molstar
Version:
A comprehensive macromolecular library.
172 lines (171 loc) • 7.38 kB
JavaScript
/**
* Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { UnitsPointsParams, UnitsPointsVisual } from '../units-visual';
import { Points } from '../../../mol-geo/geometry/points/points';
import { PointsBuilder } from '../../../mol-geo/geometry/points/points-builder';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { ElementIterator, getElementLoci, eachElement, makeElementIgnoreTest, getSerialElementLoci, eachSerialElement } from './util/element';
import { Sphere3D } from '../../../mol-math/geometry';
import { ComplexPointsParams, ComplexPointsVisual } from '../complex-visual';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const v3add = Vec3.add;
export const ElementPointParams = {
...UnitsPointsParams,
pointSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])),
traceOnly: PD.Boolean(false),
stride: PD.Numeric(1, { min: 1, max: 100, step: 1 }),
};
// TODO size
export function createElementPoint(ctx, unit, structure, theme, props, points) {
// TODO sizeFactor
const { child } = structure;
const childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id);
if (child && !childUnit)
return Points.createEmpty(points);
const { stride } = props;
const elements = unit.elements;
const n = elements.length;
const builder = PointsBuilder.create(n, n / 10, points);
const p = Vec3();
const c = unit.conformation;
const ignore = makeElementIgnoreTest(structure, unit, props);
const center = Vec3();
let count = 0;
if ((stride && stride > 1) || ignore) {
for (let i = 0; i < n; ++i) {
if (stride && i % stride !== 0)
continue;
if (ignore && ignore(elements[i]))
continue;
c.invariantPosition(elements[i], p);
v3add(center, center, p);
count += 1;
builder.add(p[0], p[1], p[2], i);
}
}
else {
for (let i = 0; i < n; ++i) {
c.invariantPosition(elements[i], p);
v3add(center, center, p);
count += 1;
builder.add(p[0], p[1], p[2], i);
}
}
const pt = builder.getPoints();
if (count === 0)
return pt;
// re-use boundingSphere if it has not changed much
let boundingSphere;
Vec3.scale(center, center, 1 / count);
const oldBoundingSphere = points ? Sphere3D.clone(points.boundingSphere) : undefined;
if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) {
boundingSphere = oldBoundingSphere;
}
else {
boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
}
pt.setBoundingSphere(boundingSphere);
return pt;
}
export function ElementPointVisual(materialId) {
return UnitsPointsVisual({
defaultProps: PD.getDefaultValues(ElementPointParams),
createGeometry: createElementPoint,
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.stride !== currentProps.stride);
}
}, materialId);
}
//
export function createStructureElementPoint(ctx, structure, theme, props, points) {
// TODO sizeFactor
const { child } = structure;
const { stride } = props;
const { getSerialIndex } = structure.serialMapping;
const structureElementCount = structure.elementCount;
const builder = PointsBuilder.create(structureElementCount, structureElementCount / 2, points);
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 Points.createEmpty(points);
const { elements, conformation: c } = unit;
const elementCount = elements.length;
const v = Vec3();
const ignore = makeElementIgnoreTest(structure, unit, props);
if ((stride && stride > 1) || ignore) {
for (let i = 0; i < elementCount; i++) {
const eI = elements[i];
if (stride && i % stride !== 0)
continue;
if (ignore && ignore(eI))
continue;
c.position(eI, v);
builder.add(v[0], v[1], v[2], getSerialIndex(unit, eI));
v3add(center, center, v);
count += 1;
}
}
else {
for (let i = 0; i < elementCount; i++) {
const eI = elements[i];
c.position(eI, v);
builder.add(v[0], v[1], v[2], getSerialIndex(unit, eI));
v3add(center, center, v);
}
count += elementCount;
}
}
const pt = builder.getPoints();
if (count === 0)
return pt;
// re-use boundingSphere if it has not changed much
let boundingSphere;
Vec3.scale(center, center, 1 / count);
const oldBoundingSphere = points ? Sphere3D.clone(points.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);
}
pt.setBoundingSphere(boundingSphere);
return pt;
}
export const StructureElementPointParams = {
...ComplexPointsParams,
pointSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])),
traceOnly: PD.Boolean(false),
stride: PD.Numeric(1, { min: 1, max: 100, step: 1 }),
};
export function StructureElementPointVisual(materialId) {
return ComplexPointsVisual({
defaultProps: PD.getDefaultValues(StructureElementPointParams),
createGeometry: createStructureElementPoint,
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.stride !== currentProps.stride);
}
}, materialId);
}