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molstar

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A comprehensive macromolecular library.

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"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 = tslib_1.__assign(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(); }