molstar
Version:
A comprehensive macromolecular library.
136 lines (135 loc) • 7.33 kB
JavaScript
"use strict";
/**
* Copyright (c) 2018-2023 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.NucleotideBlockParams = exports.DefaultNucleotideBlockMeshProps = exports.NucleotideBlockMeshParams = void 0;
exports.NucleotideBlockVisual = NucleotideBlockVisual;
const param_definition_1 = require("../../../mol-util/param-definition");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const box_1 = require("../../../mol-geo/primitive/box");
const structure_1 = require("../../../mol-model/structure");
const mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
const mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder");
const int_1 = require("../../../mol-data/int");
const types_1 = require("../../../mol-model/structure/model/types");
const cylinder_1 = require("../../../mol-geo/geometry/mesh/builder/cylinder");
const units_visual_1 = require("../units-visual");
const nucleotide_1 = require("./util/nucleotide");
const base_1 = require("../../../mol-geo/geometry/base");
const geometry_1 = require("../../../mol-math/geometry");
// TODO support blocks for multiple locations (including from microheterogeneity)
const p1 = (0, linear_algebra_1.Vec3)();
const p2 = (0, linear_algebra_1.Vec3)();
const p3 = (0, linear_algebra_1.Vec3)();
const p4 = (0, linear_algebra_1.Vec3)();
const p5 = (0, linear_algebra_1.Vec3)();
const pt = (0, linear_algebra_1.Vec3)();
const v12 = (0, linear_algebra_1.Vec3)();
const v34 = (0, linear_algebra_1.Vec3)();
const vC = (0, linear_algebra_1.Vec3)();
const center = (0, linear_algebra_1.Vec3)();
const t = linear_algebra_1.Mat4.identity();
const sVec = (0, linear_algebra_1.Vec3)();
const box = (0, box_1.Box)();
exports.NucleotideBlockMeshParams = {
sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
thicknessFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 2, step: 0.01 }),
radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo),
};
exports.DefaultNucleotideBlockMeshProps = param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideBlockMeshParams);
function createNucleotideBlockMesh(ctx, unit, structure, theme, props, mesh) {
if (!structure_1.Unit.isAtomic(unit))
return mesh_1.Mesh.createEmpty(mesh);
const nucleotideElementCount = unit.nucleotideElements.length;
if (!nucleotideElementCount)
return mesh_1.Mesh.createEmpty(mesh);
const { sizeFactor, thicknessFactor, radialSegments } = props;
const vertexCount = nucleotideElementCount * (box.vertices.length / 3 + radialSegments * 2);
const builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 4, mesh);
const { elements, model, conformation: c } = unit;
const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy;
const { moleculeType } = model.atomicHierarchy.derived.residue;
const chainIt = int_1.Segmentation.transientSegments(chainAtomSegments, elements);
const residueIt = int_1.Segmentation.transientSegments(residueAtomSegments, elements);
const radius = 1 * sizeFactor;
const width = 4.5;
const depth = thicknessFactor * sizeFactor * 2;
const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments, bottomCap: true };
let i = 0;
while (chainIt.hasNext) {
residueIt.setSegment(chainIt.move());
while (residueIt.hasNext) {
const { index: residueIndex } = residueIt.move();
if ((0, types_1.isNucleic)(moleculeType[residueIndex])) {
const idx = (0, nucleotide_1.createNucleicIndices)();
let idx1 = -1, idx2 = -1, idx3 = -1, idx4 = -1, idx5 = -1;
let height = 4.5;
const { isPurine, isPyrimidine } = (0, nucleotide_1.getNucleotideBaseType)(unit, residueIndex);
if (isPurine) {
height = 4.5;
(0, nucleotide_1.setPurinIndices)(idx, unit, residueIndex);
idx1 = idx.N1;
idx2 = idx.C4;
idx3 = idx.C6;
idx4 = idx.C2;
idx5 = idx.N9;
}
else if (isPyrimidine) {
height = 3.0;
(0, nucleotide_1.setPyrimidineIndices)(idx, unit, residueIndex);
idx1 = idx.N3;
idx2 = idx.C6;
idx3 = idx.C4;
idx4 = idx.C2;
idx5 = idx.N1;
}
if (idx5 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx5, p5);
c.invariantPosition(idx.trace, pt);
builderState.currentGroup = i;
(0, cylinder_1.addCylinder)(builderState, p5, pt, 1, cylinderProps);
if (idx1 !== -1 && idx2 !== -1 && idx3 !== -1 && idx4 !== -1) {
c.invariantPosition(idx1, p1);
c.invariantPosition(idx2, p2);
c.invariantPosition(idx3, p3);
c.invariantPosition(idx4, p4);
linear_algebra_1.Vec3.normalize(v12, linear_algebra_1.Vec3.sub(v12, p2, p1));
linear_algebra_1.Vec3.normalize(v34, linear_algebra_1.Vec3.sub(v34, p4, p3));
linear_algebra_1.Vec3.normalize(vC, linear_algebra_1.Vec3.cross(vC, v12, v34));
linear_algebra_1.Mat4.targetTo(t, p1, p2, vC);
linear_algebra_1.Vec3.scaleAndAdd(center, p1, v12, height / 2 - 0.2);
linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, width, depth, height));
linear_algebra_1.Mat4.setTranslation(t, center);
mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, box);
}
}
++i;
}
}
}
const m = mesh_builder_1.MeshBuilder.getMesh(builderState);
const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, radius);
m.setBoundingSphere(sphere);
return m;
}
exports.NucleotideBlockParams = {
...units_visual_1.UnitsMeshParams,
...exports.NucleotideBlockMeshParams
};
function NucleotideBlockVisual(materialId) {
return (0, units_visual_1.UnitsMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideBlockParams),
createGeometry: createNucleotideBlockMesh,
createLocationIterator: nucleotide_1.NucleotideLocationIterator.fromGroup,
getLoci: nucleotide_1.getNucleotideElementLoci,
eachLocation: nucleotide_1.eachNucleotideElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.thicknessFactor !== currentProps.thicknessFactor ||
newProps.radialSegments !== currentProps.radialSegments);
}
}, materialId);
}