molstar
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A comprehensive macromolecular library.
282 lines (281 loc) • 15.4 kB
JavaScript
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { __assign } from "tslib";
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Unit, StructureElement, Bond } from '../../../mol-model/structure';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { arrayEqual } from '../../../mol-util';
import { createLinkCylinderImpostors, createLinkCylinderMesh } from './util/link';
import { UnitsMeshParams, UnitsMeshVisual, UnitsCylindersParams, UnitsCylindersVisual } from '../units-visual';
import { BondType } from '../../../mol-model/structure/model/types';
import { BondCylinderParams, BondIterator, eachIntraBond, getIntraBondLoci, ignoreBondType, makeIntraBondIgnoreTest } from './util/bond';
import { Sphere3D } from '../../../mol-math/geometry';
import { IntAdjacencyGraph } from '../../../mol-math/graph';
import { Cylinders } from '../../../mol-geo/geometry/cylinders/cylinders';
import { SortedArray } from '../../../mol-data/int';
import { arrayIntersectionSize } from '../../../mol-util/array';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
var isBondType = BondType.is;
function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
var elements = unit.elements;
var bonds = unit.bonds;
var edgeCount = bonds.edgeCount, a = bonds.a, b = bonds.b, edgeProps = bonds.edgeProps, offset = bonds.offset;
var _order = edgeProps.order, _flags = edgeProps.flags;
var sizeFactor = props.sizeFactor, sizeAspectRatio = props.sizeAspectRatio, adjustCylinderLength = props.adjustCylinderLength, aromaticBonds = props.aromaticBonds, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes, multipleBonds = props.multipleBonds;
var mbOff = multipleBonds === 'off';
var mbSymmetric = multipleBonds === 'symmetric';
var include = BondType.fromNames(includeTypes);
var exclude = BondType.fromNames(excludeTypes);
var ignoreComputedAromatic = ignoreBondType(include, exclude, 32 /* BondType.Flag.Computed */);
var vRef = Vec3(), delta = Vec3();
var pos = unit.conformation.invariantPosition;
var stub;
var locE = StructureElement.Location.create(structure, unit);
var locB = Bond.Location(structure, unit, undefined, structure, unit, undefined);
var child = structure.child;
if (props.includeParent && child) {
var childUnit_1 = child.unitMap.get(unit.id);
if (!childUnit_1)
throw new Error('expected childUnit to exist');
stub = function (edgeIndex) {
var eA = elements[a[edgeIndex]];
var eB = elements[b[edgeIndex]];
return SortedArray.has(childUnit_1.elements, eA) && !SortedArray.has(childUnit_1.elements, eB);
};
}
var radius = function (edgeIndex) {
locB.aIndex = a[edgeIndex];
locB.bIndex = b[edgeIndex];
return theme.size.size(locB) * sizeFactor;
};
var radiusA = function (edgeIndex) {
locE.element = elements[a[edgeIndex]];
return theme.size.size(locE) * sizeFactor;
};
var radiusB = function (edgeIndex) {
locE.element = elements[b[edgeIndex]];
return theme.size.size(locE) * sizeFactor;
};
var _a = unit.rings, elementRingIndices = _a.elementRingIndices, elementAromaticRingIndices = _a.elementAromaticRingIndices;
var deloTriplets = aromaticBonds ? unit.resonance.delocalizedTriplets : undefined;
return {
linkCount: edgeCount * 2,
referencePosition: function (edgeIndex) {
var _a, _b;
var aI = a[edgeIndex], bI = b[edgeIndex];
var rI = deloTriplets === null || deloTriplets === void 0 ? void 0 : deloTriplets.getThirdElement(aI, bI);
if (rI !== undefined)
return pos(elements[rI], vRef);
if (aI > bI)
_a = [bI, aI], aI = _a[0], bI = _a[1];
if (offset[aI + 1] - offset[aI] === 1)
_b = [bI, aI], aI = _b[0], bI = _b[1];
var aR = elementAromaticRingIndices.get(aI) || elementRingIndices.get(aI);
var maxSize = 0;
for (var i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
var _bI = b[i];
if (_bI !== bI && _bI !== aI) {
if (aR) {
var _bR = elementAromaticRingIndices.get(_bI) || elementRingIndices.get(_bI);
if (!_bR)
continue;
var size = arrayIntersectionSize(aR, _bR);
if (size > maxSize) {
maxSize = size;
pos(elements[_bI], vRef);
}
}
else {
return pos(elements[_bI], vRef);
}
}
}
return maxSize > 0 ? vRef : null;
},
position: function (posA, posB, edgeIndex) {
pos(elements[a[edgeIndex]], posA);
pos(elements[b[edgeIndex]], posB);
if (adjustCylinderLength) {
var rA = radiusA(edgeIndex), rB = radiusB(edgeIndex);
var r = Math.min(rA, rB) * sizeAspectRatio;
var oA = Math.sqrt(Math.max(0, rA * rA - r * r)) - 0.05;
var 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: function (edgeIndex) {
var o = _order[edgeIndex];
var f = _flags[edgeIndex];
if (isBondType(f, 2 /* BondType.Flag.MetallicCoordination */) || isBondType(f, 4 /* BondType.Flag.HydrogenBond */)) {
// show metallic coordinations and hydrogen bonds with dashed cylinders
return 1 /* LinkStyle.Dashed */;
}
else if (o === 3) {
return mbOff ? 0 /* LinkStyle.Solid */ :
mbSymmetric ? 4 /* LinkStyle.Triple */ :
5 /* LinkStyle.OffsetTriple */;
}
else if (aromaticBonds) {
var aI = a[edgeIndex], bI = b[edgeIndex];
var aR = elementAromaticRingIndices.get(aI);
var bR = elementAromaticRingIndices.get(bI);
var arCount = (aR && bR) ? arrayIntersectionSize(aR, bR) : 0;
if (isBondType(f, 16 /* BondType.Flag.Aromatic */) || (arCount && !ignoreComputedAromatic)) {
if (arCount === 2) {
return 8 /* LinkStyle.MirroredAromatic */;
}
else {
return 7 /* LinkStyle.Aromatic */;
}
}
}
return (o !== 2 || mbOff) ? 0 /* LinkStyle.Solid */ :
mbSymmetric ? 2 /* LinkStyle.Double */ :
3 /* LinkStyle.OffsetDouble */;
},
radius: function (edgeIndex) {
return radius(edgeIndex) * sizeAspectRatio;
},
ignore: makeIntraBondIgnoreTest(structure, unit, props),
stub: stub
};
}
function createIntraUnitBondCylinderImpostors(ctx, unit, structure, theme, props, cylinders) {
if (!Unit.isAtomic(unit))
return Cylinders.createEmpty(cylinders);
if (!unit.bonds.edgeCount)
return Cylinders.createEmpty(cylinders);
var child = structure.child;
var childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id);
if (child && !childUnit)
return Cylinders.createEmpty(cylinders);
var builderProps = getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props);
var _a = createLinkCylinderImpostors(ctx, builderProps, props, cylinders), c = _a.cylinders, boundingSphere = _a.boundingSphere;
if (boundingSphere) {
c.setBoundingSphere(boundingSphere);
}
else if (c.cylinderCount > 0) {
var sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
c.setBoundingSphere(sphere);
}
return c;
}
function createIntraUnitBondCylinderMesh(ctx, unit, structure, theme, props, mesh) {
if (!Unit.isAtomic(unit))
return Mesh.createEmpty(mesh);
if (!unit.bonds.edgeCount)
return Mesh.createEmpty(mesh);
var child = structure.child;
var childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id);
if (child && !childUnit)
return Mesh.createEmpty(mesh);
var builderProps = getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props);
var _a = createLinkCylinderMesh(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
if (boundingSphere) {
m.setBoundingSphere(boundingSphere);
}
else if (m.triangleCount > 0) {
var sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
}
return m;
}
export var IntraUnitBondCylinderParams = __assign(__assign(__assign(__assign({}, UnitsMeshParams), UnitsCylindersParams), 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 IntraUnitBondCylinderVisual(materialId, structure, props, webgl) {
return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
? IntraUnitBondCylinderImpostorVisual(materialId)
: IntraUnitBondCylinderMeshVisual(materialId);
}
export function IntraUnitBondCylinderImpostorVisual(materialId) {
return UnitsCylindersVisual({
defaultProps: PD.getDefaultValues(IntraUnitBondCylinderParams),
createGeometry: createIntraUnitBondCylinderImpostors,
createLocationIterator: BondIterator.fromGroup,
getLoci: getIntraBondLoci,
eachLocation: eachIntraBond,
setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
state.createGeometry = (newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
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.aromaticBonds !== currentProps.aromaticBonds ||
newProps.multipleBonds !== currentProps.multipleBonds);
var newUnit = newStructureGroup.group.units[0];
var currentUnit = currentStructureGroup.group.units[0];
if (Unit.isAtomic(newUnit) && Unit.isAtomic(currentUnit)) {
if (!IntAdjacencyGraph.areEqual(newUnit.bonds, currentUnit.bonds)) {
state.createGeometry = true;
state.updateTransform = true;
state.updateColor = true;
state.updateSize = true;
}
}
},
mustRecreate: function (structureGroup, props, webgl) {
return !props.tryUseImpostor || !webgl;
}
}, materialId);
}
export function IntraUnitBondCylinderMeshVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(IntraUnitBondCylinderParams),
createGeometry: createIntraUnitBondCylinderMesh,
createLocationIterator: BondIterator.fromGroup,
getLoci: getIntraBondLoci,
eachLocation: eachIntraBond,
setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
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.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.aromaticBonds !== currentProps.aromaticBonds ||
newProps.multipleBonds !== currentProps.multipleBonds);
var newUnit = newStructureGroup.group.units[0];
var currentUnit = currentStructureGroup.group.units[0];
if (Unit.isAtomic(newUnit) && Unit.isAtomic(currentUnit)) {
if (!IntAdjacencyGraph.areEqual(newUnit.bonds, currentUnit.bonds)) {
state.createGeometry = true;
state.updateTransform = true;
state.updateColor = true;
state.updateSize = true;
}
}
},
mustRecreate: function (structureGroup, props, webgl) {
return props.tryUseImpostor && !!webgl;
}
}, materialId);
}