diff --git a/src/mol-model/structure/model/properties/utils/atomic-derived.ts b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
index 255c144473aeaa52d149d5d973bc25905b99f018..8c1a1bb429545a4bf29672b96a49615f286c2e30 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-derived.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
@@ -21,7 +21,7 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
const moleculeTypeMap = new Map<string, MoleculeType>()
- for (let i = 0; i < n; ++i) {
+ for (let i = 0 as ResidueIndex; i < n; ++i) {
const compId = label_comp_id.value(i)
const chemCompMap = chemicalComponentMap
let molType: MoleculeType
@@ -39,18 +39,18 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
moleculeType[i] = molType
const traceAtomId = getAtomIdForAtomRole(molType, 'trace')
- let traceIndex = index.findAtomsOnResidue(i as ResidueIndex, traceAtomId)
+ let traceIndex = index.findAtomsOnResidue(i, traceAtomId)
if (traceIndex === -1) {
const coarseAtomId = getAtomIdForAtomRole(molType, 'coarseBackbone')
- traceIndex = index.findAtomsOnResidue(i as ResidueIndex, coarseAtomId)
+ traceIndex = index.findAtomsOnResidue(i, coarseAtomId)
}
traceElementIndex[i] = traceIndex
const directionFromAtomId = getAtomIdForAtomRole(molType, 'directionFrom')
- directionFromElementIndex[i] = index.findAtomsOnResidue(i as ResidueIndex, directionFromAtomId)
+ directionFromElementIndex[i] = index.findAtomsOnResidue(i, directionFromAtomId)
const directionToAtomId = getAtomIdForAtomRole(molType, 'directionTo')
- directionToElementIndex[i] = index.findAtomsOnResidue(i as ResidueIndex, directionToAtomId)
+ directionToElementIndex[i] = index.findAtomsOnResidue(i, directionToAtomId)
}
return {
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index d50179acd7784097e4e6d6d3d66d1b232df8c7a4..e36aba74fc910266f3aaf50d04a88f0b40b7b08c 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -143,8 +143,9 @@ namespace Unit {
readonly model: Model;
readonly conformation: SymmetryOperator.ArrayMapping<ElementIndex>;
- /** Reference some commonly accessed things for faster access. */
+ /** Reference `residueIndex` from `model` for faster access. */
readonly residueIndex: ArrayLike<ResidueIndex>;
+ /** Reference `chainIndex` from `model` for faster access. */
readonly chainIndex: ArrayLike<ChainIndex>;
private props: AtomicProperties;
diff --git a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
index c7b4b2d9c21b6c6282890d83e485a6051785ed7a..255001edbe5f4f32d766b2506c72e33d317e7fa5 100644
--- a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-block-mesh.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>
*/
@@ -62,7 +62,7 @@ function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structure: St
const chainIt = Segmentation.transientSegments(chainAtomSegments, elements)
const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
- const cylinderProps: CylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments }
+ const cylinderProps: CylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments, bottomCap: true }
let i = 0
while (chainIt.hasNext) {
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index d7a5e39e5750156b45080691c9694589161be0c9..4f47a53f97e5ee7c70d5d144980b617780e455db 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -10,7 +10,7 @@ import { Unit, Structure } from '../../../mol-model/structure';
import { Theme } from '../../../mol-theme/theme';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
-import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment, interpolateSizes, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement } from './util/polymer';
+import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment, interpolateSizes, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement, HelixTension, NucleicShift, StandardShift, StandardTension, OverhangFactor } from './util/polymer';
import { isNucleic, SecondaryStructureType } from '../../../mol-model/structure/model/types';
import { addSheet } from '../../../mol-geo/geometry/mesh/builder/sheet';
import { addTube } from '../../../mol-geo/geometry/mesh/builder/tube';
@@ -18,9 +18,12 @@ import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '.
import { VisualUpdateState } from '../../util';
import { ComputedSecondaryStructure } from '../../../mol-model-props/computed/secondary-structure';
import { addRibbon } from '../../../mol-geo/geometry/mesh/builder/ribbon';
+import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
+import { Vec3 } from '../../../mol-math/linear-algebra';
export const PolymerTraceMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
+ detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }),
aspectRatio: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }),
@@ -29,13 +32,13 @@ export const PolymerTraceMeshParams = {
export const DefaultPolymerTraceMeshProps = PD.getDefaultValues(PolymerTraceMeshParams)
export type PolymerTraceMeshProps = typeof DefaultPolymerTraceMeshProps
-// TODO handle polymer ends properly
+const tmpV1 = Vec3()
function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerTraceMeshProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
- const { sizeFactor, linearSegments, radialSegments, aspectRatio, arrowFactor } = props
+ const { sizeFactor, detail, linearSegments, radialSegments, aspectRatio, arrowFactor } = props
const vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh)
@@ -53,8 +56,8 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
const isNucleicType = isNucleic(v.moleculeType)
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
const isHelix = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Helix)
- const tension = isHelix ? 0.9 : 0.5
- const shift = isNucleicType ? 0.3 : 0.5
+ const tension = isHelix ? HelixTension : StandardTension
+ const shift = isNucleicType ? NucleicShift : StandardShift
interpolateCurveSegment(state, v, tension, shift)
@@ -70,7 +73,28 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
const startCap = v.secStrucFirst || v.coarseBackboneFirst || v.first
const endCap = v.secStrucLast || v.coarseBackboneLast || v.last
- if (isSheet) {
+ let segmentCount = linearSegments
+ if (v.initial) {
+ segmentCount = Math.max(Math.round(linearSegments * shift), 1)
+ const offset = linearSegments - segmentCount
+ curvePoints.copyWithin(0, offset * 3)
+ binormalVectors.copyWithin(0, offset * 3)
+ normalVectors.copyWithin(0, offset * 3)
+ Vec3.fromArray(tmpV1, curvePoints, 3)
+ Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1))
+ Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * OverhangFactor)
+ Vec3.toArray(tmpV1, curvePoints, 0)
+ } else if (v.final) {
+ segmentCount = Math.max(Math.round(linearSegments * (1 - shift)), 1)
+ Vec3.fromArray(tmpV1, curvePoints, segmentCount * 3 - 3)
+ Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1))
+ Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * OverhangFactor)
+ Vec3.toArray(tmpV1, curvePoints, segmentCount * 3)
+ }
+
+ if (v.initial === true && v.final === true) {
+ addSphere(builderState, v.p2, w1 * 2, detail)
+ } else if (isSheet) {
const h0 = w0 * aspectRatio
const h1 = w1 * aspectRatio
const h2 = w2 * aspectRatio
@@ -79,9 +103,9 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
interpolateSizes(state, w0, w1, w2, h0, h1, h2, shift)
if (radialSegments === 2) {
- addRibbon(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, widthValues, heightValues, arrowHeight)
+ addRibbon(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, arrowHeight)
} else {
- addSheet(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, widthValues, heightValues, arrowHeight, startCap, endCap)
+ addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, arrowHeight, startCap, endCap)
}
} else {
let h0: number, h1: number, h2: number
@@ -108,14 +132,14 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
if (isNucleicType && !v.isCoarseBackbone) {
// TODO find a cleaner way to swap normal and binormal for nucleic types
for (let i = 0, il = binormalVectors.length; i < il; i++) binormalVectors[i] *= -1
- addRibbon(builderState, curvePoints, binormalVectors, normalVectors, linearSegments, heightValues, widthValues, 0)
+ addRibbon(builderState, curvePoints, binormalVectors, normalVectors, segmentCount, heightValues, widthValues, 0)
} else {
- addRibbon(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, widthValues, heightValues, 0)
+ addRibbon(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0)
}
} else if (radialSegments === 4) {
- addSheet(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, widthValues, heightValues, 0, startCap, endCap)
+ addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap)
} else {
- addTube(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, 1, startCap, endCap)
+ addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, 1, startCap, endCap)
}
}
@@ -141,6 +165,7 @@ export function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTrace
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTraceParams>, currentProps: PD.Values<PolymerTraceParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
+ newProps.detail !== currentProps.detail ||
newProps.linearSegments !== currentProps.linearSegments ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.aspectRatio !== currentProps.aspectRatio ||
diff --git a/src/mol-repr/structure/visual/polymer-tube-mesh.ts b/src/mol-repr/structure/visual/polymer-tube-mesh.ts
index c015f2053cbf19dd1e914debe75e95909d5eee86..09e337366801f949b4732d77cbc953ba481d3fb6 100644
--- a/src/mol-repr/structure/visual/polymer-tube-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-tube-mesh.ts
@@ -10,29 +10,32 @@ import { Unit, Structure } from '../../../mol-model/structure';
import { Theme } from '../../../mol-theme/theme';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
-import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment, interpolateSizes, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement } from './util/polymer';
-import { isNucleic } from '../../../mol-model/structure/model/types';
+import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment, interpolateSizes, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement, HelixTension, StandardTension, StandardShift, NucleicShift, OverhangFactor } from './util/polymer';
+import { isNucleic, SecondaryStructureType } from '../../../mol-model/structure/model/types';
import { addTube } from '../../../mol-geo/geometry/mesh/builder/tube';
import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
import { VisualUpdateState } from '../../util';
import { addSheet } from '../../../mol-geo/geometry/mesh/builder/sheet';
import { addRibbon } from '../../../mol-geo/geometry/mesh/builder/ribbon';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
export const PolymerTubeMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
+ detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }),
}
export const DefaultPolymerTubeMeshProps = PD.getDefaultValues(PolymerTubeMeshParams)
export type PolymerTubeMeshProps = typeof DefaultPolymerTubeMeshProps
-// TODO handle polymer ends properly
+const tmpV1 = Vec3()
function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerTubeMeshProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
- const { sizeFactor, linearSegments, radialSegments } = props
+ const { sizeFactor, detail, linearSegments, radialSegments } = props
const vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh)
@@ -47,8 +50,9 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct
builderState.currentGroup = i
const isNucleicType = isNucleic(v.moleculeType)
- const tension = isNucleicType ? 0.5 : 0.9
- const shift = isNucleicType ? 0.3 : 0.5
+ const isHelix = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Helix)
+ const tension = isHelix ? HelixTension : StandardTension
+ const shift = isNucleicType ? NucleicShift : StandardShift
interpolateCurveSegment(state, v, tension, shift)
@@ -61,12 +65,35 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct
interpolateSizes(state, s0, s1, s2, s0, s1, s2, shift)
- if (radialSegments === 2) {
- addRibbon(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, widthValues, heightValues, 0)
+ let segmentCount = linearSegments
+ if (v.initial) {
+ segmentCount = Math.max(Math.round(linearSegments * shift), 1)
+ const offset = linearSegments - segmentCount
+ curvePoints.copyWithin(0, offset * 3)
+ binormalVectors.copyWithin(0, offset * 3)
+ normalVectors.copyWithin(0, offset * 3)
+ widthValues.copyWithin(0, offset * 3)
+ heightValues.copyWithin(0, offset * 3)
+ Vec3.fromArray(tmpV1, curvePoints, 3)
+ Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1))
+ Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, s1 * OverhangFactor)
+ Vec3.toArray(tmpV1, curvePoints, 0)
+ } else if (v.final) {
+ segmentCount = Math.max(Math.round(linearSegments * (1 - shift)), 1)
+ Vec3.fromArray(tmpV1, curvePoints, segmentCount * 3 - 3)
+ Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1))
+ Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, s1 * OverhangFactor)
+ Vec3.toArray(tmpV1, curvePoints, segmentCount * 3)
+ }
+
+ if (v.initial === true && v.final === true) {
+ addSphere(builderState, v.p2, s1 * 2, detail)
+ } else if (radialSegments === 2) {
+ addRibbon(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0)
} else if (radialSegments === 4) {
- addSheet(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, widthValues, heightValues, 0, startCap, endCap)
+ addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap)
} else {
- addTube(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, 1, startCap, endCap)
+ addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, 1, startCap, endCap)
}
++i
@@ -91,6 +118,7 @@ export function PolymerTubeVisual(materialId: number): UnitsVisual<PolymerTubePa
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTubeParams>, currentProps: PD.Values<PolymerTubeParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
+ newProps.detail !== currentProps.detail ||
newProps.linearSegments !== currentProps.linearSegments ||
newProps.radialSegments !== currentProps.radialSegments
)
diff --git a/src/mol-repr/structure/visual/util/nucleotide.ts b/src/mol-repr/structure/visual/util/nucleotide.ts
index 7bc2400ddb4609887f8e4b789cd9216d0484dcec..32762da65a417d56d80136d5c42aaecc127cce33 100644
--- a/src/mol-repr/structure/visual/util/nucleotide.ts
+++ b/src/mol-repr/structure/visual/util/nucleotide.ts
@@ -35,7 +35,7 @@ export function getNucleotideElementLoci(pickingId: PickingId, structureGroup: S
const { structure, group } = structureGroup
const unit = group.units[instanceId]
if (Unit.isAtomic(unit)) {
- return getResidueLoci(structure, unit, unit.polymerElements[groupId])
+ return getResidueLoci(structure, unit, unit.nucleotideElements[groupId])
}
}
return EmptyLoci
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index 927bb2dc199f4a519265941ec3ad7fba6add65a8..5fac3e83b765cb38e0a351b4ebcb70c707ba4a14 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.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>
*/
@@ -18,6 +18,12 @@ export * from './polymer/gap-iterator'
export * from './polymer/trace-iterator'
export * from './polymer/curve-segment'
+export const StandardTension = 0.5
+export const HelixTension = 0.9
+export const StandardShift = 0.5
+export const NucleicShift = 0.3
+export const OverhangFactor = 2
+
export function getPolymerRanges(unit: Unit): SortedRanges<ElementIndex> {
switch (unit.kind) {
case Unit.Kind.Atomic: return unit.model.atomicHierarchy.polymerRanges
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 390b63bad83e32b208c315f3f3dbac1f80d1f96b..889c57ab7f373a439e97868d032c1c3f5ab6fa1c 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -34,6 +34,7 @@ interface PolymerTraceElement {
centerPrev: StructureElement.Location
centerNext: StructureElement.Location
first: boolean, last: boolean
+ initial: boolean, final: boolean
secStrucFirst: boolean, secStrucLast: boolean
secStrucType: SecondaryStructureType
moleculeType: MoleculeType
@@ -52,6 +53,7 @@ function createPolymerTraceElement (unit: Unit): PolymerTraceElement {
centerPrev: StructureElement.Location.create(unit),
centerNext: StructureElement.Location.create(unit),
first: false, last: false,
+ initial: false, final: false,
secStrucFirst: false, secStrucLast: false,
secStrucType: SecStrucTypeNA,
moleculeType: MoleculeType.unknown,
@@ -223,6 +225,9 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
const residueIndexNext2 = this.getResidueIndex(residueIndex + 2)
const residueIndexNext3 = this.getResidueIndex(residueIndex + 3)
+ value.initial = residueIndex === residueIndexPrev1
+ value.final = residueIndex === residueIndexNext1
+
value.centerPrev.element = this.traceElementIndex[residueIndexPrev1]
value.center.element = this.traceElementIndex[residueIndex]
value.centerNext.element = this.traceElementIndex[residueIndexNext1]