molstar
Version:
A comprehensive macromolecular library.
309 lines (308 loc) • 19.2 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.NucleotideAtomicBondParams = void 0;
exports.NucleotideAtomicBondVisual = NucleotideAtomicBondVisual;
exports.NucleotideAtomicBondImpostorVisual = NucleotideAtomicBondImpostorVisual;
exports.NucleotideAtomicBondMeshVisual = NucleotideAtomicBondMeshVisual;
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 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");
const cylinders_1 = require("../../../mol-geo/geometry/cylinders/cylinders");
const cylinders_builder_1 = require("../../../mol-geo/geometry/cylinders/cylinders-builder");
const pTrace = (0, linear_algebra_1.Vec3)();
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)();
exports.NucleotideAtomicBondParams = {
...units_visual_1.UnitsMeshParams,
...units_visual_1.UnitsCylindersParams,
sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo),
tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true)
};
function NucleotideAtomicBondVisual(materialId, structure, props, webgl) {
return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
? NucleotideAtomicBondImpostorVisual(materialId)
: NucleotideAtomicBondMeshVisual(materialId);
}
function createNucleotideAtomicBondImpostor(ctx, unit, structure, theme, props, cylinders) {
if (!structure_1.Unit.isAtomic(unit))
return cylinders_1.Cylinders.createEmpty(cylinders);
const nucleotideElementCount = unit.nucleotideElements.length;
if (!nucleotideElementCount)
return cylinders_1.Cylinders.createEmpty(cylinders);
const cylindersCountEstimate = nucleotideElementCount * 15; // 15 is the average purine (17) & pirimidine (13) bonds
const builder = cylinders_builder_1.CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
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);
let i = 0;
const colorModeFlag = 2.0;
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)();
(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);
// trace cylinder
c.invariantPosition(idx.trace, pTrace);
builder.add(pC3_1[0], pC3_1[1], pC3_1[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
// sugar ring
builder.add(pC3_1[0], pC3_1[1], pC3_1[2], pC4_1[0], pC4_1[1], pC4_1[2], 1, true, true, colorModeFlag, i);
builder.add(pC4_1[0], pC4_1[1], pC4_1[2], pO4_1[0], pO4_1[1], pO4_1[2], 1, true, true, colorModeFlag, i);
builder.add(pO4_1[0], pO4_1[1], pO4_1[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
builder.add(pC1_1[0], pC1_1[1], pC1_1[2], pC2_1[0], pC2_1[1], pC2_1[2], 1, true, true, colorModeFlag, i);
builder.add(pC2_1[0], pC2_1[1], pC2_1[2], pC3_1[0], pC3_1[1], pC3_1[2], 1, true, true, colorModeFlag, i);
}
const { isPurine, isPyrimidine } = (0, nucleotide_1.getNucleotideBaseType)(unit, residueIndex);
if (isPurine) {
(0, nucleotide_1.setPurinIndices)(idx, unit, residueIndex);
if (idx.C1_1 !== -1 && idx.N9 !== -1) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.N9, pN9);
builder.add(pN9[0], pN9[1], pN9[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
}
else if (idx.N9 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx.N9, pN9);
c.invariantPosition(idx.trace, pTrace);
builder.add(pN9[0], pN9[1], pN9[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
}
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
builder.add(pN9[0], pN9[1], pN9[2], pC8[0], pC8[1], pC8[2], 1, true, true, colorModeFlag, i);
builder.add(pC8[0], pC8[1], pC8[2], pN7[0], pN7[1], pN7[2], 1, true, true, colorModeFlag, i);
builder.add(pN7[0], pN7[1], pN7[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
builder.add(pC5[0], pC5[1], pC5[2], pC6[0], pC6[1], pC6[2], 1, true, true, colorModeFlag, i);
builder.add(pC6[0], pC6[1], pC6[2], pN1[0], pN1[1], pN1[2], 1, true, true, colorModeFlag, i);
builder.add(pN1[0], pN1[1], pN1[2], pC2[0], pC2[1], pC2[2], 1, true, true, colorModeFlag, i);
builder.add(pC2[0], pC2[1], pC2[2], pN3[0], pN3[1], pN3[2], 1, true, true, colorModeFlag, i);
builder.add(pN3[0], pN3[1], pN3[2], pC4[0], pC4[1], pC4[2], 1, true, true, colorModeFlag, i);
builder.add(pC4[0], pC4[1], pC4[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
builder.add(pC4[0], pC4[1], pC4[2], pN9[0], pN9[1], pN9[2], 1, true, true, colorModeFlag, i);
}
}
else if (isPyrimidine) {
(0, nucleotide_1.setPyrimidineIndices)(idx, unit, residueIndex);
if (idx.C1_1 !== -1 && idx.N1 !== -1) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C1_1, pC1_1);
builder.add(pN1[0], pN1[1], pN1[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
}
else if (idx.N1 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.trace, pTrace);
builder.add(pN1[0], pN1[1], pN1[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
}
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
builder.add(pN1[0], pN1[1], pN1[2], pC6[0], pC6[1], pC6[2], 1, true, true, colorModeFlag, i);
builder.add(pC6[0], pC6[1], pC6[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
builder.add(pC5[0], pC5[1], pC5[2], pC4[0], pC4[1], pC4[2], 1, true, true, colorModeFlag, i);
builder.add(pC4[0], pC4[1], pC4[2], pN3[0], pN3[1], pN3[2], 1, true, true, colorModeFlag, i);
builder.add(pN3[0], pN3[1], pN3[2], pC2[0], pC2[1], pC2[2], 1, true, true, colorModeFlag, i);
builder.add(pC2[0], pC2[1], pC2[2], pN1[0], pN1[1], pN1[2], 1, true, true, colorModeFlag, i);
}
}
++i;
}
}
}
const cy = builder.getCylinders();
const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor);
cy.setBoundingSphere(sphere);
return cy;
}
function NucleotideAtomicBondImpostorVisual(materialId) {
return (0, units_visual_1.UnitsCylindersVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideAtomicBondParams),
createGeometry: createNucleotideAtomicBondImpostor,
createLocationIterator: nucleotide_1.NucleotideLocationIterator.fromGroup,
getLoci: nucleotide_1.getNucleotideElementLoci,
eachLocation: nucleotide_1.eachNucleotideElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor);
},
mustRecreate: (structureGroup, props, webgl) => {
return !props.tryUseImpostor || !webgl;
}
}, materialId);
}
function createNucleotideAtomicBondMesh(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, radialSegments } = props;
const vertexCount = nucleotideElementCount * (radialSegments * 15); // 15 is the average purine (17) & pirimidine (13) bonds
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 cylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments };
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);
// trace cylinder
c.invariantPosition(idx.trace, pTrace);
(0, cylinder_1.addCylinder)(builderState, pC3_1, pTrace, 1, cylinderProps);
// sugar ring
(0, cylinder_1.addCylinder)(builderState, pC3_1, pC4_1, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC4_1, pO4_1, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pO4_1, pC1_1, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC1_1, pC2_1, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC2_1, pC3_1, 1, cylinderProps);
}
const { isPurine, isPyrimidine } = (0, nucleotide_1.getNucleotideBaseType)(unit, residueIndex);
if (isPurine) {
(0, nucleotide_1.setPurinIndices)(idx, unit, residueIndex);
if (idx.C1_1 !== -1 && idx.N9 !== -1) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.N9, pN9);
(0, cylinder_1.addCylinder)(builderState, pN9, pC1_1, 1, cylinderProps);
}
else if (idx.N9 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx.N9, pN9);
c.invariantPosition(idx.trace, pTrace);
(0, cylinder_1.addCylinder)(builderState, pN9, pTrace, 1, cylinderProps);
}
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
(0, cylinder_1.addCylinder)(builderState, pN9, pC8, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC8, pN7, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pN7, pC5, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC5, pC6, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC6, pN1, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pN1, pC2, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC2, pN3, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pN3, pC4, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC4, pC5, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC4, pN9, 1, cylinderProps);
}
}
else if (isPyrimidine) {
(0, nucleotide_1.setPyrimidineIndices)(idx, unit, residueIndex);
if (idx.C1_1 !== -1 && idx.N1 !== -1) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C1_1, pC1_1);
(0, cylinder_1.addCylinder)(builderState, pN1, pC1_1, 1, cylinderProps);
}
else if (idx.N1 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.trace, pTrace);
(0, cylinder_1.addCylinder)(builderState, pN1, pTrace, 1, cylinderProps);
}
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
(0, cylinder_1.addCylinder)(builderState, pN1, pC6, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC6, pC5, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC5, pC4, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC4, pN3, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pN3, pC2, 1, cylinderProps);
(0, cylinder_1.addCylinder)(builderState, pC2, pN1, 1, cylinderProps);
}
}
++i;
}
}
}
const m = mesh_builder_1.MeshBuilder.getMesh(builderState);
const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
return m;
}
function NucleotideAtomicBondMeshVisual(materialId) {
return (0, units_visual_1.UnitsMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideAtomicBondParams),
createGeometry: createNucleotideAtomicBondMesh,
createLocationIterator: nucleotide_1.NucleotideLocationIterator.fromGroup,
getLoci: nucleotide_1.getNucleotideElementLoci,
eachLocation: nucleotide_1.eachNucleotideElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.radialSegments !== currentProps.radialSegments);
},
mustRecreate: (structureGroup, props, webgl) => {
return props.tryUseImpostor && !!webgl;
}
}, materialId);
}