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Avogadro::QtGui::ExtensionPlugin", "Class Avogadro::QtGui::ExtensionPluginFactory", "Class Avogadro::QtGui::FileBrowseWidget", "Class Avogadro::QtGui::FileFormatDialog", "Class Avogadro::QtGui::GenericHighlighter", "Class Avogadro::QtGui::GenericHighlighter::Rule", "Class Avogadro::QtGui::HydrogenTools", "Class Avogadro::QtGui::InterfaceScript", "Class Avogadro::QtGui::InterfaceWidget", "Class Avogadro::QtGui::MeshGenerator", "Class Avogadro::QtGui::Molecule", "Class Avogadro::QtGui::MoleculeModel", "Class Avogadro::QtGui::MultiViewWidget", "Class Avogadro::QtGui::PeriodicTableScene", "Class Avogadro::QtGui::PeriodicTableView", "Class Avogadro::QtGui::PersistentAtom", "Class Avogadro::QtGui::PersistentBond", "Class Avogadro::QtGui::PythonScript", "Class Avogadro::QtGui::RWAtom", "Class Avogadro::QtGui::RWBond", "Class Avogadro::QtGui::RWMolecule", "Class Avogadro::QtGui::ScenePlugin", "Class Avogadro::QtGui::ScenePluginFactory", "Class Avogadro::QtGui::ScenePluginModel", "Class Avogadro::QtGui::ScriptLoader", "Class Avogadro::QtGui::ToolPlugin", "Class Avogadro::QtGui::ToolPluginFactory", "Class Avogadro::QtGui::ViewFactory", "Class Avogadro::QtOpenGL::ActiveObjects", "Class Avogadro::QtOpenGL::GLWidget", "Class Avogadro::QtOpenGL::QtTextRenderStrategy", "Class Avogadro::QuantumIO::GAMESSUSOutput", "Class Avogadro::QuantumIO::GUKBasisSet", "Class Avogadro::QuantumIO::GamessukOut", "Class Avogadro::QuantumIO::GaussianCube", "Class Avogadro::QuantumIO::GaussianFchk", "Class Avogadro::QuantumIO::MoldenFile", "Class Avogadro::QuantumIO::MopacAux", "Class Avogadro::QuantumIO::NWChemJson", "Class Avogadro::QuantumIO::NWChemLog", "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry", "Class Avogadro::Rendering::ArrowGeometry", "Class Avogadro::Rendering::BufferObject", "Class Avogadro::Rendering::Camera", "Class Avogadro::Rendering::Cylinder", "Class Avogadro::Rendering::CylinderGeometry", "Class Avogadro::Rendering::Drawable", "Class Avogadro::Rendering::GLRenderVisitor", "Class Avogadro::Rendering::GLRenderer", "Class Avogadro::Rendering::GeometryNode", "Class Avogadro::Rendering::GeometryVisitor", "Class Avogadro::Rendering::GroupNode", "Class Avogadro::Rendering::LineStripGeometry", "Class Avogadro::Rendering::MeshGeometry", "Class Avogadro::Rendering::Node", "Class Avogadro::Rendering::POVRayVisitor", "Class Avogadro::Rendering::Primitive", "Class Avogadro::Rendering::Scene", "Class Avogadro::Rendering::Shader", "Class Avogadro::Rendering::ShaderProgram", "Class Avogadro::Rendering::Sphere", "Class Avogadro::Rendering::SphereGeometry", "Class Avogadro::Rendering::TextLabel2D", "Class Avogadro::Rendering::TextLabel3D", "Class Avogadro::Rendering::TextLabelBase", "Class Avogadro::Rendering::TextProperties", "Class Avogadro::Rendering::TextRenderStrategy", "Class Avogadro::Rendering::Texture2D", "Class Avogadro::Rendering::TransformNode", "Class Avogadro::Rendering::VRMLVisitor", "Class Avogadro::Rendering::Visitor", "Class Avogadro::Rendering::VolumeGeometry", "Class Avogadro::TypeTraits", "Class Avogadro::TypeTraits&lt; char &gt;", "Class Avogadro::TypeTraits&lt; double &gt;", "Class Avogadro::TypeTraits&lt; float &gt;", "Class Avogadro::TypeTraits&lt; int &gt;", "Class Avogadro::TypeTraits&lt; short &gt;", "Class Avogadro::TypeTraits&lt; unsigned char &gt;", "Class Avogadro::TypeTraits&lt; unsigned int &gt;", "Class Avogadro::TypeTraits&lt; unsigned short &gt;", "Class Avogadro::VTK::VtkPlot", "Class Avogadro::VTK::vtkGLWidget", "Class vtkAvogadroActor", "Class List", "Core Classes", "Develop", "IO Classes", "MoleQueue Classes", "QtGui Classes", "Rendering Classes", "Avogadro Remote Procedure Call (RPC)", "Charges / Electrostatics", "Command Scripts", "Energy / Force Fields", "Example Plugin Script - Part 1", "Example Plugin Script - Part 2", "File Formats", "Input Generators", "Script Plugins", "Installing Script Plugins", "Script Interfaces", "VTK Classes", "License", "Avogadro: Molecular Editor and Visualization", "Table of contents", "Making a Crystal Surface Slab", "Building a Polymer Unit Cell", "Perceiving Crystall Symmetry", "Building Materials", "Building Molecule-Surface Interactions", "Reducing Crystals to a Primitive Unit Cell", "Scaling Crystal Cell Volume", "Building a Supercell", "Building a Peptide", "Building Carbon Nanotubes", "Building DNA or RNA", "Building with SMILES", "Importing from the Protein Data Bank (PDB)", "Importing Molecules by Name", "Building Molecules", "Insert Molecular Fragments", "Coloring Part of a Molecules", "Different Display Styles", "Display Types", "Drawing Molecules", "Getting Started", "Introduction", "Making Selections", "User Guide", "Build Menu", "Edit Menu", "Extension Menu", "File Menu", "Menus", "Select Menu", "View Menu", "Finding Conformers of Molecules", "Geometry Constraints", "Enabling additional force fields", "Optimizing Geometry", "Introduction to Molecular Mechanics", "Align Tool", "Auto-Optimize Tool", "Auto-Rotate Tool", "Bond-Centric Manipulate Tool", "Draw Tool", "Tools", "Manipulate Tool", "Measure Tool", "Navigate Tool", "Selection Tool", "Template Tool", "Tutorials", "Naming a Molecule", "Using QTAIM (Atoms in Molecules) Analysis", "Viewing Electrostatic Potential Maps", "Viewing Molecular Orbitals", "Viewing Vibrations", "What\u2019s New in Avogadro 2", "Interface Changes", "Major New Features", "Install", "Building Source Code", "Install", "Version History", "Release Notes v1.94.0", "Release Notes v1.95.0", "Release Notes v1.95.1", "Release Notes v1.96.0", "Release Notes v1.97.0", "Release Notes v1.98.0", "Acid-Base Properties of Amino Acids", "Alkene Isomers", "Educational Publications Using Avogadro", "Basic VSEPR", "1,3-diaxial interactions", "HCN dipole", "Hydrogen Clusters", "Hydrogen Molecule", "Teach", "Markovnikov\u2019s Rule", "Organic Hybridization", "Water"], "terms": {"If": [0, 1, 3, 5, 7, 13, 14, 15, 16, 22, 24, 27, 29, 40, 44, 49, 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168, 179, 208], "i": [1, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 72, 73, 74, 76, 79, 82, 83, 85, 86, 89, 90, 91, 92, 93, 94, 95, 96, 97, 101, 103, 104, 105, 107, 108, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 122, 124, 125, 127, 128, 129, 130, 133, 134, 135, 137, 139, 143, 146, 158, 159, 160, 161, 162, 165, 167, 168, 169, 170, 171, 172, 173, 174, 176, 177, 179, 180, 182, 183, 184, 186, 187, 188, 189, 192, 193, 194, 198, 199, 201, 203, 204, 205, 206, 207, 208, 209, 211, 212, 213, 214, 215, 217, 218, 219, 221, 222, 224, 225, 226, 227, 228, 230, 232, 233, 235, 236, 237, 238, 239, 243, 244, 245, 246, 247, 250, 251, 254, 255, 256, 257, 259], "goe": [1, 6, 63, 83, 174, 239], "here": [1, 63, 82, 83, 167, 171, 172, 177, 179, 182, 183, 184, 186, 187, 188, 189, 191, 192, 208, 214, 231, 256, 257], "void": [1, 6, 8, 9, 13, 14, 16, 18, 19, 20, 21, 23, 25, 26, 27, 28, 29, 32, 34, 36, 37, 38, 40, 42, 43, 44, 45, 49, 52, 58, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 76, 78, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 96, 97, 99, 101, 104, 105, 106, 108, 109, 111, 113, 115, 116, 117, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 158, 159], "dosometh": [1, 6], "overview": [1, 6], "add": [1, 7, 23, 25, 27, 28, 29, 34, 38, 49, 50, 63, 80, 81, 82, 83, 86, 96, 97, 101, 105, 116, 117, 121, 125, 127, 128, 129, 137, 158, 160, 162, 165, 176, 177, 183, 188, 189, 208, 210, 212, 214, 217, 228, 237, 239, 242, 243, 244, 245, 246, 247, 248, 252, 259], "path": [1, 49, 52, 63, 64, 65, 73, 74, 76, 79, 83, 84, 93, 100, 167, 169, 171, 174, 176, 177, 216, 237, 239, 243, 245, 246, 247], "user": [1, 4, 5, 24, 29, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 64, 65, 66, 69, 76, 79, 84, 85, 96, 97, 101, 105, 107, 110, 111, 112, 113, 114, 115, 163, 168, 169, 170, 171, 172, 173, 176, 177, 212, 238, 239, 243, 244, 245, 246, 247], "appropri": [1, 6, 12, 17, 52, 63, 75, 83, 169, 171, 174, 177, 203, 239, 245], "point": [1, 6, 23, 42, 44, 64, 65, 72, 79, 84, 85, 105, 116, 119, 121, 122, 125, 129, 133, 135, 137, 138, 139, 141, 168, 171, 186, 206, 212, 218, 228, 231, 239, 246, 247, 248], "out": [1, 9, 16, 29, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 74, 83, 93, 107, 110, 111, 112, 113, 114, 115, 119, 125, 127, 177, 179, 183, 184, 203, 205, 214, 217, 220, 226, 236, 237, 247, 256], "altern": [1, 170], "similar": [1, 20, 96, 174, 179, 199, 203, 228], "ideal": [1, 15], "give": [1, 5, 8, 9, 21, 24, 40, 49, 119, 172, 179, 212, 247, 259], "some": [1, 5, 24, 29, 63, 65, 83, 86, 96, 116, 137, 162, 167, 168, 172, 174, 176, 177, 182, 184, 187, 199, 236, 244, 246, 247, 254, 256, 257], "simpl": [1, 24, 32, 33, 37, 40, 41, 51, 63, 83, 177, 189, 199, 206, 239, 251], "exampl": [1, 5, 20, 118, 135, 162, 168, 169, 170, 173, 174, 179, 183, 184, 189, 199, 207, 208, 211, 212, 215, 216, 221, 225, 228, 232, 237, 239, 242, 246, 249, 251], "demonstr": [1, 199, 211], "core": [1, 3, 4, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 70, 83, 85, 86, 96, 107, 110, 111, 112, 113, 114, 115, 116, 117, 118, 122, 124, 125, 128, 129, 135, 137, 140, 143, 158, 160, 162, 174, 235, 245], "simplest": 1, "wai": [1, 86, 96, 179, 183, 189, 198, 204, 206, 208, 215, 227, 237, 238], "possibl": [1, 6, 22, 23, 50, 85, 172, 179, 205, 239, 247, 250], "molequeu": [1, 3, 83, 160, 167, 174, 239, 242], "jsonrpcclient": 1, "h": [1, 3, 6, 20, 25, 50, 62, 64, 65, 66, 67, 68, 69, 72, 75, 77, 79, 83, 84, 90, 93, 99, 106, 108, 116, 117, 119, 121, 123, 126, 128, 142, 160, 161, 162, 168, 174, 179, 184, 186, 210, 217, 242, 246, 248, 250, 255, 257, 259], "client": [1, 67, 160, 164, 179], "The": [1, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 84, 85, 86, 88, 90, 91, 92, 93, 96, 97, 98, 100, 101, 102, 103, 104, 105, 106, 107, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 133, 135, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 159, 162, 163, 165, 168, 169, 170, 172, 173, 174, 176, 177, 179, 182, 183, 186, 188, 190, 191, 192, 197, 198, 199, 201, 203, 204, 205, 206, 207, 208, 209, 211, 212, 214, 215, 217, 218, 219, 220, 221, 222, 224, 225, 226, 227, 228, 230, 232, 236, 237, 239, 248, 250], "submit": [1, 5, 62, 64, 65, 66, 69, 160, 164, 176, 183, 186], "call": [1, 8, 13, 14, 18, 19, 26, 28, 49, 52, 63, 64, 68, 69, 70, 73, 74, 76, 83, 85, 89, 90, 93, 96, 101, 105, 124, 128, 129, 135, 162, 163, 169, 170, 171, 172, 173, 174, 177, 205, 237, 239, 242, 245, 247, 257], "an": [1, 3, 5, 6, 12, 14, 15, 18, 19, 20, 23, 24, 25, 27, 28, 29, 32, 34, 37, 38, 40, 43, 44, 49, 50, 52, 62, 63, 65, 66, 68, 69, 70, 79, 80, 83, 84, 85, 86, 89, 90, 91, 92, 93, 96, 104, 105, 106, 108, 116, 137, 138, 142, 158, 159, 162, 163, 168, 169, 170, 172, 173, 174, 176, 177, 179, 183, 184, 186, 189, 190, 191, 194, 198, 199, 201, 203, 204, 208, 211, 212, 213, 214, 216, 218, 219, 220, 221, 222, 226, 227, 228, 232, 233, 234, 237, 238, 239, 245, 246, 247, 250, 255, 256, 257, 259], "rpc": [1, 66, 69, 162, 242], "server": [1, 5, 62, 66, 67, 69, 93, 167, 230], "json": [1, 46, 63, 66, 76, 83, 84, 101, 114, 162, 167, 168, 169, 170, 171, 172, 173, 174, 176, 177, 242, 247], "2": [1, 6, 16, 18, 20, 29, 63, 66, 83, 85, 133, 143, 160, 161, 167, 170, 174, 177, 181, 183, 186, 191, 194, 201, 210, 213, 222, 225, 236, 237, 238, 239, 242, 245, 246, 248, 249, 255, 256, 257, 258], "0": [1, 6, 9, 11, 14, 15, 16, 19, 20, 22, 24, 27, 29, 40, 42, 44, 49, 63, 66, 73, 74, 76, 83, 96, 97, 101, 102, 103, 106, 119, 133, 135, 139, 141, 142, 143, 160, 161, 167, 168, 170, 172, 174, 176, 177, 180, 183, 186, 194, 201, 205, 219, 222, 235, 237, 241, 244, 248, 254, 255, 259], "author": [1, 16, 19, 23, 25, 26, 28, 32, 37, 38, 39, 47, 48, 49, 50, 52, 54, 56, 58, 59, 60, 61, 63, 71, 75, 76, 77, 83, 85, 87, 88, 90, 98, 99, 101, 102, 103, 105, 114, 116, 118, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 144, 146, 147, 159, 169, 174, 176, 179, 250], "marcu": [1, 2, 4, 16, 19, 23, 25, 26, 28, 32, 37, 38, 39, 47, 49, 50, 56, 71, 76, 77, 85, 87, 88, 90, 98, 99, 103, 105, 114, 118, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 144, 146, 147, 159], "d": [1, 2, 4, 8, 16, 19, 23, 25, 26, 28, 32, 37, 38, 39, 47, 49, 50, 56, 63, 71, 76, 77, 83, 85, 87, 88, 90, 93, 98, 99, 103, 105, 108, 114, 118, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 144, 146, 147, 159, 160, 161, 179, 243, 245, 246], "hanwel": [1, 2, 4, 16, 19, 23, 25, 26, 28, 32, 37, 38, 39, 47, 49, 50, 56, 71, 76, 77, 85, 87, 88, 90, 98, 99, 103, 105, 114, 118, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 144, 146, 147, 159], "provid": [1, 14, 15, 19, 22, 23, 25, 26, 28, 29, 32, 37, 39, 42, 44, 52, 62, 63, 64, 65, 66, 67, 68, 69, 70, 75, 80, 83, 84, 86, 91, 92, 103, 104, 105, 119, 122, 124, 127, 130, 140, 146, 162, 168, 170, 171, 174, 176, 179, 187, 198, 199, 201, 204, 205, 206, 207, 208, 209, 212, 219, 222, 227, 232, 234, 237, 247], "To": [1, 12, 17, 52, 64, 66, 75, 169, 172, 179, 182, 203, 210, 215, 220, 221, 239], "creat": [1, 13, 18, 20, 22, 27, 29, 34, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 67, 79, 83, 84, 86, 91, 92, 96, 103, 105, 107, 108, 110, 111, 112, 113, 114, 115, 118, 131, 134, 135, 145, 170, 171, 174, 176, 177, 179, 183, 185, 188, 190, 199, 206, 207, 209, 210, 212, 216, 223, 231, 232, 233, 237, 239, 243, 245, 247, 248, 252, 253, 254, 255, 259], "connect": [1, 27, 62, 67, 69, 85, 96, 128, 167, 172, 179, 204, 227, 230, 231, 246], "method": [1, 6, 13, 18, 22, 24, 29, 43, 49, 52, 63, 64, 66, 68, 76, 79, 83, 85, 86, 91, 92, 96, 101, 103, 105, 118, 119, 135, 159, 168, 170, 174, 216, 217, 237, 242, 245, 247, 250], "follow": [1, 6, 20, 63, 83, 93, 143, 168, 169, 170, 171, 172, 173, 174, 177, 179, 186, 189, 214, 215, 239], "done": [1, 14, 25, 38, 40, 66, 118, 124, 134, 160, 164, 170, 172, 219, 233], "new": [1, 3, 5, 6, 7, 8, 13, 18, 27, 28, 29, 34, 40, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 67, 69, 76, 80, 82, 83, 90, 93, 96, 101, 103, 106, 107, 110, 111, 112, 113, 114, 115, 128, 129, 142, 159, 160, 167, 170, 172, 173, 175, 178, 181, 182, 190, 191, 197, 201, 203, 205, 206, 210, 211, 215, 218, 219, 222, 223, 233, 236, 242, 243, 245, 246, 247, 248], "connecttoserv": 1, "myrpcserv": 1, "qjsonobject": [1, 62, 63, 83], "emptyrequest": 1, "qlatin1str": 1, "listqueu": 1, "sendrequest": 1, "endcod": 1, "signal": [1, 3, 62, 67, 68, 69, 70, 71, 76, 78, 83, 85, 86, 87, 88, 89, 90, 93, 96, 97, 99, 101, 104, 105, 158], "order": [1, 8, 14, 18, 22, 29, 63, 76, 80, 83, 86, 90, 93, 96, 104, 106, 124, 134, 135, 143, 160, 161, 168, 169, 172, 174, 177, 199, 201, 215, 222, 225, 228, 231, 239, 243, 247, 254], "act": [1, 96, 172, 239], "result": [1, 6, 13, 14, 19, 22, 26, 39, 63, 66, 69, 83, 84, 106, 125, 135, 142, 162, 169, 172, 173, 177, 179, 182, 183, 184, 231, 239, 255, 257, 258, 259], "notif": 1, "error": [1, 13, 49, 50, 52, 62, 64, 66, 69, 70, 79, 93, 105, 118, 124, 134, 135, 143, 160, 163, 164, 165, 166, 179, 245, 246, 247, 255], "receiv": [1, 62, 83, 179], "respons": [1, 4, 62, 88, 96, 124, 171, 172, 247], "set": [1, 13, 15, 16, 18, 19, 22, 23, 25, 26, 27, 28, 29, 34, 38, 39, 40, 42, 43, 44, 49, 52, 62, 63, 64, 65, 66, 69, 70, 74, 76, 79, 80, 81, 83, 85, 91, 92, 93, 96, 97, 101, 104, 105, 108, 117, 119, 122, 124, 127, 128, 129, 130, 133, 134, 135, 137, 141, 147, 158, 159, 160, 161, 162, 165, 167, 168, 169, 171, 174, 179, 182, 183, 184, 187, 188, 191, 198, 199, 208, 210, 216, 217, 219, 239, 242, 244, 245, 247, 248], "public": [1, 3, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 243], "qobject": [1, 62, 63, 67, 68, 70, 75, 76, 80, 83, 85, 86, 87, 89, 93, 96, 97, 99, 100, 101, 102, 104], "end": [1, 3, 6, 8, 29, 44, 82, 96, 116, 117, 121, 122, 125, 131, 137, 145, 160, 161, 166, 183, 186, 198, 220, 221], "complet": [1, 28, 52, 62, 66, 69, 85, 118, 128, 164, 168, 169, 176, 186], "constructor": [1, 8, 16, 19, 25, 28, 29, 38, 63, 68, 73, 74, 83, 85, 86, 89, 90, 93], "more": [1, 3, 6, 25, 28, 38, 49, 63, 76, 83, 86, 96, 104, 105, 106, 116, 121, 124, 127, 135, 137, 162, 169, 173, 174, 175, 176, 179, 191, 198, 199, 204, 208, 211, 212, 214, 215, 217, 219, 227, 228, 232, 237, 238, 242, 243, 246, 247, 257], "construct": [1, 19, 20, 62, 65, 80, 84, 90, 96, 203, 206], "describ": [1, 14, 16, 63, 69, 83, 118, 168, 170, 173, 174, 179], "paramet": [1, 8, 14, 15, 16, 19, 22, 23, 25, 26, 28, 29, 33, 38, 39, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 64, 65, 66, 68, 69, 75, 76, 79, 82, 84, 85, 86, 90, 91, 92, 93, 96, 101, 103, 106, 107, 110, 111, 112, 113, 114, 115, 116, 117, 119, 121, 122, 125, 127, 128, 129, 130, 135, 137, 140, 142, 143, 169, 170, 189, 208, 214, 217, 219, 233, 246, 254], "input": [1, 9, 14, 22, 24, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 84, 85, 93, 96, 101, 105, 107, 110, 111, 112, 113, 114, 115, 131, 145, 158, 162, 163, 168, 169, 170, 173, 175, 176, 177, 181, 183, 193, 208, 237, 242, 243, 244, 246, 247], "job": [1, 62, 63, 64, 65, 66, 69, 83, 174], "param": [1, 167], "filenam": [1, 49, 50, 52, 63, 70, 78, 79, 83, 109, 160, 163, 164, 165, 167, 170, 174, 176, 247], "appear": [1, 63, 79, 83, 96, 174, 176, 182, 189, 208, 228], "work": [1, 4, 5, 7, 25, 104, 169, 179, 183, 191, 194, 205, 208, 211, 214, 236, 237, 238, 239, 246, 247], "directori": [1, 30, 31, 79, 157, 162, 239, 243, 247], "content": [1, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 83, 85, 105, 107, 110, 111, 112, 113, 114, 115, 116, 117, 121, 122, 128, 129, 137, 140, 158, 167, 174, 179], "specifi": [1, 14, 19, 20, 22, 23, 26, 28, 29, 34, 39, 49, 50, 52, 65, 80, 84, 86, 91, 92, 93, 96, 105, 125, 127, 128, 129, 130, 135, 143, 168, 170, 171, 172, 173, 177, 179, 182, 184, 186, 187, 211, 228], "return": [1, 6, 9, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 73, 74, 75, 76, 79, 80, 82, 83, 85, 86, 88, 90, 91, 92, 93, 96, 97, 100, 101, 103, 104, 105, 107, 108, 110, 111, 112, 113, 114, 115, 116, 118, 119, 121, 122, 124, 125, 127, 128, 129, 130, 135, 137, 143, 159, 168, 171, 172, 206, 230, 252], "true": [1, 6, 9, 13, 15, 16, 18, 22, 25, 26, 27, 28, 29, 32, 37, 38, 39, 40, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 69, 70, 76, 83, 85, 86, 91, 92, 93, 96, 97, 101, 105, 107, 108, 110, 111, 112, 113, 114, 115, 122, 125, 127, 130, 135, 143, 160, 165, 168, 169, 170, 171, 172, 177], "wa": [1, 4, 28, 29, 62, 63, 66, 69, 70, 74, 76, 83, 85, 86, 101, 105, 125, 127, 174, 187, 189, 198, 203, 205, 232, 235, 237, 243], "successfulli": [1, 52, 62, 63, 66, 67, 76, 83, 85, 239, 246], "fals": [1, 6, 15, 16, 22, 25, 26, 28, 29, 32, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 76, 83, 85, 86, 96, 97, 101, 105, 107, 110, 111, 112, 113, 114, 115, 122, 125, 127, 130, 135, 160, 165, 168, 170, 172, 174], "otherwis": [1, 15, 16, 22, 25, 26, 29, 38, 39, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 66, 68, 69, 76, 83, 96, 101, 107, 110, 111, 112, 113, 114, 115, 127, 173, 174, 179, 213, 230], "bool": [1, 8, 9, 13, 15, 16, 18, 22, 23, 25, 26, 27, 28, 29, 32, 34, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 76, 78, 83, 85, 86, 87, 91, 92, 93, 96, 97, 99, 100, 101, 105, 106, 107, 108, 110, 111, 112, 113, 114, 115, 118, 122, 124, 125, 127, 130, 132, 133, 134, 135, 141, 143, 158, 159, 160, 161], "setinputfil": 1, "const": [1, 3, 6, 8, 9, 10, 11, 13, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 73, 74, 76, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 90, 91, 92, 93, 96, 97, 99, 100, 101, 102, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158], "qstring": [1, 3, 62, 63, 64, 65, 66, 68, 69, 70, 75, 76, 78, 79, 80, 81, 83, 84, 88, 93, 96, 97, 100, 101, 102, 103, 105, 109], "yunu": [2, 4], "ak": [2, 4], "ahmad": [2, 4], "abdolmaleki": [2, 4], "acun": [2, 4], "robert": [2, 4], "adam": [2, 4, 22], "b": [2, 4, 6, 20, 22, 27, 29, 42, 48, 54, 60, 86, 92, 96, 106, 141, 160, 161, 170, 174, 179, 192, 245, 247, 254], "adarsh": [2, 4, 48, 54, 60], "aditya": [2, 4], "niskala": [2, 4], "airaha": [2, 4], "alex": [2, 4, 242, 247], "bryce": [2, 4], "anderson": [2, 4], "andre870": [2, 4, 242], "hub": [2, 4, 242], "patrick": [2, 4, 59], "averi": [2, 4, 59], "ty": [2, 4], "balduf": [2, 4], "heiko": [2, 4], "becker": [2, 4], "eric": [2, 4], "berquist": [2, 4, 242, 247], "ludovico": [2, 4], "besana": [2, 4], "nathan": [2, 4], "bonnemain": [2, 4], "brohovski": [2, 4], "libor": [2, 4], "bukata": [2, 4], "andi": [2, 4], "chandler": [2, 4], "guillaum": [2, 4], "charifi": [2, 4], "yuri": [2, 4], "chornoivan": [2, 4], "christian": [2, 4], "clauss": [2, 4], "david": [2, 4], "cole": [2, 4], "andrea": [2, 4], "cord": [2, 4], "landwehr": [2, 4], "ddinghoya": [2, 4, 247], "diazonium": [2, 4], "amanda": [2, 4], "dumi": [2, 4], "sebastian": [2, 4], "ehlert": [2, 4], "aritz": [2, 4], "erkiaga": [2, 4], "o\u011fuz": [2, 4, 242], "ersen": [2, 4, 242], "bori": [2, 4], "faur": [2, 4], "nicola": [2, 4], "fella": [2, 4], "dominik": [2, 4], "florjan": [2, 4], "funnycod": [2, 4], "alessandro": [2, 4], "genova": [2, 4], "chri": [2, 4], "harri": [2, 4], "andr\u00e9": [2, 4], "henao": [2, 4], "brenton": [2, 4], "horn": [2, 4], "geoff": [2, 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189, 192, 199, 205, 207, 208, 211, 212, 214, 215, 219, 221, 224, 225, 228, 239, 251, 256, 258], "deriv": [3, 16, 21, 22, 26, 39, 49, 86, 101, 105, 127, 159, 179, 231, 251, 252, 256], "qobject_cast": 3, "enum": [3, 16, 20, 22, 23, 25, 34, 38, 40, 43, 49, 52, 62, 66, 68, 78, 79, 82, 86, 96, 97, 108, 118, 127, 132, 134, 135, 141, 143, 148, 149, 150, 151, 152, 153, 154, 155, 156], "": [3, 13, 14, 18, 20, 22, 25, 27, 29, 38, 42, 43, 44, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 66, 76, 80, 81, 82, 83, 85, 86, 96, 105, 107, 108, 110, 111, 112, 113, 114, 115, 119, 122, 130, 143, 158, 160, 161, 163, 167, 169, 170, 171, 173, 174, 179, 181, 184, 191, 201, 206, 208, 212, 214, 215, 218, 219, 220, 221, 222, 226, 231, 232, 237, 239, 242, 247, 249, 256], "constant": [3, 24, 85, 208], "static": [3, 15, 22, 24, 29, 40, 42, 49, 50, 62, 66, 67, 69, 72, 75, 79, 82, 85, 100, 104, 117, 128, 129, 148, 149, 150, 151, 152, 153, 154, 155, 156, 159, 217], "int": [3, 6, 13, 16, 18, 19, 22, 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76, 106, 119, 121, 124, 139, 142, 199, 224, 239, 245], "framework": [4, 237, 246, 247], "so": [4, 19, 22, 25, 38, 42, 52, 63, 83, 85, 96, 135, 143, 158, 159, 162, 167, 172, 174, 176, 179, 184, 191, 197, 198, 199, 208, 219, 236, 239, 255, 257, 259], "veri": [4, 5, 23, 32, 37, 162, 184, 203, 243, 245, 246], "grate": 4, "start": [4, 5, 6, 25, 27, 93, 117, 121, 181, 182, 183, 190, 191, 206, 216, 219, 220, 223, 229, 234, 238, 243, 247], "donald": 4, "curti": 4, "effort": [4, 82, 205], "kitwar": [4, 239], "inc": 4, "shahzad": 4, "ali": 4, "kristof": 4, "bal": 4, "banck": 4, "edward": 4, "bett": 4, "ross": 4, "braithwait": 4, "jame": 4, "bunt": 4, "taylor": [4, 205], "cornel": [4, 205], "raphael": 4, "kubo": 4, "costa": 4, "reini": 4, "dann": 4, "zackari": 4, "fall": [4, 6, 242, 243, 245], "naomi": 4, "fox": 4, "raimonda": 4, "galv": 4, "dagmar": 4, "lenk": 4, "gari": 4, "kedziora": 4, "thoma": [4, 242], "margraf": 4, "jordan": 4, "mantha": 4, "carsten": 4, "niehau": 4, "katsuhiko": 4, "nishimra": 4, "simon": 4, "ochsenreith": 4, "schwab": 4, "sergei": 4, "smirnov": 4, "casper": 4, "steinmann": 4, "jen": 4, "jonathan": 4, "tinkham": 4, "toneian": 4, "jure": 4, "varlec": 4, "egon": 4, "willighagen": 4, "support": [4, 5, 13, 25, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 75, 79, 83, 96, 103, 107, 110, 111, 112, 113, 114, 115, 116, 118, 124, 135, 143, 162, 167, 168, 169, 170, 171, 173, 174, 176, 203, 230, 231, 237, 238, 239, 242, 243, 245, 246, 247], "its": [4, 9, 15, 27, 40, 50, 52, 73, 74, 82, 96, 127, 162, 171, 172, 179, 198, 206, 226, 255, 256, 257, 259], "ha": [4, 5, 14, 15, 16, 22, 25, 27, 29, 38, 42, 52, 65, 67, 69, 76, 86, 96, 97, 101, 124, 133, 135, 172, 179, 186, 188, 189, 192, 194, 198, 199, 201, 203, 206, 208, 209, 217, 219, 221, 222, 232, 234, 237, 239, 242, 247, 257], "come": [4, 194, 199, 215, 217, 221, 238], "would": [4, 76, 127, 135, 191, 203, 205, 235, 237, 238, 239, 256], "particularli": [4, 217, 235, 243, 245, 246], "googl": [4, 243, 245, 246], "summer": [4, 205, 242, 243, 245, 246], "code": [4, 5, 7, 25, 38, 63, 83, 85, 89, 162, 168, 170, 171, 172, 174, 184, 191, 192, 194, 208, 233, 234, 237, 238, 240, 242, 243, 245, 246, 247], "2007": 4, "2008": 4, "2011": 4, "2016": 4, "2018": 4, "2019": [4, 245], "2021": [4, 242, 243, 244], "2022": [4, 205, 245, 246], "univers": [4, 205, 217, 219, 250], "pittsburgh": [4, 205], "u": [4, 5, 8, 9, 21, 105, 127, 186, 191, 238, 242, 243, 245, 246], "depart": [4, 205], "defens": 4, "dod": 4, "through": [4, 5, 6, 7, 14, 65, 69, 76, 96, 101, 162, 165, 170, 172, 175, 176, 179, 182, 183, 187, 188, 189, 192, 193, 198, 199, 201, 203, 208, 209, 211, 215, 219, 222, 228, 231, 237, 239, 242, 247], "pettt": 4, "program": [4, 66, 67, 68, 69, 135, 160, 164, 167, 168, 169, 174, 183, 189, 209, 215, 235, 236, 245], "research": [4, 191, 238, 250, 256], "corpor": [4, 179], "cottrel": 4, "scholar": 4, "award": 4, "reli": 4, "number": [4, 6, 13, 15, 16, 18, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 38, 39, 40, 52, 62, 63, 64, 73, 74, 75, 80, 82, 83, 85, 86, 96, 116, 121, 127, 129, 135, 137, 143, 167, 168, 170, 172, 174, 176, 177, 186, 192, 199, 201, 203, 206, 208, 213, 214, 219, 222, 228, 239, 254], "infrastructur": 4, "blue": [4, 19, 24, 141, 143, 160, 161, 166, 198, 199, 218, 221, 232, 237], "obelisk": [4, 24], "group": [4, 6, 8, 13, 18, 20, 29, 40, 42, 62, 63, 64, 65, 66, 67, 69, 70, 79, 83, 86, 93, 96, 101, 105, 106, 117, 122, 123, 124, 127, 128, 129, 135, 137, 138, 139, 140, 141, 143, 158, 174, 184, 186, 187, 188, 189, 191, 201, 206, 211, 222, 223, 231, 237, 245, 247, 250, 252, 254], "pybind11": 4, "chemic": [4, 24, 29, 34, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 83, 107, 110, 111, 112, 113, 114, 115, 162, 173, 174, 195, 203, 207, 209, 211, 215, 230, 237], "structur": [4, 22, 23, 24, 25, 27, 29, 38, 76, 171, 172, 184, 190, 191, 195, 197, 199, 201, 207, 212, 217, 219, 222, 237, 242, 243, 245, 254], "databas": [4, 5, 24, 175, 190, 197, 209, 230], "cmake": [4, 239, 247], "eigen": [4, 6, 29, 38, 108, 119, 135, 239], "softwar": [4, 208, 231], "babel": [4, 163, 170, 203, 237, 242, 245, 246], "And": [4, 168], "cours": [4, 190, 250], "johann": 4, "loschmidt": 4, "amedeo": 4, "made": [5, 7, 8, 24, 27, 82, 101, 179, 180, 197, 198, 199, 203, 204, 209, 211, 212, 217, 227, 242], "who": 5, "want": [5, 8, 169, 186, 190, 191, 198, 201, 203, 213, 214, 222, 224, 231, 232, 238], "back": [5, 8, 84, 160, 161, 206, 212, 242, 243, 245], "great": [5, 238, 239], "place": [5, 6, 40, 50, 73, 74, 172, 174, 179, 184, 199, 207, 208, 212, 219, 224, 226, 238, 239, 252], "fellow": 5, "forum": [5, 7], "question": [5, 238], "level": [5, 63, 76, 83, 174, 239, 250], "post": [5, 214], "mai": [5, 19, 29, 40, 52, 63, 65, 68, 76, 83, 96, 97, 101, 105, 106, 118, 127, 135, 168, 169, 172, 174, 176, 177, 179, 182, 184, 186, 190, 191, 192, 195, 205, 213, 215, 219, 228, 230, 231, 233, 235, 236, 239, 251, 256, 259], "find": [5, 15, 23, 30, 31, 42, 52, 79, 85, 96, 100, 157, 171, 172, 181, 203, 215, 216, 233, 237, 238, 246, 253, 256], "experi": [5, 250], "valuabl": 5, "bug": [5, 7, 194, 238, 241], "pleas": [5, 7, 238, 242, 243, 245, 246, 256], "take": [5, 23, 29, 50, 63, 70, 73, 74, 76, 83, 88, 105, 123, 124, 138, 172, 182, 195, 199, 208, 212, 215, 219, 224, 226, 233], "moment": [5, 191, 233], "tracker": [5, 238], "issu": [5, 7, 238, 242, 247], "while": [5, 6, 27, 63, 83, 85, 96, 101, 169, 170, 174, 183, 188, 214, 219, 228, 230, 246], "move": [5, 29, 105, 139, 143, 179, 186, 194, 197, 203, 219, 224, 236, 237, 247, 248], "around": [5, 6, 16, 23, 32, 37, 64, 66, 70, 186, 188, 191, 197, 199, 203, 214, 224, 237, 251, 256], "fit": [5, 6, 29, 52, 105, 124, 158, 179, 228], "particular": [5, 24, 52, 63, 76, 83, 167, 168, 170, 174, 179, 190, 205, 228], "compon": [5, 19, 23, 24, 27, 29, 128, 129, 133, 141, 143, 162], "itself": 5, "section": [5, 22, 63, 68, 83, 96, 174, 176, 199, 204, 205, 206, 208, 214, 219, 224, 237, 256], "discuss": [5, 7, 169, 208, 238, 242, 243, 245, 246, 256], "idea": [5, 238, 256], "plan": 5, "direct": [5, 19, 42, 63, 83, 116, 119, 120, 121, 122, 125, 129, 137, 143, 160, 166, 174, 179, 194, 220, 239, 245, 248], "progress": [5, 28, 85, 209, 236], "etc": [5, 6, 18, 25, 38, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 76, 83, 101, 104, 105, 107, 110, 111, 112, 113, 114, 115, 116, 121, 134, 135, 137, 143, 158, 162, 169, 170, 171, 174, 177, 199, 203, 208, 228, 230, 231, 234, 236, 237, 238, 239, 242, 247, 251], "both": [5, 16, 27, 52, 64, 65, 162, 168, 170, 173, 174, 176, 177, 188, 215, 238, 259], "python": [5, 93, 100, 162, 169, 172, 175, 176, 216, 236, 238, 239, 241, 243, 245, 246, 247], "script": [5, 64, 65, 76, 84, 93, 100, 101, 163, 173, 215, 236, 238, 242, 243, 244, 246, 247], "util": [5, 65, 93, 100, 119, 176, 189, 199, 208], "tell": [5, 101, 167], "friend": [5, 28, 42, 68, 80, 96, 116, 117, 121, 122, 128, 129, 130, 137, 140], "cite": 5, "paper": [5, 22, 193, 238, 248], "write": [5, 6, 8, 16, 37, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 70, 79, 83, 93, 104, 107, 110, 111, 112, 113, 114, 115, 160, 163, 165, 170, 171, 174, 245, 246, 247], "edit": [5, 15, 65, 96, 162, 181, 189, 198, 199, 201, 203, 208, 210, 211, 212, 222, 224, 234, 235, 237, 239, 245, 246, 247], "tutori": [5, 181, 182, 199, 208, 237, 238, 250], "site": [5, 228, 237, 238], "up": [5, 25, 27, 28, 38, 50, 52, 85, 99, 105, 119, 143, 158, 162, 167, 171, 182, 186, 189, 190, 191, 194, 195, 197, 198, 203, 208, 209, 211, 212, 213, 225, 228, 230, 232, 235, 237, 246, 247], "lesson": [5, 186, 250, 256], "activ": [5, 25, 71, 76, 87, 88, 89, 90, 97, 101, 104, 105, 215, 237, 239, 250], "teacher": [5, 250], "send": [5, 62, 67, 93, 162, 167, 174, 242], "fragment": [5, 134, 135, 160, 166, 181, 193, 196, 204, 206, 224, 227, 228, 237, 242, 247], "report": [5, 7, 63, 83, 174, 184, 238, 243, 244, 245, 246], "encount": [5, 7, 49, 52, 105], "about": [5, 20, 24, 40, 63, 83, 119, 174, 198, 208, 212, 214, 226, 238, 245, 246], "improv": [5, 7, 235, 237, 241, 244], "translat": [5, 23, 42, 68, 75, 119, 160, 163, 166, 168, 170, 173, 177, 179, 183, 184, 186, 190, 191, 203, 205, 218, 224, 238, 241, 242], "languag": [5, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 83, 107, 110, 111, 112, 113, 114, 115, 168, 169, 170, 171, 174, 211, 238, 246], "donat": 5, "pai": [5, 205, 259], "host": [5, 245, 246, 247], "meet": 5, "bounti": 5, "when": [6, 8, 9, 14, 16, 19, 21, 25, 29, 38, 50, 52, 62, 63, 64, 65, 66, 67, 69, 70, 76, 79, 83, 89, 90, 93, 96, 101, 105, 124, 128, 129, 158, 169, 170, 171, 172, 174, 176, 188, 189, 198, 199, 203, 204, 206, 208, 212, 213, 215, 224, 233, 236, 239, 243, 246, 247, 248, 250, 251], "base": [6, 8, 9, 14, 16, 20, 29, 34, 49, 63, 76, 77, 79, 80, 83, 86, 98, 101, 102, 117, 121, 122, 123, 125, 126, 130, 131, 145, 146, 162, 170, 172, 174, 176, 177, 179, 191, 192, 206, 208, 211, 237, 246, 247, 251, 256], "larg": [6, 8, 52, 182, 186, 187, 190, 191, 203, 237, 239], "kde": 6, "format": [6, 20, 34, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 70, 76, 79, 80, 81, 83, 107, 110, 111, 112, 113, 114, 115, 141, 143, 162, 163, 167, 168, 170, 171, 172, 174, 175, 176, 179, 180, 194, 208, 231, 233, 236, 237, 242, 243, 244, 245, 246, 247], "enforc": [6, 179], "clang": [6, 246], "tool": [6, 26, 39, 76, 101, 102, 105, 160, 165, 181, 183, 186, 190, 191, 197, 199, 201, 203, 204, 205, 214, 235, 236, 238, 242, 244, 245, 247, 251, 255, 258, 259], "space": [6, 20, 22, 23, 26, 28, 29, 39, 40, 52, 96, 147, 160, 161, 170, 174, 182, 184, 186, 187, 188, 189, 212, 245, 247, 254], "tab": [6, 212, 228, 243, 246], "keep": [6, 27, 52, 66, 68, 96, 104, 106, 214, 239], "less": [6, 13, 18, 24, 29, 96, 208, 228, 232, 237, 257], "than": [6, 8, 13, 18, 24, 27, 29, 52, 63, 83, 96, 167, 179, 187, 237, 243, 254, 257], "80": 6, "charact": [6, 20, 49, 63, 83, 169, 174], "wide": [6, 205, 208, 237], "each": [6, 14, 20, 25, 27, 28, 33, 38, 41, 49, 52, 62, 63, 64, 83, 96, 135, 143, 162, 170, 171, 174, 176, 177, 213, 239, 258, 259], "separ": [6, 143, 169, 174, 179, 231], "g": [6, 20, 25, 29, 34, 49, 63, 75, 76, 83, 89, 90, 93, 101, 135, 139, 141, 143, 160, 161, 167, 168, 169, 170, 173, 174, 176, 177, 179, 182, 191, 193, 194, 201, 213, 222, 228, 230, 234, 236, 237, 239, 242, 247], "nmbr": 6, "singl": [6, 18, 29, 52, 63, 65, 67, 71, 83, 85, 96, 117, 143, 174, 191, 192, 198, 204, 227, 246, 250], "fine": [6, 63, 83, 174], "counter": [6, 63, 83, 93], "temporari": [6, 170], "obviou": 6, "wait": [6, 65, 68, 93], "until": [6, 8, 65, 66, 206, 219, 254], "unus": [6, 16, 25, 38], "ones": 6, "incorrect": [6, 243, 246, 247], "f": [6, 25, 38, 71, 88, 108, 122, 135, 137, 139, 158, 160, 161, 170, 179, 217, 243], "lower": [6, 27, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 107, 110, 111, 112, 113, 114, 115, 143, 212], "letter": [6, 24, 192, 245], "word": 6, "acronym": 6, "cmlformat": [6, 49, 160, 163], "doubl": [6, 15, 18, 24, 25, 26, 29, 38, 39, 40, 43, 52, 90, 96, 108, 117, 158, 159, 160, 161, 191, 192, 201, 204, 222, 226, 227, 246, 257], "cntr": 6, "std": [6, 8, 9, 10, 11, 13, 16, 20, 21, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 38, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 82, 86, 96, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 121, 122, 124, 125, 127, 131, 134, 135, 137, 140, 142, 143, 145], "string": [6, 7, 13, 16, 20, 23, 24, 25, 28, 29, 33, 34, 35, 40, 41, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 66, 68, 69, 70, 76, 79, 80, 81, 83, 96, 101, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 118, 124, 131, 134, 135, 140, 142, 143, 145, 160, 161, 163, 167, 169, 172, 174, 193], "rawxml": 6, "char": [6, 13, 18, 24, 25, 29, 34, 40, 43, 86, 96, 101, 106, 128, 129, 135, 140, 141, 142, 143, 148, 150, 151, 152, 153, 155, 156, 160, 161], "list_delimit": 6, "center": [6, 29, 116, 119, 126, 133, 137, 160, 166, 186, 190, 191, 192, 198, 199, 210, 228, 237, 243, 247], "listdelimit": 6, "upper": [6, 138], "m_": 6, "blank": [6, 177, 212], "togeth": [6, 96, 127, 176], "after": [6, 29, 49, 52, 63, 64, 66, 69, 83, 90, 118, 169, 170, 177, 182, 186, 187, 188, 189, 191, 195, 197, 198, 201, 206, 208, 209, 214, 222, 224, 228, 232, 234, 242], "curli": 6, "blah": [6, 63, 83, 177], "explod": 6, "5": [6, 15, 40, 42, 63, 83, 96, 160, 161, 177, 186, 239, 246, 247, 248, 251, 258, 259], "pointer": [6, 8, 24, 28, 43, 45, 66, 79, 122, 125, 127, 130, 160, 161], "refer": [6, 8, 13, 18, 43, 45, 64, 66, 67, 68, 79, 80, 86, 91, 92, 104, 105, 116, 118, 119, 121, 125, 127, 135, 137, 143, 158, 160, 161, 171, 179, 214, 218, 219, 244], "between": [6, 15, 23, 24, 27, 29, 42, 43, 44, 85, 86, 96, 167, 172, 173, 182, 183, 199, 208, 214, 219, 225, 228, 247, 254, 256, 259], "x": [6, 20, 22, 23, 28, 29, 124, 170, 173, 174, 183, 199, 206, 208, 212, 218, 220, 237, 239, 247, 257], "mystr": 6, "y": [6, 20, 23, 29, 119, 124, 170, 174, 199, 206, 208, 212, 218, 220, 239], "whoah": 6, "surround": [6, 232], "binari": [6, 239, 246], "oper": [6, 8, 13, 14, 18, 21, 22, 28, 29, 34, 35, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 70, 72, 79, 80, 85, 86, 96, 107, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 121, 122, 128, 129, 132, 135, 137, 140, 141, 143, 160, 161, 163, 165, 166, 169, 171, 173, 183], "No": [6, 22, 27, 168, 179, 246], "memoryblock": 6, "malloc": 6, "data": [6, 8, 9, 16, 19, 21, 23, 24, 25, 26, 27, 28, 29, 34, 38, 39, 40, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 68, 76, 83, 85, 86, 87, 93, 96, 99, 106, 107, 108, 110, 111, 112, 113, 114, 115, 118, 133, 135, 142, 143, 147, 158, 160, 161, 164, 165, 167, 168, 172, 173, 181, 196, 207, 210, 211, 231, 236, 237, 242, 254, 255, 257], "size": [6, 8, 19, 21, 27, 28, 44, 52, 85, 116, 118, 121, 135, 137, 143, 160, 161, 166, 182, 183, 199, 212, 242, 247, 254], "left": [6, 52, 63, 83, 106, 119, 138, 142, 143, 174, 201, 203, 204, 206, 212, 218, 219, 221, 222, 227, 239], "normal": [6, 8, 25, 28, 29, 38, 63, 76, 83, 85, 90, 116, 120, 121, 122, 125, 129, 135, 137, 160, 161, 165, 166, 174, 188, 203], "same": [6, 13, 18, 22, 27, 52, 62, 64, 128, 129, 168, 179, 198, 212, 217, 239, 248, 259], "foo": 6, "run": [6, 14, 28, 62, 65, 68, 69, 83, 84, 85, 104, 160, 161, 165, 168, 169, 170, 171, 173, 176, 203, 210, 215, 234, 237, 244, 246, 253], "implement": [6, 12, 14, 17, 22, 33, 41, 46, 47, 48, 52, 54, 55, 56, 59, 60, 61, 63, 76, 83, 85, 90, 93, 96, 106, 114, 118, 123, 135, 140, 142, 143, 162, 167, 173, 245, 246], "myfun": 6, "cout": 6, "suppli": [6, 23, 24, 25, 29, 38, 49, 50, 63, 64, 76, 79, 83, 85, 96, 97, 108, 119, 122, 125, 134, 135, 137, 158, 168, 169, 170, 179], "endl": 6, "bar": [6, 208, 212, 224, 226, 233], "bodi": 6, "condit": [6, 22, 191], "also": [6, 27, 28, 40, 49, 63, 73, 74, 83, 96, 105, 116, 133, 137, 162, 168, 170, 172, 174, 175, 176, 179, 182, 186, 188, 190, 191, 192, 194, 201, 203, 204, 205, 206, 207, 208, 209, 211, 212, 215, 217, 219, 220, 222, 225, 226, 227, 231, 237, 238, 239, 246, 256], "complex": [6, 127, 201, 222, 228, 237, 247], "42": 6, "var": [6, 171], "parent": [6, 45, 62, 66, 68, 70, 71, 72, 76, 79, 82, 85, 87, 88, 89, 96, 97, 99, 101, 102, 105, 122, 127, 130, 144, 160, 161, 164, 165, 166], "doe": [6, 8, 13, 15, 22, 29, 40, 52, 86, 93, 96, 105, 119, 135, 159, 168, 169, 170, 179, 187, 208, 217, 224, 236, 254], "wrap": [6, 42, 96, 143, 159, 160, 166], "isvalid": [6, 13, 16, 18, 25, 26, 38, 39, 63, 83, 86, 91, 92, 105, 124, 132, 160, 161, 164, 165, 166], "agooddai": 6, "ani": [6, 8, 13, 14, 18, 23, 27, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 69, 76, 79, 80, 81, 83, 93, 96, 101, 105, 107, 110, 111, 112, 113, 114, 115, 118, 119, 125, 135, 167, 168, 169, 170, 172, 173, 174, 176, 177, 179, 195, 203, 206, 209, 212, 221, 228, 235, 239, 247], "els": 6, "block": [6, 20, 63, 83, 169, 177], "element": [6, 8, 20, 21, 25, 27, 28, 29, 33, 41, 72, 73, 74, 75, 89, 90, 96, 123, 129, 131, 133, 135, 143, 145, 160, 161, 165, 168, 170, 171, 172, 174, 177, 179, 182, 189, 201, 206, 210, 217, 222, 228, 237, 243, 246, 251], "cover": [6, 169, 205, 230], "empti": [6, 8, 20, 25, 27, 29, 34, 40, 43, 44, 49, 50, 52, 76, 79, 80, 96, 118, 124, 134, 135, 160, 161, 169, 188, 242], "express": [6, 63, 83, 174, 179, 257], "intent": 6, "clearer": 6, "label": [6, 13, 20, 29, 63, 83, 96, 108, 139, 160, 161, 165, 169, 171, 174, 177, 179, 200, 214, 237, 242, 243, 245, 247], "column": [6, 22, 42, 68, 87, 99], "everi": [6, 27, 29, 179, 230], "must": [6, 16, 25, 26, 29, 38, 52, 63, 66, 76, 79, 83, 85, 96, 106, 118, 120, 128, 129, 134, 135, 142, 143, 168, 169, 170, 172, 173, 174, 176, 179, 206, 215, 239], "indic": [6, 20, 23, 27, 28, 29, 63, 64, 66, 68, 69, 76, 79, 82, 83, 86, 96, 104, 105, 116, 129, 135, 137, 168, 169, 170, 172, 173, 174, 176, 177, 179, 182, 186, 212, 214, 221, 228, 244], "omiss": 6, "anoth": [6, 40, 52, 170, 184, 189, 199, 201, 204, 222, 227, 237, 259], "immedi": [6, 176], "myenum": 6, "drawlin": [6, 117, 160, 166], "vertex": [6, 27, 28, 85, 117, 128, 129, 134, 135, 160, 161, 166, 225], "drawdot": 6, "default": [6, 16, 20, 24, 25, 26, 28, 29, 34, 38, 49, 52, 63, 65, 76, 79, 83, 96, 97, 105, 119, 128, 129, 133, 134, 139, 143, 169, 171, 174, 177, 192, 199, 201, 203, 212, 213, 219, 222, 233, 237, 247], "drawdefault": 6, "shorter": 6, "insert": [6, 8, 29, 63, 83, 160, 161, 169, 177, 181, 182, 186, 190, 191, 192, 193, 196, 210, 223, 224, 237, 242, 243, 245, 247, 248], "comma": [6, 168, 170], "broken": 6, "begin": [6, 8, 44, 85, 96, 106, 131, 142, 145, 160, 161, 166, 201, 204, 221, 222, 232, 234], "verylongexpress": 6, "anotherevenlongerexpress": 6, "justwhenyouthoughtitcouldntgetlong": 6, "vector3d": [6, 108], "posit": [6, 8, 13, 15, 22, 23, 26, 29, 39, 82, 85, 96, 116, 119, 120, 126, 133, 135, 136, 137, 139, 160, 161, 166, 186, 190, 191, 206, 212, 224, 237, 252, 257, 259], "currentposit": 6, "offset": [6, 85, 135, 160, 165], "reimplement": [6, 65, 105], "put": [6, 237, 247], "discourag": 6, "prefix": [6, 13, 18, 63, 79, 83, 173, 176, 177, 239], "clear": [6, 8, 14, 27, 28, 43, 44, 49, 63, 83, 85, 87, 90, 99, 105, 116, 117, 121, 122, 126, 127, 128, 129, 133, 137, 140, 158, 160, 161, 163, 165, 166, 183, 204, 210, 227, 242], "cpp": [6, 85], "extens": [6, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 76, 77, 79, 83, 107, 110, 111, 112, 113, 114, 115, 162, 167, 168, 169, 170, 173, 174, 181, 183, 199, 201, 210, 211, 214, 215, 219, 222, 231, 232, 237, 238, 242, 245, 246, 247], "As": [6, 7, 167, 169, 190, 199, 210, 218, 225, 228, 230, 239, 242, 245], "feel": [6, 238], "free": [6, 52, 105, 169, 174, 179, 201, 205, 222, 238, 239], "bad": 6, "local": [7, 63, 75, 83, 85, 169, 174, 176, 177, 238, 242, 245, 247], "avail": [7, 26, 29, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 67, 68, 69, 76, 83, 85, 101, 105, 107, 110, 111, 112, 113, 114, 115, 134, 159, 168, 169, 170, 171, 173, 174, 177, 179, 180, 237, 238, 246], "autom": [7, 50, 176, 237, 245, 246], "task": [7, 217, 237], "phrase": 7, "whenev": 7, "allow": [7, 8, 28, 32, 37, 43, 63, 79, 83, 162, 163, 168, 170, 173, 174, 179, 182, 183, 186, 188, 189, 190, 191, 193, 194, 199, 201, 203, 204, 206, 208, 209, 211, 212, 214, 219, 220, 221, 222, 224, 225, 226, 227, 228, 231, 233, 234, 236, 237, 242, 246, 247], "time": [7, 52, 63, 83, 93, 96, 105, 118, 127, 162, 179, 182, 187, 191, 247, 250], "freez": [7, 29], "least": [7, 76, 96, 213, 225, 232, 237, 246], "week": 7, "advanc": [7, 63, 83, 174, 238, 239], "releas": [7, 52, 118, 135, 143, 160, 166, 176, 205, 235, 239, 240, 241], "typenam": [8, 9, 10, 14, 21, 43, 45, 91, 92, 130, 148], "copi": [8, 13, 18, 23, 28, 29, 43, 50, 79, 86, 106, 142, 186, 193, 210, 215, 228, 242, 245, 247], "semant": 8, "effect": [8, 119, 179, 215, 248, 254], "share": [8, 13, 18, 27, 37, 176, 179, 180, 237, 239], "without": [8, 27, 50, 52, 66, 69, 162, 179, 203, 205, 208, 209, 235, 239, 243], "expos": 8, "access": [8, 19, 52, 65, 67, 68, 84, 104, 118, 135, 143, 170, 179, 194, 199, 209, 246, 250], "amount": [8, 186, 208], "non": [8, 9, 24, 29, 63, 83, 96, 127, 170, 172, 174, 179, 242, 243, 246, 247], "trigger": [8, 105, 172], "detach": [8, 135, 160, 161, 210, 245], "op": 8, "count": [8, 13, 29], "1": [8, 13, 16, 18, 19, 20, 22, 23, 25, 27, 29, 52, 63, 66, 69, 83, 86, 96, 106, 119, 133, 135, 142, 143, 160, 161, 168, 170, 172, 174, 176, 177, 183, 184, 186, 188, 191, 192, 194, 201, 205, 210, 213, 222, 225, 235, 237, 239, 240, 241, 242, 247, 248, 249, 255, 256, 257, 258, 259], "perform": [8, 14, 16, 22, 43, 52, 64, 85, 96, 105, 135, 169, 171, 172, 179, 183, 189, 203, 208, 213, 237, 239, 241, 248, 259], "deep": [8, 232, 239], "greater": 8, "unnam": [8, 13, 18, 20, 29, 42, 62, 64, 65, 66, 67, 69, 70, 79, 86, 93, 96, 101, 105, 106, 117, 122, 123, 124, 128, 129, 135, 138, 139, 140, 141, 143, 158], "typedef": [8, 12, 13, 14, 17, 18, 22, 29, 34, 44, 45, 49, 62, 79, 86, 91, 92, 96, 141], "value_typ": [8, 45, 118, 135, 143, 160, 161], "compat": [8, 79, 179, 208], "allocator_typ": [8, 45, 160, 161], "const_refer": [8, 45, 160, 161], "const_point": [8, 45, 160, 161], "iter": [8, 14, 44, 45, 160, 161], "const_iter": [8, 44, 45, 160, 161], "reverse_iter": [8, 45, 160, 161], "const_reverse_iter": [8, 45, 160, 161], "difference_typ": [8, 45, 160, 161], "size_typ": [8, 45, 143, 160, 161], "intern": [8, 14, 40, 52, 62, 64, 66, 67, 79, 90, 140, 143, 160, 161, 168, 170, 173, 238], "arrayrefcontain": [8, 160, 161], "valuetyp": [8, 9, 10, 11, 14, 45, 160, 161], "inlin": [8, 9, 10, 11, 12, 16, 17, 19, 20, 21, 23, 25, 26, 28, 29, 34, 35, 38, 42, 43, 44, 45, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 69, 70, 71, 76, 78, 80, 81, 83, 84, 85, 86, 87, 88, 90, 91, 92, 93, 94, 95, 96, 97, 98, 101, 105, 106, 107, 108, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 143, 145, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159], "explicit": [8, 14, 26, 27, 33, 36, 39, 41, 42, 45, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 76, 78, 80, 83, 84, 85, 87, 88, 89, 90, 91, 92, 93, 96, 97, 99, 100, 101, 105, 123, 127, 128, 129, 134, 144], "size_t": [8, 13, 27, 29, 36, 44, 45, 52, 82, 96, 116, 117, 121, 125, 127, 128, 129, 135, 137, 141], "n": [8, 16, 20, 25, 27, 28, 38, 45, 127, 129, 174, 190, 191, 217], "valu": [8, 9, 10, 16, 19, 20, 22, 23, 25, 26, 28, 29, 34, 38, 39, 43, 44, 45, 49, 50, 52, 62, 66, 68, 78, 79, 82, 85, 86, 87, 93, 97, 99, 105, 118, 119, 122, 127, 129, 130, 132, 134, 135, 141, 143, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 160, 161, 168, 170, 171, 173, 174, 176, 208, 248], "inputiter": [8, 45], "last": [8, 23, 45, 63, 69, 83, 93, 207, 243], "note": [8, 25, 29, 63, 83, 119, 129, 135, 143, 167, 170, 174, 176, 177, 184, 186, 187, 188, 191, 199, 203, 205, 239, 241, 248, 252, 253, 259], "detachwithcopi": [8, 160, 161], "explicitli": [8, 167], "implicitli": 8, "ensur": [8, 22, 29, 63, 67, 83, 86, 96, 124, 133, 174, 208, 239, 242, 247], "retriev": [8, 16, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 68, 83, 107, 110, 111, 112, 113, 114, 115], "underli": [8, 19, 65, 84, 91, 92], "constdata": [8, 160, 161], "max_siz": [8, 160, 161], "capac": [8, 160, 161], "reserv": [8, 14, 28, 160, 161, 179], "sz": 8, "resiz": [8, 21, 52, 90, 105, 124, 160, 161, 166], "rbegin": [8, 160, 161], "rend": [8, 160, 161], "front": [8, 160, 161], "assign": [8, 27, 28, 29, 33, 41, 86, 96, 160, 161, 168, 237, 245, 246], "val": 8, "push_back": [8, 160, 161], "v": [8, 40, 42, 43, 44, 128, 129, 135, 177, 179, 194, 239, 247, 249, 257], "pop_back": [8, 160, 161], "eras": [8, 160, 161], "idx": [8, 68, 80], "othert": 8, "swap": [8, 27, 42, 80, 116, 117, 121, 122, 128, 129, 137, 140, 141, 160, 161, 165, 166], "swapandpop": [8, 160, 161], "index": [8, 12, 13, 14, 17, 18, 20, 21, 23, 25, 27, 29, 34, 38, 63, 68, 80, 83, 86, 87, 91, 92, 94, 95, 96, 99, 116, 118, 121, 125, 127, 128, 129, 132, 134, 135, 137, 143, 160, 161, 164, 165, 166, 172, 174, 177, 191, 247], "delet": [8, 50, 52, 70, 96, 105, 125, 127, 134, 158, 169, 183, 201, 206, 212, 222, 243, 245, 247, 252], "valid": [8, 16, 25, 26, 28, 38, 39, 49, 63, 69, 83, 86, 91, 92, 96, 105, 124, 129, 130, 134, 160, 161, 173, 174, 177, 239, 247], "pop": [8, 171, 189, 195, 197, 198, 208, 209, 211, 212, 232], "preserv": [8, 22, 27, 52, 96, 188], "protect": [8, 9, 14, 16, 19, 23, 29, 33, 34, 41, 49, 68, 80, 85, 89, 90, 93, 96, 97, 105, 122, 125, 127, 130, 134, 135, 140, 159, 179], "attribut": [8, 9, 14, 16, 19, 23, 29, 34, 62, 63, 69, 83, 85, 93, 96, 97, 117, 118, 122, 125, 127, 128, 129, 130, 134, 135, 140, 159, 174, 176, 180], "arrai": [9, 14, 19, 21, 22, 23, 27, 28, 29, 40, 52, 63, 83, 85, 86, 96, 116, 117, 118, 122, 124, 125, 128, 129, 135, 137, 140, 143, 160, 161, 168, 170, 173, 174, 177], "store": [9, 19, 21, 24, 25, 26, 29, 38, 39, 40, 43, 52, 63, 64, 65, 80, 81, 83, 96, 116, 117, 118, 119, 122, 128, 137, 143, 209, 247], "figur": [9, 74, 214, 254], "subclass": [9, 11, 16, 29, 46, 49, 67, 122, 127, 128, 129, 130, 132, 140, 142, 146], "coordinateset": [9, 160, 161], "istyp": [9, 160, 161], "match": [9, 24, 29, 40, 50, 63, 66, 68, 69, 79, 80, 81, 83, 118, 169, 174, 233, 239], "placehold": [9, 10, 64, 160, 161], "m_content": [9, 10, 160, 161], "m_data": [9, 19, 23, 29, 160, 161], "holder": [9, 11, 160, 161, 179], "type_info": [9, 10, 11], "clone": [9, 10, 11, 16, 25, 38, 160, 161], "atomtempl": [12, 94, 160, 161], "repres": [12, 13, 17, 18, 19, 22, 24, 27, 29, 34, 40, 43, 50, 64, 65, 67, 68, 84, 96, 122, 132, 162, 172, 199, 235, 237], "moleculeclass": [12, 17], "atomtyp": [12, 18, 29, 33, 41, 86, 91, 96, 160, 161, 165], "molecule_t": [13, 18, 91, 92], "setatomicnumb": [13, 29, 96, 160, 161, 165], "unsign": [13, 15, 16, 18, 22, 23, 24, 25, 28, 29, 38, 40, 43, 45, 62, 66, 69, 85, 86, 96, 101, 106, 108, 128, 129, 135, 140, 141, 142, 143, 160, 161], "num": [13, 25, 29, 96, 172], "proton": [13, 73, 232, 248, 256], "atom": [13, 14, 16, 18, 20, 22, 24, 25, 29, 33, 34, 38, 40, 41, 63, 75, 82, 83, 86, 91, 96, 97, 108, 132, 139, 160, 161, 162, 165, 166, 170, 171, 172, 174, 181, 182, 183, 184, 186, 189, 198, 200, 201, 204, 206, 210, 211, 212, 213, 214, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 229, 230, 232, 234, 235, 237, 242, 243, 245, 246, 247, 251, 257, 259], "atomicnumb": [13, 24, 29, 86, 96, 160, 161, 165], "setposition2d": [13, 160, 161], "vector2": [13, 29, 96], "po": [13, 23, 29, 85, 96, 120, 136], "2d": [13, 29, 212, 242], "Not": 13, "current": [13, 14, 18, 27, 28, 29, 49, 52, 56, 62, 64, 65, 66, 69, 75, 76, 85, 88, 90, 96, 101, 104, 106, 116, 117, 119, 121, 122, 123, 124, 128, 129, 130, 133, 134, 135, 137, 140, 142, 167, 169, 186, 199, 209, 211, 212, 213, 224, 236, 237, 238, 251], "moleculetyp": [13, 18, 91, 92, 160, 161, 165], "compil": [13, 134, 135, 160, 166, 239], "position2d": [13, 160, 161], "setposition3d": [13, 160, 161], "vector3": [13, 22, 23, 26, 29, 39, 40, 42, 82, 86, 96], "3d": [13, 23, 29, 96, 105, 119, 128, 129, 135, 162, 170, 172, 193, 203, 212, 237, 246, 256], "position3d": [13, 29, 86, 96, 160, 161], "sethybrid": [13, 29, 96, 160, 161, 165], "atomhybrid": [13, 29, 96], "hyb": [13, 29, 96], "hybrid": [13, 29, 96, 160, 161, 165, 251, 256], "coordin": [13, 20, 21, 22, 25, 29, 40, 42, 63, 83, 96, 108, 117, 119, 124, 135, 138, 139, 143, 160, 161, 163, 183, 184, 187, 188, 206, 228, 242, 243, 247, 250], "setformalcharg": [13, 29, 96, 160, 161, 165], "sign": [13, 29, 96, 135, 239, 245], "charg": [13, 29, 63, 83, 96, 174, 175, 176, 208, 217, 228, 232, 237, 243, 245, 246, 247, 248, 259], "formal": [13, 29, 96, 228, 245, 247], "formalcharg": [13, 29, 96, 160, 161, 165], "setcolor": [13, 28, 29, 34, 96, 128, 129, 132, 160, 161, 165, 166], "vector3ub": [13, 29, 34, 96, 116, 120, 121, 128, 129, 131, 132, 135, 136, 137, 141, 145], "color": [13, 19, 24, 28, 29, 34, 63, 83, 96, 116, 121, 128, 129, 132, 133, 137, 141, 143, 158, 160, 161, 165, 166, 174, 175, 177, 181, 186, 199, 208, 210, 232, 237, 242, 243, 245, 246, 247], "setlay": [13, 29, 96, 160, 161, 165], "layer": [13, 29, 86, 96, 160, 161, 165, 243, 244, 245, 246, 247], "invalid": [13, 18, 29, 40, 49, 69, 86, 91, 92, 96, 132, 160, 166, 243], "object": [13, 14, 18, 19, 25, 28, 29, 43, 44, 50, 52, 62, 63, 64, 65, 68, 69, 73, 76, 79, 83, 84, 85, 86, 91, 92, 96, 101, 104, 105, 106, 108, 116, 117, 118, 119, 121, 122, 124, 125, 128, 129, 132, 135, 137, 142, 146, 159, 165, 168, 169, 170, 173, 174, 198, 214, 242], "increment": [13, 18], "self": [13, 18, 246], "check": [13, 16, 18, 22, 26, 28, 29, 39, 40, 49, 63, 69, 76, 83, 86, 93, 96, 105, 124, 127, 171, 172, 176, 177, 201, 212, 214, 219, 221, 222, 226, 242, 246, 247, 253, 254, 259], "postfix": [13, 18], "decrement": [13, 18], "setselect": [13, 160, 161], "select": [13, 29, 66, 69, 79, 86, 90, 96, 160, 161, 165, 177, 181, 182, 183, 186, 189, 190, 191, 192, 193, 194, 195, 197, 199, 201, 202, 203, 206, 209, 210, 212, 214, 215, 217, 218, 220, 221, 222, 223, 224, 225, 228, 230, 232, 233, 234, 242, 243, 244, 245, 246, 247, 248], "setforcevector": [13, 29, 96, 160, 161, 165], "forc": [13, 29, 86, 96, 140, 162, 175, 176, 191, 200, 210, 214, 216, 217, 228, 234, 239, 247, 253, 255, 256, 257, 259], "forcevector": [13, 29, 96, 160, 161, 165], "setlabel": [13, 29, 96, 160, 161, 165], "outputtyp": 14, "interfac": [14, 15, 24, 40, 62, 63, 65, 76, 83, 84, 85, 93, 97, 101, 142, 162, 169, 171, 172, 174, 181, 203, 205, 208, 215, 219, 246, 247], "list": [14, 22, 29, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67, 68, 69, 76, 79, 80, 103, 105, 107, 110, 111, 112, 113, 114, 115, 125, 127, 168, 169, 170, 171, 172, 174, 176, 179, 208, 209, 228, 239, 242, 246, 256], "identifi": [14, 16, 24, 29, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 69, 83, 86, 91, 92, 102, 107, 110, 111, 112, 113, 114, 115, 116, 120, 121, 122, 124, 125, 132, 135, 136, 137, 143, 160, 163, 165, 166, 174], "mol": [14, 15, 20, 22, 23, 26, 33, 34, 39, 40, 41, 57, 59, 62, 63, 64, 65, 70, 72, 76, 83, 96, 101, 168, 169, 170, 172, 208, 252, 257], "nullptr": [14, 26, 29, 33, 36, 39, 41, 50, 52, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 76, 78, 79, 80, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 96, 97, 99, 100, 101, 102, 103, 104, 105, 122, 123, 125, 127, 130, 144, 158, 243], "setmolecul": [14, 16, 20, 36, 64, 65, 70, 76, 101, 105, 158, 160, 161, 164, 165, 178], "obtain": [14, 29, 32, 37, 68, 82, 86, 91, 92, 96, 129, 172], "lookup": [14, 50, 246], "been": [14, 29, 50, 52, 67, 69, 76, 96, 97, 133, 135, 172, 179, 186, 189, 198, 199, 201, 208, 209, 212, 217, 219, 222, 225, 232, 233, 234, 237, 239, 250, 256], "previous": [14, 208, 209, 212, 225], "cach": [14, 52, 63, 67, 83, 93, 176, 246, 247], "There": [14, 63, 82, 83, 174, 192, 193, 194, 212, 238, 239], "correspond": [14, 16, 25, 29, 62, 63, 83, 96, 174, 176, 177, 179, 183, 215, 219, 248], "reset": [14, 49, 52, 63, 83, 91, 92, 93, 97, 105, 119, 124, 158, 160, 161, 164, 165, 186, 210, 220, 224, 225, 226, 242, 243], "typer": 14, "state": [14, 49, 52, 62, 63, 66, 69, 83, 91, 92, 96, 97, 126, 159, 177, 179, 243], "m_type": [14, 134, 160, 161, 166], "initi": [14, 24, 25, 27, 38, 63, 66, 69, 79, 83, 85, 86, 96, 105, 124, 160, 161, 165, 166, 176, 177, 201, 203, 206, 222, 226, 230, 231, 242, 244, 245, 246, 247], "setup": [14, 62, 170, 210, 215, 245], "prior": [14, 62, 179], "enough": [14, 52], "room": 14, "determin": [14, 33, 41, 50, 52, 62, 63, 83, 118, 126, 176, 188, 189, 191, 208, 221, 225, 228, 231, 232, 247], "m_molecul": [14, 16, 96, 160, 161, 165], "popul": [14, 16, 22, 26, 52, 96], "spglib": [15, 40, 96, 184, 242], "short": [15, 29, 40, 43, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 93, 96, 107, 110, 111, 112, 113, 114, 115, 143, 160, 161], "gethallnumb": [15, 160, 161], "carttol": [15, 40, 96], "1e": [15, 40, 96], "hall": [15, 40, 96], "crystal": [15, 40, 42, 181, 185, 189, 199, 206, 208, 210, 237, 243, 247], "unit": [15, 20, 22, 24, 29, 40, 42, 63, 83, 96, 174, 177, 181, 182, 185, 188, 189, 191, 194, 210, 212, 243, 247, 254], "cell": [15, 20, 22, 29, 40, 42, 96, 174, 181, 182, 185, 186, 189, 191, 194, 210, 212, 243, 247, 254], "exist": [15, 23, 27, 29, 44, 52, 66, 68, 86, 96, 103, 127, 135, 169, 173, 174, 219, 235, 243], "algorithm": [15, 22, 85, 96, 187, 208, 213], "fail": [15, 43, 52, 63, 66, 67, 83, 96, 128, 129, 170, 174, 179], "succe": 15, "handl": [15, 22, 49, 50, 64, 69, 76, 79, 89, 90, 93, 101, 105, 118, 134, 143, 160, 163, 164, 165, 166, 168, 169, 170, 173, 237, 242, 247], "cartesian": [15, 20, 22, 25, 38, 40, 42, 96, 170, 174, 183, 184, 187, 188, 199, 210], "toler": [15, 29, 40, 96, 184, 187, 246], "reducetoprimit": [15, 160, 161], "reduc": [15, 22, 40, 96, 179, 181, 185], "primit": [15, 25, 38, 96, 97, 116, 120, 121, 122, 124, 125, 133, 136, 137, 160, 166, 181, 185], "unless": [15, 19, 179], "miss": [15, 235, 243, 246], "conventionalizecel": [15, 96, 160, 161, 165], "refin": [15, 217], "convention": [15, 96], "symmetr": [15, 96, 160, 161, 188, 237], "basi": [16, 25, 26, 29, 38, 39, 63, 83, 108, 109, 174, 179, 208, 247], "gaussianset": [16, 26, 38, 39, 109, 160, 161], "slaterset": [16, 160, 161], "capabl": [16, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 96, 107, 110, 111, 112, 113, 114, 115, 116, 137, 173, 174, 206, 209, 217], "calcul": [16, 25, 26, 28, 29, 38, 39, 63, 64, 65, 69, 83, 85, 106, 119, 142, 164, 174, 182, 183, 184, 186, 189, 191, 210, 215, 217, 225, 228, 231, 232, 234, 237, 246, 248, 250, 259], "electrontyp": [16, 25, 26, 38, 160, 161], "electron": [16, 24, 25, 26, 29, 39, 208, 231, 232, 246], "pair": [16, 25, 26, 27, 28, 29, 35, 38, 63, 83, 86, 96, 117, 160, 161, 174, 176, 177, 208, 231, 237, 246], "alpha": [16, 25, 26, 42, 141, 143, 160, 161, 166, 170, 242, 246], "beta": [16, 25, 26, 42, 160, 161, 170, 235, 236], "cannot": [16, 22, 30, 31, 50, 52, 69, 157, 179, 237], "enumer": [16, 20, 22, 23, 25, 34, 38, 43, 49, 52, 62, 66, 68, 78, 79, 82, 86, 97, 118, 127, 132, 134, 135, 141, 143, 148, 149, 150, 151, 152, 153, 154, 155, 156, 172], "destructor": [16, 25, 28, 38, 52, 85], "setelectroncount": [16, 160, 161], "electroncount": [16, 160, 161], "molecule_": 16, "get": [16, 23, 25, 29, 40, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 76, 83, 85, 86, 88, 91, 92, 96, 103, 104, 105, 107, 110, 111, 112, 113, 114, 115, 116, 118, 119, 121, 122, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 158, 159, 162, 168, 170, 172, 181, 238, 239, 242, 256], "belong": [16, 68, 86, 91, 92], "setnam": [16, 23, 28, 160, 161], "settheorynam": [16, 160, 161], "theorynam": [16, 160, 161], "molecularorbitalcount": [16, 25, 38, 160, 161], "molecular": [16, 25, 26, 29, 38, 39, 63, 83, 105, 162, 167, 168, 169, 170, 171, 172, 174, 181, 193, 195, 196, 199, 203, 210, 212, 214, 219, 228, 229, 231, 235, 237, 238, 246, 247, 250, 251, 256], "orbit": [16, 25, 26, 38, 39, 108, 160, 161, 162, 181, 199, 210, 229, 237, 243, 255, 258], "homo": [16, 160, 161], "given": [16, 23, 24, 25, 27, 29, 40, 43, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 65, 68, 79, 84, 86, 96, 105, 107, 110, 111, 112, 113, 114, 115, 168, 171], "mo": [16, 23, 25, 26, 38, 160, 161, 247], "lumo": [16, 160, 161], "m_electron": [16, 160, 161], "total": [16, 29, 62, 228, 247], "close": [16, 49, 52, 65, 71, 160, 163, 179, 210, 214, 232, 233, 243, 245, 246, 254], "shell": [16, 25, 38, 108, 160, 163], "doubli": 16, "occupi": [16, 52], "hold": [16, 85, 108, 172, 193, 197, 203, 204, 219, 227], "possibli": 16, "bond": [16, 18, 29, 34, 63, 82, 83, 86, 92, 96, 132, 160, 161, 162, 165, 166, 172, 174, 181, 183, 189, 191, 200, 201, 204, 206, 208, 212, 213, 217, 219, 222, 223, 224, 225, 227, 228, 231, 244, 245, 246, 247, 253, 254, 255, 256, 257, 258, 259], "read": [16, 29, 37, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 70, 76, 79, 83, 107, 110, 111, 112, 113, 114, 115, 160, 163, 165, 170, 172, 174, 176, 179, 196, 206, 231, 242, 243, 244, 245, 247], "output": [16, 20, 22, 25, 30, 31, 38, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 66, 69, 83, 93, 107, 108, 110, 111, 112, 113, 114, 115, 157, 163, 164, 168, 169, 170, 173, 174, 207, 214, 217, 231, 233, 234, 246, 247], "necessarili": 16, "m_name": [16, 23, 160, 161], "usual": [16, 172, 239], "standard": [16, 63, 71, 83, 91, 92, 93, 96, 118, 135, 159, 167, 168, 169, 170, 172, 173, 174, 179, 199, 209, 243, 247], "m_theorynam": [16, 160, 161], "theori": [16, 63, 83, 174, 179, 200, 210, 247, 251], "bondtempl": [17, 95, 160, 161], "bondtyp": [17, 29, 86, 92, 96, 160, 161, 165], "atom1": [18, 29, 86, 96, 160, 161], "atom2": [18, 29, 86, 96, 160, 161], "setord": [18, 160, 161], "o": [18, 93, 119, 127, 137, 159, 168, 201, 207, 217, 222, 239, 259], "getotheratom": [18, 160, 161], "represent": [19, 22, 42, 63, 83, 135, 173, 174, 179, 199, 207], "rgb": [19, 63, 83, 141, 174], "three": [19, 24, 25, 38, 128, 129, 143, 199, 206, 225, 228], "float": [19, 23, 28, 43, 85, 116, 119, 120, 121, 122, 124, 125, 126, 128, 131, 133, 135, 136, 137, 139, 140, 141, 143, 145, 160, 161, 168, 170, 172, 246], "rang": [19, 22, 63, 83, 125, 127, 129, 135, 141, 143, 168, 170, 174, 177, 208, 228, 237, 246, 256], "intens": [19, 29, 246], "red": [19, 141, 143, 160, 161, 166, 199, 218, 232, 237], "green": [19, 141, 143, 160, 161, 166, 199, 218], "memori": [19, 25, 52, 96, 135, 245], "3": [19, 28, 63, 83, 85, 128, 129, 135, 141, 143, 160, 161, 168, 170, 177, 183, 187, 191, 201, 210, 213, 214, 222, 239, 242, 248, 249, 256, 257, 258], "pass": [19, 23, 28, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 69, 76, 83, 84, 85, 93, 101, 105, 107, 110, 111, 112, 113, 114, 115, 122, 123, 135, 167, 169, 174, 243, 246], "directli": [19, 50, 68, 168, 179, 190, 192, 196, 231], "opengl": [19, 124, 133, 162, 239, 245, 246, 247], "conveni": [19, 29, 44, 49, 50, 52, 67, 68, 86, 162, 206, 211, 247], "written": [19, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 83, 85, 107, 110, 111, 112, 113, 114, 115, 169, 174, 177, 179, 232], "emphasi": 19, "effici": [19, 211, 243], "layout": [19, 66, 88], "black": [19, 133, 201, 204, 222, 226, 227], "integ": [19, 23, 28, 143, 174], "255": [19, 63, 83, 135, 141, 174], "expect": [19, 24, 25, 28, 63, 83, 85, 104, 169, 170, 174, 179, 239, 247], "align": [20, 22, 133, 141, 174, 181, 182, 183, 186, 191, 192, 210, 223, 247], "see": [20, 29, 52, 63, 65, 79, 83, 86, 96, 106, 135, 143, 162, 169, 173, 174, 184, 187, 188, 191, 192, 208, 231, 256], "setspecif": [20, 160, 161], "detail": [20, 22, 49, 52, 62, 63, 65, 66, 73, 83, 162, 168, 169, 170, 171, 173, 174, 208], "distanceunit": [20, 160, 161], "distanc": [20, 40, 42, 119, 139, 160, 161, 166, 182, 183, 208, 214, 225, 246, 247, 254], "angstrom": [20, 22, 42, 160, 161, 191, 206, 214], "bohr": [20, 160, 161, 191, 206], "setdistanceunit": [20, 160, 161], "spec": 20, "inform": [20, 25, 29, 40, 63, 83, 96, 105, 124, 135, 169, 174, 176, 179, 188, 198, 199, 204, 206, 208, 210, 211, 214, 217, 219, 224, 227, 238, 245], "z": [20, 23, 29, 170, 174, 182, 186, 191, 192, 199, 206, 208, 212, 218, 220, 242], "6": [20, 22, 28, 63, 75, 83, 85, 124, 159, 160, 161, 168, 170, 172, 174, 191, 214, 239, 247, 251, 257], "carbon": [20, 24, 29, 75, 171, 172, 174, 176, 181, 186, 206, 221, 223, 226, 228, 250, 256, 257, 258], "l": [20, 120, 179, 239, 247], "c1": [20, 247], "gamess": [20, 108, 174, 208, 246, 247], "lattic": [20, 22, 42, 96, 174, 187, 188], "requir": [20, 25, 50, 63, 66, 83, 124, 143, 159, 168, 169, 172, 173, 174, 176, 179, 215, 233, 235, 257], "A": [20, 22, 25, 27, 29, 32, 37, 42, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 71, 76, 79, 80, 82, 83, 86, 87, 88, 91, 92, 93, 96, 97, 99, 100, 101, 103, 105, 107, 110, 111, 112, 113, 114, 115, 116, 123, 125, 127, 133, 134, 135, 137, 143, 162, 169, 174, 177, 179, 180, 183, 189, 190, 192, 194, 195, 197, 201, 206, 208, 212, 213, 221, 222, 226, 232, 233, 237, 239, 250, 256], "liter": [20, 63, 83, 174], "optim": [20, 29, 63, 83, 170, 174, 177, 181, 183, 191, 201, 210, 217, 222, 228, 237, 245, 246, 247, 248, 249, 251, 252, 253, 254, 255, 257, 258, 259], "flag": [20, 22, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 66, 68, 79, 83, 87, 99, 107, 110, 111, 112, 113, 114, 115, 141, 160, 164, 165, 169, 171, 174], "_": [20, 174], "__szxyz110": [20, 174], "replac": [20, 29, 80, 96, 169, 171, 172, 174, 179, 206, 239, 243], "text": [20, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 65, 80, 81, 96, 106, 107, 110, 111, 112, 113, 114, 115, 123, 124, 131, 138, 139, 140, 141, 142, 145, 160, 166, 168, 170, 171, 173, 174, 179, 183, 193, 194, 206, 207, 247, 250], "126214": [20, 174], "765886": [20, 174], "000000": [20, 174], "819345": [20, 174], "564955": [20, 174], "598383": [20, 174], "795127": [20, 174], "310706": [20, 174], "370165": [20, 174], "16": [20, 85, 174, 243], "285330": [20, 174], "757144": [20, 174], "130424": [20, 174], "185837": [20, 174], "548377": [20, 174], "375303": [20, 174], "033768": [20, 174], "794407": [20, 174], "396173": [20, 174], "450760": [20, 174], "generatecoordinateblock": [20, 160, 161], "arrayset": [21, 160, 161], "concret": 21, "_size": 21, "_index": 21, "collect": [22, 62, 63, 65, 66, 83, 105, 116, 121, 122, 125, 133, 137, 162, 172, 174, 179], "common": [22, 49, 63, 83, 122, 125, 127, 130, 146, 168, 169, 174, 180, 197, 208, 217, 228, 237], "crystallograph": [22, 184], "option": [22, 49, 50, 52, 62, 64, 65, 66, 69, 73, 74, 76, 84, 93, 96, 101, 116, 135, 137, 141, 143, 160, 161, 163, 164, 165, 167, 168, 170, 171, 172, 173, 177, 183, 186, 191, 208, 210, 216, 218, 219, 232, 236, 237, 243], "bitwis": [22, 50, 66, 141], "variou": [22, 25, 38, 63, 83, 169, 174, 198, 199, 208, 209, 211, 232, 234, 237, 238, 239, 245], "none": [22, 23, 25, 29, 40, 49, 50, 62, 79, 103, 127, 134, 135, 160, 161, 163, 164, 166, 210, 228, 245], "transformatom": [22, 96, 160, 161], "transform": [22, 40, 96, 119, 144, 179], "along": [22, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 71, 73, 74, 96, 107, 110, 111, 112, 113, 114, 115, 162, 168, 170, 173, 186, 191, 203], "wrapatomstounitcel": [22, 160, 161], "adjust": [22, 42, 82, 96, 160, 165, 188, 198, 199, 201, 206, 208, 212, 214, 219, 220, 222, 223, 224, 233, 234, 242, 247, 251], "fraction": [22, 40, 42, 96, 188, 206], "success": [22, 25, 26, 28, 29, 32, 37, 38, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 66, 69, 70, 83, 86, 96, 107, 110, 111, 112, 113, 114, 115, 135, 160, 165, 170], "rotatetostandardorient": [22, 160, 161], "opt": [22, 62, 96, 143, 171, 172], "rotat": [22, 96, 119, 141, 160, 166, 181, 182, 186, 190, 203, 213, 218, 221, 224, 226, 237, 242, 247, 250, 254], "axi": [22, 29, 119, 121, 133, 182, 183, 186, 191, 212, 218], "xy": [22, 38, 160, 161, 182, 186, 191], "plane": [22, 29, 119, 138, 182, 186, 191, 212, 217, 221], "trig": 22, "sinc": [22, 52, 168, 170, 172, 176, 177, 184, 187, 190, 194, 230, 237, 254], "fragil": 22, "neg": [22, 82, 237], "angl": [22, 42, 119, 201, 208, 212, 214, 222, 223, 225, 245, 246, 247, 258, 259], "found": [22, 29, 40, 44, 50, 63, 68, 79, 80, 81, 83, 85, 86, 125, 127, 162, 171, 174, 199, 204, 206, 207, 208, 211, 227, 230, 233, 238, 239, 242, 243, 244, 245, 246], "http": [22, 52, 85, 173, 176, 179, 191, 194, 195, 208, 239, 242, 243, 245, 246], "xtalopt": [22, 167], "openmolecul": 22, "net": [22, 199, 248], "misc": 22, "rotatetostdorient": 22, "pdf": 22, "setvolum": [22, 160, 161], "real": [22, 42, 43, 170, 247], "newvolum": [22, 96], "isotrop": 22, "scale": [22, 96, 119, 160, 166, 181, 185, 220, 226, 246], "volum": [22, 42, 96, 158, 160, 161, 181, 185, 187], "cubic": [22, 42], "failur": [22, 25, 26, 29, 32, 37, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 83, 96, 107, 110, 111, 112, 113, 114, 115, 135, 179, 244], "nigglireduc": [22, 160, 161], "niggli": [22, 96, 187], "reduct": [22, 96, 187], "produc": [22, 65, 123, 173, 179, 191], "canon": 22, "strive": 22, "gross": 22, "kunstlev": 22, "rw": 22, "sauter": 22, "nk": 22, "pd": 22, "numer": [22, 63, 83, 116, 135, 137, 168, 169, 170, 174, 242], "stabl": [22, 28, 160, 161], "comput": [22, 119, 168, 203, 205, 208, 212, 219, 237, 238, 256], "acta": 22, "crystallographica": 22, "foundat": 22, "crystallographi": [22, 182, 189, 194], "2003": 22, "60": 22, "modifi": [22, 28, 29, 50, 65, 82, 86, 96, 105, 119, 158, 160, 165, 169, 171, 172, 179, 189, 203, 210, 230, 237, 238], "extend": [22, 162, 175, 238, 242, 250, 251], "isnigglireduc": [22, 160, 161], "alreadi": [22, 40, 67, 86, 96, 108, 173, 189, 201, 215, 222, 247], "gruber": 22, "cryst": 22, "1973": 22, "29": 22, "4": [22, 85, 106, 129, 141, 142, 160, 161, 167, 170, 180, 182, 187, 191, 213, 219, 237, 249, 251, 257], "433": 22, "440": [22, 242], "buildsupercel": [22, 96, 160, 161, 165], "supercel": [22, 96, 181, 182, 185, 187], "expand": [22, 66, 69, 188, 189, 212], "upon": [22, 96, 127, 179], "setcellmatrix": [22, 42, 160, 161], "matrix3": [22, 42, 96], "newcellcolmatrix": 22, "ignor": [22, 29, 63, 83, 96, 97, 105, 143, 160, 165, 174, 176, 210, 214, 239, 246], "fractionalcoordin": [22, 160, 161], "unitcel": [22, 29, 86, 160, 161, 165, 170], "cart": [22, 42], "frac": [22, 42], "coord": [22, 29, 63, 83, 170, 172, 174, 243, 246], "atompositions3d": [22, 29, 96, 160, 161, 165], "setfractionalcoordin": [22, 160, 161], "regularli": [23, 147], "grid": [23, 168], "relat": [23, 179, 205, 232, 238], "vdw": [23, 160, 161, 243], "solventaccess": [23, 160, 161], "solventexclud": [23, 160, 161], "esp": [23, 160, 161], "electrondens": [23, 160, 161], "spindens": [23, 160, 161], "fromfil": [23, 160, 161], "min": [23, 160, 161], "max": [23, 160, 161], "maximum": [23, 29, 63, 82, 83, 85, 135, 177], "vector3i": [23, 85], "dimens": [23, 52, 85, 106, 119, 142, 143, 160, 161, 182], "setlimit": [23, 160, 161], "limit": [23, 79, 135, 208], "interv": 23, "dim": [23, 52, 106, 142, 143], "pad": [23, 129, 160, 166, 186], "regular": [23, 63, 83, 174, 247], "dimension": [23, 28, 52, 250], "setdata": [23, 29, 74, 87, 99, 160, 161, 165], "those": [23, 62, 172, 179], "adddata": [23, 160, 161], "closestindex": [23, 160, 161], "closest": 23, "indexvector": [23, 160, 161], "j": [23, 42, 179, 242, 245, 250], "k": [23, 42, 179], "quick": [23, 208, 210, 213, 221, 233, 237], "just": [23, 56, 63, 83, 129, 133, 169, 170, 177, 186, 237, 239], "valuef": [23, 160, 161], "vector3f": [23, 28, 85, 116, 117, 119, 120, 121, 122, 124, 125, 126, 128, 129, 133, 135, 136, 137, 139, 140], "trilinear": 23, "interpol": [23, 143], "quit": [23, 85, 243], "computation": 23, "expens": [23, 52, 85, 179], "setvalu": [23, 43, 44, 160, 161], "fill": [23, 40, 96, 106, 142, 160, 161, 212, 247], "fillstrip": [23, 160, 161], "kfirst": 23, "klast": 23, "stripe": 23, "minvalu": [23, 160, 161], "maxvalu": [23, 160, 161], "name_": [23, 28], "setcubetyp": 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143, 167, 168, 170, 173, 174], "radii": [24, 29, 82], "random": [24, 168, 172, 242], "consist": [24, 27, 63, 83, 172, 174], "mass": [24, 29, 73, 160, 161, 245, 247], "elementcount": [24, 160, 161], "atomicnumberfromnam": [24, 160, 161], "capit": 24, "recognis": 24, "invalidel": [24, 29, 96], "dummi": [24, 228, 242], "atomicnumberfromsymbol": [24, 160, 161], "xx": [24, 169], "guessatomicnumb": [24, 160, 161], "str": [24, 140], "attempt": [24, 32, 37, 52, 67, 126, 130, 135, 239], "slower": [24, 219], "reliabl": [24, 251], "atomicnumberfrom": 24, "best": [24, 29, 170, 208, 217, 228, 238, 239], "radiusvdw": [24, 160, 161], "van": [24, 182, 200, 208, 237], "der": [24, 182, 200, 208, 237], "waal": [24, 182, 200, 208, 237], "radiu": [24, 29, 116, 120, 121, 126, 133, 136, 137, 139, 140, 160, 161, 166, 237, 242], "radiuscoval": [24, 160, 161], "coval": [24, 82, 246], "valenceelectron": [24, 160, 161], "valenc": [24, 82, 201, 206, 222, 247], "basisset": [25, 26, 29, 38, 108, 160, 161], 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[[20, "class-avogadro-core-coordinateblockgenerator"]], "Contribute": [[5, "contribute"]], "How to Help": [[5, "how-to-help"]], "Coding Style (C++)": [[6, "coding-style-c"]], "Indentation": [[6, "indentation"]], "Line Width": [[6, "line-width"]], "Declaring Variables": [[6, "declaring-variables"]], "Whitespace": [[6, "whitespace"]], "Braces": [[6, "braces"]], "Parentheses": [[6, "parentheses"]], "Switch Statements": [[6, "switch-statements"]], "Line Breaks": [[6, "line-breaks"]], "Inheritance and the \u201cvirtual\u201d Keyword": [[6, "inheritance-and-the-virtual-keyword"]], "Referencing Members": [[6, "referencing-members"]], "File Naming": [[6, "file-naming"]], "Breaking Rules": [[6, "breaking-rules"]], "Translations": [[7, "translations"]], "Current Status": [[7, "current-status"]], "Credits": [[7, "credits"], [247, "credits"], [243, "credits"], [245, "credits"], [244, "credits"], [246, "credits"], [242, "credits"]], "Thanks": [[4, "thanks"], [205, "thanks"]], "Creators": [[4, "creators"]], "Contributors to Avogadro v2": [[4, "contributors-to-avogadro-v2"]], "Contributors to Avogadro v1": [[4, "contributors-to-avogadro-v1"]], "Avogadro Translators": [[4, "avogadro-translators"]], "Funding": [[4, "funding"]], "Other Projects": [[4, "other-projects"]], "Class Avogadro::Core::Array": [[8, "class-avogadro-core-array"]], "Class Avogadro::Core::CrystalTools": [[22, "class-avogadro-core-crystaltools"]], "Contributing Code": [[0, "contributing-code"], [0, null]], "Class Avogadro::Core::BondTemplate": [[18, "class-avogadro-core-bondtemplate"]], "Class Avogadro::Core::ArraySet::Holder": [[10, "class-avogadro-core-arrayset-holder"]], "Class Avogadro::Core::AvoSpglib": [[15, "class-avogadro-core-avospglib"]], "Class Avogadro::Core::Bond": [[17, "class-avogadro-core-bond"]], "Class Avogadro::Core::CoordinateSet": [[21, "class-avogadro-core-coordinateset"]], "Coding Conventions (C++)": [[3, "coding-conventions-c"]], "C++ Features": [[3, "c-features"]], "Including Headers": [[3, "including-headers"]], "Export Macro Headers": [[3, "export-macro-headers"]], "Private Headers": [[3, "private-headers"]], "Qt Headers": [[3, "qt-headers"]], "Namespaces": [[3, "namespaces"]], "Casting": [[3, "casting"]], "Aesthetics": [[3, "aesthetics"]], "Class Avogadro::Core::BasisSet": [[16, "class-avogadro-core-basisset"]], "Class Avogadro::Core::ArraySet": [[9, "class-avogadro-core-arrayset"]], "Class Avogadro::Core::ArraySet::PlaceHolder": [[11, "class-avogadro-core-arrayset-placeholder"]], "Class Avogadro::Core::Cube": [[23, "class-avogadro-core-cube"]], "Hydrogen Molecule": [[255, "hydrogen-molecule"]], "Task": [[255, "task"], [258, "task"], [257, "task"], [254, "task"], [253, "task"], [251, "task"], [259, "task"], [249, "task"]], "Solution": [[255, "solution"], [258, "solution"], [257, "solution"], [254, "solution"], [252, "solution"], [259, "solution"], [248, "solution"]], "See also": [[255, "see-also"], [258, "see-also"], [257, "see-also"], [254, "see-also"], [253, "see-also"], [251, "see-also"], [259, "see-also"], [249, "see-also"]], "Sources": [[255, "sources"], [254, "sources"], [259, "sources"]], "Organic Hybridization": [[258, "organic-hybridization"]], "Further reading": [[258, "further-reading"], [257, "further-reading"], [251, "further-reading"], [248, "further-reading"]], "Educational Publications Using Avogadro": [[250, "educational-publications-using-avogadro"]], "Yes We Chem": [[250, "yes-we-chem"]], "Computational Chemistry": [[250, "computational-chemistry"]], "Spectra / Spectroscopy": [[250, "spectra-spectroscopy"]], "Chemical Reactions and Mechanisms": [[250, "chemical-reactions-and-mechanisms"]], "Materials / Nano": [[250, "materials-nano"]], "Cheminformatics": [[250, "cheminformatics"]], "3D Printing and VR": [[250, "d-printing-and-vr"]], "Remote Teaching": [[250, "remote-teaching"]], "Markovnikov\u2019s Rule": [[257, "markovnikovs-rule"]], "Hydrogen Clusters": [[254, "hydrogen-clusters"]], "Issues": [[254, "issues"]], "HCN dipole": [[253, "hcn-dipole"]], "1,3-diaxial interactions": [[252, "diaxial-interactions"]], "Tasks": [[252, "tasks"], [248, "tasks"]], "Basic VSEPR": [[251, "basic-vsepr"]], "Water": [[259, "water"]], "Teach": [[256, "teach"]], "Publications": [[256, "publications"]], "Activities": [[256, "activities"]], "General Chemistry": [[256, "general-chemistry"]], "Organic Chemistry": [[256, "organic-chemistry"]], "Biochemistry:": [[256, "biochemistry"]], "Class Avogadro::MoleQueue::InputGenerator": [[63, "class-avogadro-molequeue-inputgenerator"]], "Script Entry Points": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md0"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md14"], [169, "script-entry-points"], [174, "script-entry-points"]], "Specifying parameters with <tt>\u2013print-options</tt>": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md1"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md15"]], "Fixed Mutually-Exclusive Parameter Lists": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md2"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md16"]], "Short Free-Form Text Parameters": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md3"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md17"], [177, "short-free-form-text-parameters"]], "Existing files": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md4"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md18"], [177, "existing-files"]], "Clamped Integer Values": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md5"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md19"]], "Boolean Parameters": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md6"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md20"], [177, "boolean-parameters"]], "Special Parameters": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md7"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md21"], [174, "special-parameters"]], "Syntax Highlighting": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md8"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md22"], [174, "syntax-highlighting"]], "Requesting Full Structure of Current Molecule": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md9"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md23"], [174, "requesting-full-structure-of-current-molecule"]], "Handling User Selections: <tt>\u2013generate-input</tt>": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md10"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md24"]], "Automatic Generation of Geometry": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md11"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md25"], [174, "automatic-generation-of-geometry"]], "Error Handling": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md12"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md26"], [174, "error-handling"]], "Debugging": [[63, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md13"], [83, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md27"], [169, "debugging"], [174, "debugging"]], "Class Avogadro::QtGui::BackgroundFileFormat": [[70, "class-avogadro-qtgui-backgroundfileformat"]], "Class Avogadro::QtGui::CustomElementDialog": [[72, "class-avogadro-qtgui-customelementdialog"]], "Class Avogadro::MoleQueue::MoleQueueWidget": [[69, "class-avogadro-molequeue-molequeuewidget"]], "Class Avogadro::Io::PoscarFormat": [[59, "class-avogadro-io-poscarformat"]], "Class Avogadro::Io::LammpsDataFormat": [[53, "class-avogadro-io-lammpsdataformat"]], "Class Avogadro::QtGui::ContainerWidget": [[71, "class-avogadro-qtgui-containerwidget"]], "Class Avogadro::Io::MMTFFormat": [[55, "class-avogadro-io-mmtfformat"]], "Class Avogadro::Io::MdlFormat": [[56, "class-avogadro-io-mdlformat"]], "Class Avogadro::MoleQueue::InputGeneratorWidget": [[65, "class-avogadro-molequeue-inputgeneratorwidget"]], "Class Avogadro::Io::Hdf5DataFormat": [[52, "class-avogadro-io-hdf5dataformat"]], "Class Avogadro::Io::OutcarFormat": [[57, "class-avogadro-io-outcarformat"]], "Class Avogadro::QtGui::ElementItem": [[74, "class-avogadro-qtgui-elementitem"]], "Class Avogadro::QtGui::ElementDetail": [[73, "class-avogadro-qtgui-elementdetail"]], "Class Avogadro::MoleQueue::InputGeneratorDialog": [[64, "class-avogadro-molequeue-inputgeneratordialog"]], "Class Avogadro::MoleQueue::MoleQueueQueueListModel": [[68, "class-avogadro-molequeue-molequeuequeuelistmodel"]], "Class Avogadro::MoleQueue::BatchJob": [[62, "class-avogadro-molequeue-batchjob"]], "Class Avogadro::Io::LammpsTrajectoryFormat": [[54, "class-avogadro-io-lammpstrajectoryformat"]], "Class Avogadro::Io::XyzFormat": [[61, "class-avogadro-io-xyzformat"]], "Class Avogadro::Io::TrrFormat": [[60, "class-avogadro-io-trrformat"]], "Class Avogadro::Io::GromacsFormat": [[51, "class-avogadro-io-gromacsformat"]], "Class Avogadro::Io::PdbFormat": [[58, "class-avogadro-io-pdbformat"]], "Class Avogadro::Io::FileFormatManager": [[50, "class-avogadro-io-fileformatmanager"]], "Class Avogadro::MoleQueue::MoleQueueManager": [[67, "class-avogadro-molequeue-molequeuemanager"]], "Class Avogadro::MoleQueue::MoleQueueDialog": [[66, "class-avogadro-molequeue-molequeuedialog"]], "Building Source Code": [[239, "building-source-code"]], "Cloning Repositories": [[239, "cloning-repositories"]], "Updating": [[239, "updating"]], "Prerequisites": [[239, "prerequisites"]], "Debian-based Distribution or Ubuntu": [[239, "debian-based-distribution-or-ubuntu"]], "Building": [[239, "building"]], "Finding Qt, Windows Generators": [[239, "finding-qt-windows-generators"]], "Normal Development": [[239, "normal-development"]], "Build Tree Layout": [[239, "build-tree-layout"]], "Running Executables": [[239, "running-executables"]], "Building Packages": [[239, "building-packages"]], "Viewing Molecular Orbitals": [[233, "viewing-molecular-orbitals"]], "Configure": [[233, "configure"]], "Release Notes v1.98.0": [[247, "release-notes-v1-98-0"]], "\ud83c\udf1f Highlights (tldr)": [[247, "highlights-tldr"]], "\u2728 Features": [[247, "features"], [243, "features"], [245, "features"], [244, "features"], [246, "features"]], "\ud83d\udc1b Bug Fixes": [[247, "bug-fixes"], [243, "bug-fixes"], [245, "bug-fixes"], [244, "bug-fixes"], [246, "bug-fixes"], [242, "bug-fixes"]], "\ud83d\ude80 Performance Improvements": [[247, "performance-improvements"], [246, "performance-improvements"]], "\ud83e\uddf0 Maintenance": [[247, "maintenance"], [243, "maintenance"], [245, "maintenance"], [244, "maintenance"], [246, "maintenance"], [242, "maintenance"]], "\ud83d\udcda Translations": [[247, "translations"], [243, "translations"], [245, "translations"], [244, "translations"], [246, "translations"]], "Selection Tool": [[227, "selection-tool"]], "What\u2019s New in Avogadro 2": [[235, "whats-new-in-avogadro-2"]], "Install": [[238, "install"], [240, "install"]], "Features": [[238, "features"], [242, "features"]], "Resources": [[238, "resources"]], "Connecting with the Avogadro community": [[238, "connecting-with-the-avogadro-community"]], "Tutorials": [[229, "tutorials"], [229, null]], "Release Notes v1.95.0": [[243, "release-notes-v1-95-0"]], "Changes": [[243, "changes"], [245, "changes"]], "Navigate Tool": [[226, "navigate-tool"]], "Viewing Electrostatic Potential Maps": [[232, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[232, "changing-surface-settings"]], "Release Notes v1.96.0": [[245, "release-notes-v1-96-0"]], "\ud83d\ude80 Performance Fixes": [[245, "performance-fixes"]], "Template Tool": [[228, "template-tool"], [237, "template-tool"]], "Inserting Atoms with Specific Geometry": [[228, "inserting-atoms-with-specific-geometry"]], "Attaching Ligands": [[228, "attaching-ligands"]], "Attaching Functional Groups": [[228, "attaching-functional-groups"]], "Creating New Ligands": [[228, "creating-new-ligands"]], "Creating New Haptic Ligands": [[228, "creating-new-haptic-ligands"]], "Measure Tool": [[225, "measure-tool"]], "Viewing Vibrations": [[234, "viewing-vibrations"]], "Naming a Molecule": [[230, "naming-a-molecule"]], "Acid-Base Properties of Amino Acids": [[248, "acid-base-properties-of-amino-acids"]], "Alkene Isomers": [[249, "alkene-isomers"]], "Major New Features": [[237, "major-new-features"]], "Speed and Stability": [[237, "speed-and-stability"]], "Rendering": [[237, "rendering"]], "New real-time shadows and depth effects": [[237, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[237, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[237, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[237, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[237, "layers"]], "Symmetry Properties": [[237, "symmetry-properties"]], "Solvent Accessible and Solvent Excluded Surfaces": [[237, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[237, "flexible-electrostatics-models"]], "New Analysis Tools": [[237, "new-analysis-tools"]], "Python Commands / Plugins": [[237, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[237, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[237, "new-and-updated-interfaces-to-external-programs"]], "Using QTAIM (Atoms in Molecules) Analysis": [[231, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[231, "start-with-a-wfn-file"]], "Version History": [[241, "version-history"], [241, null]], "Interface Changes": [[236, "interface-changes"]], "Input Generators": [[236, "input-generators"], [174, "input-generators"]], "Release Notes v1.95.1": [[244, "release-notes-v1-95-1"]], "Release Notes v1.97.0": [[246, "release-notes-v1-97-0"]], "Highlights (tldr)": [[246, "highlights-tldr"]], "Release Notes v1.94.0": [[242, "release-notes-v1-94-0"]], "\ud83d\udc0d Python Improvements": [[242, "python-improvements"]], "Class Avogadro::QtGui::FileFormatDialog": [[79, "class-avogadro-qtgui-fileformatdialog"]], "Class Avogadro::QtGui::PeriodicTableScene": [[89, "class-avogadro-qtgui-periodictablescene"]], "Class Avogadro::QtGui::InterfaceWidget": [[84, "class-avogadro-qtgui-interfacewidget"]], "Class Avogadro::QtGui::InterfaceScript": [[83, "class-avogadro-qtgui-interfacescript"]], "Class Avogadro::QtGui::GenericHighlighter::Rule": [[81, "class-avogadro-qtgui-generichighlighter-rule"]], "Class Avogadro::QtGui::HydrogenTools": [[82, "class-avogadro-qtgui-hydrogentools"]], "Class Avogadro::QtGui::MeshGenerator": [[85, "class-avogadro-qtgui-meshgenerator"]], "Class Avogadro::QtGui::PythonScript": [[93, "class-avogadro-qtgui-pythonscript"]], "Class Avogadro::QtGui::PersistentBond": [[92, "class-avogadro-qtgui-persistentbond"]], "Class Avogadro::QtGui::RWAtom": [[94, "class-avogadro-qtgui-rwatom"]], "Class Avogadro::QtGui::RWBond": [[95, "class-avogadro-qtgui-rwbond"]], "Class Avogadro::QtGui::Molecule": [[86, "class-avogadro-qtgui-molecule"]], "Class Avogadro::QtGui::ScenePluginModel": [[99, "class-avogadro-qtgui-scenepluginmodel"]], "Class Avogadro::QtGui::FileBrowseWidget": [[78, "class-avogadro-qtgui-filebrowsewidget"]], "Class Avogadro::QtGui::PeriodicTableView": [[90, "class-avogadro-qtgui-periodictableview"]], "Class Avogadro::QtGui::MultiViewWidget": [[88, "class-avogadro-qtgui-multiviewwidget"]], "Class Avogadro::QtGui::MoleculeModel": [[87, "class-avogadro-qtgui-moleculemodel"]], "Class Avogadro::QtGui::ExtensionPlugin": [[76, "class-avogadro-qtgui-extensionplugin"]], "Class Avogadro::QtGui::GenericHighlighter": [[80, "class-avogadro-qtgui-generichighlighter"]], "Class Avogadro::QtGui::ScenePlugin": [[97, "class-avogadro-qtgui-sceneplugin"]], "Class Avogadro::QtGui::ScenePluginFactory": [[98, "class-avogadro-qtgui-scenepluginfactory"]], "Class Avogadro::QtGui::PersistentAtom": [[91, "class-avogadro-qtgui-persistentatom"]], "Class Avogadro::QtGui::RWMolecule": [[96, "class-avogadro-qtgui-rwmolecule"]], "Class Avogadro::QtGui::ExtensionPluginFactory": [[77, "class-avogadro-qtgui-extensionpluginfactory"]], "Class Avogadro::QtGui::ElementTranslator": [[75, "class-avogadro-qtgui-elementtranslator"]], "Display Types": [[200, "display-types"], [200, null]], "Auto-Optimize Tool": [[219, "auto-optimize-tool"]], "Force Fields & Algorithms": [[219, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[219, "fixing-ignoring-selections"]], "File Menu": [[209, "file-menu"]], "New": [[209, "new"]], "Open": [[209, "open"]], "Open Recent": [[209, "open-recent"]], "Close": [[209, "close"]], "Save": [[209, "save"]], "Save As\u2026": [[209, "save-as"]], "Revert to Saved": [[209, "revert-to-saved"]], "Import": [[209, "import"]], "Export": [[209, "export"]], "Optimizing Geometry": [[216, "optimizing-geometry"]], "Optimization": [[216, null]], "Introduction": [[203, "introduction"]], "Opening a File": [[203, "opening-a-file"]], "Importing by Name": [[203, "importing-by-name"]], "Navigation": [[203, "navigation"]], "Enabling additional force fields": [[215, "enabling-additional-force-fields"]], "Creating an avogadro conda environment": [[215, "creating-an-avogadro-conda-environment"]], "Setting the Python path": [[215, "setting-the-python-path"]], "Manipulate Tool": [[224, "manipulate-tool"]], "Auto-Rotate Tool": [[220, "auto-rotate-tool"]], "Extension Menu": [[208, "extension-menu"]], "Animation": [[208, "animation"]], "Optimize Geometry": [[208, "optimize-geometry"]], "Molecular Mechanics": [[208, "molecular-mechanics"]], "Setup Force Field\u2026": [[208, "setup-force-field"]], "Calculate Energy": [[208, "calculate-energy"]], "Conformer Search": [[208, "conformer-search"]], "Constraints": [[208, "constraints"], [214, "constraints"]], "Ignore Selection": [[208, "ignore-selection"]], "Fix Selected Atoms": [[208, "fix-selected-atoms"]], "Avogadro Extensions\u2013Plugins": [[208, "avogadro-extensionsplugins"]], "General \u201cHow To\u201d for Plugins": [[208, "general-how-to-for-plugins"]], "Running Gaussian": [[208, "running-gaussian"]], "Molecular Orbitals": [[208, "molecular-orbitals"]], "QTAIM (Quantum Theory of Atoms in Molecules)": [[208, "qtaim-quantum-theory-of-atoms-in-molecules"], [199, "qtaim-quantum-theory-of-atoms-in-molecules"]], "Spectra\u2026": [[208, "spectra"]], "Create Surfaces\u2026": [[208, "create-surfaces"]], "Tools": [[223, "tools"], [223, null]], "Build Menu": [[206, "build-menu"]], "Cartesian Editor\u2026": [[206, "cartesian-editor"]], "1. Sort by\u2026": [[206, "sort-by"]], "2. Unit of Measure": [[206, "unit-of-measure"]], "3. Editing & Modifying Data": [[206, "editing-modifying-data"]], "Change H to Methyl": [[206, "change-h-to-methyl"]], "Add Hydrogens": [[206, "add-hydrogens"]], "Add Hydrogens for pH\u2026": [[206, "add-hydrogens-for-ph"]], "Remove Hydrogens": [[206, "remove-hydrogens"]], "Insert": [[206, "insert"]], "Invert Chirality": [[206, "invert-chirality"]], "Super Cell Builder\u2026": [[206, "super-cell-builder"]], "Nanotube Builder\u2026": [[206, "nanotube-builder"]], "View Menu": [[212, "view-menu"]], "New View": [[212, "new-view"]], "Duplicate View": [[212, "duplicate-view"]], "Detach View": [[212, "detach-view"]], "Close View": [[212, "close-view"]], "Center": [[212, "center"]], "Align View to Axes": [[212, "align-view-to-axes"]], "Full Screen": [[212, "full-screen"]], "Reset Display Types": [[212, "reset-display-types"]], "Set Background Color\u2026": [[212, "set-background-color"]], "Projection": [[212, "projection"]], "Display Axes": [[212, "display-axes"]], "Debug Information": [[212, "debug-information"]], "Use Quick Render": [[212, "use-quick-render"]], "All Molecules in File\u2026": [[212, "all-molecules-in-file"]], "Crystal View Options\u2026": [[212, "crystal-view-options"]], "Properties": [[212, "properties"]], "Menus": [[210, "menus"], [210, null]], "Drawing Molecules": [[201, "drawing-molecules"]], "Creating Carbon Dioxide": [[201, "creating-carbon-dioxide"], [222, "creating-carbon-dioxide"]], "Getting Started": [[202, "getting-started"]], "Align Tool": [[218, "align-tool"]], "Making Selections": [[204, "making-selections"]], "User Guide": [[205, "user-guide"]], "Avogadro: Molecular Editor and Visualization": [[205, "avogadro-molecular-editor-and-visualization"], [180, "avogadro-molecular-editor-and-visualization"]], "Avogadro 2": [[205, "avogadro-2"]], "Finding Conformers of Molecules": [[213, "finding-conformers-of-molecules"]], "Start with your molecule of interest": [[213, "start-with-your-molecule-of-interest"]], "Optimize the geometry": [[213, "optimize-the-geometry"]], "Change the force field options": [[213, "change-the-force-field-options"]], "Set the conformer search options": [[213, "set-the-conformer-search-options"]], "Pick a search method and start the search": [[213, "pick-a-search-method-and-start-the-search"]], "Select Menu": [[211, "select-menu"]], "Select All": [[211, "select-all"], [207, "select-all"]], "Select None": [[211, "select-none"], [207, "select-none"]], "Invert Selection": [[211, "invert-selection"]], "Select SMARTS\u2026": [[211, "select-smarts"]], "Select by Element\u2026": [[211, "select-by-element"]], "Select by Residue\u2026": [[211, "select-by-residue"]], "Select Solvent": [[211, "select-solvent"]], "Add Name Selection\u2026": [[211, "add-name-selection"]], "Geometry Constraints": [[214, "geometry-constraints"]], "Example": [[214, "example"]], "Optimizations": [[214, "optimizations"]], "Example cont.": [[214, "example-cont"]], "Edit Menu": [[207, "edit-menu"]], "Undo": [[207, "undo"]], "Redo": [[207, "redo"]], "Cut": [[207, "cut"]], "Copy": [[207, "copy"]], "Copy As": [[207, "copy-as"]], "Paste": [[207, "paste"]], "Clear": [[207, "clear"]], "Draw Tool": [[222, "draw-tool"]], "Bond-Centric Manipulate Tool": [[221, "bond-centric-manipulate-tool"]], "Starting with the basics:": [[221, "starting-with-the-basics"]], "Adjusting Bonds and Torsion Angles": [[221, "adjusting-bonds-and-torsion-angles"]], "Introduction to Molecular Mechanics": [[217, "introduction-to-molecular-mechanics"]], "UFF": [[217, "uff"]], "MMFF94(s)": [[217, "mmff94-s"]], "GAFF": [[217, "gaff"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[45, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Io::DcdFormat": [[48, "class-avogadro-io-dcdformat"]], "Class Avogadro::Core::SlaterSetTools": [[39, "class-avogadro-core-slatersettools"]], "Class Avogadro::Core::NameAtomTyper": [[33, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::GaussianSet": [[25, "class-avogadro-core-gaussianset"]], "Class Avogadro::Io::CjsonFormat": [[46, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Core::SpaceGroups": [[40, "class-avogadro-core-spacegroups"]], "Class Avogadro::Io::FileFormat": [[49, "class-avogadro-io-fileformat"]], "Class Avogadro::Core::Molecule": [[29, "class-avogadro-core-molecule"]], "Class Avogadro::Io::CmlFormat": [[47, "class-avogadro-io-cmlformat"]], "Class Avogadro::Core::MoleculeDeserializer": [[30, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::RingPerceiver": [[36, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::UnitCell": [[42, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::Mesh": [[28, "class-avogadro-core-mesh"]], "Class Avogadro::Core::VariantMap": [[44, "class-avogadro-core-variantmap"]], "Class Avogadro::Core::SlaterSet": [[38, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::GaussianSetTools": [[26, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::MoleculeSerializer": [[31, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Core::Residue": [[34, "class-avogadro-core-residue"]], "Class Avogadro::Core::SharedMutex": [[37, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::ResidueData": [[35, "class-avogadro-core-residuedata"]], "Class Avogadro::Core::Variant": [[43, "class-avogadro-core-variant"]], "Class Avogadro::Core::SymbolAtomTyper": [[41, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::Graph": [[27, "class-avogadro-core-graph"]], "Class Avogadro::Core::Mutex": [[32, "class-avogadro-core-mutex"]], "Installing Script Plugins": [[176, "installing-script-plugins"]], "Directories": [[176, "directories"]], "Plugin Packages and Repositories": [[176, "plugin-packages-and-repositories"]], "Adding to the Plugin Directory": [[176, "adding-to-the-plugin-directory"]], "Building a Peptide": [[190, "building-a-peptide"]], "Different Display Styles": [[199, "different-display-styles"]], "Locating Display Types": [[199, "locating-display-types"]], "Axes": [[199, "axes"]], "Ball and Stick": [[199, "ball-and-stick"]], "Cartoon": [[199, "cartoon"]], "Dipole": [[199, "dipole"]], "Force": [[199, "force"]], "Hydrogen Bond": [[199, "hydrogen-bond"]], "Label": [[199, "label"]], "Polygon": [[199, "polygon"]], "Ribbon": [[199, "ribbon"]], "Ring": [[199, "ring"]], "Stick": [[199, "stick"]], "Surfaces": [[199, "surfaces"]], "Van der Waals Spheres": [[199, "van-der-waals-spheres"]], "Wireframe": [[199, "wireframe"]], "License": [[179, "license"]], "Creative Commons Attribution-ShareAlike 4.0 International": [[179, "creative-commons-attribution-sharealike-4-0-international"]], "Using Creative Commons Public Licenses": [[179, "using-creative-commons-public-licenses"]], "Creative Commons Attribution-ShareAlike 4.0 International Public License": [[179, "creative-commons-attribution-sharealike-4-0-international-public-license"]], "Section 1 \u2013 Definitions.": [[179, "section-1-definitions"]], "Section 2 \u2013 Scope.": [[179, "section-2-scope"]], "Section 3 \u2013 License Conditions.": [[179, "section-3-license-conditions"]], "Section 4 \u2013 Sui Generis Database Rights.": [[179, "section-4-sui-generis-database-rights"]], "Section 5 \u2013 Disclaimer of Warranties and Limitation of Liability.": [[179, "section-5-disclaimer-of-warranties-and-limitation-of-liability"]], "Section 6 \u2013 Term and Termination.": [[179, "section-6-term-and-termination"]], "Section 7 \u2013 Other Terms and Conditions.": [[179, "section-7-other-terms-and-conditions"]], "Section 8 \u2013 Interpretation.": [[179, "section-8-interpretation"]], "Coloring Part of a Molecules": [[198, "coloring-part-of-a-molecules"]], "Hemoglobin": [[198, "hemoglobin"]], "Select by Residue": [[198, "select-by-residue"]], "Select by Element": [[198, "select-by-element"]], "Building Molecule-Surface Interactions": [[186, "building-molecule-surface-interactions"]], "Start with a generated Crystal Surface": [[186, "start-with-a-generated-crystal-surface"]], "New Window: Create our Molecule": [[186, "new-window-create-our-molecule"]], "Building a Polymer Unit Cell": [[183, "building-a-polymer-unit-cell"]], "Importing from the Protein Data Bank (PDB)": [[194, "importing-from-the-protein-data-bank-pdb"]], "Importing Directly": [[194, "importing-directly"]], "Reading a Downloaded PDB file": [[194, "reading-a-downloaded-pdb-file"]], "Building with SMILES": [[193, "building-with-smiles"]], "Insert Molecular Fragments": [[197, "insert-molecular-fragments"]], "Script Interfaces": [[177, "script-interfaces"]], "Fixed String Lists (Pop-up menus)": [[177, "fixed-string-lists-pop-up-menus"]], "Integer Values": [[177, "integer-values"]], "Floating-point values": [[177, "floating-point-values"]], "Reducing Crystals to a Primitive Unit Cell": [[187, "reducing-crystals-to-a-primitive-unit-cell"]], "Script Plugins": [[175, "script-plugins"], [162, "script-plugins"]], "Building DNA or RNA": [[192, "building-dna-or-rna"]], "Building a Supercell": [[189, "building-a-supercell"]], "Creating a Surface": [[189, "creating-a-surface"]], "Perceiving Crystall Symmetry": [[184, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[184, "open-a-crystal-file"]], "Scaling Crystal Cell Volume": [[188, "scaling-crystal-cell-volume"]], "Importing Molecules by Name": [[195, "importing-molecules-by-name"]], "Building Materials": [[185, "building-materials"], [185, null]], "Building Carbon Nanotubes": [[191, "building-carbon-nanotubes"]], "Table of contents": [[181, "table-of-contents"]], "VTK Classes": [[178, "vtk-classes"]], "Building Molecules": [[196, "building-molecules"], [196, null]], "Making a Crystal Surface Slab": [[182, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[182, "import-the-appropriate-crystal-structure"]], "Command Scripts": [[169, "command-scripts"]], "Specifying UI options with \u2013print-options": [[169, "specifying-ui-options-with-print-options"]], "Returning Data": [[169, "returning-data"]], "Returning Data in a Specific File Format": [[169, "returning-data-in-a-specific-file-format"]], "Appending New Atoms and Bonds": [[169, "appending-new-atoms-and-bonds"]], "Bonding New Atoms": [[169, "bonding-new-atoms"]], "Selected Atoms": [[169, "selected-atoms"]], "Core Classes": [[161, "core-classes"]], "MoleQueue Classes": [[164, "molequeue-classes"]], "Specifying parameters with --print-options": [[174, "specifying-parameters-with-print-options"]], "Handling User Selections: --generate-input": [[174, "handling-user-selections-generate-input"]], "Coordinate Blocks": [[174, "coordinate-blocks"]], "QtGui Classes": [[165, "qtgui-classes"]], "IO Classes": [[163, "io-classes"]], "Develop": [[162, "develop"]], "External Scripting": [[162, "external-scripting"]], "Libraries": [[162, "libraries"]], "Main Classes": [[162, "main-classes"]], "Class Avogadro::TypeTraits< float >": [[151, "class-avogadro-typetraits-float"]], "Class Avogadro::TypeTraits< unsigned char >": [[154, "class-avogadro-typetraits-unsigned-char"]], "Rendering Classes": [[166, "rendering-classes"]], "Class Avogadro::TypeTraits< unsigned int >": [[155, "class-avogadro-typetraits-unsigned-int"]], "Avogadro Remote Procedure Call (RPC)": [[167, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[167, "rpc-protocol"]], "Methods": [[167, "methods"]], "Class Avogadro::TypeTraits< unsigned short >": [[156, "class-avogadro-typetraits-unsigned-short"]], "Example Plugin Script - Part 2": [[172, "example-plugin-script-part-2"]], "Providing Input to Run Command": [[172, "providing-input-to-run-command"]], "runCommand() Function": [[172, "runcommand-function"]], "Operation Function": [[172, "operation-function"]], "Retrieving necessary components": [[172, "retrieving-necessary-components"]], "Support for Selection": [[172, "support-for-selection"]], "Sample Input and Output": [[172, "sample-input-and-output"]], "Class vtkAvogadroActor": [[159, "class-vtkavogadroactor"]], "Example Plugin Script - Part 1": [[171, "example-plugin-script-part-1"]], "The Main function:": [[171, "the-main-function"]], "Input Arguments": [[171, "input-arguments"]], "getOptions() Function": [[171, "getoptions-function"]], "Charges / Electrostatics": [[168, "charges-electrostatics"]], "Identify the Script with --metadata": [[168, "identify-the-script-with-metadata"], [170, "identify-the-script-with-metadata"]], "Calculating Atomic Partial Charges with --charge": [[168, "calculating-atomic-partial-charges-with-charge"]], "Generating Electrostatic Potentials with --potential": [[168, "generating-electrostatic-potentials-with-potential"]], "Class Avogadro::VTK::VtkPlot": [[157, "class-avogadro-vtk-vtkplot"]], "Class List": [[160, "class-list"]], "Energy / Force Fields": [[170, "energy-force-fields"]], "Calculating Energies and Gradients": [[170, "calculating-energies-and-gradients"]], "Unit Cells, Total Charge, and Spin Multiplicity": [[170, "unit-cells-total-charge-and-spin-multiplicity"]], "Lattice Vectors and Fractional Coordinates": [[170, "lattice-vectors-and-fractional-coordinates"]], "Class Avogadro::TypeTraits< int >": [[152, "class-avogadro-typetraits-int"]], "Class Avogadro::VTK::vtkGLWidget": [[158, "class-avogadro-vtk-vtkglwidget"]], "Class Avogadro::TypeTraits< double >": [[150, "class-avogadro-typetraits-double"]], "Class Avogadro::TypeTraits< short >": [[153, "class-avogadro-typetraits-short"]], "File Formats": [[173, "file-formats"]], "Identify the Format with --metadata": [[173, "identify-the-format-with-metadata"]], "Reading a format with --read": [[173, "reading-a-format-with-read"]], "Writing a format with --write": [[173, "writing-a-format-with-write"]], "Class Avogadro::Rendering::Shader": [[134, "class-avogadro-rendering-shader"]], "Class Avogadro::Rendering::Node": [[130, "class-avogadro-rendering-node"]], "Class Avogadro::Rendering::LineStripGeometry": [[128, "class-avogadro-rendering-linestripgeometry"]], "Class Avogadro::Rendering::TransformNode": [[144, "class-avogadro-rendering-transformnode"]], "Class Avogadro::Rendering::ShaderProgram": [[135, "class-avogadro-rendering-shaderprogram"]], "Class Avogadro::Rendering::Primitive": [[132, "class-avogadro-rendering-primitive"]], "Class Avogadro::TypeTraits": [[148, "class-avogadro-typetraits"]], "Class Avogadro::Rendering::TextProperties": [[141, "class-avogadro-rendering-textproperties"]], "Class Avogadro::Rendering::SphereGeometry": [[137, "class-avogadro-rendering-spheregeometry"]], "Class Avogadro::Rendering::Sphere": [[136, "class-avogadro-rendering-sphere"]], "Class Avogadro::Rendering::TextLabelBase": [[140, "class-avogadro-rendering-textlabelbase"]], "Class Avogadro::Rendering::TextLabel3D": [[139, "class-avogadro-rendering-textlabel3d"]], "Class Avogadro::TypeTraits< char >": [[149, "class-avogadro-typetraits-char"]], "Class Avogadro::Rendering::VolumeGeometry": [[147, "class-avogadro-rendering-volumegeometry"]], "Class Avogadro::Rendering::Visitor": [[146, "class-avogadro-rendering-visitor"]], "Class Avogadro::Rendering::GeometryNode": [[125, "class-avogadro-rendering-geometrynode"]], "Class Avogadro::Rendering::Texture2D": [[143, "class-avogadro-rendering-texture2d"]], "Class Avogadro::Rendering::MeshGeometry": [[129, "class-avogadro-rendering-meshgeometry"]], "Class Avogadro::Rendering::Scene": [[133, "class-avogadro-rendering-scene"]], "Class Avogadro::Rendering::TextRenderStrategy": [[142, "class-avogadro-rendering-textrenderstrategy"]], "Class Avogadro::Rendering::TextLabel2D": [[138, "class-avogadro-rendering-textlabel2d"]], "Class Avogadro::Rendering::VRMLVisitor": [[145, "class-avogadro-rendering-vrmlvisitor"]], "Class Avogadro::Rendering::GeometryVisitor": [[126, "class-avogadro-rendering-geometryvisitor"]], "Class Avogadro::Rendering::POVRayVisitor": [[131, "class-avogadro-rendering-povrayvisitor"]], "Class Avogadro::Rendering::GroupNode": [[127, "class-avogadro-rendering-groupnode"]], "Class Avogadro::QtOpenGL::QtTextRenderStrategy": [[106, "class-avogadro-qtopengl-qttextrenderstrategy"]], "Class Avogadro::Rendering::GLRenderVisitor": [[123, "class-avogadro-rendering-glrendervisitor"]], "Class Avogadro::QtOpenGL::ActiveObjects": [[104, "class-avogadro-qtopengl-activeobjects"]], "Class Avogadro::QuantumIO::MoldenFile": [[112, "class-avogadro-quantumio-moldenfile"]], "Class Avogadro::QtGui::ScriptLoader": [[100, "class-avogadro-qtgui-scriptloader"]], "Class Avogadro::Rendering::ArrowGeometry": [[117, "class-avogadro-rendering-arrowgeometry"]], "Class Avogadro::QuantumIO::GamessukOut": [[109, "class-avogadro-quantumio-gamessukout"]], "Class Avogadro::QtGui::ToolPlugin": [[101, "class-avogadro-qtgui-toolplugin"]], "Class Avogadro::Rendering::BufferObject": [[118, "class-avogadro-rendering-bufferobject"]], "Class Avogadro::QuantumIO::MopacAux": [[113, "class-avogadro-quantumio-mopacaux"]], "Class Avogadro::Rendering::GLRenderer": [[124, "class-avogadro-rendering-glrenderer"]], "Class Avogadro::Rendering::Camera": [[119, "class-avogadro-rendering-camera"]], "Class Avogadro::Rendering::CylinderGeometry": [[121, "class-avogadro-rendering-cylindergeometry"]], "Class Avogadro::QuantumIO::GUKBasisSet": [[108, "class-avogadro-quantumio-gukbasisset"]], "Class Avogadro::QuantumIO::GaussianCube": [[110, "class-avogadro-quantumio-gaussiancube"]], "Class Avogadro::QtGui::ViewFactory": [[103, "class-avogadro-qtgui-viewfactory"]], "Class Avogadro::QtOpenGL::GLWidget": [[105, "class-avogadro-qtopengl-glwidget"]], "Class Avogadro::Rendering::Drawable": [[122, "class-avogadro-rendering-drawable"]], "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry": [[116, "class-avogadro-rendering-ambientocclusionspheregeometry"]], "Class Avogadro::QuantumIO::NWChemLog": [[115, "class-avogadro-quantumio-nwchemlog"]], "Class Avogadro::QuantumIO::NWChemJson": [[114, "class-avogadro-quantumio-nwchemjson"]], "Class Avogadro::QuantumIO::GAMESSUSOutput": [[107, "class-avogadro-quantumio-gamessusoutput"]], "Class Avogadro::QuantumIO::GaussianFchk": [[111, "class-avogadro-quantumio-gaussianfchk"]], "Class Avogadro::QtGui::ToolPluginFactory": [[102, "class-avogadro-qtgui-toolpluginfactory"]], "Class Avogadro::Rendering::Cylinder": [[120, "class-avogadro-rendering-cylinder"]]}, "indexentries": {"avogadro::core::array (c++ class)": [[8, "_CPPv4I0EN8Avogadro4Core5ArrayE"]], "avogadro::core::array::array (c++ function)": [[8, "_CPPv4I0EN8Avogadro4Core5Array5ArrayE13InputIterator13InputIterator"], [8, "_CPPv4N8Avogadro4Core5Array5ArrayEK6size_tRK9ValueType"], [8, "_CPPv4N8Avogadro4Core5Array5ArrayERK5Array"], [8, "_CPPv4N8Avogadro4Core5Array5ArrayEv"]], "avogadro::core::array::container (c++ type)": [[8, "_CPPv4N8Avogadro4Core5Array9ContainerE"]], "avogadro::core::array::valuetype (c++ type)": [[8, 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"docs/building-molecules/importing-molecules-by-name.md", "docs/building-molecules/index.md", "docs/building-molecules/insert-fragments.md", "docs/display-types/coloring-part-of-a-molecule.md", "docs/display-types/display-types.md", "docs/display-types/index.md", "docs/getting-started/drawing-molecules.md", "docs/getting-started/index.md", "docs/getting-started/introduction.md", "docs/getting-started/making-selections.md", "docs/index.md", "docs/menus/build-menu.md", "docs/menus/edit-menu.md", "docs/menus/extensions-menu.md", "docs/menus/file-menu.md", "docs/menus/index.md", "docs/menus/select-menu.md", "docs/menus/view-menu.md", "docs/optimizing-geometry/conformers.md", "docs/optimizing-geometry/constraints.md", "docs/optimizing-geometry/enabling-ff.md", "docs/optimizing-geometry/index.md", "docs/optimizing-geometry/molecular-mechanics.md", "docs/tools/align-tool.md", "docs/tools/auto-optimize-tool.md", "docs/tools/auto-rotate-tool.md", "docs/tools/bond-centric-manipulate-tool.md", "docs/tools/draw-tool.md", "docs/tools/index.md", "docs/tools/manipulate-tool.md", "docs/tools/measure-tool.md", "docs/tools/navigate-tool.md", "docs/tools/selection-tool.md", "docs/tools/template-tool.md", "docs/tutorials/index.md", "docs/tutorials/naming-a-molecule.md", "docs/tutorials/using-qtaim-and-wfn.md", "docs/tutorials/viewing-electrostatic-potential.md", "docs/tutorials/viewing-molecular-orbitals.md", "docs/tutorials/viewing-vibrations.md", "docs/whats-new-in-avogadro-2/index.md", "docs/whats-new-in-avogadro-2/interface-changes.md", "docs/whats-new-in-avogadro-2/major-new-features.md", "index.md", "install/build.md", "install/index.md", "install/versions/index.md", "install/versions/v194.md", "install/versions/v195.md", "install/versions/v1951.md", "install/versions/v196.md", "install/versions/v197.md", "install/versions/v198.md", "teach/acid_base.md", "teach/alkene_isomers.md", "teach/articles.md", "teach/basic_vsepr.md", "teach/diaxial_interactions.md", "teach/hcn_dipole.md", "teach/hydrogen_clusters.md", "teach/hydrogen_molecule.md", "teach/index.md", "teach/markovnikovs_rule.md", "teach/organic_hybridization.md", "teach/water.md"], "titles": ["Contributing Code", "Documenting Code", "&lt;no title&gt;", "Coding Conventions (C++)", "Thanks", "Contribute", "Coding Style (C++)", "Translations", "Class Avogadro::Core::Array", "Class Avogadro::Core::ArraySet", "Class Avogadro::Core::ArraySet::Holder", "Class Avogadro::Core::ArraySet::PlaceHolder", "Class Avogadro::Core::Atom", "Class Avogadro::Core::AtomTemplate", "Class Avogadro::Core::AtomTyper", "Class Avogadro::Core::AvoSpglib", "Class Avogadro::Core::BasisSet", "Class Avogadro::Core::Bond", "Class Avogadro::Core::BondTemplate", "Class Avogadro::Core::Color3f", "Class Avogadro::Core::CoordinateBlockGenerator", "Class Avogadro::Core::CoordinateSet", "Class Avogadro::Core::CrystalTools", "Class Avogadro::Core::Cube", "Class Avogadro::Core::Elements", "Class Avogadro::Core::GaussianSet", "Class Avogadro::Core::GaussianSetTools", "Class Avogadro::Core::Graph", "Class Avogadro::Core::Mesh", "Class Avogadro::Core::Molecule", "Class Avogadro::Core::MoleculeDeserializer", "Class Avogadro::Core::MoleculeSerializer", "Class Avogadro::Core::Mutex", "Class Avogadro::Core::NameAtomTyper", "Class Avogadro::Core::Residue", "Class Avogadro::Core::ResidueData", "Class Avogadro::Core::RingPerceiver", "Class Avogadro::Core::SharedMutex", "Class Avogadro::Core::SlaterSet", "Class Avogadro::Core::SlaterSetTools", "Class Avogadro::Core::SpaceGroups", "Class Avogadro::Core::SymbolAtomTyper", "Class Avogadro::Core::UnitCell", "Class Avogadro::Core::Variant", "Class Avogadro::Core::VariantMap", "Class Avogadro::Core::internal::ArrayRefContainer", "Class Avogadro::Io::CjsonFormat", "Class Avogadro::Io::CmlFormat", "Class Avogadro::Io::DcdFormat", "Class Avogadro::Io::FileFormat", "Class Avogadro::Io::FileFormatManager", "Class Avogadro::Io::GromacsFormat", "Class Avogadro::Io::Hdf5DataFormat", "Class Avogadro::Io::LammpsDataFormat", "Class Avogadro::Io::LammpsTrajectoryFormat", "Class Avogadro::Io::MMTFFormat", "Class Avogadro::Io::MdlFormat", "Class Avogadro::Io::OutcarFormat", "Class Avogadro::Io::PdbFormat", "Class Avogadro::Io::PoscarFormat", "Class Avogadro::Io::TrrFormat", "Class Avogadro::Io::XyzFormat", "Class Avogadro::MoleQueue::BatchJob", "Class Avogadro::MoleQueue::InputGenerator", "Class Avogadro::MoleQueue::InputGeneratorDialog", "Class Avogadro::MoleQueue::InputGeneratorWidget", "Class Avogadro::MoleQueue::MoleQueueDialog", "Class Avogadro::MoleQueue::MoleQueueManager", "Class Avogadro::MoleQueue::MoleQueueQueueListModel", "Class Avogadro::MoleQueue::MoleQueueWidget", "Class Avogadro::QtGui::BackgroundFileFormat", "Class Avogadro::QtGui::ContainerWidget", "Class Avogadro::QtGui::CustomElementDialog", "Class Avogadro::QtGui::ElementDetail", "Class Avogadro::QtGui::ElementItem", "Class Avogadro::QtGui::ElementTranslator", "Class Avogadro::QtGui::ExtensionPlugin", "Class Avogadro::QtGui::ExtensionPluginFactory", "Class Avogadro::QtGui::FileBrowseWidget", "Class Avogadro::QtGui::FileFormatDialog", "Class Avogadro::QtGui::GenericHighlighter", "Class Avogadro::QtGui::GenericHighlighter::Rule", "Class Avogadro::QtGui::HydrogenTools", "Class Avogadro::QtGui::InterfaceScript", "Class Avogadro::QtGui::InterfaceWidget", "Class Avogadro::QtGui::MeshGenerator", "Class Avogadro::QtGui::Molecule", "Class Avogadro::QtGui::MoleculeModel", "Class Avogadro::QtGui::MultiViewWidget", "Class Avogadro::QtGui::PeriodicTableScene", "Class Avogadro::QtGui::PeriodicTableView", "Class Avogadro::QtGui::PersistentAtom", "Class Avogadro::QtGui::PersistentBond", "Class Avogadro::QtGui::PythonScript", "Class Avogadro::QtGui::RWAtom", "Class Avogadro::QtGui::RWBond", "Class Avogadro::QtGui::RWMolecule", "Class Avogadro::QtGui::ScenePlugin", "Class Avogadro::QtGui::ScenePluginFactory", "Class Avogadro::QtGui::ScenePluginModel", "Class Avogadro::QtGui::ScriptLoader", "Class Avogadro::QtGui::ToolPlugin", "Class Avogadro::QtGui::ToolPluginFactory", "Class Avogadro::QtGui::ViewFactory", "Class Avogadro::QtOpenGL::ActiveObjects", "Class Avogadro::QtOpenGL::GLWidget", "Class Avogadro::QtOpenGL::QtTextRenderStrategy", "Class Avogadro::QuantumIO::GAMESSUSOutput", "Class Avogadro::QuantumIO::GUKBasisSet", "Class Avogadro::QuantumIO::GamessukOut", "Class Avogadro::QuantumIO::GaussianCube", "Class Avogadro::QuantumIO::GaussianFchk", "Class Avogadro::QuantumIO::MoldenFile", "Class Avogadro::QuantumIO::MopacAux", "Class Avogadro::QuantumIO::NWChemJson", "Class Avogadro::QuantumIO::NWChemLog", "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry", "Class Avogadro::Rendering::ArrowGeometry", "Class Avogadro::Rendering::BufferObject", "Class Avogadro::Rendering::Camera", "Class Avogadro::Rendering::Cylinder", "Class Avogadro::Rendering::CylinderGeometry", "Class Avogadro::Rendering::Drawable", "Class 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71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 162, 175, 176, 201, 208, 217, 222, 223, 237, 247], "us": [1, 3, 6, 8, 9, 12, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 34, 38, 39, 40, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 72, 74, 75, 76, 79, 80, 83, 84, 85, 86, 91, 92, 96, 101, 104, 105, 106, 107, 108, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 121, 123, 124, 127, 128, 129, 132, 133, 135, 137, 139, 140, 141, 143, 158, 162, 165, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 181, 182, 183, 184, 186, 187, 191, 192, 194, 195, 199, 201, 203, 204, 205, 206, 208, 210, 211, 213, 215, 217, 218, 219, 221, 222, 225, 226, 228, 229, 230, 235, 236, 237, 238, 239, 242, 243, 245, 246, 247, 248, 251, 253, 254, 255, 256, 257, 258, 259], "gener": [1, 3, 7, 14, 20, 21, 24, 25, 28, 29, 40, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 82, 84, 85, 93, 96, 104, 105, 107, 110, 111, 112, 113, 114, 115, 140, 142, 158, 162, 169, 175, 176, 177, 181, 182, 189, 191, 201, 204, 210, 211, 212, 217, 219, 222, 235, 237, 242, 243, 244, 245, 246, 247, 250], "javadoc": 1, "thei": [1, 3, 5, 7, 14, 52, 63, 65, 83, 85, 116, 137, 174, 176, 177, 179, 186, 190, 217, 219, 228, 239], "go": [1, 6, 76, 82, 101, 192, 194, 198, 214, 215, 219, 224, 239], "next": [1, 63, 83, 140, 170, 177, 183, 198, 213, 232, 235, 237], "all": [1, 4, 5, 6, 8, 9, 13, 22, 23, 24, 25, 27, 28, 29, 42, 49, 50, 52, 63, 66, 69, 76, 79, 82, 83, 90, 93, 96, 100, 104, 105, 122, 125, 127, 128, 129, 130, 133, 144, 146, 160, 162, 163, 166, 169, 172, 174, 176, 179, 182, 184, 194, 198, 199, 201, 204, 206, 210, 214, 217, 221, 222, 224, 227, 228, 231, 233, 235, 236, 238, 239, 243, 244, 251, 254], "should": [1, 3, 6, 9, 21, 23, 28, 29, 40, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 69, 73, 74, 76, 83, 85, 86, 90, 91, 92, 96, 97, 101, 105, 107, 110, 111, 112, 113, 114, 115, 118, 122, 124, 134, 135, 168, 169, 170, 173, 174, 176, 177, 179, 183, 203, 206, 213, 215, 228, 239, 243, 247, 255], "minimum": [1, 23, 29, 42, 50, 63, 83, 85, 177, 179, 213, 247], "brief": [1, 176], "one": [1, 3, 6, 14, 16, 20, 23, 25, 27, 28, 38, 49, 63, 76, 79, 83, 86, 96, 116, 118, 121, 135, 137, 169, 174, 179, 182, 183, 191, 192, 193, 199, 203, 208, 212, 214, 221, 228, 237, 247], "two": [1, 16, 27, 76, 85, 143, 167, 168, 172, 183, 187, 203, 212, 214, 218, 242, 243, 245, 246, 247, 250, 253, 257, 259], "sentenc": 1, "explain": 1, "what": [1, 29, 44, 86, 96, 181, 198, 208, 212, 226], "intend": [1, 24, 52, 173, 179, 256], "purpos": [1, 3, 6, 52, 66, 116, 127, 137, 168, 179, 208], "i": [1, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 72, 73, 74, 76, 79, 82, 83, 85, 86, 89, 90, 91, 92, 93, 94, 95, 96, 97, 101, 103, 104, 105, 107, 108, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 122, 124, 125, 127, 128, 129, 130, 133, 134, 135, 137, 139, 143, 146, 158, 159, 160, 161, 162, 165, 167, 168, 169, 170, 171, 172, 173, 174, 176, 177, 179, 180, 182, 183, 184, 186, 187, 188, 189, 192, 193, 194, 198, 199, 201, 203, 204, 205, 206, 207, 208, 209, 211, 212, 213, 214, 215, 217, 218, 219, 221, 222, 224, 225, 226, 227, 228, 230, 232, 233, 235, 236, 237, 238, 239, 243, 244, 245, 246, 247, 250, 251, 254, 255, 256, 257, 259], "goe": [1, 6, 63, 83, 174, 239], "here": [1, 63, 82, 83, 167, 171, 172, 177, 179, 182, 183, 184, 186, 187, 188, 189, 191, 192, 208, 214, 231, 256, 257], "void": [1, 6, 8, 9, 13, 14, 16, 18, 19, 20, 21, 23, 25, 26, 27, 28, 29, 32, 34, 36, 37, 38, 40, 42, 43, 44, 45, 49, 52, 58, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 76, 78, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 96, 97, 99, 101, 104, 105, 106, 108, 109, 111, 113, 115, 116, 117, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 158, 159], "dosometh": [1, 6], "overview": [1, 6], "add": [1, 7, 23, 25, 27, 28, 29, 34, 38, 49, 50, 63, 80, 81, 82, 83, 86, 96, 97, 101, 105, 116, 117, 121, 125, 127, 128, 129, 137, 158, 160, 162, 165, 176, 177, 183, 188, 189, 208, 210, 212, 214, 217, 228, 237, 239, 242, 243, 244, 245, 246, 247, 248, 252, 259], "path": [1, 49, 52, 63, 64, 65, 73, 74, 76, 79, 83, 84, 93, 100, 167, 169, 171, 174, 176, 177, 216, 237, 239, 243, 245, 246, 247], "user": [1, 4, 5, 24, 29, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 64, 65, 66, 69, 76, 79, 84, 85, 96, 97, 101, 105, 107, 110, 111, 112, 113, 114, 115, 163, 168, 169, 170, 171, 172, 173, 176, 177, 212, 238, 239, 243, 244, 245, 246, 247], "appropri": [1, 6, 12, 17, 52, 63, 75, 83, 169, 171, 174, 177, 203, 239, 245], "point": [1, 6, 23, 42, 44, 64, 65, 72, 79, 84, 85, 105, 116, 119, 121, 122, 125, 129, 133, 135, 137, 138, 139, 141, 168, 171, 186, 206, 212, 218, 228, 231, 239, 246, 247, 248], "out": [1, 9, 16, 29, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 74, 83, 93, 107, 110, 111, 112, 113, 114, 115, 119, 125, 127, 177, 179, 183, 184, 203, 205, 214, 217, 220, 226, 236, 237, 247, 256], "altern": [1, 170], "similar": [1, 20, 96, 174, 179, 199, 203, 228], "ideal": [1, 15], "give": [1, 5, 8, 9, 21, 24, 40, 49, 119, 172, 179, 212, 247, 259], "some": [1, 5, 24, 29, 63, 65, 83, 86, 96, 116, 137, 162, 167, 168, 172, 174, 176, 177, 182, 184, 187, 199, 236, 244, 246, 247, 254, 256, 257], "simpl": [1, 24, 32, 33, 37, 40, 41, 51, 63, 83, 177, 189, 199, 206, 239, 251], "exampl": [1, 5, 20, 118, 135, 162, 168, 169, 170, 173, 174, 179, 183, 184, 189, 199, 207, 208, 211, 212, 215, 216, 221, 225, 228, 232, 237, 239, 242, 246, 249, 251], "demonstr": [1, 199, 211], "core": [1, 3, 4, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 70, 83, 85, 86, 96, 107, 110, 111, 112, 113, 114, 115, 116, 117, 118, 122, 124, 125, 128, 129, 135, 137, 140, 143, 158, 160, 162, 174, 235, 245], "simplest": 1, "wai": [1, 86, 96, 179, 183, 189, 198, 204, 206, 208, 215, 227, 237, 238], "possibl": [1, 6, 22, 23, 50, 85, 172, 179, 205, 239, 247, 250], "molequeu": [1, 3, 83, 160, 167, 174, 239, 242], "jsonrpcclient": 1, "h": [1, 3, 6, 20, 25, 50, 62, 64, 65, 66, 67, 68, 69, 72, 75, 77, 79, 83, 84, 90, 93, 99, 106, 108, 116, 117, 119, 121, 123, 126, 128, 142, 160, 161, 162, 168, 174, 179, 184, 186, 210, 217, 242, 246, 248, 250, 255, 257, 259], "client": [1, 67, 160, 164, 179], "The": [1, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 84, 85, 86, 88, 90, 91, 92, 93, 96, 97, 98, 100, 101, 102, 103, 104, 105, 106, 107, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 133, 135, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 159, 162, 163, 165, 168, 169, 170, 172, 173, 174, 176, 177, 179, 182, 183, 186, 188, 190, 191, 192, 197, 198, 199, 201, 203, 204, 205, 206, 207, 208, 209, 211, 212, 214, 215, 217, 218, 219, 220, 221, 222, 224, 225, 226, 227, 228, 230, 232, 236, 237, 239, 248, 250], "submit": [1, 5, 62, 64, 65, 66, 69, 160, 164, 176, 183, 186], "call": [1, 8, 13, 14, 18, 19, 26, 28, 49, 52, 63, 64, 68, 69, 70, 73, 74, 76, 83, 85, 89, 90, 93, 96, 101, 105, 124, 128, 129, 135, 162, 163, 169, 170, 171, 172, 173, 174, 177, 205, 237, 239, 242, 245, 247, 257], "an": [1, 3, 5, 6, 12, 14, 15, 18, 19, 20, 23, 24, 25, 27, 28, 29, 32, 34, 37, 38, 40, 43, 44, 49, 50, 52, 62, 63, 65, 66, 68, 69, 70, 79, 80, 83, 84, 85, 86, 89, 90, 91, 92, 93, 96, 104, 105, 106, 108, 116, 137, 138, 142, 158, 159, 162, 163, 168, 169, 170, 172, 173, 174, 176, 177, 179, 183, 184, 186, 189, 190, 191, 194, 198, 199, 201, 203, 204, 208, 211, 212, 213, 214, 216, 218, 219, 220, 221, 222, 226, 227, 228, 232, 233, 234, 237, 238, 239, 245, 246, 247, 250, 255, 256, 257, 259], "rpc": [1, 66, 69, 162, 242], "server": [1, 5, 62, 66, 67, 69, 93, 167, 230], "json": [1, 46, 63, 66, 76, 83, 84, 101, 114, 162, 167, 168, 169, 170, 171, 172, 173, 174, 176, 177, 242, 247], "2": [1, 6, 16, 18, 20, 29, 63, 66, 83, 85, 133, 143, 160, 161, 167, 170, 174, 177, 181, 183, 186, 191, 194, 201, 210, 213, 222, 225, 236, 237, 238, 239, 242, 245, 246, 248, 249, 255, 256, 257, 258], "0": [1, 6, 9, 11, 14, 15, 16, 19, 20, 22, 24, 27, 29, 40, 42, 44, 49, 63, 66, 73, 74, 76, 83, 96, 97, 101, 102, 103, 106, 119, 133, 135, 139, 141, 142, 143, 160, 161, 167, 168, 170, 172, 174, 176, 177, 180, 183, 186, 194, 201, 205, 219, 222, 235, 237, 241, 244, 248, 254, 255, 259], "author": [1, 16, 19, 23, 25, 26, 28, 32, 37, 38, 39, 47, 48, 49, 50, 52, 54, 56, 58, 59, 60, 61, 63, 71, 75, 76, 77, 83, 85, 87, 88, 90, 98, 99, 101, 102, 103, 105, 114, 116, 118, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 144, 146, 147, 159, 169, 174, 176, 179, 250], "marcu": [1, 2, 4, 16, 19, 23, 25, 26, 28, 32, 37, 38, 39, 47, 49, 50, 56, 71, 76, 77, 85, 87, 88, 90, 98, 99, 103, 105, 114, 118, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 144, 146, 147, 159], "d": [1, 2, 4, 8, 16, 19, 23, 25, 26, 28, 32, 37, 38, 39, 47, 49, 50, 56, 63, 71, 76, 77, 83, 85, 87, 88, 90, 93, 98, 99, 103, 105, 108, 114, 118, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 144, 146, 147, 159, 160, 161, 179, 243, 245, 246], "hanwel": [1, 2, 4, 16, 19, 23, 25, 26, 28, 32, 37, 38, 39, 47, 49, 50, 56, 71, 76, 77, 85, 87, 88, 90, 98, 99, 103, 105, 114, 118, 119, 121, 122, 123, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 144, 146, 147, 159], "provid": [1, 14, 15, 19, 22, 23, 25, 26, 28, 29, 32, 37, 39, 42, 44, 52, 62, 63, 64, 65, 66, 67, 68, 69, 70, 75, 80, 83, 84, 86, 91, 92, 103, 104, 105, 119, 122, 124, 127, 130, 140, 146, 162, 168, 170, 171, 174, 176, 179, 187, 198, 199, 201, 204, 205, 206, 207, 208, 209, 212, 219, 222, 227, 232, 234, 237, 247], "To": [1, 12, 17, 52, 64, 66, 75, 169, 172, 179, 182, 203, 210, 215, 220, 221, 239], "creat": [1, 13, 18, 20, 22, 27, 29, 34, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 67, 79, 83, 84, 86, 91, 92, 96, 103, 105, 107, 108, 110, 111, 112, 113, 114, 115, 118, 131, 134, 135, 145, 170, 171, 174, 176, 177, 179, 183, 185, 188, 190, 199, 206, 207, 209, 210, 212, 216, 223, 231, 232, 233, 237, 239, 243, 245, 247, 248, 252, 253, 254, 255, 259], "connect": [1, 27, 62, 67, 69, 85, 96, 128, 167, 172, 179, 204, 227, 230, 231, 246], "method": [1, 6, 13, 18, 22, 24, 29, 43, 49, 52, 63, 64, 66, 68, 76, 79, 83, 85, 86, 91, 92, 96, 101, 103, 105, 118, 119, 135, 159, 168, 170, 174, 216, 217, 237, 242, 245, 247, 250], "follow": [1, 6, 20, 63, 83, 93, 143, 168, 169, 170, 171, 172, 173, 174, 177, 179, 186, 189, 214, 215, 239], "done": [1, 14, 25, 38, 40, 66, 118, 124, 134, 160, 164, 170, 172, 219, 233], "new": [1, 3, 5, 6, 7, 8, 13, 18, 27, 28, 29, 34, 40, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 67, 69, 76, 80, 82, 83, 90, 93, 96, 101, 103, 106, 107, 110, 111, 112, 113, 114, 115, 128, 129, 142, 159, 160, 167, 170, 172, 173, 175, 178, 181, 182, 190, 191, 197, 201, 203, 205, 206, 210, 211, 215, 218, 219, 222, 223, 233, 236, 242, 243, 245, 246, 247, 248], "connecttoserv": 1, "myrpcserv": 1, "qjsonobject": [1, 62, 63, 83], "emptyrequest": 1, "qlatin1str": 1, "listqueu": 1, "sendrequest": 1, "endcod": 1, "signal": [1, 3, 62, 67, 68, 69, 70, 71, 76, 78, 83, 85, 86, 87, 88, 89, 90, 93, 96, 97, 99, 101, 104, 105, 158], "order": [1, 8, 14, 18, 22, 29, 63, 76, 80, 83, 86, 90, 93, 96, 104, 106, 124, 134, 135, 143, 160, 161, 168, 169, 172, 174, 177, 199, 201, 215, 222, 225, 228, 231, 239, 243, 247, 254], "act": [1, 96, 172, 239], "result": [1, 6, 13, 14, 19, 22, 26, 39, 63, 66, 69, 83, 84, 106, 125, 135, 142, 162, 169, 172, 173, 177, 179, 182, 183, 184, 231, 239, 255, 257, 258, 259], "notif": 1, "error": [1, 13, 49, 50, 52, 62, 64, 66, 69, 70, 79, 93, 105, 118, 124, 134, 135, 143, 160, 163, 164, 165, 166, 179, 245, 246, 247, 255], "receiv": [1, 62, 83, 179], "respons": [1, 4, 62, 88, 96, 124, 171, 172, 247], "set": [1, 13, 15, 16, 18, 19, 22, 23, 25, 26, 27, 28, 29, 34, 38, 39, 40, 42, 43, 44, 49, 52, 62, 63, 64, 65, 66, 69, 70, 74, 76, 79, 80, 81, 83, 85, 91, 92, 93, 96, 97, 101, 104, 105, 108, 117, 119, 122, 124, 127, 128, 129, 130, 133, 134, 135, 137, 141, 147, 158, 159, 160, 161, 162, 165, 167, 168, 169, 171, 174, 179, 182, 183, 184, 187, 188, 191, 198, 199, 208, 210, 216, 217, 219, 239, 242, 244, 245, 247, 248], "public": [1, 3, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 243], "qobject": [1, 62, 63, 67, 68, 70, 75, 76, 80, 83, 85, 86, 87, 89, 93, 96, 97, 99, 100, 101, 102, 104], "end": [1, 3, 6, 8, 29, 44, 82, 96, 116, 117, 121, 122, 125, 131, 137, 145, 160, 161, 166, 183, 186, 198, 220, 221], "complet": [1, 28, 52, 62, 66, 69, 85, 118, 128, 164, 168, 169, 176, 186], "constructor": [1, 8, 16, 19, 25, 28, 29, 38, 63, 68, 73, 74, 83, 85, 86, 89, 90, 93], "more": [1, 3, 6, 25, 28, 38, 49, 63, 76, 83, 86, 96, 104, 105, 106, 116, 121, 124, 127, 135, 137, 162, 169, 173, 174, 175, 176, 179, 191, 198, 199, 204, 208, 211, 212, 214, 215, 217, 219, 227, 228, 232, 237, 238, 242, 243, 246, 247, 257], "construct": [1, 19, 20, 62, 65, 80, 84, 90, 96, 203, 206], "describ": [1, 14, 16, 63, 69, 83, 118, 168, 170, 173, 174, 179], "paramet": [1, 8, 14, 15, 16, 19, 22, 23, 25, 26, 28, 29, 33, 38, 39, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 64, 65, 66, 68, 69, 75, 76, 79, 82, 84, 85, 86, 90, 91, 92, 93, 96, 101, 103, 106, 107, 110, 111, 112, 113, 114, 115, 116, 117, 119, 121, 122, 125, 127, 128, 129, 130, 135, 137, 140, 142, 143, 169, 170, 189, 208, 214, 217, 219, 233, 246, 254], "input": [1, 9, 14, 22, 24, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 84, 85, 93, 96, 101, 105, 107, 110, 111, 112, 113, 114, 115, 131, 145, 158, 162, 163, 168, 169, 170, 173, 175, 176, 177, 181, 183, 193, 208, 237, 242, 243, 244, 246, 247], "job": [1, 62, 63, 64, 65, 66, 69, 83, 174], "param": [1, 167], "filenam": [1, 49, 50, 52, 63, 70, 78, 79, 83, 109, 160, 163, 164, 165, 167, 170, 174, 176, 247], "appear": [1, 63, 79, 83, 96, 174, 176, 182, 189, 208, 228], "work": [1, 4, 5, 7, 25, 104, 169, 179, 183, 191, 194, 205, 208, 211, 214, 236, 237, 238, 239, 246, 247], "directori": [1, 30, 31, 79, 157, 162, 239, 243, 247], "content": [1, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 83, 85, 105, 107, 110, 111, 112, 113, 114, 115, 116, 117, 121, 122, 128, 129, 137, 140, 158, 167, 174, 179], "specifi": [1, 14, 19, 20, 22, 23, 26, 28, 29, 34, 39, 49, 50, 52, 65, 80, 84, 86, 91, 92, 93, 96, 105, 125, 127, 128, 129, 130, 135, 143, 168, 170, 171, 172, 173, 177, 179, 182, 184, 186, 187, 211, 228], "return": [1, 6, 9, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 73, 74, 75, 76, 79, 80, 82, 83, 85, 86, 88, 90, 91, 92, 93, 96, 97, 100, 101, 103, 104, 105, 107, 108, 110, 111, 112, 113, 114, 115, 116, 118, 119, 121, 122, 124, 125, 127, 128, 129, 130, 135, 137, 143, 159, 168, 171, 172, 206, 230, 252], "true": [1, 6, 9, 13, 15, 16, 18, 22, 25, 26, 27, 28, 29, 32, 37, 38, 39, 40, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 69, 70, 76, 83, 85, 86, 91, 92, 93, 96, 97, 101, 105, 107, 108, 110, 111, 112, 113, 114, 115, 122, 125, 127, 130, 135, 143, 160, 165, 168, 169, 170, 171, 172, 177], "wa": [1, 4, 28, 29, 62, 63, 66, 69, 70, 74, 76, 83, 85, 86, 101, 105, 125, 127, 174, 187, 189, 198, 203, 205, 232, 235, 237, 243], "successfulli": [1, 52, 62, 63, 66, 67, 76, 83, 85, 239, 246], "fals": [1, 6, 15, 16, 22, 25, 26, 28, 29, 32, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 76, 83, 85, 86, 96, 97, 101, 105, 107, 110, 111, 112, 113, 114, 115, 122, 125, 127, 130, 135, 160, 165, 168, 170, 172, 174], "otherwis": [1, 15, 16, 22, 25, 26, 29, 38, 39, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 66, 68, 69, 76, 83, 96, 101, 107, 110, 111, 112, 113, 114, 115, 127, 173, 174, 179, 213, 230], "bool": [1, 8, 9, 13, 15, 16, 18, 22, 23, 25, 26, 27, 28, 29, 32, 34, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 76, 78, 83, 85, 86, 87, 91, 92, 93, 96, 97, 99, 100, 101, 105, 106, 107, 108, 110, 111, 112, 113, 114, 115, 118, 122, 124, 125, 127, 130, 132, 133, 134, 135, 141, 143, 158, 159, 160, 161], "setinputfil": 1, "const": [1, 3, 6, 8, 9, 10, 11, 13, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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28, 29, 30, 31, 34, 38, 40, 44, 49, 50, 52, 62, 63, 66, 68, 69, 70, 76, 79, 82, 83, 84, 85, 86, 91, 92, 96, 101, 105, 108, 116, 117, 119, 121, 122, 125, 127, 128, 129, 130, 135, 137, 138, 139, 157, 159, 162, 167, 169, 170, 172, 173, 174, 175, 176, 177, 179, 181, 182, 183, 184, 187, 188, 190, 191, 193, 196, 198, 199, 201, 203, 205, 207, 208, 209, 212, 214, 215, 218, 220, 221, 222, 228, 231, 232, 233, 234, 235, 237, 238, 239, 240, 242, 243, 244, 245, 246, 247, 250, 251, 256], "librari": [3, 5, 52, 104, 143, 176, 182, 228, 239, 243, 247], "over": [3, 183, 187, 193, 194, 197, 219, 228, 230, 235, 237, 242, 243], "boost": [3, 239], "depend": [3, 4, 106, 172, 182, 199, 208, 219, 239, 242, 248, 256], "In": [3, 7, 28, 63, 83, 85, 169, 172, 174, 179, 183, 186, 201, 205, 215, 222, 231, 237, 239, 240, 248], "11": [3, 32, 179, 183], "17": [3, 37, 239], "where": [3, 6, 19, 23, 24, 25, 27, 28, 38, 63, 73, 74, 83, 105, 162, 167, 171, 172, 174, 179, 184, 195, 203, 212, 217, 228, 232, 237, 239, 247, 257], "necessari": [3, 6, 8, 97, 179, 212, 215, 219], "offer": [3, 4, 96, 174, 179, 203, 205, 238], "avo_overrid": 3, "avo_fin": 3, "defin": [3, 42, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 83, 88, 107, 110, 111, 112, 113, 114, 115, 116, 122, 137, 141, 142, 143, 169, 171, 174, 179, 182, 183, 186, 206, 228, 237], "overrid": [3, 25, 29, 33, 38, 41, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 76, 77, 78, 80, 83, 84, 85, 86, 87, 88, 89, 90, 93, 96, 97, 98, 99, 100, 101, 105, 106, 107, 110, 111, 112, 113, 114, 115, 116, 117, 121, 123, 125, 126, 127, 128, 129, 131, 137, 138, 139, 140, 144, 145, 147, 159, 174, 246], "final": [3, 62, 96, 169, 172, 191, 198, 247], "minim": [3, 63, 83, 141, 174, 191], "third": [3, 183, 239], "parti": [3, 179, 239], "think": [3, 168, 238, 250], "carefulli": [3, 76], "befor": [3, 6, 13, 18, 25, 38, 52, 63, 67, 83, 86, 93, 96, 108, 177, 179, 188, 198, 213, 214, 219, 228, 233, 239, 247], "ad": [3, 7, 25, 27, 29, 34, 38, 49, 62, 63, 82, 83, 86, 103, 121, 125, 127, 128, 129, 160, 165, 177, 189, 190, 191, 199, 201, 215, 222, 228, 230, 237, 242, 247], "templat": [3, 7, 8, 9, 10, 13, 14, 18, 21, 43, 45, 63, 65, 66, 69, 83, 91, 92, 118, 130, 135, 143, 148, 149, 150, 151, 152, 153, 154, 155, 156, 174, 201, 222, 223, 243, 247], "sens": [3, 69], "alwai": [3, 6, 69, 175, 179, 213, 243, 245, 246], "form": [3, 15, 27, 84, 96, 105, 128, 168, 169, 170, 173, 174, 179, 198, 214, 217, 243, 245, 246, 250, 257], "project": [3, 5, 6, 30, 31, 119, 139, 157, 160, 166, 183, 186, 207, 210, 238, 239, 243, 247, 250], "someth": [3, 85, 101, 171, 205], "type": [3, 6, 8, 9, 10, 11, 13, 14, 16, 18, 19, 21, 22, 23, 25, 26, 29, 33, 34, 38, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 66, 68, 72, 76, 78, 79, 82, 83, 86, 90, 91, 92, 96, 97, 100, 103, 104, 107, 108, 110, 111, 112, 113, 114, 115, 118, 119, 122, 125, 127, 130, 132, 134, 135, 141, 143, 148, 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242], "nest": [3, 191], "everyth": [3, 207, 211, 218], "insid": [3, 6, 176, 239], "mongochem": [3, 247], "contain": [3, 6, 8, 9, 13, 16, 18, 19, 21, 22, 23, 25, 27, 28, 29, 34, 38, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 66, 68, 69, 71, 76, 79, 83, 87, 88, 91, 92, 93, 96, 99, 105, 107, 110, 111, 112, 113, 114, 115, 116, 118, 121, 125, 127, 131, 133, 135, 137, 143, 145, 147, 159, 160, 161, 168, 169, 170, 172, 173, 174, 176, 213, 215, 239, 246], "most": [3, 16, 62, 63, 73, 74, 76, 79, 83, 126, 127, 165, 169, 174, 179, 203, 205, 206, 208, 212, 217, 219, 231, 232, 237, 239], "overspecifi": 3, "e": [3, 6, 20, 27, 28, 29, 34, 38, 44, 49, 63, 65, 75, 76, 83, 85, 86, 89, 90, 93, 96, 101, 133, 135, 139, 143, 167, 168, 169, 170, 173, 174, 176, 177, 179, 182, 186, 191, 193, 194, 201, 213, 222, 228, 230, 234, 235, 236, 237, 239, 242, 243, 246, 247], "doesn": [3, 194, 198, 219], "slot": [3, 62, 63, 64, 66, 67, 69, 70, 72, 76, 78, 83, 86, 87, 88, 89, 90, 93, 96, 99, 101, 104, 105, 158], "moc": 3, "often": [3, 184, 217], "littl": 3, "help": [3, 4, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 107, 110, 111, 112, 113, 114, 115, 162, 168, 170, 173, 205, 206, 217, 232, 236, 237, 238, 243, 245, 246, 256], "onli": [3, 6, 16, 22, 24, 29, 44, 52, 63, 66, 69, 82, 83, 86, 96, 105, 118, 122, 125, 134, 168, 169, 170, 172, 173, 174, 179, 191, 198, 199, 203, 208, 211, 215, 217, 219, 221, 231, 237, 239, 244, 245, 246, 247, 256, 259], "specif": [3, 12, 17, 20, 29, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 76, 83, 107, 110, 111, 112, 113, 114, 115, 160, 161, 172, 173, 174, 183, 198, 208, 211, 214, 217, 218, 219, 220, 223, 232, 242, 247], "symbol": [3, 20, 24, 40, 41, 73, 74, 160, 161, 174, 201, 222, 245, 247], "avoid": [3, 6, 23, 85, 179, 239, 246, 247, 257], "static_cast": 3, "dynamic_cast": [3, 130], "const_cast": 3, "reinterpret_cast": [3, 6], "For": [3, 5, 6, 16, 20, 24, 52, 62, 96, 135, 162, 168, 170, 171, 172, 173, 174, 177, 179, 183, 189, 192, 199, 205, 207, 208, 211, 212, 214, 215, 219, 221, 224, 225, 228, 239, 251, 256, 258], "deriv": [3, 16, 21, 22, 26, 39, 49, 86, 101, 105, 127, 159, 179, 231, 251, 252, 256], "qobject_cast": 3, "enum": [3, 16, 20, 22, 23, 25, 34, 38, 40, 43, 49, 52, 62, 66, 68, 78, 79, 82, 86, 96, 97, 108, 118, 127, 132, 134, 135, 141, 143, 148, 149, 150, 151, 152, 153, 154, 155, 156], "": [3, 13, 14, 18, 20, 22, 25, 27, 29, 38, 42, 43, 44, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 66, 76, 80, 81, 82, 83, 85, 86, 96, 105, 107, 108, 110, 111, 112, 113, 114, 115, 119, 122, 130, 143, 158, 160, 161, 163, 167, 169, 170, 171, 173, 174, 179, 181, 184, 191, 201, 206, 208, 212, 214, 215, 218, 219, 220, 221, 222, 226, 231, 232, 237, 239, 242, 247, 249, 256], "constant": [3, 24, 85, 208], "static": [3, 15, 22, 24, 29, 40, 42, 49, 50, 62, 66, 67, 69, 72, 75, 79, 82, 85, 100, 104, 117, 128, 129, 148, 149, 150, 151, 152, 153, 154, 155, 156, 159, 217], "int": [3, 6, 13, 16, 18, 19, 22, 23, 25, 26, 28, 29, 34, 35, 38, 39, 42, 43, 45, 49, 52, 62, 63, 66, 68, 69, 73, 74, 75, 76, 80, 82, 83, 85, 86, 87, 89, 90, 93, 96, 99, 105, 106, 108, 119, 124, 128, 129, 135, 141, 142, 143, 159, 160, 161, 172], "verbos": 3, "argument": [3, 29, 44, 63, 66, 83, 86, 168, 169, 170, 172, 173, 174, 239], "id": [3, 27, 28, 29, 34, 50, 62, 66, 69, 86, 91, 92, 96, 116, 120, 132, 136, 137, 167, 239, 243], "show": [3, 29, 66, 79, 90, 182, 186, 188, 191, 192, 203, 208, 221, 230, 231, 237, 246], "autocomplet": 3, "It": [3, 15, 16, 19, 22, 25, 28, 29, 38, 44, 50, 63, 82, 83, 86, 96, 122, 169, 171, 172, 174, 195, 203, 205, 209, 215, 235, 237, 238, 239], "look": [3, 6, 50, 119, 171, 172, 176, 184, 203, 212, 237, 239], "better": [3, 5, 205, 213, 219, 237, 238, 247], "poor": 3, "peopl": [3, 205], "guess": [3, 24], "abbrevi": [3, 6], "ambigu": 3, "can": [3, 8, 14, 21, 22, 24, 26, 28, 29, 39, 49, 50, 52, 62, 63, 65, 66, 67, 68, 69, 76, 79, 82, 83, 85, 86, 91, 92, 96, 101, 104, 116, 122, 131, 133, 134, 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76, 106, 119, 121, 124, 139, 142, 199, 224, 239, 245], "framework": [4, 237, 246, 247], "so": [4, 19, 22, 25, 38, 42, 52, 63, 83, 85, 96, 135, 143, 158, 159, 162, 167, 172, 174, 176, 179, 184, 191, 197, 198, 199, 208, 219, 236, 239, 255, 257, 259], "veri": [4, 5, 23, 32, 37, 162, 184, 203, 243, 245, 246], "grate": 4, "start": [4, 5, 6, 25, 27, 93, 117, 121, 181, 182, 183, 190, 191, 206, 216, 219, 220, 223, 229, 234, 238, 243, 247], "donald": 4, "curti": 4, "effort": [4, 82, 205], "kitwar": [4, 239], "inc": 4, "shahzad": 4, "ali": 4, "kristof": 4, "bal": 4, "banck": 4, "edward": 4, "bett": 4, "ross": 4, "braithwait": 4, "jame": 4, "bunt": 4, "taylor": [4, 205], "cornel": [4, 205], "raphael": 4, "kubo": 4, "costa": 4, "reini": 4, "dann": 4, "zackari": 4, "fall": [4, 6, 242, 243, 245], "naomi": 4, "fox": 4, "raimonda": 4, "galv": 4, "dagmar": 4, "lenk": 4, "gari": 4, "kedziora": 4, "thoma": [4, 242], "margraf": 4, "jordan": 4, "mantha": 4, "carsten": 4, "niehau": 4, "katsuhiko": 4, 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243, 245, 246], "summer": [4, 205, 242, 243, 245, 246], "code": [4, 5, 7, 25, 38, 63, 83, 85, 89, 162, 168, 170, 171, 172, 174, 184, 191, 192, 194, 208, 233, 234, 237, 238, 240, 242, 243, 245, 246, 247], "2007": 4, "2008": 4, "2011": 4, "2016": 4, "2018": 4, "2019": [4, 245], "2021": [4, 242, 243, 244], "2022": [4, 205, 245, 246], "univers": [4, 205, 217, 219, 250], "pittsburgh": [4, 205], "u": [4, 5, 8, 9, 21, 105, 127, 186, 191, 238, 242, 243, 245, 246], "depart": [4, 205], "defens": 4, "dod": 4, "through": [4, 5, 6, 7, 14, 65, 69, 76, 96, 101, 162, 165, 170, 172, 175, 176, 179, 182, 183, 187, 188, 189, 192, 193, 198, 199, 201, 203, 208, 209, 211, 215, 219, 222, 228, 231, 237, 239, 242, 247], "pettt": 4, "program": [4, 66, 67, 68, 69, 135, 160, 164, 167, 168, 169, 174, 183, 189, 209, 215, 235, 236, 245], "research": [4, 191, 238, 250, 256], "corpor": [4, 179], "cottrel": 4, "scholar": 4, "award": 4, "reli": 4, "number": [4, 6, 13, 15, 16, 18, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 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172, 181, 203, 215, 216, 233, 237, 238, 246, 253, 256], "experi": [5, 250], "valuabl": 5, "bug": [5, 7, 194, 238, 241], "pleas": [5, 7, 238, 242, 243, 245, 246, 256], "take": [5, 23, 29, 50, 63, 70, 73, 74, 76, 83, 88, 105, 123, 124, 138, 172, 182, 195, 199, 208, 212, 215, 219, 224, 226, 233], "moment": [5, 191, 233], "tracker": [5, 238], "issu": [5, 7, 238, 242, 247], "while": [5, 6, 27, 63, 83, 85, 96, 101, 169, 170, 174, 183, 188, 214, 219, 228, 230, 246], "move": [5, 29, 105, 139, 143, 179, 186, 194, 197, 203, 219, 224, 236, 237, 247, 248], "around": [5, 6, 16, 23, 32, 37, 64, 66, 70, 186, 188, 191, 197, 199, 203, 214, 224, 237, 251, 256], "fit": [5, 6, 29, 52, 105, 124, 158, 179, 228], "particular": [5, 24, 52, 63, 76, 83, 167, 168, 170, 174, 179, 190, 205, 228], "compon": [5, 19, 23, 24, 27, 29, 128, 129, 133, 141, 143, 162], "itself": 5, "section": [5, 22, 63, 68, 83, 96, 174, 176, 199, 204, 205, 206, 208, 214, 219, 224, 237, 256], "discuss": [5, 7, 169, 208, 238, 242, 243, 245, 246, 256], "idea": [5, 238, 256], "plan": 5, "direct": [5, 19, 42, 63, 83, 116, 119, 120, 121, 122, 125, 129, 137, 143, 160, 166, 174, 179, 194, 220, 239, 245, 248], "progress": [5, 28, 85, 209, 236], "etc": [5, 6, 18, 25, 38, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 76, 83, 101, 104, 105, 107, 110, 111, 112, 113, 114, 115, 116, 121, 134, 135, 137, 143, 158, 162, 169, 170, 171, 174, 177, 199, 203, 208, 228, 230, 231, 234, 236, 237, 238, 239, 242, 247, 251], "both": [5, 16, 27, 52, 64, 65, 162, 168, 170, 173, 174, 176, 177, 188, 215, 238, 259], "python": [5, 93, 100, 162, 169, 172, 175, 176, 216, 236, 238, 239, 241, 243, 245, 246, 247], "script": [5, 64, 65, 76, 84, 93, 100, 101, 163, 173, 215, 236, 238, 242, 243, 244, 246, 247], "util": [5, 65, 93, 100, 119, 176, 189, 199, 208], "tell": [5, 101, 167], "friend": [5, 28, 42, 68, 80, 96, 116, 117, 121, 122, 128, 129, 130, 137, 140], "cite": 5, "paper": [5, 22, 193, 238, 248], "write": [5, 6, 8, 16, 37, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 70, 79, 83, 93, 104, 107, 110, 111, 112, 113, 114, 115, 160, 163, 165, 170, 171, 174, 245, 246, 247], "edit": [5, 15, 65, 96, 162, 181, 189, 198, 199, 201, 203, 208, 210, 211, 212, 222, 224, 234, 235, 237, 239, 245, 246, 247], "tutori": [5, 181, 182, 199, 208, 237, 238, 250], "site": [5, 228, 237, 238], "up": [5, 25, 27, 28, 38, 50, 52, 85, 99, 105, 119, 143, 158, 162, 167, 171, 182, 186, 189, 190, 191, 194, 195, 197, 198, 203, 208, 209, 211, 212, 213, 225, 228, 230, 232, 235, 237, 246, 247], "lesson": [5, 186, 250, 256], "activ": [5, 25, 71, 76, 87, 88, 89, 90, 97, 101, 104, 105, 215, 237, 239, 250], "teacher": [5, 250], "send": [5, 62, 67, 93, 162, 167, 174, 242], "fragment": [5, 134, 135, 160, 166, 181, 193, 196, 204, 206, 224, 227, 228, 237, 242, 247], "report": [5, 7, 63, 83, 174, 184, 238, 243, 244, 245, 246], "encount": [5, 7, 49, 52, 105], "about": [5, 20, 24, 40, 63, 83, 119, 174, 198, 208, 212, 214, 226, 238, 245, 246], "improv": [5, 7, 235, 237, 241, 244], "translat": [5, 23, 42, 68, 75, 119, 160, 163, 166, 168, 170, 173, 177, 179, 183, 184, 186, 190, 191, 203, 205, 218, 224, 238, 241, 242], "languag": [5, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 83, 107, 110, 111, 112, 113, 114, 115, 168, 169, 170, 171, 174, 211, 238, 246], "donat": 5, "pai": [5, 205, 259], "host": [5, 245, 246, 247], "meet": 5, "bounti": 5, "when": [6, 8, 9, 14, 16, 19, 21, 25, 29, 38, 50, 52, 62, 63, 64, 65, 66, 67, 69, 70, 76, 79, 83, 89, 90, 93, 96, 101, 105, 124, 128, 129, 158, 169, 170, 171, 172, 174, 176, 188, 189, 198, 199, 203, 204, 206, 208, 212, 213, 215, 224, 233, 236, 239, 243, 246, 247, 248, 250, 251], "base": [6, 8, 9, 14, 16, 20, 29, 34, 49, 63, 76, 77, 79, 80, 83, 86, 98, 101, 102, 117, 121, 122, 123, 125, 126, 130, 131, 145, 146, 162, 170, 172, 174, 176, 177, 179, 191, 192, 206, 208, 211, 237, 246, 247, 251, 256], "larg": [6, 8, 52, 182, 186, 187, 190, 191, 203, 237, 239], "kde": 6, "format": [6, 20, 34, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 70, 76, 79, 80, 81, 83, 107, 110, 111, 112, 113, 114, 115, 141, 143, 162, 163, 167, 168, 170, 171, 172, 174, 175, 176, 179, 180, 194, 208, 231, 233, 236, 237, 242, 243, 244, 245, 246, 247], "enforc": [6, 179], "clang": [6, 246], "tool": [6, 26, 39, 76, 101, 102, 105, 160, 165, 181, 183, 186, 190, 191, 197, 199, 201, 203, 204, 205, 214, 235, 236, 238, 242, 244, 245, 247, 251, 255, 258, 259], "space": [6, 20, 22, 23, 26, 28, 29, 39, 40, 52, 96, 147, 160, 161, 170, 174, 182, 184, 186, 187, 188, 189, 212, 245, 247, 254], "tab": [6, 212, 228, 243, 246], "keep": [6, 27, 52, 66, 68, 96, 104, 106, 214, 239], "less": [6, 13, 18, 24, 29, 96, 208, 228, 232, 237, 257], "than": [6, 8, 13, 18, 24, 27, 29, 52, 63, 83, 96, 167, 179, 187, 237, 243, 254, 257], "80": 6, "charact": [6, 20, 49, 63, 83, 169, 174], "wide": [6, 205, 208, 237], "each": [6, 14, 20, 25, 27, 28, 33, 38, 41, 49, 52, 62, 63, 64, 83, 96, 135, 143, 162, 170, 171, 174, 176, 177, 213, 239, 258, 259], "separ": [6, 143, 169, 174, 179, 231], "g": [6, 20, 25, 29, 34, 49, 63, 75, 76, 83, 89, 90, 93, 101, 135, 139, 141, 143, 160, 161, 167, 168, 169, 170, 173, 174, 176, 177, 179, 182, 191, 193, 194, 201, 213, 222, 228, 230, 234, 236, 237, 239, 242, 247], "nmbr": 6, "singl": [6, 18, 29, 52, 63, 65, 67, 71, 83, 85, 96, 117, 143, 174, 191, 192, 198, 204, 227, 246, 250], "fine": [6, 63, 83, 174], "counter": [6, 63, 83, 93], "temporari": [6, 170], "obviou": 6, "wait": [6, 65, 68, 93], "until": [6, 8, 65, 66, 206, 219, 254], "unus": [6, 16, 25, 38], "ones": 6, "incorrect": [6, 243, 246, 247], "f": [6, 25, 38, 71, 88, 108, 122, 135, 137, 139, 158, 160, 161, 170, 179, 217, 243], "lower": [6, 27, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 107, 110, 111, 112, 113, 114, 115, 143, 212], "letter": [6, 24, 192, 245], "word": 6, "acronym": 6, "cmlformat": [6, 49, 160, 163], "doubl": [6, 15, 18, 24, 25, 26, 29, 38, 39, 40, 43, 52, 90, 96, 108, 117, 158, 159, 160, 161, 191, 192, 201, 204, 222, 226, 227, 246, 257], "cntr": 6, "std": [6, 8, 9, 10, 11, 13, 16, 20, 21, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 38, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 82, 86, 96, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 121, 122, 124, 125, 127, 131, 134, 135, 137, 140, 142, 143, 145], "string": [6, 7, 13, 16, 20, 23, 24, 25, 28, 29, 33, 34, 35, 40, 41, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 66, 68, 69, 70, 76, 79, 80, 81, 83, 96, 101, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 118, 124, 131, 134, 135, 140, 142, 143, 145, 160, 161, 163, 167, 169, 172, 174, 193], "rawxml": 6, "char": [6, 13, 18, 24, 25, 29, 34, 40, 43, 86, 96, 101, 106, 128, 129, 135, 140, 141, 142, 143, 148, 150, 151, 152, 153, 155, 156, 160, 161], "list_delimit": 6, "center": [6, 29, 116, 119, 126, 133, 137, 160, 166, 186, 190, 191, 192, 198, 199, 210, 228, 237, 243, 247], "listdelimit": 6, "upper": [6, 138], "m_": 6, "blank": [6, 177, 212], "togeth": [6, 96, 127, 176], "after": [6, 29, 49, 52, 63, 64, 66, 69, 83, 90, 118, 169, 170, 177, 182, 186, 187, 188, 189, 191, 195, 197, 198, 201, 206, 208, 209, 214, 222, 224, 228, 232, 234, 242], "curli": 6, "blah": [6, 63, 83, 177], "explod": 6, "5": [6, 15, 40, 42, 63, 83, 96, 160, 161, 177, 186, 239, 246, 247, 248, 251, 258, 259], "pointer": [6, 8, 24, 28, 43, 45, 66, 79, 122, 125, 127, 130, 160, 161], "refer": [6, 8, 13, 18, 43, 45, 64, 66, 67, 68, 79, 80, 86, 91, 92, 104, 105, 116, 118, 119, 121, 125, 127, 135, 137, 143, 158, 160, 161, 171, 179, 214, 218, 219, 244], "between": [6, 15, 23, 24, 27, 29, 42, 43, 44, 85, 86, 96, 167, 172, 173, 182, 183, 199, 208, 214, 219, 225, 228, 247, 254, 256, 259], "x": [6, 20, 22, 23, 28, 29, 124, 170, 173, 174, 183, 199, 206, 208, 212, 218, 220, 237, 239, 247, 257], "mystr": 6, "y": [6, 20, 23, 29, 119, 124, 170, 174, 199, 206, 208, 212, 218, 220, 239], "whoah": 6, "surround": [6, 232], "binari": [6, 239, 246], "oper": [6, 8, 13, 14, 18, 21, 22, 28, 29, 34, 35, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 70, 72, 79, 80, 85, 86, 96, 107, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 121, 122, 128, 129, 132, 135, 137, 140, 141, 143, 160, 161, 163, 165, 166, 169, 171, 173, 183], "No": [6, 22, 27, 168, 179, 246], "memoryblock": 6, "malloc": 6, "data": [6, 8, 9, 16, 19, 21, 23, 24, 25, 26, 27, 28, 29, 34, 38, 39, 40, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 68, 76, 83, 85, 86, 87, 93, 96, 99, 106, 107, 108, 110, 111, 112, 113, 114, 115, 118, 133, 135, 142, 143, 147, 158, 160, 161, 164, 165, 167, 168, 172, 173, 181, 196, 207, 210, 211, 231, 236, 237, 242, 254, 255, 257], "size": [6, 8, 19, 21, 27, 28, 44, 52, 85, 116, 118, 121, 135, 137, 143, 160, 161, 166, 182, 183, 199, 212, 242, 247, 254], "left": [6, 52, 63, 83, 106, 119, 138, 142, 143, 174, 201, 203, 204, 206, 212, 218, 219, 221, 222, 227, 239], "normal": [6, 8, 25, 28, 29, 38, 63, 76, 83, 85, 90, 116, 120, 121, 122, 125, 129, 135, 137, 160, 161, 165, 166, 174, 188, 203], "same": [6, 13, 18, 22, 27, 52, 62, 64, 128, 129, 168, 179, 198, 212, 217, 239, 248, 259], "foo": 6, "run": [6, 14, 28, 62, 65, 68, 69, 83, 84, 85, 104, 160, 161, 165, 168, 169, 170, 171, 173, 176, 203, 210, 215, 234, 237, 244, 246, 253], "implement": [6, 12, 14, 17, 22, 33, 41, 46, 47, 48, 52, 54, 55, 56, 59, 60, 61, 63, 76, 83, 85, 90, 93, 96, 106, 114, 118, 123, 135, 140, 142, 143, 162, 167, 173, 245, 246], "myfun": 6, "cout": 6, "suppli": [6, 23, 24, 25, 29, 38, 49, 50, 63, 64, 76, 79, 83, 85, 96, 97, 108, 119, 122, 125, 134, 135, 137, 158, 168, 169, 170, 179], "endl": 6, "bar": [6, 208, 212, 224, 226, 233], "bodi": 6, "condit": [6, 22, 191], "also": [6, 27, 28, 40, 49, 63, 73, 74, 83, 96, 105, 116, 133, 137, 162, 168, 170, 172, 174, 175, 176, 179, 182, 186, 188, 190, 191, 192, 194, 201, 203, 204, 205, 206, 207, 208, 209, 211, 212, 215, 217, 219, 220, 222, 225, 226, 227, 231, 237, 238, 239, 246, 256], "complex": [6, 127, 201, 222, 228, 237, 247], "42": 6, "var": [6, 171], "parent": [6, 45, 62, 66, 68, 70, 71, 72, 76, 79, 82, 85, 87, 88, 89, 96, 97, 99, 101, 102, 105, 122, 127, 130, 144, 160, 161, 164, 165, 166], "doe": [6, 8, 13, 15, 22, 29, 40, 52, 86, 93, 96, 105, 119, 135, 159, 168, 169, 170, 179, 187, 208, 217, 224, 236, 254], "wrap": [6, 42, 96, 143, 159, 160, 166], "isvalid": [6, 13, 16, 18, 25, 26, 38, 39, 63, 83, 86, 91, 92, 105, 124, 132, 160, 161, 164, 165, 166], "agooddai": 6, "ani": [6, 8, 13, 14, 18, 23, 27, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 69, 76, 79, 80, 81, 83, 93, 96, 101, 105, 107, 110, 111, 112, 113, 114, 115, 118, 119, 125, 135, 167, 168, 169, 170, 172, 173, 174, 176, 177, 179, 195, 203, 206, 209, 212, 221, 228, 235, 239, 247], "els": 6, "block": [6, 20, 63, 83, 169, 177], "element": [6, 8, 20, 21, 25, 27, 28, 29, 33, 41, 72, 73, 74, 75, 89, 90, 96, 123, 129, 131, 133, 135, 143, 145, 160, 161, 165, 168, 170, 171, 172, 174, 177, 179, 182, 189, 201, 206, 210, 217, 222, 228, 237, 243, 246, 251], "cover": [6, 169, 205, 230], "empti": [6, 8, 20, 25, 27, 29, 34, 40, 43, 44, 49, 50, 52, 76, 79, 80, 96, 118, 124, 134, 135, 160, 161, 169, 188, 242], "express": [6, 63, 83, 174, 179, 257], "intent": 6, "clearer": 6, "label": [6, 13, 20, 29, 63, 83, 96, 108, 139, 160, 161, 165, 169, 171, 174, 177, 179, 200, 214, 237, 242, 243, 245, 247], "column": [6, 22, 42, 68, 87, 99], "everi": [6, 27, 29, 179, 230], "must": [6, 16, 25, 26, 29, 38, 52, 63, 66, 76, 79, 83, 85, 96, 106, 118, 120, 128, 129, 134, 135, 142, 143, 168, 169, 170, 172, 173, 174, 176, 179, 206, 215, 239], "indic": [6, 20, 23, 27, 28, 29, 63, 64, 66, 68, 69, 76, 79, 82, 83, 86, 96, 104, 105, 116, 129, 135, 137, 168, 169, 170, 172, 173, 174, 176, 177, 179, 182, 186, 212, 214, 221, 228, 244], "omiss": 6, "anoth": [6, 40, 52, 170, 184, 189, 199, 201, 204, 222, 227, 237, 259], "immedi": [6, 176], "myenum": 6, "drawlin": [6, 117, 160, 166], "vertex": [6, 27, 28, 85, 117, 128, 129, 134, 135, 160, 161, 166, 225], "drawdot": 6, "default": [6, 16, 20, 24, 25, 26, 28, 29, 34, 38, 49, 52, 63, 65, 76, 79, 83, 96, 97, 105, 119, 128, 129, 133, 134, 139, 143, 169, 171, 174, 177, 192, 199, 201, 203, 212, 213, 219, 222, 233, 237, 247], "drawdefault": 6, "shorter": 6, "insert": [6, 8, 29, 63, 83, 160, 161, 169, 177, 181, 182, 186, 190, 191, 192, 193, 196, 210, 223, 224, 237, 242, 243, 245, 247, 248], "comma": [6, 168, 170], "broken": 6, "begin": [6, 8, 44, 85, 96, 106, 131, 142, 145, 160, 161, 166, 201, 204, 221, 222, 232, 234], "verylongexpress": 6, "anotherevenlongerexpress": 6, "justwhenyouthoughtitcouldntgetlong": 6, "vector3d": [6, 108], "posit": [6, 8, 13, 15, 22, 23, 26, 29, 39, 82, 85, 96, 116, 119, 120, 126, 133, 135, 136, 137, 139, 160, 161, 166, 186, 190, 191, 206, 212, 224, 237, 252, 257, 259], "currentposit": 6, "offset": [6, 85, 135, 160, 165], "reimplement": [6, 65, 105], "put": [6, 237, 247], "discourag": 6, "prefix": [6, 13, 18, 63, 79, 83, 173, 176, 177, 239], "clear": [6, 8, 14, 27, 28, 43, 44, 49, 63, 83, 85, 87, 90, 99, 105, 116, 117, 121, 122, 126, 127, 128, 129, 133, 137, 140, 158, 160, 161, 163, 165, 166, 183, 204, 210, 227, 242], "cpp": [6, 85], "extens": [6, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 76, 77, 79, 83, 107, 110, 111, 112, 113, 114, 115, 162, 167, 168, 169, 170, 173, 174, 181, 183, 199, 201, 210, 211, 214, 215, 219, 222, 231, 232, 237, 238, 242, 245, 246, 247], "As": [6, 7, 167, 169, 190, 199, 210, 218, 225, 228, 230, 239, 242, 245], "feel": [6, 238], "free": [6, 52, 105, 169, 174, 179, 201, 205, 222, 238, 239], "bad": 6, "local": [7, 63, 75, 83, 85, 169, 174, 176, 177, 238, 242, 245, 247], "avail": [7, 26, 29, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 67, 68, 69, 76, 83, 85, 101, 105, 107, 110, 111, 112, 113, 114, 115, 134, 159, 168, 169, 170, 171, 173, 174, 177, 179, 180, 237, 238, 246], "autom": [7, 50, 176, 237, 245, 246], "task": [7, 217, 237], "phrase": 7, "whenev": 7, "allow": [7, 8, 28, 32, 37, 43, 63, 79, 83, 162, 163, 168, 170, 173, 174, 179, 182, 183, 186, 188, 189, 190, 191, 193, 194, 199, 201, 203, 204, 206, 208, 209, 211, 212, 214, 219, 220, 221, 222, 224, 225, 226, 227, 228, 231, 233, 234, 236, 237, 242, 246, 247], "time": [7, 52, 63, 83, 93, 96, 105, 118, 127, 162, 179, 182, 187, 191, 247, 250], "freez": [7, 29], "least": [7, 76, 96, 213, 225, 232, 237, 246], "week": 7, "advanc": [7, 63, 83, 174, 238, 239], "releas": [7, 52, 118, 135, 143, 160, 166, 176, 205, 235, 239, 240, 241], "typenam": [8, 9, 10, 14, 21, 43, 45, 91, 92, 130, 148], "copi": [8, 13, 18, 23, 28, 29, 43, 50, 79, 86, 106, 142, 186, 193, 210, 215, 228, 242, 245, 247], "semant": 8, "effect": [8, 119, 179, 215, 248, 254], "share": [8, 13, 18, 27, 37, 176, 179, 180, 237, 239], "without": [8, 27, 50, 52, 66, 69, 162, 179, 203, 205, 208, 209, 235, 239, 243], "expos": 8, "access": [8, 19, 52, 65, 67, 68, 84, 104, 118, 135, 143, 170, 179, 194, 199, 209, 246, 250], "amount": [8, 186, 208], "non": [8, 9, 24, 29, 63, 83, 96, 127, 170, 172, 174, 179, 242, 243, 246, 247], "trigger": [8, 105, 172], "detach": [8, 135, 160, 161, 210, 245], "op": 8, "count": [8, 13, 29], "1": [8, 13, 16, 18, 19, 20, 22, 23, 25, 27, 29, 52, 63, 66, 69, 83, 86, 96, 106, 119, 133, 135, 142, 143, 160, 161, 168, 170, 172, 174, 176, 177, 183, 184, 186, 188, 191, 192, 194, 201, 205, 210, 213, 222, 225, 235, 237, 239, 240, 241, 242, 247, 248, 249, 255, 256, 257, 258, 259], "perform": [8, 14, 16, 22, 43, 52, 64, 85, 96, 105, 135, 169, 171, 172, 179, 183, 189, 203, 208, 213, 237, 239, 241, 248, 259], "deep": [8, 232, 239], "greater": 8, "unnam": [8, 13, 18, 20, 29, 42, 62, 64, 65, 66, 67, 69, 70, 79, 86, 93, 96, 101, 105, 106, 117, 122, 123, 124, 128, 129, 135, 138, 139, 140, 141, 143, 158], "typedef": [8, 12, 13, 14, 17, 18, 22, 29, 34, 44, 45, 49, 62, 79, 86, 91, 92, 96, 141], "value_typ": [8, 45, 118, 135, 143, 160, 161], "compat": [8, 79, 179, 208], "allocator_typ": [8, 45, 160, 161], "const_refer": [8, 45, 160, 161], "const_point": [8, 45, 160, 161], "iter": [8, 14, 44, 45, 160, 161], "const_iter": [8, 44, 45, 160, 161], "reverse_iter": [8, 45, 160, 161], "const_reverse_iter": [8, 45, 160, 161], "difference_typ": [8, 45, 160, 161], "size_typ": [8, 45, 143, 160, 161], "intern": [8, 14, 40, 52, 62, 64, 66, 67, 79, 90, 140, 143, 160, 161, 168, 170, 173, 238], "arrayrefcontain": [8, 160, 161], "valuetyp": [8, 9, 10, 11, 14, 45, 160, 161], "inlin": [8, 9, 10, 11, 12, 16, 17, 19, 20, 21, 23, 25, 26, 28, 29, 34, 35, 38, 42, 43, 44, 45, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 69, 70, 71, 76, 78, 80, 81, 83, 84, 85, 86, 87, 88, 90, 91, 92, 93, 94, 95, 96, 97, 98, 101, 105, 106, 107, 108, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 143, 145, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159], "explicit": [8, 14, 26, 27, 33, 36, 39, 41, 42, 45, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 76, 78, 80, 83, 84, 85, 87, 88, 89, 90, 91, 92, 93, 96, 97, 99, 100, 101, 105, 123, 127, 128, 129, 134, 144], "size_t": [8, 13, 27, 29, 36, 44, 45, 52, 82, 96, 116, 117, 121, 125, 127, 128, 129, 135, 137, 141], "n": [8, 16, 20, 25, 27, 28, 38, 45, 127, 129, 174, 190, 191, 217], "valu": [8, 9, 10, 16, 19, 20, 22, 23, 25, 26, 28, 29, 34, 38, 39, 43, 44, 45, 49, 50, 52, 62, 66, 68, 78, 79, 82, 85, 86, 87, 93, 97, 99, 105, 118, 119, 122, 127, 129, 130, 132, 134, 135, 141, 143, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 160, 161, 168, 170, 171, 173, 174, 176, 208, 248], "inputiter": [8, 45], "last": [8, 23, 45, 63, 69, 83, 93, 207, 243], "note": [8, 25, 29, 63, 83, 119, 129, 135, 143, 167, 170, 174, 176, 177, 184, 186, 187, 188, 191, 199, 203, 205, 239, 241, 248, 252, 253, 259], "detachwithcopi": [8, 160, 161], "explicitli": [8, 167], "implicitli": 8, "ensur": [8, 22, 29, 63, 67, 83, 86, 96, 124, 133, 174, 208, 239, 242, 247], "retriev": [8, 16, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 68, 83, 107, 110, 111, 112, 113, 114, 115], "underli": [8, 19, 65, 84, 91, 92], "constdata": [8, 160, 161], "max_siz": [8, 160, 161], "capac": [8, 160, 161], "reserv": [8, 14, 28, 160, 161, 179], "sz": 8, "resiz": [8, 21, 52, 90, 105, 124, 160, 161, 166], "rbegin": [8, 160, 161], "rend": [8, 160, 161], "front": [8, 160, 161], "assign": [8, 27, 28, 29, 33, 41, 86, 96, 160, 161, 168, 237, 245, 246], "val": 8, "push_back": [8, 160, 161], "v": [8, 40, 42, 43, 44, 128, 129, 135, 177, 179, 194, 239, 247, 249, 257], "pop_back": [8, 160, 161], "eras": [8, 160, 161], "idx": [8, 68, 80], "othert": 8, "swap": [8, 27, 42, 80, 116, 117, 121, 122, 128, 129, 137, 140, 141, 160, 161, 165, 166], "swapandpop": [8, 160, 161], "index": [8, 12, 13, 14, 17, 18, 20, 21, 23, 25, 27, 29, 34, 38, 63, 68, 80, 83, 86, 87, 91, 92, 94, 95, 96, 99, 116, 118, 121, 125, 127, 128, 129, 132, 134, 135, 137, 143, 160, 161, 164, 165, 166, 172, 174, 177, 191, 247], "delet": [8, 50, 52, 70, 96, 105, 125, 127, 134, 158, 169, 183, 201, 206, 212, 222, 243, 245, 247, 252], "valid": [8, 16, 25, 26, 28, 38, 39, 49, 63, 69, 83, 86, 91, 92, 96, 105, 124, 129, 130, 134, 160, 161, 173, 174, 177, 239, 247], "pop": [8, 171, 189, 195, 197, 198, 208, 209, 211, 212, 232], "preserv": [8, 22, 27, 52, 96, 188], "protect": [8, 9, 14, 16, 19, 23, 29, 33, 34, 41, 49, 68, 80, 85, 89, 90, 93, 96, 97, 105, 122, 125, 127, 130, 134, 135, 140, 159, 179], "attribut": [8, 9, 14, 16, 19, 23, 29, 34, 62, 63, 69, 83, 85, 93, 96, 97, 117, 118, 122, 125, 127, 128, 129, 130, 134, 135, 140, 159, 174, 176, 180], "arrai": [9, 14, 19, 21, 22, 23, 27, 28, 29, 40, 52, 63, 83, 85, 86, 96, 116, 117, 118, 122, 124, 125, 128, 129, 135, 137, 140, 143, 160, 161, 168, 170, 173, 174, 177], "store": [9, 19, 21, 24, 25, 26, 29, 38, 39, 40, 43, 52, 63, 64, 65, 80, 81, 83, 96, 116, 117, 118, 119, 122, 128, 137, 143, 209, 247], "figur": [9, 74, 214, 254], "subclass": [9, 11, 16, 29, 46, 49, 67, 122, 127, 128, 129, 130, 132, 140, 142, 146], "coordinateset": [9, 160, 161], "istyp": [9, 160, 161], "match": [9, 24, 29, 40, 50, 63, 66, 68, 69, 79, 80, 81, 83, 118, 169, 174, 233, 239], "placehold": [9, 10, 64, 160, 161], "m_content": [9, 10, 160, 161], "m_data": [9, 19, 23, 29, 160, 161], "holder": [9, 11, 160, 161, 179], "type_info": [9, 10, 11], "clone": [9, 10, 11, 16, 25, 38, 160, 161], "atomtempl": [12, 94, 160, 161], "repres": [12, 13, 17, 18, 19, 22, 24, 27, 29, 34, 40, 43, 50, 64, 65, 67, 68, 84, 96, 122, 132, 162, 172, 199, 235, 237], "moleculeclass": [12, 17], "atomtyp": [12, 18, 29, 33, 41, 86, 91, 96, 160, 161, 165], "molecule_t": [13, 18, 91, 92], "setatomicnumb": [13, 29, 96, 160, 161, 165], "unsign": [13, 15, 16, 18, 22, 23, 24, 25, 28, 29, 38, 40, 43, 45, 62, 66, 69, 85, 86, 96, 101, 106, 108, 128, 129, 135, 140, 141, 142, 143, 160, 161], "num": [13, 25, 29, 96, 172], "proton": [13, 73, 232, 248, 256], "atom": [13, 14, 16, 18, 20, 22, 24, 25, 29, 33, 34, 38, 40, 41, 63, 75, 82, 83, 86, 91, 96, 97, 108, 132, 139, 160, 161, 162, 165, 166, 170, 171, 172, 174, 181, 182, 183, 184, 186, 189, 198, 200, 201, 204, 206, 210, 211, 212, 213, 214, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 229, 230, 232, 234, 235, 237, 242, 243, 245, 246, 247, 251, 257, 259], "atomicnumb": [13, 24, 29, 86, 96, 160, 161, 165], "setposition2d": [13, 160, 161], "vector2": [13, 29, 96], "po": [13, 23, 29, 85, 96, 120, 136], "2d": [13, 29, 212, 242], "Not": 13, "current": [13, 14, 18, 27, 28, 29, 49, 52, 56, 62, 64, 65, 66, 69, 75, 76, 85, 88, 90, 96, 101, 104, 106, 116, 117, 119, 121, 122, 123, 124, 128, 129, 130, 133, 134, 135, 137, 140, 142, 167, 169, 186, 199, 209, 211, 212, 213, 224, 236, 237, 238, 251], "moleculetyp": [13, 18, 91, 92, 160, 161, 165], "compil": [13, 134, 135, 160, 166, 239], "position2d": [13, 160, 161], "setposition3d": [13, 160, 161], "vector3": [13, 22, 23, 26, 29, 39, 40, 42, 82, 86, 96], "3d": [13, 23, 29, 96, 105, 119, 128, 129, 135, 162, 170, 172, 193, 203, 212, 237, 246, 256], "position3d": [13, 29, 86, 96, 160, 161], "sethybrid": [13, 29, 96, 160, 161, 165], "atomhybrid": [13, 29, 96], "hyb": [13, 29, 96], "hybrid": [13, 29, 96, 160, 161, 165, 251, 256], "coordin": [13, 20, 21, 22, 25, 29, 40, 42, 63, 83, 96, 108, 117, 119, 124, 135, 138, 139, 143, 160, 161, 163, 183, 184, 187, 188, 206, 228, 242, 243, 247, 250], "setformalcharg": [13, 29, 96, 160, 161, 165], "sign": [13, 29, 96, 135, 239, 245], "charg": [13, 29, 63, 83, 96, 174, 175, 176, 208, 217, 228, 232, 237, 243, 245, 246, 247, 248, 259], "formal": [13, 29, 96, 228, 245, 247], "formalcharg": [13, 29, 96, 160, 161, 165], "setcolor": [13, 28, 29, 34, 96, 128, 129, 132, 160, 161, 165, 166], "vector3ub": [13, 29, 34, 96, 116, 120, 121, 128, 129, 131, 132, 135, 136, 137, 141, 145], "color": [13, 19, 24, 28, 29, 34, 63, 83, 96, 116, 121, 128, 129, 132, 133, 137, 141, 143, 158, 160, 161, 165, 166, 174, 175, 177, 181, 186, 199, 208, 210, 232, 237, 242, 243, 245, 246, 247], "setlay": [13, 29, 96, 160, 161, 165], "layer": [13, 29, 86, 96, 160, 161, 165, 243, 244, 245, 246, 247], "invalid": [13, 18, 29, 40, 49, 69, 86, 91, 92, 96, 132, 160, 166, 243], "object": [13, 14, 18, 19, 25, 28, 29, 43, 44, 50, 52, 62, 63, 64, 65, 68, 69, 73, 76, 79, 83, 84, 85, 86, 91, 92, 96, 101, 104, 105, 106, 108, 116, 117, 118, 119, 121, 122, 124, 125, 128, 129, 132, 135, 137, 142, 146, 159, 165, 168, 169, 170, 173, 174, 198, 214, 242], "increment": [13, 18], "self": [13, 18, 246], "check": [13, 16, 18, 22, 26, 28, 29, 39, 40, 49, 63, 69, 76, 83, 86, 93, 96, 105, 124, 127, 171, 172, 176, 177, 201, 212, 214, 219, 221, 222, 226, 242, 246, 247, 253, 254, 259], "postfix": [13, 18], "decrement": [13, 18], "setselect": [13, 160, 161], "select": [13, 29, 66, 69, 79, 86, 90, 96, 160, 161, 165, 177, 181, 182, 183, 186, 189, 190, 191, 192, 193, 194, 195, 197, 199, 201, 202, 203, 206, 209, 210, 212, 214, 215, 217, 218, 220, 221, 222, 223, 224, 225, 228, 230, 232, 233, 234, 242, 243, 244, 245, 246, 247, 248], "setforcevector": [13, 29, 96, 160, 161, 165], "forc": [13, 29, 86, 96, 140, 162, 175, 176, 191, 200, 210, 214, 216, 217, 228, 234, 239, 247, 253, 255, 256, 257, 259], "forcevector": [13, 29, 96, 160, 161, 165], "setlabel": [13, 29, 96, 160, 161, 165], "outputtyp": 14, "interfac": [14, 15, 24, 40, 62, 63, 65, 76, 83, 84, 85, 93, 97, 101, 142, 162, 169, 171, 172, 174, 181, 203, 205, 208, 215, 219, 246, 247], "list": [14, 22, 29, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67, 68, 69, 76, 79, 80, 103, 105, 107, 110, 111, 112, 113, 114, 115, 125, 127, 168, 169, 170, 171, 172, 174, 176, 179, 208, 209, 228, 239, 242, 246, 256], "identifi": [14, 16, 24, 29, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 69, 83, 86, 91, 92, 102, 107, 110, 111, 112, 113, 114, 115, 116, 120, 121, 122, 124, 125, 132, 135, 136, 137, 143, 160, 163, 165, 166, 174], "mol": [14, 15, 20, 22, 23, 26, 33, 34, 39, 40, 41, 57, 59, 62, 63, 64, 65, 70, 72, 76, 83, 96, 101, 168, 169, 170, 172, 208, 252, 257], "nullptr": [14, 26, 29, 33, 36, 39, 41, 50, 52, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 76, 78, 79, 80, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 96, 97, 99, 100, 101, 102, 103, 104, 105, 122, 123, 125, 127, 130, 144, 158, 243], "setmolecul": [14, 16, 20, 36, 64, 65, 70, 76, 101, 105, 158, 160, 161, 164, 165, 178], "obtain": [14, 29, 32, 37, 68, 82, 86, 91, 92, 96, 129, 172], "lookup": [14, 50, 246], "been": [14, 29, 50, 52, 67, 69, 76, 96, 97, 133, 135, 172, 179, 186, 189, 198, 199, 201, 208, 209, 212, 217, 219, 222, 225, 232, 233, 234, 237, 239, 250, 256], "previous": [14, 208, 209, 212, 225], "cach": [14, 52, 63, 67, 83, 93, 176, 246, 247], "There": [14, 63, 82, 83, 174, 192, 193, 194, 212, 238, 239], "correspond": [14, 16, 25, 29, 62, 63, 83, 96, 174, 176, 177, 179, 183, 215, 219, 248], "reset": [14, 49, 52, 63, 83, 91, 92, 93, 97, 105, 119, 124, 158, 160, 161, 164, 165, 186, 210, 220, 224, 225, 226, 242, 243], "typer": 14, "state": [14, 49, 52, 62, 63, 66, 69, 83, 91, 92, 96, 97, 126, 159, 177, 179, 243], "m_type": [14, 134, 160, 161, 166], "initi": [14, 24, 25, 27, 38, 63, 66, 69, 79, 83, 85, 86, 96, 105, 124, 160, 161, 165, 166, 176, 177, 201, 203, 206, 222, 226, 230, 231, 242, 244, 245, 246, 247], "setup": [14, 62, 170, 210, 215, 245], "prior": [14, 62, 179], "enough": [14, 52], "room": 14, "determin": [14, 33, 41, 50, 52, 62, 63, 83, 118, 126, 176, 188, 189, 191, 208, 221, 225, 228, 231, 232, 247], "m_molecul": [14, 16, 96, 160, 161, 165], "popul": [14, 16, 22, 26, 52, 96], "spglib": [15, 40, 96, 184, 242], "short": [15, 29, 40, 43, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 93, 96, 107, 110, 111, 112, 113, 114, 115, 143, 160, 161], "gethallnumb": [15, 160, 161], "carttol": [15, 40, 96], "1e": [15, 40, 96], "hall": [15, 40, 96], "crystal": [15, 40, 42, 181, 185, 189, 199, 206, 208, 210, 237, 243, 247], "unit": [15, 20, 22, 24, 29, 40, 42, 63, 83, 96, 174, 177, 181, 182, 185, 188, 189, 191, 194, 210, 212, 243, 247, 254], "cell": [15, 20, 22, 29, 40, 42, 96, 174, 181, 182, 185, 186, 189, 191, 194, 210, 212, 243, 247, 254], "exist": [15, 23, 27, 29, 44, 52, 66, 68, 86, 96, 103, 127, 135, 169, 173, 174, 219, 235, 243], "algorithm": [15, 22, 85, 96, 187, 208, 213], "fail": [15, 43, 52, 63, 66, 67, 83, 96, 128, 129, 170, 174, 179], "succe": 15, "handl": [15, 22, 49, 50, 64, 69, 76, 79, 89, 90, 93, 101, 105, 118, 134, 143, 160, 163, 164, 165, 166, 168, 169, 170, 173, 237, 242, 247], "cartesian": [15, 20, 22, 25, 38, 40, 42, 96, 170, 174, 183, 184, 187, 188, 199, 210], "toler": [15, 29, 40, 96, 184, 187, 246], "reducetoprimit": [15, 160, 161], "reduc": [15, 22, 40, 96, 179, 181, 185], "primit": [15, 25, 38, 96, 97, 116, 120, 121, 122, 124, 125, 133, 136, 137, 160, 166, 181, 185], "unless": [15, 19, 179], "miss": [15, 235, 243, 246], "conventionalizecel": [15, 96, 160, 161, 165], "refin": [15, 217], "convention": [15, 96], "symmetr": [15, 96, 160, 161, 188, 237], "basi": [16, 25, 26, 29, 38, 39, 63, 83, 108, 109, 174, 179, 208, 247], "gaussianset": [16, 26, 38, 39, 109, 160, 161], "slaterset": [16, 160, 161], "capabl": [16, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 96, 107, 110, 111, 112, 113, 114, 115, 116, 137, 173, 174, 206, 209, 217], "calcul": [16, 25, 26, 28, 29, 38, 39, 63, 64, 65, 69, 83, 85, 106, 119, 142, 164, 174, 182, 183, 184, 186, 189, 191, 210, 215, 217, 225, 228, 231, 232, 234, 237, 246, 248, 250, 259], "electrontyp": [16, 25, 26, 38, 160, 161], "electron": [16, 24, 25, 26, 29, 39, 208, 231, 232, 246], "pair": [16, 25, 26, 27, 28, 29, 35, 38, 63, 83, 86, 96, 117, 160, 161, 174, 176, 177, 208, 231, 237, 246], "alpha": [16, 25, 26, 42, 141, 143, 160, 161, 166, 170, 242, 246], "beta": [16, 25, 26, 42, 160, 161, 170, 235, 236], "cannot": [16, 22, 30, 31, 50, 52, 69, 157, 179, 237], "enumer": [16, 20, 22, 23, 25, 34, 38, 43, 49, 52, 62, 66, 68, 78, 79, 82, 86, 97, 118, 127, 132, 134, 135, 141, 143, 148, 149, 150, 151, 152, 153, 154, 155, 156, 172], "destructor": [16, 25, 28, 38, 52, 85], "setelectroncount": [16, 160, 161], "electroncount": [16, 160, 161], "molecule_": 16, "get": [16, 23, 25, 29, 40, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 76, 83, 85, 86, 88, 91, 92, 96, 103, 104, 105, 107, 110, 111, 112, 113, 114, 115, 116, 118, 119, 121, 122, 124, 125, 126, 127, 129, 130, 133, 134, 135, 137, 158, 159, 162, 168, 170, 172, 181, 238, 239, 242, 256], "belong": [16, 68, 86, 91, 92], "setnam": [16, 23, 28, 160, 161], "settheorynam": [16, 160, 161], "theorynam": [16, 160, 161], "molecularorbitalcount": [16, 25, 38, 160, 161], "molecular": [16, 25, 26, 29, 38, 39, 63, 83, 105, 162, 167, 168, 169, 170, 171, 172, 174, 181, 193, 195, 196, 199, 203, 210, 212, 214, 219, 228, 229, 231, 235, 237, 238, 246, 247, 250, 251, 256], "orbit": [16, 25, 26, 38, 39, 108, 160, 161, 162, 181, 199, 210, 229, 237, 243, 255, 258], "homo": [16, 160, 161], "given": [16, 23, 24, 25, 27, 29, 40, 43, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 65, 68, 79, 84, 86, 96, 105, 107, 110, 111, 112, 113, 114, 115, 168, 171], "mo": [16, 23, 25, 26, 38, 160, 161, 247], "lumo": [16, 160, 161], "m_electron": [16, 160, 161], "total": [16, 29, 62, 228, 247], "close": [16, 49, 52, 65, 71, 160, 163, 179, 210, 214, 232, 233, 243, 245, 246, 254], "shell": [16, 25, 38, 108, 160, 163], "doubli": 16, "occupi": [16, 52], "hold": [16, 85, 108, 172, 193, 197, 203, 204, 219, 227], "possibli": 16, "bond": [16, 18, 29, 34, 63, 82, 83, 86, 92, 96, 132, 160, 161, 162, 165, 166, 172, 174, 181, 183, 189, 191, 200, 201, 204, 206, 208, 212, 213, 217, 219, 222, 223, 224, 225, 227, 228, 231, 244, 245, 246, 247, 253, 254, 255, 256, 257, 258, 259], "read": [16, 29, 37, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 70, 76, 79, 83, 107, 110, 111, 112, 113, 114, 115, 160, 163, 165, 170, 172, 174, 176, 179, 196, 206, 231, 242, 243, 244, 245, 247], "output": [16, 20, 22, 25, 30, 31, 38, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 66, 69, 83, 93, 107, 108, 110, 111, 112, 113, 114, 115, 157, 163, 164, 168, 169, 170, 173, 174, 207, 214, 217, 231, 233, 234, 246, 247], "necessarili": 16, "m_name": [16, 23, 160, 161], "usual": [16, 172, 239], "standard": [16, 63, 71, 83, 91, 92, 93, 96, 118, 135, 159, 167, 168, 169, 170, 172, 173, 174, 179, 199, 209, 243, 247], "m_theorynam": [16, 160, 161], "theori": [16, 63, 83, 174, 179, 200, 210, 247, 251], "bondtempl": [17, 95, 160, 161], "bondtyp": [17, 29, 86, 92, 96, 160, 161, 165], "atom1": [18, 29, 86, 96, 160, 161], "atom2": [18, 29, 86, 96, 160, 161], "setord": [18, 160, 161], "o": [18, 93, 119, 127, 137, 159, 168, 201, 207, 217, 222, 239, 259], "getotheratom": [18, 160, 161], "represent": [19, 22, 42, 63, 83, 135, 173, 174, 179, 199, 207], "rgb": [19, 63, 83, 141, 174], "three": [19, 24, 25, 38, 128, 129, 143, 199, 206, 225, 228], "float": [19, 23, 28, 43, 85, 116, 119, 120, 121, 122, 124, 125, 126, 128, 131, 133, 135, 136, 137, 139, 140, 141, 143, 145, 160, 161, 168, 170, 172, 246], "rang": [19, 22, 63, 83, 125, 127, 129, 135, 141, 143, 168, 170, 174, 177, 208, 228, 237, 246, 256], "intens": [19, 29, 246], "red": [19, 141, 143, 160, 161, 166, 199, 218, 232, 237], "green": [19, 141, 143, 160, 161, 166, 199, 218], "memori": [19, 25, 52, 96, 135, 245], "3": [19, 28, 63, 83, 85, 128, 129, 135, 141, 143, 160, 161, 168, 170, 177, 183, 187, 191, 201, 210, 213, 214, 222, 239, 242, 248, 249, 256, 257, 258], "pass": [19, 23, 28, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 69, 76, 83, 84, 85, 93, 101, 105, 107, 110, 111, 112, 113, 114, 115, 122, 123, 135, 167, 169, 174, 243, 246], "directli": [19, 50, 68, 168, 179, 190, 192, 196, 231], "opengl": [19, 124, 133, 162, 239, 245, 246, 247], "conveni": [19, 29, 44, 49, 50, 52, 67, 68, 86, 162, 206, 211, 247], "written": [19, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 65, 83, 85, 107, 110, 111, 112, 113, 114, 115, 169, 174, 177, 179, 232], "emphasi": 19, "effici": [19, 211, 243], "layout": [19, 66, 88], "black": [19, 133, 201, 204, 222, 226, 227], "integ": [19, 23, 28, 143, 174], "255": [19, 63, 83, 135, 141, 174], "expect": [19, 24, 25, 28, 63, 83, 85, 104, 169, 170, 174, 179, 239, 247], "align": [20, 22, 133, 141, 174, 181, 182, 183, 186, 191, 192, 210, 223, 247], "see": [20, 29, 52, 63, 65, 79, 83, 86, 96, 106, 135, 143, 162, 169, 173, 174, 184, 187, 188, 191, 192, 208, 231, 256], "setspecif": [20, 160, 161], "detail": [20, 22, 49, 52, 62, 63, 65, 66, 73, 83, 162, 168, 169, 170, 171, 173, 174, 208], "distanceunit": [20, 160, 161], "distanc": [20, 40, 42, 119, 139, 160, 161, 166, 182, 183, 208, 214, 225, 246, 247, 254], "angstrom": [20, 22, 42, 160, 161, 191, 206, 214], "bohr": [20, 160, 161, 191, 206], "setdistanceunit": [20, 160, 161], "spec": 20, "inform": [20, 25, 29, 40, 63, 83, 96, 105, 124, 135, 169, 174, 176, 179, 188, 198, 199, 204, 206, 208, 210, 211, 214, 217, 219, 224, 227, 238, 245], "z": [20, 23, 29, 170, 174, 182, 186, 191, 192, 199, 206, 208, 212, 218, 220, 242], "6": [20, 22, 28, 63, 75, 83, 85, 124, 159, 160, 161, 168, 170, 172, 174, 191, 214, 239, 247, 251, 257], "carbon": [20, 24, 29, 75, 171, 172, 174, 176, 181, 186, 206, 221, 223, 226, 228, 250, 256, 257, 258], "l": [20, 120, 179, 239, 247], "c1": [20, 247], "gamess": [20, 108, 174, 208, 246, 247], "lattic": [20, 22, 42, 96, 174, 187, 188], "requir": [20, 25, 50, 63, 66, 83, 124, 143, 159, 168, 169, 172, 173, 174, 176, 179, 215, 233, 235, 257], "A": [20, 22, 25, 27, 29, 32, 37, 42, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 71, 76, 79, 80, 82, 83, 86, 87, 88, 91, 92, 93, 96, 97, 99, 100, 101, 103, 105, 107, 110, 111, 112, 113, 114, 115, 116, 123, 125, 127, 133, 134, 135, 137, 143, 162, 169, 174, 177, 179, 180, 183, 189, 190, 192, 194, 195, 197, 201, 206, 208, 212, 213, 221, 222, 226, 232, 233, 237, 239, 250, 256], "liter": [20, 63, 83, 174], "optim": [20, 29, 63, 83, 170, 174, 177, 181, 183, 191, 201, 210, 217, 222, 228, 237, 245, 246, 247, 248, 249, 251, 252, 253, 254, 255, 257, 258, 259], "flag": [20, 22, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 66, 68, 79, 83, 87, 99, 107, 110, 111, 112, 113, 114, 115, 141, 160, 164, 165, 169, 171, 174], "_": [20, 174], "__szxyz110": [20, 174], "replac": [20, 29, 80, 96, 169, 171, 172, 174, 179, 206, 239, 243], "text": [20, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 65, 80, 81, 96, 106, 107, 110, 111, 112, 113, 114, 115, 123, 124, 131, 138, 139, 140, 141, 142, 145, 160, 166, 168, 170, 171, 173, 174, 179, 183, 193, 194, 206, 207, 247, 250], "126214": [20, 174], "765886": [20, 174], "000000": [20, 174], "819345": [20, 174], "564955": [20, 174], "598383": [20, 174], "795127": [20, 174], "310706": [20, 174], "370165": [20, 174], "16": [20, 85, 174, 243], "285330": [20, 174], "757144": [20, 174], "130424": [20, 174], "185837": [20, 174], "548377": [20, 174], "375303": [20, 174], "033768": [20, 174], "794407": [20, 174], "396173": [20, 174], "450760": [20, 174], "generatecoordinateblock": [20, 160, 161], "arrayset": [21, 160, 161], "concret": 21, "_size": 21, "_index": 21, "collect": [22, 62, 63, 65, 66, 83, 105, 116, 121, 122, 125, 133, 137, 162, 172, 174, 179], "common": [22, 49, 63, 83, 122, 125, 127, 130, 146, 168, 169, 174, 180, 197, 208, 217, 228, 237], "crystallograph": [22, 184], "option": [22, 49, 50, 52, 62, 64, 65, 66, 69, 73, 74, 76, 84, 93, 96, 101, 116, 135, 137, 141, 143, 160, 161, 163, 164, 165, 167, 168, 170, 171, 172, 173, 177, 183, 186, 191, 208, 210, 216, 218, 219, 232, 236, 237, 243], "bitwis": [22, 50, 66, 141], "variou": [22, 25, 38, 63, 83, 169, 174, 198, 199, 208, 209, 211, 232, 234, 237, 238, 239, 245], "none": [22, 23, 25, 29, 40, 49, 50, 62, 79, 103, 127, 134, 135, 160, 161, 163, 164, 166, 210, 228, 245], "transformatom": [22, 96, 160, 161], "transform": [22, 40, 96, 119, 144, 179], "along": [22, 46, 47, 48, 49, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 71, 73, 74, 96, 107, 110, 111, 112, 113, 114, 115, 162, 168, 170, 173, 186, 191, 203], "wrapatomstounitcel": [22, 160, 161], "adjust": [22, 42, 82, 96, 160, 165, 188, 198, 199, 201, 206, 208, 212, 214, 219, 220, 222, 223, 224, 233, 234, 242, 247, 251], "fraction": [22, 40, 42, 96, 188, 206], "success": [22, 25, 26, 28, 29, 32, 37, 38, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 66, 69, 70, 83, 86, 96, 107, 110, 111, 112, 113, 114, 115, 135, 160, 165, 170], "rotatetostandardorient": [22, 160, 161], "opt": [22, 62, 96, 143, 171, 172], "rotat": [22, 96, 119, 141, 160, 166, 181, 182, 186, 190, 203, 213, 218, 221, 224, 226, 237, 242, 247, 250, 254], "axi": [22, 29, 119, 121, 133, 182, 183, 186, 191, 212, 218], "xy": [22, 38, 160, 161, 182, 186, 191], "plane": [22, 29, 119, 138, 182, 186, 191, 212, 217, 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"markovnikov": 257, "hybrid": 258, "water": 259}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"Class Avogadro::Core::Elements": [[24, "class-avogadro-core-elements"]], "Class Avogadro::Core::Bond": [[17, "class-avogadro-core-bond"]], "Contributing Code": [[0, "contributing-code"], [0, null]], "Documenting Code": [[1, "documenting-code"]], "Class Descriptions": [[1, "class-descriptions"]], "Function Descriptions": [[1, "function-descriptions"]], "Class Avogadro::Core::CoordinateBlockGenerator": [[20, "class-avogadro-core-coordinateblockgenerator"]], "Class Avogadro::Core::ArraySet::PlaceHolder": [[11, "class-avogadro-core-arrayset-placeholder"]], "Class Avogadro::Core::Atom": [[12, "class-avogadro-core-atom"]], "Class Avogadro::Core::AtomTyper": [[14, "class-avogadro-core-atomtyper"]], "Class Avogadro::Core::ArraySet::Holder": [[10, "class-avogadro-core-arrayset-holder"]], "Class Avogadro::Core::CrystalTools": [[22, "class-avogadro-core-crystaltools"]], "Coding Style (C++)": [[6, "coding-style-c"]], "Indentation": [[6, "indentation"]], "Line Width": [[6, "line-width"]], "Declaring Variables": [[6, "declaring-variables"]], "Whitespace": [[6, "whitespace"]], "Braces": [[6, "braces"]], "Parentheses": [[6, "parentheses"]], "Switch Statements": [[6, "switch-statements"]], "Line Breaks": [[6, "line-breaks"]], "Inheritance and the \u201cvirtual\u201d Keyword": [[6, "inheritance-and-the-virtual-keyword"]], "Referencing Members": [[6, "referencing-members"]], "File Naming": [[6, "file-naming"]], "Breaking Rules": [[6, "breaking-rules"]], "Class Avogadro::Core::ArraySet": [[9, "class-avogadro-core-arrayset"]], "Class Avogadro::Core::Array": [[8, "class-avogadro-core-array"]], "Class Avogadro::Core::AvoSpglib": [[15, "class-avogadro-core-avospglib"]], "Coding Conventions (C++)": [[3, "coding-conventions-c"]], "C++ Features": [[3, "c-features"]], "Including Headers": [[3, "including-headers"]], "Export Macro Headers": [[3, "export-macro-headers"]], "Private Headers": [[3, "private-headers"]], "Qt Headers": [[3, "qt-headers"]], "Namespaces": [[3, "namespaces"]], "Casting": [[3, "casting"]], "Aesthetics": [[3, "aesthetics"]], "Class Avogadro::Core::BondTemplate": [[18, "class-avogadro-core-bondtemplate"]], "Class Avogadro::Core::CoordinateSet": [[21, "class-avogadro-core-coordinateset"]], "Class Avogadro::Core::AtomTemplate": [[13, "class-avogadro-core-atomtemplate"]], "Class Avogadro::Core::Color3f": [[19, "class-avogadro-core-color3f"]], "Class Avogadro::Core::BasisSet": [[16, "class-avogadro-core-basisset"]], "Class Avogadro::Core::Cube": [[23, "class-avogadro-core-cube"]], "Thanks": [[4, "thanks"], [205, "thanks"]], "Creators": [[4, "creators"]], "Contributors to Avogadro v2": [[4, "contributors-to-avogadro-v2"]], "Contributors to Avogadro v1": [[4, "contributors-to-avogadro-v1"]], "Avogadro Translators": [[4, "avogadro-translators"]], "Funding": [[4, "funding"]], "Other Projects": [[4, "other-projects"]], "Translations": [[7, "translations"]], "Current Status": [[7, "current-status"]], "Credits": [[7, "credits"], [244, "credits"], [247, "credits"], [242, "credits"], [243, "credits"], [246, "credits"], [245, "credits"]], "Contribute": [[5, "contribute"]], "How to Help": [[5, "how-to-help"]], "Teach": [[256, "teach"]], "Publications": [[256, "publications"]], "Activities": [[256, "activities"]], "General Chemistry": [[256, "general-chemistry"]], "Organic Chemistry": [[256, "organic-chemistry"]], "Biochemistry:": [[256, "biochemistry"]], "Organic Hybridization": [[258, "organic-hybridization"]], "Task": [[258, "task"], [254, "task"], [259, "task"], [257, "task"], [253, "task"], [251, "task"], [255, "task"], [249, "task"]], "Solution": [[258, "solution"], [254, "solution"], [259, "solution"], [257, "solution"], [252, "solution"], [255, "solution"], [248, "solution"]], "See also": [[258, "see-also"], [254, "see-also"], [259, "see-also"], [257, "see-also"], [253, "see-also"], [251, "see-also"], [255, "see-also"], [249, "see-also"]], "Further reading": [[258, "further-reading"], [257, "further-reading"], [251, "further-reading"], [248, "further-reading"]], "Hydrogen Clusters": [[254, "hydrogen-clusters"]], "Issues": [[254, "issues"]], "Sources": [[254, "sources"], [259, "sources"], [255, "sources"]], "Water": [[259, "water"]], "Markovnikov\u2019s Rule": [[257, "markovnikovs-rule"]], "HCN dipole": [[253, "hcn-dipole"]], "1,3-diaxial interactions": [[252, "diaxial-interactions"]], "Tasks": [[252, "tasks"], [248, "tasks"]], "Educational Publications Using Avogadro": [[250, "educational-publications-using-avogadro"]], "Yes We Chem": [[250, "yes-we-chem"]], "Computational Chemistry": [[250, "computational-chemistry"]], "Spectra / Spectroscopy": [[250, "spectra-spectroscopy"]], "Chemical Reactions and Mechanisms": [[250, "chemical-reactions-and-mechanisms"]], "Materials / Nano": [[250, "materials-nano"]], "Cheminformatics": [[250, "cheminformatics"]], "3D Printing and VR": [[250, "d-printing-and-vr"]], "Remote Teaching": [[250, "remote-teaching"]], "Basic VSEPR": [[251, "basic-vsepr"]], "Hydrogen Molecule": [[255, "hydrogen-molecule"]], "Class Avogadro::Io::MMTFFormat": [[55, "class-avogadro-io-mmtfformat"]], "Class Avogadro::MoleQueue::MoleQueueDialog": [[66, "class-avogadro-molequeue-molequeuedialog"]], "Class Avogadro::Io::GromacsFormat": [[51, "class-avogadro-io-gromacsformat"]], "Class Avogadro::MoleQueue::InputGeneratorDialog": [[64, "class-avogadro-molequeue-inputgeneratordialog"]], "Class Avogadro::QtGui::BackgroundFileFormat": [[70, "class-avogadro-qtgui-backgroundfileformat"]], "Class Avogadro::Io::PdbFormat": [[58, "class-avogadro-io-pdbformat"]], "Class 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Repositories": [[239, "cloning-repositories"]], "Updating": [[239, "updating"]], "Prerequisites": [[239, "prerequisites"]], "Debian-based Distribution or Ubuntu": [[239, "debian-based-distribution-or-ubuntu"]], "Building": [[239, "building"]], "Finding Qt, Windows Generators": [[239, "finding-qt-windows-generators"]], "Normal Development": [[239, "normal-development"]], "Build Tree Layout": [[239, "build-tree-layout"]], "Running Executables": [[239, "running-executables"]], "Building Packages": [[239, "building-packages"]], "Tutorials": [[229, "tutorials"], [229, null]], "Viewing Vibrations": [[234, "viewing-vibrations"]], "Major New Features": [[237, "major-new-features"]], "Speed and Stability": [[237, "speed-and-stability"]], "Rendering": [[237, "rendering"]], "New real-time shadows and depth effects": [[237, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[237, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[237, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[237, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[237, "layers"]], "Symmetry Properties": [[237, "symmetry-properties"]], "Template Tool": [[237, "template-tool"], [228, "template-tool"]], "Solvent Accessible and Solvent Excluded Surfaces": [[237, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[237, "flexible-electrostatics-models"]], "New Analysis Tools": [[237, "new-analysis-tools"]], "Python Commands / Plugins": [[237, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[237, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[237, "new-and-updated-interfaces-to-external-programs"]], "Release Notes v1.95.1": [[244, "release-notes-v1-95-1"]], "\ud83d\udc1b Bug Fixes": [[244, "bug-fixes"], [247, "bug-fixes"], [242, "bug-fixes"], [243, "bug-fixes"], [246, "bug-fixes"], [245, "bug-fixes"]], "\u2728 Features": [[244, "features"], [247, "features"], [243, "features"], [246, "features"], [245, "features"]], "\ud83e\uddf0 Maintenance": [[244, "maintenance"], [247, "maintenance"], [242, "maintenance"], [243, "maintenance"], [246, "maintenance"], [245, "maintenance"]], "\ud83d\udcda Translations": [[244, "translations"], [247, "translations"], [243, "translations"], [246, "translations"], [245, "translations"]], "Release Notes v1.98.0": [[247, "release-notes-v1-98-0"]], "\ud83c\udf1f Highlights (tldr)": [[247, "highlights-tldr"]], "\ud83d\ude80 Performance Improvements": [[247, "performance-improvements"], [246, "performance-improvements"]], "Interface Changes": [[236, "interface-changes"]], "Input Generators": [[236, "input-generators"], [174, "input-generators"]], "Acid-Base Properties of Amino Acids": [[248, "acid-base-properties-of-amino-acids"]], "Using QTAIM (Atoms in Molecules) Analysis": [[231, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[231, "start-with-a-wfn-file"]], "Install": [[240, "install"], [238, "install"]], "Version History": [[241, "version-history"], [241, null]], "Release Notes v1.94.0": [[242, "release-notes-v1-94-0"]], "Features": [[242, "features"], [238, "features"]], "\ud83d\udc0d Python Improvements": [[242, "python-improvements"]], "Viewing Electrostatic Potential Maps": [[232, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[232, "changing-surface-settings"]], "Resources": [[238, "resources"]], "Connecting with the Avogadro community": [[238, "connecting-with-the-avogadro-community"]], "Navigate Tool": [[226, "navigate-tool"]], "Release Notes v1.95.0": [[243, "release-notes-v1-95-0"]], "Changes": [[243, "changes"], [245, "changes"]], "Release Notes v1.97.0": [[246, "release-notes-v1-97-0"]], "Highlights (tldr)": [[246, "highlights-tldr"]], "Inserting Atoms with Specific Geometry": [[228, "inserting-atoms-with-specific-geometry"]], "Attaching Ligands": [[228, "attaching-ligands"]], "Attaching Functional Groups": [[228, "attaching-functional-groups"]], "Creating New Ligands": [[228, "creating-new-ligands"]], "Creating New Haptic Ligands": [[228, "creating-new-haptic-ligands"]], "Alkene Isomers": [[249, "alkene-isomers"]], "Release Notes v1.96.0": [[245, "release-notes-v1-96-0"]], "\ud83d\ude80 Performance Fixes": [[245, "performance-fixes"]], "What\u2019s New in Avogadro 2": [[235, "whats-new-in-avogadro-2"]], "Viewing Molecular Orbitals": [[233, "viewing-molecular-orbitals"]], "Configure": [[233, "configure"]], "Selection Tool": [[227, "selection-tool"]], "User Guide": [[205, "user-guide"]], "Avogadro: Molecular Editor and Visualization": [[205, "avogadro-molecular-editor-and-visualization"], [180, "avogadro-molecular-editor-and-visualization"]], "Avogadro 2": [[205, "avogadro-2"]], "Select Menu": [[211, "select-menu"]], "Select All": [[211, "select-all"], [207, "select-all"]], "Select None": [[211, "select-none"], [207, "select-none"]], "Invert Selection": [[211, "invert-selection"]], "Select SMARTS\u2026": [[211, "select-smarts"]], "Select by Element\u2026": [[211, "select-by-element"]], "Select by Residue\u2026": [[211, "select-by-residue"]], "Select Solvent": [[211, "select-solvent"]], "Add Name Selection\u2026": [[211, "add-name-selection"]], "Enabling additional force fields": [[215, "enabling-additional-force-fields"]], "Creating an avogadro conda environment": [[215, "creating-an-avogadro-conda-environment"]], "Setting the Python path": [[215, "setting-the-python-path"]], "Geometry Constraints": [[214, "geometry-constraints"]], "Constraints": [[214, "constraints"], [208, "constraints"]], "Example": [[214, "example"]], "Optimizations": [[214, "optimizations"]], "Example cont.": [[214, "example-cont"]], "Drawing Molecules": [[201, "drawing-molecules"]], "Creating Carbon Dioxide": [[201, "creating-carbon-dioxide"], [222, "creating-carbon-dioxide"]], "Making Selections": [[204, "making-selections"]], "Getting Started": [[202, "getting-started"]], "Manipulate Tool": [[224, "manipulate-tool"]], "Tools": [[223, "tools"], [223, null]], "Bond-Centric Manipulate Tool": [[221, "bond-centric-manipulate-tool"]], "Starting with the basics:": [[221, "starting-with-the-basics"]], "Adjusting Bonds and Torsion Angles": [[221, "adjusting-bonds-and-torsion-angles"]], "Finding Conformers of Molecules": [[213, "finding-conformers-of-molecules"]], "Start with your molecule of interest": [[213, "start-with-your-molecule-of-interest"]], "Optimize the geometry": [[213, "optimize-the-geometry"]], "Change the force field options": [[213, "change-the-force-field-options"]], "Set the conformer search options": [[213, "set-the-conformer-search-options"]], "Pick a search method and start the search": [[213, "pick-a-search-method-and-start-the-search"]], "Build Menu": [[206, "build-menu"]], "Cartesian Editor\u2026": [[206, "cartesian-editor"]], "1. Sort by\u2026": [[206, "sort-by"]], "2. Unit of Measure": [[206, "unit-of-measure"]], "3. Editing & Modifying Data": [[206, "editing-modifying-data"]], "Change H to Methyl": [[206, "change-h-to-methyl"]], "Add Hydrogens": [[206, "add-hydrogens"]], "Add Hydrogens for pH\u2026": [[206, "add-hydrogens-for-ph"]], "Remove Hydrogens": [[206, "remove-hydrogens"]], "Insert": [[206, "insert"]], "Invert Chirality": [[206, "invert-chirality"]], "Super Cell Builder\u2026": [[206, "super-cell-builder"]], "Nanotube Builder\u2026": [[206, "nanotube-builder"]], "Auto-Optimize Tool": [[219, "auto-optimize-tool"]], "Force Fields & Algorithms": [[219, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[219, "fixing-ignoring-selections"]], "Display Types": [[200, "display-types"], [200, null]], "Menus": [[210, "menus"], [210, null]], "Introduction": [[203, "introduction"]], "Opening a File": [[203, "opening-a-file"]], "Importing by Name": [[203, "importing-by-name"]], "Navigation": [[203, "navigation"]], "View Menu": [[212, "view-menu"]], "New View": [[212, "new-view"]], "Duplicate View": [[212, "duplicate-view"]], "Detach View": [[212, "detach-view"]], "Close View": [[212, "close-view"]], "Center": [[212, "center"]], "Align View to Axes": [[212, "align-view-to-axes"]], "Full Screen": [[212, "full-screen"]], "Reset Display Types": [[212, "reset-display-types"]], "Set Background Color\u2026": [[212, "set-background-color"]], "Projection": [[212, "projection"]], "Display Axes": [[212, "display-axes"]], "Debug Information": [[212, "debug-information"]], "Use Quick Render": [[212, "use-quick-render"]], "All Molecules in File\u2026": [[212, "all-molecules-in-file"]], "Crystal View Options\u2026": [[212, "crystal-view-options"]], "Properties": [[212, "properties"]], "Extension Menu": [[208, "extension-menu"]], "Animation": [[208, "animation"]], "Optimize Geometry": [[208, "optimize-geometry"]], "Molecular Mechanics": [[208, "molecular-mechanics"]], "Setup Force Field\u2026": [[208, "setup-force-field"]], "Calculate Energy": [[208, "calculate-energy"]], "Conformer Search": [[208, "conformer-search"]], "Ignore Selection": [[208, "ignore-selection"]], "Fix Selected Atoms": [[208, "fix-selected-atoms"]], "Avogadro Extensions\u2013Plugins": [[208, "avogadro-extensionsplugins"]], "General \u201cHow To\u201d for Plugins": [[208, "general-how-to-for-plugins"]], "Running Gaussian": [[208, "running-gaussian"]], "Molecular Orbitals": [[208, "molecular-orbitals"]], "QTAIM (Quantum Theory of Atoms in Molecules)": [[208, "qtaim-quantum-theory-of-atoms-in-molecules"], [199, "qtaim-quantum-theory-of-atoms-in-molecules"]], "Spectra\u2026": [[208, "spectra"]], "Create Surfaces\u2026": [[208, "create-surfaces"]], "Auto-Rotate Tool": [[220, "auto-rotate-tool"]], "Introduction to Molecular Mechanics": [[217, "introduction-to-molecular-mechanics"]], "UFF": [[217, "uff"]], "MMFF94(s)": [[217, "mmff94-s"]], "GAFF": [[217, "gaff"]], "Align Tool": [[218, "align-tool"]], "File Menu": [[209, "file-menu"]], "New": [[209, "new"]], "Open": [[209, "open"]], "Open Recent": [[209, "open-recent"]], "Close": [[209, "close"]], "Save": [[209, "save"]], "Save As\u2026": [[209, "save-as"]], "Revert to Saved": [[209, "revert-to-saved"]], "Import": [[209, "import"]], "Export": [[209, "export"]], "Draw Tool": [[222, "draw-tool"]], "Optimizing Geometry": [[216, "optimizing-geometry"]], "Optimization": [[216, null]], "Edit Menu": [[207, "edit-menu"]], "Undo": [[207, "undo"]], "Redo": [[207, "redo"]], "Cut": [[207, "cut"]], "Copy": [[207, "copy"]], "Copy As": [[207, "copy-as"]], "Paste": [[207, "paste"]], "Clear": [[207, "clear"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[45, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Core::GaussianSetTools": [[26, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::SpaceGroups": [[40, "class-avogadro-core-spacegroups"]], "Class Avogadro::Core::SlaterSet": [[38, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::SharedMutex": [[37, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::UnitCell": [[42, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::Mesh": [[28, "class-avogadro-core-mesh"]], "Class Avogadro::Core::SlaterSetTools": [[39, "class-avogadro-core-slatersettools"]], "Class Avogadro::Core::Molecule": [[29, "class-avogadro-core-molecule"]], "Class Avogadro::Core::Mutex": [[32, "class-avogadro-core-mutex"]], "Class Avogadro::Io::DcdFormat": [[48, "class-avogadro-io-dcdformat"]], "Class Avogadro::Core::NameAtomTyper": [[33, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::SymbolAtomTyper": [[41, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::Variant": [[43, "class-avogadro-core-variant"]], "Class Avogadro::Io::CjsonFormat": [[46, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Core::Residue": [[34, "class-avogadro-core-residue"]], "Class Avogadro::Core::MoleculeSerializer": [[31, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Core::RingPerceiver": [[36, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::Graph": [[27, "class-avogadro-core-graph"]], "Class Avogadro::Core::ResidueData": [[35, "class-avogadro-core-residuedata"]], "Class Avogadro::Io::CmlFormat": [[47, "class-avogadro-io-cmlformat"]], "Class Avogadro::Core::MoleculeDeserializer": [[30, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::GaussianSet": [[25, "class-avogadro-core-gaussianset"]], "Class Avogadro::Core::VariantMap": [[44, "class-avogadro-core-variantmap"]], "Class Avogadro::Io::FileFormat": [[49, "class-avogadro-io-fileformat"]], "Script Plugins": [[175, "script-plugins"], [162, "script-plugins"]], "Building with SMILES": [[193, "building-with-smiles"]], "Scaling Crystal Cell Volume": [[188, "scaling-crystal-cell-volume"]], "License": [[179, "license"]], "Creative Commons Attribution-ShareAlike 4.0 International": [[179, "creative-commons-attribution-sharealike-4-0-international"]], "Using Creative Commons Public Licenses": [[179, "using-creative-commons-public-licenses"]], "Creative Commons Attribution-ShareAlike 4.0 International Public License": [[179, "creative-commons-attribution-sharealike-4-0-international-public-license"]], "Section 1 \u2013 Definitions.": [[179, "section-1-definitions"]], "Section 2 \u2013 Scope.": [[179, "section-2-scope"]], "Section 3 \u2013 License Conditions.": [[179, "section-3-license-conditions"]], "Section 4 \u2013 Sui Generis Database Rights.": [[179, "section-4-sui-generis-database-rights"]], "Section 5 \u2013 Disclaimer of Warranties and Limitation of Liability.": [[179, "section-5-disclaimer-of-warranties-and-limitation-of-liability"]], "Section 6 \u2013 Term and Termination.": [[179, "section-6-term-and-termination"]], "Section 7 \u2013 Other Terms and Conditions.": [[179, "section-7-other-terms-and-conditions"]], "Section 8 \u2013 Interpretation.": [[179, "section-8-interpretation"]], "Building a Supercell": [[189, "building-a-supercell"]], "Creating a Surface": [[189, "creating-a-surface"]], "Building DNA or RNA": [[192, "building-dna-or-rna"]], "Building Materials": [[185, "building-materials"], [185, null]], "Perceiving Crystall Symmetry": [[184, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[184, "open-a-crystal-file"]], "Reducing Crystals to a Primitive Unit Cell": [[187, "reducing-crystals-to-a-primitive-unit-cell"]], "VTK Classes": [[178, "vtk-classes"]], "Making a Crystal Surface Slab": [[182, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[182, "import-the-appropriate-crystal-structure"]], "Importing Molecules by Name": [[195, "importing-molecules-by-name"]], "Building Carbon Nanotubes": [[191, "building-carbon-nanotubes"]], "Insert Molecular Fragments": [[197, "insert-molecular-fragments"]], "Building a Polymer Unit Cell": [[183, "building-a-polymer-unit-cell"]], "Different Display Styles": [[199, "different-display-styles"]], "Locating Display Types": [[199, "locating-display-types"]], "Axes": [[199, "axes"]], "Ball and Stick": [[199, "ball-and-stick"]], "Cartoon": [[199, "cartoon"]], "Dipole": [[199, "dipole"]], "Force": [[199, "force"]], "Hydrogen Bond": [[199, "hydrogen-bond"]], "Label": [[199, "label"]], "Polygon": [[199, "polygon"]], "Ribbon": [[199, "ribbon"]], "Ring": [[199, "ring"]], "Stick": [[199, "stick"]], "Surfaces": [[199, "surfaces"]], "Van der Waals Spheres": [[199, "van-der-waals-spheres"]], "Wireframe": [[199, "wireframe"]], "Installing Script Plugins": [[176, "installing-script-plugins"]], "Directories": [[176, "directories"]], "Plugin Packages and Repositories": [[176, "plugin-packages-and-repositories"]], "Adding to the Plugin Directory": [[176, "adding-to-the-plugin-directory"]], "Script Interfaces": [[177, "script-interfaces"]], "Fixed String Lists (Pop-up menus)": [[177, "fixed-string-lists-pop-up-menus"]], "Integer Values": [[177, "integer-values"]], "Floating-point values": [[177, "floating-point-values"]], "Coloring Part of a Molecules": [[198, "coloring-part-of-a-molecules"]], "Hemoglobin": [[198, "hemoglobin"]], "Select by Residue": [[198, "select-by-residue"]], "Select by Element": [[198, "select-by-element"]], "Table of contents": [[181, "table-of-contents"]], "Building a Peptide": [[190, "building-a-peptide"]], "Building Molecules": [[196, "building-molecules"], [196, null]], "Building Molecule-Surface Interactions": [[186, "building-molecule-surface-interactions"]], "Start with a generated Crystal Surface": [[186, "start-with-a-generated-crystal-surface"]], "New Window: Create our Molecule": [[186, "new-window-create-our-molecule"]], "Importing from the Protein Data Bank (PDB)": [[194, "importing-from-the-protein-data-bank-pdb"]], "Importing Directly": [[194, "importing-directly"]], "Reading a Downloaded PDB file": [[194, "reading-a-downloaded-pdb-file"]], "File Formats": [[173, "file-formats"]], "Identify the Format with --metadata": [[173, "identify-the-format-with-metadata"]], "Reading a format with --read": [[173, "reading-a-format-with-read"]], "Writing a format with --write": [[173, "writing-a-format-with-write"]], "Example Plugin Script - Part 2": [[172, "example-plugin-script-part-2"]], "Providing Input to Run Command": [[172, "providing-input-to-run-command"]], "runCommand() Function": [[172, "runcommand-function"]], "Operation Function": [[172, "operation-function"]], "Retrieving necessary components": [[172, "retrieving-necessary-components"]], "Support for Selection": [[172, "support-for-selection"]], "Sample Input and Output": [[172, "sample-input-and-output"]], "Class List": [[160, "class-list"]], "Class Avogadro::TypeTraits< unsigned char >": [[154, "class-avogadro-typetraits-unsigned-char"]], "Specifying parameters with --print-options": [[174, "specifying-parameters-with-print-options"]], "Handling User Selections: --generate-input": [[174, "handling-user-selections-generate-input"]], "Coordinate Blocks": [[174, "coordinate-blocks"]], "Class Avogadro::TypeTraits< float >": [[151, "class-avogadro-typetraits-float"]], "Charges / Electrostatics": [[168, "charges-electrostatics"]], "Identify the Script with --metadata": [[168, "identify-the-script-with-metadata"], [170, "identify-the-script-with-metadata"]], "Calculating Atomic Partial Charges with --charge": [[168, "calculating-atomic-partial-charges-with-charge"]], "Generating Electrostatic Potentials with --potential": [[168, "generating-electrostatic-potentials-with-potential"]], "Class Avogadro::TypeTraits< unsigned int >": [[155, "class-avogadro-typetraits-unsigned-int"]], "Command Scripts": [[169, "command-scripts"]], "Specifying UI options with \u2013print-options": [[169, "specifying-ui-options-with-print-options"]], "Returning Data": [[169, "returning-data"]], "Returning Data in a Specific File Format": [[169, "returning-data-in-a-specific-file-format"]], "Appending New Atoms and Bonds": [[169, "appending-new-atoms-and-bonds"]], "Bonding New Atoms": [[169, "bonding-new-atoms"]], "Selected Atoms": [[169, "selected-atoms"]], "QtGui Classes": [[165, "qtgui-classes"]], "Avogadro Remote Procedure Call (RPC)": [[167, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[167, "rpc-protocol"]], "Methods": [[167, "methods"]], "Core Classes": [[161, "core-classes"]], "Example Plugin Script - Part 1": [[171, "example-plugin-script-part-1"]], "The Main function:": [[171, "the-main-function"]], "Input Arguments": [[171, "input-arguments"]], "getOptions() Function": [[171, "getoptions-function"]], "Class Avogadro::TypeTraits< double >": [[150, "class-avogadro-typetraits-double"]], "MoleQueue Classes": [[164, "molequeue-classes"]], "Class vtkAvogadroActor": [[159, "class-vtkavogadroactor"]], "Class Avogadro::TypeTraits< int >": [[152, "class-avogadro-typetraits-int"]], "Develop": [[162, "develop"]], "External Scripting": [[162, "external-scripting"]], "Libraries": [[162, "libraries"]], "Main Classes": [[162, "main-classes"]], "Class Avogadro::VTK::vtkGLWidget": [[158, "class-avogadro-vtk-vtkglwidget"]], "Class Avogadro::VTK::VtkPlot": [[157, "class-avogadro-vtk-vtkplot"]], "Rendering Classes": [[166, "rendering-classes"]], "Energy / Force Fields": [[170, "energy-force-fields"]], "Calculating Energies and Gradients": [[170, "calculating-energies-and-gradients"]], "Unit Cells, Total Charge, and Spin Multiplicity": [[170, "unit-cells-total-charge-and-spin-multiplicity"]], "Lattice Vectors and Fractional Coordinates": [[170, "lattice-vectors-and-fractional-coordinates"]], "IO Classes": [[163, "io-classes"]], "Class Avogadro::TypeTraits< short >": [[153, "class-avogadro-typetraits-short"]], "Class Avogadro::TypeTraits< unsigned short >": [[156, "class-avogadro-typetraits-unsigned-short"]], "Class Avogadro::QuantumIO::GamessukOut": [[109, "class-avogadro-quantumio-gamessukout"]], "Class Avogadro::Rendering::Cylinder": [[120, "class-avogadro-rendering-cylinder"]], "Class Avogadro::QuantumIO::GaussianFchk": [[111, "class-avogadro-quantumio-gaussianfchk"]], "Class Avogadro::Rendering::GLRenderer": [[124, "class-avogadro-rendering-glrenderer"]], "Class Avogadro::QuantumIO::NWChemLog": [[115, "class-avogadro-quantumio-nwchemlog"]], "Class Avogadro::Rendering::Drawable": [[122, "class-avogadro-rendering-drawable"]], "Class Avogadro::QtOpenGL::ActiveObjects": [[104, "class-avogadro-qtopengl-activeobjects"]], "Class Avogadro::QtGui::ViewFactory": [[103, "class-avogadro-qtgui-viewfactory"]], "Class Avogadro::QuantumIO::MopacAux": [[113, "class-avogadro-quantumio-mopacaux"]], "Class Avogadro::QuantumIO::GUKBasisSet": [[108, "class-avogadro-quantumio-gukbasisset"]], "Class Avogadro::Rendering::GLRenderVisitor": [[123, "class-avogadro-rendering-glrendervisitor"]], "Class Avogadro::Rendering::BufferObject": [[118, "class-avogadro-rendering-bufferobject"]], "Class Avogadro::QuantumIO::MoldenFile": [[112, "class-avogadro-quantumio-moldenfile"]], "Class Avogadro::QtGui::ToolPlugin": [[101, "class-avogadro-qtgui-toolplugin"]], "Class Avogadro::QtGui::ToolPluginFactory": [[102, "class-avogadro-qtgui-toolpluginfactory"]], "Class Avogadro::QtOpenGL::QtTextRenderStrategy": [[106, "class-avogadro-qtopengl-qttextrenderstrategy"]], "Class Avogadro::QuantumIO::GaussianCube": [[110, "class-avogadro-quantumio-gaussiancube"]], "Class Avogadro::QtGui::ScriptLoader": [[100, "class-avogadro-qtgui-scriptloader"]], "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry": [[116, "class-avogadro-rendering-ambientocclusionspheregeometry"]], "Class Avogadro::Rendering::CylinderGeometry": [[121, "class-avogadro-rendering-cylindergeometry"]], "Class Avogadro::Rendering::ArrowGeometry": [[117, "class-avogadro-rendering-arrowgeometry"]], "Class Avogadro::QuantumIO::NWChemJson": [[114, "class-avogadro-quantumio-nwchemjson"]], "Class Avogadro::QuantumIO::GAMESSUSOutput": [[107, "class-avogadro-quantumio-gamessusoutput"]], "Class Avogadro::QtOpenGL::GLWidget": [[105, "class-avogadro-qtopengl-glwidget"]], "Class Avogadro::Rendering::Camera": [[119, "class-avogadro-rendering-camera"]], "Class Avogadro::Rendering::Shader": [[134, "class-avogadro-rendering-shader"]], "Class Avogadro::Rendering::VRMLVisitor": [[145, "class-avogadro-rendering-vrmlvisitor"]], "Class Avogadro::Rendering::SphereGeometry": [[137, "class-avogadro-rendering-spheregeometry"]], "Class Avogadro::Rendering::TextLabelBase": [[140, "class-avogadro-rendering-textlabelbase"]], "Class Avogadro::Rendering::TextRenderStrategy": [[142, "class-avogadro-rendering-textrenderstrategy"]], "Class Avogadro::TypeTraits": [[148, "class-avogadro-typetraits"]], "Class Avogadro::Rendering::LineStripGeometry": [[128, "class-avogadro-rendering-linestripgeometry"]], "Class Avogadro::Rendering::GeometryNode": [[125, "class-avogadro-rendering-geometrynode"]], "Class Avogadro::Rendering::GeometryVisitor": [[126, "class-avogadro-rendering-geometryvisitor"]], "Class Avogadro::Rendering::Sphere": [[136, "class-avogadro-rendering-sphere"]], "Class 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\ No newline at end of file