molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-repr/structure/visual/label-text.js

@@ -1,137 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2021 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>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.LabelTextVisual = exports.LabelTextParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var structure_1 = require("../../../mol-model/structure");
-var text_builder_1 = require("../../../mol-geo/geometry/text/text-builder");
-var complex_visual_1 = require("../complex-visual");
-var element_1 = require("./util/element");
-var names_1 = require("../../../mol-util/color/names");
-var linear_algebra_1 = require("../../../mol-math/linear-algebra");
-var boundary_helper_1 = require("../../../mol-math/geometry/boundary-helper");
-exports.LabelTextParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexTextParams), { background: param_definition_1.ParamDefinition.Boolean(false), backgroundMargin: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }), backgroundColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.black), backgroundOpacity: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.01 }), borderWidth: param_definition_1.ParamDefinition.Numeric(0.25, { min: 0, max: 0.5, step: 0.01 }), level: param_definition_1.ParamDefinition.Select('residue', [['chain', 'Chain'], ['residue', 'Residue'], ['element', 'Element']], { isEssential: true }), chainScale: param_definition_1.ParamDefinition.Numeric(10, { min: 0, max: 20, step: 0.1 }), residueScale: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 20, step: 0.1 }), elementScale: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 20, step: 0.1 }) });
-function LabelTextVisual(materialId) {
-    return (0, complex_visual_1.ComplexTextVisual)({
-        defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.LabelTextParams),
-        createGeometry: createLabelText,
-        createLocationIterator: element_1.ElementIterator.fromStructure,
-        getLoci: element_1.getSerialElementLoci,
-        eachLocation: element_1.eachSerialElement,
-        setUpdateState: function (state, newProps, currentProps) {
-            state.createGeometry = (newProps.level !== currentProps.level ||
-                (newProps.level === 'chain' && newProps.chainScale !== currentProps.chainScale) ||
-                (newProps.level === 'residue' && newProps.residueScale !== currentProps.residueScale) ||
-                (newProps.level === 'element' && newProps.elementScale !== currentProps.elementScale));
-        }
-    }, materialId);
-}
-exports.LabelTextVisual = LabelTextVisual;
-function createLabelText(ctx, structure, theme, props, text) {
-    switch (props.level) {
-        case 'chain': return createChainText(ctx, structure, theme, props, text);
-        case 'residue': return createResidueText(ctx, structure, theme, props, text);
-        case 'element': return createElementText(ctx, structure, theme, props, text);
-    }
-}
-//
-var tmpVec = (0, linear_algebra_1.Vec3)();
-var boundaryHelper = new boundary_helper_1.BoundaryHelper('98');
-function createChainText(ctx, structure, theme, props, text) {
-    var l = structure_1.StructureElement.Location.create(structure);
-    var units = structure.units, serialMapping = structure.serialMapping;
-    var _a = structure_1.StructureProperties.chain, auth_asym_id = _a.auth_asym_id, label_asym_id = _a.label_asym_id;
-    var cumulativeUnitElementCount = serialMapping.cumulativeUnitElementCount;
-    var count = units.length;
-    var chainScale = props.chainScale;
-    var builder = text_builder_1.TextBuilder.create(props, count, count / 2, text);
-    for (var i = 0, il = units.length; i < il; ++i) {
-        var unit = units[i];
-        l.unit = unit;
-        l.element = unit.elements[0];
-        var _b = unit.lookup3d.boundary.sphere, center = _b.center, radius = _b.radius;
-        linear_algebra_1.Vec3.transformMat4(tmpVec, center, unit.conformation.operator.matrix);
-        var authId = auth_asym_id(l);
-        var labelId = label_asym_id(l);
-        var text_1 = authId === labelId ? labelId : "".concat(labelId, " [").concat(authId, "]");
-        builder.add(text_1, tmpVec[0], tmpVec[1], tmpVec[2], radius, chainScale, cumulativeUnitElementCount[i]);
-    }
-    return builder.getText();
-}
-function createResidueText(ctx, structure, theme, props, text) {
-    var l = structure_1.StructureElement.Location.create(structure);
-    var units = structure.units, serialMapping = structure.serialMapping;
-    var label_comp_id = structure_1.StructureProperties.atom.label_comp_id;
-    var auth_seq_id = structure_1.StructureProperties.residue.auth_seq_id;
-    var cumulativeUnitElementCount = serialMapping.cumulativeUnitElementCount;
-    var count = structure.polymerResidueCount * 2;
-    var residueScale = props.residueScale;
-    var builder = text_builder_1.TextBuilder.create(props, count, count / 2, text);
-    for (var i = 0, il = units.length; i < il; ++i) {
-        var unit = units[i];
-        var pos = unit.conformation.position;
-        var elements = unit.elements;
-        l.unit = unit;
-        l.element = unit.elements[0];
-        var residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index;
-        var groupOffset = cumulativeUnitElementCount[i];
-        var j = 0;
-        var jl = elements.length;
-        while (j < jl) {
-            var start = j, rI = residueIndex[elements[j]];
-            j++;
-            while (j < jl && residueIndex[elements[j]] === rI)
-                j++;
-            boundaryHelper.reset();
-            for (var eI = start; eI < j; eI++) {
-                pos(elements[eI], tmpVec);
-                boundaryHelper.includePosition(tmpVec);
-            }
-            boundaryHelper.finishedIncludeStep();
-            for (var eI = start; eI < j; eI++) {
-                pos(elements[eI], tmpVec);
-                boundaryHelper.radiusPosition(tmpVec);
-            }
-            l.element = elements[start];
-            var _a = boundaryHelper.getSphere(), center = _a.center, radius = _a.radius;
-            var authSeqId = auth_seq_id(l);
-            var compId = label_comp_id(l);
-            var text_2 = "".concat(compId, " ").concat(authSeqId);
-            builder.add(text_2, center[0], center[1], center[2], radius, residueScale, groupOffset + start);
-        }
-    }
-    return builder.getText();
-}
-function createElementText(ctx, structure, theme, props, text) {
-    var l = structure_1.StructureElement.Location.create(structure);
-    var units = structure.units, serialMapping = structure.serialMapping;
-    var _a = structure_1.StructureProperties.atom, label_atom_id = _a.label_atom_id, label_alt_id = _a.label_alt_id;
-    var cumulativeUnitElementCount = serialMapping.cumulativeUnitElementCount;
-    var sizeTheme = theme.size;
-    var count = structure.elementCount;
-    var elementScale = props.elementScale;
-    var builder = text_builder_1.TextBuilder.create(props, count, count / 2, text);
-    for (var i = 0, il = units.length; i < il; ++i) {
-        var unit = units[i];
-        var pos = unit.conformation.position;
-        var elements = unit.elements;
-        l.unit = unit;
-        var groupOffset = cumulativeUnitElementCount[i];
-        for (var j = 0, _j = elements.length; j < _j; j++) {
-            l.element = elements[j];
-            pos(l.element, tmpVec);
-            var atomId = label_atom_id(l);
-            var altId = label_alt_id(l);
-            var text_3 = altId ? "".concat(atomId, "%").concat(altId) : atomId;
-            builder.add(text_3, tmpVec[0], tmpVec[1], tmpVec[2], sizeTheme.size(l), elementScale, groupOffset + j);
-        }
-    }
-    return builder.getText();
-}
-//# sourceMappingURL=label-text.js.map

package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js

@@ -1,99 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2021 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.MolecularSurfaceMeshVisual = exports.MolecularSurfaceMeshParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var units_visual_1 = require("../units-visual");
-var molecular_surface_1 = require("../../../mol-math/geometry/molecular-surface");
-var mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
-var molecular_surface_2 = require("./util/molecular-surface");
-var algorithm_1 = require("../../../mol-geo/util/marching-cubes/algorithm");
-var element_1 = require("./util/element");
-var common_1 = require("./util/common");
-var geometry_1 = require("../../../mol-math/geometry");
-var color_smoothing_1 = require("../../../mol-geo/geometry/mesh/color-smoothing");
-var base_1 = require("../../../mol-geo/geometry/base");
-exports.MolecularSurfaceMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), molecular_surface_1.MolecularSurfaceCalculationParams), common_1.CommonSurfaceParams), base_1.ColorSmoothingParams);
-//
-function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var _a, transform, field, idField, resolution, params, surface, iterations, sphere;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0: return [4 /*yield*/, (0, molecular_surface_2.computeUnitMolecularSurface)(structure, unit, theme.size, props).runInContext(ctx.runtime)];
-                case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, resolution = _a.resolution;
-                    params = {
-                        isoLevel: props.probeRadius,
-                        scalarField: field,
-                        idField: idField
-                    };
-                    return [4 /*yield*/, (0, algorithm_1.computeMarchingCubesMesh)(params, mesh).runAsChild(ctx.runtime)];
-                case 2:
-                    surface = _b.sent();
-                    if (props.includeParent) {
-                        iterations = Math.ceil(2 / props.resolution);
-                        mesh_1.Mesh.smoothEdges(surface, { iterations: iterations, maxNewEdgeLength: Math.sqrt(2) });
-                    }
-                    mesh_1.Mesh.transform(surface, transform);
-                    if (ctx.webgl && !ctx.webgl.isWebGL2)
-                        mesh_1.Mesh.uniformTriangleGroup(surface);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.probeRadius + (0, common_1.getUnitExtraRadius)(unit));
-                    surface.setBoundingSphere(sphere);
-                    surface.meta.resolution = resolution;
-                    return [2 /*return*/, surface];
-            }
-        });
-    });
-}
-function MolecularSurfaceMeshVisual(materialId) {
-    return (0, units_visual_1.UnitsMeshVisual)({
-        defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.MolecularSurfaceMeshParams),
-        createGeometry: createMolecularSurfaceMesh,
-        createLocationIterator: element_1.ElementIterator.fromGroup,
-        getLoci: element_1.getElementLoci,
-        eachLocation: element_1.eachElement,
-        setUpdateState: function (state, newProps, currentProps) {
-            if (newProps.resolution !== currentProps.resolution)
-                state.createGeometry = true;
-            if (newProps.probeRadius !== currentProps.probeRadius)
-                state.createGeometry = true;
-            if (newProps.probePositions !== currentProps.probePositions)
-                state.createGeometry = true;
-            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
-                state.createGeometry = true;
-            if (newProps.traceOnly !== currentProps.traceOnly)
-                state.createGeometry = true;
-            if (newProps.includeParent !== currentProps.includeParent)
-                state.createGeometry = true;
-            if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
-                state.updateColor = true;
-            }
-            else if (newProps.smoothColors.name === 'on' && currentProps.smoothColors.name === 'on') {
-                if (newProps.smoothColors.params.resolutionFactor !== currentProps.smoothColors.params.resolutionFactor)
-                    state.updateColor = true;
-                if (newProps.smoothColors.params.sampleStride !== currentProps.smoothColors.params.sampleStride)
-                    state.updateColor = true;
-            }
-        },
-        processValues: function (values, geometry, props, theme, webgl) {
-            var _a = geometry.meta, resolution = _a.resolution, colorTexture = _a.colorTexture;
-            var csp = (0, base_1.getColorSmoothingProps)(props.smoothColors, theme.color.preferSmoothing, resolution);
-            if (csp) {
-                (0, color_smoothing_1.applyMeshColorSmoothing)(values, csp.resolution, csp.stride, webgl, colorTexture);
-                geometry.meta.colorTexture = values.tColorGrid.ref.value;
-            }
-        },
-        dispose: function (geometry) {
-            var _a;
-            (_a = geometry.meta.colorTexture) === null || _a === void 0 ? void 0 : _a.destroy();
-        }
-    }, materialId);
-}
-exports.MolecularSurfaceMeshVisual = MolecularSurfaceMeshVisual;
-//# sourceMappingURL=molecular-surface-mesh.js.map

package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js

@@ -1,67 +0,0 @@
-"use strict";
-/**
- * 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.MolecularSurfaceWireframeVisual = exports.MolecularSurfaceWireframeParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var units_visual_1 = require("../units-visual");
-var molecular_surface_1 = require("../../../mol-math/geometry/molecular-surface");
-var lines_1 = require("../../../mol-geo/geometry/lines/lines");
-var molecular_surface_2 = require("./util/molecular-surface");
-var algorithm_1 = require("../../../mol-geo/util/marching-cubes/algorithm");
-var element_1 = require("./util/element");
-var common_1 = require("./util/common");
-var geometry_1 = require("../../../mol-math/geometry");
-exports.MolecularSurfaceWireframeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsLinesParams), molecular_surface_1.MolecularSurfaceCalculationParams), common_1.CommonSurfaceParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1.5, { min: 0, max: 10, step: 0.1 }) });
-//
-function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lines) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var _a, transform, field, idField, params, wireframe, sphere;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0: return [4 /*yield*/, (0, molecular_surface_2.computeUnitMolecularSurface)(structure, unit, theme.size, props).runInContext(ctx.runtime)];
-                case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField;
-                    params = {
-                        isoLevel: props.probeRadius,
-                        scalarField: field,
-                        idField: idField
-                    };
-                    return [4 /*yield*/, (0, algorithm_1.computeMarchingCubesLines)(params, lines).runAsChild(ctx.runtime)];
-                case 2:
-                    wireframe = _b.sent();
-                    lines_1.Lines.transform(wireframe, transform);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.probeRadius + (0, common_1.getUnitExtraRadius)(unit));
-                    wireframe.setBoundingSphere(sphere);
-                    return [2 /*return*/, wireframe];
-            }
-        });
-    });
-}
-function MolecularSurfaceWireframeVisual(materialId) {
-    return (0, units_visual_1.UnitsLinesVisual)({
-        defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.MolecularSurfaceWireframeParams),
-        createGeometry: createMolecularSurfaceWireframe,
-        createLocationIterator: element_1.ElementIterator.fromGroup,
-        getLoci: element_1.getElementLoci,
-        eachLocation: element_1.eachElement,
-        setUpdateState: function (state, newProps, currentProps) {
-            if (newProps.resolution !== currentProps.resolution)
-                state.createGeometry = true;
-            if (newProps.probeRadius !== currentProps.probeRadius)
-                state.createGeometry = true;
-            if (newProps.probePositions !== currentProps.probePositions)
-                state.createGeometry = true;
-            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
-                state.createGeometry = true;
-            if (newProps.includeParent !== currentProps.includeParent)
-                state.createGeometry = true;
-        }
-    }, materialId);
-}
-exports.MolecularSurfaceWireframeVisual = MolecularSurfaceWireframeVisual;
-//# sourceMappingURL=molecular-surface-wireframe.js.map

package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.js

@@ -1,148 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2019 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.NucleotideBlockVisual = exports.NucleotideBlockParams = exports.DefaultNucleotideBlockMeshProps = exports.NucleotideBlockMeshParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var linear_algebra_1 = require("../../../mol-math/linear-algebra");
-var box_1 = require("../../../mol-geo/primitive/box");
-var structure_1 = require("../../../mol-model/structure");
-var mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
-var mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder");
-var int_1 = require("../../../mol-data/int");
-var types_1 = require("../../../mol-model/structure/model/types");
-var cylinder_1 = require("../../../mol-geo/geometry/mesh/builder/cylinder");
-var units_visual_1 = require("../units-visual");
-var nucleotide_1 = require("./util/nucleotide");
-var base_1 = require("../../../mol-geo/geometry/base");
-var geometry_1 = require("../../../mol-math/geometry");
-// TODO support blocks for multiple locations (including from microheterogeneity)
-var p1 = (0, linear_algebra_1.Vec3)();
-var p2 = (0, linear_algebra_1.Vec3)();
-var p3 = (0, linear_algebra_1.Vec3)();
-var p4 = (0, linear_algebra_1.Vec3)();
-var p5 = (0, linear_algebra_1.Vec3)();
-var p6 = (0, linear_algebra_1.Vec3)();
-var v12 = (0, linear_algebra_1.Vec3)();
-var v34 = (0, linear_algebra_1.Vec3)();
-var vC = (0, linear_algebra_1.Vec3)();
-var center = (0, linear_algebra_1.Vec3)();
-var t = linear_algebra_1.Mat4.identity();
-var sVec = (0, linear_algebra_1.Vec3)();
-var box = (0, box_1.Box)();
-exports.NucleotideBlockMeshParams = {
-    sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
-    radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo),
-};
-exports.DefaultNucleotideBlockMeshProps = param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideBlockMeshParams);
-function createNucleotideBlockMesh(ctx, unit, structure, theme, props, mesh) {
-    if (!structure_1.Unit.isAtomic(unit))
-        return mesh_1.Mesh.createEmpty(mesh);
-    var nucleotideElementCount = unit.nucleotideElements.length;
-    if (!nucleotideElementCount)
-        return mesh_1.Mesh.createEmpty(mesh);
-    var sizeFactor = props.sizeFactor, radialSegments = props.radialSegments;
-    var vertexCount = nucleotideElementCount * (box.vertices.length / 3 + radialSegments * 2);
-    var builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 4, mesh);
-    var elements = unit.elements, model = unit.model;
-    var _a = model.atomicHierarchy, chainAtomSegments = _a.chainAtomSegments, residueAtomSegments = _a.residueAtomSegments, atoms = _a.atoms, atomicIndex = _a.index;
-    var _b = model.atomicHierarchy.derived.residue, moleculeType = _b.moleculeType, traceElementIndex = _b.traceElementIndex;
-    var label_comp_id = atoms.label_comp_id;
-    var pos = unit.conformation.invariantPosition;
-    var chainIt = int_1.Segmentation.transientSegments(chainAtomSegments, elements);
-    var residueIt = int_1.Segmentation.transientSegments(residueAtomSegments, elements);
-    var cylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments: radialSegments, bottomCap: true };
-    var i = 0;
-    while (chainIt.hasNext) {
-        residueIt.setSegment(chainIt.move());
-        while (residueIt.hasNext) {
-            var residueIndex = residueIt.move().index;
-            if ((0, types_1.isNucleic)(moleculeType[residueIndex])) {
-                var compId = label_comp_id.value(residueAtomSegments.offsets[residueIndex]);
-                var idx1 = -1, idx2 = -1, idx3 = -1, idx4 = -1, idx5 = -1, idx6 = -1;
-                var width = 4.5, depth = 2.5 * sizeFactor;
-                var height = 4.5;
-                var isPurine = (0, types_1.isPurineBase)(compId);
-                var isPyrimidine = (0, types_1.isPyrimidineBase)(compId);
-                if (!isPurine && !isPyrimidine) {
-                    // detect Purine or Pyrimidin based on geometry
-                    var idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
-                    var idxN9 = atomicIndex.findAtomOnResidue(residueIndex, 'N9');
-                    if (idxC4 !== -1 && idxN9 !== -1 && linear_algebra_1.Vec3.distance(pos(idxC4, p1), pos(idxN9, p2)) < 1.6) {
-                        isPurine = true;
-                    }
-                    else {
-                        isPyrimidine = true;
-                    }
-                }
-                if (isPurine) {
-                    height = 4.5;
-                    idx1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1');
-                    idx2 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
-                    idx3 = atomicIndex.findAtomOnResidue(residueIndex, 'C6');
-                    idx4 = atomicIndex.findAtomOnResidue(residueIndex, 'C2');
-                    idx5 = atomicIndex.findAtomOnResidue(residueIndex, 'N9');
-                    idx6 = traceElementIndex[residueIndex];
-                }
-                else if (isPyrimidine) {
-                    height = 3.0;
-                    idx1 = atomicIndex.findAtomOnResidue(residueIndex, 'N3');
-                    idx2 = atomicIndex.findAtomOnResidue(residueIndex, 'C6');
-                    idx3 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
-                    idx4 = atomicIndex.findAtomOnResidue(residueIndex, 'C2');
-                    idx5 = atomicIndex.findAtomOnResidue(residueIndex, 'N1');
-                    if (idx5 === -1) {
-                        // modified ring, e.g. DZ
-                        idx5 = atomicIndex.findAtomOnResidue(residueIndex, 'C1');
-                    }
-                    idx6 = traceElementIndex[residueIndex];
-                }
-                if (idx5 !== -1 && idx6 !== -1) {
-                    pos(idx5, p5);
-                    pos(idx6, p6);
-                    builderState.currentGroup = i;
-                    (0, cylinder_1.addCylinder)(builderState, p5, p6, 1, cylinderProps);
-                    if (idx1 !== -1 && idx2 !== -1 && idx3 !== -1 && idx4 !== -1) {
-                        pos(idx1, p1);
-                        pos(idx2, p2);
-                        pos(idx3, p3);
-                        pos(idx4, p4);
-                        linear_algebra_1.Vec3.normalize(v12, linear_algebra_1.Vec3.sub(v12, p2, p1));
-                        linear_algebra_1.Vec3.normalize(v34, linear_algebra_1.Vec3.sub(v34, p4, p3));
-                        linear_algebra_1.Vec3.normalize(vC, linear_algebra_1.Vec3.cross(vC, v12, v34));
-                        linear_algebra_1.Mat4.targetTo(t, p1, p2, vC);
-                        linear_algebra_1.Vec3.scaleAndAdd(center, p1, v12, height / 2 - 0.2);
-                        linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, width, depth, height));
-                        linear_algebra_1.Mat4.setTranslation(t, center);
-                        mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, box);
-                    }
-                }
-                ++i;
-            }
-        }
-    }
-    var m = mesh_builder_1.MeshBuilder.getMesh(builderState);
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
-    return m;
-}
-exports.NucleotideBlockParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), exports.NucleotideBlockMeshParams);
-function NucleotideBlockVisual(materialId) {
-    return (0, units_visual_1.UnitsMeshVisual)({
-        defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideBlockParams),
-        createGeometry: createNucleotideBlockMesh,
-        createLocationIterator: nucleotide_1.NucleotideLocationIterator.fromGroup,
-        getLoci: nucleotide_1.getNucleotideElementLoci,
-        eachLocation: nucleotide_1.eachNucleotideElement,
-        setUpdateState: function (state, newProps, currentProps) {
-            state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
-                newProps.radialSegments !== currentProps.radialSegments);
-        }
-    }, materialId);
-}
-exports.NucleotideBlockVisual = NucleotideBlockVisual;
-//# sourceMappingURL=nucleotide-block-mesh.js.map

package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.js

@@ -1,202 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 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.NucleotideRingVisual = exports.NucleotideRingParams = exports.DefaultNucleotideRingMeshProps = exports.NucleotideRingMeshParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var linear_algebra_1 = require("../../../mol-math/linear-algebra");
-var structure_1 = require("../../../mol-model/structure");
-var mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
-var mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder");
-var int_1 = require("../../../mol-data/int");
-var types_1 = require("../../../mol-model/structure/model/types");
-var cylinder_1 = require("../../../mol-geo/geometry/mesh/builder/cylinder");
-var sphere_1 = require("../../../mol-geo/geometry/mesh/builder/sphere");
-var units_visual_1 = require("../units-visual");
-var nucleotide_1 = require("./util/nucleotide");
-var base_1 = require("../../../mol-geo/geometry/base");
-var geometry_1 = require("../../../mol-math/geometry");
-// TODO support rings for multiple locations (including from microheterogeneity)
-var pTrace = linear_algebra_1.Vec3.zero();
-var pN1 = linear_algebra_1.Vec3.zero();
-var pC2 = linear_algebra_1.Vec3.zero();
-var pN3 = linear_algebra_1.Vec3.zero();
-var pC4 = linear_algebra_1.Vec3.zero();
-var pC5 = linear_algebra_1.Vec3.zero();
-var pC6 = linear_algebra_1.Vec3.zero();
-var pN7 = linear_algebra_1.Vec3.zero();
-var pC8 = linear_algebra_1.Vec3.zero();
-var pN9 = linear_algebra_1.Vec3.zero();
-var normal = linear_algebra_1.Vec3.zero();
-exports.NucleotideRingMeshParams = {
-    sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
-    radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo),
-    detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo),
-};
-exports.DefaultNucleotideRingMeshProps = param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideRingMeshParams);
-var positionsRing5_6 = new Float32Array(2 * 9 * 3);
-var stripIndicesRing5_6 = new Uint32Array([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 14, 15, 12, 13, 8, 9, 10, 11, 0, 1]);
-var fanIndicesTopRing5_6 = new Uint32Array([8, 12, 14, 16, 6, 4, 2, 0, 10]);
-var fanIndicesBottomRing5_6 = new Uint32Array([9, 11, 1, 3, 5, 7, 17, 15, 13]);
-var positionsRing6 = new Float32Array(2 * 6 * 3);
-var stripIndicesRing6 = new Uint32Array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 1]);
-var fanIndicesTopRing6 = new Uint32Array([0, 10, 8, 6, 4, 2]);
-var fanIndicesBottomRing6 = new Uint32Array([1, 3, 5, 7, 9, 11]);
-var tmpShiftV = linear_algebra_1.Vec3.zero();
-function shiftPositions(out, dir) {
-    var positions = [];
-    for (var _i = 2; _i < arguments.length; _i++) {
-        positions[_i - 2] = arguments[_i];
-    }
-    for (var i = 0, il = positions.length; i < il; ++i) {
-        var v = positions[i];
-        linear_algebra_1.Vec3.toArray(linear_algebra_1.Vec3.add(tmpShiftV, v, dir), out, (i * 2) * 3);
-        linear_algebra_1.Vec3.toArray(linear_algebra_1.Vec3.sub(tmpShiftV, v, dir), out, (i * 2 + 1) * 3);
-    }
-}
-function createNucleotideRingMesh(ctx, unit, structure, theme, props, mesh) {
-    if (!structure_1.Unit.isAtomic(unit))
-        return mesh_1.Mesh.createEmpty(mesh);
-    var nucleotideElementCount = unit.nucleotideElements.length;
-    if (!nucleotideElementCount)
-        return mesh_1.Mesh.createEmpty(mesh);
-    var sizeFactor = props.sizeFactor, radialSegments = props.radialSegments, detail = props.detail;
-    var vertexCount = nucleotideElementCount * (26 + radialSegments * 2);
-    var builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 4, mesh);
-    var elements = unit.elements, model = unit.model;
-    var _a = model.atomicHierarchy, chainAtomSegments = _a.chainAtomSegments, residueAtomSegments = _a.residueAtomSegments, atoms = _a.atoms, atomicIndex = _a.index;
-    var _b = model.atomicHierarchy.derived.residue, moleculeType = _b.moleculeType, traceElementIndex = _b.traceElementIndex;
-    var label_comp_id = atoms.label_comp_id;
-    var pos = unit.conformation.invariantPosition;
-    var chainIt = int_1.Segmentation.transientSegments(chainAtomSegments, elements);
-    var residueIt = int_1.Segmentation.transientSegments(residueAtomSegments, elements);
-    var radius = 1 * sizeFactor;
-    var halfThickness = 1.25 * sizeFactor;
-    var cylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments: radialSegments };
-    var i = 0;
-    while (chainIt.hasNext) {
-        residueIt.setSegment(chainIt.move());
-        while (residueIt.hasNext) {
-            var residueIndex = residueIt.move().index;
-            if ((0, types_1.isNucleic)(moleculeType[residueIndex])) {
-                var compId = label_comp_id.value(residueAtomSegments.offsets[residueIndex]);
-                var idxTrace = -1, idxN1 = -1, idxC2 = -1, idxN3 = -1, idxC4 = -1, idxC5 = -1, idxC6 = -1, idxN7 = -1, idxC8 = -1, idxN9 = -1;
-                builderState.currentGroup = i;
-                var isPurine = (0, types_1.isPurineBase)(compId);
-                var isPyrimidine = (0, types_1.isPyrimidineBase)(compId);
-                if (!isPurine && !isPyrimidine) {
-                    // detect Purine or Pyrimidin based on geometry
-                    var idxC4_1 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
-                    var idxN9_1 = atomicIndex.findAtomOnResidue(residueIndex, 'N9');
-                    if (idxC4_1 !== -1 && idxN9_1 !== -1 && linear_algebra_1.Vec3.distance(pos(idxC4_1, pC4), pos(idxN9_1, pN9)) < 1.6) {
-                        isPurine = true;
-                    }
-                    else {
-                        isPyrimidine = true;
-                    }
-                }
-                if (isPurine) {
-                    idxTrace = traceElementIndex[residueIndex];
-                    idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1');
-                    idxC2 = atomicIndex.findAtomOnResidue(residueIndex, 'C2');
-                    idxN3 = atomicIndex.findAtomOnResidue(residueIndex, 'N3');
-                    idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
-                    idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'C5');
-                    if (idxC5 === -1) {
-                        // modified ring, e.g. DP
-                        idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'N5');
-                    }
-                    idxC6 = atomicIndex.findAtomOnResidue(residueIndex, 'C6');
-                    idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'N7');
-                    if (idxN7 === -1) {
-                        // modified ring, e.g. DP
-                        idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'C7');
-                    }
-                    idxC8 = atomicIndex.findAtomOnResidue(residueIndex, 'C8');
-                    idxN9 = atomicIndex.findAtomOnResidue(residueIndex, 'N9');
-                    if (idxN9 !== -1 && idxTrace !== -1) {
-                        pos(idxN9, pN9);
-                        pos(idxTrace, pTrace);
-                        builderState.currentGroup = i;
-                        (0, cylinder_1.addCylinder)(builderState, pN9, pTrace, 1, cylinderProps);
-                        (0, sphere_1.addSphere)(builderState, pN9, radius, detail);
-                    }
-                    if (idxN1 !== -1 && idxC2 !== -1 && idxN3 !== -1 && idxC4 !== -1 && idxC5 !== -1 && idxC6 !== -1 && idxN7 !== -1 && idxC8 !== -1 && idxN9 !== -1) {
-                        pos(idxN1, pN1);
-                        pos(idxC2, pC2);
-                        pos(idxN3, pN3);
-                        pos(idxC4, pC4);
-                        pos(idxC5, pC5);
-                        pos(idxC6, pC6);
-                        pos(idxN7, pN7);
-                        pos(idxC8, pC8);
-                        linear_algebra_1.Vec3.triangleNormal(normal, pN1, pC4, pC5);
-                        linear_algebra_1.Vec3.scale(normal, normal, halfThickness);
-                        shiftPositions(positionsRing5_6, normal, pN1, pC2, pN3, pC4, pC5, pC6, pN7, pC8, pN9);
-                        mesh_builder_1.MeshBuilder.addTriangleStrip(builderState, positionsRing5_6, stripIndicesRing5_6);
-                        mesh_builder_1.MeshBuilder.addTriangleFan(builderState, positionsRing5_6, fanIndicesTopRing5_6);
-                        mesh_builder_1.MeshBuilder.addTriangleFan(builderState, positionsRing5_6, fanIndicesBottomRing5_6);
-                    }
-                }
-                else if (isPyrimidine) {
-                    idxTrace = traceElementIndex[residueIndex];
-                    idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1');
-                    if (idxN1 === -1) {
-                        // modified ring, e.g. DZ
-                        idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'C1');
-                    }
-                    idxC2 = atomicIndex.findAtomOnResidue(residueIndex, 'C2');
-                    idxN3 = atomicIndex.findAtomOnResidue(residueIndex, 'N3');
-                    idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4');
-                    idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'C5');
-                    idxC6 = atomicIndex.findAtomOnResidue(residueIndex, 'C6');
-                    if (idxN1 !== -1 && idxTrace !== -1) {
-                        pos(idxN1, pN1);
-                        pos(idxTrace, pTrace);
-                        builderState.currentGroup = i;
-                        (0, cylinder_1.addCylinder)(builderState, pN1, pTrace, 1, cylinderProps);
-                        (0, sphere_1.addSphere)(builderState, pN1, radius, detail);
-                    }
-                    if (idxN1 !== -1 && idxC2 !== -1 && idxN3 !== -1 && idxC4 !== -1 && idxC5 !== -1 && idxC6 !== -1) {
-                        pos(idxC2, pC2);
-                        pos(idxN3, pN3);
-                        pos(idxC4, pC4);
-                        pos(idxC5, pC5);
-                        pos(idxC6, pC6);
-                        linear_algebra_1.Vec3.triangleNormal(normal, pN1, pC4, pC5);
-                        linear_algebra_1.Vec3.scale(normal, normal, halfThickness);
-                        shiftPositions(positionsRing6, normal, pN1, pC2, pN3, pC4, pC5, pC6);
-                        mesh_builder_1.MeshBuilder.addTriangleStrip(builderState, positionsRing6, stripIndicesRing6);
-                        mesh_builder_1.MeshBuilder.addTriangleFan(builderState, positionsRing6, fanIndicesTopRing6);
-                        mesh_builder_1.MeshBuilder.addTriangleFan(builderState, positionsRing6, fanIndicesBottomRing6);
-                    }
-                }
-                ++i;
-            }
-        }
-    }
-    var m = mesh_builder_1.MeshBuilder.getMesh(builderState);
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
-    return m;
-}
-exports.NucleotideRingParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), exports.NucleotideRingMeshParams);
-function NucleotideRingVisual(materialId) {
-    return (0, units_visual_1.UnitsMeshVisual)({
-        defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideRingParams),
-        createGeometry: createNucleotideRingMesh,
-        createLocationIterator: nucleotide_1.NucleotideLocationIterator.fromGroup,
-        getLoci: nucleotide_1.getNucleotideElementLoci,
-        eachLocation: nucleotide_1.eachNucleotideElement,
-        setUpdateState: function (state, newProps, currentProps) {
-            state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
-                newProps.radialSegments !== currentProps.radialSegments);
-        }
-    }, materialId);
-}
-exports.NucleotideRingVisual = NucleotideRingVisual;
-//# sourceMappingURL=nucleotide-ring-mesh.js.map