nucleotide ring visual

src/mol-repr/structure/representation/cartoon.ts

@@ -14,11 +14,13 @@ import { Representation, RepresentationParamsGetter, RepresentationContext } fro
 import { PolymerDirectionVisual, PolymerDirectionParams } from '../visual/polymer-direction-wedge';
 import { Structure, Unit } from 'mol-model/structure';
 import { ThemeRegistryContext } from 'mol-theme/theme';
+import { NucleotideRingParams, NucleotideRingVisual } from '../visual/nucleotide-ring-mesh';
 
 const CartoonVisuals = {
     'polymer-trace': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerTraceParams>) => UnitsRepresentation('Polymer trace mesh', ctx, getParams, PolymerTraceVisual),
     'polymer-gap': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerGapParams>) => UnitsRepresentation('Polymer gap cylinder', ctx, getParams, PolymerGapVisual),
     'nucleotide-block': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, NucleotideBlockParams>) => UnitsRepresentation('Nucleotide block mesh', ctx, getParams, NucleotideBlockVisual),
+    'nucleotide-ring': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, NucleotideRingParams>) => UnitsRepresentation('Nucleotide ring mesh', ctx, getParams, NucleotideRingVisual),
     'direction-wedge': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerDirectionParams>) => UnitsRepresentation('Polymer direction wedge', ctx, getParams, PolymerDirectionVisual)
 }
 type CartoonVisualName = keyof typeof CartoonVisuals
@@ -28,6 +30,7 @@ export const CartoonParams = {
     ...PolymerTraceParams,
     ...PolymerGapParams,
     ...NucleotideBlockParams,
+    ...NucleotideRingParams,
     ...PolymerDirectionParams,
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
     visuals: PD.MultiSelect<CartoonVisualName>(['polymer-trace', 'polymer-gap', 'nucleotide-block'], CartoonVisualOptions),

src/mol-repr/structure/visual/nucleotide-ring-mesh.ts

+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Unit, Structure, ElementIndex } from 'mol-model/structure';
+import { UnitsVisual } from '../representation';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { Segmentation } from 'mol-data/int';
+import { isNucleic, isPurinBase, isPyrimidineBase } from 'mol-model/structure/model/types';
+import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
+import { NucleotideLocationIterator, eachNucleotideElement, getNucleotideElementLoci } from './util/nucleotide';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { Mesh } from 'mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
+import { addCylinder } from 'mol-geo/geometry/mesh/builder/cylinder';
+import { VisualContext } from 'mol-repr/visual';
+import { Theme } from 'mol-theme/theme';
+import { VisualUpdateState } from 'mol-repr/util';
+import { CylinderProps } from 'mol-geo/primitive/cylinder';
+import { NumberArray } from 'mol-util/type-helpers';
+import { addSphere } from 'mol-geo/geometry/mesh/builder/sphere';
+
+const pTrace = Vec3.zero()
+const pN1 = Vec3.zero()
+const pC2 = Vec3.zero()
+const pN3 = Vec3.zero()
+const pC4 = Vec3.zero()
+const pC5 = Vec3.zero()
+const pC6 = Vec3.zero()
+const pN7 = Vec3.zero()
+const pC8 = Vec3.zero()
+const pN9 = Vec3.zero()
+const normal = Vec3.zero()
+
+export const NucleotideRingMeshParams = {
+    sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
+    radialSegments: PD.Numeric(16, { min: 3, max: 56, step: 1 }),
+    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+}
+export const DefaultNucleotideRingMeshProps = PD.getDefaultValues(NucleotideRingMeshParams)
+export type NucleotideRingProps = typeof DefaultNucleotideRingMeshProps
+
+const positionsRing5_6 = new Float32Array(2 * 9 * 3)
+const stripIndicesRing5_6 = new Uint32Array([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 14, 15, 12, 13, 8, 9, 10, 11, 0, 1])
+const fanIndicesTopRing5_6 = new Uint32Array([8, 12, 14, 16, 6, 4, 2, 0, 10])
+const fanIndicesBottomRing5_6 = new Uint32Array([9, 11, 1, 3, 5, 7, 17, 15, 13])
+
+const positionsRing6 = new Float32Array(2 * 6 * 3)
+const stripIndicesRing6 = new Uint32Array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 1])
+const fanIndicesTopRing6 = new Uint32Array([0, 10, 8, 6, 4, 2])
+const fanIndicesBottomRing6 = new Uint32Array([1, 3, 5, 7, 9, 11])
+
+const tmpShiftV = Vec3.zero()
+function shiftPositions(out: NumberArray, dir: Vec3, ...positions: Vec3[]) {
+    for (let i = 0, il = positions.length; i < il; ++i) {
+        const v = positions[i]
+        Vec3.toArray(Vec3.add(tmpShiftV, v, dir), out, (i * 2) * 3)
+        Vec3.toArray(Vec3.sub(tmpShiftV, v, dir), out, (i * 2 + 1) * 3)
+    }
+}
+
+function createNucleotideRingMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: NucleotideRingProps, mesh?: Mesh) {
+    if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
+
+    const nucleotideElementCount = unit.nucleotideElements.length
+    if (!nucleotideElementCount) return Mesh.createEmpty(mesh)
+
+    const { sizeFactor, radialSegments, detail } = props
+
+    const vertexCount = nucleotideElementCount * (26 + radialSegments * 2)
+    const builderState = MeshBuilder.createState(vertexCount, vertexCount / 4, mesh)
+
+    const { elements, model } = unit
+    const { modifiedResidues } = model.properties
+    const { chainAtomSegments, residueAtomSegments, residues, index: atomicIndex } = model.atomicHierarchy
+    const { moleculeType, traceElementIndex } = model.atomicHierarchy.derived.residue
+    const { label_comp_id } = residues
+    const pos = unit.conformation.invariantPosition
+
+    const chainIt = Segmentation.transientSegments(chainAtomSegments, elements)
+    const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
+
+    const radius = 1 * sizeFactor
+    const halfThickness = 1.25 * sizeFactor
+    const cylinderProps: CylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments }
+
+    let i = 0
+    while (chainIt.hasNext) {
+        residueIt.setSegment(chainIt.move());
+
+        while (residueIt.hasNext) {
+            const { index: residueIndex } = residueIt.move();
+
+            if (isNucleic(moleculeType[residueIndex])) {
+                let compId = label_comp_id.value(residueIndex)
+                const parentId = modifiedResidues.parentId.get(compId)
+                if (parentId !== undefined) compId = parentId
+
+                let idxTrace: ElementIndex | -1 = -1, idxN1: ElementIndex | -1 = -1, idxC2: ElementIndex | -1 = -1, idxN3: ElementIndex | -1 = -1, idxC4: ElementIndex | -1 = -1, idxC5: ElementIndex | -1 = -1, idxC6: ElementIndex | -1 = -1, idxN7: ElementIndex | -1 = -1, idxC8: ElementIndex | -1 = -1, idxN9: ElementIndex | -1 = -1
+
+                builderState.currentGroup = i
+
+                if (isPurinBase(compId)) {
+                    idxTrace = traceElementIndex[residueIndex]
+                    idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1')
+                    idxC2 = atomicIndex.findAtomOnResidue(residueIndex, 'C2')
+                    idxN3 = atomicIndex.findAtomOnResidue(residueIndex, 'N3')
+                    idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4')
+                    idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'C5')
+                    idxC6 = atomicIndex.findAtomOnResidue(residueIndex, 'C6')
+                    idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'N7')
+                    idxC8 = atomicIndex.findAtomOnResidue(residueIndex, 'C8')
+                    idxN9 = atomicIndex.findAtomOnResidue(residueIndex, 'N9')
+
+                    if (idxN9 !== -1 && idxTrace !== -1) {
+                        pos(idxN9, pN9); pos(idxTrace, pTrace)
+                        builderState.currentGroup = i
+                        addCylinder(builderState, pN9, pTrace, 1, cylinderProps)
+                        addSphere(builderState, pN9, radius, detail)
+                    }
+
+                    if (idxN1 !== -1 && idxC2 !== -1 && idxN3 !== -1 && idxC4 !== -1 && idxC5 !== -1 && idxC6 !== -1 && idxN7 !== -1 && idxC8 !== -1 && idxN9 !== -1 ) {
+                        pos(idxN1, pN1); pos(idxC2, pC2); pos(idxN3, pN3); pos(idxC4, pC4); pos(idxC5, pC5); pos(idxC6, pC6); pos(idxN7, pN7); pos(idxC8, pC8)
+
+                        Vec3.triangleNormal(normal, pN1, pC4, pC5)
+                        Vec3.scale(normal, normal, halfThickness)
+                        shiftPositions(positionsRing5_6, normal, pN1, pC2, pN3, pC4, pC5, pC6, pN7, pC8, pN9)
+
+                        MeshBuilder.addTriangleStrip(builderState, positionsRing5_6, stripIndicesRing5_6)
+                        MeshBuilder.addTriangleFan(builderState, positionsRing5_6, fanIndicesTopRing5_6)
+                        MeshBuilder.addTriangleFan(builderState, positionsRing5_6, fanIndicesBottomRing5_6)
+                    }
+                } else if (isPyrimidineBase(compId)) {
+                    idxTrace = traceElementIndex[residueIndex]
+                    idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1')
+                    idxC2 = atomicIndex.findAtomOnResidue(residueIndex, 'C2')
+                    idxN3 = atomicIndex.findAtomOnResidue(residueIndex, 'N3')
+                    idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4')
+                    idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'C5')
+                    idxC6 = atomicIndex.findAtomOnResidue(residueIndex, 'C6')
+
+                    if (idxN1 !== -1 && idxTrace !== -1) {
+                        pos(idxN1, pN1); pos(idxTrace, pTrace)
+                        builderState.currentGroup = i
+                        addCylinder(builderState, pN1, pTrace, 1, cylinderProps)
+                        addSphere(builderState, pN1, radius, detail)
+                    }
+
+                    if (idxN1 !== -1 && idxC2 !== -1 && idxN3 !== -1 && idxC4 !== -1 && idxC5 !== -1 && idxC6 !== -1) {
+                        pos(idxC2, pC2); pos(idxN3, pN3); pos(idxC4, pC4); pos(idxC5, pC5); pos(idxC6, pC6);
+
+                        Vec3.triangleNormal(normal, pN1, pC4, pC5)
+                        Vec3.scale(normal, normal, halfThickness)
+                        shiftPositions(positionsRing6, normal, pN1, pC2, pN3, pC4, pC5, pC6)
+
+                        MeshBuilder.addTriangleStrip(builderState, positionsRing6, stripIndicesRing6)
+                        MeshBuilder.addTriangleFan(builderState, positionsRing6, fanIndicesTopRing6)
+                        MeshBuilder.addTriangleFan(builderState, positionsRing6, fanIndicesBottomRing6)
+                    }
+                }
+
+                ++i
+            }
+        }
+    }
+
+    return MeshBuilder.getMesh(builderState)
+}
+
+export const NucleotideRingParams = {
+    ...UnitsMeshParams,
+    ...NucleotideRingMeshParams
+}
+export type NucleotideRingParams = typeof NucleotideRingParams
+
+export function NucleotideRingVisual(): UnitsVisual<NucleotideRingParams> {
+    return UnitsMeshVisual<NucleotideRingParams>({
+        defaultProps: PD.getDefaultValues(NucleotideRingParams),
+        createGeometry: createNucleotideRingMesh,
+        createLocationIterator: NucleotideLocationIterator.fromGroup,
+        getLoci: getNucleotideElementLoci,
+        eachLocation: eachNucleotideElement,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<NucleotideRingParams>, currentProps: PD.Values<NucleotideRingParams>) => {
+            state.createGeometry = (
+                newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.radialSegments !== currentProps.radialSegments
+            )
+        }
+    })
+}
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