molstar
Version:
A comprehensive macromolecular library.
201 lines (200 loc) • 11.3 kB
JavaScript
/**
* Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Gianluca Tomasello <giagitom@gmail.com>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Unit } from '../../../mol-model/structure';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment, interpolateSizes, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement, HelixTension, NucleicShift, StandardShift, StandardTension, OverhangFactor } from './util/polymer';
import { isNucleic, SecondaryStructureType } from '../../../mol-model/structure/model/types';
import { addSheet } from '../../../mol-geo/geometry/mesh/builder/sheet';
import { addTube } from '../../../mol-geo/geometry/mesh/builder/tube';
import { UnitsMeshParams, UnitsMeshVisual } from '../units-visual';
import { SecondaryStructureProvider } from '../../../mol-model-props/computed/secondary-structure';
import { addRibbon } from '../../../mol-geo/geometry/mesh/builder/ribbon';
import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
export const PolymerTraceMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
aspectRatio: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }),
arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Size factor for sheet arrows' }),
tubularHelices: PD.Boolean(false, { description: 'Draw alpha helices as tubes' }),
roundCap: PD.Boolean(false, { description: 'Draw round caps on tubular alpha helices' }),
helixProfile: PD.Select('elliptical', PD.arrayToOptions(['elliptical', 'rounded', 'square']), { description: 'Protein helix trace profile' }),
nucleicProfile: PD.Select('square', PD.arrayToOptions(['elliptical', 'rounded', 'square']), { description: 'Nucleic strand trace profile' }),
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }, BaseGeometry.CustomQualityParamInfo),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo)
};
export const DefaultPolymerTraceMeshProps = PD.getDefaultValues(PolymerTraceMeshParams);
const tmpV1 = Vec3();
function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
const polymerElementCount = unit.polymerElements.length;
if (!polymerElementCount)
return Mesh.createEmpty(mesh);
const { sizeFactor, detail, linearSegments, radialSegments, aspectRatio, arrowFactor, tubularHelices, roundCap, helixProfile, nucleicProfile } = props;
const vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2;
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh);
const isCoarse = Unit.isCoarse(unit);
const state = createCurveSegmentState(linearSegments);
const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state;
let i = 0;
const polymerTraceIt = PolymerTraceIterator(unit, structure, { ignoreSecondaryStructure: false, useHelixOrientation: tubularHelices });
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move();
builderState.currentGroup = i;
const isNucleicType = isNucleic(v.moleculeType);
const isSheet = SecondaryStructureType.is(v.secStrucType, 4 /* SecondaryStructureType.Flag.Beta */);
const isHelix = SecondaryStructureType.is(v.secStrucType, 2 /* SecondaryStructureType.Flag.Helix */);
const tension = isHelix && !tubularHelices ? HelixTension : StandardTension;
const shift = isNucleicType ? NucleicShift : StandardShift;
interpolateCurveSegment(state, v, tension, shift);
let w0 = theme.size.size(v.centerPrev) * sizeFactor;
let w1 = theme.size.size(v.center) * sizeFactor;
let w2 = theme.size.size(v.centerNext) * sizeFactor;
if (isCoarse) {
w0 *= aspectRatio / 2;
w1 *= aspectRatio / 2;
w2 *= aspectRatio / 2;
}
const startCap = v.secStrucFirst || v.coarseBackboneFirst || v.first;
const endCap = v.secStrucLast || v.coarseBackboneLast || v.last;
const hasRoundCap = isHelix && tubularHelices && roundCap;
let segmentCount = linearSegments;
if (v.initial) {
segmentCount = Math.max(Math.round(linearSegments * shift), 1);
const offset = linearSegments - segmentCount;
curvePoints.copyWithin(0, offset * 3);
binormalVectors.copyWithin(0, offset * 3);
normalVectors.copyWithin(0, offset * 3);
Vec3.fromArray(tmpV1, curvePoints, 3);
Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1));
Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * OverhangFactor);
Vec3.toArray(tmpV1, curvePoints, 0);
}
else if (v.final) {
segmentCount = Math.max(Math.round(linearSegments * (1 - shift)), 1);
Vec3.fromArray(tmpV1, curvePoints, segmentCount * 3 - 3);
Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1));
Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * OverhangFactor);
Vec3.toArray(tmpV1, curvePoints, segmentCount * 3);
}
if (v.initial === true && v.final === true) {
addSphere(builderState, v.p2, w1 * 2, detail);
}
else if (isSheet) {
const h0 = w0 * aspectRatio;
const h1 = w1 * aspectRatio;
const h2 = w2 * aspectRatio;
const arrowHeight = v.secStrucLast ? h1 * arrowFactor : 0;
interpolateSizes(state, w0, w1, w2, h0, h1, h2, shift);
if (radialSegments === 2) {
addRibbon(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, arrowHeight);
}
else {
addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, arrowHeight, startCap, endCap);
}
}
else {
let h0, h1, h2;
if (isHelix) {
if (tubularHelices) {
w0 *= aspectRatio * 1.5;
w1 *= aspectRatio * 1.5;
w2 *= aspectRatio * 1.5;
h0 = w0;
h1 = w1;
h2 = w2;
}
else {
h0 = w0 * aspectRatio;
h1 = w1 * aspectRatio;
h2 = w2 * aspectRatio;
}
}
else if (isNucleicType) {
h0 = w0 * aspectRatio;
h1 = w1 * aspectRatio;
h2 = w2 * aspectRatio;
}
else {
h0 = w0;
h1 = w1;
h2 = w2;
}
interpolateSizes(state, w0, w1, w2, h0, h1, h2, shift);
const [normals, binormals] = isNucleicType ? [binormalVectors, normalVectors] : [normalVectors, binormalVectors];
if (isNucleicType) {
// TODO: find a cleaner way to swap normal and binormal for nucleic types
for (let i = 0, il = normals.length; i < il; i++)
normals[i] *= -1;
}
const profile = isNucleicType ? nucleicProfile : helixProfile;
if (radialSegments === 2) {
if (isNucleicType) {
addRibbon(builderState, curvePoints, normals, binormals, segmentCount, heightValues, widthValues, 0);
}
else {
addRibbon(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0);
}
}
else if (radialSegments === 4) {
addSheet(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
}
else if (h1 === w1) {
addTube(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical', hasRoundCap);
}
else if (profile === 'square') {
addSheet(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
}
else {
addTube(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, profile);
}
}
++i;
}
const m = MeshBuilder.getMesh(builderState);
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
return m;
}
export const PolymerTraceParams = {
...UnitsMeshParams,
...PolymerTraceMeshParams
};
export function PolymerTraceVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(PolymerTraceParams),
createGeometry: createPolymerTraceMesh,
createLocationIterator: (structureGroup) => PolymerLocationIterator.fromGroup(structureGroup, { asSecondary: true }),
getLoci: getPolymerElementLoci,
eachLocation: eachPolymerElement,
setUpdateState: (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.tubularHelices !== currentProps.tubularHelices ||
newProps.roundCap !== currentProps.roundCap ||
newProps.detail !== currentProps.detail ||
newProps.linearSegments !== currentProps.linearSegments ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.aspectRatio !== currentProps.aspectRatio ||
newProps.arrowFactor !== currentProps.arrowFactor ||
newProps.helixProfile !== currentProps.helixProfile ||
newProps.nucleicProfile !== currentProps.nucleicProfile);
const secondaryStructureHash = SecondaryStructureProvider.get(newStructureGroup.structure).version;
if (state.info.secondaryStructureHash !== secondaryStructureHash) {
if (state.info.secondaryStructureHash !== undefined)
state.createGeometry = true;
state.info.secondaryStructureHash = secondaryStructureHash;
}
},
initUpdateState: (state, newProps, newTheme, newStructureGroup) => {
const secondaryStructureHash = SecondaryStructureProvider.get(newStructureGroup.structure).version;
state.info.secondaryStructureHash = secondaryStructureHash;
}
}, materialId);
}