molstar
Version:
A comprehensive macromolecular library.
179 lines (178 loc) • 8.11 kB
JavaScript
/**
* Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { UnitsLinesParams, UnitsLinesVisual } from '../units-visual';
import { Unit } from '../../../mol-model/structure';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { ElementIterator, getElementLoci, eachElement, makeElementIgnoreTest, getSerialElementLoci, eachSerialElement } from './util/element';
import { Sphere3D } from '../../../mol-math/geometry';
import { Lines } from '../../../mol-geo/geometry/lines/lines';
import { LinesBuilder } from '../../../mol-geo/geometry/lines/lines-builder';
import { bondCount } from '../../../mol-model-props/computed/chemistry/util';
import { hasUnitVisibleBonds } from './util/bond';
import { ComplexLinesParams, ComplexLinesVisual } from '../complex-visual';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const v3add = Vec3.add;
const v3scaleAndAdd = Vec3.scaleAndAdd;
const v3unitX = Vec3.unitX;
const v3unitY = Vec3.unitY;
const v3unitZ = Vec3.unitZ;
export const ElementCrossParams = {
...UnitsLinesParams,
lineSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])),
traceOnly: PD.Boolean(false),
crosses: PD.Select('lone', PD.arrayToOptions(['lone', 'all'])),
crossSize: PD.Numeric(0.35, { min: 0, max: 2, step: 0.01 }),
};
export function createElementCross(ctx, unit, structure, theme, props, lines) {
const { child } = structure;
if (child && !child.unitMap.get(unit.id))
return Lines.createEmpty(lines);
const elements = unit.elements;
const n = elements.length;
const builder = LinesBuilder.create(n, n / 10, lines);
const p = Vec3();
const s = Vec3();
const e = Vec3();
const c = unit.conformation;
const ignore = makeElementIgnoreTest(structure, unit, props);
const r = props.crossSize / 2;
const lone = props.crosses === 'lone';
const center = Vec3();
let count = 0;
for (let i = 0; i < n; ++i) {
if (ignore && ignore(elements[i]))
continue;
if (lone && Unit.isAtomic(unit) && hasUnitVisibleBonds(unit, props) && bondCount(structure, unit, i) !== 0)
continue;
c.invariantPosition(elements[i], p);
v3add(center, center, p);
count += 1;
v3scaleAndAdd(s, p, v3unitX, r);
v3scaleAndAdd(e, p, v3unitX, -r);
builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
v3scaleAndAdd(s, p, v3unitY, r);
v3scaleAndAdd(e, p, v3unitY, -r);
builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
v3scaleAndAdd(s, p, v3unitZ, r);
v3scaleAndAdd(e, p, v3unitZ, -r);
builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
}
const l = builder.getLines();
if (count === 0)
return l;
// re-use boundingSphere if it has not changed much
let boundingSphere;
Vec3.scale(center, center, 1 / count);
const oldBoundingSphere = lines ? Sphere3D.clone(lines.boundingSphere) : undefined;
if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) {
boundingSphere = oldBoundingSphere;
}
else {
boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
}
l.setBoundingSphere(boundingSphere);
return l;
}
export function ElementCrossVisual(materialId) {
return UnitsLinesVisual({
defaultProps: PD.getDefaultValues(ElementCrossParams),
createGeometry: createElementCross,
createLocationIterator: ElementIterator.fromGroup,
getLoci: getElementLoci,
eachLocation: eachElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.traceOnly !== currentProps.traceOnly ||
newProps.crosses !== currentProps.crosses ||
newProps.crossSize !== currentProps.crossSize);
}
}, materialId);
}
//
export function createStructureElementCross(ctx, structure, theme, props, lines) {
const { child } = structure;
const { getSerialIndex } = structure.serialMapping;
const structureElementCount = structure.elementCount;
const builder = LinesBuilder.create(structureElementCount, structureElementCount / 2, lines);
const p = Vec3();
const s = Vec3();
const e = Vec3();
const r = props.crossSize / 2;
const lone = props.crosses === 'lone';
const center = Vec3();
let count = 0;
for (const unit of structure.units) {
const childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id);
if (child && !childUnit)
return Lines.createEmpty(lines);
const { elements, conformation: c } = unit;
const elementCount = elements.length;
const ignore = makeElementIgnoreTest(structure, unit, props);
for (let i = 0; i < elementCount; i++) {
if (ignore && ignore(elements[i]))
continue;
if (lone && Unit.isAtomic(unit) && hasUnitVisibleBonds(unit, props) && bondCount(structure, unit, i) !== 0)
continue;
c.position(elements[i], p);
v3add(center, center, p);
count += 1;
const si = getSerialIndex(unit, elements[i]);
v3scaleAndAdd(s, p, v3unitX, r);
v3scaleAndAdd(e, p, v3unitX, -r);
builder.add(s[0], s[1], s[2], e[0], e[1], e[2], si);
v3scaleAndAdd(s, p, v3unitY, r);
v3scaleAndAdd(e, p, v3unitY, -r);
builder.add(s[0], s[1], s[2], e[0], e[1], e[2], si);
v3scaleAndAdd(s, p, v3unitZ, r);
v3scaleAndAdd(e, p, v3unitZ, -r);
builder.add(s[0], s[1], s[2], e[0], e[1], e[2], si);
}
}
const l = builder.getLines();
if (count === 0)
return l;
// re-use boundingSphere if it has not changed much
let boundingSphere;
Vec3.scale(center, center, 1 / count);
const oldBoundingSphere = lines ? Sphere3D.clone(lines.boundingSphere) : undefined;
if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
boundingSphere = oldBoundingSphere;
}
else {
boundingSphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
}
l.setBoundingSphere(boundingSphere);
return l;
}
export const StructureElementCrossParams = {
...ComplexLinesParams,
lineSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])),
traceOnly: PD.Boolean(false),
crosses: PD.Select('lone', PD.arrayToOptions(['lone', 'all'])),
crossSize: PD.Numeric(0.35, { min: 0, max: 2, step: 0.01 }),
};
export function StructureElementCrossVisual(materialId) {
return ComplexLinesVisual({
defaultProps: PD.getDefaultValues(StructureElementCrossParams),
createGeometry: createStructureElementCross,
createLocationIterator: ElementIterator.fromStructure,
getLoci: getSerialElementLoci,
eachLocation: eachSerialElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.traceOnly !== currentProps.traceOnly ||
newProps.crosses !== currentProps.crosses ||
newProps.crossSize !== currentProps.crossSize);
}
}, materialId);
}