UNPKG

molstar

Version:

A comprehensive macromolecular library.

202 lines (201 loc) 12.4 kB
"use strict"; /** * Copyright (c) 2019 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.NucleotideRingVisual = exports.NucleotideRingParams = exports.DefaultNucleotideRingMeshProps = exports.NucleotideRingMeshParams = void 0; var tslib_1 = require("tslib"); var param_definition_1 = require("../../../mol-util/param-definition"); var linear_algebra_1 = require("../../../mol-math/linear-algebra"); var structure_1 = require("../../../mol-model/structure"); var mesh_1 = require("../../../mol-geo/geometry/mesh/mesh"); var mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder"); var int_1 = require("../../../mol-data/int"); var types_1 = require("../../../mol-model/structure/model/types"); var cylinder_1 = require("../../../mol-geo/geometry/mesh/builder/cylinder"); var sphere_1 = require("../../../mol-geo/geometry/mesh/builder/sphere"); var units_visual_1 = require("../units-visual"); var nucleotide_1 = require("./util/nucleotide"); var base_1 = require("../../../mol-geo/geometry/base"); var geometry_1 = require("../../../mol-math/geometry"); // TODO support rings for multiple locations (including from microheterogeneity) var pTrace = linear_algebra_1.Vec3.zero(); var pN1 = linear_algebra_1.Vec3.zero(); var pC2 = linear_algebra_1.Vec3.zero(); var pN3 = linear_algebra_1.Vec3.zero(); var pC4 = linear_algebra_1.Vec3.zero(); var pC5 = linear_algebra_1.Vec3.zero(); var pC6 = linear_algebra_1.Vec3.zero(); var pN7 = linear_algebra_1.Vec3.zero(); var pC8 = linear_algebra_1.Vec3.zero(); var pN9 = linear_algebra_1.Vec3.zero(); var normal = linear_algebra_1.Vec3.zero(); exports.NucleotideRingMeshParams = { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), }; exports.DefaultNucleotideRingMeshProps = param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideRingMeshParams); var positionsRing5_6 = new Float32Array(2 * 9 * 3); var stripIndicesRing5_6 = new Uint32Array([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 14, 15, 12, 13, 8, 9, 10, 11, 0, 1]); var fanIndicesTopRing5_6 = new Uint32Array([8, 12, 14, 16, 6, 4, 2, 0, 10]); var fanIndicesBottomRing5_6 = new Uint32Array([9, 11, 1, 3, 5, 7, 17, 15, 13]); var positionsRing6 = new Float32Array(2 * 6 * 3); var stripIndicesRing6 = new Uint32Array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 1]); var fanIndicesTopRing6 = new Uint32Array([0, 10, 8, 6, 4, 2]); var fanIndicesBottomRing6 = new Uint32Array([1, 3, 5, 7, 9, 11]); var tmpShiftV = linear_algebra_1.Vec3.zero(); function shiftPositions(out, dir) { var positions = []; for (var _i = 2; _i < arguments.length; _i++) { positions[_i - 2] = arguments[_i]; } for (var i = 0, il = positions.length; i < il; ++i) { var 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 createNucleotideRingMesh(ctx, unit, structure, theme, props, mesh) { if (!structure_1.Unit.isAtomic(unit)) return mesh_1.Mesh.createEmpty(mesh); var nucleotideElementCount = unit.nucleotideElements.length; if (!nucleotideElementCount) return mesh_1.Mesh.createEmpty(mesh); var sizeFactor = props.sizeFactor, radialSegments = props.radialSegments, detail = props.detail; var vertexCount = nucleotideElementCount * (26 + radialSegments * 2); var builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 4, mesh); var elements = unit.elements, model = unit.model; var _a = model.atomicHierarchy, chainAtomSegments = _a.chainAtomSegments, residueAtomSegments = _a.residueAtomSegments, atoms = _a.atoms, atomicIndex = _a.index; var _b = model.atomicHierarchy.derived.residue, moleculeType = _b.moleculeType, traceElementIndex = _b.traceElementIndex; var label_comp_id = atoms.label_comp_id; var pos = unit.conformation.invariantPosition; var chainIt = int_1.Segmentation.transientSegments(chainAtomSegments, elements); var residueIt = int_1.Segmentation.transientSegments(residueAtomSegments, elements); var radius = 1 * sizeFactor; var halfThickness = 1.25 * sizeFactor; var cylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments: radialSegments }; var i = 0; while (chainIt.hasNext) { residueIt.setSegment(chainIt.move()); while (residueIt.hasNext) { var residueIndex = residueIt.move().index; if ((0, types_1.isNucleic)(moleculeType[residueIndex])) { var compId = label_comp_id.value(residueAtomSegments.offsets[residueIndex]); var idxTrace = -1, idxN1 = -1, idxC2 = -1, idxN3 = -1, idxC4 = -1, idxC5 = -1, idxC6 = -1, idxN7 = -1, idxC8 = -1, idxN9 = -1; builderState.currentGroup = i; var isPurine = (0, types_1.isPurineBase)(compId); var isPyrimidine = (0, types_1.isPyrimidineBase)(compId); if (!isPurine && !isPyrimidine) { // detect Purine or Pyrimidin based on geometry var idxC4_1 = atomicIndex.findAtomOnResidue(residueIndex, 'C4'); var idxN9_1 = atomicIndex.findAtomOnResidue(residueIndex, 'N9'); if (idxC4_1 !== -1 && idxN9_1 !== -1 && linear_algebra_1.Vec3.distance(pos(idxC4_1, pC4), pos(idxN9_1, pN9)) < 1.6) { isPurine = true; } else { isPyrimidine = true; } } if (isPurine) { idxTrace = traceElementIndex[residueIndex]; idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1'); idxC2 = atomicIndex.findAtomOnResidue(residueIndex, 'C2'); idxN3 = atomicIndex.findAtomOnResidue(residueIndex, 'N3'); idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4'); idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'C5'); if (idxC5 === -1) { // modified ring, e.g. DP idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'N5'); } idxC6 = atomicIndex.findAtomOnResidue(residueIndex, 'C6'); idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'N7'); if (idxN7 === -1) { // modified ring, e.g. DP idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'C7'); } idxC8 = atomicIndex.findAtomOnResidue(residueIndex, 'C8'); idxN9 = atomicIndex.findAtomOnResidue(residueIndex, 'N9'); if (idxN9 !== -1 && idxTrace !== -1) { pos(idxN9, pN9); pos(idxTrace, pTrace); builderState.currentGroup = i; (0, cylinder_1.addCylinder)(builderState, pN9, pTrace, 1, cylinderProps); (0, sphere_1.addSphere)(builderState, pN9, radius, detail); } if (idxN1 !== -1 && idxC2 !== -1 && idxN3 !== -1 && idxC4 !== -1 && idxC5 !== -1 && idxC6 !== -1 && idxN7 !== -1 && idxC8 !== -1 && idxN9 !== -1) { pos(idxN1, pN1); pos(idxC2, pC2); pos(idxN3, pN3); pos(idxC4, pC4); pos(idxC5, pC5); pos(idxC6, pC6); pos(idxN7, pN7); pos(idxC8, pC8); linear_algebra_1.Vec3.triangleNormal(normal, pN1, pC4, pC5); linear_algebra_1.Vec3.scale(normal, normal, halfThickness); shiftPositions(positionsRing5_6, normal, pN1, pC2, pN3, pC4, pC5, pC6, pN7, pC8, pN9); mesh_builder_1.MeshBuilder.addTriangleStrip(builderState, positionsRing5_6, stripIndicesRing5_6); mesh_builder_1.MeshBuilder.addTriangleFan(builderState, positionsRing5_6, fanIndicesTopRing5_6); mesh_builder_1.MeshBuilder.addTriangleFan(builderState, positionsRing5_6, fanIndicesBottomRing5_6); } } else if (isPyrimidine) { idxTrace = traceElementIndex[residueIndex]; idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1'); if (idxN1 === -1) { // modified ring, e.g. DZ idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'C1'); } idxC2 = atomicIndex.findAtomOnResidue(residueIndex, 'C2'); idxN3 = atomicIndex.findAtomOnResidue(residueIndex, 'N3'); idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4'); idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'C5'); idxC6 = atomicIndex.findAtomOnResidue(residueIndex, 'C6'); if (idxN1 !== -1 && idxTrace !== -1) { pos(idxN1, pN1); pos(idxTrace, pTrace); builderState.currentGroup = i; (0, cylinder_1.addCylinder)(builderState, pN1, pTrace, 1, cylinderProps); (0, sphere_1.addSphere)(builderState, pN1, radius, detail); } if (idxN1 !== -1 && idxC2 !== -1 && idxN3 !== -1 && idxC4 !== -1 && idxC5 !== -1 && idxC6 !== -1) { pos(idxC2, pC2); pos(idxN3, pN3); pos(idxC4, pC4); pos(idxC5, pC5); pos(idxC6, pC6); linear_algebra_1.Vec3.triangleNormal(normal, pN1, pC4, pC5); linear_algebra_1.Vec3.scale(normal, normal, halfThickness); shiftPositions(positionsRing6, normal, pN1, pC2, pN3, pC4, pC5, pC6); mesh_builder_1.MeshBuilder.addTriangleStrip(builderState, positionsRing6, stripIndicesRing6); mesh_builder_1.MeshBuilder.addTriangleFan(builderState, positionsRing6, fanIndicesTopRing6); mesh_builder_1.MeshBuilder.addTriangleFan(builderState, positionsRing6, fanIndicesBottomRing6); } } ++i; } } } var m = mesh_builder_1.MeshBuilder.getMesh(builderState); var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor); m.setBoundingSphere(sphere); return m; } exports.NucleotideRingParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), exports.NucleotideRingMeshParams); function NucleotideRingVisual(materialId) { return (0, units_visual_1.UnitsMeshVisual)({ defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideRingParams), createGeometry: createNucleotideRingMesh, createLocationIterator: nucleotide_1.NucleotideLocationIterator.fromGroup, getLoci: nucleotide_1.getNucleotideElementLoci, eachLocation: nucleotide_1.eachNucleotideElement, setUpdateState: function (state, newProps, currentProps) { state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor || newProps.radialSegments !== currentProps.radialSegments); } }, materialId); } exports.NucleotideRingVisual = NucleotideRingVisual;