molstar
Version:
A comprehensive macromolecular library.
144 lines (143 loc) • 7.65 kB
JavaScript
/**
* Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __assign } from "tslib";
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, isPurineBase, isPyrimidineBase } 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 } 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)
var p1 = Vec3();
var p2 = Vec3();
var p3 = Vec3();
var p4 = Vec3();
var p5 = Vec3();
var p6 = Vec3();
var v12 = Vec3();
var v34 = Vec3();
var vC = Vec3();
var center = Vec3();
var t = Mat4.identity();
var sVec = Vec3();
var box = Box();
export var NucleotideBlockMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
};
export var DefaultNucleotideBlockMeshProps = PD.getDefaultValues(NucleotideBlockMeshParams);
function createNucleotideBlockMesh(ctx, unit, structure, theme, props, mesh) {
if (!Unit.isAtomic(unit))
return Mesh.createEmpty(mesh);
var nucleotideElementCount = unit.nucleotideElements.length;
if (!nucleotideElementCount)
return Mesh.createEmpty(mesh);
var sizeFactor = props.sizeFactor, radialSegments = props.radialSegments;
var vertexCount = nucleotideElementCount * (box.vertices.length / 3 + radialSegments * 2);
var builderState = MeshBuilder.createState(vertexCount, vertexCount / 4, mesh);
var elements = unit.elements, model = unit.model;
var _a = model.atomicHierarchy, chainAtomSegments = _a.chainAtomSegments, residueAtomSegments = _a.residueAtomSegments, atoms = _a.atoms, atomicIndex = _a.index;
var _b = model.atomicHierarchy.derived.residue, moleculeType = _b.moleculeType, traceElementIndex = _b.traceElementIndex;
var label_comp_id = atoms.label_comp_id;
var pos = unit.conformation.invariantPosition;
var chainIt = Segmentation.transientSegments(chainAtomSegments, elements);
var residueIt = Segmentation.transientSegments(residueAtomSegments, elements);
var cylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments: radialSegments, bottomCap: true };
var i = 0;
while (chainIt.hasNext) {
residueIt.setSegment(chainIt.move());
while (residueIt.hasNext) {
var residueIndex = residueIt.move().index;
if (isNucleic(moleculeType[residueIndex])) {
var compId = label_comp_id.value(residueAtomSegments.offsets[residueIndex]);
var idx1 = -1, idx2 = -1, idx3 = -1, idx4 = -1, idx5 = -1, idx6 = -1;
var width = 4.5, depth = 2.5 * sizeFactor;
var height = 4.5;
var isPurine = isPurineBase(compId);
var isPyrimidine = isPyrimidineBase(compId);
if (!isPurine && !isPyrimidine) {
// detect Purine or Pyrimidin based on geometry
var idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
var idxN9 = atomicIndex.findAtomOnResidue(residueIndex, 'N9');
if (idxC4 !== -1 && idxN9 !== -1 && Vec3.distance(pos(idxC4, p1), pos(idxN9, p2)) < 1.6) {
isPurine = true;
}
else {
isPyrimidine = true;
}
}
if (isPurine) {
height = 4.5;
idx1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1');
idx2 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
idx3 = atomicIndex.findAtomOnResidue(residueIndex, 'C6');
idx4 = atomicIndex.findAtomOnResidue(residueIndex, 'C2');
idx5 = atomicIndex.findAtomOnResidue(residueIndex, 'N9');
idx6 = traceElementIndex[residueIndex];
}
else if (isPyrimidine) {
height = 3.0;
idx1 = atomicIndex.findAtomOnResidue(residueIndex, 'N3');
idx2 = atomicIndex.findAtomOnResidue(residueIndex, 'C6');
idx3 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
idx4 = atomicIndex.findAtomOnResidue(residueIndex, 'C2');
idx5 = atomicIndex.findAtomOnResidue(residueIndex, 'N1');
if (idx5 === -1) {
// modified ring, e.g. DZ
idx5 = atomicIndex.findAtomOnResidue(residueIndex, 'C1');
}
idx6 = traceElementIndex[residueIndex];
}
if (idx5 !== -1 && idx6 !== -1) {
pos(idx5, p5);
pos(idx6, p6);
builderState.currentGroup = i;
addCylinder(builderState, p5, p6, 1, cylinderProps);
if (idx1 !== -1 && idx2 !== -1 && idx3 !== -1 && idx4 !== -1) {
pos(idx1, p1);
pos(idx2, p2);
pos(idx3, p3);
pos(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;
}
}
}
var m = MeshBuilder.getMesh(builderState);
var sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
return m;
}
export var NucleotideBlockParams = __assign(__assign({}, UnitsMeshParams), NucleotideBlockMeshParams);
export function NucleotideBlockVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(NucleotideBlockParams),
createGeometry: createNucleotideBlockMesh,
createLocationIterator: NucleotideLocationIterator.fromGroup,
getLoci: getNucleotideElementLoci,
eachLocation: eachNucleotideElement,
setUpdateState: function (state, newProps, currentProps) {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.radialSegments !== currentProps.radialSegments);
}
}, materialId);
}