diff --git a/.doctrees/docs/getting-started/making-selections.doctree b/.doctrees/docs/getting-started/making-selections.doctree index 06a4af13..7a5495c0 100644 Binary files a/.doctrees/docs/getting-started/making-selections.doctree and b/.doctrees/docs/getting-started/making-selections.doctree differ diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 4a8a7628..45112931 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/_images/09e78cf6-0516-40eb-a1c4-16c791ea442c.png b/_images/09e78cf6-0516-40eb-a1c4-16c791ea442c.png deleted file mode 100644 index 871ef232..00000000 Binary files a/_images/09e78cf6-0516-40eb-a1c4-16c791ea442c.png and /dev/null differ diff --git a/_images/300264d3-31a2-4380-8c24-205fe639ae4d.png b/_images/300264d3-31a2-4380-8c24-205fe639ae4d.png deleted file mode 100644 index 26702e4a..00000000 Binary files a/_images/300264d3-31a2-4380-8c24-205fe639ae4d.png and /dev/null differ diff --git a/_images/bc9d312e-427a-4214-91da-87c3ff071342.png b/_images/bc9d312e-427a-4214-91da-87c3ff071342.png deleted file mode 100644 index dd692fcd..00000000 Binary files a/_images/bc9d312e-427a-4214-91da-87c3ff071342.png and /dev/null differ diff --git a/_images/bd548110-2ddd-46fb-b6f2-20b18b136fb4.png b/_images/bd548110-2ddd-46fb-b6f2-20b18b136fb4.png deleted file mode 100644 index 2332ff11..00000000 Binary files a/_images/bd548110-2ddd-46fb-b6f2-20b18b136fb4.png and /dev/null differ diff --git a/_images/fed929fc-c444-4b2b-bfc6-68222818c459.png b/_images/fed929fc-c444-4b2b-bfc6-68222818c459.png deleted file mode 100644 index 3432c502..00000000 Binary files a/_images/fed929fc-c444-4b2b-bfc6-68222818c459.png and /dev/null differ diff --git a/_images/tutorial-select-all.png b/_images/tutorial-select-all.png new file mode 100644 index 00000000..2c5508a8 Binary files /dev/null and b/_images/tutorial-select-all.png differ diff --git a/_images/tutorial-select-atom.png b/_images/tutorial-select-atom.png new file mode 100644 index 00000000..46d41b1b Binary files /dev/null and b/_images/tutorial-select-atom.png differ diff --git a/_images/tutorial-select-drag.png b/_images/tutorial-select-drag.png new file mode 100644 index 00000000..ad4ec41e Binary files /dev/null and b/_images/tutorial-select-drag.png differ diff --git a/_images/tutorial-select-tool.png b/_images/tutorial-select-tool.png new file mode 100644 index 00000000..66d1949b Binary files /dev/null and b/_images/tutorial-select-tool.png differ diff --git a/_sources/docs/getting-started/making-selections.md.txt b/_sources/docs/getting-started/making-selections.md.txt index c9819de0..265643d4 100644 --- a/_sources/docs/getting-started/making-selections.md.txt +++ b/_sources/docs/getting-started/making-selections.md.txt @@ -2,26 +2,20 @@ The selection tool is also a useful feature to master when beginning to learn Avogadro. Generally, the selection tool allows for the individual selection of atoms, bonds, or fragments. -![](../../_static/fed929fc-c444-4b2b-bfc6-68222818c459.png) +![](../../_static/tutorial-select-tool.png) -There are three types of selection modes: "Atom/Bond", "Residue", and "Molecule". - -The "Atom/Bond" selection mode provides you with the ability to select a single atom within a molecule. This is achieved by left clicking the atom. Press and holding the "shift" key allows for the selection of multiple atoms. +The select provides you with the ability to select a single atom within a molecule. This is achieved by left clicking the atom. Press and holding the "shift" key allows for the selection of multiple atoms. Right clicking on the black display will clear the selection made. -![](../../_static/09e78cf6-0516-40eb-a1c4-16c791ea442c.png) - -The "Residue" selection mode selects an entire residue within a molecule. A residue is selected by clicking on a single atom within the residue. - -![](../../_static/bc9d312e-427a-4214-91da-87c3ff071342.png) +![](../../_static/tutorial-select-atom.png) -The "Molecule" selection mode selects the entire molecule by clicking on an atom. Double clicking an atom in the molecule will also select the entire molecule. +You can also double-click on an atom to select all atoms connected in that fragment or molecule. -![](../../_static/bd548110-2ddd-46fb-b6f2-20b18b136fb4.png) +![](../../_static/tutorial-select-all.png) Clicking and dragging your cursor is another way molecules, or fragments of molecules can be selected. -![](../../_static/300264d3-31a2-4380-8c24-205fe639ae4d.png) +![](../../_static/tutorial-select-drag.png) -More information on selections can be found in the ["Tools" section](tools). +More information on selections can be found in the ["Tools" section](tools) and the "Select" menu. diff --git a/_static/tutorial-select-all.png b/_static/tutorial-select-all.png new file mode 100644 index 00000000..2c5508a8 Binary files /dev/null and b/_static/tutorial-select-all.png differ diff --git a/_static/tutorial-select-atom.png b/_static/tutorial-select-atom.png new file mode 100644 index 00000000..46d41b1b Binary files /dev/null and b/_static/tutorial-select-atom.png differ diff --git a/_static/tutorial-select-drag.png b/_static/tutorial-select-drag.png new file mode 100644 index 00000000..ad4ec41e Binary files /dev/null and b/_static/tutorial-select-drag.png differ diff --git a/_static/tutorial-select-tool.png b/_static/tutorial-select-tool.png new file mode 100644 index 00000000..66d1949b Binary files /dev/null and b/_static/tutorial-select-tool.png differ diff --git a/docs/getting-started/making-selections.html b/docs/getting-started/making-selections.html index 37ce3962..d4dd7c9c 100644 --- a/docs/getting-started/making-selections.html +++ b/docs/getting-started/making-selections.html @@ -508,18 +508,15 @@

Making Selections#

The selection tool is also a useful feature to master when beginning to learn Avogadro. Generally, the selection tool allows for the individual selection of atoms, bonds, or fragments.

-

-

There are three types of selection modes: “Atom/Bond”, “Residue”, and “Molecule”.

-

The “Atom/Bond” selection mode provides you with the ability to select a single atom within a molecule. This is achieved by left clicking the atom. Press and holding the “shift” key allows for the selection of multiple atoms.

+

+

The select provides you with the ability to select a single atom within a molecule. This is achieved by left clicking the atom. Press and holding the “shift” key allows for the selection of multiple atoms.

Right clicking on the black display will clear the selection made.

-

-

The “Residue” selection mode selects an entire residue within a molecule. A residue is selected by clicking on a single atom within the residue.

-

-

The “Molecule” selection mode selects the entire molecule by clicking on an atom. Double clicking an atom in the molecule will also select the entire molecule.

-

+

+

You can also double-click on an atom to select all atoms connected in that fragment or molecule.

+

Clicking and dragging your cursor is another way molecules, or fragments of molecules can be selected.

-

-

More information on selections can be found in the “Tools” section.

+

+

More information on selections can be found in the “Tools” section and the “Select” menu.

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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< char >", "Class Avogadro::TypeTraits< double >", "Class Avogadro::TypeTraits< float >", "Class Avogadro::TypeTraits< int >", "Class Avogadro::TypeTraits< short >", "Class Avogadro::TypeTraits< unsigned char >", "Class Avogadro::TypeTraits< unsigned int >", "Class Avogadro::TypeTraits< unsigned short >", "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, 2, 4, 6, 12, 13, 14, 15, 21, 23, 26, 28, 39, 43, 48, 51, 61, 62, 65, 68, 75, 78, 82, 95, 100, 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245, 248, 250], "demonstr": [1, 198, 210], "core": [1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 69, 82, 84, 85, 95, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 121, 123, 124, 127, 128, 134, 136, 139, 142, 157, 159, 161, 173, 234, 244], "simplest": 1, "wai": [1, 85, 95, 178, 182, 188, 197, 203, 205, 207, 214, 236, 237], "possibl": [1, 5, 21, 22, 49, 84, 171, 178, 204, 238, 246, 249], "molequeu": [1, 2, 82, 159, 166, 173, 238, 241], "jsonrpcclient": 1, "h": [1, 2, 5, 19, 24, 49, 61, 63, 64, 65, 66, 67, 68, 71, 74, 76, 78, 82, 83, 89, 92, 98, 105, 107, 115, 116, 118, 120, 122, 125, 127, 141, 159, 160, 161, 167, 173, 178, 183, 185, 209, 216, 241, 245, 247, 249, 254, 256, 258], "client": [1, 66, 159, 163, 178], "The": [1, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 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, 72, 73, 74, 75, 76, 78, 79, 80, 81, 82, 83, 84, 85, 87, 89, 90, 91, 92, 95, 96, 97, 99, 100, 101, 102, 103, 104, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 132, 134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 158, 161, 162, 164, 167, 168, 169, 171, 172, 173, 175, 176, 178, 181, 182, 185, 187, 189, 190, 191, 196, 197, 198, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 213, 214, 216, 217, 218, 219, 220, 223, 224, 225, 226, 227, 229, 231, 236, 238, 247, 249], "submit": [1, 4, 61, 63, 64, 65, 68, 159, 163, 175, 182, 185], "call": [1, 7, 12, 13, 17, 18, 25, 27, 48, 51, 62, 63, 67, 68, 69, 72, 73, 75, 82, 84, 88, 89, 92, 95, 100, 104, 123, 127, 128, 134, 161, 162, 168, 169, 170, 171, 172, 173, 176, 204, 236, 238, 241, 244, 246, 256], "an": [1, 2, 4, 5, 11, 13, 14, 17, 18, 19, 22, 23, 24, 26, 27, 28, 31, 33, 36, 37, 39, 42, 43, 48, 49, 51, 61, 62, 64, 65, 67, 68, 69, 78, 79, 82, 83, 84, 85, 88, 89, 90, 91, 92, 95, 103, 104, 105, 107, 115, 136, 137, 141, 157, 158, 161, 162, 167, 168, 169, 171, 172, 173, 175, 176, 178, 182, 183, 185, 188, 189, 190, 193, 197, 198, 200, 202, 203, 207, 210, 211, 212, 213, 215, 217, 218, 219, 220, 221, 225, 226, 227, 231, 232, 233, 236, 237, 238, 244, 245, 246, 249, 254, 255, 256, 258], "rpc": [1, 65, 68, 161, 241], "server": [1, 4, 61, 65, 66, 68, 92, 166, 229], "json": [1, 45, 62, 65, 75, 82, 83, 100, 113, 161, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 241, 246], "2": [1, 5, 15, 17, 19, 28, 62, 65, 82, 84, 132, 142, 159, 160, 166, 169, 173, 176, 180, 182, 185, 190, 193, 200, 209, 212, 222, 224, 235, 236, 237, 238, 241, 244, 245, 247, 248, 254, 255, 256, 257], "0": [1, 5, 8, 10, 13, 14, 15, 18, 19, 21, 23, 26, 28, 39, 41, 43, 48, 62, 65, 72, 73, 75, 82, 95, 96, 100, 101, 102, 105, 118, 132, 134, 138, 140, 141, 142, 159, 160, 166, 167, 169, 171, 173, 175, 176, 179, 182, 185, 193, 200, 204, 218, 234, 236, 240, 243, 247, 253, 254, 258], "author": [1, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 47, 48, 49, 51, 53, 55, 57, 58, 59, 60, 62, 70, 74, 75, 76, 82, 84, 86, 87, 89, 97, 98, 100, 101, 102, 104, 113, 115, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158, 168, 173, 175, 178, 249], "marcu": [1, 3, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 70, 75, 76, 84, 86, 87, 89, 97, 98, 102, 104, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158], "d": [1, 3, 7, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 62, 70, 75, 76, 82, 84, 86, 87, 89, 92, 97, 98, 102, 104, 107, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158, 159, 160, 178, 242, 244, 245], "hanwel": [1, 3, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 70, 75, 76, 84, 86, 87, 89, 97, 98, 102, 104, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158], "provid": [1, 13, 14, 18, 21, 22, 24, 25, 27, 28, 31, 36, 38, 41, 43, 51, 61, 62, 63, 64, 65, 66, 67, 68, 69, 74, 79, 82, 83, 85, 90, 91, 102, 103, 104, 118, 121, 123, 126, 129, 139, 145, 161, 167, 169, 170, 173, 175, 178, 186, 197, 198, 200, 203, 204, 205, 206, 207, 208, 211, 218, 221, 226, 231, 233, 236, 246], "To": [1, 11, 16, 51, 63, 65, 74, 168, 171, 178, 181, 202, 209, 214, 219, 220, 238], "creat": [1, 12, 17, 19, 21, 26, 28, 33, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 66, 78, 82, 83, 85, 90, 91, 95, 102, 104, 106, 107, 109, 110, 111, 112, 113, 114, 117, 130, 133, 134, 144, 169, 170, 173, 175, 176, 178, 182, 184, 187, 189, 198, 205, 206, 208, 209, 211, 215, 222, 230, 231, 232, 236, 238, 242, 244, 246, 247, 251, 252, 253, 254, 258], "connect": [1, 26, 61, 66, 68, 84, 95, 127, 166, 171, 178, 229, 230, 245], "method": [1, 5, 12, 17, 21, 23, 28, 42, 48, 51, 62, 63, 65, 67, 75, 78, 82, 84, 85, 90, 91, 95, 100, 102, 104, 117, 118, 134, 158, 167, 169, 173, 215, 216, 236, 241, 244, 246, 249], "follow": [1, 5, 19, 62, 82, 92, 142, 167, 168, 169, 170, 171, 172, 173, 176, 178, 185, 188, 213, 214, 238], "done": [1, 13, 24, 37, 39, 65, 117, 123, 133, 159, 163, 169, 171, 218, 232], "new": [1, 2, 4, 5, 6, 7, 12, 17, 26, 27, 28, 33, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 66, 68, 75, 79, 81, 82, 89, 92, 95, 100, 102, 105, 106, 109, 110, 111, 112, 113, 114, 127, 128, 141, 158, 159, 166, 169, 171, 172, 174, 177, 180, 181, 189, 190, 196, 200, 202, 204, 205, 209, 210, 214, 217, 218, 222, 232, 241, 242, 244, 245, 246, 247], "connecttoserv": 1, "myrpcserv": 1, "qjsonobject": [1, 61, 62, 82], "emptyrequest": 1, "qlatin1str": 1, "listqueu": 1, "sendrequest": 1, "endcod": 1, "signal": [1, 2, 61, 66, 67, 68, 69, 70, 75, 77, 82, 84, 85, 86, 87, 88, 89, 92, 95, 96, 98, 100, 103, 104, 157], "order": [1, 7, 13, 17, 21, 28, 62, 75, 79, 82, 85, 89, 92, 95, 103, 105, 123, 133, 134, 142, 159, 160, 167, 168, 171, 173, 176, 198, 200, 214, 221, 224, 227, 230, 238, 242, 246, 253], "act": [1, 95, 171, 238], "result": [1, 5, 12, 13, 18, 21, 25, 38, 62, 65, 68, 82, 83, 105, 124, 134, 141, 161, 168, 171, 172, 176, 178, 181, 182, 183, 230, 238, 254, 256, 257, 258], "notif": 1, "error": [1, 12, 48, 49, 51, 61, 63, 65, 68, 69, 78, 92, 104, 117, 123, 133, 134, 142, 159, 162, 163, 164, 165, 178, 244, 245, 246, 254], "receiv": [1, 61, 82, 178], "respons": [1, 3, 61, 87, 95, 123, 170, 171, 246], "set": [1, 12, 14, 15, 17, 18, 21, 22, 24, 25, 26, 27, 28, 33, 37, 38, 39, 41, 42, 43, 48, 51, 61, 62, 63, 64, 65, 68, 69, 73, 75, 78, 79, 80, 82, 84, 90, 91, 92, 95, 96, 100, 103, 104, 107, 116, 118, 121, 123, 126, 127, 128, 129, 132, 133, 134, 136, 140, 146, 157, 158, 159, 160, 161, 164, 166, 167, 168, 170, 173, 178, 181, 182, 183, 186, 187, 190, 197, 198, 207, 209, 215, 216, 218, 238, 241, 243, 244, 246, 247], "public": [1, 2, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 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, 157, 158, 242], "qobject": [1, 61, 62, 66, 67, 69, 74, 75, 79, 82, 84, 85, 86, 88, 92, 95, 96, 98, 99, 100, 101, 103], "end": [1, 2, 5, 7, 28, 43, 81, 95, 115, 116, 120, 121, 124, 130, 136, 144, 159, 160, 165, 182, 185, 197, 219, 220], "complet": [1, 27, 51, 61, 65, 68, 84, 117, 127, 163, 167, 168, 175, 185], "constructor": [1, 7, 15, 18, 24, 27, 28, 37, 62, 67, 72, 73, 82, 84, 85, 88, 89, 92], "more": [1, 2, 5, 24, 27, 37, 48, 62, 75, 82, 85, 95, 103, 104, 105, 115, 120, 123, 126, 134, 136, 161, 168, 172, 173, 174, 175, 178, 190, 197, 198, 203, 207, 210, 211, 213, 214, 216, 218, 227, 231, 236, 237, 241, 242, 245, 246, 256], "construct": [1, 18, 19, 61, 64, 79, 83, 89, 95, 202, 205], "describ": [1, 13, 15, 62, 68, 82, 117, 167, 169, 172, 173, 178], "paramet": [1, 7, 13, 14, 15, 18, 21, 22, 24, 25, 27, 28, 32, 37, 38, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 63, 64, 65, 67, 68, 74, 75, 78, 81, 83, 84, 85, 89, 90, 91, 92, 95, 100, 102, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 118, 120, 121, 124, 126, 127, 128, 129, 134, 136, 139, 141, 142, 168, 169, 188, 207, 213, 216, 218, 232, 245, 253], "input": [1, 8, 13, 21, 23, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 83, 84, 92, 95, 100, 104, 106, 109, 110, 111, 112, 113, 114, 130, 144, 157, 161, 162, 167, 168, 169, 172, 174, 175, 176, 180, 182, 192, 207, 236, 241, 242, 243, 245, 246], "job": [1, 61, 62, 63, 64, 65, 68, 82, 173], "param": [1, 166], "filenam": [1, 48, 49, 51, 62, 69, 77, 78, 82, 108, 159, 162, 163, 164, 166, 169, 173, 175, 246], "appear": [1, 62, 78, 82, 95, 173, 175, 181, 188, 207, 227], "work": [1, 3, 4, 6, 24, 103, 168, 178, 182, 190, 193, 204, 207, 210, 213, 236, 237, 238, 245, 246], "directori": [1, 29, 30, 78, 156, 161, 238, 242, 246], "content": [1, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 84, 104, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 121, 127, 128, 136, 139, 157, 166, 173, 178], "specifi": [1, 13, 18, 19, 21, 22, 25, 27, 28, 33, 38, 48, 49, 51, 64, 79, 83, 85, 90, 91, 92, 95, 104, 124, 126, 127, 128, 129, 134, 142, 167, 169, 170, 171, 172, 176, 178, 181, 183, 185, 186, 210, 227], "return": [1, 5, 8, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 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, 72, 73, 74, 75, 78, 79, 81, 82, 84, 85, 87, 89, 90, 91, 92, 95, 96, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 117, 118, 120, 121, 123, 124, 126, 127, 128, 129, 134, 136, 142, 158, 167, 170, 171, 205, 229, 251], "true": [1, 5, 8, 12, 14, 15, 17, 21, 24, 25, 26, 27, 28, 31, 36, 37, 38, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 75, 82, 84, 85, 90, 91, 92, 95, 96, 100, 104, 106, 107, 109, 110, 111, 112, 113, 114, 121, 124, 126, 129, 134, 142, 159, 164, 167, 168, 169, 170, 171, 176], "wa": [1, 27, 28, 61, 62, 65, 68, 69, 73, 75, 82, 84, 85, 100, 104, 124, 126, 173, 186, 188, 197, 202, 204, 231, 234, 236, 242], "successfulli": [1, 51, 61, 62, 65, 66, 75, 82, 84, 238, 245], "fals": [1, 5, 14, 15, 21, 24, 25, 27, 28, 31, 36, 37, 38, 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, 75, 82, 84, 85, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 121, 124, 126, 129, 134, 159, 164, 167, 169, 171, 173], "otherwis": [1, 14, 15, 21, 24, 25, 28, 37, 38, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 75, 82, 95, 100, 106, 109, 110, 111, 112, 113, 114, 126, 172, 173, 178, 212, 229], "bool": [1, 7, 8, 12, 14, 15, 17, 21, 22, 24, 25, 26, 27, 28, 31, 33, 36, 37, 38, 39, 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, 75, 77, 82, 84, 85, 86, 90, 91, 92, 95, 96, 98, 99, 100, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 117, 121, 123, 124, 126, 129, 131, 132, 133, 134, 140, 142, 157, 158, 159, 160], "setinputfil": 1, "const": [1, 2, 5, 7, 8, 9, 10, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 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, 72, 73, 75, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 89, 90, 91, 92, 95, 96, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 144, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157], "qstring": [1, 2, 61, 62, 63, 64, 65, 67, 68, 69, 74, 75, 77, 78, 79, 80, 82, 83, 87, 92, 95, 96, 99, 100, 101, 102, 104, 108], "don": [2, 5, 68, 218, 242, 246], "t": [2, 5, 7, 8, 20, 37, 42, 44, 68, 129, 142, 147, 178, 183, 185, 193, 197, 207, 218, 242, 243, 246], "except": [2, 5, 167, 169, 178, 246], "assert": [2, 178], "product": [2, 197, 256], "never": [2, 169, 178], "crash": [2, 62, 82, 168, 173, 234, 236, 242, 244, 245, 246], "prefer": [2, 49, 62, 82, 134, 167, 171, 173, 192, 205, 207, 212, 245], "solut": 2, "from": [2, 3, 7, 15, 18, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 37, 39, 43, 48, 49, 51, 61, 62, 65, 67, 68, 69, 75, 78, 81, 82, 83, 84, 85, 90, 91, 95, 100, 104, 107, 115, 116, 118, 120, 121, 124, 126, 127, 128, 129, 134, 136, 137, 138, 156, 158, 161, 166, 168, 169, 171, 172, 173, 174, 175, 176, 178, 180, 181, 182, 183, 186, 187, 189, 190, 192, 195, 197, 198, 200, 202, 204, 206, 207, 208, 211, 213, 214, 217, 219, 220, 221, 227, 230, 231, 232, 233, 234, 236, 237, 238, 239, 241, 242, 243, 244, 245, 246, 249, 250, 255], "librari": [2, 4, 51, 103, 142, 175, 181, 227, 238, 242, 246], "over": [2, 182, 186, 192, 193, 196, 218, 227, 229, 234, 236, 241, 242], "boost": [2, 238], "depend": [2, 3, 105, 171, 181, 198, 207, 218, 238, 241, 247, 255], "In": [2, 6, 27, 62, 82, 84, 168, 171, 173, 178, 182, 185, 200, 204, 214, 221, 230, 236, 238, 239, 247], "11": [2, 31, 178, 182], "17": [2, 36, 238], "where": [2, 5, 18, 22, 23, 24, 26, 27, 37, 62, 72, 73, 82, 104, 161, 166, 170, 171, 173, 178, 183, 194, 202, 211, 216, 226, 227, 231, 236, 238, 246, 256], "necessari": [2, 5, 7, 96, 178, 211, 214, 218], "offer": [2, 3, 95, 173, 178, 202, 204, 237], "avo_overrid": 2, "avo_fin": 2, "defin": [2, 41, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 82, 87, 106, 109, 110, 111, 112, 113, 114, 115, 121, 136, 140, 141, 142, 168, 170, 173, 178, 181, 182, 185, 205, 227, 236], "overrid": [2, 24, 28, 32, 37, 40, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 72, 73, 75, 76, 77, 79, 82, 83, 84, 85, 86, 87, 88, 89, 92, 95, 96, 97, 98, 99, 100, 104, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 122, 124, 125, 126, 127, 128, 130, 136, 137, 138, 139, 143, 144, 146, 158, 173, 245], "final": [2, 61, 95, 168, 171, 190, 197, 246], "minim": [2, 62, 82, 140, 173, 190], "third": [2, 182, 238], "parti": [2, 178, 238], "think": [2, 167, 237, 249], "carefulli": [2, 75], "befor": [2, 5, 12, 17, 24, 37, 51, 62, 66, 82, 85, 92, 95, 107, 176, 178, 187, 197, 212, 213, 218, 227, 232, 238, 246], "ad": [2, 6, 24, 26, 28, 33, 37, 48, 61, 62, 81, 82, 85, 102, 120, 124, 126, 127, 128, 159, 164, 176, 188, 189, 190, 198, 200, 214, 221, 227, 229, 236, 241, 246], "templat": [2, 6, 7, 8, 9, 12, 13, 17, 20, 42, 44, 62, 64, 65, 68, 82, 90, 91, 117, 129, 134, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 173, 200, 222, 242, 246], "sens": [2, 68], "alwai": [2, 5, 68, 174, 178, 212, 242, 244, 245], "form": [2, 14, 26, 83, 95, 104, 127, 167, 168, 169, 172, 173, 178, 197, 213, 216, 242, 244, 245, 249, 256], "project": [2, 4, 5, 29, 30, 118, 138, 156, 159, 165, 182, 185, 206, 209, 237, 238, 242, 246, 249], "someth": [2, 84, 100, 170, 204], "type": [2, 5, 7, 8, 9, 10, 12, 13, 15, 17, 18, 20, 21, 22, 24, 25, 28, 32, 33, 37, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 67, 71, 75, 77, 78, 81, 82, 85, 89, 90, 91, 95, 96, 99, 102, 103, 106, 107, 109, 110, 111, 112, 113, 114, 117, 118, 121, 124, 126, 129, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 158, 159, 160, 165, 168, 170, 172, 173, 174, 175, 176, 180, 181, 189, 190, 191, 194, 197, 200, 202, 203, 205, 207, 209, 210, 213, 214, 217, 221, 225, 226, 227, 230, 231, 236, 242, 250], 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199, 200, 214, 216, 221, 230, 236, 247, 253, 254, 255], "modul": [2, 170, 175, 214, 236, 238], "qtcore": 2, "vector": [2, 7, 18, 20, 21, 22, 24, 26, 27, 28, 33, 34, 35, 37, 39, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 81, 84, 95, 106, 107, 109, 110, 111, 112, 113, 114, 117, 118, 120, 124, 134, 142, 182, 183, 233], "stl": [2, 7], "do": [2, 5, 12, 17, 84, 95, 122, 125, 130, 134, 144, 145, 171, 172, 178, 183, 190, 200, 202, 214, 221, 238, 241, 246, 247, 250], "avogadrorenderingexport": 2, "ar": [2, 3, 4, 5, 6, 13, 14, 15, 18, 21, 23, 24, 25, 26, 28, 37, 39, 41, 48, 49, 51, 61, 62, 63, 64, 65, 66, 67, 68, 75, 78, 79, 80, 81, 82, 84, 92, 95, 103, 104, 115, 117, 120, 121, 124, 128, 134, 136, 140, 142, 161, 167, 168, 169, 172, 173, 174, 175, 176, 178, 181, 185, 187, 200, 202, 203, 211, 212, 214, 217, 218, 220, 221, 224, 226, 227, 229, 236, 237, 238, 239, 241, 242, 244, 245, 246, 250, 253, 258], "denot": [2, 121, 129], "_p": 2, "camel": [2, 5], "case": [2, 5, 15, 24, 37, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 72, 73, 82, 84, 106, 109, 110, 111, 112, 113, 114, 166, 169, 171, 173, 178, 197, 200, 210, 220, 221, 244, 245, 246, 256], "qtgui": [2, 28, 62, 63, 64, 103, 104, 157, 159, 161], "instead": [2, 39, 75, 167, 168, 169, 227, 245], "being": [2, 5, 15, 24, 27, 48, 84, 90, 91, 104, 120, 124, 157, 158, 198, 218, 220, 225, 238, 255], "wrong": [2, 5, 242], "qdialog": [2, 63, 65, 71], "correct": [2, 5, 49, 62, 82, 123, 126, 173, 190, 238, 246, 253], "open": [2, 3, 4, 5, 48, 51, 65, 68, 75, 78, 159, 161, 162, 163, 166, 169, 181, 182, 184, 185, 186, 187, 193, 198, 204, 207, 209, 211, 229, 232, 233, 236, 237, 238, 241, 243, 244, 245, 246, 247], "chemistri": [2, 3, 4, 5, 204, 230, 232, 233, 237, 238, 241], "nest": [2, 190], "everyth": [2, 206, 210, 217], "insid": [2, 5, 175, 238], "mongochem": [2, 246], "contain": [2, 5, 7, 8, 12, 15, 17, 18, 20, 21, 22, 24, 26, 27, 28, 33, 37, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 70, 75, 78, 82, 86, 87, 90, 91, 92, 95, 98, 104, 106, 109, 110, 111, 112, 113, 114, 115, 117, 120, 124, 126, 130, 132, 134, 136, 142, 144, 146, 158, 159, 160, 167, 168, 169, 171, 172, 173, 175, 212, 214, 238, 245], "most": [2, 15, 61, 62, 72, 73, 75, 78, 82, 125, 126, 164, 168, 173, 178, 202, 204, 205, 207, 211, 216, 218, 230, 231, 236, 238], "overspecifi": 2, "e": [2, 5, 19, 26, 27, 28, 33, 37, 43, 48, 62, 64, 74, 75, 82, 84, 85, 88, 89, 92, 95, 100, 132, 134, 138, 142, 166, 167, 168, 169, 172, 173, 175, 176, 178, 181, 185, 190, 192, 193, 200, 212, 221, 227, 229, 233, 234, 236, 238, 241, 242, 245, 246], "doesn": [2, 193, 197, 218], "slot": [2, 61, 62, 63, 65, 66, 68, 69, 71, 75, 77, 82, 85, 86, 87, 88, 89, 92, 95, 98, 100, 103, 104, 157], "moc": 2, "often": [2, 183, 216], "littl": 2, "help": [2, 3, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 106, 109, 110, 111, 112, 113, 114, 161, 167, 169, 172, 204, 205, 216, 231, 236, 237, 242, 244, 245, 255], "onli": [2, 5, 15, 21, 23, 28, 43, 51, 62, 65, 68, 81, 82, 85, 95, 104, 117, 121, 124, 133, 167, 168, 169, 171, 172, 173, 178, 190, 197, 198, 202, 207, 210, 214, 216, 218, 220, 230, 236, 238, 243, 244, 245, 246, 255, 258], "specif": [2, 11, 16, 19, 28, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 106, 109, 110, 111, 112, 113, 114, 159, 160, 171, 172, 173, 182, 197, 207, 210, 213, 216, 217, 218, 219, 222, 231, 241, 246], "symbol": [2, 19, 23, 39, 40, 72, 73, 159, 160, 173, 200, 221, 244, 246], "avoid": [2, 5, 22, 84, 178, 238, 245, 246, 256], "static_cast": 2, "dynamic_cast": [2, 129], "const_cast": 2, "reinterpret_cast": [2, 5], "For": [2, 4, 5, 15, 19, 23, 51, 61, 95, 134, 161, 167, 169, 170, 171, 172, 173, 176, 178, 182, 188, 191, 198, 204, 206, 207, 210, 211, 213, 214, 218, 220, 223, 224, 227, 238, 250, 255, 257], "deriv": [2, 15, 20, 21, 25, 38, 48, 85, 100, 104, 126, 158, 178, 230, 250, 251, 255], "qobject_cast": 2, "enum": [2, 15, 19, 21, 22, 24, 33, 37, 39, 42, 48, 51, 61, 65, 67, 77, 78, 81, 85, 95, 96, 107, 117, 126, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155], "": [2, 12, 13, 17, 19, 21, 24, 26, 28, 37, 41, 42, 43, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 65, 75, 79, 80, 81, 82, 84, 85, 95, 104, 106, 107, 109, 110, 111, 112, 113, 114, 118, 121, 129, 142, 157, 159, 160, 162, 166, 168, 169, 170, 172, 173, 178, 180, 183, 190, 200, 205, 207, 211, 213, 214, 217, 218, 219, 220, 221, 225, 230, 231, 236, 238, 241, 246, 248, 255], "constant": [2, 23, 84, 207], "static": [2, 14, 21, 23, 28, 39, 41, 48, 49, 61, 65, 66, 68, 71, 74, 78, 81, 84, 99, 103, 116, 127, 128, 147, 148, 149, 150, 151, 152, 153, 154, 155, 158, 216], "int": [2, 5, 12, 15, 17, 18, 21, 22, 24, 25, 27, 28, 33, 34, 37, 38, 41, 42, 44, 48, 51, 61, 62, 65, 67, 68, 72, 73, 74, 75, 79, 81, 82, 84, 85, 86, 88, 89, 92, 95, 98, 104, 105, 107, 118, 123, 127, 128, 134, 140, 141, 142, 158, 159, 160, 171], "verbos": 2, 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219, 220, 221, 225, 226, 227, 230, 231, 232, 236, 237, 238, 239, 241, 242, 244, 245], "afford": 2, "few": [2, 175, 190, 194, 234, 236, 246], "extra": [2, 62, 82, 168, 173, 182], "byte": [2, 51, 105, 141], "like": [3, 15, 24, 37, 61, 65, 78, 162, 166, 169, 170, 171, 172, 190, 211, 212, 236, 237, 238, 242, 243, 244, 245, 246, 255], "mani": [3, 24, 37, 161, 167, 204, 207, 220, 223, 227, 234, 235, 236, 241, 242, 243, 244, 245, 246], "fundament": 3, "commun": [3, 4, 66, 166, 178, 255], "aim": [3, 230], "develop": [3, 4, 204, 230, 234, 236, 237, 241, 242, 244, 245, 249], "contributor": [3, 234, 241, 242, 243, 244, 245, 246], "alik": [3, 179], "hope": 3, "build": [3, 21, 29, 30, 95, 98, 156, 168, 170, 180, 181, 196, 209, 216, 227, 229, 234, 236, 237, 239, 241, 242, 244, 245, 246, 247, 248, 250, 256, 257], "top": [3, 75, 105, 118, 120, 123, 138, 141, 198, 223, 238, 244], "framework": [3, 236, 245, 246], "so": [3, 18, 21, 24, 37, 41, 51, 62, 82, 84, 95, 134, 142, 157, 158, 161, 166, 171, 173, 175, 178, 183, 190, 196, 197, 198, 207, 218, 238, 254, 256, 258], "veri": [3, 4, 22, 31, 36, 161, 183, 202, 242, 244, 245], "grate": 3, "shahzad": 3, "ali": 3, "michael": 3, "banck": 3, "ross": 3, "braithwait": 3, "jame": 3, "bunt": 3, "donald": 3, "curti": 3, "naomi": 3, "fox": 3, "geoff": [3, 74], "hutchison": [3, 74, 175, 204], "beno\u00eet": 3, "jacob": 3, "jordan": 3, "mantha": 3, "thoma": [3, 241], "margraf": 3, "carsten": 3, "niehau": 3, "simon": 3, "ochsenreith": 3, "konstantin": 3, "tokarev": 3, "allison": [3, 51, 60, 100, 101], "vacanti": [3, 51, 60, 100, 101], "tim": [3, 115], "vandermeersch": [3, 115], "translat": [3, 4, 22, 41, 67, 74, 118, 159, 162, 165, 167, 169, 172, 176, 178, 182, 183, 185, 189, 190, 202, 204, 217, 223, 237, 240, 241], "support": [3, 4, 12, 24, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 74, 78, 82, 95, 102, 106, 109, 110, 111, 112, 113, 114, 115, 117, 123, 134, 142, 161, 166, 167, 168, 169, 170, 172, 173, 175, 202, 229, 230, 236, 237, 238, 241, 242, 244, 245, 246], "its": [3, 8, 14, 26, 39, 49, 51, 72, 73, 81, 95, 126, 161, 170, 171, 178, 197, 205, 225, 254, 255, 256, 258], "ha": [3, 4, 13, 14, 15, 21, 24, 26, 28, 37, 41, 51, 64, 66, 68, 75, 85, 95, 96, 100, 123, 132, 134, 171, 178, 185, 187, 188, 191, 193, 197, 198, 200, 202, 205, 207, 208, 216, 218, 220, 221, 231, 233, 236, 238, 241, 246, 256], "come": [3, 193, 198, 214, 216, 220, 237], "would": [3, 75, 126, 134, 190, 202, 204, 234, 236, 237, 238, 255], "particularli": [3, 216, 234, 235, 242, 244, 245], "googl": [3, 242, 244, 245], "summer": [3, 204, 241, 242, 244, 245], "2007": 3, "2008": 3, "2011": 3, "2016": 3, "2018": 3, "2019": [3, 244], "2021": [3, 241, 242, 243], "2022": [3, 204, 244, 245], "kitwar": [3, 238], "inc": 3, "univers": [3, 204, 216, 218, 249], "pittsburgh": [3, 204], "u": [3, 4, 7, 8, 20, 104, 126, 185, 190, 237, 241, 242, 244, 245], "depart": [3, 204], "defens": 3, "dod": 3, "through": [3, 4, 5, 6, 13, 64, 68, 75, 95, 100, 161, 164, 169, 171, 174, 175, 178, 181, 182, 186, 187, 188, 191, 192, 197, 198, 200, 202, 207, 208, 210, 214, 218, 221, 227, 230, 236, 238, 241, 246], "pettt": 3, "program": [3, 65, 66, 67, 68, 134, 159, 163, 166, 167, 168, 173, 182, 188, 208, 214, 234, 244], "research": [3, 190, 237, 249, 255], "corpor": [3, 178], "cottrel": 3, "scholar": 3, "award": 3, "reli": 3, "number": [3, 5, 12, 14, 15, 17, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 37, 38, 39, 51, 61, 62, 63, 72, 73, 74, 79, 81, 82, 84, 85, 95, 115, 120, 126, 128, 134, 136, 142, 166, 167, 169, 171, 173, 175, 176, 185, 191, 198, 200, 202, 205, 207, 212, 213, 218, 221, 227, 238, 253], "infrastructur": 3, "blue": [3, 18, 23, 140, 142, 159, 160, 165, 197, 198, 217, 220, 231, 236], "obelisk": [3, 23], "group": [3, 5, 7, 12, 17, 19, 28, 39, 41, 61, 62, 63, 64, 65, 66, 68, 69, 78, 82, 85, 92, 95, 100, 104, 105, 116, 121, 122, 123, 126, 127, 128, 134, 136, 137, 138, 139, 140, 142, 157, 173, 183, 185, 186, 187, 188, 190, 200, 205, 210, 222, 230, 235, 236, 244, 246, 249, 251, 253], "pybind11": 3, "chemic": [3, 23, 28, 33, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 106, 109, 110, 111, 112, 113, 114, 161, 172, 173, 194, 202, 206, 208, 210, 214, 229, 236], "structur": [3, 21, 22, 23, 24, 26, 28, 37, 75, 170, 171, 183, 189, 190, 194, 196, 198, 200, 206, 211, 216, 218, 221, 236, 241, 242, 244, 253], "databas": [3, 4, 23, 174, 189, 196, 208, 229], "cmake": [3, 238, 246], "eigen": [3, 5, 28, 37, 107, 118, 134, 238], "softwar": [3, 207, 230], "babel": [3, 162, 169, 202, 236, 241, 244, 245], "And": [3, 167], "cours": [3, 189, 249], "johann": 3, "loschmidt": 3, "amedeo": 3, "made": [4, 6, 7, 23, 26, 81, 100, 178, 179, 196, 197, 198, 202, 203, 208, 210, 211, 216, 226, 241], "who": 4, "want": [4, 7, 168, 185, 189, 190, 197, 200, 202, 212, 213, 221, 223, 230, 231, 237], "back": [4, 7, 83, 159, 160, 205, 211, 241, 242, 244], "great": [4, 237, 238], "place": [4, 5, 39, 49, 72, 73, 171, 173, 178, 183, 198, 206, 207, 211, 218, 223, 225, 237, 238, 251], "start": [4, 5, 24, 26, 92, 116, 120, 180, 181, 182, 189, 190, 205, 215, 218, 219, 222, 228, 233, 237, 242, 246], "fellow": 4, "forum": [4, 6], "question": [4, 237], "level": [4, 62, 75, 82, 173, 238, 249], "post": [4, 213], "mai": [4, 18, 28, 39, 51, 62, 64, 67, 75, 82, 95, 96, 100, 104, 105, 117, 126, 134, 167, 168, 171, 173, 175, 176, 178, 181, 183, 185, 189, 190, 191, 194, 204, 212, 214, 218, 227, 229, 230, 232, 234, 238, 250, 255, 258], "find": [4, 14, 22, 29, 30, 41, 51, 78, 84, 95, 99, 156, 170, 171, 180, 202, 214, 215, 232, 236, 237, 245, 252, 255], "experi": [4, 249], "valuabl": 4, "bug": [4, 6, 193, 237, 240], "pleas": [4, 6, 237, 241, 242, 244, 245, 255], "take": [4, 22, 28, 49, 62, 69, 72, 73, 75, 82, 87, 104, 122, 123, 137, 171, 181, 194, 198, 207, 211, 214, 218, 223, 225, 232], "moment": [4, 190, 232], "tracker": [4, 237], "issu": [4, 6, 237, 241, 246], "code": [4, 6, 24, 37, 62, 82, 84, 88, 161, 167, 169, 170, 171, 173, 183, 190, 191, 193, 207, 232, 233, 236, 237, 239, 241, 242, 244, 245, 246], "while": [4, 5, 26, 62, 82, 84, 95, 100, 168, 169, 173, 182, 187, 213, 218, 227, 229, 245], "move": [4, 28, 104, 138, 142, 178, 185, 193, 196, 202, 218, 223, 236, 246, 247], "around": [4, 5, 15, 22, 31, 36, 63, 65, 69, 185, 187, 190, 196, 198, 202, 213, 223, 236, 250, 255], "fit": [4, 5, 28, 51, 104, 123, 157, 178, 227], "particular": [4, 23, 51, 62, 75, 82, 166, 167, 169, 173, 178, 189, 204, 227], "compon": [4, 18, 22, 23, 26, 28, 127, 128, 132, 140, 142, 161], "itself": 4, "section": [4, 21, 62, 67, 82, 95, 173, 175, 198, 203, 204, 205, 207, 213, 218, 223, 236, 255], "discuss": [4, 6, 168, 207, 237, 241, 242, 244, 245, 255], "idea": [4, 237, 255], "plan": 4, "direct": [4, 18, 41, 62, 82, 115, 118, 119, 120, 121, 124, 128, 136, 142, 159, 165, 173, 178, 193, 219, 238, 244, 247], "progress": [4, 27, 84, 208], "etc": [4, 5, 17, 24, 37, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 100, 103, 104, 106, 109, 110, 111, 112, 113, 114, 115, 120, 133, 134, 136, 142, 157, 161, 168, 169, 170, 173, 176, 198, 202, 207, 227, 229, 230, 233, 236, 237, 238, 241, 246, 250], "both": [4, 15, 26, 51, 63, 64, 161, 167, 169, 172, 173, 175, 176, 187, 214, 237, 258], "python": [4, 92, 99, 161, 168, 171, 174, 175, 215, 237, 238, 240, 242, 244, 245, 246], "script": [4, 63, 64, 75, 83, 92, 99, 100, 162, 172, 214, 237, 241, 242, 243, 245, 246], "util": [4, 64, 92, 99, 118, 175, 188, 198, 207], "tell": [4, 100, 166], "friend": [4, 27, 41, 67, 79, 95, 115, 116, 120, 121, 127, 128, 129, 136, 139], "cite": 4, "paper": [4, 21, 192, 237, 247], "write": [4, 5, 7, 15, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 78, 82, 92, 103, 106, 109, 110, 111, 112, 113, 114, 159, 162, 164, 169, 170, 173, 244, 245, 246], "edit": [4, 14, 64, 95, 161, 180, 188, 197, 198, 200, 202, 207, 209, 210, 211, 221, 223, 233, 234, 236, 238, 244, 245, 246], "tutori": [4, 180, 181, 198, 207, 236, 237, 249], "site": [4, 227, 236, 237], "up": [4, 24, 26, 27, 37, 49, 51, 84, 98, 104, 118, 142, 157, 161, 166, 170, 181, 185, 188, 189, 190, 193, 194, 196, 197, 202, 207, 208, 210, 211, 212, 224, 227, 229, 231, 234, 236, 245, 246], "lesson": [4, 185, 249, 255], "activ": [4, 24, 70, 75, 86, 87, 88, 89, 96, 100, 103, 104, 214, 236, 238, 249], "teacher": [4, 249], "send": [4, 61, 66, 92, 161, 166, 173, 241], "fragment": [4, 133, 134, 159, 165, 180, 192, 195, 203, 205, 223, 226, 227, 236, 241, 246], "report": [4, 6, 62, 82, 173, 183, 237, 242, 243, 244, 245], "encount": [4, 6, 48, 51, 104], "about": [4, 19, 23, 39, 62, 82, 118, 173, 197, 207, 211, 213, 225, 237, 244, 245], "improv": [4, 6, 234, 236, 240, 243], "languag": [4, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 106, 109, 110, 111, 112, 113, 114, 167, 168, 169, 170, 173, 210, 237, 245], "donat": 4, "pai": [4, 204, 258], "host": [4, 244, 245, 246], "meet": 4, "bounti": 4, "when": [5, 7, 8, 13, 15, 18, 20, 24, 28, 37, 49, 51, 61, 62, 63, 64, 65, 66, 68, 69, 75, 78, 82, 88, 89, 92, 95, 100, 104, 123, 127, 128, 157, 168, 169, 170, 171, 173, 175, 187, 188, 197, 198, 202, 203, 205, 207, 211, 212, 214, 223, 232, 238, 242, 245, 246, 247, 249, 250], "base": [5, 7, 8, 13, 15, 19, 28, 33, 48, 62, 75, 76, 78, 79, 82, 85, 97, 100, 101, 116, 120, 121, 122, 124, 125, 129, 130, 144, 145, 161, 169, 171, 173, 175, 176, 178, 190, 191, 205, 207, 210, 236, 245, 246, 250, 255], "larg": [5, 7, 51, 181, 185, 186, 189, 190, 202, 236, 238], "kde": 5, "format": [5, 19, 33, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 75, 78, 79, 80, 82, 106, 109, 110, 111, 112, 113, 114, 140, 142, 161, 162, 166, 167, 169, 170, 171, 173, 174, 175, 178, 179, 193, 207, 230, 232, 236, 241, 242, 243, 244, 245, 246], "enforc": [5, 178], "clang": [5, 245], "tool": [5, 25, 38, 75, 100, 101, 104, 159, 164, 180, 182, 185, 189, 190, 196, 198, 200, 202, 203, 204, 213, 234, 237, 241, 243, 244, 246, 250, 254, 257, 258], "space": [5, 19, 21, 22, 25, 27, 28, 38, 39, 51, 95, 146, 159, 160, 169, 173, 181, 183, 185, 186, 187, 188, 211, 244, 246, 253], "tab": [5, 211, 227, 242, 245], "keep": [5, 26, 51, 65, 67, 95, 103, 105, 213, 238], "less": [5, 12, 17, 23, 28, 95, 207, 227, 231, 236, 256], "than": [5, 7, 12, 17, 23, 26, 28, 51, 62, 82, 95, 166, 178, 186, 236, 242, 253, 256], "80": 5, "charact": [5, 19, 48, 62, 82, 168, 173], "wide": [5, 204, 207, 236], "each": [5, 13, 19, 24, 26, 27, 32, 37, 40, 48, 51, 61, 62, 63, 82, 95, 134, 142, 161, 169, 170, 173, 175, 176, 212, 238, 257, 258], "separ": [5, 142, 168, 173, 178, 230, 235], "g": [5, 19, 24, 28, 33, 48, 62, 74, 75, 82, 88, 89, 92, 100, 134, 138, 140, 142, 159, 160, 166, 167, 168, 169, 172, 173, 175, 176, 178, 181, 190, 192, 193, 200, 212, 221, 227, 229, 233, 236, 238, 241, 246], "nmbr": 5, "singl": [5, 17, 28, 51, 62, 64, 66, 70, 82, 84, 95, 116, 142, 173, 190, 191, 197, 203, 226, 245, 249], "fine": [5, 62, 82, 173], "counter": [5, 62, 82, 92], "temporari": [5, 169], "obviou": 5, "wait": [5, 64, 67, 92], "until": [5, 7, 64, 65, 205, 218, 253], "unus": [5, 15, 24, 37], "ones": 5, "incorrect": [5, 242, 245, 246], "f": [5, 24, 37, 70, 87, 107, 121, 134, 136, 138, 157, 159, 160, 169, 178, 216, 242], "lower": [5, 26, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 106, 109, 110, 111, 112, 113, 114, 142, 211], "letter": [5, 23, 191, 244], "word": 5, "acronym": 5, "cmlformat": [5, 48, 159, 162], "doubl": [5, 14, 17, 23, 24, 25, 28, 37, 38, 39, 42, 51, 89, 95, 107, 116, 157, 158, 159, 160, 190, 191, 200, 203, 221, 225, 226, 245, 256], "cntr": 5, "std": [5, 7, 8, 9, 10, 12, 15, 19, 20, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 37, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 81, 85, 95, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 120, 121, 123, 124, 126, 130, 133, 134, 136, 139, 141, 142, 144], "string": [5, 6, 12, 15, 19, 22, 23, 24, 27, 28, 32, 33, 34, 39, 40, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 67, 68, 69, 75, 78, 79, 80, 82, 95, 100, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 117, 123, 130, 133, 134, 139, 141, 142, 144, 159, 160, 162, 166, 168, 171, 173, 192], "rawxml": 5, "char": [5, 12, 17, 23, 24, 28, 33, 39, 42, 85, 95, 100, 105, 127, 128, 134, 139, 140, 141, 142, 147, 149, 150, 151, 152, 154, 155, 159, 160], "list_delimit": 5, "center": [5, 28, 115, 118, 125, 132, 136, 159, 165, 185, 189, 190, 191, 197, 198, 209, 226, 227, 236, 242, 246], "listdelimit": 5, "upper": [5, 137], "m_": 5, "blank": [5, 176, 211], "togeth": [5, 95, 126, 175], "after": [5, 28, 48, 51, 62, 63, 65, 68, 82, 89, 117, 168, 169, 176, 181, 185, 186, 187, 188, 190, 194, 196, 197, 200, 205, 207, 208, 213, 221, 223, 227, 231, 233, 241], "curli": 5, "blah": [5, 62, 82, 176], "explod": 5, "5": [5, 14, 39, 41, 62, 82, 95, 159, 160, 176, 185, 222, 238, 245, 246, 247, 250, 257, 258], "pointer": [5, 7, 23, 27, 42, 44, 65, 78, 121, 124, 126, 129, 159, 160], "refer": [5, 7, 12, 17, 42, 44, 63, 65, 66, 67, 78, 79, 85, 90, 91, 103, 104, 115, 117, 118, 120, 124, 126, 134, 136, 142, 157, 159, 160, 170, 178, 213, 217, 218, 243], "between": [5, 14, 22, 23, 26, 28, 41, 42, 43, 84, 85, 95, 166, 171, 172, 181, 182, 198, 207, 213, 218, 224, 227, 246, 253, 255, 258], "x": [5, 19, 21, 22, 27, 28, 123, 169, 172, 173, 182, 198, 205, 207, 211, 217, 219, 236, 238, 246, 256], "mystr": 5, "y": [5, 19, 22, 28, 118, 123, 169, 173, 198, 205, 207, 211, 217, 219, 238], "whoah": 5, "surround": [5, 231], "binari": [5, 238, 245], "oper": [5, 7, 12, 13, 17, 20, 21, 27, 28, 33, 34, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 69, 71, 78, 79, 84, 85, 95, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 127, 128, 131, 134, 136, 139, 140, 142, 159, 160, 162, 164, 165, 168, 170, 172, 182], "No": [5, 21, 26, 167, 178, 245], "memoryblock": 5, "malloc": 5, "data": [5, 7, 8, 15, 18, 20, 22, 23, 24, 25, 26, 27, 28, 33, 37, 38, 39, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 75, 82, 84, 85, 86, 92, 95, 98, 105, 106, 107, 109, 110, 111, 112, 113, 114, 117, 132, 134, 141, 142, 146, 157, 159, 160, 163, 164, 166, 167, 171, 172, 180, 195, 206, 209, 210, 230, 236, 241, 253, 254, 256], "size": [5, 7, 18, 20, 26, 27, 43, 51, 84, 115, 117, 120, 134, 136, 142, 159, 160, 165, 181, 182, 198, 211, 241, 246, 253], "left": [5, 51, 62, 82, 105, 118, 137, 141, 142, 173, 200, 202, 203, 205, 211, 217, 218, 220, 221, 226, 238], "normal": [5, 7, 24, 27, 28, 37, 62, 75, 82, 84, 89, 115, 119, 120, 121, 124, 128, 134, 136, 159, 160, 164, 165, 173, 187, 202], "same": [5, 12, 17, 21, 26, 51, 61, 63, 127, 128, 167, 178, 197, 211, 216, 238, 247, 258], "foo": 5, "run": [5, 13, 27, 61, 64, 67, 68, 82, 83, 84, 103, 159, 160, 164, 167, 168, 169, 170, 172, 175, 202, 209, 214, 233, 236, 243, 245, 252], "implement": [5, 11, 13, 16, 21, 32, 40, 45, 46, 47, 51, 53, 54, 55, 58, 59, 60, 62, 75, 82, 84, 89, 92, 95, 105, 113, 117, 122, 134, 139, 141, 142, 161, 166, 172, 244, 245], "myfun": 5, "cout": 5, "suppli": [5, 22, 23, 24, 28, 37, 48, 49, 62, 63, 75, 78, 82, 84, 95, 96, 107, 118, 121, 124, 133, 134, 136, 157, 167, 168, 169, 178], "endl": 5, "bar": [5, 207, 211, 223, 225, 232], "bodi": 5, "condit": [5, 21, 190], "also": [5, 26, 27, 39, 48, 62, 72, 73, 82, 95, 104, 115, 132, 136, 161, 167, 169, 171, 173, 174, 175, 178, 181, 185, 187, 189, 190, 191, 193, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 214, 216, 218, 219, 221, 224, 225, 226, 230, 236, 237, 238, 245, 255], "complex": [5, 126, 200, 227, 236, 246], "42": 5, "var": [5, 170], "parent": [5, 44, 61, 65, 67, 69, 70, 71, 75, 78, 81, 84, 86, 87, 88, 95, 96, 98, 100, 101, 104, 121, 126, 129, 143, 159, 160, 163, 164, 165], "doe": [5, 7, 12, 14, 21, 28, 39, 51, 85, 92, 95, 104, 118, 134, 158, 167, 168, 169, 178, 186, 207, 216, 223, 253], "wrap": [5, 41, 95, 142, 158, 159, 165], "isvalid": [5, 12, 15, 17, 24, 25, 37, 38, 62, 82, 85, 90, 91, 104, 123, 131, 159, 160, 163, 164, 165], "agooddai": 5, "ani": [5, 7, 12, 13, 17, 22, 26, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 68, 75, 78, 79, 80, 82, 92, 95, 100, 104, 106, 109, 110, 111, 112, 113, 114, 117, 118, 124, 134, 166, 167, 168, 169, 171, 172, 173, 175, 176, 178, 194, 202, 205, 208, 211, 220, 227, 234, 238, 246], "els": 5, "block": [5, 19, 62, 82, 168, 176], "element": [5, 7, 19, 20, 24, 26, 27, 28, 32, 40, 71, 72, 73, 74, 88, 89, 95, 122, 128, 130, 132, 134, 142, 144, 159, 160, 164, 167, 169, 170, 171, 173, 176, 178, 181, 188, 200, 205, 209, 216, 221, 227, 236, 242, 245, 250], "cover": [5, 168, 204, 229], "b": [5, 19, 21, 26, 28, 41, 47, 53, 59, 85, 91, 95, 105, 140, 159, 160, 169, 173, 178, 191, 244, 246, 253], "empti": [5, 7, 19, 24, 26, 28, 33, 39, 42, 43, 48, 49, 51, 75, 78, 79, 95, 117, 123, 133, 134, 159, 160, 168, 187, 241], "express": [5, 62, 82, 173, 178, 256], "intent": 5, "clearer": 5, "label": [5, 12, 19, 28, 62, 82, 95, 107, 138, 159, 160, 164, 168, 170, 173, 176, 178, 199, 213, 236, 241, 242, 244, 246], "column": [5, 21, 41, 67, 86, 98], "everi": [5, 26, 28, 178, 229], "must": [5, 15, 24, 25, 28, 37, 51, 62, 65, 75, 78, 82, 84, 95, 105, 117, 119, 127, 128, 133, 134, 141, 142, 167, 168, 169, 171, 172, 173, 175, 178, 205, 214, 238], "indic": [5, 19, 22, 26, 27, 28, 62, 63, 65, 67, 68, 75, 78, 81, 82, 85, 95, 103, 104, 115, 128, 134, 136, 167, 168, 169, 171, 172, 173, 175, 176, 178, 181, 185, 211, 213, 220, 227, 243], "omiss": 5, "anoth": [5, 39, 51, 169, 183, 188, 198, 200, 203, 221, 236, 258], "immedi": [5, 175], "myenum": 5, "drawlin": [5, 116, 159, 165], "vertex": [5, 26, 27, 84, 116, 127, 128, 133, 134, 159, 160, 165, 224], "drawdot": 5, "fall": [5, 241, 242, 244], "default": [5, 15, 19, 23, 24, 25, 27, 28, 33, 37, 48, 51, 62, 64, 75, 78, 82, 95, 96, 104, 118, 127, 128, 132, 133, 138, 142, 168, 170, 173, 176, 191, 198, 200, 202, 211, 212, 218, 221, 232, 236, 246], "drawdefault": 5, "shorter": 5, "insert": [5, 7, 28, 62, 82, 159, 160, 168, 176, 180, 181, 185, 189, 190, 191, 192, 195, 209, 222, 223, 236, 241, 242, 244, 246, 247], "comma": [5, 167, 169], "broken": 5, "begin": [5, 7, 43, 84, 95, 105, 130, 141, 144, 159, 160, 165, 200, 203, 220, 221, 231, 233], "verylongexpress": 5, "anotherevenlongerexpress": 5, "justwhenyouthoughtitcouldntgetlong": 5, "vector3d": [5, 107], "posit": [5, 7, 12, 14, 21, 22, 25, 28, 38, 81, 84, 95, 115, 118, 119, 125, 132, 134, 135, 136, 138, 159, 160, 165, 185, 189, 190, 205, 211, 223, 236, 251, 256, 258], "currentposit": 5, "offset": [5, 84, 134, 159, 164], "reimplement": [5, 64, 104], "put": [5, 236, 246], "discourag": 5, "prefix": [5, 12, 17, 62, 78, 82, 172, 175, 176, 238], "clear": [5, 7, 13, 26, 27, 42, 43, 48, 62, 82, 84, 86, 89, 98, 104, 115, 116, 120, 121, 125, 126, 127, 128, 132, 136, 139, 157, 159, 160, 162, 164, 165, 182, 203, 209, 226, 241], "cpp": [5, 84], "extens": [5, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 76, 78, 82, 106, 109, 110, 111, 112, 113, 114, 161, 166, 167, 168, 169, 172, 173, 180, 182, 198, 200, 209, 210, 213, 214, 218, 221, 230, 231, 236, 237, 241, 244, 245, 246], "As": [5, 6, 166, 168, 189, 198, 209, 217, 224, 227, 229, 238, 241, 244], "feel": [5, 237], "free": [5, 51, 104, 168, 173, 178, 200, 204, 237, 238], "bad": 5, "local": [6, 62, 74, 82, 84, 168, 173, 175, 176, 237, 241, 244, 246], "avail": [6, 25, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 66, 67, 68, 75, 82, 84, 100, 104, 106, 109, 110, 111, 112, 113, 114, 133, 158, 167, 168, 169, 170, 172, 173, 176, 178, 179, 236, 237, 245], "weblat": [6, 241, 242, 243, 244, 245, 246], "autom": [6, 49, 175, 236, 244, 245], "task": [6, 216, 236], "phrase": 6, "whenev": 6, "allow": [6, 7, 27, 31, 36, 42, 62, 78, 82, 161, 162, 167, 169, 172, 173, 178, 181, 182, 185, 187, 188, 189, 190, 192, 193, 198, 200, 202, 203, 205, 207, 208, 210, 211, 213, 218, 219, 220, 223, 224, 225, 226, 227, 230, 232, 233, 236, 241, 245, 246], "time": [6, 51, 62, 82, 92, 95, 104, 117, 126, 161, 178, 181, 186, 190, 246, 249], "freez": [6, 28], "least": [6, 75, 95, 212, 224, 231, 236, 245], "week": 6, "advanc": [6, 62, 82, 173, 237, 238], "releas": [6, 51, 117, 134, 142, 159, 165, 175, 204, 234, 238, 239, 240], "typenam": [7, 8, 9, 13, 20, 42, 44, 90, 91, 129, 147], "copi": [7, 12, 17, 22, 27, 28, 42, 49, 78, 85, 105, 141, 185, 192, 209, 214, 227, 241, 244, 246], "semant": 7, "effect": [7, 118, 178, 214, 247, 253], "share": [7, 12, 17, 26, 36, 175, 178, 179, 236, 238], "without": [7, 26, 49, 51, 65, 68, 161, 178, 202, 204, 207, 208, 234, 238, 242], "expos": 7, "access": [7, 18, 51, 64, 66, 67, 83, 103, 117, 134, 142, 169, 178, 193, 198, 208, 245, 249], "amount": [7, 185, 207], "non": [7, 8, 23, 28, 62, 82, 95, 126, 169, 171, 173, 178, 241, 242, 245, 246], "trigger": [7, 104, 171], "detach": [7, 134, 159, 160, 209, 244], "op": 7, "count": [7, 12, 28], "1": [7, 12, 15, 17, 18, 19, 21, 22, 24, 26, 28, 51, 62, 65, 68, 82, 85, 95, 105, 118, 132, 134, 141, 142, 159, 160, 167, 169, 171, 173, 175, 176, 182, 183, 185, 187, 190, 191, 193, 200, 204, 209, 212, 222, 224, 234, 236, 238, 239, 240, 241, 246, 247, 248, 254, 255, 256, 257, 258], "perform": [7, 13, 15, 21, 42, 51, 63, 84, 95, 104, 134, 168, 170, 171, 178, 182, 188, 202, 207, 212, 236, 238, 240, 247, 258], "deep": [7, 231, 238], "greater": 7, "unnam": [7, 12, 17, 19, 28, 41, 61, 63, 64, 65, 66, 68, 69, 78, 85, 92, 95, 100, 104, 105, 116, 121, 122, 123, 127, 128, 134, 137, 138, 139, 140, 142, 157], "typedef": [7, 11, 12, 13, 16, 17, 21, 28, 33, 43, 44, 48, 61, 78, 85, 90, 91, 95, 140], "value_typ": [7, 44, 117, 134, 142, 159, 160], "compat": [7, 78, 178, 207], "allocator_typ": [7, 44, 159, 160], "const_refer": [7, 44, 159, 160], "const_point": [7, 44, 159, 160], "iter": [7, 13, 43, 44, 159, 160], "const_iter": [7, 43, 44, 159, 160], "reverse_iter": [7, 44, 159, 160], "const_reverse_iter": [7, 44, 159, 160], "difference_typ": [7, 44, 159, 160], "size_typ": [7, 44, 142, 159, 160], "intern": [7, 13, 39, 51, 61, 63, 65, 66, 78, 89, 139, 142, 159, 160, 167, 169, 172, 237], "arrayrefcontain": [7, 159, 160], "valuetyp": [7, 8, 9, 10, 13, 44, 159, 160], "inlin": [7, 8, 9, 10, 11, 15, 16, 18, 19, 20, 22, 24, 25, 27, 28, 33, 34, 37, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 68, 69, 70, 75, 77, 79, 80, 82, 83, 84, 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96, 97, 100, 104, 105, 106, 107, 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, 139, 140, 142, 144, 145, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 158], "explicit": [7, 13, 25, 26, 32, 35, 38, 40, 41, 44, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 75, 77, 79, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 99, 100, 104, 122, 126, 127, 128, 133, 143], "size_t": [7, 12, 26, 28, 35, 43, 44, 51, 81, 95, 115, 116, 120, 124, 126, 127, 128, 134, 136, 140], "n": [7, 15, 19, 24, 26, 27, 37, 44, 126, 128, 173, 189, 190, 216], "valu": [7, 8, 9, 15, 18, 19, 21, 22, 24, 25, 27, 28, 33, 37, 38, 42, 43, 44, 48, 49, 51, 61, 65, 67, 77, 78, 81, 84, 85, 86, 92, 96, 98, 104, 117, 118, 121, 126, 128, 129, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 159, 160, 167, 169, 170, 172, 173, 175, 207, 247], "inputiter": [7, 44], "last": [7, 22, 44, 62, 68, 82, 92, 206, 242], "note": [7, 24, 28, 62, 82, 118, 128, 134, 142, 166, 169, 173, 175, 176, 183, 185, 186, 187, 190, 198, 202, 204, 238, 240, 247, 251, 252, 258], "detachwithcopi": [7, 159, 160], "explicitli": [7, 166], "implicitli": 7, "ensur": [7, 21, 28, 62, 66, 82, 85, 95, 123, 132, 173, 207, 238, 241, 246], "retriev": [7, 15, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 82, 106, 109, 110, 111, 112, 113, 114], "underli": [7, 18, 64, 83, 90, 91], "constdata": [7, 159, 160], "max_siz": [7, 159, 160], "capac": [7, 159, 160], "reserv": [7, 13, 27, 159, 160, 178], "sz": 7, "resiz": [7, 20, 51, 89, 104, 123, 159, 160, 165], "rbegin": [7, 159, 160], "rend": [7, 159, 160], "front": [7, 159, 160], "assign": [7, 26, 27, 28, 32, 40, 85, 95, 159, 160, 167, 236, 244, 245], "val": 7, "push_back": [7, 159, 160], "v": [7, 39, 41, 42, 43, 127, 128, 134, 176, 178, 193, 238, 246, 248, 256], "pop_back": [7, 159, 160], "eras": [7, 159, 160], "idx": [7, 67, 79], "othert": 7, "swap": [7, 26, 41, 79, 115, 116, 120, 121, 127, 128, 136, 139, 140, 159, 160, 164, 165], "swapandpop": [7, 159, 160], "index": [7, 11, 12, 13, 16, 17, 19, 20, 22, 24, 26, 28, 33, 37, 62, 67, 79, 82, 85, 86, 90, 91, 93, 94, 95, 98, 115, 117, 120, 124, 126, 127, 128, 131, 133, 134, 136, 142, 159, 160, 163, 164, 165, 171, 173, 176, 190, 246], "delet": [7, 49, 51, 69, 95, 104, 124, 126, 133, 157, 168, 182, 200, 205, 211, 221, 242, 244, 246, 251], "valid": [7, 15, 24, 25, 27, 37, 38, 48, 62, 68, 82, 85, 90, 91, 95, 104, 123, 128, 129, 133, 159, 160, 172, 173, 176, 238, 246], "pop": [7, 170, 188, 194, 196, 197, 207, 208, 210, 211, 231], "preserv": [7, 21, 26, 51, 95, 187], "protect": [7, 8, 13, 15, 18, 22, 28, 32, 33, 40, 48, 67, 79, 84, 88, 89, 92, 95, 96, 104, 121, 124, 126, 129, 133, 134, 139, 158, 178], "attribut": [7, 8, 13, 15, 18, 22, 28, 33, 61, 62, 68, 82, 84, 92, 95, 96, 116, 117, 121, 124, 126, 127, 128, 129, 133, 134, 139, 158, 173, 175, 179], "arrai": [8, 13, 18, 20, 21, 22, 26, 27, 28, 39, 51, 62, 82, 84, 85, 95, 115, 116, 117, 121, 123, 124, 127, 128, 134, 136, 139, 142, 159, 160, 167, 169, 172, 173, 176], "store": [8, 18, 20, 23, 24, 25, 28, 37, 38, 39, 42, 51, 62, 63, 64, 79, 80, 82, 95, 115, 116, 117, 118, 121, 127, 136, 142, 208, 246], "figur": [8, 73, 213, 253], "subclass": [8, 10, 15, 28, 45, 48, 66, 121, 126, 127, 128, 129, 131, 139, 141, 145], "coordinateset": [8, 159, 160], "istyp": [8, 159, 160], "match": [8, 23, 28, 39, 49, 62, 65, 67, 68, 78, 79, 80, 82, 117, 168, 173, 232, 238], "placehold": [8, 9, 63, 159, 160], "m_content": [8, 9, 159, 160], "m_data": [8, 18, 22, 28, 159, 160], "holder": [8, 10, 159, 160, 178], "type_info": [8, 9, 10], "clone": [8, 9, 10, 15, 24, 37, 159, 160], "atomtempl": [11, 93, 159, 160], "repres": [11, 12, 16, 17, 18, 21, 23, 26, 28, 33, 39, 42, 49, 63, 64, 66, 67, 83, 95, 121, 131, 161, 171, 198, 234, 236], "moleculeclass": [11, 16], "atomtyp": [11, 17, 28, 32, 40, 85, 90, 95, 159, 160, 164], "m": [11, 12, 16, 17, 24, 35, 37, 41, 64, 77, 90, 91, 93, 94, 95, 178, 187, 190], "molecule_t": [12, 17, 90, 91], "setatomicnumb": [12, 28, 95, 159, 160, 164], "unsign": [12, 14, 15, 17, 21, 22, 23, 24, 27, 28, 37, 39, 42, 44, 61, 65, 68, 84, 85, 95, 100, 105, 107, 127, 128, 134, 139, 140, 141, 142, 159, 160], "num": [12, 24, 28, 95, 171], "proton": [12, 72, 231, 247, 255], "atom": [12, 13, 15, 17, 19, 21, 23, 24, 28, 32, 33, 37, 39, 40, 62, 74, 81, 82, 85, 90, 95, 96, 107, 131, 138, 159, 160, 161, 164, 165, 169, 170, 171, 173, 180, 181, 182, 183, 185, 188, 197, 199, 200, 203, 205, 209, 210, 211, 212, 213, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 229, 231, 233, 234, 236, 241, 242, 244, 245, 246, 250, 256, 258], "atomicnumb": [12, 23, 28, 85, 95, 159, 160, 164], "setposition2d": [12, 159, 160], "vector2": [12, 28, 95], "po": [12, 22, 28, 84, 95, 119, 135], "2d": [12, 28, 211, 241], "Not": 12, "current": [12, 13, 17, 26, 27, 28, 48, 51, 55, 61, 63, 64, 65, 68, 74, 75, 84, 87, 89, 95, 100, 103, 105, 115, 116, 118, 120, 121, 122, 123, 127, 128, 129, 132, 133, 134, 136, 139, 141, 166, 168, 185, 198, 208, 210, 211, 212, 223, 236, 237, 250], "moleculetyp": [12, 17, 90, 91, 159, 160, 164], "compil": [12, 133, 134, 159, 165, 238], "position2d": [12, 159, 160], "setposition3d": [12, 159, 160], "vector3": [12, 21, 22, 25, 28, 38, 39, 41, 81, 85, 95], "3d": [12, 22, 28, 95, 104, 118, 127, 128, 134, 161, 169, 171, 192, 202, 211, 236, 245, 255], "position3d": [12, 28, 85, 95, 159, 160], "sethybrid": [12, 28, 95, 159, 160, 164], "atomhybrid": [12, 28, 95], "hyb": [12, 28, 95], "hybrid": [12, 28, 95, 159, 160, 164, 250, 255], "coordin": [12, 19, 20, 21, 24, 28, 39, 41, 62, 82, 95, 107, 116, 118, 123, 134, 137, 138, 142, 159, 160, 162, 182, 183, 186, 187, 205, 227, 241, 242, 246, 249], "setformalcharg": [12, 28, 95, 159, 160, 164], "sign": [12, 28, 95, 134, 238, 244], "charg": [12, 28, 62, 82, 95, 173, 174, 175, 207, 216, 227, 231, 236, 242, 244, 245, 246, 247, 258], "formal": [12, 28, 95, 227, 244, 246], "formalcharg": [12, 28, 95, 159, 160, 164], "setcolor": [12, 27, 28, 33, 95, 127, 128, 131, 159, 160, 164, 165], "vector3ub": [12, 28, 33, 95, 115, 119, 120, 127, 128, 130, 131, 134, 135, 136, 140, 144], "color": [12, 18, 23, 27, 28, 33, 62, 82, 95, 115, 120, 127, 128, 131, 132, 136, 140, 142, 157, 159, 160, 164, 165, 173, 174, 176, 180, 185, 198, 207, 209, 231, 236, 241, 242, 244, 245, 246], "setlay": [12, 28, 95, 159, 160, 164], "layer": [12, 28, 85, 95, 159, 160, 164, 242, 243, 244, 245, 246], "invalid": [12, 17, 28, 39, 48, 68, 85, 90, 91, 95, 131, 159, 165, 242], "object": [12, 13, 17, 18, 24, 27, 28, 42, 43, 49, 51, 61, 62, 63, 64, 67, 68, 72, 75, 78, 82, 83, 84, 85, 90, 91, 95, 100, 103, 104, 105, 107, 115, 116, 117, 118, 120, 121, 123, 124, 127, 128, 131, 134, 136, 141, 145, 158, 164, 167, 168, 169, 172, 173, 197, 213, 241], "increment": [12, 17], "self": [12, 17, 245], "check": [12, 15, 17, 21, 25, 27, 28, 38, 39, 48, 62, 68, 75, 82, 85, 92, 95, 104, 123, 126, 170, 171, 175, 176, 200, 211, 213, 218, 220, 221, 225, 241, 245, 246, 252, 253, 258], "postfix": [12, 17], "decrement": [12, 17], "setselect": [12, 159, 160], "select": [12, 28, 65, 68, 78, 85, 89, 95, 159, 160, 164, 176, 180, 181, 182, 185, 188, 189, 190, 191, 192, 193, 194, 196, 198, 200, 201, 202, 205, 208, 209, 211, 213, 214, 216, 217, 219, 220, 221, 222, 223, 224, 227, 229, 231, 232, 233, 241, 242, 243, 244, 245, 246, 247], "setforcevector": [12, 28, 95, 159, 160, 164], "forc": [12, 28, 85, 95, 139, 161, 174, 175, 190, 199, 209, 213, 215, 216, 227, 233, 238, 246, 252, 254, 255, 256, 258], "forcevector": [12, 28, 95, 159, 160, 164], "setlabel": [12, 28, 95, 159, 160, 164], "outputtyp": 13, "interfac": [13, 14, 23, 39, 61, 62, 64, 75, 82, 83, 84, 92, 96, 100, 141, 161, 168, 170, 171, 173, 180, 202, 204, 207, 214, 218, 245, 246], "list": [13, 21, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 66, 67, 68, 75, 78, 79, 102, 104, 106, 109, 110, 111, 112, 113, 114, 124, 126, 167, 168, 169, 170, 171, 173, 175, 178, 207, 208, 227, 238, 241, 245, 255], "identifi": [13, 15, 23, 28, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 68, 82, 85, 90, 91, 101, 106, 109, 110, 111, 112, 113, 114, 115, 119, 120, 121, 123, 124, 131, 134, 135, 136, 142, 159, 162, 164, 165, 173], "mol": [13, 14, 19, 21, 22, 25, 32, 33, 38, 39, 40, 56, 58, 61, 62, 63, 64, 69, 71, 75, 82, 95, 100, 167, 168, 169, 171, 207, 251, 256], "nullptr": [13, 25, 28, 32, 35, 38, 40, 49, 51, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 75, 77, 78, 79, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 99, 100, 101, 102, 103, 104, 121, 122, 124, 126, 129, 143, 157, 242], "setmolecul": [13, 15, 19, 35, 63, 64, 69, 75, 100, 104, 157, 159, 160, 163, 164, 177], "obtain": [13, 28, 31, 36, 67, 81, 85, 90, 91, 95, 128, 171], "lookup": [13, 49, 245], "been": [13, 28, 49, 51, 66, 68, 75, 95, 96, 132, 134, 171, 178, 185, 188, 197, 198, 200, 207, 208, 211, 216, 218, 221, 224, 231, 232, 233, 236, 238, 249, 255], "previous": [13, 207, 208, 211, 224], "cach": [13, 51, 62, 66, 82, 92, 175, 245, 246], "There": [13, 62, 81, 82, 173, 191, 192, 193, 203, 211, 226, 237, 238], "correspond": [13, 15, 24, 28, 61, 62, 82, 95, 173, 175, 176, 178, 182, 214, 218, 247], "reset": [13, 48, 51, 62, 82, 90, 91, 92, 96, 104, 118, 123, 157, 159, 160, 163, 164, 185, 209, 219, 223, 224, 225, 241, 242], "typer": 13, "state": [13, 48, 51, 61, 62, 65, 68, 82, 90, 91, 95, 96, 125, 158, 176, 178, 242], "m_type": [13, 133, 159, 160, 165], "initi": [13, 23, 24, 26, 37, 62, 65, 68, 78, 82, 84, 85, 95, 104, 123, 159, 160, 164, 165, 175, 176, 200, 202, 205, 221, 225, 229, 230, 241, 243, 244, 245, 246], "setup": [13, 61, 169, 209, 214, 244], "prior": [13, 61, 178], "enough": [13, 51], "room": 13, "determin": [13, 32, 40, 49, 51, 61, 62, 82, 117, 125, 175, 187, 188, 190, 207, 220, 224, 227, 230, 231, 246], "m_molecul": [13, 15, 95, 159, 160, 164], "popul": [13, 15, 21, 25, 51, 95], "spglib": [14, 39, 95, 183, 241], "short": [14, 28, 39, 42, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 92, 95, 106, 109, 110, 111, 112, 113, 114, 142, 159, 160], "gethallnumb": [14, 159, 160], "carttol": [14, 39, 95], "1e": [14, 39, 95], "hall": [14, 39, 95], "crystal": [14, 39, 41, 180, 184, 188, 198, 205, 207, 209, 236, 242, 246], "unit": [14, 19, 21, 23, 28, 39, 41, 62, 82, 95, 173, 176, 180, 181, 184, 187, 188, 190, 193, 209, 211, 242, 246, 253], "cell": [14, 19, 21, 28, 39, 41, 95, 173, 180, 181, 184, 185, 188, 190, 193, 209, 211, 242, 246, 253], "exist": [14, 22, 26, 28, 43, 51, 65, 67, 85, 95, 102, 126, 134, 168, 172, 173, 218, 234, 242], "algorithm": [14, 21, 84, 95, 186, 207, 212], "fail": [14, 42, 51, 62, 65, 66, 82, 95, 127, 128, 169, 173, 178], "succe": 14, "handl": [14, 21, 48, 49, 63, 68, 75, 78, 88, 89, 92, 100, 104, 117, 133, 142, 159, 162, 163, 164, 165, 167, 168, 169, 172, 236, 241, 246], "cartesian": [14, 19, 21, 24, 37, 39, 41, 95, 169, 173, 182, 183, 186, 187, 198, 209], "toler": [14, 28, 39, 95, 183, 186, 245], "reducetoprimit": [14, 159, 160], "reduc": [14, 21, 39, 95, 178, 180, 184], "primit": [14, 24, 37, 95, 96, 115, 119, 120, 121, 123, 124, 132, 135, 136, 159, 165, 180, 184], "unless": [14, 18, 178], "miss": [14, 234, 242, 245], "conventionalizecel": [14, 95, 159, 160, 164], "refin": [14, 216], "convention": [14, 95], "symmetr": [14, 95, 159, 160, 187, 236], "basi": [15, 24, 25, 28, 37, 38, 62, 82, 107, 108, 173, 178, 207, 246], "gaussianset": [15, 25, 37, 38, 108, 159, 160], "slaterset": [15, 159, 160], "capabl": [15, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95, 106, 109, 110, 111, 112, 113, 114, 115, 136, 172, 173, 205, 208, 216], "calcul": [15, 24, 25, 27, 28, 37, 38, 62, 63, 64, 68, 82, 84, 105, 118, 141, 163, 173, 181, 182, 183, 185, 188, 190, 209, 214, 216, 224, 227, 230, 231, 233, 236, 245, 247, 249, 258], "electrontyp": [15, 24, 25, 37, 159, 160], "electron": [15, 23, 24, 25, 28, 38, 207, 230, 231, 245], "pair": [15, 24, 25, 26, 27, 28, 34, 37, 62, 82, 85, 95, 116, 159, 160, 173, 175, 176, 207, 230, 236, 245], "alpha": [15, 24, 25, 41, 140, 142, 159, 160, 165, 169, 241, 245], "beta": [15, 24, 25, 41, 159, 160, 169, 234], "cannot": [15, 21, 29, 30, 49, 51, 68, 156, 178, 236], "enumer": [15, 19, 21, 22, 24, 33, 37, 42, 48, 51, 61, 65, 67, 77, 78, 81, 85, 96, 117, 126, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 171], "destructor": [15, 24, 27, 37, 51, 84], "setelectroncount": [15, 159, 160], "electroncount": [15, 159, 160], "molecule_": 15, "get": [15, 22, 24, 28, 39, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 84, 85, 87, 90, 91, 95, 102, 103, 104, 106, 109, 110, 111, 112, 113, 114, 115, 117, 118, 120, 121, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 157, 158, 161, 167, 169, 171, 180, 237, 238, 241, 255], "belong": [15, 67, 85, 90, 91], "setnam": [15, 22, 27, 159, 160], "settheorynam": [15, 159, 160], "theorynam": [15, 159, 160], "molecularorbitalcount": [15, 24, 37, 159, 160], "molecular": [15, 24, 25, 28, 37, 38, 62, 82, 104, 161, 166, 167, 168, 169, 170, 171, 173, 180, 192, 194, 195, 198, 202, 209, 211, 213, 218, 227, 228, 230, 234, 236, 237, 245, 246, 249, 250, 255], "orbit": [15, 24, 25, 37, 38, 107, 159, 160, 161, 180, 198, 209, 228, 236, 242, 254, 257], "homo": [15, 159, 160], "given": [15, 22, 23, 24, 26, 28, 39, 42, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 67, 78, 83, 85, 95, 104, 106, 109, 110, 111, 112, 113, 114, 167, 170], "mo": [15, 22, 24, 25, 37, 159, 160, 246], "lumo": [15, 159, 160], "m_electron": [15, 159, 160], "total": [15, 28, 61, 227, 246], "close": [15, 48, 51, 64, 70, 159, 162, 178, 209, 213, 231, 232, 242, 244, 245, 253], "shell": [15, 24, 37, 107, 159, 162], "doubli": 15, "occupi": [15, 51], "hold": [15, 84, 107, 171, 192, 196, 202, 203, 218], "possibli": 15, "bond": [15, 17, 28, 33, 62, 81, 82, 85, 91, 95, 131, 159, 160, 161, 164, 165, 171, 173, 180, 182, 188, 190, 199, 200, 203, 205, 207, 211, 212, 216, 218, 221, 222, 223, 224, 226, 227, 230, 243, 244, 245, 246, 252, 253, 254, 255, 256, 257, 258], "read": [15, 28, 36, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 75, 78, 82, 106, 109, 110, 111, 112, 113, 114, 159, 162, 164, 169, 171, 173, 175, 178, 195, 205, 230, 241, 242, 243, 244, 246], "output": [15, 19, 21, 24, 29, 30, 37, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 65, 68, 82, 92, 106, 107, 109, 110, 111, 112, 113, 114, 156, 162, 163, 167, 168, 169, 172, 173, 206, 213, 216, 230, 232, 233, 245, 246], "necessarili": 15, "m_name": [15, 22, 159, 160], "usual": [15, 171, 238], "standard": [15, 62, 70, 82, 90, 91, 92, 95, 117, 134, 158, 166, 167, 168, 169, 171, 172, 173, 178, 198, 208, 242, 246], "m_theorynam": [15, 159, 160], "theori": [15, 62, 82, 173, 178, 199, 209, 246, 250], "bondtempl": [16, 94, 159, 160], "bondtyp": [16, 28, 85, 91, 95, 159, 160, 164], "atom1": [17, 28, 85, 95, 159, 160], "atom2": [17, 28, 85, 95, 159, 160], "setord": [17, 159, 160], "o": [17, 92, 118, 126, 136, 158, 167, 200, 206, 216, 221, 238, 258], "getotheratom": [17, 159, 160], "represent": [18, 21, 41, 62, 82, 134, 172, 173, 178, 198, 206], "rgb": [18, 62, 82, 140, 173], "three": [18, 23, 24, 37, 127, 128, 142, 198, 203, 205, 224, 226, 227], "float": [18, 22, 27, 42, 84, 115, 118, 119, 120, 121, 123, 124, 125, 127, 130, 132, 134, 135, 136, 138, 139, 140, 142, 144, 159, 160, 167, 169, 171, 245], "rang": [18, 21, 62, 82, 124, 126, 128, 134, 140, 142, 167, 169, 173, 176, 207, 227, 236, 245, 255], "intens": [18, 28, 245], "red": [18, 140, 142, 159, 160, 165, 198, 217, 231, 236], "green": [18, 140, 142, 159, 160, 165, 198, 217], "memori": [18, 24, 51, 95, 134, 244], "3": [18, 27, 62, 82, 84, 127, 128, 134, 140, 142, 159, 160, 167, 169, 176, 182, 186, 190, 200, 209, 212, 213, 222, 238, 241, 247, 248, 255, 256, 257], "pass": [18, 22, 27, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 68, 75, 82, 83, 84, 92, 100, 104, 106, 109, 110, 111, 112, 113, 114, 121, 122, 134, 166, 168, 173, 242, 245], "directli": [18, 49, 67, 167, 178, 189, 191, 195, 230], "opengl": [18, 123, 132, 161, 238, 244, 245, 246], "conveni": [18, 28, 43, 48, 49, 51, 66, 67, 85, 161, 205, 210, 246], "written": [18, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 82, 84, 106, 109, 110, 111, 112, 113, 114, 168, 173, 176, 178, 231], "emphasi": 18, "effici": [18, 210, 242], "layout": [18, 65, 87], "black": [18, 132, 200, 203, 221, 225, 226], "integ": [18, 22, 27, 142, 173], "255": [18, 62, 82, 134, 140, 173], "expect": [18, 23, 24, 27, 62, 82, 84, 103, 168, 169, 173, 178, 238, 246], "align": [19, 21, 132, 140, 173, 180, 181, 182, 185, 190, 191, 209, 222, 246], "see": [19, 28, 51, 62, 64, 78, 82, 85, 95, 105, 134, 142, 161, 168, 172, 173, 183, 186, 187, 190, 191, 207, 230, 255], "setspecif": [19, 159, 160], "detail": [19, 21, 48, 51, 61, 62, 64, 65, 72, 82, 161, 167, 168, 169, 170, 172, 173, 207], "distanceunit": [19, 159, 160], "distanc": [19, 39, 41, 118, 138, 159, 160, 165, 181, 182, 207, 213, 224, 245, 246, 253], "angstrom": [19, 21, 41, 159, 160, 190, 205, 213], "bohr": [19, 159, 160, 190, 205], "setdistanceunit": [19, 159, 160], "spec": 19, "inform": [19, 24, 28, 39, 62, 82, 95, 104, 123, 134, 168, 173, 175, 178, 187, 197, 198, 203, 205, 207, 209, 210, 213, 216, 218, 223, 237, 244], "z": [19, 22, 28, 169, 173, 181, 185, 190, 191, 198, 205, 207, 211, 217, 219, 241], "6": [19, 21, 27, 62, 74, 82, 84, 123, 158, 159, 160, 167, 169, 171, 173, 190, 213, 222, 238, 246, 250, 256], "carbon": [19, 23, 28, 74, 170, 171, 173, 175, 180, 185, 205, 220, 221, 225, 227, 249, 255, 256, 257], "l": [19, 119, 178, 238, 246], "c1": [19, 246], "gamess": [19, 107, 173, 207, 245, 246], "lattic": [19, 21, 41, 95, 173, 186, 187], "requir": [19, 24, 49, 62, 65, 82, 123, 142, 158, 167, 168, 171, 172, 173, 175, 178, 214, 232, 234, 256], "A": [19, 21, 24, 26, 28, 31, 36, 41, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 70, 75, 78, 79, 81, 82, 85, 86, 87, 90, 91, 92, 95, 96, 98, 99, 100, 102, 104, 106, 109, 110, 111, 112, 113, 114, 115, 122, 124, 126, 132, 133, 134, 136, 142, 161, 168, 173, 176, 178, 179, 182, 188, 189, 191, 193, 194, 196, 200, 203, 205, 207, 211, 212, 220, 221, 225, 231, 232, 236, 238, 249, 255], "liter": [19, 62, 82, 173], "optim": [19, 28, 62, 82, 169, 173, 176, 180, 182, 190, 200, 209, 216, 221, 227, 236, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 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78, 79, 80, 82, 84, 85, 124, 126, 161, 170, 173, 198, 203, 205, 206, 207, 210, 226, 229, 232, 237, 238, 241, 242, 243, 244, 245], "http": [21, 51, 84, 172, 175, 178, 190, 193, 194, 207, 238, 241, 242, 244, 245], "xtalopt": [21, 166], "openmolecul": 21, "net": [21, 198, 247], "misc": 21, "rotatetostdorient": 21, "pdf": 21, "setvolum": [21, 159, 160], "real": [21, 41, 42, 169, 246], "newvolum": [21, 95], "isotrop": 21, "scale": [21, 95, 118, 159, 165, 180, 184, 219, 225, 245], "volum": [21, 41, 95, 157, 159, 160, 180, 184, 186], "cubic": [21, 41], "failur": [21, 24, 25, 28, 31, 36, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 95, 106, 109, 110, 111, 112, 113, 114, 134, 178, 243], "nigglireduc": [21, 159, 160], "niggli": [21, 95, 186], "reduct": [21, 95, 186], "produc": [21, 64, 122, 172, 178, 190], "canon": 21, "strive": 21, "gross": 21, "kunstlev": 21, "rw": 21, "sauter": 21, "nk": 21, "adam": 21, "pd": 21, "numer": [21, 62, 82, 115, 134, 136, 167, 168, 169, 173, 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249, 253], "mechan": [24, 37, 90, 91, 180, 209, 213, 218, 230, 253, 255, 256], "certain": [24, 28, 37, 95, 178, 207], "hierarchi": [24, 37], "built": [24, 37, 103, 181, 182, 188, 190, 200, 221, 237, 238], "gto": 24, "p": [24, 37, 86, 107, 157, 159, 160, 183, 216], "compos": [24, 27, 37, 95], "contract": [24, 37, 178], "coeffici": [24, 37], "expon": [24, 37], "orthogon": [24, 37], "independ": [24, 37, 49, 178], "That": [24, 37, 236], "px": [24, 37, 159, 160], "py": [24, 37, 159, 160, 169, 171, 175, 244], "pz": [24, 37, 159, 160], "five": [24, 37, 198, 227], "six": [24, 37, 198], "sp": [24, 107, 159, 160, 255, 257], "d5": [24, 107, 159, 160], "f7": [24, 107, 159, 160], "g9": [24, 159, 160], "h11": [24, 159, 160], "i13": [24, 159, 160], "uu": [24, 37, 107, 159, 160], "addbasi": [24, 159, 160], "addgto": [24, 159, 160], "setmolecularorbit": [24, 159, 160], "correctli": [24, 104, 167, 169, 186, 214], "sequenc": [24, 62, 82, 95, 173, 189, 191], "setcount": [24, 159, 160], "setactivesetstep": 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159, 160], "scftype": [24, 159, 160], "setfunctionalnam": [24, 159, 160], "applic": [24, 62, 75, 82, 100, 103, 161, 173, 175, 178, 193, 238, 249], "functionalnam": [24, 159, 160], "initcalcul": [24, 37, 159, 160], "anyth": [24, 37, 100, 124, 230], "symmetri": [24, 37, 159, 160, 180, 184, 241], "accessor": [24, 37], "properti": [24, 28, 37, 62, 82, 105, 139, 141, 173, 207, 209, 229, 231, 243, 244, 245, 246, 255, 258], "atomindic": [24, 159, 160], "moindic": [24, 159, 160], "gtoindic": [24, 159, 160], "cindic": [24, 159, 160], "gtoa": [24, 159, 160], "gtoc": [24, 159, 160], "gtocn": [24, 159, 160], "momatrix": [24, 159, 160], "moenergi": [24, 107, 159, 160, 162], "mooccup": [24, 159, 160], "monumb": [24, 159, 160], "densitymatrix": [24, 37, 159, 160], "spindensitymatrix": [24, 159, 160], "setelectrontyp": [25, 159, 160], "onc": [25, 51, 84, 133, 182, 185, 188, 198, 200, 207, 214, 220, 221, 227, 232, 238], "calculatemolecularorbit": [25, 38, 159, 160], "cube": [25, 27, 28, 84, 157, 159, 160, 164, 177, 244, 245], "molecularorbitalnumb": [25, 38], "calculateelectrondens": [25, 38, 159, 160], "calculatespindens": [25, 38, 159, 160], "vertic": [26, 27, 116, 118, 127, 128, 140, 159, 160, 165], "edg": [26, 142, 159, 160, 187, 246], "wherein": 26, "edgecount": [26, 159, 160], "destroi": [26, 28, 42, 43, 85], "setsiz": [26, 159, 160], "smaller": [26, 186, 236], "remov": [26, 27, 28, 39, 49, 51, 61, 81, 85, 95, 124, 126, 134, 159, 164, 178, 193, 206, 209, 238, 241, 242, 244, 246], "higher": [26, 232], "them": [26, 48, 62, 82, 128, 134, 167, 170, 178, 182, 198, 238], "These": [26, 28, 61, 62, 64, 82, 84, 161, 167, 207, 211, 214, 216, 232, 236, 241], "guarante": [26, 81], "regard": [26, 178, 216], "larger": [26, 51, 186, 196, 236], "unconnect": 26, "isempti": [26, 43, 159, 160], "addvertex": [26, 159, 160], "unchang": 26, "removevertex": [26, 159, 160], "highest": [26, 74], "swapvertexindic": [26, 159, 160], "affect": [26, 51, 85, 118, 178], "vertexcount": [26, 128, 159, 160, 165], "addedg": [26, 159, 160], "removeedg": [26, 159, 160], "remain": [26, 178], "edgeindex": 26, "editedgeinplac": [26, 159, 160], "swapedgeindic": [26, 159, 160], "edgeindex1": 26, "edgeindex2": 26, "neighbor": [26, 142, 159, 160, 246, 258], "endpoint": [26, 159, 160], "incid": 26, "degre": [26, 118, 159, 160, 220, 223, 246], "containsedg": [26, 159, 160], "edgepair": [26, 159, 160], "equal": 26, "connectedcompon": [26, 159, 160], "subgraphscount": [26, 159, 160], "subgraph": [26, 159, 160, 244], "li": [26, 41, 183], "subgraphcount": [26, 159, 160], "getconnectedid": [26, 159, 160], "encapsul": 27, "triangular": 27, "surfac": [27, 84, 167, 180, 184, 199, 209, 245, 246], "own": [27, 49, 103, 104, 227], "associ": [27, 61, 62, 68, 82, 173], "caus": [27, 62, 82, 95, 100, 118, 168, 173, 204], "storag": [27, 42, 142], "too": [27, 37, 246], "setstabl": [27, 159, 160], "long": [27, 42, 84, 85, 159, 160, 244, 253], "mark": [27, 62, 82, 132, 173, 178], "whether": [27, 28, 33, 61, 62, 82, 84, 95, 123, 167, 169, 173, 178], "unstabl": 27, "advis": [27, 178], "setisovalu": [27, 157, 159, 160, 177], "iso": [27, 84, 207], "isovalu": [27, 157, 159, 160], "setothermesh": [27, 159, 160], "othermesh": [27, 159, 160], "setcub": [27, 157, 159, 160, 177], "cube_": 27, "numvertic": [27, 159, 160], "triangl": [27, 128, 159, 165, 227], "setvertic": [27, 159, 160], "addvertic": [27, 128, 159, 160, 165], "length": [27, 28, 41, 81, 95, 119, 127, 128, 159, 165, 190, 200, 205, 213, 220, 221, 223, 224, 252, 254, 255, 257, 258], "numnorm": [27, 159, 160], "setnorm": [27, 159, 160], "addnorm": [27, 159, 160], "color3f": [27, 159, 160], "addcolor": [27, 159, 160], "saniti": [27, 245], "sane": 27, "right": [27, 105, 118, 141, 142, 189, 197, 198, 200, 202, 203, 205, 207, 213, 221, 224, 225, 226, 245], "overload": [27, 28, 43, 85, 122, 125, 130, 144, 145], "smooth": [27, 84, 159, 160, 245, 246], "iterationcount": 27, "appli": [27, 62, 71, 79, 80, 82, 143, 159, 164, 173, 178, 185, 198, 205, 207, 213, 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"Line Breaks": [[5, "line-breaks"]], "Inheritance and the \u201cvirtual\u201d Keyword": [[5, "inheritance-and-the-virtual-keyword"]], "Referencing Members": [[5, "referencing-members"]], "File Naming": [[5, "file-naming"]], "Breaking Rules": [[5, "breaking-rules"]], "Class Avogadro::Core::Color3f": [[18, "class-avogadro-core-color3f"]], "Class Avogadro::Core::AtomTemplate": [[12, "class-avogadro-core-atomtemplate"]], "Class Avogadro::Core::BondTemplate": [[17, "class-avogadro-core-bondtemplate"]], "Class Avogadro::Core::ArraySet": [[8, "class-avogadro-core-arrayset"]], "Class Avogadro::Core::Elements": [[23, "class-avogadro-core-elements"]], "Class Avogadro::Core::AvoSpglib": [[14, "class-avogadro-core-avospglib"]], "Class Avogadro::Core::BasisSet": [[15, "class-avogadro-core-basisset"]], "Coding Conventions (C++)": [[2, "coding-conventions-c"]], "C++ Features": [[2, "c-features"]], "Including Headers": [[2, "including-headers"]], "Export Macro Headers": [[2, "export-macro-headers"]], "Private Headers": [[2, "private-headers"]], "Qt Headers": [[2, "qt-headers"]], "Namespaces": [[2, "namespaces"]], "Casting": [[2, "casting"]], "Aesthetics": [[2, "aesthetics"]], "Class Avogadro::Core::Atom": [[11, "class-avogadro-core-atom"]], "Hydrogen Molecule": [[254, "hydrogen-molecule"]], "Task": [[254, "task"], [250, "task"], [252, "task"], [257, "task"], [258, "task"], [253, "task"], [256, "task"], [248, "task"]], "Solution": [[254, "solution"], [251, "solution"], [257, "solution"], [258, "solution"], [253, "solution"], [256, "solution"], [247, "solution"]], "See also": [[254, "see-also"], [250, "see-also"], [252, "see-also"], [257, "see-also"], [258, "see-also"], [253, "see-also"], [256, "see-also"], [248, "see-also"]], "Sources": [[254, "sources"], [258, "sources"], [253, "sources"]], "Teach": [[255, "teach"]], "Publications": [[255, "publications"]], "Activities": [[255, "activities"]], "General Chemistry": [[255, "general-chemistry"]], "Organic Chemistry": [[255, 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Avogadro::QtGui::PersistentAtom": [[90, "class-avogadro-qtgui-persistentatom"]], "Tools": [[222, "tools"], [222, null]], "Build Menu": [[205, "build-menu"]], "Cartesian Editor\u2026": [[205, "cartesian-editor"]], "1. Sort by\u2026": [[205, "sort-by"]], "2. Unit of Measure": [[205, "unit-of-measure"]], "3. Editing & Modifying Data": [[205, "editing-modifying-data"]], "Change H to Methyl": [[205, "change-h-to-methyl"]], "Add Hydrogens": [[205, "add-hydrogens"]], "Add Hydrogens for pH\u2026": [[205, "add-hydrogens-for-ph"]], "Remove Hydrogens": [[205, "remove-hydrogens"]], "Insert": [[205, "insert"]], "Invert Chirality": [[205, "invert-chirality"]], "Super Cell Builder\u2026": [[205, "super-cell-builder"]], "Nanotube Builder\u2026": [[205, "nanotube-builder"]], "Introduction": [[202, "introduction"]], "Opening a File": [[202, "opening-a-file"]], "Importing by Name": [[202, "importing-by-name"]], "Navigation": [[202, "navigation"]], "Edit Menu": [[206, "edit-menu"]], "Undo": [[206, "undo"]], "Redo": [[206, "redo"]], "Cut": [[206, "cut"]], "Copy": [[206, "copy"]], "Copy As": [[206, "copy-as"]], "Paste": [[206, "paste"]], "Clear": [[206, "clear"]], "Select All": [[206, "select-all"], [210, "select-all"]], "Select None": [[206, "select-none"], [210, "select-none"]], "View Menu": [[211, "view-menu"]], "New View": [[211, "new-view"]], "Duplicate View": [[211, "duplicate-view"]], "Detach View": [[211, "detach-view"]], "Close View": [[211, "close-view"]], "Center": [[211, "center"]], "Align View to Axes": [[211, "align-view-to-axes"]], "Full Screen": [[211, "full-screen"]], "Reset Display Types": [[211, "reset-display-types"]], "Set Background Color\u2026": [[211, "set-background-color"]], "Projection": [[211, "projection"]], "Display Axes": [[211, "display-axes"]], "Debug Information": [[211, "debug-information"]], "Use Quick Render": [[211, "use-quick-render"]], "All Molecules in File\u2026": [[211, "all-molecules-in-file"]], "Crystal View Options\u2026": [[211, "crystal-view-options"]], "Properties": [[211, "properties"]], "Select Menu": [[210, "select-menu"]], "Invert Selection": [[210, "invert-selection"]], "Select SMARTS\u2026": [[210, "select-smarts"]], "Select by Element\u2026": [[210, "select-by-element"]], "Select by Residue\u2026": [[210, "select-by-residue"]], "Select Solvent": [[210, "select-solvent"]], "Add Name Selection\u2026": [[210, "add-name-selection"]], "Optimizing Geometry": [[215, "optimizing-geometry"]], "Optimization": [[215, null]], "Drawing Molecules": [[200, "drawing-molecules"]], "Creating Carbon Dioxide": [[200, "creating-carbon-dioxide"]], "File Menu": [[208, "file-menu"]], "New": [[208, "new"]], "Open": [[208, "open"]], "Open Recent": [[208, "open-recent"]], "Close": [[208, "close"]], "Save": [[208, "save"]], "Save As\u2026": [[208, "save-as"]], "Revert to Saved": [[208, "revert-to-saved"]], "Import": [[208, "import"]], "Export": [[208, "export"]], "Draw Tool": [[221, "draw-tool"]], "1. Creating a Molecule": [[221, "creating-a-molecule"]], "2.": [[221, "id2"]], "3.": [[221, "id3"]], "4.": [[221, "id4"]], "5.": [[221, "id5"]], "6.": [[221, "id6"]], "7.": [[221, "id7"]], "8.": [[221, "id8"]], "9.": [[221, "id9"]], "Geometry Constraints": [[213, "geometry-constraints"]], "Constraints": [[213, "constraints"], [207, "constraints"]], "Example": [[213, "example"]], "Optimizations": [[213, "optimizations"]], "Example cont.": [[213, "example-cont"]], "Auto-Optimize Tool": [[218, "auto-optimize-tool"]], "Force Fields & Algorithms": [[218, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[218, "fixing-ignoring-selections"]], "User Guide": [[204, "user-guide"]], "Avogadro: Molecular Editor and Visualization": [[204, "avogadro-molecular-editor-and-visualization"], [179, "avogadro-molecular-editor-and-visualization"]], "Avogadro 2": [[204, "avogadro-2"]], "Align Tool": [[217, "align-tool"]], "Enabling additional force fields": [[214, "enabling-additional-force-fields"]], "Creating an avogadro conda environment": [[214, "creating-an-avogadro-conda-environment"]], "Setting the Python path": [[214, "setting-the-python-path"]], "Menus": [[209, "menus"], [209, null]], "Auto-Rotate Tool": [[219, "auto-rotate-tool"]], "Making Selections": [[203, "making-selections"]], "Bond-Centric Manipulate Tool": [[220, "bond-centric-manipulate-tool"]], "Starting with the basics:": [[220, "starting-with-the-basics"]], "Adjusting Bonds and Torsion Angles": [[220, "adjusting-bonds-and-torsion-angles"]], "Measure Tool": [[224, "measure-tool"]], "Extension Menu": [[207, "extension-menu"]], "Animation": [[207, "animation"]], "Optimize Geometry": [[207, "optimize-geometry"]], "Molecular Mechanics": [[207, "molecular-mechanics"]], "Setup Force Field\u2026": [[207, "setup-force-field"]], "Calculate Energy": [[207, "calculate-energy"]], "Conformer Search": [[207, "conformer-search"]], "Ignore Selection": [[207, "ignore-selection"]], "Fix Selected Atoms": [[207, "fix-selected-atoms"]], "Avogadro Extensions\u2013Plugins": [[207, "avogadro-extensionsplugins"]], "General \u201cHow To\u201d for Plugins": [[207, "general-how-to-for-plugins"]], "Running Gaussian": [[207, "running-gaussian"]], "Molecular Orbitals": [[207, "molecular-orbitals"]], "QTAIM (Quantum Theory of Atoms in Molecules)": [[207, "qtaim-quantum-theory-of-atoms-in-molecules"], [198, "qtaim-quantum-theory-of-atoms-in-molecules"]], "Spectra\u2026": [[207, "spectra"]], "Create Surfaces\u2026": [[207, "create-surfaces"]], "Getting Started": [[201, "getting-started"]], "Manipulate Tool": [[223, "manipulate-tool"]], "Introduction to Molecular Mechanics": [[216, "introduction-to-molecular-mechanics"]], "UFF": [[216, "uff"]], "MMFF94(s)": [[216, "mmff94-s"]], "GAFF": [[216, "gaff"]], "Finding Conformers of Molecules": [[212, "finding-conformers-of-molecules"]], "Start with your molecule of interest": [[212, "start-with-your-molecule-of-interest"]], "Optimize the geometry": [[212, "optimize-the-geometry"]], "Change the force field options": [[212, "change-the-force-field-options"]], "Set the conformer search options": [[212, "set-the-conformer-search-options"]], "Pick a search method and start the search": [[212, "pick-a-search-method-and-start-the-search"]], "Class Avogadro::Io::DcdFormat": [[47, "class-avogadro-io-dcdformat"]], "Class Avogadro::Core::MoleculeDeserializer": [[29, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::RingPerceiver": [[35, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::NameAtomTyper": [[32, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::MoleculeSerializer": [[30, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Core::Mesh": [[27, "class-avogadro-core-mesh"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[44, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Io::CmlFormat": [[46, "class-avogadro-io-cmlformat"]], "Class Avogadro::Core::SlaterSet": [[37, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::Variant": [[42, "class-avogadro-core-variant"]], "Class Avogadro::Core::GaussianSetTools": [[25, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::Residue": [[33, "class-avogadro-core-residue"]], "Class Avogadro::Core::Molecule": [[28, "class-avogadro-core-molecule"]], "Class Avogadro::Core::VariantMap": [[43, "class-avogadro-core-variantmap"]], "Class Avogadro::Core::SharedMutex": [[36, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::SlaterSetTools": [[38, "class-avogadro-core-slatersettools"]], "Class Avogadro::Io::CjsonFormat": [[45, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Io::FileFormatManager": [[49, "class-avogadro-io-fileformatmanager"]], "Class Avogadro::Io::FileFormat": [[48, "class-avogadro-io-fileformat"]], "Class Avogadro::Core::SpaceGroups": [[39, "class-avogadro-core-spacegroups"]], "Class Avogadro::Core::SymbolAtomTyper": [[40, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::Mutex": [[31, "class-avogadro-core-mutex"]], "Class Avogadro::Core::ResidueData": [[34, "class-avogadro-core-residuedata"]], "Class Avogadro::Core::UnitCell": [[41, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::Graph": [[26, "class-avogadro-core-graph"]], "Building Source Code": [[238, "building-source-code"]], "Cloning Repositories": [[238, "cloning-repositories"]], "Updating": [[238, "updating"]], "Prerequisites": [[238, "prerequisites"]], "Debian-based Distribution or Ubuntu": [[238, "debian-based-distribution-or-ubuntu"]], "Building": [[238, "building"]], "Finding Qt, Windows Generators": [[238, "finding-qt-windows-generators"]], "Normal Development": [[238, "normal-development"]], "Build Tree Layout": [[238, "build-tree-layout"]], "Running Executables": [[238, "running-executables"]], "Building Packages": [[238, "building-packages"]], "Release Notes v1.94.0": [[241, "release-notes-v1-94-0"]], "Features": [[241, "features"], [237, "features"]], "\ud83d\udc1b Bug Fixes": [[241, "bug-fixes"], [246, "bug-fixes"], [242, "bug-fixes"], [244, "bug-fixes"], [243, "bug-fixes"], [245, "bug-fixes"]], "\ud83d\udc0d Python Improvements": [[241, "python-improvements"]], "\ud83e\uddf0 Maintenance": [[241, "maintenance"], [246, "maintenance"], [242, "maintenance"], [244, "maintenance"], [243, "maintenance"], [245, "maintenance"]], "Selection Tool": [[226, "selection-tool"]], "Release Notes v1.98.0": [[246, "release-notes-v1-98-0"]], "\ud83c\udf1f Highlights (tldr)": [[246, "highlights-tldr"]], "\u2728 Features": [[246, "features"], [242, "features"], [244, "features"], [243, "features"], [245, "features"]], "\ud83d\ude80 Performance Improvements": [[246, "performance-improvements"], [245, "performance-improvements"]], "\ud83d\udcda Translations": [[246, "translations"], [242, "translations"], [244, "translations"], [243, "translations"], [245, "translations"]], "Install": [[239, "install"], [237, "install"]], "Template Tool": [[227, "template-tool"], [236, "template-tool"]], "Inserting Atoms with Specific Geometry": [[227, "inserting-atoms-with-specific-geometry"]], "Attaching Ligands": [[227, "attaching-ligands"]], "Attaching Functional Groups": [[227, "attaching-functional-groups"]], "Creating New Ligands": [[227, "creating-new-ligands"]], "Creating New Haptic Ligands": [[227, "creating-new-haptic-ligands"]], "Release Notes v1.95.0": [[242, "release-notes-v1-95-0"]], "Changes": [[242, "changes"], [244, "changes"]], "Viewing Molecular Orbitals": [[232, "viewing-molecular-orbitals"]], "Configure": [[232, "configure"]], "Release Notes v1.96.0": [[244, "release-notes-v1-96-0"]], "\ud83d\ude80 Performance Fixes": [[244, "performance-fixes"]], "Tutorials": [[228, "tutorials"], [228, null]], "Viewing Electrostatic Potential Maps": [[231, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[231, "changing-surface-settings"]], "Release Notes v1.95.1": [[243, "release-notes-v1-95-1"]], "Major New Features": [[236, "major-new-features"]], "Speed and Stability": [[236, "speed-and-stability"]], "Rendering": [[236, "rendering"]], "New real-time shadows and depth effects": [[236, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[236, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[236, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[236, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[236, "layers"]], "Symmetry Properties": [[236, "symmetry-properties"]], "Solvent Accessible and Solvent Excluded Surfaces": [[236, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[236, "flexible-electrostatics-models"]], "New Analysis Tools": [[236, "new-analysis-tools"]], "Python Commands / Plugins": [[236, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[236, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[236, "new-and-updated-interfaces-to-external-programs"]], "Resources": [[237, "resources"]], "Connecting with the Avogadro community": [[237, "connecting-with-the-avogadro-community"]], "Alkene Isomers": [[248, "alkene-isomers"]], "Acid-Base Properties of Amino Acids": [[247, "acid-base-properties-of-amino-acids"]], "Version History": [[240, "version-history"], [240, null]], "Naming a Molecule": [[229, "naming-a-molecule"]], "Educational Publications Using Avogadro": [[249, "educational-publications-using-avogadro"]], "Yes We Chem": [[249, "yes-we-chem"]], "Computational Chemistry": [[249, "computational-chemistry"]], "Spectra / Spectroscopy": [[249, "spectra-spectroscopy"]], "Chemical Reactions and Mechanisms": [[249, "chemical-reactions-and-mechanisms"]], "Materials / Nano": [[249, "materials-nano"]], "Cheminformatics": [[249, "cheminformatics"]], "3D Printing and VR": [[249, "d-printing-and-vr"]], "Remote Teaching": [[249, "remote-teaching"]], "Using QTAIM (Atoms in Molecules) Analysis": [[230, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[230, "start-with-a-wfn-file"]], "Interface Changes": [[235, "interface-changes"]], "Viewing Vibrations": [[233, "viewing-vibrations"]], "What\u2019s New in Avogadro 2": [[234, "whats-new-in-avogadro-2"]], "Navigate Tool": [[225, "navigate-tool"]], "Release Notes v1.97.0": [[245, "release-notes-v1-97-0"]], "Highlights (tldr)": [[245, "highlights-tldr"]], "Building Materials": [[184, "building-materials"], [184, null]], "License": [[178, "license"]], "Creative Commons Attribution-ShareAlike 4.0 International": [[178, "creative-commons-attribution-sharealike-4-0-international"]], "Using Creative Commons Public Licenses": [[178, "using-creative-commons-public-licenses"]], "Creative Commons Attribution-ShareAlike 4.0 International Public License": [[178, "creative-commons-attribution-sharealike-4-0-international-public-license"]], "Section 1 \u2013 Definitions.": [[178, "section-1-definitions"]], "Section 2 \u2013 Scope.": [[178, "section-2-scope"]], "Section 3 \u2013 License Conditions.": [[178, "section-3-license-conditions"]], "Section 4 \u2013 Sui Generis Database Rights.": [[178, "section-4-sui-generis-database-rights"]], "Section 5 \u2013 Disclaimer of Warranties and Limitation of Liability.": [[178, "section-5-disclaimer-of-warranties-and-limitation-of-liability"]], "Section 6 \u2013 Term and Termination.": [[178, "section-6-term-and-termination"]], "Section 7 \u2013 Other Terms and Conditions.": [[178, "section-7-other-terms-and-conditions"]], "Section 8 \u2013 Interpretation.": [[178, "section-8-interpretation"]], "Reducing Crystals to a Primitive Unit Cell": [[186, "reducing-crystals-to-a-primitive-unit-cell"]], "Building Molecules": [[195, "building-molecules"], [195, null]], "Insert Molecular Fragments": [[196, "insert-molecular-fragments"]], "Scaling Crystal Cell Volume": [[187, "scaling-crystal-cell-volume"]], "Making a Crystal Surface Slab": [[181, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[181, "import-the-appropriate-crystal-structure"]], "Building Molecule-Surface Interactions": [[185, "building-molecule-surface-interactions"]], "Start with a generated Crystal Surface": [[185, "start-with-a-generated-crystal-surface"]], "New Window: Create our Molecule": [[185, "new-window-create-our-molecule"]], "Building Carbon Nanotubes": [[190, "building-carbon-nanotubes"]], "Importing Molecules by Name": [[194, "importing-molecules-by-name"]], "VTK Classes": [[177, "vtk-classes"]], "Building a Supercell": [[188, "building-a-supercell"]], "Creating a Surface": [[188, "creating-a-surface"]], "Building a Polymer Unit Cell": [[182, "building-a-polymer-unit-cell"]], "Installing Script Plugins": [[175, "installing-script-plugins"]], "Directories": [[175, "directories"]], "Plugin Packages and Repositories": [[175, "plugin-packages-and-repositories"]], "Adding to the Plugin Directory": [[175, "adding-to-the-plugin-directory"]], "Display Types": [[199, "display-types"], [199, null]], "Building a Peptide": [[189, "building-a-peptide"]], "Building DNA or RNA": [[191, "building-dna-or-rna"]], "Coloring Part of a Molecules": [[197, "coloring-part-of-a-molecules"]], "Hemoglobin": [[197, "hemoglobin"]], "Select by Residue": [[197, "select-by-residue"]], "Select by Element": [[197, "select-by-element"]], "Table of contents": [[180, "table-of-contents"]], "Different Display Styles": [[198, "different-display-styles"]], "Locating Display Types": [[198, "locating-display-types"]], "Axes": [[198, "axes"]], "Ball and Stick": [[198, "ball-and-stick"]], "Cartoon": [[198, "cartoon"]], "Dipole": [[198, "dipole"]], "Force": [[198, "force"]], "Hydrogen Bond": [[198, "hydrogen-bond"]], "Label": [[198, "label"]], "Polygon": [[198, "polygon"]], "Ribbon": [[198, "ribbon"]], "Ring": [[198, "ring"]], "Stick": [[198, "stick"]], "Surfaces": [[198, "surfaces"]], "Van der Waals Spheres": [[198, "van-der-waals-spheres"]], "Wireframe": [[198, "wireframe"]], "Importing from the Protein Data Bank (PDB)": [[193, "importing-from-the-protein-data-bank-pdb"]], "Importing Directly": [[193, "importing-directly"]], "Reading a Downloaded PDB file": [[193, "reading-a-downloaded-pdb-file"]], "Script Interfaces": [[176, "script-interfaces"]], "Fixed String Lists (Pop-up menus)": [[176, "fixed-string-lists-pop-up-menus"]], "Integer Values": [[176, "integer-values"]], "Floating-point values": [[176, "floating-point-values"]], "Building with SMILES": [[192, "building-with-smiles"]], "Perceiving Crystall Symmetry": [[183, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[183, "open-a-crystal-file"]], "Class Avogadro::Rendering::MeshGeometry": [[128, "class-avogadro-rendering-meshgeometry"]], "Class Avogadro::Rendering::ShaderProgram": [[134, "class-avogadro-rendering-shaderprogram"]], "Class Avogadro::Rendering::POVRayVisitor": [[130, "class-avogadro-rendering-povrayvisitor"]], "Class Avogadro::Rendering::TextLabel2D": [[137, "class-avogadro-rendering-textlabel2d"]], "Class Avogadro::Rendering::SphereGeometry": [[136, "class-avogadro-rendering-spheregeometry"]], "Class Avogadro::Rendering::TransformNode": [[143, "class-avogadro-rendering-transformnode"]], "Class Avogadro::Rendering::Visitor": [[145, "class-avogadro-rendering-visitor"]], "Class Avogadro::Rendering::TextRenderStrategy": [[141, "class-avogadro-rendering-textrenderstrategy"]], "Class Avogadro::Rendering::Node": [[129, "class-avogadro-rendering-node"]], "Class Avogadro::Rendering::Scene": [[132, "class-avogadro-rendering-scene"]], "Class Avogadro::TypeTraits< char >": [[148, "class-avogadro-typetraits-char"]], "Class Avogadro::Rendering::VRMLVisitor": [[144, "class-avogadro-rendering-vrmlvisitor"]], "Class Avogadro::TypeTraits< double >": [[149, "class-avogadro-typetraits-double"]], "Class Avogadro::Rendering::GroupNode": [[126, "class-avogadro-rendering-groupnode"]], "Class Avogadro::Rendering::Sphere": [[135, "class-avogadro-rendering-sphere"]], "Class Avogadro::Rendering::LineStripGeometry": [[127, "class-avogadro-rendering-linestripgeometry"]], "Class Avogadro::Rendering::TextLabel3D": [[138, "class-avogadro-rendering-textlabel3d"]], "Class Avogadro::Rendering::TextProperties": [[140, "class-avogadro-rendering-textproperties"]], "Class Avogadro::Rendering::GeometryVisitor": [[125, "class-avogadro-rendering-geometryvisitor"]], "Class Avogadro::Rendering::VolumeGeometry": [[146, "class-avogadro-rendering-volumegeometry"]], "Class Avogadro::Rendering::TextLabelBase": [[139, "class-avogadro-rendering-textlabelbase"]], "Class Avogadro::Rendering::Texture2D": [[142, "class-avogadro-rendering-texture2d"]], "Class Avogadro::Rendering::Primitive": [[131, "class-avogadro-rendering-primitive"]], "Class Avogadro::TypeTraits": [[147, "class-avogadro-typetraits"]], "Class Avogadro::Rendering::Shader": [[133, "class-avogadro-rendering-shader"]], "Class Avogadro::VTK::VtkPlot": [[156, "class-avogadro-vtk-vtkplot"]], "Example Plugin Script - Part 2": [[171, "example-plugin-script-part-2"]], "Providing Input to Run Command": [[171, "providing-input-to-run-command"]], "runCommand() Function": [[171, "runcommand-function"]], "Operation Function": [[171, "operation-function"]], "Retrieving necessary components": [[171, "retrieving-necessary-components"]], "Support for Selection": [[171, "support-for-selection"]], "Sample Input and Output": [[171, "sample-input-and-output"]], "QtGui Classes": [[164, "qtgui-classes"]], "Rendering Classes": [[165, "rendering-classes"]], "Class Avogadro::TypeTraits< unsigned short >": [[155, "class-avogadro-typetraits-unsigned-short"]], "Class List": [[159, "class-list"]], "Core Classes": [[160, "core-classes"]], "Class Avogadro::TypeTraits< unsigned int >": [[154, "class-avogadro-typetraits-unsigned-int"]], "IO Classes": [[162, "io-classes"]], "Class Avogadro::TypeTraits< short >": [[152, "class-avogadro-typetraits-short"]], "Develop": [[161, "develop"]], "Script Plugins": [[161, "script-plugins"], [174, "script-plugins"]], "External Scripting": [[161, "external-scripting"]], "Libraries": [[161, "libraries"]], "Main Classes": [[161, "main-classes"]], "Class Avogadro::TypeTraits< unsigned char >": [[153, "class-avogadro-typetraits-unsigned-char"]], "Command Scripts": [[168, "command-scripts"]], "Specifying UI options with \u2013print-options": [[168, "specifying-ui-options-with-print-options"]], "Returning Data": [[168, "returning-data"]], "Returning Data in a Specific File Format": [[168, "returning-data-in-a-specific-file-format"]], "Appending New Atoms and Bonds": [[168, "appending-new-atoms-and-bonds"]], "Bonding New Atoms": [[168, "bonding-new-atoms"]], "Selected Atoms": [[168, "selected-atoms"]], "Class vtkAvogadroActor": [[158, "class-vtkavogadroactor"]], "Input Generators": [[173, "input-generators"]], "Specifying parameters with --print-options": [[173, "specifying-parameters-with-print-options"]], "Handling User Selections: --generate-input": [[173, "handling-user-selections-generate-input"]], "Coordinate Blocks": [[173, "coordinate-blocks"]], "MoleQueue Classes": [[163, "molequeue-classes"]], "Example Plugin Script - Part 1": [[170, "example-plugin-script-part-1"]], "The Main function:": [[170, "the-main-function"]], "Input Arguments": [[170, "input-arguments"]], "getOptions() Function": [[170, "getoptions-function"]], "Avogadro Remote Procedure Call (RPC)": [[166, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[166, "rpc-protocol"]], "Methods": [[166, "methods"]], "Class Avogadro::TypeTraits< float >": [[150, "class-avogadro-typetraits-float"]], "Class Avogadro::VTK::vtkGLWidget": [[157, "class-avogadro-vtk-vtkglwidget"]], "File Formats": [[172, "file-formats"]], "Identify the Format with --metadata": [[172, "identify-the-format-with-metadata"]], "Reading a format with --read": [[172, "reading-a-format-with-read"]], "Writing a format with --write": [[172, "writing-a-format-with-write"]], "Energy / Force Fields": [[169, "energy-force-fields"]], "Identify the Script with --metadata": [[169, "identify-the-script-with-metadata"], [167, "identify-the-script-with-metadata"]], "Calculating Energies and Gradients": [[169, "calculating-energies-and-gradients"]], "Unit Cells, Total Charge, and Spin Multiplicity": [[169, "unit-cells-total-charge-and-spin-multiplicity"]], "Lattice Vectors and Fractional Coordinates": [[169, "lattice-vectors-and-fractional-coordinates"]], "Charges / Electrostatics": [[167, "charges-electrostatics"]], "Calculating Atomic Partial Charges with --charge": [[167, "calculating-atomic-partial-charges-with-charge"]], "Generating Electrostatic Potentials 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244, 245, 249, 255], "sever": [0, 4, 5, 18, 48, 173, 178, 190, 218, 236, 238, 241, 242, 243, 245, 246], "suggest": [0, 4, 28, 168, 174, 175, 234, 237, 241, 242, 244, 245], "far": [0, 118], "style": [0, 1, 2, 19, 62, 82, 140, 173, 180, 199], "convent": [0, 5, 14, 95], "c": [0, 1, 4, 18, 19, 21, 24, 31, 33, 36, 37, 41, 84, 95, 127, 128, 130, 131, 144, 159, 160, 161, 169, 173, 175, 178, 186, 187, 200, 206, 214, 216, 221, 237, 238, 246, 253, 257], "well": [0, 26, 168, 175, 178, 190, 191, 207, 208, 213, 216, 227, 236, 238, 244], "need": [0, 2, 5, 13, 19, 21, 28, 51, 62, 81, 82, 84, 95, 100, 103, 161, 166, 169, 172, 173, 175, 176, 178, 181, 183, 185, 186, 188, 190, 196, 200, 207, 213, 214, 218, 221, 227, 232, 238, 242, 246, 256], "document": [0, 2, 4, 19, 62, 64, 78, 82, 161, 172, 173, 185, 206, 208, 237, 241, 242, 244, 245, 255], "your": [0, 1, 4, 5, 169, 175, 178, 187, 188, 192, 193, 196, 200, 202, 203, 205, 207, 208, 210, 211, 213, 214, 215, 217, 218, 220, 221, 223, 226, 227, 229, 231, 236, 237, 238, 245], "comment": [0, 5, 62, 82, 173, 241, 242, 244, 245], "doxygen": [0, 1, 29, 30, 156], "api": [0, 1, 48, 49, 75, 95, 121, 126, 129, 145, 237], "doc": [0, 29, 30, 51, 105, 156, 171, 241], "which": [0, 4, 13, 18, 28, 51, 62, 64, 68, 72, 73, 81, 82, 104, 121, 122, 125, 127, 130, 132, 144, 145, 167, 168, 169, 170, 171, 172, 173, 175, 176, 178, 182, 185, 186, 187, 200, 202, 210, 214, 227, 229, 230, 236, 238, 242, 246, 247, 250, 256], "ultim": 0, "becom": [0, 100, 142, 256], "part": [0, 27, 90, 91, 166, 168, 173, 178, 180, 207, 235, 236, 241, 242, 244, 245], "thi": [0, 1, 2, 4, 5, 7, 8, 12, 13, 15, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 33, 37, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 69, 71, 72, 73, 74, 75, 78, 79, 80, 81, 82, 84, 85, 88, 89, 92, 95, 96, 100, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 117, 118, 121, 122, 123, 124, 125, 126, 127, 128, 130, 132, 133, 134, 136, 144, 157, 158, 161, 166, 168, 169, 170, 171, 172, 173, 176, 178, 179, 181, 182, 183, 185, 186, 187, 188, 191, 197, 198, 200, 202, 203, 204, 205, 206, 207, 210, 211, 213, 214, 216, 218, 220, 221, 223, 226, 227, 230, 231, 232, 233, 236, 237, 238, 242, 243, 244, 245, 249, 253, 255, 256], "websit": [0, 190, 192, 193, 207, 244, 245, 249], "featur": [0, 4, 6, 103, 123, 161, 180, 181, 185, 197, 198, 203, 204, 205, 206, 207, 210, 211, 216, 218, 232, 233, 234, 240], "header": [0, 1, 5, 33, 241, 245], "export": [0, 161, 188, 209, 241, 246], "macro": [0, 95, 158], "privat": [0, 78, 242], "qt": [0, 1, 3, 5, 67, 70, 86, 87, 98, 105, 157, 164, 241, 245, 246], "namespac": [0, 1, 5, 161], "cast": [0, 3, 5, 20, 42, 75, 129, 159, 165, 218, 244], "aesthet": 0, "indent": [0, 158], "line": [0, 48, 62, 82, 83, 116, 127, 167, 168, 169, 170, 171, 172, 173, 182, 192, 220, 227, 236, 245, 246], "width": [0, 104, 118, 123, 127, 142, 159, 165, 245], "declar": [0, 1, 2, 169, 246], "variabl": [0, 65, 85, 92, 95, 170, 213, 238], "whitespac": 0, "brace": 0, "parenthes": 0, "switch": [0, 182, 185, 202, 212, 241, 245, 246], "statement": 0, "break": [0, 171], "inherit": 0, "virtual": [0, 8, 9, 10, 13, 15, 24, 28, 32, 33, 37, 40, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 64, 75, 85, 96, 100, 101, 102, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 121, 122, 124, 125, 126, 127, 128, 129, 130, 136, 137, 138, 139, 141, 144, 145], "keyword": [0, 62, 82, 173, 207, 233], "referenc": [0, 15, 65, 85], "member": [0, 8, 9, 27, 28, 42, 43, 44, 62, 82, 85, 107, 123, 126, 127, 128, 131, 158, 161, 167, 169, 172, 173, 178, 198], "file": [0, 1, 2, 4, 6, 15, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 68, 69, 75, 78, 92, 106, 109, 110, 111, 112, 113, 114, 130, 144, 159, 161, 162, 163, 166, 167, 169, 173, 174, 175, 180, 181, 184, 185, 186, 188, 194, 195, 197, 198, 206, 207, 209, 210, 227, 228, 232, 233, 236, 241, 242, 244, 245, 246], "name": [0, 1, 2, 15, 19, 22, 23, 24, 27, 28, 32, 33, 34, 43, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 69, 72, 74, 75, 82, 95, 96, 99, 100, 102, 104, 106, 109, 110, 111, 112, 113, 114, 134, 147, 148, 149, 150, 151, 152, 153, 154, 155, 159, 160, 162, 164, 167, 168, 169, 170, 171, 172, 173, 175, 176, 178, 180, 181, 195, 197, 209, 213, 214, 227, 228, 238, 245, 246], "rule": [0, 62, 79, 82, 159, 164, 173, 248, 250, 255], "class": [0, 2, 5, 173, 236, 242, 246], "descript": [0, 4, 13, 21, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 75, 82, 95, 96, 100, 106, 109, 110, 111, 112, 113, 114, 159, 162, 163, 164, 167, 169, 172, 173, 175, 244], "function": [0, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 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, 157, 158, 161, 174, 175, 200, 207, 216, 222, 236, 246], "us": [1, 2, 5, 7, 8, 11, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 33, 37, 38, 39, 41, 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, 71, 73, 74, 75, 78, 79, 82, 83, 84, 85, 90, 91, 95, 100, 103, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 122, 123, 126, 127, 128, 131, 132, 134, 136, 138, 139, 140, 142, 157, 161, 164, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 180, 181, 182, 183, 185, 186, 190, 191, 193, 194, 198, 200, 202, 203, 204, 205, 207, 209, 210, 212, 214, 216, 217, 218, 220, 221, 224, 225, 227, 228, 229, 234, 236, 237, 238, 241, 242, 244, 245, 246, 247, 250, 252, 253, 254, 255, 256, 257, 258], "gener": [1, 2, 6, 13, 19, 20, 23, 24, 27, 28, 39, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 81, 83, 84, 92, 95, 103, 104, 106, 109, 110, 111, 112, 113, 114, 139, 141, 157, 161, 168, 174, 175, 176, 180, 181, 188, 190, 200, 203, 209, 210, 211, 216, 218, 221, 234, 236, 241, 242, 243, 244, 245, 246, 249], "javadoc": 1, "thei": [1, 2, 4, 6, 13, 51, 62, 64, 82, 84, 115, 136, 173, 175, 176, 178, 185, 189, 216, 218, 227, 238], "go": [1, 5, 75, 81, 100, 191, 193, 197, 213, 214, 218, 223, 238], "next": [1, 62, 82, 139, 169, 176, 182, 197, 212, 231, 234, 236], "all": [1, 3, 4, 5, 7, 8, 12, 21, 22, 23, 24, 26, 27, 28, 41, 48, 49, 51, 62, 65, 68, 75, 78, 81, 82, 89, 92, 95, 99, 103, 104, 121, 124, 126, 127, 128, 129, 132, 143, 145, 159, 161, 162, 165, 168, 171, 173, 175, 178, 181, 183, 193, 197, 198, 200, 203, 205, 209, 213, 216, 220, 221, 223, 227, 230, 232, 234, 237, 238, 242, 243, 250, 253], "should": [1, 2, 5, 8, 20, 22, 27, 28, 39, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 68, 72, 73, 75, 82, 84, 85, 89, 90, 91, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 117, 121, 123, 133, 134, 167, 168, 169, 172, 173, 175, 176, 178, 182, 202, 205, 212, 214, 227, 238, 242, 246, 254], "minimum": [1, 22, 28, 41, 49, 62, 82, 84, 176, 178, 212, 246], "brief": [1, 175], "one": [1, 2, 5, 13, 15, 19, 22, 24, 26, 27, 37, 48, 62, 75, 78, 82, 85, 95, 115, 117, 120, 134, 136, 168, 173, 178, 181, 182, 190, 191, 192, 198, 202, 207, 211, 213, 220, 227, 236, 246], "two": [1, 15, 26, 75, 84, 142, 166, 167, 171, 182, 186, 202, 211, 213, 217, 241, 242, 244, 245, 246, 249, 252, 256, 258], "sentenc": 1, "explain": 1, "what": [1, 28, 43, 85, 95, 180, 197, 207, 211, 225], "intend": [1, 23, 51, 172, 178, 255], "purpos": [1, 2, 5, 51, 65, 115, 126, 136, 167, 178, 207], "i": [1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 37, 38, 39, 40, 41, 42, 43, 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, 71, 72, 73, 75, 78, 81, 82, 84, 85, 88, 89, 90, 91, 92, 93, 94, 95, 96, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 121, 123, 124, 126, 127, 128, 129, 132, 133, 134, 136, 138, 142, 145, 157, 158, 159, 160, 161, 164, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 178, 179, 181, 182, 183, 185, 186, 187, 188, 191, 192, 193, 197, 198, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 212, 213, 214, 216, 217, 218, 220, 221, 223, 224, 225, 226, 227, 229, 231, 232, 234, 236, 237, 238, 242, 243, 244, 245, 246, 249, 250, 253, 254, 255, 256, 258], "goe": [1, 5, 62, 82, 173, 238], "here": [1, 62, 81, 82, 166, 170, 171, 176, 178, 181, 182, 183, 185, 186, 187, 188, 190, 191, 207, 213, 230, 255, 256], "void": [1, 5, 7, 8, 12, 13, 15, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28, 31, 33, 35, 36, 37, 39, 41, 42, 43, 44, 48, 51, 57, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 75, 77, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 100, 103, 104, 105, 107, 108, 110, 112, 114, 115, 116, 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, 144, 145, 157, 158], "dosometh": [1, 5], "overview": [1, 5], "add": [1, 6, 22, 24, 26, 27, 28, 33, 37, 48, 49, 62, 79, 80, 81, 82, 85, 95, 96, 100, 104, 115, 116, 120, 124, 126, 127, 128, 136, 157, 159, 161, 164, 175, 176, 182, 187, 188, 207, 209, 211, 213, 216, 226, 227, 236, 238, 241, 242, 243, 244, 245, 246, 247, 251, 258], "path": [1, 48, 51, 62, 63, 64, 72, 73, 75, 78, 82, 83, 92, 99, 166, 168, 170, 173, 175, 176, 215, 236, 238, 242, 244, 245, 246], "user": [1, 3, 4, 23, 28, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 63, 64, 65, 68, 75, 78, 83, 84, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 162, 167, 168, 169, 170, 171, 172, 175, 176, 211, 237, 238, 242, 243, 244, 245, 246], "appropri": [1, 5, 11, 16, 51, 62, 74, 82, 168, 170, 173, 176, 202, 238, 244], "point": [1, 5, 22, 41, 43, 63, 64, 71, 78, 83, 84, 104, 115, 118, 120, 121, 124, 128, 132, 134, 136, 137, 138, 140, 167, 170, 185, 205, 211, 217, 227, 230, 238, 245, 246, 247], "out": [1, 8, 15, 28, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 73, 82, 92, 106, 109, 110, 111, 112, 113, 114, 118, 124, 126, 176, 178, 182, 183, 202, 204, 213, 216, 219, 225, 235, 236, 246, 255], "altern": [1, 169], "similar": [1, 19, 95, 173, 178, 198, 202, 227], "ideal": [1, 14], "give": [1, 4, 7, 8, 20, 23, 39, 48, 118, 171, 178, 211, 246, 258], "some": [1, 4, 23, 28, 62, 64, 82, 85, 95, 115, 136, 161, 166, 167, 171, 173, 175, 176, 181, 183, 186, 198, 243, 245, 246, 253, 255, 256], "simpl": [1, 23, 31, 32, 36, 39, 40, 50, 62, 82, 176, 188, 198, 205, 238, 250], "exampl": [1, 4, 19, 117, 134, 161, 167, 168, 169, 172, 173, 178, 182, 183, 188, 198, 206, 207, 210, 211, 214, 215, 220, 224, 227, 231, 236, 238, 241, 245, 248, 250], "demonstr": [1, 198, 210], "core": [1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 69, 82, 84, 85, 95, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 121, 123, 124, 127, 128, 134, 136, 139, 142, 157, 159, 161, 173, 234, 244], "simplest": 1, "wai": [1, 85, 95, 178, 182, 188, 197, 203, 205, 207, 214, 236, 237], "possibl": [1, 5, 21, 22, 49, 84, 171, 178, 204, 238, 246, 249], "molequeu": [1, 2, 82, 159, 166, 173, 238, 241], "jsonrpcclient": 1, "h": [1, 2, 5, 19, 24, 49, 61, 63, 64, 65, 66, 67, 68, 71, 74, 76, 78, 82, 83, 89, 92, 98, 105, 107, 115, 116, 118, 120, 122, 125, 127, 141, 159, 160, 161, 167, 173, 178, 183, 185, 209, 216, 241, 245, 247, 249, 254, 256, 258], "client": [1, 66, 159, 163, 178], "The": [1, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 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, 72, 73, 74, 75, 76, 78, 79, 80, 81, 82, 83, 84, 85, 87, 89, 90, 91, 92, 95, 96, 97, 99, 100, 101, 102, 103, 104, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 132, 134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 158, 161, 162, 164, 167, 168, 169, 171, 172, 173, 175, 176, 178, 181, 182, 185, 187, 189, 190, 191, 196, 197, 198, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 213, 214, 216, 217, 218, 219, 220, 223, 224, 225, 226, 227, 229, 231, 236, 238, 247, 249], "submit": [1, 4, 61, 63, 64, 65, 68, 159, 163, 175, 182, 185], "call": [1, 7, 12, 13, 17, 18, 25, 27, 48, 51, 62, 63, 67, 68, 69, 72, 73, 75, 82, 84, 88, 89, 92, 95, 100, 104, 123, 127, 128, 134, 161, 162, 168, 169, 170, 171, 172, 173, 176, 204, 236, 238, 241, 244, 246, 256], "an": [1, 2, 4, 5, 11, 13, 14, 17, 18, 19, 22, 23, 24, 26, 27, 28, 31, 33, 36, 37, 39, 42, 43, 48, 49, 51, 61, 62, 64, 65, 67, 68, 69, 78, 79, 82, 83, 84, 85, 88, 89, 90, 91, 92, 95, 103, 104, 105, 107, 115, 136, 137, 141, 157, 158, 161, 162, 167, 168, 169, 171, 172, 173, 175, 176, 178, 182, 183, 185, 188, 189, 190, 193, 197, 198, 200, 202, 203, 207, 210, 211, 212, 213, 215, 217, 218, 219, 220, 221, 225, 226, 227, 231, 232, 233, 236, 237, 238, 244, 245, 246, 249, 254, 255, 256, 258], "rpc": [1, 65, 68, 161, 241], "server": [1, 4, 61, 65, 66, 68, 92, 166, 229], "json": [1, 45, 62, 65, 75, 82, 83, 100, 113, 161, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 241, 246], "2": [1, 5, 15, 17, 19, 28, 62, 65, 82, 84, 132, 142, 159, 160, 166, 169, 173, 176, 180, 182, 185, 190, 193, 200, 209, 212, 222, 224, 235, 236, 237, 238, 241, 244, 245, 247, 248, 254, 255, 256, 257], "0": [1, 5, 8, 10, 13, 14, 15, 18, 19, 21, 23, 26, 28, 39, 41, 43, 48, 62, 65, 72, 73, 75, 82, 95, 96, 100, 101, 102, 105, 118, 132, 134, 138, 140, 141, 142, 159, 160, 166, 167, 169, 171, 173, 175, 176, 179, 182, 185, 193, 200, 204, 218, 234, 236, 240, 243, 247, 253, 254, 258], "author": [1, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 47, 48, 49, 51, 53, 55, 57, 58, 59, 60, 62, 70, 74, 75, 76, 82, 84, 86, 87, 89, 97, 98, 100, 101, 102, 104, 113, 115, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158, 168, 173, 175, 178, 249], "marcu": [1, 3, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 70, 75, 76, 84, 86, 87, 89, 97, 98, 102, 104, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158], "d": [1, 3, 7, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 62, 70, 75, 76, 82, 84, 86, 87, 89, 92, 97, 98, 102, 104, 107, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158, 159, 160, 178, 242, 244, 245], "hanwel": [1, 3, 15, 18, 22, 24, 25, 27, 31, 36, 37, 38, 46, 48, 49, 55, 70, 75, 76, 84, 86, 87, 89, 97, 98, 102, 104, 113, 117, 118, 120, 121, 122, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 143, 145, 146, 158], "provid": [1, 13, 14, 18, 21, 22, 24, 25, 27, 28, 31, 36, 38, 41, 43, 51, 61, 62, 63, 64, 65, 66, 67, 68, 69, 74, 79, 82, 83, 85, 90, 91, 102, 103, 104, 118, 121, 123, 126, 129, 139, 145, 161, 167, 169, 170, 173, 175, 178, 186, 197, 198, 200, 203, 204, 205, 206, 207, 208, 211, 218, 221, 226, 231, 233, 236, 246], "To": [1, 11, 16, 51, 63, 65, 74, 168, 171, 178, 181, 202, 209, 214, 219, 220, 238], "creat": [1, 12, 17, 19, 21, 26, 28, 33, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 66, 78, 82, 83, 85, 90, 91, 95, 102, 104, 106, 107, 109, 110, 111, 112, 113, 114, 117, 130, 133, 134, 144, 169, 170, 173, 175, 176, 178, 182, 184, 187, 189, 198, 205, 206, 208, 209, 211, 215, 222, 230, 231, 232, 236, 238, 242, 244, 246, 247, 251, 252, 253, 254, 258], "connect": [1, 26, 61, 66, 68, 84, 95, 127, 166, 171, 178, 203, 229, 230, 245], "method": [1, 5, 12, 17, 21, 23, 28, 42, 48, 51, 62, 63, 65, 67, 75, 78, 82, 84, 85, 90, 91, 95, 100, 102, 104, 117, 118, 134, 158, 167, 169, 173, 215, 216, 236, 241, 244, 246, 249], "follow": [1, 5, 19, 62, 82, 92, 142, 167, 168, 169, 170, 171, 172, 173, 176, 178, 185, 188, 213, 214, 238], "done": [1, 13, 24, 37, 39, 65, 117, 123, 133, 159, 163, 169, 171, 218, 232], "new": [1, 2, 4, 5, 6, 7, 12, 17, 26, 27, 28, 33, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 66, 68, 75, 79, 81, 82, 89, 92, 95, 100, 102, 105, 106, 109, 110, 111, 112, 113, 114, 127, 128, 141, 158, 159, 166, 169, 171, 172, 174, 177, 180, 181, 189, 190, 196, 200, 202, 204, 205, 209, 210, 214, 217, 218, 222, 232, 241, 242, 244, 245, 246, 247], "connecttoserv": 1, "myrpcserv": 1, "qjsonobject": [1, 61, 62, 82], "emptyrequest": 1, "qlatin1str": 1, "listqueu": 1, "sendrequest": 1, "endcod": 1, "signal": [1, 2, 61, 66, 67, 68, 69, 70, 75, 77, 82, 84, 85, 86, 87, 88, 89, 92, 95, 96, 98, 100, 103, 104, 157], "order": [1, 7, 13, 17, 21, 28, 62, 75, 79, 82, 85, 89, 92, 95, 103, 105, 123, 133, 134, 142, 159, 160, 167, 168, 171, 173, 176, 198, 200, 214, 221, 224, 227, 230, 238, 242, 246, 253], "act": [1, 95, 171, 238], "result": [1, 5, 12, 13, 18, 21, 25, 38, 62, 65, 68, 82, 83, 105, 124, 134, 141, 161, 168, 171, 172, 176, 178, 181, 182, 183, 230, 238, 254, 256, 257, 258], "notif": 1, "error": [1, 12, 48, 49, 51, 61, 63, 65, 68, 69, 78, 92, 104, 117, 123, 133, 134, 142, 159, 162, 163, 164, 165, 178, 244, 245, 246, 254], "receiv": [1, 61, 82, 178], "respons": [1, 3, 61, 87, 95, 123, 170, 171, 246], "set": [1, 12, 14, 15, 17, 18, 21, 22, 24, 25, 26, 27, 28, 33, 37, 38, 39, 41, 42, 43, 48, 51, 61, 62, 63, 64, 65, 68, 69, 73, 75, 78, 79, 80, 82, 84, 90, 91, 92, 95, 96, 100, 103, 104, 107, 116, 118, 121, 123, 126, 127, 128, 129, 132, 133, 134, 136, 140, 146, 157, 158, 159, 160, 161, 164, 166, 167, 168, 170, 173, 178, 181, 182, 183, 186, 187, 190, 197, 198, 207, 209, 215, 216, 218, 238, 241, 243, 244, 246, 247], "public": [1, 2, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 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, 157, 158, 242], "qobject": [1, 61, 62, 66, 67, 69, 74, 75, 79, 82, 84, 85, 86, 88, 92, 95, 96, 98, 99, 100, 101, 103], "end": [1, 2, 5, 7, 28, 43, 81, 95, 115, 116, 120, 121, 124, 130, 136, 144, 159, 160, 165, 182, 185, 197, 219, 220], "complet": [1, 27, 51, 61, 65, 68, 84, 117, 127, 163, 167, 168, 175, 185], "constructor": [1, 7, 15, 18, 24, 27, 28, 37, 62, 67, 72, 73, 82, 84, 85, 88, 89, 92], "more": [1, 2, 5, 24, 27, 37, 48, 62, 75, 82, 85, 95, 103, 104, 105, 115, 120, 123, 126, 134, 136, 161, 168, 172, 173, 174, 175, 178, 190, 197, 198, 203, 207, 210, 211, 213, 214, 216, 218, 227, 231, 236, 237, 241, 242, 245, 246, 256], "construct": [1, 18, 19, 61, 64, 79, 83, 89, 95, 202, 205], "describ": [1, 13, 15, 62, 68, 82, 117, 167, 169, 172, 173, 178], "paramet": [1, 7, 13, 14, 15, 18, 21, 22, 24, 25, 27, 28, 32, 37, 38, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 63, 64, 65, 67, 68, 74, 75, 78, 81, 83, 84, 85, 89, 90, 91, 92, 95, 100, 102, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 118, 120, 121, 124, 126, 127, 128, 129, 134, 136, 139, 141, 142, 168, 169, 188, 207, 213, 216, 218, 232, 245, 253], "input": [1, 8, 13, 21, 23, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 83, 84, 92, 95, 100, 104, 106, 109, 110, 111, 112, 113, 114, 130, 144, 157, 161, 162, 167, 168, 169, 172, 174, 175, 176, 180, 182, 192, 207, 236, 241, 242, 243, 245, 246], "job": [1, 61, 62, 63, 64, 65, 68, 82, 173], "param": [1, 166], "filenam": [1, 48, 49, 51, 62, 69, 77, 78, 82, 108, 159, 162, 163, 164, 166, 169, 173, 175, 246], "appear": [1, 62, 78, 82, 95, 173, 175, 181, 188, 207, 227], "work": [1, 3, 4, 6, 24, 103, 168, 178, 182, 190, 193, 204, 207, 210, 213, 236, 237, 238, 245, 246], "directori": [1, 29, 30, 78, 156, 161, 238, 242, 246], "content": [1, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 84, 104, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 121, 127, 128, 136, 139, 157, 166, 173, 178], "specifi": [1, 13, 18, 19, 21, 22, 25, 27, 28, 33, 38, 48, 49, 51, 64, 79, 83, 85, 90, 91, 92, 95, 104, 124, 126, 127, 128, 129, 134, 142, 167, 169, 170, 171, 172, 176, 178, 181, 183, 185, 186, 210, 227], "return": [1, 5, 8, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 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, 72, 73, 74, 75, 78, 79, 81, 82, 84, 85, 87, 89, 90, 91, 92, 95, 96, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 114, 115, 117, 118, 120, 121, 123, 124, 126, 127, 128, 129, 134, 136, 142, 158, 167, 170, 171, 205, 229, 251], "true": [1, 5, 8, 12, 14, 15, 17, 21, 24, 25, 26, 27, 28, 31, 36, 37, 38, 39, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 75, 82, 84, 85, 90, 91, 92, 95, 96, 100, 104, 106, 107, 109, 110, 111, 112, 113, 114, 121, 124, 126, 129, 134, 142, 159, 164, 167, 168, 169, 170, 171, 176], "wa": [1, 27, 28, 61, 62, 65, 68, 69, 73, 75, 82, 84, 85, 100, 104, 124, 126, 173, 186, 188, 197, 202, 204, 231, 234, 236, 242], "successfulli": [1, 51, 61, 62, 65, 66, 75, 82, 84, 238, 245], "fals": [1, 5, 14, 15, 21, 24, 25, 27, 28, 31, 36, 37, 38, 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, 75, 82, 84, 85, 95, 96, 100, 104, 106, 109, 110, 111, 112, 113, 114, 121, 124, 126, 129, 134, 159, 164, 167, 169, 171, 173], "otherwis": [1, 14, 15, 21, 24, 25, 28, 37, 38, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 75, 82, 95, 100, 106, 109, 110, 111, 112, 113, 114, 126, 172, 173, 178, 212, 229], "bool": [1, 7, 8, 12, 14, 15, 17, 21, 22, 24, 25, 26, 27, 28, 31, 33, 36, 37, 38, 39, 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, 75, 77, 82, 84, 85, 86, 90, 91, 92, 95, 96, 98, 99, 100, 104, 105, 106, 107, 109, 110, 111, 112, 113, 114, 117, 121, 123, 124, 126, 129, 131, 132, 133, 134, 140, 142, 157, 158, 159, 160], "setinputfil": 1, "const": [1, 2, 5, 7, 8, 9, 10, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 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, 72, 73, 75, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 89, 90, 91, 92, 95, 96, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 144, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157], "qstring": [1, 2, 61, 62, 63, 64, 65, 67, 68, 69, 74, 75, 77, 78, 79, 80, 82, 83, 87, 92, 95, 96, 99, 100, 101, 102, 104, 108], "don": [2, 5, 68, 218, 242, 246], "t": [2, 5, 7, 8, 20, 37, 42, 44, 68, 129, 142, 147, 178, 183, 185, 193, 197, 207, 218, 242, 243, 246], "except": [2, 5, 167, 169, 178, 246], "assert": [2, 178], "product": [2, 197, 256], "never": [2, 169, 178], "crash": [2, 62, 82, 168, 173, 234, 236, 242, 244, 245, 246], "prefer": [2, 49, 62, 82, 134, 167, 171, 173, 192, 205, 207, 212, 245], "solut": 2, "from": [2, 3, 7, 15, 18, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 37, 39, 43, 48, 49, 51, 61, 62, 65, 67, 68, 69, 75, 78, 81, 82, 83, 84, 85, 90, 91, 95, 100, 104, 107, 115, 116, 118, 120, 121, 124, 126, 127, 128, 129, 134, 136, 137, 138, 156, 158, 161, 166, 168, 169, 171, 172, 173, 174, 175, 176, 178, 180, 181, 182, 183, 186, 187, 189, 190, 192, 195, 197, 198, 200, 202, 204, 206, 207, 208, 211, 213, 214, 217, 219, 220, 221, 227, 230, 231, 232, 233, 234, 236, 237, 238, 239, 241, 242, 243, 244, 245, 246, 249, 250, 255], "librari": [2, 4, 51, 103, 142, 175, 181, 227, 238, 242, 246], "over": [2, 182, 186, 192, 193, 196, 218, 227, 229, 234, 236, 241, 242], "boost": [2, 238], "depend": [2, 3, 105, 171, 181, 198, 207, 218, 238, 241, 247, 255], "In": [2, 6, 27, 62, 82, 84, 168, 171, 173, 178, 182, 185, 200, 204, 214, 221, 230, 236, 238, 239, 247], "11": [2, 31, 178, 182], "17": [2, 36, 238], "where": [2, 5, 18, 22, 23, 24, 26, 27, 37, 62, 72, 73, 82, 104, 161, 166, 170, 171, 173, 178, 183, 194, 202, 211, 216, 226, 227, 231, 236, 238, 246, 256], "necessari": [2, 5, 7, 96, 178, 211, 214, 218], "offer": [2, 3, 95, 173, 178, 202, 204, 237], "avo_overrid": 2, "avo_fin": 2, "defin": [2, 41, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 82, 87, 106, 109, 110, 111, 112, 113, 114, 115, 121, 136, 140, 141, 142, 168, 170, 173, 178, 181, 182, 185, 205, 227, 236], "overrid": [2, 24, 28, 32, 37, 40, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 72, 73, 75, 76, 77, 79, 82, 83, 84, 85, 86, 87, 88, 89, 92, 95, 96, 97, 98, 99, 100, 104, 105, 106, 109, 110, 111, 112, 113, 114, 115, 116, 120, 122, 124, 125, 126, 127, 128, 130, 136, 137, 138, 139, 143, 144, 146, 158, 173, 245], "final": [2, 61, 95, 168, 171, 190, 197, 246], "minim": [2, 62, 82, 140, 173, 190], "third": [2, 182, 238], "parti": [2, 178, 238], "think": [2, 167, 237, 249], "carefulli": [2, 75], "befor": [2, 5, 12, 17, 24, 37, 51, 62, 66, 82, 85, 92, 95, 107, 176, 178, 187, 197, 212, 213, 218, 227, 232, 238, 246], "ad": [2, 6, 24, 26, 28, 33, 37, 48, 61, 62, 81, 82, 85, 102, 120, 124, 126, 127, 128, 159, 164, 176, 188, 189, 190, 198, 200, 214, 221, 227, 229, 236, 241, 246], "templat": [2, 6, 7, 8, 9, 12, 13, 17, 20, 42, 44, 62, 64, 65, 68, 82, 90, 91, 117, 129, 134, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 173, 200, 222, 242, 246], "sens": [2, 68], "alwai": [2, 5, 68, 174, 178, 212, 242, 244, 245], "form": [2, 14, 26, 83, 95, 104, 127, 167, 168, 169, 172, 173, 178, 197, 213, 216, 242, 244, 245, 249, 256], "project": [2, 4, 5, 29, 30, 118, 138, 156, 159, 165, 182, 185, 206, 209, 237, 238, 242, 246, 249], "someth": [2, 84, 100, 170, 204], "type": [2, 5, 7, 8, 9, 10, 12, 13, 15, 17, 18, 20, 21, 22, 24, 25, 28, 32, 33, 37, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 67, 71, 75, 77, 78, 81, 82, 85, 89, 90, 91, 95, 96, 99, 102, 103, 106, 107, 109, 110, 111, 112, 113, 114, 117, 118, 121, 124, 126, 129, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 158, 159, 160, 165, 168, 170, 172, 173, 174, 175, 176, 180, 181, 189, 190, 191, 194, 197, 200, 202, 205, 207, 209, 210, 213, 214, 217, 221, 225, 226, 227, 230, 231, 236, 242, 250], "myclass": 2, "sourc": [2, 3, 5, 84, 133, 159, 161, 165, 183, 202, 204, 237, 239, 241, 245], "special": [2, 75, 178], "first": [2, 7, 19, 22, 23, 24, 27, 28, 44, 51, 62, 65, 68, 79, 82, 84, 85, 95, 104, 127, 128, 142, 168, 169, 173, 182, 187, 202, 207, 210, 231, 245, 249], "myapihead": 2, "our": [2, 3, 6, 115, 116, 120, 121, 124, 126, 127, 128, 129, 136, 137, 138, 167, 178, 183, 190, 237, 256], "molecul": [2, 11, 12, 13, 14, 15, 16, 17, 19, 21, 22, 25, 27, 32, 33, 35, 38, 39, 40, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 69, 71, 75, 81, 86, 90, 91, 95, 96, 100, 103, 104, 106, 109, 110, 111, 112, 113, 114, 121, 131, 157, 159, 160, 161, 164, 165, 166, 167, 168, 169, 171, 177, 180, 181, 182, 191, 192, 196, 199, 201, 202, 203, 205, 206, 209, 210, 213, 215, 216, 217, 218, 219, 220, 222, 223, 225, 226, 227, 228, 231, 233, 234, 236, 237, 241, 242, 244, 246, 247, 249, 250, 251, 252, 253, 255, 256, 257, 258], "differ": [2, 4, 22, 28, 42, 43, 85, 99, 176, 178, 180, 199, 200, 214, 216, 221, 230, 236, 247, 253, 254, 255], "modul": [2, 170, 175, 214, 236, 238], "qtcore": 2, "vector": [2, 7, 18, 20, 21, 22, 24, 26, 27, 28, 33, 34, 35, 37, 39, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 81, 84, 95, 106, 107, 109, 110, 111, 112, 113, 114, 117, 118, 120, 124, 134, 142, 182, 183, 233], "stl": [2, 7], "do": [2, 5, 12, 17, 84, 95, 122, 125, 130, 134, 144, 145, 171, 172, 178, 183, 190, 200, 202, 214, 221, 238, 241, 246, 247, 250], "avogadrorenderingexport": 2, "ar": [2, 3, 4, 5, 6, 13, 14, 15, 18, 21, 23, 24, 25, 26, 28, 37, 39, 41, 48, 49, 51, 61, 62, 63, 64, 65, 66, 67, 68, 75, 78, 79, 80, 81, 82, 84, 92, 95, 103, 104, 115, 117, 120, 121, 124, 128, 134, 136, 140, 142, 161, 167, 168, 169, 172, 173, 174, 175, 176, 178, 181, 185, 187, 200, 202, 211, 212, 214, 217, 218, 220, 221, 224, 226, 227, 229, 236, 237, 238, 239, 241, 242, 244, 245, 246, 250, 253, 258], "denot": [2, 121, 129], "_p": 2, "camel": [2, 5], "case": [2, 5, 15, 24, 37, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 72, 73, 82, 84, 106, 109, 110, 111, 112, 113, 114, 166, 169, 171, 173, 178, 197, 200, 210, 220, 221, 244, 245, 246, 256], "qtgui": [2, 28, 62, 63, 64, 103, 104, 157, 159, 161], "instead": [2, 39, 75, 167, 168, 169, 227, 245], "being": [2, 5, 15, 24, 27, 48, 84, 90, 91, 104, 120, 124, 157, 158, 198, 218, 220, 225, 238, 255], "wrong": [2, 5, 242], "qdialog": [2, 63, 65, 71], "correct": [2, 5, 49, 62, 82, 123, 126, 173, 190, 238, 246, 253], "open": [2, 3, 4, 5, 48, 51, 65, 68, 75, 78, 159, 161, 162, 163, 166, 169, 181, 182, 184, 185, 186, 187, 193, 198, 204, 207, 209, 211, 229, 232, 233, 236, 237, 238, 241, 243, 244, 245, 246, 247], "chemistri": [2, 3, 4, 5, 204, 230, 232, 233, 237, 238, 241], "nest": [2, 190], "everyth": [2, 206, 210, 217], "insid": [2, 5, 175, 238], "mongochem": [2, 246], "contain": [2, 5, 7, 8, 12, 15, 17, 18, 20, 21, 22, 24, 26, 27, 28, 33, 37, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 68, 70, 75, 78, 82, 86, 87, 90, 91, 92, 95, 98, 104, 106, 109, 110, 111, 112, 113, 114, 115, 117, 120, 124, 126, 130, 132, 134, 136, 142, 144, 146, 158, 159, 160, 167, 168, 169, 171, 172, 173, 175, 212, 214, 238, 245], "most": [2, 15, 61, 62, 72, 73, 75, 78, 82, 125, 126, 164, 168, 173, 178, 202, 204, 205, 207, 211, 216, 218, 230, 231, 236, 238], "overspecifi": 2, "e": [2, 5, 19, 26, 27, 28, 33, 37, 43, 48, 62, 64, 74, 75, 82, 84, 85, 88, 89, 92, 95, 100, 132, 134, 138, 142, 166, 167, 168, 169, 172, 173, 175, 176, 178, 181, 185, 190, 192, 193, 200, 212, 221, 227, 229, 233, 234, 236, 238, 241, 242, 245, 246], "doesn": [2, 193, 197, 218], "slot": [2, 61, 62, 63, 65, 66, 68, 69, 71, 75, 77, 82, 85, 86, 87, 88, 89, 92, 95, 98, 100, 103, 104, 157], "moc": 2, "often": [2, 183, 216], "littl": 2, "help": [2, 3, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 106, 109, 110, 111, 112, 113, 114, 161, 167, 169, 172, 204, 205, 216, 231, 236, 237, 242, 244, 245, 255], "onli": [2, 5, 15, 21, 23, 28, 43, 51, 62, 65, 68, 81, 82, 85, 95, 104, 117, 121, 124, 133, 167, 168, 169, 171, 172, 173, 178, 190, 197, 198, 202, 207, 210, 214, 216, 218, 220, 230, 236, 238, 243, 244, 245, 246, 255, 258], "specif": [2, 11, 16, 19, 28, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 106, 109, 110, 111, 112, 113, 114, 159, 160, 171, 172, 173, 182, 197, 207, 210, 213, 216, 217, 218, 219, 222, 231, 241, 246], "symbol": [2, 19, 23, 39, 40, 72, 73, 159, 160, 173, 200, 221, 244, 246], "avoid": [2, 5, 22, 84, 178, 238, 245, 246, 256], "static_cast": 2, "dynamic_cast": [2, 129], "const_cast": 2, "reinterpret_cast": [2, 5], "For": [2, 4, 5, 15, 19, 23, 51, 61, 95, 134, 161, 167, 169, 170, 171, 172, 173, 176, 178, 182, 188, 191, 198, 204, 206, 207, 210, 211, 213, 214, 218, 220, 223, 224, 227, 238, 250, 255, 257], "deriv": [2, 15, 20, 21, 25, 38, 48, 85, 100, 104, 126, 158, 178, 230, 250, 251, 255], "qobject_cast": 2, "enum": [2, 15, 19, 21, 22, 24, 33, 37, 39, 42, 48, 51, 61, 65, 67, 77, 78, 81, 85, 95, 96, 107, 117, 126, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155], "": [2, 12, 13, 17, 19, 21, 24, 26, 28, 37, 41, 42, 43, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 65, 75, 79, 80, 81, 82, 84, 85, 95, 104, 106, 107, 109, 110, 111, 112, 113, 114, 118, 121, 129, 142, 157, 159, 160, 162, 166, 168, 169, 170, 172, 173, 178, 180, 183, 190, 200, 205, 207, 211, 213, 214, 217, 218, 219, 220, 221, 225, 230, 231, 236, 238, 241, 246, 248, 255], "constant": [2, 23, 84, 207], "static": [2, 14, 21, 23, 28, 39, 41, 48, 49, 61, 65, 66, 68, 71, 74, 78, 81, 84, 99, 103, 116, 127, 128, 147, 148, 149, 150, 151, 152, 153, 154, 155, 158, 216], "int": [2, 5, 12, 15, 17, 18, 21, 22, 24, 25, 27, 28, 33, 34, 37, 38, 41, 42, 44, 48, 51, 61, 62, 65, 67, 68, 72, 73, 74, 75, 79, 81, 82, 84, 85, 86, 88, 89, 92, 95, 98, 104, 105, 107, 118, 123, 127, 128, 134, 140, 141, 142, 158, 159, 160, 171], "verbos": 2, "argument": [2, 28, 43, 62, 65, 82, 85, 167, 168, 169, 171, 172, 173, 238], "id": [2, 26, 27, 28, 33, 49, 61, 65, 68, 85, 90, 91, 95, 115, 119, 131, 135, 136, 166, 238, 242], "show": [2, 28, 65, 78, 89, 181, 185, 187, 190, 191, 202, 207, 220, 229, 230, 236, 245], "autocomplet": 2, "It": [2, 14, 15, 18, 21, 24, 27, 28, 37, 43, 49, 62, 81, 82, 85, 95, 121, 168, 170, 171, 173, 194, 202, 204, 208, 214, 234, 236, 237, 238], "look": [2, 5, 49, 118, 170, 171, 175, 183, 202, 211, 236, 238], "better": [2, 4, 204, 212, 218, 236, 237, 246], "poor": 2, "peopl": [2, 204], "guess": [2, 23], "abbrevi": [2, 5], "ambigu": 2, "can": [2, 7, 13, 20, 21, 23, 25, 27, 28, 38, 48, 49, 51, 61, 62, 64, 65, 66, 67, 68, 75, 78, 81, 82, 84, 85, 90, 91, 95, 100, 103, 115, 121, 130, 132, 133, 134, 136, 144, 157, 158, 161, 166, 167, 168, 169, 170, 172, 173, 174, 175, 176, 178, 182, 183, 185, 186, 187, 188, 189, 190, 191, 193, 194, 196, 197, 198, 200, 202, 203, 204, 205, 206, 207, 210, 211, 213, 214, 216, 217, 218, 219, 220, 221, 225, 226, 227, 230, 231, 232, 236, 237, 238, 239, 241, 242, 244, 245], "afford": 2, "few": [2, 175, 190, 194, 234, 236, 246], "extra": [2, 62, 82, 168, 173, 182], "byte": [2, 51, 105, 141], "like": [3, 15, 24, 37, 61, 65, 78, 162, 166, 169, 170, 171, 172, 190, 211, 212, 236, 237, 238, 242, 243, 244, 245, 246, 255], "mani": [3, 24, 37, 161, 167, 204, 207, 220, 223, 227, 234, 235, 236, 241, 242, 243, 244, 245, 246], "fundament": 3, "commun": [3, 4, 66, 166, 178, 255], "aim": [3, 230], "develop": [3, 4, 204, 230, 234, 236, 237, 241, 242, 244, 245, 249], "contributor": [3, 234, 241, 242, 243, 244, 245, 246], "alik": [3, 179], "hope": 3, "build": [3, 21, 29, 30, 95, 98, 156, 168, 170, 180, 181, 196, 209, 216, 227, 229, 234, 236, 237, 239, 241, 242, 244, 245, 246, 247, 248, 250, 256, 257], "top": [3, 75, 105, 118, 120, 123, 138, 141, 198, 223, 238, 244], "framework": [3, 236, 245, 246], "so": [3, 18, 21, 24, 37, 41, 51, 62, 82, 84, 95, 134, 142, 157, 158, 161, 166, 171, 173, 175, 178, 183, 190, 196, 197, 198, 207, 218, 238, 254, 256, 258], "veri": [3, 4, 22, 31, 36, 161, 183, 202, 242, 244, 245], "grate": 3, "shahzad": 3, "ali": 3, "michael": 3, "banck": 3, "ross": 3, "braithwait": 3, "jame": 3, "bunt": 3, "donald": 3, "curti": 3, "naomi": 3, "fox": 3, "geoff": [3, 74], "hutchison": [3, 74, 175, 204], "beno\u00eet": 3, "jacob": 3, "jordan": 3, "mantha": 3, "thoma": [3, 241], "margraf": 3, "carsten": 3, "niehau": 3, "simon": 3, "ochsenreith": 3, "konstantin": 3, "tokarev": 3, "allison": [3, 51, 60, 100, 101], "vacanti": [3, 51, 60, 100, 101], "tim": [3, 115], "vandermeersch": [3, 115], "translat": [3, 4, 22, 41, 67, 74, 118, 159, 162, 165, 167, 169, 172, 176, 178, 182, 183, 185, 189, 190, 202, 204, 217, 223, 237, 240, 241], "support": [3, 4, 12, 24, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 74, 78, 82, 95, 102, 106, 109, 110, 111, 112, 113, 114, 115, 117, 123, 134, 142, 161, 166, 167, 168, 169, 170, 172, 173, 175, 202, 229, 230, 236, 237, 238, 241, 242, 244, 245, 246], "its": [3, 8, 14, 26, 39, 49, 51, 72, 73, 81, 95, 126, 161, 170, 171, 178, 197, 205, 225, 254, 255, 256, 258], "ha": [3, 4, 13, 14, 15, 21, 24, 26, 28, 37, 41, 51, 64, 66, 68, 75, 85, 95, 96, 100, 123, 132, 134, 171, 178, 185, 187, 188, 191, 193, 197, 198, 200, 202, 205, 207, 208, 216, 218, 220, 221, 231, 233, 236, 238, 241, 246, 256], "come": [3, 193, 198, 214, 216, 220, 237], "would": [3, 75, 126, 134, 190, 202, 204, 234, 236, 237, 238, 255], "particularli": [3, 216, 234, 235, 242, 244, 245], "googl": [3, 242, 244, 245], "summer": [3, 204, 241, 242, 244, 245], "2007": 3, "2008": 3, "2011": 3, "2016": 3, "2018": 3, "2019": [3, 244], "2021": [3, 241, 242, 243], "2022": [3, 204, 244, 245], "kitwar": [3, 238], "inc": 3, "univers": [3, 204, 216, 218, 249], "pittsburgh": [3, 204], "u": [3, 4, 7, 8, 20, 104, 126, 185, 190, 237, 241, 242, 244, 245], "depart": [3, 204], "defens": 3, "dod": 3, "through": [3, 4, 5, 6, 13, 64, 68, 75, 95, 100, 161, 164, 169, 171, 174, 175, 178, 181, 182, 186, 187, 188, 191, 192, 197, 198, 200, 202, 207, 208, 210, 214, 218, 221, 227, 230, 236, 238, 241, 246], "pettt": 3, "program": [3, 65, 66, 67, 68, 134, 159, 163, 166, 167, 168, 173, 182, 188, 208, 214, 234, 244], "research": [3, 190, 237, 249, 255], "corpor": [3, 178], "cottrel": 3, "scholar": 3, "award": 3, "reli": 3, "number": [3, 5, 12, 14, 15, 17, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 37, 38, 39, 51, 61, 62, 63, 72, 73, 74, 79, 81, 82, 84, 85, 95, 115, 120, 126, 128, 134, 136, 142, 166, 167, 169, 171, 173, 175, 176, 185, 191, 198, 200, 202, 205, 207, 212, 213, 218, 221, 227, 238, 253], "infrastructur": 3, "blue": [3, 18, 23, 140, 142, 159, 160, 165, 197, 198, 217, 220, 231, 236], "obelisk": [3, 23], "group": [3, 5, 7, 12, 17, 19, 28, 39, 41, 61, 62, 63, 64, 65, 66, 68, 69, 78, 82, 85, 92, 95, 100, 104, 105, 116, 121, 122, 123, 126, 127, 128, 134, 136, 137, 138, 139, 140, 142, 157, 173, 183, 185, 186, 187, 188, 190, 200, 205, 210, 222, 230, 235, 236, 244, 246, 249, 251, 253], "pybind11": 3, "chemic": [3, 23, 28, 33, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 106, 109, 110, 111, 112, 113, 114, 161, 172, 173, 194, 202, 206, 208, 210, 214, 229, 236], "structur": [3, 21, 22, 23, 24, 26, 28, 37, 75, 170, 171, 183, 189, 190, 194, 196, 198, 200, 206, 211, 216, 218, 221, 236, 241, 242, 244, 253], "databas": [3, 4, 23, 174, 189, 196, 208, 229], "cmake": [3, 238, 246], "eigen": [3, 5, 28, 37, 107, 118, 134, 238], "softwar": [3, 207, 230], "babel": [3, 162, 169, 202, 236, 241, 244, 245], "And": [3, 167], "cours": [3, 189, 249], "johann": 3, "loschmidt": 3, "amedeo": 3, "made": [4, 6, 7, 23, 26, 81, 100, 178, 179, 196, 197, 198, 202, 203, 208, 210, 211, 216, 226, 241], "who": 4, "want": [4, 7, 168, 185, 189, 190, 197, 200, 202, 212, 213, 221, 223, 230, 231, 237], "back": [4, 7, 83, 159, 160, 205, 211, 241, 242, 244], "great": [4, 237, 238], "place": [4, 5, 39, 49, 72, 73, 171, 173, 178, 183, 198, 206, 207, 211, 218, 223, 225, 237, 238, 251], "start": [4, 5, 24, 26, 92, 116, 120, 180, 181, 182, 189, 190, 205, 215, 218, 219, 222, 228, 233, 237, 242, 246], "fellow": 4, "forum": [4, 6], "question": [4, 237], "level": [4, 62, 75, 82, 173, 238, 249], "post": [4, 213], "mai": [4, 18, 28, 39, 51, 62, 64, 67, 75, 82, 95, 96, 100, 104, 105, 117, 126, 134, 167, 168, 171, 173, 175, 176, 178, 181, 183, 185, 189, 190, 191, 194, 204, 212, 214, 218, 227, 229, 230, 232, 234, 238, 250, 255, 258], "find": [4, 14, 22, 29, 30, 41, 51, 78, 84, 95, 99, 156, 170, 171, 180, 202, 214, 215, 232, 236, 237, 245, 252, 255], "experi": [4, 249], "valuabl": 4, "bug": [4, 6, 193, 237, 240], "pleas": [4, 6, 237, 241, 242, 244, 245, 255], "take": [4, 22, 28, 49, 62, 69, 72, 73, 75, 82, 87, 104, 122, 123, 137, 171, 181, 194, 198, 207, 211, 214, 218, 223, 225, 232], "moment": [4, 190, 232], "tracker": [4, 237], "issu": [4, 6, 237, 241, 246], "code": [4, 6, 24, 37, 62, 82, 84, 88, 161, 167, 169, 170, 171, 173, 183, 190, 191, 193, 207, 232, 233, 236, 237, 239, 241, 242, 244, 245, 246], "while": [4, 5, 26, 62, 82, 84, 95, 100, 168, 169, 173, 182, 187, 213, 218, 227, 229, 245], "move": [4, 28, 104, 138, 142, 178, 185, 193, 196, 202, 218, 223, 236, 246, 247], "around": [4, 5, 15, 22, 31, 36, 63, 65, 69, 185, 187, 190, 196, 198, 202, 213, 223, 236, 250, 255], "fit": [4, 5, 28, 51, 104, 123, 157, 178, 227], "particular": [4, 23, 51, 62, 75, 82, 166, 167, 169, 173, 178, 189, 204, 227], "compon": [4, 18, 22, 23, 26, 28, 127, 128, 132, 140, 142, 161], "itself": 4, "section": [4, 21, 62, 67, 82, 95, 173, 175, 198, 203, 204, 205, 207, 213, 218, 223, 236, 255], "discuss": [4, 6, 168, 207, 237, 241, 242, 244, 245, 255], "idea": [4, 237, 255], "plan": 4, "direct": [4, 18, 41, 62, 82, 115, 118, 119, 120, 121, 124, 128, 136, 142, 159, 165, 173, 178, 193, 219, 238, 244, 247], "progress": [4, 27, 84, 208], "etc": [4, 5, 17, 24, 37, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 100, 103, 104, 106, 109, 110, 111, 112, 113, 114, 115, 120, 133, 134, 136, 142, 157, 161, 168, 169, 170, 173, 176, 198, 202, 207, 227, 229, 230, 233, 236, 237, 238, 241, 246, 250], "both": [4, 15, 26, 51, 63, 64, 161, 167, 169, 172, 173, 175, 176, 187, 214, 237, 258], "python": [4, 92, 99, 161, 168, 171, 174, 175, 215, 237, 238, 240, 242, 244, 245, 246], "script": [4, 63, 64, 75, 83, 92, 99, 100, 162, 172, 214, 237, 241, 242, 243, 245, 246], "util": [4, 64, 92, 99, 118, 175, 188, 198, 207], "tell": [4, 100, 166], "friend": [4, 27, 41, 67, 79, 95, 115, 116, 120, 121, 127, 128, 129, 136, 139], "cite": 4, "paper": [4, 21, 192, 237, 247], "write": [4, 5, 7, 15, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 78, 82, 92, 103, 106, 109, 110, 111, 112, 113, 114, 159, 162, 164, 169, 170, 173, 244, 245, 246], "edit": [4, 14, 64, 95, 161, 180, 188, 197, 198, 200, 202, 207, 209, 210, 211, 221, 223, 233, 234, 236, 238, 244, 245, 246], "tutori": [4, 180, 181, 198, 207, 236, 237, 249], "site": [4, 227, 236, 237], "up": [4, 24, 26, 27, 37, 49, 51, 84, 98, 104, 118, 142, 157, 161, 166, 170, 181, 185, 188, 189, 190, 193, 194, 196, 197, 202, 207, 208, 210, 211, 212, 224, 227, 229, 231, 234, 236, 245, 246], "lesson": [4, 185, 249, 255], "activ": [4, 24, 70, 75, 86, 87, 88, 89, 96, 100, 103, 104, 214, 236, 238, 249], "teacher": [4, 249], "send": [4, 61, 66, 92, 161, 166, 173, 241], "fragment": [4, 133, 134, 159, 165, 180, 192, 195, 203, 205, 223, 226, 227, 236, 241, 246], "report": [4, 6, 62, 82, 173, 183, 237, 242, 243, 244, 245], "encount": [4, 6, 48, 51, 104], "about": [4, 19, 23, 39, 62, 82, 118, 173, 197, 207, 211, 213, 225, 237, 244, 245], "improv": [4, 6, 234, 236, 240, 243], "languag": [4, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 106, 109, 110, 111, 112, 113, 114, 167, 168, 169, 170, 173, 210, 237, 245], "donat": 4, "pai": [4, 204, 258], "host": [4, 244, 245, 246], "meet": 4, "bounti": 4, "when": [5, 7, 8, 13, 15, 18, 20, 24, 28, 37, 49, 51, 61, 62, 63, 64, 65, 66, 68, 69, 75, 78, 82, 88, 89, 92, 95, 100, 104, 123, 127, 128, 157, 168, 169, 170, 171, 173, 175, 187, 188, 197, 198, 202, 203, 205, 207, 211, 212, 214, 223, 232, 238, 242, 245, 246, 247, 249, 250], "base": [5, 7, 8, 13, 15, 19, 28, 33, 48, 62, 75, 76, 78, 79, 82, 85, 97, 100, 101, 116, 120, 121, 122, 124, 125, 129, 130, 144, 145, 161, 169, 171, 173, 175, 176, 178, 190, 191, 205, 207, 210, 236, 245, 246, 250, 255], "larg": [5, 7, 51, 181, 185, 186, 189, 190, 202, 236, 238], "kde": 5, "format": [5, 19, 33, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 75, 78, 79, 80, 82, 106, 109, 110, 111, 112, 113, 114, 140, 142, 161, 162, 166, 167, 169, 170, 171, 173, 174, 175, 178, 179, 193, 207, 230, 232, 236, 241, 242, 243, 244, 245, 246], "enforc": [5, 178], "clang": [5, 245], "tool": [5, 25, 38, 75, 100, 101, 104, 159, 164, 180, 182, 185, 189, 190, 196, 198, 200, 202, 203, 204, 213, 234, 237, 241, 243, 244, 246, 250, 254, 257, 258], "space": [5, 19, 21, 22, 25, 27, 28, 38, 39, 51, 95, 146, 159, 160, 169, 173, 181, 183, 185, 186, 187, 188, 211, 244, 246, 253], "tab": [5, 211, 227, 242, 245], "keep": [5, 26, 51, 65, 67, 95, 103, 105, 213, 238], "less": [5, 12, 17, 23, 28, 95, 207, 227, 231, 236, 256], "than": [5, 7, 12, 17, 23, 26, 28, 51, 62, 82, 95, 166, 178, 186, 236, 242, 253, 256], "80": 5, "charact": [5, 19, 48, 62, 82, 168, 173], "wide": [5, 204, 207, 236], "each": [5, 13, 19, 24, 26, 27, 32, 37, 40, 48, 51, 61, 62, 63, 82, 95, 134, 142, 161, 169, 170, 173, 175, 176, 212, 238, 257, 258], "separ": [5, 142, 168, 173, 178, 230, 235], "g": [5, 19, 24, 28, 33, 48, 62, 74, 75, 82, 88, 89, 92, 100, 134, 138, 140, 142, 159, 160, 166, 167, 168, 169, 172, 173, 175, 176, 178, 181, 190, 192, 193, 200, 212, 221, 227, 229, 233, 236, 238, 241, 246], "nmbr": 5, "singl": [5, 17, 28, 51, 62, 64, 66, 70, 82, 84, 95, 116, 142, 173, 190, 191, 197, 203, 226, 245, 249], "fine": [5, 62, 82, 173], "counter": [5, 62, 82, 92], "temporari": [5, 169], "obviou": 5, 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53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 67, 68, 69, 75, 78, 79, 80, 82, 95, 100, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 117, 123, 130, 133, 134, 139, 141, 142, 144, 159, 160, 162, 166, 168, 171, 173, 192], "rawxml": 5, "char": [5, 12, 17, 23, 24, 28, 33, 39, 42, 85, 95, 100, 105, 127, 128, 134, 139, 140, 141, 142, 147, 149, 150, 151, 152, 154, 155, 159, 160], "list_delimit": 5, "center": [5, 28, 115, 118, 125, 132, 136, 159, 165, 185, 189, 190, 191, 197, 198, 209, 226, 227, 236, 242, 246], "listdelimit": 5, "upper": [5, 137], "m_": 5, "blank": [5, 176, 211], "togeth": [5, 95, 126, 175], "after": [5, 28, 48, 51, 62, 63, 65, 68, 82, 89, 117, 168, 169, 176, 181, 185, 186, 187, 188, 190, 194, 196, 197, 200, 205, 207, 208, 213, 221, 223, 227, 231, 233, 241], "curli": 5, "blah": [5, 62, 82, 176], "explod": 5, "5": [5, 14, 39, 41, 62, 82, 95, 159, 160, 176, 185, 222, 238, 245, 246, 247, 250, 257, 258], "pointer": [5, 7, 23, 27, 42, 44, 65, 78, 121, 124, 126, 129, 159, 160], "refer": [5, 7, 12, 17, 42, 44, 63, 65, 66, 67, 78, 79, 85, 90, 91, 103, 104, 115, 117, 118, 120, 124, 126, 134, 136, 142, 157, 159, 160, 170, 178, 213, 217, 218, 243], "between": [5, 14, 22, 23, 26, 28, 41, 42, 43, 84, 85, 95, 166, 171, 172, 181, 182, 198, 207, 213, 218, 224, 227, 246, 253, 255, 258], "x": [5, 19, 21, 22, 27, 28, 123, 169, 172, 173, 182, 198, 205, 207, 211, 217, 219, 236, 238, 246, 256], "mystr": 5, "y": [5, 19, 22, 28, 118, 123, 169, 173, 198, 205, 207, 211, 217, 219, 238], "whoah": 5, "surround": [5, 231], "binari": [5, 238, 245], "oper": [5, 7, 12, 13, 17, 20, 21, 27, 28, 33, 34, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 69, 71, 78, 79, 84, 85, 95, 106, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 127, 128, 131, 134, 136, 139, 140, 142, 159, 160, 162, 164, 165, 168, 170, 172, 182], "No": [5, 21, 26, 167, 178, 245], "memoryblock": 5, "malloc": 5, "data": [5, 7, 8, 15, 18, 20, 22, 23, 24, 25, 26, 27, 28, 33, 37, 38, 39, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 75, 82, 84, 85, 86, 92, 95, 98, 105, 106, 107, 109, 110, 111, 112, 113, 114, 117, 132, 134, 141, 142, 146, 157, 159, 160, 163, 164, 166, 167, 171, 172, 180, 195, 206, 209, 210, 230, 236, 241, 253, 254, 256], "size": [5, 7, 18, 20, 26, 27, 43, 51, 84, 115, 117, 120, 134, 136, 142, 159, 160, 165, 181, 182, 198, 211, 241, 246, 253], "left": [5, 51, 62, 82, 105, 118, 137, 141, 142, 173, 200, 202, 203, 205, 211, 217, 218, 220, 221, 226, 238], "normal": [5, 7, 24, 27, 28, 37, 62, 75, 82, 84, 89, 115, 119, 120, 121, 124, 128, 134, 136, 159, 160, 164, 165, 173, 187, 202], "same": [5, 12, 17, 21, 26, 51, 61, 63, 127, 128, 167, 178, 197, 211, 216, 238, 247, 258], "foo": 5, "run": [5, 13, 27, 61, 64, 67, 68, 82, 83, 84, 103, 159, 160, 164, 167, 168, 169, 170, 172, 175, 202, 209, 214, 233, 236, 243, 245, 252], "implement": [5, 11, 13, 16, 21, 32, 40, 45, 46, 47, 51, 53, 54, 55, 58, 59, 60, 62, 75, 82, 84, 89, 92, 95, 105, 113, 117, 122, 134, 139, 141, 142, 161, 166, 172, 244, 245], "myfun": 5, "cout": 5, "suppli": [5, 22, 23, 24, 28, 37, 48, 49, 62, 63, 75, 78, 82, 84, 95, 96, 107, 118, 121, 124, 133, 134, 136, 157, 167, 168, 169, 178], "endl": 5, "bar": [5, 207, 211, 223, 225, 232], "bodi": 5, "condit": [5, 21, 190], "also": [5, 26, 27, 39, 48, 62, 72, 73, 82, 95, 104, 115, 132, 136, 161, 167, 169, 171, 173, 174, 175, 178, 181, 185, 187, 189, 190, 191, 193, 200, 202, 203, 204, 205, 206, 207, 208, 210, 211, 214, 216, 218, 219, 221, 224, 225, 226, 230, 236, 237, 238, 245, 255], "complex": [5, 126, 200, 227, 236, 246], "42": 5, "var": [5, 170], "parent": [5, 44, 61, 65, 67, 69, 70, 71, 75, 78, 81, 84, 86, 87, 88, 95, 96, 98, 100, 101, 104, 121, 126, 129, 143, 159, 160, 163, 164, 165], "doe": [5, 7, 12, 14, 21, 28, 39, 51, 85, 92, 95, 104, 118, 134, 158, 167, 168, 169, 178, 186, 207, 216, 223, 253], "wrap": [5, 41, 95, 142, 158, 159, 165], "isvalid": [5, 12, 15, 17, 24, 25, 37, 38, 62, 82, 85, 90, 91, 104, 123, 131, 159, 160, 163, 164, 165], "agooddai": 5, "ani": [5, 7, 12, 13, 17, 22, 26, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 68, 75, 78, 79, 80, 82, 92, 95, 100, 104, 106, 109, 110, 111, 112, 113, 114, 117, 118, 124, 134, 166, 167, 168, 169, 171, 172, 173, 175, 176, 178, 194, 202, 205, 208, 211, 220, 227, 234, 238, 246], "els": 5, "block": [5, 19, 62, 82, 168, 176], "element": [5, 7, 19, 20, 24, 26, 27, 28, 32, 40, 71, 72, 73, 74, 88, 89, 95, 122, 128, 130, 132, 134, 142, 144, 159, 160, 164, 167, 169, 170, 171, 173, 176, 178, 181, 188, 200, 205, 209, 216, 221, 227, 236, 242, 245, 250], "cover": [5, 168, 204, 229], "b": [5, 19, 21, 26, 28, 41, 47, 53, 59, 85, 91, 95, 105, 140, 159, 160, 169, 173, 178, 191, 244, 246, 253], "empti": [5, 7, 19, 24, 26, 28, 33, 39, 42, 43, 48, 49, 51, 75, 78, 79, 95, 117, 123, 133, 134, 159, 160, 168, 187, 241], "express": [5, 62, 82, 173, 178, 256], "intent": 5, "clearer": 5, "label": [5, 12, 19, 28, 62, 82, 95, 107, 138, 159, 160, 164, 168, 170, 173, 176, 178, 199, 213, 236, 241, 242, 244, 246], "column": [5, 21, 41, 67, 86, 98], "everi": [5, 26, 28, 178, 229], "must": [5, 15, 24, 25, 28, 37, 51, 62, 65, 75, 78, 82, 84, 95, 105, 117, 119, 127, 128, 133, 134, 141, 142, 167, 168, 169, 171, 172, 173, 175, 178, 205, 214, 238], "indic": [5, 19, 22, 26, 27, 28, 62, 63, 65, 67, 68, 75, 78, 81, 82, 85, 95, 103, 104, 115, 128, 134, 136, 167, 168, 169, 171, 172, 173, 175, 176, 178, 181, 185, 211, 213, 220, 227, 243], "omiss": 5, "anoth": [5, 39, 51, 169, 183, 188, 198, 200, 203, 221, 236, 258], "immedi": [5, 175], "myenum": 5, "drawlin": [5, 116, 159, 165], "vertex": [5, 26, 27, 84, 116, 127, 128, 133, 134, 159, 160, 165, 224], "drawdot": 5, "fall": [5, 241, 242, 244], "default": [5, 15, 19, 23, 24, 25, 27, 28, 33, 37, 48, 51, 62, 64, 75, 78, 82, 95, 96, 104, 118, 127, 128, 132, 133, 138, 142, 168, 170, 173, 176, 191, 198, 200, 202, 211, 212, 218, 221, 232, 236, 246], "drawdefault": 5, "shorter": 5, "insert": [5, 7, 28, 62, 82, 159, 160, 168, 176, 180, 181, 185, 189, 190, 191, 192, 195, 209, 222, 223, 236, 241, 242, 244, 246, 247], "comma": [5, 167, 169], "broken": 5, "begin": [5, 7, 43, 84, 95, 105, 130, 141, 144, 159, 160, 165, 200, 203, 220, 221, 231, 233], "verylongexpress": 5, "anotherevenlongerexpress": 5, "justwhenyouthoughtitcouldntgetlong": 5, "vector3d": [5, 107], "posit": [5, 7, 12, 14, 21, 22, 25, 28, 38, 81, 84, 95, 115, 118, 119, 125, 132, 134, 135, 136, 138, 159, 160, 165, 185, 189, 190, 205, 211, 223, 236, 251, 256, 258], "currentposit": 5, "offset": [5, 84, 134, 159, 164], "reimplement": [5, 64, 104], "put": [5, 236, 246], "discourag": 5, "prefix": [5, 12, 17, 62, 78, 82, 172, 175, 176, 238], "clear": [5, 7, 13, 26, 27, 42, 43, 48, 62, 82, 84, 86, 89, 98, 104, 115, 116, 120, 121, 125, 126, 127, 128, 132, 136, 139, 157, 159, 160, 162, 164, 165, 182, 203, 209, 226, 241], "cpp": [5, 84], "extens": [5, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 76, 78, 82, 106, 109, 110, 111, 112, 113, 114, 161, 166, 167, 168, 169, 172, 173, 180, 182, 198, 200, 209, 210, 213, 214, 218, 221, 230, 231, 236, 237, 241, 244, 245, 246], "As": [5, 6, 166, 168, 189, 198, 209, 217, 224, 227, 229, 238, 241, 244], "feel": [5, 237], "free": [5, 51, 104, 168, 173, 178, 200, 204, 237, 238], "bad": 5, "local": [6, 62, 74, 82, 84, 168, 173, 175, 176, 237, 241, 244, 246], "avail": [6, 25, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 66, 67, 68, 75, 82, 84, 100, 104, 106, 109, 110, 111, 112, 113, 114, 133, 158, 167, 168, 169, 170, 172, 173, 176, 178, 179, 236, 237, 245], "weblat": [6, 241, 242, 243, 244, 245, 246], "autom": [6, 49, 175, 236, 244, 245], "task": [6, 216, 236], "phrase": 6, "whenev": 6, "allow": [6, 7, 27, 31, 36, 42, 62, 78, 82, 161, 162, 167, 169, 172, 173, 178, 181, 182, 185, 187, 188, 189, 190, 192, 193, 198, 200, 202, 203, 205, 207, 208, 210, 211, 213, 218, 219, 220, 223, 224, 225, 226, 227, 230, 232, 233, 236, 241, 245, 246], "time": [6, 51, 62, 82, 92, 95, 104, 117, 126, 161, 178, 181, 186, 190, 246, 249], "freez": [6, 28], "least": [6, 75, 95, 212, 224, 231, 236, 245], "week": 6, "advanc": [6, 62, 82, 173, 237, 238], "releas": [6, 51, 117, 134, 142, 159, 165, 175, 204, 234, 238, 239, 240], "typenam": [7, 8, 9, 13, 20, 42, 44, 90, 91, 129, 147], "copi": [7, 12, 17, 22, 27, 28, 42, 49, 78, 85, 105, 141, 185, 192, 209, 214, 227, 241, 244, 246], "semant": 7, "effect": [7, 118, 178, 214, 247, 253], "share": [7, 12, 17, 26, 36, 175, 178, 179, 236, 238], "without": [7, 26, 49, 51, 65, 68, 161, 178, 202, 204, 207, 208, 234, 238, 242], "expos": 7, "access": [7, 18, 51, 64, 66, 67, 83, 103, 117, 134, 142, 169, 178, 193, 198, 208, 245, 249], "amount": [7, 185, 207], "non": [7, 8, 23, 28, 62, 82, 95, 126, 169, 171, 173, 178, 241, 242, 245, 246], "trigger": [7, 104, 171], "detach": [7, 134, 159, 160, 209, 244], "op": 7, "count": [7, 12, 28], "1": [7, 12, 15, 17, 18, 19, 21, 22, 24, 26, 28, 51, 62, 65, 68, 82, 85, 95, 105, 118, 132, 134, 141, 142, 159, 160, 167, 169, 171, 173, 175, 176, 182, 183, 185, 187, 190, 191, 193, 200, 204, 209, 212, 222, 224, 234, 236, 238, 239, 240, 241, 246, 247, 248, 254, 255, 256, 257, 258], "perform": [7, 13, 15, 21, 42, 51, 63, 84, 95, 104, 134, 168, 170, 171, 178, 182, 188, 202, 207, 212, 236, 238, 240, 247, 258], "deep": [7, 231, 238], "greater": 7, "unnam": [7, 12, 17, 19, 28, 41, 61, 63, 64, 65, 66, 68, 69, 78, 85, 92, 95, 100, 104, 105, 116, 121, 122, 123, 127, 128, 134, 137, 138, 139, 140, 142, 157], "typedef": [7, 11, 12, 13, 16, 17, 21, 28, 33, 43, 44, 48, 61, 78, 85, 90, 91, 95, 140], "value_typ": [7, 44, 117, 134, 142, 159, 160], "compat": [7, 78, 178, 207], "allocator_typ": [7, 44, 159, 160], "const_refer": [7, 44, 159, 160], "const_point": [7, 44, 159, 160], "iter": [7, 13, 43, 44, 159, 160], "const_iter": [7, 43, 44, 159, 160], "reverse_iter": [7, 44, 159, 160], "const_reverse_iter": [7, 44, 159, 160], "difference_typ": [7, 44, 159, 160], "size_typ": [7, 44, 142, 159, 160], "intern": [7, 13, 39, 51, 61, 63, 65, 66, 78, 89, 139, 142, 159, 160, 167, 169, 172, 237], "arrayrefcontain": [7, 159, 160], "valuetyp": [7, 8, 9, 10, 13, 44, 159, 160], "inlin": [7, 8, 9, 10, 11, 15, 16, 18, 19, 20, 22, 24, 25, 27, 28, 33, 34, 37, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 68, 69, 70, 75, 77, 79, 80, 82, 83, 84, 85, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96, 97, 100, 104, 105, 106, 107, 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, 139, 140, 142, 144, 145, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 158], "explicit": [7, 13, 25, 26, 32, 35, 38, 40, 41, 44, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 75, 77, 79, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 99, 100, 104, 122, 126, 127, 128, 133, 143], "size_t": [7, 12, 26, 28, 35, 43, 44, 51, 81, 95, 115, 116, 120, 124, 126, 127, 128, 134, 136, 140], "n": [7, 15, 19, 24, 26, 27, 37, 44, 126, 128, 173, 189, 190, 216], "valu": [7, 8, 9, 15, 18, 19, 21, 22, 24, 25, 27, 28, 33, 37, 38, 42, 43, 44, 48, 49, 51, 61, 65, 67, 77, 78, 81, 84, 85, 86, 92, 96, 98, 104, 117, 118, 121, 126, 128, 129, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 157, 159, 160, 167, 169, 170, 172, 173, 175, 207, 247], "inputiter": [7, 44], "last": [7, 22, 44, 62, 68, 82, 92, 206, 242], "note": [7, 24, 28, 62, 82, 118, 128, 134, 142, 166, 169, 173, 175, 176, 183, 185, 186, 187, 190, 198, 202, 204, 238, 240, 247, 251, 252, 258], "detachwithcopi": [7, 159, 160], "explicitli": [7, 166], "implicitli": 7, "ensur": [7, 21, 28, 62, 66, 82, 85, 95, 123, 132, 173, 207, 238, 241, 246], "retriev": [7, 15, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 67, 82, 106, 109, 110, 111, 112, 113, 114], "underli": [7, 18, 64, 83, 90, 91], "constdata": [7, 159, 160], "max_siz": [7, 159, 160], "capac": [7, 159, 160], "reserv": [7, 13, 27, 159, 160, 178], "sz": 7, "resiz": [7, 20, 51, 89, 104, 123, 159, 160, 165], "rbegin": [7, 159, 160], "rend": [7, 159, 160], "front": [7, 159, 160], "assign": [7, 26, 27, 28, 32, 40, 85, 95, 159, 160, 167, 236, 244, 245], "val": 7, "push_back": [7, 159, 160], "v": [7, 39, 41, 42, 43, 127, 128, 134, 176, 178, 193, 238, 246, 248, 256], "pop_back": [7, 159, 160], "eras": [7, 159, 160], "idx": [7, 67, 79], "othert": 7, "swap": [7, 26, 41, 79, 115, 116, 120, 121, 127, 128, 136, 139, 140, 159, 160, 164, 165], "swapandpop": [7, 159, 160], "index": [7, 11, 12, 13, 16, 17, 19, 20, 22, 24, 26, 28, 33, 37, 62, 67, 79, 82, 85, 86, 90, 91, 93, 94, 95, 98, 115, 117, 120, 124, 126, 127, 128, 131, 133, 134, 136, 142, 159, 160, 163, 164, 165, 171, 173, 176, 190, 246], "delet": [7, 49, 51, 69, 95, 104, 124, 126, 133, 157, 168, 182, 200, 205, 211, 221, 242, 244, 246, 251], "valid": [7, 15, 24, 25, 27, 37, 38, 48, 62, 68, 82, 85, 90, 91, 95, 104, 123, 128, 129, 133, 159, 160, 172, 173, 176, 238, 246], "pop": [7, 170, 188, 194, 196, 197, 207, 208, 210, 211, 231], "preserv": [7, 21, 26, 51, 95, 187], "protect": [7, 8, 13, 15, 18, 22, 28, 32, 33, 40, 48, 67, 79, 84, 88, 89, 92, 95, 96, 104, 121, 124, 126, 129, 133, 134, 139, 158, 178], "attribut": [7, 8, 13, 15, 18, 22, 28, 33, 61, 62, 68, 82, 84, 92, 95, 96, 116, 117, 121, 124, 126, 127, 128, 129, 133, 134, 139, 158, 173, 175, 179], "arrai": [8, 13, 18, 20, 21, 22, 26, 27, 28, 39, 51, 62, 82, 84, 85, 95, 115, 116, 117, 121, 123, 124, 127, 128, 134, 136, 139, 142, 159, 160, 167, 169, 172, 173, 176], "store": [8, 18, 20, 23, 24, 25, 28, 37, 38, 39, 42, 51, 62, 63, 64, 79, 80, 82, 95, 115, 116, 117, 118, 121, 127, 136, 142, 208, 246], "figur": [8, 73, 213, 253], "subclass": [8, 10, 15, 28, 45, 48, 66, 121, 126, 127, 128, 129, 131, 139, 141, 145], "coordinateset": [8, 159, 160], "istyp": [8, 159, 160], "match": [8, 23, 28, 39, 49, 62, 65, 67, 68, 78, 79, 80, 82, 117, 168, 173, 232, 238], "placehold": [8, 9, 63, 159, 160], "m_content": [8, 9, 159, 160], "m_data": [8, 18, 22, 28, 159, 160], "holder": [8, 10, 159, 160, 178], "type_info": [8, 9, 10], "clone": [8, 9, 10, 15, 24, 37, 159, 160], "atomtempl": [11, 93, 159, 160], "repres": [11, 12, 16, 17, 18, 21, 23, 26, 28, 33, 39, 42, 49, 63, 64, 66, 67, 83, 95, 121, 131, 161, 171, 198, 234, 236], "moleculeclass": [11, 16], "atomtyp": [11, 17, 28, 32, 40, 85, 90, 95, 159, 160, 164], "m": [11, 12, 16, 17, 24, 35, 37, 41, 64, 77, 90, 91, 93, 94, 95, 178, 187, 190], "molecule_t": [12, 17, 90, 91], "setatomicnumb": [12, 28, 95, 159, 160, 164], "unsign": [12, 14, 15, 17, 21, 22, 23, 24, 27, 28, 37, 39, 42, 44, 61, 65, 68, 84, 85, 95, 100, 105, 107, 127, 128, 134, 139, 140, 141, 142, 159, 160], "num": [12, 24, 28, 95, 171], "proton": [12, 72, 231, 247, 255], "atom": [12, 13, 15, 17, 19, 21, 23, 24, 28, 32, 33, 37, 39, 40, 62, 74, 81, 82, 85, 90, 95, 96, 107, 131, 138, 159, 160, 161, 164, 165, 169, 170, 171, 173, 180, 181, 182, 183, 185, 188, 197, 199, 200, 203, 205, 209, 210, 211, 212, 213, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 228, 229, 231, 233, 234, 236, 241, 242, 244, 245, 246, 250, 256, 258], "atomicnumb": [12, 23, 28, 85, 95, 159, 160, 164], "setposition2d": [12, 159, 160], "vector2": [12, 28, 95], "po": [12, 22, 28, 84, 95, 119, 135], "2d": [12, 28, 211, 241], "Not": 12, "current": [12, 13, 17, 26, 27, 28, 48, 51, 55, 61, 63, 64, 65, 68, 74, 75, 84, 87, 89, 95, 100, 103, 105, 115, 116, 118, 120, 121, 122, 123, 127, 128, 129, 132, 133, 134, 136, 139, 141, 166, 168, 185, 198, 208, 210, 211, 212, 223, 236, 237, 250], "moleculetyp": [12, 17, 90, 91, 159, 160, 164], "compil": [12, 133, 134, 159, 165, 238], "position2d": [12, 159, 160], "setposition3d": [12, 159, 160], "vector3": [12, 21, 22, 25, 28, 38, 39, 41, 81, 85, 95], "3d": [12, 22, 28, 95, 104, 118, 127, 128, 134, 161, 169, 171, 192, 202, 211, 236, 245, 255], "position3d": [12, 28, 85, 95, 159, 160], "sethybrid": [12, 28, 95, 159, 160, 164], "atomhybrid": [12, 28, 95], "hyb": [12, 28, 95], "hybrid": [12, 28, 95, 159, 160, 164, 250, 255], "coordin": [12, 19, 20, 21, 24, 28, 39, 41, 62, 82, 95, 107, 116, 118, 123, 134, 137, 138, 142, 159, 160, 162, 182, 183, 186, 187, 205, 227, 241, 242, 246, 249], "setformalcharg": [12, 28, 95, 159, 160, 164], "sign": [12, 28, 95, 134, 238, 244], "charg": [12, 28, 62, 82, 95, 173, 174, 175, 207, 216, 227, 231, 236, 242, 244, 245, 246, 247, 258], "formal": [12, 28, 95, 227, 244, 246], "formalcharg": [12, 28, 95, 159, 160, 164], "setcolor": [12, 27, 28, 33, 95, 127, 128, 131, 159, 160, 164, 165], "vector3ub": [12, 28, 33, 95, 115, 119, 120, 127, 128, 130, 131, 134, 135, 136, 140, 144], "color": [12, 18, 23, 27, 28, 33, 62, 82, 95, 115, 120, 127, 128, 131, 132, 136, 140, 142, 157, 159, 160, 164, 165, 173, 174, 176, 180, 185, 198, 207, 209, 231, 236, 241, 242, 244, 245, 246], "setlay": [12, 28, 95, 159, 160, 164], "layer": [12, 28, 85, 95, 159, 160, 164, 242, 243, 244, 245, 246], "invalid": [12, 17, 28, 39, 48, 68, 85, 90, 91, 95, 131, 159, 165, 242], "object": [12, 13, 17, 18, 24, 27, 28, 42, 43, 49, 51, 61, 62, 63, 64, 67, 68, 72, 75, 78, 82, 83, 84, 85, 90, 91, 95, 100, 103, 104, 105, 107, 115, 116, 117, 118, 120, 121, 123, 124, 127, 128, 131, 134, 136, 141, 145, 158, 164, 167, 168, 169, 172, 173, 197, 213, 241], "increment": [12, 17], "self": [12, 17, 245], "check": [12, 15, 17, 21, 25, 27, 28, 38, 39, 48, 62, 68, 75, 82, 85, 92, 95, 104, 123, 126, 170, 171, 175, 176, 200, 211, 213, 218, 220, 221, 225, 241, 245, 246, 252, 253, 258], "postfix": [12, 17], "decrement": [12, 17], "setselect": [12, 159, 160], "select": [12, 28, 65, 68, 78, 85, 89, 95, 159, 160, 164, 176, 180, 181, 182, 185, 188, 189, 190, 191, 192, 193, 194, 196, 198, 200, 201, 202, 205, 208, 209, 211, 213, 214, 216, 217, 219, 220, 221, 222, 223, 224, 227, 229, 231, 232, 233, 241, 242, 243, 244, 245, 246, 247], "setforcevector": [12, 28, 95, 159, 160, 164], "forc": [12, 28, 85, 95, 139, 161, 174, 175, 190, 199, 209, 213, 215, 216, 227, 233, 238, 246, 252, 254, 255, 256, 258], "forcevector": [12, 28, 95, 159, 160, 164], "setlabel": [12, 28, 95, 159, 160, 164], "outputtyp": 13, "interfac": [13, 14, 23, 39, 61, 62, 64, 75, 82, 83, 84, 92, 96, 100, 141, 161, 168, 170, 171, 173, 180, 202, 204, 207, 214, 218, 245, 246], "list": [13, 21, 28, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 66, 67, 68, 75, 78, 79, 102, 104, 106, 109, 110, 111, 112, 113, 114, 124, 126, 167, 168, 169, 170, 171, 173, 175, 178, 207, 208, 227, 238, 241, 245, 255], "identifi": [13, 15, 23, 28, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 68, 82, 85, 90, 91, 101, 106, 109, 110, 111, 112, 113, 114, 115, 119, 120, 121, 123, 124, 131, 134, 135, 136, 142, 159, 162, 164, 165, 173], "mol": [13, 14, 19, 21, 22, 25, 32, 33, 38, 39, 40, 56, 58, 61, 62, 63, 64, 69, 71, 75, 82, 95, 100, 167, 168, 169, 171, 207, 251, 256], "nullptr": [13, 25, 28, 32, 35, 38, 40, 49, 51, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 75, 77, 78, 79, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 95, 96, 98, 99, 100, 101, 102, 103, 104, 121, 122, 124, 126, 129, 143, 157, 242], "setmolecul": [13, 15, 19, 35, 63, 64, 69, 75, 100, 104, 157, 159, 160, 163, 164, 177], "obtain": [13, 28, 31, 36, 67, 81, 85, 90, 91, 95, 128, 171], "lookup": [13, 49, 245], "been": [13, 28, 49, 51, 66, 68, 75, 95, 96, 132, 134, 171, 178, 185, 188, 197, 198, 200, 207, 208, 211, 216, 218, 221, 224, 231, 232, 233, 236, 238, 249, 255], "previous": [13, 207, 208, 211, 224], "cach": [13, 51, 62, 66, 82, 92, 175, 245, 246], "There": [13, 62, 81, 82, 173, 191, 192, 193, 211, 226, 237, 238], "correspond": [13, 15, 24, 28, 61, 62, 82, 95, 173, 175, 176, 178, 182, 214, 218, 247], "reset": [13, 48, 51, 62, 82, 90, 91, 92, 96, 104, 118, 123, 157, 159, 160, 163, 164, 185, 209, 219, 223, 224, 225, 241, 242], "typer": 13, "state": [13, 48, 51, 61, 62, 65, 68, 82, 90, 91, 95, 96, 125, 158, 176, 178, 242], "m_type": [13, 133, 159, 160, 165], "initi": [13, 23, 24, 26, 37, 62, 65, 68, 78, 82, 84, 85, 95, 104, 123, 159, 160, 164, 165, 175, 176, 200, 202, 205, 221, 225, 229, 230, 241, 243, 244, 245, 246], "setup": [13, 61, 169, 209, 214, 244], "prior": [13, 61, 178], "enough": [13, 51], "room": 13, "determin": [13, 32, 40, 49, 51, 61, 62, 82, 117, 125, 175, 187, 188, 190, 207, 220, 224, 227, 230, 231, 246], "m_molecul": [13, 15, 95, 159, 160, 164], "popul": [13, 15, 21, 25, 51, 95], "spglib": [14, 39, 95, 183, 241], "short": [14, 28, 39, 42, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 92, 95, 106, 109, 110, 111, 112, 113, 114, 142, 159, 160], "gethallnumb": [14, 159, 160], "carttol": [14, 39, 95], "1e": [14, 39, 95], "hall": [14, 39, 95], "crystal": [14, 39, 41, 180, 184, 188, 198, 205, 207, 209, 236, 242, 246], "unit": [14, 19, 21, 23, 28, 39, 41, 62, 82, 95, 173, 176, 180, 181, 184, 187, 188, 190, 193, 209, 211, 242, 246, 253], "cell": [14, 19, 21, 28, 39, 41, 95, 173, 180, 181, 184, 185, 188, 190, 193, 209, 211, 242, 246, 253], "exist": [14, 22, 26, 28, 43, 51, 65, 67, 85, 95, 102, 126, 134, 168, 172, 173, 218, 234, 242], "algorithm": [14, 21, 84, 95, 186, 207, 212], "fail": [14, 42, 51, 62, 65, 66, 82, 95, 127, 128, 169, 173, 178], "succe": 14, "handl": [14, 21, 48, 49, 63, 68, 75, 78, 88, 89, 92, 100, 104, 117, 133, 142, 159, 162, 163, 164, 165, 167, 168, 169, 172, 236, 241, 246], "cartesian": [14, 19, 21, 24, 37, 39, 41, 95, 169, 173, 182, 183, 186, 187, 198, 209], "toler": [14, 28, 39, 95, 183, 186, 245], "reducetoprimit": [14, 159, 160], "reduc": [14, 21, 39, 95, 178, 180, 184], "primit": [14, 24, 37, 95, 96, 115, 119, 120, 121, 123, 124, 132, 135, 136, 159, 165, 180, 184], "unless": [14, 18, 178], "miss": [14, 234, 242, 245], "conventionalizecel": [14, 95, 159, 160, 164], "refin": [14, 216], "convention": [14, 95], "symmetr": [14, 95, 159, 160, 187, 236], "basi": [15, 24, 25, 28, 37, 38, 62, 82, 107, 108, 173, 178, 207, 246], "gaussianset": [15, 25, 37, 38, 108, 159, 160], "slaterset": [15, 159, 160], "capabl": [15, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95, 106, 109, 110, 111, 112, 113, 114, 115, 136, 172, 173, 205, 208, 216], "calcul": [15, 24, 25, 27, 28, 37, 38, 62, 63, 64, 68, 82, 84, 105, 118, 141, 163, 173, 181, 182, 183, 185, 188, 190, 209, 214, 216, 224, 227, 230, 231, 233, 236, 245, 247, 249, 258], "electrontyp": [15, 24, 25, 37, 159, 160], "electron": [15, 23, 24, 25, 28, 38, 207, 230, 231, 245], "pair": [15, 24, 25, 26, 27, 28, 34, 37, 62, 82, 85, 95, 116, 159, 160, 173, 175, 176, 207, 230, 236, 245], "alpha": [15, 24, 25, 41, 140, 142, 159, 160, 165, 169, 241, 245], "beta": [15, 24, 25, 41, 159, 160, 169, 234], "cannot": [15, 21, 29, 30, 49, 51, 68, 156, 178, 236], "enumer": [15, 19, 21, 22, 24, 33, 37, 42, 48, 51, 61, 65, 67, 77, 78, 81, 85, 96, 117, 126, 131, 133, 134, 140, 142, 147, 148, 149, 150, 151, 152, 153, 154, 155, 171], "destructor": [15, 24, 27, 37, 51, 84], "setelectroncount": [15, 159, 160], "electroncount": [15, 159, 160], "molecule_": 15, "get": [15, 22, 24, 28, 39, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 75, 82, 84, 85, 87, 90, 91, 95, 102, 103, 104, 106, 109, 110, 111, 112, 113, 114, 115, 117, 118, 120, 121, 123, 124, 125, 126, 128, 129, 132, 133, 134, 136, 157, 158, 161, 167, 169, 171, 180, 237, 238, 241, 255], "belong": [15, 67, 85, 90, 91], "setnam": [15, 22, 27, 159, 160], "settheorynam": [15, 159, 160], "theorynam": [15, 159, 160], "molecularorbitalcount": [15, 24, 37, 159, 160], "molecular": [15, 24, 25, 28, 37, 38, 62, 82, 104, 161, 166, 167, 168, 169, 170, 171, 173, 180, 192, 194, 195, 198, 202, 209, 211, 213, 218, 227, 228, 230, 234, 236, 237, 245, 246, 249, 250, 255], "orbit": [15, 24, 25, 37, 38, 107, 159, 160, 161, 180, 198, 209, 228, 236, 242, 254, 257], "homo": [15, 159, 160], "given": [15, 22, 23, 24, 26, 28, 39, 42, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 67, 78, 83, 85, 95, 104, 106, 109, 110, 111, 112, 113, 114, 167, 170], "mo": [15, 22, 24, 25, 37, 159, 160, 246], "lumo": [15, 159, 160], "m_electron": [15, 159, 160], "total": [15, 28, 61, 227, 246], "close": [15, 48, 51, 64, 70, 159, 162, 178, 209, 213, 231, 232, 242, 244, 245, 253], "shell": [15, 24, 37, 107, 159, 162], "doubli": 15, "occupi": [15, 51], "hold": [15, 84, 107, 171, 192, 196, 202, 203, 218], "possibli": 15, "bond": [15, 17, 28, 33, 62, 81, 82, 85, 91, 95, 131, 159, 160, 161, 164, 165, 171, 173, 180, 182, 188, 190, 199, 200, 203, 205, 207, 211, 212, 216, 218, 221, 222, 223, 224, 226, 227, 230, 243, 244, 245, 246, 252, 253, 254, 255, 256, 257, 258], "read": [15, 28, 36, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 69, 75, 78, 82, 106, 109, 110, 111, 112, 113, 114, 159, 162, 164, 169, 171, 173, 175, 178, 195, 205, 230, 241, 242, 243, 244, 246], "output": [15, 19, 21, 24, 29, 30, 37, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 65, 68, 82, 92, 106, 107, 109, 110, 111, 112, 113, 114, 156, 162, 163, 167, 168, 169, 172, 173, 206, 213, 216, 230, 232, 233, 245, 246], "necessarili": 15, "m_name": [15, 22, 159, 160], "usual": [15, 171, 238], "standard": [15, 62, 70, 82, 90, 91, 92, 95, 117, 134, 158, 166, 167, 168, 169, 171, 172, 173, 178, 198, 208, 242, 246], "m_theorynam": [15, 159, 160], "theori": [15, 62, 82, 173, 178, 199, 209, 246, 250], "bondtempl": [16, 94, 159, 160], "bondtyp": [16, 28, 85, 91, 95, 159, 160, 164], "atom1": [17, 28, 85, 95, 159, 160], "atom2": [17, 28, 85, 95, 159, 160], "setord": [17, 159, 160], "o": [17, 92, 118, 126, 136, 158, 167, 200, 206, 216, 221, 238, 258], "getotheratom": [17, 159, 160], "represent": [18, 21, 41, 62, 82, 134, 172, 173, 178, 198, 206], "rgb": [18, 62, 82, 140, 173], "three": [18, 23, 24, 37, 127, 128, 142, 198, 205, 224, 226, 227], "float": [18, 22, 27, 42, 84, 115, 118, 119, 120, 121, 123, 124, 125, 127, 130, 132, 134, 135, 136, 138, 139, 140, 142, 144, 159, 160, 167, 169, 171, 245], "rang": [18, 21, 62, 82, 124, 126, 128, 134, 140, 142, 167, 169, 173, 176, 207, 227, 236, 245, 255], "intens": [18, 28, 245], "red": [18, 140, 142, 159, 160, 165, 198, 217, 231, 236], "green": [18, 140, 142, 159, 160, 165, 198, 217], "memori": [18, 24, 51, 95, 134, 244], "3": [18, 27, 62, 82, 84, 127, 128, 134, 140, 142, 159, 160, 167, 169, 176, 182, 186, 190, 200, 209, 212, 213, 222, 238, 241, 247, 248, 255, 256, 257], "pass": [18, 22, 27, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 68, 75, 82, 83, 84, 92, 100, 104, 106, 109, 110, 111, 112, 113, 114, 121, 122, 134, 166, 168, 173, 242, 245], "directli": [18, 49, 67, 167, 178, 189, 191, 195, 230], "opengl": [18, 123, 132, 161, 238, 244, 245, 246], "conveni": [18, 28, 43, 48, 49, 51, 66, 67, 85, 161, 205, 210, 246], "written": [18, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 64, 82, 84, 106, 109, 110, 111, 112, 113, 114, 168, 173, 176, 178, 231], "emphasi": 18, "effici": [18, 210, 242], "layout": [18, 65, 87], "black": [18, 132, 200, 203, 221, 225, 226], "integ": [18, 22, 27, 142, 173], "255": [18, 62, 82, 134, 140, 173], "expect": [18, 23, 24, 27, 62, 82, 84, 103, 168, 169, 173, 178, 238, 246], "align": [19, 21, 132, 140, 173, 180, 181, 182, 185, 190, 191, 209, 222, 246], "see": [19, 28, 51, 62, 64, 78, 82, 85, 95, 105, 134, 142, 161, 168, 172, 173, 183, 186, 187, 190, 191, 207, 230, 255], "setspecif": [19, 159, 160], "detail": [19, 21, 48, 51, 61, 62, 64, 65, 72, 82, 161, 167, 168, 169, 170, 172, 173, 207], "distanceunit": [19, 159, 160], "distanc": [19, 39, 41, 118, 138, 159, 160, 165, 181, 182, 207, 213, 224, 245, 246, 253], "angstrom": [19, 21, 41, 159, 160, 190, 205, 213], "bohr": [19, 159, 160, 190, 205], "setdistanceunit": [19, 159, 160], "spec": 19, "inform": [19, 24, 28, 39, 62, 82, 95, 104, 123, 134, 168, 173, 175, 178, 187, 197, 198, 203, 205, 207, 209, 210, 213, 216, 218, 223, 237, 244], "z": [19, 22, 28, 169, 173, 181, 185, 190, 191, 198, 205, 207, 211, 217, 219, 241], "6": [19, 21, 27, 62, 74, 82, 84, 123, 158, 159, 160, 167, 169, 171, 173, 190, 213, 222, 238, 246, 250, 256], "carbon": [19, 23, 28, 74, 170, 171, 173, 175, 180, 185, 205, 220, 221, 225, 227, 249, 255, 256, 257], "l": [19, 119, 178, 238, 246], "c1": [19, 246], "gamess": [19, 107, 173, 207, 245, 246], "lattic": [19, 21, 41, 95, 173, 186, 187], "requir": [19, 24, 49, 62, 65, 82, 123, 142, 158, 167, 168, 171, 172, 173, 175, 178, 214, 232, 234, 256], "A": [19, 21, 24, 26, 28, 31, 36, 41, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 70, 75, 78, 79, 81, 82, 85, 86, 87, 90, 91, 92, 95, 96, 98, 99, 100, 102, 104, 106, 109, 110, 111, 112, 113, 114, 115, 122, 124, 126, 132, 133, 134, 136, 142, 161, 168, 173, 176, 178, 179, 182, 188, 189, 191, 193, 194, 196, 200, 205, 207, 211, 212, 220, 221, 225, 231, 232, 236, 238, 249, 255], "liter": [19, 62, 82, 173], "optim": [19, 28, 62, 82, 169, 173, 176, 180, 182, 190, 200, 209, 216, 221, 227, 236, 244, 245, 246, 247, 248, 250, 251, 252, 253, 254, 256, 257, 258], "flag": [19, 21, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 65, 67, 78, 82, 86, 98, 106, 109, 110, 111, 112, 113, 114, 140, 159, 163, 164, 168, 170, 173], "_": [19, 173], "__szxyz110": [19, 173], "replac": [19, 28, 79, 95, 168, 170, 171, 173, 178, 205, 238, 242], "text": [19, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 64, 79, 80, 95, 105, 106, 109, 110, 111, 112, 113, 114, 122, 123, 130, 137, 138, 139, 140, 141, 144, 159, 165, 167, 169, 170, 172, 173, 178, 182, 192, 193, 205, 206, 246, 249], "126214": [19, 173], "765886": [19, 173], "000000": [19, 173], "819345": [19, 173], "564955": [19, 173], "598383": [19, 173], "795127": [19, 173], "310706": [19, 173], "370165": [19, 173], "16": [19, 84, 173, 242], "285330": [19, 173], "757144": [19, 173], "130424": [19, 173], "185837": [19, 173], "548377": [19, 173], "375303": [19, 173], "033768": [19, 173], "794407": [19, 173], "396173": [19, 173], "450760": [19, 173], "generatecoordinateblock": [19, 159, 160], "arrayset": [20, 159, 160], "concret": 20, "_size": 20, "_index": 20, "collect": [21, 61, 62, 64, 65, 82, 104, 115, 120, 121, 124, 132, 136, 161, 171, 173, 178], "common": [21, 48, 62, 82, 121, 124, 126, 129, 145, 167, 168, 173, 179, 196, 207, 216, 227, 236], "crystallograph": [21, 183], "option": [21, 48, 49, 51, 61, 63, 64, 65, 68, 72, 73, 75, 83, 92, 95, 100, 115, 134, 136, 140, 142, 159, 160, 162, 163, 164, 166, 167, 169, 170, 171, 172, 176, 182, 185, 190, 207, 209, 215, 217, 218, 231, 236, 242], "bitwis": [21, 49, 65, 140], "variou": [21, 24, 37, 62, 82, 168, 173, 197, 198, 207, 208, 210, 231, 233, 236, 237, 238, 244], "none": [21, 22, 24, 28, 39, 48, 49, 61, 78, 102, 126, 133, 134, 159, 160, 162, 163, 165, 209, 227, 244], "transformatom": [21, 95, 159, 160], "transform": [21, 39, 95, 118, 143, 178], "along": [21, 45, 46, 47, 48, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 72, 73, 95, 106, 109, 110, 111, 112, 113, 114, 161, 167, 169, 172, 185, 190, 202], "wrapatomstounitcel": [21, 159, 160], "adjust": [21, 41, 81, 95, 159, 164, 187, 197, 198, 200, 205, 207, 211, 213, 218, 219, 221, 222, 223, 232, 233, 241, 246, 250], "fraction": [21, 39, 41, 95, 187, 205], "success": [21, 24, 25, 27, 28, 31, 36, 37, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 65, 68, 69, 82, 85, 95, 106, 109, 110, 111, 112, 113, 114, 134, 159, 164, 169], "rotatetostandardorient": [21, 159, 160], "opt": [21, 61, 95, 142, 170, 171], "rotat": [21, 95, 118, 140, 159, 165, 180, 181, 185, 189, 202, 212, 217, 220, 223, 225, 236, 241, 246, 249, 253], "axi": [21, 28, 118, 120, 132, 181, 182, 185, 190, 211, 217], "xy": [21, 37, 159, 160, 181, 185, 190], "plane": [21, 28, 118, 137, 181, 185, 190, 211, 216, 220], "trig": 21, "sinc": [21, 51, 167, 169, 171, 175, 176, 183, 186, 189, 193, 229, 236, 253], "fragil": 21, "neg": [21, 81, 236], "angl": [21, 41, 118, 200, 207, 211, 213, 221, 222, 224, 244, 245, 246, 257, 258], "found": [21, 28, 39, 43, 49, 62, 67, 78, 79, 80, 82, 84, 85, 124, 126, 161, 170, 173, 198, 203, 205, 206, 207, 210, 226, 229, 232, 237, 238, 241, 242, 243, 244, 245], "http": [21, 51, 84, 172, 175, 178, 190, 193, 194, 207, 238, 241, 242, 244, 245], "xtalopt": [21, 166], "openmolecul": 21, "net": [21, 198, 247], "misc": 21, "rotatetostdorient": 21, "pdf": 21, "setvolum": [21, 159, 160], "real": [21, 41, 42, 169, 246], "newvolum": [21, 95], "isotrop": 21, "scale": [21, 95, 118, 159, 165, 180, 184, 219, 225, 245], "volum": [21, 41, 95, 157, 159, 160, 180, 184, 186], "cubic": [21, 41], "failur": [21, 24, 25, 28, 31, 36, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 82, 95, 106, 109, 110, 111, 112, 113, 114, 134, 178, 243], "nigglireduc": [21, 159, 160], "niggli": [21, 95, 186], "reduct": [21, 95, 186], "produc": [21, 64, 122, 172, 178, 190], "canon": 21, "strive": 21, "gross": 21, "kunstlev": 21, "rw": 21, "sauter": 21, "nk": 21, "adam": 21, "pd": 21, "numer": [21, 62, 82, 115, 134, 136, 167, 168, 169, 173, 241], "stabl": [21, 27, 159, 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"line-width"]], "Declaring Variables": [[5, "declaring-variables"]], "Whitespace": [[5, "whitespace"]], "Braces": [[5, "braces"]], "Parentheses": [[5, "parentheses"]], "Switch Statements": [[5, "switch-statements"]], "Line Breaks": [[5, "line-breaks"]], "Inheritance and the \u201cvirtual\u201d Keyword": [[5, "inheritance-and-the-virtual-keyword"]], "Referencing Members": [[5, "referencing-members"]], "File Naming": [[5, "file-naming"]], "Breaking Rules": [[5, "breaking-rules"]], "Class Avogadro::Core::Bond": [[16, "class-avogadro-core-bond"]], "Class Avogadro::Core::AvoSpglib": [[14, "class-avogadro-core-avospglib"]], "Thanks": [[3, "thanks"], [204, "thanks"]], "Code": [[3, "code"]], "Funding": [[3, "funding"]], "Other Projects": [[3, "other-projects"]], "Class Avogadro::Core::BondTemplate": [[17, "class-avogadro-core-bondtemplate"]], "Translations": [[6, "translations"]], "Current Status": [[6, "current-status"]], "Credits": [[6, "credits"], [244, "credits"], [243, "credits"], [241, "credits"], [246, "credits"], [242, "credits"], [245, "credits"]], "Class Avogadro::Core::CoordinateSet": [[20, "class-avogadro-core-coordinateset"]], "Class Avogadro::Core::AtomTyper": [[13, "class-avogadro-core-atomtyper"]], "Class Avogadro::Core::ArraySet::PlaceHolder": [[10, "class-avogadro-core-arrayset-placeholder"]], "Class Avogadro::Core::Atom": [[11, "class-avogadro-core-atom"]], "Class Avogadro::Core::Cube": [[22, "class-avogadro-core-cube"]], "Class Avogadro::Core::Color3f": [[18, "class-avogadro-core-color3f"]], "Class Avogadro::Core::ArraySet": [[8, "class-avogadro-core-arrayset"]], "Class Avogadro::Core::CoordinateBlockGenerator": [[19, "class-avogadro-core-coordinateblockgenerator"]], "Class Avogadro::Core::AtomTemplate": [[12, "class-avogadro-core-atomtemplate"]], "Documenting Code": [[1, "documenting-code"]], "Class Descriptions": [[1, "class-descriptions"]], "Function Descriptions": [[1, "function-descriptions"]], "Class Avogadro::Core::Elements": [[23, "class-avogadro-core-elements"]], "Class Avogadro::Core::GaussianSet": [[24, "class-avogadro-core-gaussianset"]], "Class Avogadro::Core::Array": [[7, "class-avogadro-core-array"]], "Class Avogadro::Core::ArraySet::Holder": [[9, "class-avogadro-core-arrayset-holder"]], "Basic VSEPR": [[250, "basic-vsepr"]], "Task": [[250, "task"], [253, "task"], [256, "task"], [254, "task"], [252, "task"], [257, "task"], [258, "task"], [248, "task"]], "See also": [[250, "see-also"], [253, "see-also"], [256, "see-also"], [254, "see-also"], [252, "see-also"], [257, "see-also"], [258, "see-also"], [248, "see-also"]], "Further reading": [[250, "further-reading"], [256, "further-reading"], [257, "further-reading"], [247, "further-reading"]], "Hydrogen Clusters": [[253, "hydrogen-clusters"]], "Solution": [[253, "solution"], [256, "solution"], [254, "solution"], [251, "solution"], [257, "solution"], [258, "solution"], [247, "solution"]], "Issues": [[253, "issues"]], "Sources": [[253, "sources"], [254, "sources"], [258, "sources"]], "Markovnikov\u2019s Rule": [[256, "markovnikovs-rule"]], "Hydrogen Molecule": [[254, "hydrogen-molecule"]], "HCN dipole": [[252, "hcn-dipole"]], "1,3-diaxial interactions": [[251, "diaxial-interactions"]], "Tasks": [[251, "tasks"], [247, "tasks"]], "Organic Hybridization": [[257, "organic-hybridization"]], "Water": [[258, "water"]], "Teach": [[255, "teach"]], "Publications": [[255, "publications"]], "Activities": [[255, "activities"]], "General Chemistry": [[255, "general-chemistry"]], "Organic Chemistry": [[255, "organic-chemistry"]], "Biochemistry:": [[255, "biochemistry"]], "Class Avogadro::QtGui::ContainerWidget": [[70, "class-avogadro-qtgui-containerwidget"]], "Class Avogadro::Io::OutcarFormat": [[56, "class-avogadro-io-outcarformat"]], "Class Avogadro::Io::XyzFormat": [[60, "class-avogadro-io-xyzformat"]], "Class Avogadro::MoleQueue::MoleQueueWidget": [[68, "class-avogadro-molequeue-molequeuewidget"]], "Class Avogadro::Io::Hdf5DataFormat": [[51, "class-avogadro-io-hdf5dataformat"]], "Class Avogadro::Io::MMTFFormat": [[54, "class-avogadro-io-mmtfformat"]], "Class Avogadro::Io::LammpsTrajectoryFormat": [[53, "class-avogadro-io-lammpstrajectoryformat"]], "Class Avogadro::Io::GromacsFormat": [[50, "class-avogadro-io-gromacsformat"]], "Class Avogadro::Io::PdbFormat": [[57, "class-avogadro-io-pdbformat"]], "Class Avogadro::QtGui::CustomElementDialog": [[71, "class-avogadro-qtgui-customelementdialog"]], "Class Avogadro::Io::MdlFormat": [[55, "class-avogadro-io-mdlformat"]], "Class Avogadro::QtGui::ElementItem": [[73, "class-avogadro-qtgui-elementitem"]], "Class Avogadro::MoleQueue::BatchJob": [[61, "class-avogadro-molequeue-batchjob"]], "Class Avogadro::Io::PoscarFormat": [[58, "class-avogadro-io-poscarformat"]], "Class Avogadro::QtGui::ElementTranslator": [[74, "class-avogadro-qtgui-elementtranslator"]], "Class Avogadro::MoleQueue::MoleQueueQueueListModel": [[67, "class-avogadro-molequeue-molequeuequeuelistmodel"]], "Class Avogadro::Io::TrrFormat": [[59, "class-avogadro-io-trrformat"]], "Class Avogadro::MoleQueue::InputGenerator": [[62, "class-avogadro-molequeue-inputgenerator"]], "Script Entry Points": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md0"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md14"], [168, "script-entry-points"], [173, "script-entry-points"]], "Specifying parameters with \u2013print-options": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md1"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md15"]], "Fixed Mutually-Exclusive Parameter Lists": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md2"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md16"]], "Short Free-Form Text Parameters": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md3"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md17"], [176, "short-free-form-text-parameters"]], "Existing files": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md4"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md18"], [176, "existing-files"]], "Clamped Integer Values": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md5"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md19"]], "Boolean Parameters": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md6"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md20"], [176, "boolean-parameters"]], "Special Parameters": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md7"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md21"], [173, "special-parameters"]], "Syntax Highlighting": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md8"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md22"], [173, "syntax-highlighting"]], "Requesting Full Structure of Current Molecule": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md9"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md23"], [173, "requesting-full-structure-of-current-molecule"]], "Handling User Selections: \u2013generate-input": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md10"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md24"]], "Automatic Generation of Geometry": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md11"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md25"], [173, "automatic-generation-of-geometry"]], "Error Handling": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md12"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md26"], [173, "error-handling"]], "Debugging": [[62, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md13"], [82, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md27"], [168, "debugging"], [173, "debugging"]], "Class Avogadro::MoleQueue::InputGeneratorWidget": [[64, "class-avogadro-molequeue-inputgeneratorwidget"]], "Class Avogadro::MoleQueue::InputGeneratorDialog": [[63, "class-avogadro-molequeue-inputgeneratordialog"]], "Class Avogadro::MoleQueue::MoleQueueManager": [[66, "class-avogadro-molequeue-molequeuemanager"]], "Class Avogadro::QtGui::BackgroundFileFormat": [[69, "class-avogadro-qtgui-backgroundfileformat"]], "Class Avogadro::QtGui::ElementDetail": [[72, "class-avogadro-qtgui-elementdetail"]], "Class Avogadro::Io::LammpsDataFormat": [[52, "class-avogadro-io-lammpsdataformat"]], "Class Avogadro::MoleQueue::MoleQueueDialog": [[65, "class-avogadro-molequeue-molequeuedialog"]], "Class Avogadro::QtGui::ScenePlugin": [[96, "class-avogadro-qtgui-sceneplugin"]], "Class Avogadro::QtGui::MultiViewWidget": [[87, "class-avogadro-qtgui-multiviewwidget"]], "Class Avogadro::QtGui::FileBrowseWidget": [[77, "class-avogadro-qtgui-filebrowsewidget"]], "Class Avogadro::QtGui::Molecule": [[85, "class-avogadro-qtgui-molecule"]], "Class Avogadro::QtGui::ScriptLoader": [[99, "class-avogadro-qtgui-scriptloader"]], "Class Avogadro::QtGui::MeshGenerator": [[84, "class-avogadro-qtgui-meshgenerator"]], "Class Avogadro::QtGui::MoleculeModel": [[86, "class-avogadro-qtgui-moleculemodel"]], "Class Avogadro::QtGui::HydrogenTools": [[81, "class-avogadro-qtgui-hydrogentools"]], "Class Avogadro::QtGui::RWAtom": [[93, "class-avogadro-qtgui-rwatom"]], "Class Avogadro::QtGui::RWBond": [[94, "class-avogadro-qtgui-rwbond"]], "Class Avogadro::QtGui::GenericHighlighter": [[79, "class-avogadro-qtgui-generichighlighter"]], "Class Avogadro::QtGui::PersistentAtom": [[90, "class-avogadro-qtgui-persistentatom"]], "Class Avogadro::QtGui::PeriodicTableView": [[89, "class-avogadro-qtgui-periodictableview"]], "Class Avogadro::QtGui::ExtensionPlugin": [[75, "class-avogadro-qtgui-extensionplugin"]], "Class Avogadro::QtGui::GenericHighlighter::Rule": [[80, "class-avogadro-qtgui-generichighlighter-rule"]], "Class Avogadro::QtGui::PeriodicTableScene": [[88, "class-avogadro-qtgui-periodictablescene"]], "Class Avogadro::QtGui::ScenePluginFactory": [[97, "class-avogadro-qtgui-scenepluginfactory"]], "Class Avogadro::QtGui::InterfaceWidget": [[83, "class-avogadro-qtgui-interfacewidget"]], "Class Avogadro::QtGui::PythonScript": [[92, "class-avogadro-qtgui-pythonscript"]], "Class Avogadro::QtGui::InterfaceScript": [[82, "class-avogadro-qtgui-interfacescript"]], "Class Avogadro::QtGui::FileFormatDialog": [[78, "class-avogadro-qtgui-fileformatdialog"]], "Class Avogadro::QtGui::RWMolecule": [[95, "class-avogadro-qtgui-rwmolecule"]], "Class Avogadro::QtGui::PersistentBond": [[91, "class-avogadro-qtgui-persistentbond"]], "Class Avogadro::QtGui::ExtensionPluginFactory": [[76, "class-avogadro-qtgui-extensionpluginfactory"]], "Class Avogadro::QtGui::ScenePluginModel": [[98, "class-avogadro-qtgui-scenepluginmodel"]], "View Menu": [[211, "view-menu"]], "New View": [[211, "new-view"]], "Duplicate View": [[211, "duplicate-view"]], "Detach View": [[211, "detach-view"]], "Close View": [[211, "close-view"]], "Center": [[211, "center"]], "Align View to Axes": [[211, "align-view-to-axes"]], "Full Screen": [[211, "full-screen"]], "Reset Display Types": [[211, "reset-display-types"]], "Set Background Color\u2026": [[211, "set-background-color"]], "Projection": [[211, "projection"]], "Display Axes": [[211, "display-axes"]], "Debug Information": [[211, "debug-information"]], "Use Quick Render": [[211, "use-quick-render"]], "All Molecules in File\u2026": [[211, "all-molecules-in-file"]], "Crystal View Options\u2026": [[211, "crystal-view-options"]], "Properties": [[211, "properties"]], "Making Selections": [[203, "making-selections"]], "Bond-Centric Manipulate Tool": [[220, "bond-centric-manipulate-tool"]], "Starting with the basics:": [[220, "starting-with-the-basics"]], "Adjusting Bonds and Torsion Angles": [[220, "adjusting-bonds-and-torsion-angles"]], "Measure Tool": [[224, "measure-tool"]], "Drawing Molecules": [[200, "drawing-molecules"]], "Creating Carbon Dioxide": [[200, "creating-carbon-dioxide"]], "Extension Menu": [[207, "extension-menu"]], "Animation": [[207, "animation"]], "Optimize Geometry": [[207, "optimize-geometry"]], "Molecular Mechanics": [[207, "molecular-mechanics"]], "Setup Force Field\u2026": [[207, "setup-force-field"]], "Calculate Energy": [[207, "calculate-energy"]], "Conformer Search": [[207, "conformer-search"]], "Constraints": [[207, "constraints"], [213, "constraints"]], "Ignore Selection": [[207, "ignore-selection"]], "Fix Selected Atoms": [[207, "fix-selected-atoms"]], "Avogadro Extensions\u2013Plugins": [[207, "avogadro-extensionsplugins"]], "General \u201cHow To\u201d for Plugins": [[207, "general-how-to-for-plugins"]], "Running Gaussian": [[207, "running-gaussian"]], "Molecular Orbitals": [[207, "molecular-orbitals"]], "QTAIM (Quantum Theory of Atoms in Molecules)": [[207, "qtaim-quantum-theory-of-atoms-in-molecules"], [198, "qtaim-quantum-theory-of-atoms-in-molecules"]], "Spectra\u2026": [[207, "spectra"]], "Create Surfaces\u2026": [[207, "create-surfaces"]], "Finding Conformers of Molecules": [[212, "finding-conformers-of-molecules"]], "Start with your molecule of interest": [[212, "start-with-your-molecule-of-interest"]], "Optimize the geometry": [[212, "optimize-the-geometry"]], "Change the force field options": [[212, "change-the-force-field-options"]], "Set the conformer search options": [[212, "set-the-conformer-search-options"]], "Pick a search method and start the search": [[212, "pick-a-search-method-and-start-the-search"]], "Auto-Rotate Tool": [[219, "auto-rotate-tool"]], "Introduction to Molecular Mechanics": [[216, "introduction-to-molecular-mechanics"]], "UFF": [[216, "uff"]], "MMFF94(s)": [[216, "mmff94-s"]], "GAFF": [[216, "gaff"]], "File Menu": [[208, "file-menu"]], "New": [[208, "new"]], "Open": [[208, "open"]], "Open Recent": [[208, "open-recent"]], "Close": [[208, "close"]], "Save": [[208, "save"]], "Save As\u2026": [[208, "save-as"]], "Revert to Saved": [[208, "revert-to-saved"]], "Import": [[208, "import"]], "Export": [[208, "export"]], "Build Menu": [[205, "build-menu"]], "Cartesian Editor\u2026": [[205, "cartesian-editor"]], "1. Sort by\u2026": [[205, "sort-by"]], "2. Unit of Measure": [[205, "unit-of-measure"]], "3. Editing & Modifying Data": [[205, "editing-modifying-data"]], "Change H to Methyl": [[205, "change-h-to-methyl"]], "Add Hydrogens": [[205, "add-hydrogens"]], "Add Hydrogens for pH\u2026": [[205, "add-hydrogens-for-ph"]], "Remove Hydrogens": [[205, "remove-hydrogens"]], "Insert": [[205, "insert"]], "Invert Chirality": [[205, "invert-chirality"]], "Super Cell Builder\u2026": [[205, "super-cell-builder"]], "Nanotube Builder\u2026": [[205, "nanotube-builder"]], "Introduction": [[202, "introduction"]], "Opening a File": [[202, "opening-a-file"]], "Importing by Name": [[202, "importing-by-name"]], "Navigation": [[202, "navigation"]], "Menus": [[209, "menus"], [209, null]], "Align Tool": [[217, "align-tool"]], "Draw Tool": [[221, "draw-tool"]], "1. Creating a Molecule": [[221, "creating-a-molecule"]], "2.": [[221, "id2"]], "3.": [[221, "id3"]], "4.": [[221, "id4"]], "5.": [[221, "id5"]], "6.": [[221, "id6"]], "7.": [[221, "id7"]], "8.": [[221, "id8"]], "9.": [[221, "id9"]], "Enabling additional force fields": [[214, "enabling-additional-force-fields"]], "Creating an avogadro conda environment": [[214, "creating-an-avogadro-conda-environment"]], "Setting the Python path": [[214, "setting-the-python-path"]], "Optimizing Geometry": [[215, "optimizing-geometry"]], "Optimization": [[215, null]], "User Guide": [[204, "user-guide"]], "Avogadro: Molecular Editor and Visualization": [[204, "avogadro-molecular-editor-and-visualization"], [179, "avogadro-molecular-editor-and-visualization"]], "Avogadro 2": [[204, "avogadro-2"]], "Edit Menu": [[206, "edit-menu"]], "Undo": [[206, "undo"]], "Redo": [[206, "redo"]], "Cut": [[206, "cut"]], "Copy": [[206, "copy"]], "Copy As": [[206, "copy-as"]], "Paste": [[206, "paste"]], "Clear": [[206, "clear"]], "Select All": [[206, "select-all"], [210, "select-all"]], "Select None": [[206, "select-none"], [210, "select-none"]], "Auto-Optimize Tool": [[218, "auto-optimize-tool"]], "Force Fields & Algorithms": [[218, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[218, "fixing-ignoring-selections"]], "Manipulate Tool": [[223, "manipulate-tool"]], "Getting Started": [[201, "getting-started"]], "Tools": [[222, "tools"], [222, null]], "Geometry Constraints": [[213, "geometry-constraints"]], "Example": [[213, "example"]], "Optimizations": [[213, "optimizations"]], "Example cont.": [[213, "example-cont"]], "Select Menu": [[210, "select-menu"]], "Invert Selection": [[210, "invert-selection"]], "Select SMARTS\u2026": [[210, "select-smarts"]], "Select by Element\u2026": [[210, "select-by-element"]], "Select by Residue\u2026": [[210, "select-by-residue"]], "Select Solvent": [[210, "select-solvent"]], "Add Name Selection\u2026": [[210, "add-name-selection"]], "Class Avogadro::Io::FileFormatManager": [[49, "class-avogadro-io-fileformatmanager"]], "Class Avogadro::Io::CmlFormat": [[46, "class-avogadro-io-cmlformat"]], "Class Avogadro::Core::RingPerceiver": [[35, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::SymbolAtomTyper": [[40, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::Mutex": [[31, "class-avogadro-core-mutex"]], "Class Avogadro::Core::Graph": [[26, "class-avogadro-core-graph"]], "Class Avogadro::Core::Residue": [[33, "class-avogadro-core-residue"]], "Class Avogadro::Core::SlaterSetTools": [[38, "class-avogadro-core-slatersettools"]], "Class Avogadro::Core::SpaceGroups": [[39, "class-avogadro-core-spacegroups"]], "Class Avogadro::Core::NameAtomTyper": [[32, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[44, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Core::SharedMutex": [[36, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::Variant": [[42, "class-avogadro-core-variant"]], "Class Avogadro::Core::UnitCell": [[41, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::VariantMap": [[43, "class-avogadro-core-variantmap"]], "Class Avogadro::Io::CjsonFormat": [[45, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Io::FileFormat": [[48, "class-avogadro-io-fileformat"]], "Class Avogadro::Core::Mesh": [[27, "class-avogadro-core-mesh"]], "Class Avogadro::Core::Molecule": [[28, "class-avogadro-core-molecule"]], "Class Avogadro::Core::ResidueData": [[34, "class-avogadro-core-residuedata"]], "Class Avogadro::Core::GaussianSetTools": [[25, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::SlaterSet": [[37, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::MoleculeDeserializer": [[29, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::MoleculeSerializer": [[30, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Io::DcdFormat": [[47, "class-avogadro-io-dcdformat"]], "Install": [[237, "install"], [239, "install"]], "Features": [[237, "features"], [241, "features"]], "Resources": [[237, "resources"]], "Connecting with the Avogadro community": [[237, "connecting-with-the-avogadro-community"]], "Release Notes v1.96.0": [[244, "release-notes-v1-96-0"]], "Changes": [[244, "changes"], [242, "changes"]], "\u2728 Features": [[244, "features"], [243, "features"], [246, "features"], [242, "features"], [245, "features"]], "\ud83d\ude80 Performance Fixes": [[244, "performance-fixes"]], "\ud83d\udc1b Bug Fixes": [[244, "bug-fixes"], [243, "bug-fixes"], [241, "bug-fixes"], [246, "bug-fixes"], [242, "bug-fixes"], [245, "bug-fixes"]], "\ud83e\uddf0 Maintenance": [[244, "maintenance"], [243, "maintenance"], [241, "maintenance"], [246, "maintenance"], [242, "maintenance"], [245, "maintenance"]], "\ud83d\udcda Translations": [[244, "translations"], [243, "translations"], [246, "translations"], [242, "translations"], [245, "translations"]], "Naming a Molecule": [[229, "naming-a-molecule"]], "Selection Tool": [[226, "selection-tool"]], "Viewing Vibrations": [[233, "viewing-vibrations"]], "Release Notes v1.95.1": [[243, "release-notes-v1-95-1"]], "What\u2019s New in Avogadro 2": [[234, "whats-new-in-avogadro-2"]], "Acid-Base Properties of Amino Acids": [[247, "acid-base-properties-of-amino-acids"]], "Building Source Code": [[238, "building-source-code"]], "Cloning Repositories": [[238, "cloning-repositories"]], "Updating": [[238, "updating"]], "Prerequisites": [[238, "prerequisites"]], "Debian-based Distribution or Ubuntu": [[238, "debian-based-distribution-or-ubuntu"]], "Building": [[238, "building"]], "Finding Qt, Windows Generators": [[238, "finding-qt-windows-generators"]], "Normal Development": [[238, "normal-development"]], "Build Tree Layout": [[238, "build-tree-layout"]], "Running Executables": [[238, "running-executables"]], "Building Packages": [[238, "building-packages"]], "Template Tool": [[227, "template-tool"], [236, "template-tool"]], "Inserting Atoms with Specific Geometry": [[227, "inserting-atoms-with-specific-geometry"]], "Attaching Ligands": [[227, "attaching-ligands"]], "Attaching Functional Groups": [[227, "attaching-functional-groups"]], "Creating New Ligands": [[227, "creating-new-ligands"]], "Creating New Haptic Ligands": [[227, "creating-new-haptic-ligands"]], "Version History": [[240, "version-history"], [240, null]], "Viewing Electrostatic Potential Maps": [[231, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[231, "changing-surface-settings"]], "Using QTAIM (Atoms in Molecules) Analysis": [[230, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[230, "start-with-a-wfn-file"]], "Alkene Isomers": [[248, "alkene-isomers"]], "Release Notes v1.94.0": [[241, "release-notes-v1-94-0"]], "\ud83d\udc0d Python Improvements": [[241, "python-improvements"]], "Release Notes v1.98.0": [[246, "release-notes-v1-98-0"]], "\ud83c\udf1f Highlights (tldr)": [[246, "highlights-tldr"]], "\ud83d\ude80 Performance Improvements": [[246, "performance-improvements"], [245, "performance-improvements"]], "Major New Features": [[236, "major-new-features"]], "Speed and Stability": [[236, "speed-and-stability"]], "Rendering": [[236, "rendering"]], "New real-time shadows and depth effects": [[236, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[236, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[236, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[236, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[236, "layers"]], "Symmetry Properties": [[236, "symmetry-properties"]], "Solvent Accessible and Solvent Excluded Surfaces": [[236, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[236, "flexible-electrostatics-models"]], "New Analysis Tools": [[236, "new-analysis-tools"]], "Python Commands / Plugins": [[236, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[236, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[236, "new-and-updated-interfaces-to-external-programs"]], "Viewing Molecular Orbitals": [[232, "viewing-molecular-orbitals"]], "Configure": [[232, "configure"]], "Release Notes v1.95.0": [[242, "release-notes-v1-95-0"]], "Tutorials": [[228, "tutorials"], [228, null]], "Navigate Tool": [[225, "navigate-tool"]], "Educational Publications Using Avogadro": [[249, "educational-publications-using-avogadro"]], "Yes We Chem": [[249, "yes-we-chem"]], "Computational Chemistry": [[249, "computational-chemistry"]], "Spectra / Spectroscopy": [[249, "spectra-spectroscopy"]], "Chemical Reactions and Mechanisms": [[249, "chemical-reactions-and-mechanisms"]], "Materials / Nano": [[249, "materials-nano"]], "Cheminformatics": [[249, "cheminformatics"]], "3D Printing and VR": [[249, "d-printing-and-vr"]], "Remote Teaching": [[249, "remote-teaching"]], "Interface Changes": [[235, "interface-changes"]], "Release Notes v1.97.0": [[245, "release-notes-v1-97-0"]], "Highlights (tldr)": [[245, "highlights-tldr"]], "VTK Classes": [[177, "vtk-classes"]], "Reducing Crystals to a Primitive Unit Cell": [[186, "reducing-crystals-to-a-primitive-unit-cell"]], "Building a Supercell": [[188, "building-a-supercell"]], "Creating a Surface": [[188, "creating-a-surface"]], "Importing Molecules by Name": [[194, "importing-molecules-by-name"]], "Insert Molecular Fragments": [[196, "insert-molecular-fragments"]], "Display Types": [[199, "display-types"], [199, null]], "Building Molecule-Surface Interactions": [[185, "building-molecule-surface-interactions"]], "Start with a generated Crystal Surface": [[185, "start-with-a-generated-crystal-surface"]], "New Window: Create our Molecule": [[185, "new-window-create-our-molecule"]], "Script Interfaces": [[176, "script-interfaces"]], "Fixed String Lists (Pop-up menus)": [[176, "fixed-string-lists-pop-up-menus"]], "Integer Values": [[176, "integer-values"]], "Floating-point values": [[176, "floating-point-values"]], "Coloring Part of a Molecules": [[197, "coloring-part-of-a-molecules"]], "Hemoglobin": [[197, "hemoglobin"]], "Select by Residue": [[197, "select-by-residue"]], "Select by Element": [[197, "select-by-element"]], "Installing Script Plugins": [[175, "installing-script-plugins"]], "Directories": [[175, "directories"]], "Plugin Packages and Repositories": [[175, "plugin-packages-and-repositories"]], "Adding to the Plugin Directory": [[175, "adding-to-the-plugin-directory"]], "Building Molecules": [[195, "building-molecules"], [195, null]], "Building a Polymer Unit Cell": [[182, "building-a-polymer-unit-cell"]], "Building with SMILES": [[192, "building-with-smiles"]], "Importing from the Protein Data Bank (PDB)": [[193, "importing-from-the-protein-data-bank-pdb"]], "Importing Directly": [[193, "importing-directly"]], "Reading a Downloaded PDB file": [[193, "reading-a-downloaded-pdb-file"]], "Building Materials": [[184, "building-materials"], [184, null]], "Making a Crystal Surface Slab": [[181, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[181, "import-the-appropriate-crystal-structure"]], "Perceiving Crystall Symmetry": [[183, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[183, "open-a-crystal-file"]], "Scaling Crystal Cell Volume": [[187, "scaling-crystal-cell-volume"]], "Building DNA or RNA": [[191, "building-dna-or-rna"]], "Building a Peptide": [[189, "building-a-peptide"]], "Different Display Styles": [[198, "different-display-styles"]], "Locating Display Types": [[198, "locating-display-types"]], "Axes": [[198, "axes"]], "Ball and Stick": [[198, "ball-and-stick"]], "Cartoon": [[198, "cartoon"]], "Dipole": [[198, "dipole"]], "Force": [[198, "force"]], "Hydrogen Bond": [[198, "hydrogen-bond"]], "Label": [[198, "label"]], "Polygon": [[198, "polygon"]], "Ribbon": [[198, "ribbon"]], "Ring": [[198, "ring"]], "Stick": [[198, "stick"]], "Surfaces": [[198, "surfaces"]], "Van der Waals Spheres": [[198, "van-der-waals-spheres"]], "Wireframe": [[198, "wireframe"]], "License": [[178, "license"]], "Creative Commons Attribution-ShareAlike 4.0 International": [[178, "creative-commons-attribution-sharealike-4-0-international"]], "Using Creative Commons Public Licenses": [[178, "using-creative-commons-public-licenses"]], "Creative Commons Attribution-ShareAlike 4.0 International Public License": [[178, "creative-commons-attribution-sharealike-4-0-international-public-license"]], "Section 1 \u2013 Definitions.": [[178, "section-1-definitions"]], "Section 2 \u2013 Scope.": [[178, "section-2-scope"]], "Section 3 \u2013 License Conditions.": [[178, "section-3-license-conditions"]], "Section 4 \u2013 Sui Generis Database Rights.": [[178, "section-4-sui-generis-database-rights"]], "Section 5 \u2013 Disclaimer of Warranties and Limitation of Liability.": [[178, "section-5-disclaimer-of-warranties-and-limitation-of-liability"]], "Section 6 \u2013 Term and Termination.": [[178, "section-6-term-and-termination"]], "Section 7 \u2013 Other Terms and Conditions.": [[178, "section-7-other-terms-and-conditions"]], "Section 8 \u2013 Interpretation.": [[178, "section-8-interpretation"]], "Table of contents": [[180, "table-of-contents"]], "Building Carbon Nanotubes": [[190, "building-carbon-nanotubes"]], "Class Avogadro::Rendering::TextProperties": [[140, "class-avogadro-rendering-textproperties"]], "Class Avogadro::Rendering::TextRenderStrategy": [[141, "class-avogadro-rendering-textrenderstrategy"]], "Class Avogadro::Rendering::VolumeGeometry": [[146, "class-avogadro-rendering-volumegeometry"]], "Class Avogadro::Rendering::ShaderProgram": [[134, "class-avogadro-rendering-shaderprogram"]], "Class Avogadro::Rendering::TextLabel2D": [[137, "class-avogadro-rendering-textlabel2d"]], "Class Avogadro::Rendering::Visitor": [[145, "class-avogadro-rendering-visitor"]], "Class Avogadro::Rendering::Texture2D": [[142, "class-avogadro-rendering-texture2d"]], "Class Avogadro::Rendering::Primitive": [[131, "class-avogadro-rendering-primitive"]], "Class Avogadro::TypeTraits< char >": [[148, "class-avogadro-typetraits-char"]], "Class Avogadro::Rendering::GeometryVisitor": [[125, "class-avogadro-rendering-geometryvisitor"]], "Class Avogadro::Rendering::TextLabelBase": [[139, "class-avogadro-rendering-textlabelbase"]], "Class Avogadro::TypeTraits< double >": [[149, "class-avogadro-typetraits-double"]], "Class Avogadro::Rendering::Shader": [[133, "class-avogadro-rendering-shader"]], "Class Avogadro::Rendering::TextLabel3D": [[138, "class-avogadro-rendering-textlabel3d"]], "Class Avogadro::Rendering::Sphere": [[135, "class-avogadro-rendering-sphere"]], "Class Avogadro::Rendering::LineStripGeometry": [[127, "class-avogadro-rendering-linestripgeometry"]], "Class Avogadro::Rendering::SphereGeometry": [[136, "class-avogadro-rendering-spheregeometry"]], "Class Avogadro::Rendering::Scene": [[132, "class-avogadro-rendering-scene"]], "Class Avogadro::Rendering::Node": [[129, "class-avogadro-rendering-node"]], "Class Avogadro::Rendering::MeshGeometry": [[128, "class-avogadro-rendering-meshgeometry"]], "Class Avogadro::TypeTraits": [[147, "class-avogadro-typetraits"]], "Class Avogadro::Rendering::TransformNode": [[143, "class-avogadro-rendering-transformnode"]], "Class Avogadro::Rendering::POVRayVisitor": [[130, "class-avogadro-rendering-povrayvisitor"]], "Class Avogadro::Rendering::GroupNode": [[126, "class-avogadro-rendering-groupnode"]], "Class Avogadro::Rendering::VRMLVisitor": [[144, "class-avogadro-rendering-vrmlvisitor"]], "Class List": [[159, "class-list"]], "Charges / Electrostatics": [[167, "charges-electrostatics"]], "Identify the Script with --metadata": [[167, "identify-the-script-with-metadata"], [169, "identify-the-script-with-metadata"]], "Calculating Atomic Partial Charges with --charge": [[167, "calculating-atomic-partial-charges-with-charge"]], "Generating Electrostatic Potentials with --potential": [[167, "generating-electrostatic-potentials-with-potential"]], "Class Avogadro::VTK::vtkGLWidget": [[157, "class-avogadro-vtk-vtkglwidget"]], "Command Scripts": [[168, "command-scripts"]], "Specifying UI options with \u2013print-options": [[168, "specifying-ui-options-with-print-options"]], "Returning Data": [[168, "returning-data"]], "Returning Data in a Specific File Format": [[168, "returning-data-in-a-specific-file-format"]], "Appending New Atoms and Bonds": [[168, "appending-new-atoms-and-bonds"]], "Bonding New Atoms": [[168, "bonding-new-atoms"]], "Selected Atoms": [[168, "selected-atoms"]], "Class Avogadro::TypeTraits< unsigned int >": [[154, "class-avogadro-typetraits-unsigned-int"]], "Avogadro Remote Procedure Call (RPC)": [[166, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[166, "rpc-protocol"]], "Methods": [[166, "methods"]], "Class Avogadro::TypeTraits< int >": [[151, "class-avogadro-typetraits-int"]], "Class Avogadro::VTK::VtkPlot": [[156, "class-avogadro-vtk-vtkplot"]], "File Formats": [[172, "file-formats"]], "Identify the Format with --metadata": [[172, "identify-the-format-with-metadata"]], "Reading a format with --read": [[172, "reading-a-format-with-read"]], "Writing a format with --write": [[172, "writing-a-format-with-write"]], "MoleQueue Classes": [[163, "molequeue-classes"]], "Rendering Classes": [[165, "rendering-classes"]], "Class Avogadro::TypeTraits< short >": [[152, "class-avogadro-typetraits-short"]], "Class Avogadro::TypeTraits< unsigned char >": [[153, "class-avogadro-typetraits-unsigned-char"]], "Class Avogadro::TypeTraits< float >": [[150, "class-avogadro-typetraits-float"]], "IO Classes": [[162, "io-classes"]], "Class vtkAvogadroActor": [[158, "class-vtkavogadroactor"]], "QtGui Classes": [[164, "qtgui-classes"]], "Core Classes": [[160, "core-classes"]], "Develop": [[161, "develop"]], "Script Plugins": [[161, "script-plugins"], [174, "script-plugins"]], "External Scripting": [[161, "external-scripting"]], "Libraries": [[161, "libraries"]], "Main Classes": [[161, "main-classes"]], "Example Plugin Script - Part 2": [[171, "example-plugin-script-part-2"]], "Providing Input to Run Command": [[171, "providing-input-to-run-command"]], "runCommand() Function": [[171, "runcommand-function"]], "Operation Function": [[171, "operation-function"]], "Retrieving necessary components": [[171, "retrieving-necessary-components"]], "Support for Selection": [[171, "support-for-selection"]], "Sample Input and Output": [[171, "sample-input-and-output"]], "Example Plugin Script - Part 1": [[170, "example-plugin-script-part-1"]], "The Main function:": [[170, "the-main-function"]], "Input Arguments": [[170, "input-arguments"]], "getOptions() Function": [[170, "getoptions-function"]], "Class Avogadro::TypeTraits< unsigned short >": [[155, "class-avogadro-typetraits-unsigned-short"]], "Energy / Force Fields": [[169, "energy-force-fields"]], "Calculating Energies and Gradients": [[169, "calculating-energies-and-gradients"]], "Unit Cells, Total Charge, and Spin Multiplicity": [[169, "unit-cells-total-charge-and-spin-multiplicity"]], "Lattice Vectors and Fractional Coordinates": [[169, "lattice-vectors-and-fractional-coordinates"]], "Input Generators": [[173, "input-generators"]], "Specifying parameters with --print-options": [[173, "specifying-parameters-with-print-options"]], "Handling User Selections: --generate-input": [[173, "handling-user-selections-generate-input"]], "Coordinate Blocks": [[173, "coordinate-blocks"]], "Class Avogadro::Rendering::Cylinder": [[119, "class-avogadro-rendering-cylinder"]], "Class Avogadro::QuantumIO::NWChemJson": [[113, "class-avogadro-quantumio-nwchemjson"]], "Class Avogadro::QtOpenGL::ActiveObjects": [[103, "class-avogadro-qtopengl-activeobjects"]], "Class Avogadro::QtGui::ViewFactory": [[102, "class-avogadro-qtgui-viewfactory"]], "Class Avogadro::Rendering::Drawable": [[121, "class-avogadro-rendering-drawable"]], "Class Avogadro::QtGui::ToolPluginFactory": [[101, "class-avogadro-qtgui-toolpluginfactory"]], "Class Avogadro::QuantumIO::GUKBasisSet": [[107, "class-avogadro-quantumio-gukbasisset"]], "Class Avogadro::QtOpenGL::QtTextRenderStrategy": [[105, "class-avogadro-qtopengl-qttextrenderstrategy"]], "Class Avogadro::Rendering::ArrowGeometry": [[116, "class-avogadro-rendering-arrowgeometry"]], "Class Avogadro::Rendering::GeometryNode": [[124, "class-avogadro-rendering-geometrynode"]], "Class Avogadro::QuantumIO::GaussianCube": [[109, "class-avogadro-quantumio-gaussiancube"]], "Class Avogadro::QtGui::ToolPlugin": [[100, "class-avogadro-qtgui-toolplugin"]], "Class Avogadro::Rendering::BufferObject": [[117, 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