit.polymerElements, e.unit.elements[Interval.max(e.indices)])
+ if (min !== -1 && max !== -1) {
+ if (apply(Interval.ofRange(unitIdx * groupCount + min, unitIdx * groupCount + max))) changed = true
+ }
} else {
for (let i = 0, _i = e.indices.length; i < _i; i++) {
- const idx = unitIdx * groupCount + OrderedSet.findPredecessorIndex(e.unit.polymerElements, e.unit.elements[e.indices[i]])
- if (apply(Interval.ofSingleton(idx))) changed = true
+ const idx = OrderedSet.indexOf(e.unit.polymerElements, e.unit.elements[e.indices[i]])
+ if (idx !== -1) {
+ if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
+ }
}
}
}
}
}
return changed
+}
+
+export function getPolymerGapElementLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number) {
+ const { objectId, instanceId, groupId } = pickingId
+ if (id === objectId) {
+ const unit = group.units[instanceId]
+ const unitIndexA = OrderedSet.indexOf(unit.elements, unit.gapElements[groupId]) as StructureElement.UnitIndex
+ const unitIndexB = OrderedSet.indexOf(unit.elements, unit.gapElements[groupId % 2 ? groupId - 1 : groupId + 1]) as StructureElement.UnitIndex
+ if (unitIndexA !== -1 && unitIndexB !== -1) {
+ return Link.Loci([ Link.Location(unit, unitIndexA, unit, unitIndexB) ])
+ }
+ }
+ return EmptyLoci
+}
+
+export function markPolymerGapElement(loci: Loci, group: Unit.SymmetryGroup, apply: (interval: Interval) => boolean) {
+ let changed = false
+ if (Link.isLoci(loci)) {
+ const groupCount = group.units[0].gapElements.length
+ for (const b of loci.links) {
+ const unitIdx = group.unitIndexMap.get(b.aUnit.id)
+ if (unitIdx !== undefined) {
+ const idxA = OrderedSet.indexOf(b.aUnit.gapElements, b.aUnit.elements[b.aIndex])
+ const idxB = OrderedSet.indexOf(b.bUnit.gapElements, b.bUnit.elements[b.bIndex])
+ if (idxA !== -1 && idxB !== -1) {
+ if (apply(Interval.ofSingleton(unitIdx * groupCount + idxA))) changed = true
+ }
+ }
+ }
+ }
+ return changed
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 3cd9ed382ce7a881dc88d94ed80fd3678855d5dd..4092d9d3cbb5521fe300c6c8cf45e35e9f845c0b 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -17,6 +17,7 @@ import { ChainIndex, ResidueIndex, ElementIndex } from '../model/indexing';
import { IntMap, SortedArray } from 'mol-data/int';
import { hash2 } from 'mol-data/util';
import { getAtomicPolymerElements, getCoarsePolymerElements, getAtomicGapElements, getCoarseGapElements } from './util/polymer';
+import { getNucleotideElements } from './util/nucleotide';
// A building block of a structure that corresponds to an atomic or a coarse grained representation
// 'conveniently grouped together'.
@@ -169,6 +170,12 @@ namespace Unit {
return this.props.gapElements.ref;
}
+ get nucleotideElements() {
+ if (this.props.nucleotideElements.ref) return this.props.nucleotideElements.ref;
+ this.props.nucleotideElements.ref = getNucleotideElements(this);
+ return this.props.nucleotideElements.ref;
+ }
+
getResidueIndex(elementIndex: StructureElement.UnitIndex) {
return this.model.atomicHierarchy.residueAtomSegments.index[this.elements[elementIndex]];
}
@@ -192,6 +199,7 @@ namespace Unit {
rings: ValueRef<UnitRings | undefined>
polymerElements: ValueRef<SortedArray<ElementIndex> | undefined>
gapElements: ValueRef<SortedArray<ElementIndex> | undefined>
+ nucleotideElements: ValueRef<SortedArray<ElementIndex> | undefined>
}
function AtomicProperties(): AtomicProperties {
@@ -201,6 +209,7 @@ namespace Unit {
rings: ValueRef.create(void 0),
polymerElements: ValueRef.create(void 0),
gapElements: ValueRef.create(void 0),
+ nucleotideElements: ValueRef.create(void 0),
};
}
diff --git a/src/mol-model/structure/structure/util/nucleotide.ts b/src/mol-model/structure/structure/util/nucleotide.ts
new file mode 100644
index 0000000000000000000000000000000000000000..8dbb668b74a5330781041f33c30c7d3d23713351
--- /dev/null
+++ b/src/mol-model/structure/structure/util/nucleotide.ts
@@ -0,0 +1,35 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Unit, ElementIndex } from 'mol-model/structure';
+import { Segmentation, SortedArray } from 'mol-data/int';
+import { isNucleic, MoleculeType } from 'mol-model/structure/model/types';
+import { getElementIndexForAtomRole } from 'mol-model/structure/util';
+
+export function getNucleotideElements(unit: Unit.Atomic) {
+ 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 SortedArray.ofSortedArray<ElementIndex>(indices)
+}
\ No newline at end of file