molstar
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A comprehensive macromolecular library.
282 lines (281 loc) • 14.2 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 { StructureElement, Bond } from '../../../mol-model/structure';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { BitFlags, arrayEqual } from '../../../mol-util';
import { createLinkCylinderImpostors, createLinkCylinderMesh, LinkStyle } from './util/link';
import { ComplexMeshParams, ComplexMeshVisual, ComplexCylindersParams, ComplexCylindersVisual } from '../complex-visual';
import { BondType } from '../../../mol-model/structure/model/types';
import { BondCylinderParams, BondIterator, getInterBondLoci, eachInterBond, makeInterBondIgnoreTest, hasStructureVisibleBonds } from './util/bond';
import { Sphere3D } from '../../../mol-math/geometry';
import { Cylinders } from '../../../mol-geo/geometry/cylinders/cylinders';
import { SortedArray } from '../../../mol-data/int/sorted-array';
import { SizeTheme } from '../../../mol-theme/size';
import { EmptyLocationIterator } from '../../../mol-geo/util/location-iterator';
const tmpRefPosBondIt = new Bond.ElementBondIterator();
function setRefPosition(pos, structure, unit, index) {
tmpRefPosBondIt.setElement(structure, unit, index);
while (tmpRefPosBondIt.hasNext) {
const bA = tmpRefPosBondIt.move();
bA.otherUnit.conformation.position(bA.otherUnit.elements[bA.otherIndex], pos);
return pos;
}
return null;
}
const tmpRef = Vec3();
function getInterUnitBondCylinderBuilderProps(structure, theme, props) {
const locE = StructureElement.Location.create(structure);
const locB = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
const bonds = structure.interUnitBonds;
const { edgeCount, edges } = bonds;
const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds, multipleBonds } = props;
const mbOff = multipleBonds === 'off';
const mbSymmetric = multipleBonds === 'symmetric';
const delta = Vec3();
let stub;
const { child } = structure;
if (props.includeParent && child) {
stub = (edgeIndex) => {
const b = edges[edgeIndex];
const childUnitA = child.unitMap.get(b.unitA);
const childUnitB = child.unitMap.get(b.unitB);
const unitA = structure.unitMap.get(b.unitA);
const eA = unitA.elements[b.indexA];
const unitB = structure.unitMap.get(b.unitB);
const eB = unitB.elements[b.indexB];
return (childUnitA && SortedArray.has(childUnitA.elements, eA) &&
(!childUnitB || !SortedArray.has(childUnitB.elements, eB)));
};
}
const radius = (edgeIndex) => {
const b = edges[edgeIndex];
locB.aUnit = structure.unitMap.get(b.unitA);
locB.aIndex = b.indexA;
locB.bUnit = structure.unitMap.get(b.unitB);
locB.bIndex = b.indexB;
return theme.size.size(locB) * sizeFactor;
};
const radiusA = (edgeIndex) => {
const b = edges[edgeIndex];
locE.unit = structure.unitMap.get(b.unitA);
locE.element = locE.unit.elements[b.indexA];
return theme.size.size(locE) * sizeFactor;
};
const radiusB = (edgeIndex) => {
const b = edges[edgeIndex];
locE.unit = structure.unitMap.get(b.unitB);
locE.element = locE.unit.elements[b.indexB];
return theme.size.size(locE) * sizeFactor;
};
return {
linkCount: edgeCount,
referencePosition: (edgeIndex) => {
const b = edges[edgeIndex];
let unitA, unitB;
let indexA, indexB;
if (b.unitA < b.unitB) {
unitA = structure.unitMap.get(b.unitA);
unitB = structure.unitMap.get(b.unitB);
indexA = b.indexA;
indexB = b.indexB;
}
else if (b.unitA > b.unitB) {
unitA = structure.unitMap.get(b.unitB);
unitB = structure.unitMap.get(b.unitA);
indexA = b.indexB;
indexB = b.indexA;
}
else {
throw new Error('same units in createInterUnitBondCylinderMesh');
}
return setRefPosition(tmpRef, structure, unitA, indexA) || setRefPosition(tmpRef, structure, unitB, indexB);
},
position: (posA, posB, edgeIndex, adjust) => {
const b = edges[edgeIndex];
const uA = structure.unitMap.get(b.unitA);
const uB = structure.unitMap.get(b.unitB);
uA.conformation.position(uA.elements[b.indexA], posA);
uB.conformation.position(uB.elements[b.indexB], posB);
if (adjust && adjustCylinderLength) {
const rA = radiusA(edgeIndex), rB = radiusB(edgeIndex);
const r = Math.min(rA, rB) * sizeAspectRatio;
const oA = Math.sqrt(Math.max(0, rA * rA - r * r)) - 0.05;
const oB = Math.sqrt(Math.max(0, rB * rB - r * r)) - 0.05;
if (oA <= 0.01 && oB <= 0.01)
return;
Vec3.normalize(delta, Vec3.sub(delta, posB, posA));
Vec3.scaleAndAdd(posA, posA, delta, oA);
Vec3.scaleAndAdd(posB, posB, delta, -oB);
}
},
style: (edgeIndex) => {
const o = edges[edgeIndex].props.order;
const f = BitFlags.create(edges[edgeIndex].props.flag);
if (BondType.is(f, BondType.Flag.MetallicCoordination) || BondType.is(f, BondType.Flag.HydrogenBond)) {
// show metallic coordinations and hydrogen bonds with dashed cylinders
return LinkStyle.Dashed;
}
else if (o === 3) {
return mbOff ? LinkStyle.Solid :
mbSymmetric ? LinkStyle.Triple :
LinkStyle.OffsetTriple;
}
else if (aromaticBonds && BondType.is(f, BondType.Flag.Aromatic)) {
return LinkStyle.Aromatic;
}
return (o !== 2 || mbOff) ? LinkStyle.Solid :
mbSymmetric ? LinkStyle.Double :
LinkStyle.OffsetDouble;
},
radius: (edgeIndex) => {
return radius(edgeIndex) * sizeAspectRatio;
},
ignore: makeInterBondIgnoreTest(structure, props),
stub
};
}
function createInterUnitBondCylinderImpostors(ctx, structure, theme, props, cylinders) {
if (!hasStructureVisibleBonds(structure, props))
return Cylinders.createEmpty(cylinders);
if (!structure.interUnitBonds.edgeCount)
return Cylinders.createEmpty(cylinders);
const builderProps = getInterUnitBondCylinderBuilderProps(structure, theme, props);
const { cylinders: c, boundingSphere } = createLinkCylinderImpostors(ctx, builderProps, props, cylinders);
if (boundingSphere) {
c.setBoundingSphere(boundingSphere);
}
else if (c.cylinderCount > 0) {
const { child } = structure;
const sphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
c.setBoundingSphere(sphere);
}
return c;
}
function createInterUnitBondCylinderMesh(ctx, structure, theme, props, mesh) {
if (!hasStructureVisibleBonds(structure, props))
return Mesh.createEmpty(mesh);
if (!structure.interUnitBonds.edgeCount)
return Mesh.createEmpty(mesh);
const builderProps = getInterUnitBondCylinderBuilderProps(structure, theme, props);
const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);
if (boundingSphere) {
m.setBoundingSphere(boundingSphere);
}
else if (m.triangleCount > 0) {
const { child } = structure;
const sphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
}
return m;
}
export const InterUnitBondCylinderParams = {
...ComplexMeshParams,
...ComplexCylindersParams,
...BondCylinderParams,
sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
sizeAspectRatio: PD.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }),
tryUseImpostor: PD.Boolean(true),
includeParent: PD.Boolean(false),
};
export function InterUnitBondCylinderVisual(materialId, structure, props, webgl) {
return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
? InterUnitBondCylinderImpostorVisual(materialId)
: InterUnitBondCylinderMeshVisual(materialId);
}
export function InterUnitBondCylinderImpostorVisual(materialId) {
return ComplexCylindersVisual({
defaultProps: PD.getDefaultValues(InterUnitBondCylinderParams),
createGeometry: createInterUnitBondCylinderImpostors,
createLocationIterator: (structure, props) => {
return !hasStructureVisibleBonds(structure, props)
? EmptyLocationIterator
: BondIterator.fromStructure(structure, { includeLocation2: props.colorMode === 'interpolate' });
},
getLoci: getInterBondLoci,
eachLocation: eachInterBond,
setUpdateState: (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.linkCap !== currentProps.linkCap ||
newProps.aromaticScale !== currentProps.aromaticScale ||
newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
newProps.stubCap !== currentProps.stubCap ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
newProps.multipleBonds !== currentProps.multipleBonds);
if (newProps.colorMode !== currentProps.colorMode) {
state.createGeometry = true;
state.updateTransform = true;
state.updateColor = true;
}
if (hasStructureVisibleBonds(newStructure, newProps) && newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
state.createGeometry = true;
state.updateTransform = true;
state.updateColor = true;
state.updateSize = true;
}
},
mustRecreate: (structure, props, webgl) => {
return !props.tryUseImpostor || !webgl;
}
}, materialId);
}
export function InterUnitBondCylinderMeshVisual(materialId) {
return ComplexMeshVisual({
defaultProps: PD.getDefaultValues(InterUnitBondCylinderParams),
createGeometry: createInterUnitBondCylinderMesh,
createLocationIterator: (structure, props) => {
return !hasStructureVisibleBonds(structure, props)
? EmptyLocationIterator
: BondIterator.fromStructure(structure);
},
getLoci: getInterBondLoci,
eachLocation: eachInterBond,
setUpdateState: (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.linkCap !== currentProps.linkCap ||
newProps.aromaticScale !== currentProps.aromaticScale ||
newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
newProps.stubCap !== currentProps.stubCap ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
newProps.multipleBonds !== currentProps.multipleBonds ||
newProps.adjustCylinderLength && !SizeTheme.areEqual(newTheme.size, currentTheme.size));
if (hasStructureVisibleBonds(newStructure, newProps) && newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
state.createGeometry = true;
state.updateTransform = true;
state.updateColor = true;
state.updateSize = true;
}
},
mustRecreate: (structure, props, webgl) => {
return props.tryUseImpostor && !!webgl;
}
}, materialId);
}