molstar
Version:
A comprehensive macromolecular library.
171 lines (170 loc) • 10.5 kB
JavaScript
"use strict";
/**
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Gianluca Tomasello <giagitom@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.NucleotideAtomicRingFillParams = exports.DefaultNucleotideAtomicRingFillMeshProps = exports.NucleotideAtomicRingFillMeshParams = void 0;
exports.NucleotideAtomicRingFillVisual = NucleotideAtomicRingFillVisual;
const param_definition_1 = require("../../../mol-util/param-definition");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
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 units_visual_1 = require("../units-visual");
const nucleotide_1 = require("./util/nucleotide");
const geometry_1 = require("../../../mol-math/geometry");
// TODO support ring-fills for multiple locations (including from microheterogeneity)
const pN1 = (0, linear_algebra_1.Vec3)();
const pC2 = (0, linear_algebra_1.Vec3)();
const pN3 = (0, linear_algebra_1.Vec3)();
const pC4 = (0, linear_algebra_1.Vec3)();
const pC5 = (0, linear_algebra_1.Vec3)();
const pC6 = (0, linear_algebra_1.Vec3)();
const pN7 = (0, linear_algebra_1.Vec3)();
const pC8 = (0, linear_algebra_1.Vec3)();
const pN9 = (0, linear_algebra_1.Vec3)();
const pC1_1 = (0, linear_algebra_1.Vec3)();
const pC2_1 = (0, linear_algebra_1.Vec3)();
const pC3_1 = (0, linear_algebra_1.Vec3)();
const pC4_1 = (0, linear_algebra_1.Vec3)();
const pO4_1 = (0, linear_algebra_1.Vec3)();
const mid = (0, linear_algebra_1.Vec3)();
const normal = (0, linear_algebra_1.Vec3)();
const shift = (0, linear_algebra_1.Vec3)();
exports.NucleotideAtomicRingFillMeshParams = {
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 }),
};
exports.DefaultNucleotideAtomicRingFillMeshProps = param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideAtomicRingFillMeshParams);
const positionsRing5_6 = new Float32Array(2 * 9 * 3);
const stripIndicesRing5_6 = new Uint32Array([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 14, 15, 12, 13, 8, 9, 10, 11, 0, 1]);
const fanIndicesTopRing5_6 = new Uint32Array([8, 12, 14, 16, 6, 4, 2, 0, 10]);
const fanIndicesBottomRing5_6 = new Uint32Array([9, 11, 1, 3, 5, 7, 17, 15, 13]);
const positionsRing5 = new Float32Array(2 * 6 * 3);
const stripIndicesRing5 = new Uint32Array([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 2, 3]);
const fanIndicesTopRing5 = new Uint32Array([0, 10, 8, 6, 4, 2, 10]);
const fanIndicesBottomRing5 = new Uint32Array([1, 3, 5, 7, 9, 11, 3]);
const positionsRing6 = new Float32Array(2 * 6 * 3);
const stripIndicesRing6 = new Uint32Array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 1]);
const fanIndicesTopRing6 = new Uint32Array([0, 10, 8, 6, 4, 2]);
const fanIndicesBottomRing6 = new Uint32Array([1, 3, 5, 7, 9, 11]);
const tmpShiftV = (0, linear_algebra_1.Vec3)();
function shiftPositions(out, dir, ...positions) {
for (let i = 0, il = positions.length; i < il; ++i) {
const v = positions[i];
linear_algebra_1.Vec3.toArray(linear_algebra_1.Vec3.add(tmpShiftV, v, dir), out, (i * 2) * 3);
linear_algebra_1.Vec3.toArray(linear_algebra_1.Vec3.sub(tmpShiftV, v, dir), out, (i * 2 + 1) * 3);
}
}
function createNucleotideAtomicRingFillMesh(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 } = props;
const vertexCount = nucleotideElementCount * 25;
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 thickness = sizeFactor * thicknessFactor;
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)();
builderState.currentGroup = i;
(0, nucleotide_1.setSugarIndices)(idx, unit, residueIndex);
if ((0, nucleotide_1.hasSugarIndices)(idx)) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.C2_1, pC2_1);
c.invariantPosition(idx.C3_1, pC3_1);
c.invariantPosition(idx.C4_1, pC4_1);
c.invariantPosition(idx.O4_1, pO4_1);
// sugar ring
linear_algebra_1.Vec3.triangleNormal(normal, pC3_1, pC4_1, pC1_1);
linear_algebra_1.Vec3.scale(mid, linear_algebra_1.Vec3.add(mid, pO4_1, linear_algebra_1.Vec3.add(mid, pC4_1, linear_algebra_1.Vec3.add(mid, pC3_1, linear_algebra_1.Vec3.add(mid, pC1_1, pC2_1)))), 0.2 /* 1 / 5 */);
linear_algebra_1.Vec3.scale(shift, normal, thickness);
shiftPositions(positionsRing5, shift, mid, pC3_1, pC4_1, pO4_1, pC1_1, pC2_1);
mesh_builder_1.MeshBuilder.addTriangleStrip(builderState, positionsRing5, stripIndicesRing5);
mesh_builder_1.MeshBuilder.addTriangleFanWithNormal(builderState, positionsRing5, fanIndicesTopRing5, normal);
linear_algebra_1.Vec3.negate(normal, normal);
mesh_builder_1.MeshBuilder.addTriangleFanWithNormal(builderState, positionsRing5, fanIndicesBottomRing5, normal);
}
const { isPurine, isPyrimidine } = (0, nucleotide_1.getNucleotideBaseType)(unit, residueIndex);
if (isPurine) {
(0, nucleotide_1.setPurinIndices)(idx, unit, residueIndex);
if ((0, nucleotide_1.hasPurinIndices)(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
c.invariantPosition(idx.N7, pN7);
c.invariantPosition(idx.C8, pC8), c.invariantPosition(idx.N9, pN9);
// base ring
linear_algebra_1.Vec3.triangleNormal(normal, pN1, pC4, pC5);
linear_algebra_1.Vec3.scale(shift, normal, thickness);
shiftPositions(positionsRing5_6, shift, pN1, pC2, pN3, pC4, pC5, pC6, pN7, pC8, pN9);
mesh_builder_1.MeshBuilder.addTriangleStrip(builderState, positionsRing5_6, stripIndicesRing5_6);
mesh_builder_1.MeshBuilder.addTriangleFanWithNormal(builderState, positionsRing5_6, fanIndicesTopRing5_6, normal);
linear_algebra_1.Vec3.negate(normal, normal);
mesh_builder_1.MeshBuilder.addTriangleFanWithNormal(builderState, positionsRing5_6, fanIndicesBottomRing5_6, normal);
}
}
else if (isPyrimidine) {
(0, nucleotide_1.setPyrimidineIndices)(idx, unit, residueIndex);
if ((0, nucleotide_1.hasPyrimidineIndices)(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
// base ring
linear_algebra_1.Vec3.triangleNormal(normal, pN1, pC4, pC5);
linear_algebra_1.Vec3.scale(shift, normal, thickness);
shiftPositions(positionsRing6, shift, pN1, pC2, pN3, pC4, pC5, pC6);
mesh_builder_1.MeshBuilder.addTriangleStrip(builderState, positionsRing6, stripIndicesRing6);
mesh_builder_1.MeshBuilder.addTriangleFanWithNormal(builderState, positionsRing6, fanIndicesTopRing6, normal);
linear_algebra_1.Vec3.negate(normal, normal);
mesh_builder_1.MeshBuilder.addTriangleFanWithNormal(builderState, positionsRing6, fanIndicesBottomRing6, normal);
}
}
++i;
}
}
}
const m = mesh_builder_1.MeshBuilder.getMesh(builderState);
const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, thickness);
m.setBoundingSphere(sphere);
return m;
}
exports.NucleotideAtomicRingFillParams = {
...units_visual_1.UnitsMeshParams,
...exports.NucleotideAtomicRingFillMeshParams
};
function NucleotideAtomicRingFillVisual(materialId) {
return (0, units_visual_1.UnitsMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideAtomicRingFillParams),
createGeometry: createNucleotideAtomicRingFillMesh,
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);
}
}, materialId);
}