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nucleotide-ring-mesh.ts 11.18 KiB
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { NumberArray } from '../../../mol-util/type-helpers';
import { VisualContext } from '../../visual';
import { Unit, Structure, ElementIndex } 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 { Segmentation } from '../../../mol-data/int';
import { CylinderProps } from '../../../mol-geo/primitive/cylinder';
import { isNucleic, isPurineBase, isPyrimidineBase } from '../../../mol-model/structure/model/types';
import { addCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
import { NucleotideLocationIterator, getNucleotideElementLoci, eachNucleotideElement } from './util/nucleotide';
import { VisualUpdateState } from '../../util';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
// TODO support rings for multiple locations (including from microheterogeneity)
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: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
};
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 { chainAtomSegments, residueAtomSegments, atoms, index: atomicIndex } = model.atomicHierarchy;
const { moleculeType, traceElementIndex } = model.atomicHierarchy.derived.residue;
const { label_comp_id } = atoms;
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])) {
const compId = label_comp_id.value(residueAtomSegments.offsets[residueIndex]);
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;
let isPurine = isPurineBase(compId);
let isPyrimidine = isPyrimidineBase(compId);
if (!isPurine && !isPyrimidine) {
// detect Purine or Pyrimidin based on geometry
const idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
const idxN9 = atomicIndex.findAtomOnResidue(residueIndex, 'N9');
if (idxC4 !== -1 && idxN9 !== -1 && Vec3.distance(pos(idxC4, pC4), pos(idxN9, pN9)) < 1.6) {
isPurine = true;
} else {
isPyrimidine = true;
}
}
if (isPurine) {
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');
if (idxC5 === -1) {
// modified ring, e.g. DP
idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'N5');
}
idxC6 = atomicIndex.findAtomOnResidue(residueIndex, 'C6');
idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'N7');
if (idxN7 === -1) {
// modified ring, e.g. DP
idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'C7');
}
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 (isPyrimidine) {
idxTrace = traceElementIndex[residueIndex];
idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1');
if (idxN1 === -1) {
// modified ring, e.g. DZ
idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'C1');
}
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;
}
}
}
const m = MeshBuilder.getMesh(builderState);
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
return m;
}
export const NucleotideRingParams = {
...UnitsMeshParams,
...NucleotideRingMeshParams
};
export type NucleotideRingParams = typeof NucleotideRingParams
export function NucleotideRingVisual(materialId: number): 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
);
}
}, materialId);
}