molstar
Version:
A comprehensive macromolecular library.
262 lines (261 loc) • 13.5 kB
JavaScript
/**
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Gianluca Tomasello <giagitom@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { Unit } from '../../../mol-model/structure';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { Segmentation } from '../../../mol-data/int';
import { isNucleic } from '../../../mol-model/structure/model/types';
import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
import { UnitsMeshParams, UnitsMeshVisual, UnitsSpheresParams, UnitsSpheresVisual } from '../units-visual';
import { NucleotideLocationIterator, getNucleotideElementLoci, eachNucleotideElement, getNucleotideBaseType, createNucleicIndices, setSugarIndices, hasSugarIndices, setPurinIndices, hasPurinIndices, setPyrimidineIndices, hasPyrimidineIndices } from './util/nucleotide';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
import { Spheres } from '../../../mol-geo/geometry/spheres/spheres';
import { sphereVertexCount } from '../../../mol-geo/primitive/sphere';
import { SpheresBuilder } from '../../../mol-geo/geometry/spheres/spheres-builder';
const pTrace = Vec3();
const pN1 = Vec3();
const pC2 = Vec3();
const pN3 = Vec3();
const pC4 = Vec3();
const pC5 = Vec3();
const pC6 = Vec3();
const pN7 = Vec3();
const pC8 = Vec3();
const pN9 = Vec3();
const pC1_1 = Vec3();
const pC2_1 = Vec3();
const pC3_1 = Vec3();
const pC4_1 = Vec3();
const pO4_1 = Vec3();
export const NucleotideAtomicElementParams = {
...UnitsMeshParams,
...UnitsSpheresParams,
sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
tryUseImpostor: PD.Boolean(true)
};
export function NucleotideAtomicElementVisual(materialId, structure, props, webgl) {
return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
? NucleotideAtomicElementImpostorVisual(materialId)
: NucleotideAtomicElementMeshVisual(materialId);
}
function createNucleotideAtomicElementImpostor(ctx, unit, structure, theme, props, spheres) {
if (!Unit.isAtomic(unit))
return Spheres.createEmpty(spheres);
const nucleotideElementCount = unit.nucleotideElements.length;
if (!nucleotideElementCount)
return Spheres.createEmpty(spheres);
const spheresCountEstimate = nucleotideElementCount * 15; // 15 is the average purine (17) & pirimidine (13) bonds
const builder = SpheresBuilder.create(spheresCountEstimate, spheresCountEstimate / 4, spheres);
const { elements, model, conformation: c } = unit;
const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy;
const { moleculeType } = model.atomicHierarchy.derived.residue;
const chainIt = Segmentation.transientSegments(chainAtomSegments, elements);
const residueIt = Segmentation.transientSegments(residueAtomSegments, elements);
let i = 0;
while (chainIt.hasNext) {
residueIt.setSegment(chainIt.move());
while (residueIt.hasNext) {
const { index: residueIndex } = residueIt.move();
if (isNucleic(moleculeType[residueIndex])) {
const idx = createNucleicIndices();
setSugarIndices(idx, unit, residueIndex);
if (hasSugarIndices(idx)) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.C2_1, pC2_1);
c.invariantPosition(idx.C3_1, pC3_1);
c.invariantPosition(idx.C4_1, pC4_1);
c.invariantPosition(idx.O4_1, pO4_1);
// trace cylinder
c.invariantPosition(idx.trace, pTrace);
builder.add(pTrace[0], pTrace[1], pTrace[2], i);
// sugar ring
builder.add(pC3_1[0], pC3_1[1], pC3_1[2], i);
builder.add(pC4_1[0], pC4_1[1], pC4_1[2], i);
builder.add(pO4_1[0], pO4_1[1], pO4_1[2], i);
builder.add(pC1_1[0], pC1_1[1], pC1_1[2], i);
builder.add(pC2_1[0], pC2_1[1], pC2_1[2], i);
}
const { isPurine, isPyrimidine } = getNucleotideBaseType(unit, residueIndex);
if (isPurine) {
setPurinIndices(idx, unit, residueIndex);
if (hasPurinIndices(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
c.invariantPosition(idx.N7, pN7);
c.invariantPosition(idx.C8, pC8);
c.invariantPosition(idx.N9, pN9);
// base ring
builder.add(pN9[0], pN9[1], pN9[2], i);
builder.add(pC8[0], pC8[1], pC8[2], i);
builder.add(pN7[0], pN7[1], pN7[2], i);
builder.add(pC5[0], pC5[1], pC5[2], i);
builder.add(pC6[0], pC6[1], pC6[2], i);
builder.add(pN1[0], pN1[1], pN1[2], i);
builder.add(pC2[0], pC2[1], pC2[2], i);
builder.add(pN3[0], pN3[1], pN3[2], i);
builder.add(pC4[0], pC4[1], pC4[2], i);
}
}
else if (isPyrimidine) {
setPyrimidineIndices(idx, unit, residueIndex);
if (hasPyrimidineIndices(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
// base ring
builder.add(pN1[0], pN1[1], pN1[2], i);
builder.add(pC6[0], pC6[1], pC6[2], i);
builder.add(pC5[0], pC5[1], pC5[2], i);
builder.add(pC4[0], pC4[1], pC4[2], i);
builder.add(pN3[0], pN3[1], pN3[2], i);
builder.add(pC2[0], pC2[1], pC2[2], i);
}
}
++i;
}
}
}
const s = builder.getSpheres();
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
s.setBoundingSphere(sphere);
return s;
}
export function NucleotideAtomicElementImpostorVisual(materialId) {
return UnitsSpheresVisual({
defaultProps: PD.getDefaultValues(NucleotideAtomicElementParams),
createGeometry: createNucleotideAtomicElementImpostor,
createLocationIterator: NucleotideLocationIterator.fromGroup,
getLoci: getNucleotideElementLoci,
eachLocation: eachNucleotideElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor);
},
mustRecreate: (structureGroup, props, webgl) => {
return !props.tryUseImpostor || !webgl;
}
}, materialId);
}
function createNucleotideAtomicElementMesh(ctx, unit, structure, theme, props, mesh) {
if (!Unit.isAtomic(unit))
return Mesh.createEmpty(mesh);
const nucleotideElementCount = unit.nucleotideElements.length;
if (!nucleotideElementCount)
return Mesh.createEmpty(mesh);
const { sizeFactor, detail } = props;
const vertexCount = nucleotideElementCount * sphereVertexCount(detail);
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
const { elements, model, conformation: c } = unit;
const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy;
const { moleculeType } = model.atomicHierarchy.derived.residue;
const chainIt = Segmentation.transientSegments(chainAtomSegments, elements);
const residueIt = Segmentation.transientSegments(residueAtomSegments, elements);
const radius = 1 * sizeFactor;
let i = 0;
while (chainIt.hasNext) {
residueIt.setSegment(chainIt.move());
while (residueIt.hasNext) {
const { index: residueIndex } = residueIt.move();
if (isNucleic(moleculeType[residueIndex])) {
const idx = createNucleicIndices();
builderState.currentGroup = i;
setSugarIndices(idx, unit, residueIndex);
if (hasSugarIndices(idx)) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.C2_1, pC2_1);
c.invariantPosition(idx.C3_1, pC3_1);
c.invariantPosition(idx.C4_1, pC4_1);
c.invariantPosition(idx.O4_1, pO4_1);
// trace cylinder
c.invariantPosition(idx.trace, pTrace);
addSphere(builderState, pTrace, radius, detail);
// sugar ring
addSphere(builderState, pC4_1, radius, detail);
addSphere(builderState, pO4_1, radius, detail);
addSphere(builderState, pC1_1, radius, detail);
addSphere(builderState, pC2_1, radius, detail);
addSphere(builderState, pC3_1, radius, detail);
}
const { isPurine, isPyrimidine } = getNucleotideBaseType(unit, residueIndex);
if (isPurine) {
setPurinIndices(idx, unit, residueIndex);
if (hasPurinIndices(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
c.invariantPosition(idx.N7, pN7);
c.invariantPosition(idx.C8, pC8);
c.invariantPosition(idx.N9, pN9);
// base ring
addSphere(builderState, pC8, radius, detail);
addSphere(builderState, pN7, radius, detail);
addSphere(builderState, pC5, radius, detail);
addSphere(builderState, pC6, radius, detail);
addSphere(builderState, pN1, radius, detail);
addSphere(builderState, pC2, radius, detail);
addSphere(builderState, pN3, radius, detail);
addSphere(builderState, pC4, radius, detail);
addSphere(builderState, pC5, radius, detail);
addSphere(builderState, pN9, radius, detail);
}
}
else if (isPyrimidine) {
setPyrimidineIndices(idx, unit, residueIndex);
if (hasPyrimidineIndices(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
// base ring
addSphere(builderState, pC6, radius, detail);
addSphere(builderState, pC5, radius, detail);
addSphere(builderState, pC4, radius, detail);
addSphere(builderState, pN3, radius, detail);
addSphere(builderState, pC2, radius, detail);
addSphere(builderState, pN1, radius, detail);
}
}
++i;
}
}
}
const m = MeshBuilder.getMesh(builderState);
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
return m;
}
export function NucleotideAtomicElementMeshVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(NucleotideAtomicElementParams),
createGeometry: createNucleotideAtomicElementMesh,
createLocationIterator: NucleotideLocationIterator.fromGroup,
getLoci: getNucleotideElementLoci,
eachLocation: eachNucleotideElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.detail !== currentProps.detail);
},
mustRecreate: (structureGroup, props, webgl) => {
return props.tryUseImpostor && !!webgl;
}
}, materialId);
}