molstar
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A comprehensive macromolecular library.
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JavaScript
/**
* Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3 } from '../../../../mol-math/linear-algebra';
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { Mesh } from '../../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../../mol-geo/geometry/mesh/mesh-builder';
import { addFixedCountDashedCylinder, addCylinder, addDoubleCylinder } from '../../../../mol-geo/geometry/mesh/builder/cylinder';
import { BaseGeometry } from '../../../../mol-geo/geometry/base';
import { Lines } from '../../../../mol-geo/geometry/lines/lines';
import { LinesBuilder } from '../../../../mol-geo/geometry/lines/lines-builder';
import { Cylinders } from '../../../../mol-geo/geometry/cylinders/cylinders';
import { CylindersBuilder } from '../../../../mol-geo/geometry/cylinders/cylinders-builder';
export var LinkCylinderParams = {
linkScale: PD.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
linkSpacing: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
linkCap: PD.Boolean(false),
dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
dashScale: PD.Numeric(0.8, { min: 0, max: 2, step: 0.1 }),
dashCap: PD.Boolean(true),
stubCap: PD.Boolean(true),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
};
export var DefaultLinkCylinderProps = PD.getDefaultValues(LinkCylinderParams);
export var LinkLineParams = {
linkScale: PD.Numeric(0.5, { min: 0, max: 1, step: 0.1 }),
linkSpacing: PD.Numeric(0.1, { min: 0, max: 2, step: 0.01 }),
dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
};
export var DefaultLinkLineProps = PD.getDefaultValues(LinkLineParams);
var tmpV12 = Vec3();
var tmpShiftV12 = Vec3();
var tmpShiftV13 = Vec3();
var up = Vec3.create(0, 1, 0);
/** Calculate 'shift' direction that is perpendiculat to v1 - v2 and goes through v3 */
export function calculateShiftDir(out, v1, v2, v3) {
Vec3.normalize(tmpShiftV12, Vec3.sub(tmpShiftV12, v1, v2));
if (v3 !== null) {
Vec3.sub(tmpShiftV13, v1, v3);
}
else {
Vec3.copy(tmpShiftV13, v1); // no reference point, use v1
}
Vec3.normalize(tmpShiftV13, tmpShiftV13);
// ensure v13 and v12 are not colinear
var dp = Vec3.dot(tmpShiftV12, tmpShiftV13);
if (1 - Math.abs(dp) < 1e-5) {
Vec3.set(tmpShiftV13, 1, 0, 0);
dp = Vec3.dot(tmpShiftV12, tmpShiftV13);
if (1 - Math.abs(dp) < 1e-5) {
Vec3.set(tmpShiftV13, 0, 1, 0);
dp = Vec3.dot(tmpShiftV12, tmpShiftV13);
}
}
Vec3.setMagnitude(tmpShiftV12, tmpShiftV12, dp);
Vec3.sub(tmpShiftV13, tmpShiftV13, tmpShiftV12);
return Vec3.normalize(out, tmpShiftV13);
}
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
var v3scale = Vec3.scale;
var v3add = Vec3.add;
var v3sub = Vec3.sub;
var v3setMagnitude = Vec3.setMagnitude;
var v3dot = Vec3.dot;
/**
* Each edge is included twice to allow for coloring/picking
* the half closer to the first vertex, i.e. vertex a.
*/
export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
if (!linkCount)
return Mesh.createEmpty(mesh);
var linkScale = props.linkScale, linkSpacing = props.linkSpacing, radialSegments = props.radialSegments, linkCap = props.linkCap, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
var vertexCountEstimate = radialSegments * 2 * linkCount * 2;
var builderState = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 4, mesh);
var va = Vec3();
var vb = Vec3();
var vShift = Vec3();
var cylinderProps = {
radiusTop: 1,
radiusBottom: 1,
radialSegments: radialSegments,
topCap: linkCap,
bottomCap: linkCap
};
var segmentCount = dashCount + 1;
for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
if (ignore && ignore(edgeIndex))
continue;
position(va, vb, edgeIndex);
v3sub(tmpV12, vb, va);
var dirFlag = v3dot(tmpV12, up) > 0;
var linkRadius = radius(edgeIndex);
var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
var _a = dirFlag ? [linkStub, linkCap] : [linkCap, linkStub], topCap = _a[0], bottomCap = _a[1];
builderState.currentGroup = edgeIndex;
var aromaticOffsetFactor = 5.5;
var multipleOffsetFactor = 4;
if (linkStyle === 0 /* Solid */) {
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
cylinderProps.topCap = topCap;
cylinderProps.bottomCap = bottomCap;
addCylinder(builderState, va, vb, 0.5, cylinderProps);
}
else if (linkStyle === 1 /* Dashed */) {
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * dashScale;
cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
}
else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
var multiRadius = linkRadius * (linkScale / (0.5 * order));
var absOffset = (linkRadius - multiRadius) * linkSpacing;
calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
cylinderProps.topCap = topCap;
cylinderProps.bottomCap = bottomCap;
if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
addCylinder(builderState, va, vb, 0.5, cylinderProps);
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * linkScale;
cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
if (linkStyle === 8 /* MirroredAromatic */) {
v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
}
}
else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
v3setMagnitude(vShift, vShift, absOffset);
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
addCylinder(builderState, va, vb, 0.5, cylinderProps);
v3scale(tmpV12, tmpV12, linkSpacing * linkScale * 0.2);
v3add(va, va, tmpV12);
v3sub(vb, vb, tmpV12);
cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
cylinderProps.topCap = dirFlag ? linkStub : dashCap;
cylinderProps.bottomCap = dirFlag ? dashCap : linkStub;
v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
addCylinder(builderState, va, vb, 0.5, cylinderProps);
if (order === 3) {
v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
addCylinder(builderState, va, vb, 0.5, cylinderProps);
}
}
else {
v3setMagnitude(vShift, vShift, absOffset);
cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
if (order === 3)
addCylinder(builderState, va, vb, 0.5, cylinderProps);
addDoubleCylinder(builderState, va, vb, 0.5, vShift, cylinderProps);
}
}
else if (linkStyle === 6 /* Disk */) {
v3scale(tmpV12, tmpV12, 0.475);
v3add(va, va, tmpV12);
v3sub(vb, vb, tmpV12);
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
cylinderProps.topCap = topCap;
cylinderProps.bottomCap = bottomCap;
addCylinder(builderState, va, vb, 0.5, cylinderProps);
}
}
return MeshBuilder.getMesh(builderState);
}
/**
* Each edge is included twice to allow for coloring/picking
* the half closer to the first vertex, i.e. vertex a.
*/
export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
if (!linkCount)
return Cylinders.createEmpty(cylinders);
var linkScale = props.linkScale, linkSpacing = props.linkSpacing, linkCap = props.linkCap, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
var cylindersCountEstimate = linkCount * 2;
var builder = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
var va = Vec3();
var vb = Vec3();
var vm = Vec3();
var vShift = Vec3();
// automatically adjust length for evenly spaced dashed cylinders
var segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
var aromaticSegmentCount = 3;
var aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
var aromaticOffsetFactor = 5.5;
var multipleOffsetFactor = 4;
for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
if (ignore && ignore(edgeIndex))
continue;
position(va, vb, edgeIndex);
var linkRadius = radius(edgeIndex);
var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
if (linkStyle === 0 /* Solid */) {
v3scale(vm, v3add(vm, va, vb), 0.5);
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
}
else if (linkStyle === 1 /* Dashed */) {
v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
v3sub(vb, vb, tmpV12);
builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
}
else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
var multiScale = linkScale / (0.5 * order);
var absOffset = (linkRadius - multiScale * linkRadius) * linkSpacing;
v3scale(vm, v3add(vm, va, vb), 0.5);
calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
v3sub(vb, vb, tmpV12);
v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
if (linkStyle === 8 /* MirroredAromatic */) {
v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
}
}
else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale * 0.2);
v3sub(va, va, tmpV12);
if (order === 3)
builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, dashCap, linkStub, edgeIndex);
}
else {
v3setMagnitude(vShift, vShift, absOffset);
if (order === 3)
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, linkStub, edgeIndex);
builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, linkCap, linkStub, edgeIndex);
}
}
else if (linkStyle === 6 /* Disk */) {
v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
v3add(va, va, tmpV12);
v3sub(vb, vb, tmpV12);
builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], 1, linkCap, linkStub, edgeIndex);
}
}
return builder.getCylinders();
}
/**
* Each edge is included twice to allow for coloring/picking
* the half closer to the first vertex, i.e. vertex a.
*/
export function createLinkLines(ctx, linkBuilder, props, lines) {
var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, ignore = linkBuilder.ignore;
if (!linkCount)
return Lines.createEmpty(lines);
var linkScale = props.linkScale, linkSpacing = props.linkSpacing, dashCount = props.dashCount;
var linesCountEstimate = linkCount * 2;
var builder = LinesBuilder.create(linesCountEstimate, linesCountEstimate / 4, lines);
var va = Vec3();
var vb = Vec3();
var vm = Vec3();
var vShift = Vec3();
// automatically adjust length for evenly spaced dashed lines
var segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
var aromaticSegmentCount = 3;
var aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
var aromaticOffsetFactor = 4.5;
var multipleOffsetFactor = 3;
for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
if (ignore && ignore(edgeIndex))
continue;
position(va, vb, edgeIndex);
var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
if (linkStyle === 0 /* Solid */) {
v3scale(vm, v3add(vm, va, vb), 0.5);
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
}
else if (linkStyle === 1 /* Dashed */) {
v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
v3sub(vb, vb, tmpV12);
builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
}
else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
var multiRadius = 1 * (linkScale / (0.5 * order));
var absOffset = (1 - multiRadius) * linkSpacing;
v3scale(vm, v3add(vm, va, vb), 0.5);
calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
v3sub(vb, vb, tmpV12);
v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
if (linkStyle === 8 /* MirroredAromatic */) {
v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
}
}
else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale);
v3sub(va, va, tmpV12);
if (order === 3)
builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], edgeIndex);
builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], edgeIndex);
}
else {
v3setMagnitude(vShift, vShift, absOffset * 1.5);
if (order === 3)
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], edgeIndex);
builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], edgeIndex);
}
}
else if (linkStyle === 6 /* Disk */) {
v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
v3add(va, va, tmpV12);
v3sub(vb, vb, tmpV12);
// TODO what to do here? Line as disk doesn't work well.
builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], edgeIndex);
}
}
return builder.getLines();
}
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