molstar
Version:
A comprehensive macromolecular library.
283 lines (282 loc) • 15.1 kB
JavaScript
;
/**
* Copyright (c) 2019-2020 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.DihedralParams = void 0;
exports.DihedralRepresentation = DihedralRepresentation;
const loci_1 = require("../../../mol-model/loci");
const lines_1 = require("../../../mol-geo/geometry/lines/lines");
const text_1 = require("../../../mol-geo/geometry/text/text");
const param_definition_1 = require("../../../mol-util/param-definition");
const names_1 = require("../../../mol-util/color/names");
const representation_1 = require("../representation");
const representation_2 = require("../../representation");
const shape_1 = require("../../../mol-model/shape");
const lines_builder_1 = require("../../../mol-geo/geometry/lines/lines-builder");
const text_builder_1 = require("../../../mol-geo/geometry/text/text-builder");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
const mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder");
const misc_1 = require("../../../mol-math/misc");
const circle_1 = require("../../../mol-geo/primitive/circle");
const primitive_1 = require("../../../mol-geo/primitive/primitive");
const marker_action_1 = require("../../../mol-util/marker-action");
const label_1 = require("../../../mol-theme/label");
const common_1 = require("./common");
const geometry_1 = require("../../../mol-math/geometry");
const SharedParams = {
color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen),
arcScale: param_definition_1.ParamDefinition.Numeric(0.7, { min: 0.01, max: 1, step: 0.01 })
};
const LinesParams = {
...lines_1.Lines.Params,
...SharedParams,
lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true),
linesSize: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 5, step: 0.01 }),
dashLength: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 0.2, step: 0.01 }),
};
const VectorsParams = {
...LinesParams
};
const ExtendersParams = {
...LinesParams
};
const ArmsParams = {
...LinesParams
};
const ArcParams = {
...LinesParams
};
const SectorParams = {
...mesh_1.Mesh.Params,
...SharedParams,
ignoreLight: param_definition_1.ParamDefinition.Boolean(true),
sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.75, { min: 0, max: 1, step: 0.01 }),
};
const DihedralVisuals = {
'vectors': (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: s => ({ ...s, pickable: false }) }),
'extenders': (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getExtendersShape, lines_1.Lines.Utils, { modifyState: s => ({ ...s, pickable: false }) }),
'connector': (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getConnectorShape, lines_1.Lines.Utils, { modifyState: s => ({ ...s, pickable: false }) }),
'arms': (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getArmsShape, lines_1.Lines.Utils, { modifyState: s => ({ ...s, pickable: false }) }),
'arc': (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: s => ({ ...s, pickable: false }) }),
'sector': (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: p => ({ ...p, alpha: p.sectorOpacity }), modifyState: s => ({ ...s, markerActions: marker_action_1.MarkerActions.Highlighting }) }),
'text': (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: s => ({ ...s, markerActions: marker_action_1.MarkerAction.None }) }),
};
exports.DihedralParams = {
...VectorsParams,
...ExtendersParams,
...ArmsParams,
...ArcParams,
...SectorParams,
...common_1.LociLabelTextParams,
visuals: param_definition_1.ParamDefinition.MultiSelect(['extenders', 'arms', 'sector', 'text'], param_definition_1.ParamDefinition.objectToOptions(DihedralVisuals)),
};
//
function getDihedralState() {
return {
sphereA: (0, geometry_1.Sphere3D)(),
sphereB: (0, geometry_1.Sphere3D)(),
sphereC: (0, geometry_1.Sphere3D)(),
sphereD: (0, geometry_1.Sphere3D)(),
dirBA: (0, linear_algebra_1.Vec3)(),
dirCD: (0, linear_algebra_1.Vec3)(),
projA: (0, linear_algebra_1.Vec3)(),
projD: (0, linear_algebra_1.Vec3)(),
arcPointA: (0, linear_algebra_1.Vec3)(),
arcPointD: (0, linear_algebra_1.Vec3)(),
arcDirA: (0, linear_algebra_1.Vec3)(),
arcDirD: (0, linear_algebra_1.Vec3)(),
arcCenter: (0, linear_algebra_1.Vec3)(),
arcNormal: (0, linear_algebra_1.Vec3)(),
radius: 0,
angle: 0,
};
}
const tmpVec = (0, linear_algebra_1.Vec3)();
const tmpMat = (0, linear_algebra_1.Mat4)();
// TODO improper dihedrals are not handled correctly
function setDihedralState(quad, state, arcScale) {
const { sphereA, sphereB, sphereC, sphereD, dirBA, dirCD, projA, projD } = state;
const { arcPointA, arcPointD, arcDirA, arcDirD, arcCenter, arcNormal } = state;
const [lociA, lociB, lociC, lociD] = quad.loci;
loci_1.Loci.getBoundingSphere(lociA, sphereA);
loci_1.Loci.getBoundingSphere(lociB, sphereB);
loci_1.Loci.getBoundingSphere(lociC, sphereC);
loci_1.Loci.getBoundingSphere(lociD, sphereD);
linear_algebra_1.Vec3.add(arcCenter, sphereB.center, sphereC.center);
linear_algebra_1.Vec3.scale(arcCenter, arcCenter, 0.5);
linear_algebra_1.Vec3.sub(dirBA, sphereA.center, sphereB.center);
linear_algebra_1.Vec3.sub(dirCD, sphereD.center, sphereC.center);
linear_algebra_1.Vec3.add(arcPointA, arcCenter, dirBA);
linear_algebra_1.Vec3.add(arcPointD, arcCenter, dirCD);
linear_algebra_1.Vec3.sub(arcNormal, sphereC.center, sphereB.center);
linear_algebra_1.Vec3.orthogonalize(arcDirA, arcNormal, dirBA);
linear_algebra_1.Vec3.orthogonalize(arcDirD, arcNormal, dirCD);
linear_algebra_1.Vec3.projectPointOnVector(projA, arcPointA, arcDirA, arcCenter);
linear_algebra_1.Vec3.projectPointOnVector(projD, arcPointD, arcDirD, arcCenter);
const len = Math.min(linear_algebra_1.Vec3.distance(projA, arcCenter), linear_algebra_1.Vec3.distance(projD, arcCenter));
const radius = len * arcScale;
linear_algebra_1.Vec3.setMagnitude(arcDirA, arcDirA, radius);
linear_algebra_1.Vec3.setMagnitude(arcDirD, arcDirD, radius);
linear_algebra_1.Vec3.add(arcPointA, arcCenter, arcDirA);
linear_algebra_1.Vec3.add(arcPointD, arcCenter, arcDirD);
state.radius = radius;
state.angle = linear_algebra_1.Vec3.dihedralAngle(sphereA.center, sphereB.center, sphereC.center, sphereD.center);
linear_algebra_1.Vec3.matchDirection(tmpVec, arcNormal, linear_algebra_1.Vec3.sub(tmpVec, arcPointA, sphereA.center));
const angleA = linear_algebra_1.Vec3.angle(dirBA, tmpVec);
const lenA = radius / Math.cos(angleA - misc_1.halfPI);
linear_algebra_1.Vec3.add(projA, sphereB.center, linear_algebra_1.Vec3.setMagnitude(tmpVec, dirBA, lenA));
linear_algebra_1.Vec3.matchDirection(tmpVec, arcNormal, linear_algebra_1.Vec3.sub(tmpVec, arcPointD, sphereD.center));
const angleD = linear_algebra_1.Vec3.angle(dirCD, tmpVec);
const lenD = radius / Math.cos(angleD - misc_1.halfPI);
linear_algebra_1.Vec3.add(projD, sphereC.center, linear_algebra_1.Vec3.setMagnitude(tmpVec, dirCD, lenD));
return state;
}
function getCircle(state, segmentLength) {
const { radius, angle } = state;
const segments = segmentLength ? (0, misc_1.arcLength)(angle, radius) / segmentLength : 32;
linear_algebra_1.Mat4.targetTo(tmpMat, state.arcCenter, angle < 0 ? state.arcPointD : state.arcPointA, state.arcNormal);
linear_algebra_1.Mat4.setTranslation(tmpMat, state.arcCenter);
linear_algebra_1.Mat4.mul(tmpMat, tmpMat, linear_algebra_1.Mat4.rotY180);
const circle = (0, circle_1.Circle)({ radius, thetaLength: Math.abs(angle), segments });
return (0, primitive_1.transformPrimitive)(circle, tmpMat);
}
const tmpState = getDihedralState();
function getDihedralName(data) {
return data.quads.length === 1 ? `Dihedral ${(0, label_1.dihedralLabel)(data.quads[0], { measureOnly: true })}` : `${data.quads.length} Dihedrals`;
}
//
function buildVectorsLines(data, props, lines) {
const builder = lines_builder_1.LinesBuilder.create(128, 64, lines);
for (let i = 0, il = data.quads.length; i < il; ++i) {
setDihedralState(data.quads[i], tmpState, props.arcScale);
builder.addFixedLengthDashes(tmpState.arcCenter, tmpState.arcPointA, props.dashLength, i);
builder.addFixedLengthDashes(tmpState.arcCenter, tmpState.arcPointD, props.dashLength, i);
}
return builder.getLines();
}
function getVectorsShape(ctx, data, props, shape) {
const lines = buildVectorsLines(data, props, shape && shape.geometry);
const name = getDihedralName(data);
return shape_1.Shape.create(name, data, lines, () => props.color, () => props.linesSize, () => '');
}
//
function buildConnectorLine(data, props, lines) {
const builder = lines_builder_1.LinesBuilder.create(128, 64, lines);
for (let i = 0, il = data.quads.length; i < il; ++i) {
setDihedralState(data.quads[i], tmpState, props.arcScale);
builder.addFixedLengthDashes(tmpState.sphereB.center, tmpState.sphereC.center, props.dashLength, i);
}
return builder.getLines();
}
function getConnectorShape(ctx, data, props, shape) {
const lines = buildConnectorLine(data, props, shape && shape.geometry);
const name = getDihedralName(data);
return shape_1.Shape.create(name, data, lines, () => props.color, () => props.linesSize, () => '');
}
//
function buildArmsLines(data, props, lines) {
const builder = lines_builder_1.LinesBuilder.create(128, 64, lines);
for (let i = 0, il = data.quads.length; i < il; ++i) {
setDihedralState(data.quads[i], tmpState, props.arcScale);
builder.addFixedLengthDashes(tmpState.sphereB.center, tmpState.sphereA.center, props.dashLength, i);
builder.addFixedLengthDashes(tmpState.sphereC.center, tmpState.sphereD.center, props.dashLength, i);
}
return builder.getLines();
}
function getArmsShape(ctx, data, props, shape) {
const lines = buildArmsLines(data, props, shape && shape.geometry);
const name = getDihedralName(data);
return shape_1.Shape.create(name, data, lines, () => props.color, () => props.linesSize, () => '');
}
//
function buildExtendersLines(data, props, lines) {
const builder = lines_builder_1.LinesBuilder.create(128, 64, lines);
for (let i = 0, il = data.quads.length; i < il; ++i) {
setDihedralState(data.quads[i], tmpState, props.arcScale);
builder.addFixedLengthDashes(tmpState.arcPointA, tmpState.projA, props.dashLength, i);
builder.addFixedLengthDashes(tmpState.arcPointD, tmpState.projD, props.dashLength, i);
}
return builder.getLines();
}
function getExtendersShape(ctx, data, props, shape) {
const lines = buildExtendersLines(data, props, shape && shape.geometry);
const name = getDihedralName(data);
return shape_1.Shape.create(name, data, lines, () => props.color, () => props.linesSize, () => '');
}
//
function buildArcLines(data, props, lines) {
const builder = lines_builder_1.LinesBuilder.create(128, 64, lines);
for (let i = 0, il = data.quads.length; i < il; ++i) {
setDihedralState(data.quads[i], tmpState, props.arcScale);
const circle = getCircle(tmpState, props.dashLength);
const { indices, vertices } = circle;
for (let j = 0, jl = indices.length; j < jl; j += 3) {
if (j % 2 === 1)
continue; // draw every other segment to get dashes
const start = indices[j] * 3;
const end = indices[j + 1] * 3;
const startX = vertices[start];
const startY = vertices[start + 1];
const startZ = vertices[start + 2];
const endX = vertices[end];
const endY = vertices[end + 1];
const endZ = vertices[end + 2];
builder.add(startX, startY, startZ, endX, endY, endZ, i);
}
}
return builder.getLines();
}
function getArcShape(ctx, data, props, shape) {
const lines = buildArcLines(data, props, shape && shape.geometry);
const name = getDihedralName(data);
return shape_1.Shape.create(name, data, lines, () => props.color, () => props.linesSize, () => '');
}
//
function buildSectorMesh(data, props, mesh) {
const state = mesh_builder_1.MeshBuilder.createState(128, 64, mesh);
for (let i = 0, il = data.quads.length; i < il; ++i) {
setDihedralState(data.quads[i], tmpState, props.arcScale);
const circle = getCircle(tmpState);
state.currentGroup = i;
mesh_builder_1.MeshBuilder.addPrimitive(state, linear_algebra_1.Mat4.id, circle);
mesh_builder_1.MeshBuilder.addPrimitiveFlipped(state, linear_algebra_1.Mat4.id, circle);
}
return mesh_builder_1.MeshBuilder.getMesh(state);
}
function getSectorShape(ctx, data, props, shape) {
const mesh = buildSectorMesh(data, props, shape && shape.geometry);
const name = getDihedralName(data);
const getLabel = (groupId) => (0, label_1.dihedralLabel)(data.quads[groupId]);
return shape_1.Shape.create(name, data, mesh, () => props.color, () => 1, getLabel);
}
//
function buildText(data, props, text) {
const builder = text_builder_1.TextBuilder.create(props, 128, 64, text);
for (let i = 0, il = data.quads.length; i < il; ++i) {
setDihedralState(data.quads[i], tmpState, props.arcScale);
linear_algebra_1.Vec3.add(tmpVec, tmpState.arcDirA, tmpState.arcDirD);
linear_algebra_1.Vec3.setMagnitude(tmpVec, tmpVec, tmpState.radius);
linear_algebra_1.Vec3.add(tmpVec, tmpState.arcCenter, tmpVec);
let angle = (0, misc_1.radToDeg)(tmpState.angle).toFixed(2);
if (angle === '-0.00')
angle = '0.00';
const label = props.customText || `${angle}\u00B0`;
const radius = Math.max(2, tmpState.sphereA.radius, tmpState.sphereB.radius, tmpState.sphereC.radius, tmpState.sphereD.radius);
const scale = radius / 2;
builder.add(label, tmpVec[0], tmpVec[1], tmpVec[2], 0.1, scale, i);
}
return builder.getText();
}
function getTextShape(ctx, data, props, shape) {
const text = buildText(data, props, shape && shape.geometry);
const name = getDihedralName(data);
const getLabel = (groupId) => (0, label_1.dihedralLabel)(data.quads[groupId]);
return shape_1.Shape.create(name, data, text, () => props.textColor, () => props.textSize, getLabel);
}
function DihedralRepresentation(ctx, getParams) {
return representation_2.Representation.createMulti('Dihedral', ctx, getParams, representation_2.Representation.StateBuilder, DihedralVisuals);
}