molstar
Version:
A comprehensive macromolecular library.
141 lines (140 loc) • 7.17 kB
JavaScript
;
/**
* Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.InterUnitBondLineVisual = exports.InterUnitBondLineParams = void 0;
var tslib_1 = require("tslib");
var param_definition_1 = require("../../../mol-util/param-definition");
var structure_1 = require("../../../mol-model/structure");
var linear_algebra_1 = require("../../../mol-math/linear-algebra");
var mol_util_1 = require("../../../mol-util");
var link_1 = require("./util/link");
var complex_visual_1 = require("../complex-visual");
var types_1 = require("../../../mol-model/structure/model/types");
var bond_1 = require("./util/bond");
var lines_1 = require("../../../mol-geo/geometry/lines/lines");
var geometry_1 = require("../../../mol-math/geometry");
var tmpRefPosBondIt = new structure_1.Bond.ElementBondIterator();
function setRefPosition(pos, structure, unit, index) {
tmpRefPosBondIt.setElement(structure, unit, index);
while (tmpRefPosBondIt.hasNext) {
var bA = tmpRefPosBondIt.move();
bA.otherUnit.conformation.position(bA.otherUnit.elements[bA.otherIndex], pos);
return pos;
}
return null;
}
function createInterUnitBondLines(ctx, structure, theme, props, lines) {
var bonds = structure.interUnitBonds;
var edgeCount = bonds.edgeCount, edges = bonds.edges;
if (!edgeCount)
return lines_1.Lines.createEmpty(lines);
var sizeFactor = props.sizeFactor, aromaticBonds = props.aromaticBonds, multipleBonds = props.multipleBonds;
var mbOff = multipleBonds === 'off';
var mbSymmetric = multipleBonds === 'symmetric';
var ref = (0, linear_algebra_1.Vec3)();
var loc = structure_1.StructureElement.Location.create();
var builderProps = {
linkCount: edgeCount,
referencePosition: function (edgeIndex) {
var b = edges[edgeIndex];
var unitA, unitB;
var 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 createInterUnitBondLines');
}
return setRefPosition(ref, structure, unitA, indexA) || setRefPosition(ref, structure, unitB, indexB);
},
position: function (posA, posB, edgeIndex) {
var b = edges[edgeIndex];
var uA = structure.unitMap.get(b.unitA);
var uB = structure.unitMap.get(b.unitB);
uA.conformation.position(uA.elements[b.indexA], posA);
uB.conformation.position(uB.elements[b.indexB], posB);
},
style: function (edgeIndex) {
var o = edges[edgeIndex].props.order;
var f = mol_util_1.BitFlags.create(edges[edgeIndex].props.flag);
if (types_1.BondType.is(f, 2 /* BondType.Flag.MetallicCoordination */) || types_1.BondType.is(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 && types_1.BondType.is(f, 16 /* BondType.Flag.Aromatic */)) {
return 7 /* LinkStyle.Aromatic */;
}
return (o !== 2 || mbOff) ? 0 /* LinkStyle.Solid */ :
mbSymmetric ? 2 /* LinkStyle.Double */ :
3 /* LinkStyle.OffsetDouble */;
},
radius: function (edgeIndex) {
var b = edges[edgeIndex];
loc.structure = structure;
loc.unit = structure.unitMap.get(b.unitA);
loc.element = loc.unit.elements[b.indexA];
var sizeA = theme.size.size(loc);
loc.unit = structure.unitMap.get(b.unitB);
loc.element = loc.unit.elements[b.indexB];
var sizeB = theme.size.size(loc);
return Math.min(sizeA, sizeB) * sizeFactor;
},
ignore: (0, bond_1.makeInterBondIgnoreTest)(structure, props)
};
var _a = (0, link_1.createLinkLines)(ctx, builderProps, props, lines), l = _a.lines, boundingSphere = _a.boundingSphere;
if (boundingSphere) {
l.setBoundingSphere(boundingSphere);
}
else if (l.lineCount > 0) {
var child = structure.child;
var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * sizeFactor);
l.setBoundingSphere(sphere);
}
return l;
}
exports.InterUnitBondLineParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexLinesParams), bond_1.BondLineParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false) });
function InterUnitBondLineVisual(materialId) {
return (0, complex_visual_1.ComplexLinesVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InterUnitBondLineParams),
createGeometry: createInterUnitBondLines,
createLocationIterator: bond_1.BondIterator.fromStructure,
getLoci: bond_1.getInterBondLoci,
eachLocation: bond_1.eachInterBond,
setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
!(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
!(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
newProps.multipleBonds !== currentProps.multipleBonds);
if (newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
state.createGeometry = true;
state.updateTransform = true;
state.updateColor = true;
state.updateSize = true;
}
}
}, materialId);
}
exports.InterUnitBondLineVisual = InterUnitBondLineVisual;