molstar
Version:
A comprehensive macromolecular library.
215 lines (214 loc) • 11 kB
JavaScript
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __assign } from "tslib";
import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
import { Box, PerforatedBox } from '../../../mol-geo/primitive/box';
import { OctagonalPyramid, PerforatedOctagonalPyramid } from '../../../mol-geo/primitive/pyramid';
import { Star } from '../../../mol-geo/primitive/star';
import { Octahedron, PerforatedOctahedron } from '../../../mol-geo/primitive/octahedron';
import { DiamondPrism, PentagonalPrism, ShiftedHexagonalPrism, HexagonalPrism, HeptagonalPrism } from '../../../mol-geo/primitive/prism';
import { Structure, StructureElement, Unit } from '../../../mol-model/structure';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { getSaccharideShape } from '../../../mol-model/structure/structure/carbohydrates/constants';
import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
import { ComplexMeshParams, ComplexMeshVisual } from '../complex-visual';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { OrderedSet, Interval } from '../../../mol-data/int';
import { EmptyLoci } from '../../../mol-model/loci';
import { getAltResidueLociFromId } from './util/common';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
var t = Mat4.identity();
var sVec = Vec3();
var pd = Vec3();
var SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
var box = Box();
var perforatedBox = PerforatedBox();
var octagonalPyramid = OctagonalPyramid();
var perforatedOctagonalPyramid = PerforatedOctagonalPyramid();
var star = Star({ outerRadius: 1, innerRadius: 0.5, thickness: 0.5, pointCount: 5 });
var octahedron = Octahedron();
var perforatedOctahedron = PerforatedOctahedron();
var diamondPrism = DiamondPrism();
var pentagonalPrism = PentagonalPrism();
var hexagonalPrism = HexagonalPrism();
var shiftedHexagonalPrism = ShiftedHexagonalPrism();
var heptagonalPrism = HeptagonalPrism();
function createCarbohydrateSymbolMesh(ctx, structure, theme, props, mesh) {
var builderState = MeshBuilder.createState(256, 128, mesh);
var detail = props.detail, sizeFactor = props.sizeFactor;
var carbohydrates = structure.carbohydrates;
var n = carbohydrates.elements.length;
var l = StructureElement.Location.create(structure);
for (var i = 0; i < n; ++i) {
var c = carbohydrates.elements[i];
var ring = c.unit.rings.all[c.ringIndex];
var shapeType = getSaccharideShape(c.component.type, ring.length);
l.unit = c.unit;
l.element = c.unit.elements[ring[0]];
var size = theme.size.size(l);
var radius = size * sizeFactor;
var side = size * sizeFactor * SideFactor;
var _a = c.geometry, center = _a.center, normal = _a.normal, direction = _a.direction;
Vec3.add(pd, center, direction);
Mat4.targetTo(t, center, pd, normal);
Mat4.setTranslation(t, center);
builderState.currentGroup = i * 2;
switch (shapeType) {
case 0 /* SaccharideShape.FilledSphere */:
addSphere(builderState, center, radius, detail);
break;
case 1 /* SaccharideShape.FilledCube */:
Mat4.scaleUniformly(t, t, side);
MeshBuilder.addPrimitive(builderState, t, box);
break;
case 2 /* SaccharideShape.CrossedCube */:
Mat4.scaleUniformly(t, t, side);
MeshBuilder.addPrimitive(builderState, t, perforatedBox);
Mat4.mul(t, t, Mat4.rotZ90X180);
builderState.currentGroup += 1;
MeshBuilder.addPrimitive(builderState, t, perforatedBox);
break;
case 4 /* SaccharideShape.FilledCone */:
Mat4.scaleUniformly(t, t, side * 1.2);
MeshBuilder.addPrimitive(builderState, t, octagonalPyramid);
break;
case 5 /* SaccharideShape.DevidedCone */:
Mat4.scaleUniformly(t, t, side * 1.2);
MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid);
Mat4.mul(t, t, Mat4.rotZ90);
builderState.currentGroup += 1;
MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid);
break;
case 6 /* SaccharideShape.FlatBox */:
Mat4.mul(t, t, Mat4.rotZY90);
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
MeshBuilder.addPrimitive(builderState, t, box);
break;
case 7 /* SaccharideShape.FilledStar */:
Mat4.scaleUniformly(t, t, side);
Mat4.mul(t, t, Mat4.rotZY90);
MeshBuilder.addPrimitive(builderState, t, star);
break;
case 8 /* SaccharideShape.FilledDiamond */:
Mat4.mul(t, t, Mat4.rotZY90);
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4));
MeshBuilder.addPrimitive(builderState, t, octahedron);
break;
case 3 /* SaccharideShape.DividedDiamond */:
Mat4.mul(t, t, Mat4.rotZY90);
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4));
MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron);
Mat4.mul(t, t, Mat4.rotY90);
builderState.currentGroup += 1;
MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron);
break;
case 9 /* SaccharideShape.FlatDiamond */:
Mat4.mul(t, t, Mat4.rotZY90);
Mat4.scale(t, t, Vec3.set(sVec, side, side / 2, side / 2));
MeshBuilder.addPrimitive(builderState, t, diamondPrism);
break;
case 12 /* SaccharideShape.DiamondPrism */:
Mat4.mul(t, t, Mat4.rotZY90);
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
MeshBuilder.addPrimitive(builderState, t, diamondPrism);
break;
case 13 /* SaccharideShape.PentagonalPrism */:
case 11 /* SaccharideShape.Pentagon */:
Mat4.mul(t, t, Mat4.rotZY90);
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
MeshBuilder.addPrimitive(builderState, t, pentagonalPrism);
break;
case 14 /* SaccharideShape.HexagonalPrism */:
Mat4.mul(t, t, Mat4.rotZY90);
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
MeshBuilder.addPrimitive(builderState, t, hexagonalPrism);
break;
case 15 /* SaccharideShape.HeptagonalPrism */:
Mat4.mul(t, t, Mat4.rotZY90);
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
MeshBuilder.addPrimitive(builderState, t, heptagonalPrism);
break;
case 10 /* SaccharideShape.FlatHexagon */:
default:
Mat4.mul(t, t, Mat4.rotZYZ90);
Mat4.scale(t, t, Vec3.set(sVec, side / 1.5, side, side / 2));
MeshBuilder.addPrimitive(builderState, t, shiftedHexagonalPrism);
break;
}
}
return MeshBuilder.getMesh(builderState);
}
export var CarbohydrateSymbolParams = __assign(__assign({}, ComplexMeshParams), { detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo), sizeFactor: PD.Numeric(1.75, { min: 0, max: 10, step: 0.01 }) });
export function CarbohydrateSymbolVisual(materialId) {
return ComplexMeshVisual({
defaultProps: PD.getDefaultValues(CarbohydrateSymbolParams),
createGeometry: createCarbohydrateSymbolMesh,
createLocationIterator: CarbohydrateElementIterator,
getLoci: getCarbohydrateLoci,
eachLocation: eachCarbohydrate,
setUpdateState: function (state, newProps, currentProps) {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.detail !== currentProps.detail);
}
}, materialId);
}
function CarbohydrateElementIterator(structure) {
var carbElements = structure.carbohydrates.elements;
var groupCount = carbElements.length * 2;
var instanceCount = 1;
var location = StructureElement.Location.create(structure);
function getLocation(groupIndex, instanceIndex) {
var carb = carbElements[Math.floor(groupIndex / 2)];
var ring = carb.unit.rings.all[carb.ringIndex];
location.unit = carb.unit;
location.element = carb.unit.elements[ring[0]];
return location;
}
function isSecondary(elementIndex, instanceIndex) {
return (elementIndex % 2) === 1;
}
return LocationIterator(groupCount, instanceCount, 1, getLocation, true, isSecondary);
}
/** Return a Loci for the elements of the whole residue of a carbohydrate. */
function getCarbohydrateLoci(pickingId, structure, id) {
var objectId = pickingId.objectId, groupId = pickingId.groupId;
if (id === objectId) {
var carb = structure.carbohydrates.elements[Math.floor(groupId / 2)];
return getAltResidueLociFromId(structure, carb.unit, carb.residueIndex, carb.altId);
}
return EmptyLoci;
}
var __elementIndicesSet = new Set();
/** For each carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */
function eachCarbohydrate(loci, structure, apply) {
var getElementIndices = structure.carbohydrates.getElementIndices;
var changed = false;
if (!StructureElement.Loci.is(loci))
return false;
if (!Structure.areEquivalent(loci.structure, structure))
return false;
var _loop_1 = function (unit, indices) {
if (!Unit.isAtomic(unit))
return "continue";
__elementIndicesSet.clear();
OrderedSet.forEach(indices, function (v) {
var elementIndices = getElementIndices(unit, unit.elements[v]);
for (var i = 0, il = elementIndices.length; i < il; ++i) {
if (!__elementIndicesSet.has(elementIndices[i])) {
__elementIndicesSet.add(elementIndices[i]);
if (apply(Interval.ofSingleton(elementIndices[i] * 2)))
changed = true;
}
}
});
};
for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
var _b = _a[_i], unit = _b.unit, indices = _b.indices;
_loop_1(unit, indices);
}
return changed;
}