molstar
Version:
A comprehensive macromolecular library.
132 lines (131 loc) • 6.32 kB
JavaScript
/**
* Copyright (c) 2018-2023 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, Mat4 } from '../../../mol-math/linear-algebra';
import { Box } from '../../../mol-geo/primitive/box';
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 { addCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
import { UnitsMeshParams, UnitsMeshVisual } from '../units-visual';
import { NucleotideLocationIterator, getNucleotideElementLoci, eachNucleotideElement, getNucleotideBaseType, createNucleicIndices, setPurinIndices, setPyrimidineIndices } from './util/nucleotide';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
// TODO support blocks for multiple locations (including from microheterogeneity)
const p1 = Vec3();
const p2 = Vec3();
const p3 = Vec3();
const p4 = Vec3();
const p5 = Vec3();
const pt = Vec3();
const v12 = Vec3();
const v34 = Vec3();
const vC = Vec3();
const center = Vec3();
const t = Mat4.identity();
const sVec = Vec3();
const box = Box();
export const NucleotideBlockMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
thicknessFactor: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
};
export const DefaultNucleotideBlockMeshProps = PD.getDefaultValues(NucleotideBlockMeshParams);
function createNucleotideBlockMesh(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, thicknessFactor, radialSegments } = props;
const vertexCount = nucleotideElementCount * (box.vertices.length / 3 + radialSegments * 2);
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 4, 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;
const width = 4.5;
const depth = thicknessFactor * sizeFactor * 2;
const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments, bottomCap: true };
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();
let idx1 = -1, idx2 = -1, idx3 = -1, idx4 = -1, idx5 = -1;
let height = 4.5;
const { isPurine, isPyrimidine } = getNucleotideBaseType(unit, residueIndex);
if (isPurine) {
height = 4.5;
setPurinIndices(idx, unit, residueIndex);
idx1 = idx.N1;
idx2 = idx.C4;
idx3 = idx.C6;
idx4 = idx.C2;
idx5 = idx.N9;
}
else if (isPyrimidine) {
height = 3.0;
setPyrimidineIndices(idx, unit, residueIndex);
idx1 = idx.N3;
idx2 = idx.C6;
idx3 = idx.C4;
idx4 = idx.C2;
idx5 = idx.N1;
}
if (idx5 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx5, p5);
c.invariantPosition(idx.trace, pt);
builderState.currentGroup = i;
addCylinder(builderState, p5, pt, 1, cylinderProps);
if (idx1 !== -1 && idx2 !== -1 && idx3 !== -1 && idx4 !== -1) {
c.invariantPosition(idx1, p1);
c.invariantPosition(idx2, p2);
c.invariantPosition(idx3, p3);
c.invariantPosition(idx4, p4);
Vec3.normalize(v12, Vec3.sub(v12, p2, p1));
Vec3.normalize(v34, Vec3.sub(v34, p4, p3));
Vec3.normalize(vC, Vec3.cross(vC, v12, v34));
Mat4.targetTo(t, p1, p2, vC);
Vec3.scaleAndAdd(center, p1, v12, height / 2 - 0.2);
Mat4.scale(t, t, Vec3.set(sVec, width, depth, height));
Mat4.setTranslation(t, center);
MeshBuilder.addPrimitive(builderState, t, box);
}
}
++i;
}
}
}
const m = MeshBuilder.getMesh(builderState);
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, radius);
m.setBoundingSphere(sphere);
return m;
}
export const NucleotideBlockParams = {
...UnitsMeshParams,
...NucleotideBlockMeshParams
};
export function NucleotideBlockVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(NucleotideBlockParams),
createGeometry: createNucleotideBlockMesh,
createLocationIterator: NucleotideLocationIterator.fromGroup,
getLoci: getNucleotideElementLoci,
eachLocation: eachNucleotideElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.thicknessFactor !== currentProps.thicknessFactor ||
newProps.radialSegments !== currentProps.radialSegments);
}
}, materialId);
}