diff --git a/.doctrees/develop/scripts/example1.doctree b/.doctrees/develop/scripts/example1.doctree index 948bd7b0..a6bf41f9 100644 Binary files a/.doctrees/develop/scripts/example1.doctree and b/.doctrees/develop/scripts/example1.doctree differ diff --git a/.doctrees/develop/scripts/interface.doctree b/.doctrees/develop/scripts/interface.doctree index 09078147..3c0b2d5c 100644 Binary files a/.doctrees/develop/scripts/interface.doctree and b/.doctrees/develop/scripts/interface.doctree differ diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 109bd637..67043f98 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/_images/image-1.png b/_images/image-1.png new file mode 100644 index 00000000..0f78a175 Binary files /dev/null and b/_images/image-1.png differ diff --git a/_images/image-2.png b/_images/image-2.png new file mode 100644 index 00000000..20674197 Binary files /dev/null and b/_images/image-2.png differ diff --git a/_images/image-3.png b/_images/image-3.png new file mode 100644 index 00000000..3f2a002c Binary files /dev/null and b/_images/image-3.png differ diff --git a/_images/image-4.png b/_images/image-4.png new file mode 100644 index 00000000..33e55f21 Binary files /dev/null and b/_images/image-4.png differ diff --git a/_images/image-5.png b/_images/image-5.png new file mode 100644 index 00000000..0c8ce3bd Binary files /dev/null and b/_images/image-5.png differ diff --git a/_images/image-6.png b/_images/image-6.png new file mode 100644 index 00000000..b6a9bcdc Binary files /dev/null and b/_images/image-6.png differ diff --git a/_images/image.png b/_images/image.png new file mode 100644 index 00000000..53674863 Binary files /dev/null and b/_images/image.png differ diff --git a/_sources/develop/scripts/example1.md.txt b/_sources/develop/scripts/example1.md.txt index d4606b25..b175c7ef 100644 --- a/_sources/develop/scripts/example1.md.txt +++ b/_sources/develop/scripts/example1.md.txt @@ -75,5 +75,9 @@ def getOptions(): return opts ``` The getOptions function is used to specify the [script Interfaces](https://two.avogadro.cc/scripts/inte**rface.html#script-interfaces) or **the pop-up menu** for the script. For each option in the userOptions list, Avogadro will create appropriate labels, menus, text boxes, check boxes, etc. -It is called when `--print-options` is given as the input argument. +Interface will look something like this: + +7th + +It is called in the command line when `--print-options` is given as the input argument. diff --git a/_sources/develop/scripts/interface.md.txt b/_sources/develop/scripts/interface.md.txt index faafd3de..fa53dede 100644 --- a/_sources/develop/scripts/interface.md.txt +++ b/_sources/develop/scripts/interface.md.txt @@ -23,6 +23,7 @@ be specified in the `userOptions` block as: } } ``` +1st Here, "Parameter Name" is the default label that will be displayed in the GUI as a label next to the combo box. If you wish to have the label @@ -38,6 +39,7 @@ differ from the JSON key, you can add a "label" key pair: } } ``` +2nd Use of the "label" is optional, but encouraged, since it greatly facilitates translation and localization (e.g., "color" vs. "colour"). @@ -62,10 +64,11 @@ optimization) via: } } ``` - This will add a blank text box to the GUI, initialized with the text specified by default. +3rd + ## Existing files A script can ask for the absolute path to an existing file using the @@ -81,10 +84,11 @@ following option block: } } ``` - This will add an option to select a file to the GUI, initialized to the file pointed to by default. +4th + ## Integer Values Scripts may request integer values from a specified range by adding a @@ -104,9 +108,10 @@ user-option of the following form: } } ``` - This block will result in a QSpinBox, configured as follows: +5th + - minimum and maximum indicate the valid range of integers for the parameter. - default is the integer value that will be shown initially. @@ -154,3 +159,5 @@ requested: This will result in a check box in the dynamically generated GUI, with the initial check state shown in default. + +6th \ No newline at end of file diff --git a/_static/image-1.png b/_static/image-1.png new file mode 100644 index 00000000..0f78a175 Binary files /dev/null and b/_static/image-1.png differ diff --git a/_static/image-2.png b/_static/image-2.png new file mode 100644 index 00000000..20674197 Binary files /dev/null and b/_static/image-2.png differ diff --git a/_static/image-3.png b/_static/image-3.png new file mode 100644 index 00000000..3f2a002c Binary files /dev/null and b/_static/image-3.png differ diff --git a/_static/image-4.png b/_static/image-4.png new file mode 100644 index 00000000..33e55f21 Binary files /dev/null and b/_static/image-4.png differ diff --git a/_static/image-5.png b/_static/image-5.png new file mode 100644 index 00000000..0c8ce3bd Binary files /dev/null and b/_static/image-5.png differ diff --git a/_static/image-6.png b/_static/image-6.png new file mode 100644 index 00000000..b6a9bcdc Binary files /dev/null and b/_static/image-6.png differ diff --git a/_static/image.png b/_static/image.png new file mode 100644 index 00000000..53674863 Binary files /dev/null and b/_static/image.png differ diff --git a/develop/scripts/example1.html b/develop/scripts/example1.html index a175074e..4a7227c1 100644 --- a/develop/scripts/example1.html +++ b/develop/scripts/example1.html @@ -591,7 +591,9 @@

getOptions() Function

The getOptions function is used to specify the script Interfaces or the pop-up menu for the script. For each option in the userOptions list, Avogadro will create appropriate labels, menus, text boxes, check boxes, etc. -It is called when --print-options is given as the input argument.

+Interface will look something like this:

+7th +

It is called in the command line when --print-options is given as the input argument.

diff --git a/develop/scripts/interface.html b/develop/scripts/interface.html index 8ae73c92..213bcb52 100644 --- a/develop/scripts/interface.html +++ b/develop/scripts/interface.html @@ -523,6 +523,7 @@

Fixed String Lists (Pop-up menus)} +1st

Here, “Parameter Name” is the default label that will be displayed in the GUI as a label next to the combo box. If you wish to have the label differ from the JSON key, you can add a “label” key pair:

@@ -536,6 +537,7 @@

Fixed String Lists (Pop-up menus)} +2nd

Use of the “label” is optional, but encouraged, since it greatly facilitates translation and localization (e.g., “color” vs. “colour”).

The array of strings in values will be used as the available entries in @@ -559,6 +561,7 @@

Short Free-Form Text Parameters

Existing files#

@@ -576,6 +579,7 @@

Existing files

Integer Values#

@@ -596,6 +600,7 @@

Integer Values

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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", "Introduction to Molecular Mechanics", "Optimizing Geometry", "Align Tool", "Auto-Optimize Tool", "Auto-Rotate Tool", "Bond-Centric Manipulate Tool", "Draw Tool", "Tools", "Manipulate Tool", "Measure Tool", "Navigate Tool", "Selection 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", "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, 103, 104, 115, 122, 127, 128, 134, 136, 161, 166, 168, 169, 170, 171, 172, 173, 176, 178, 182, 187, 192, 193, 200, 212, 214, 218, 220, 221, 224, 225, 233, 235, 236, 237, 240, 241, 243, 244, 253], "you": [0, 1, 2, 4, 6, 7, 8, 28, 84, 95, 103, 161, 169, 171, 175, 176, 178, 181, 182, 185, 186, 187, 188, 189, 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176, 182, 187, 188, 207, 209, 211, 213, 215, 226, 235, 237, 240, 241, 242, 243, 244, 245, 246, 249, 256], "path": [1, 48, 51, 62, 63, 64, 72, 73, 75, 78, 82, 83, 92, 99, 166, 168, 170, 173, 175, 176, 216, 235, 237, 241, 243, 244, 245], "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, 236, 237, 241, 242, 243, 244, 245], "appropri": [1, 5, 11, 16, 51, 62, 74, 82, 168, 170, 173, 176, 202, 237, 243], "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, 229, 237, 244, 245, 246], "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, 215, 219, 225, 234, 235, 245, 253], "altern": [1, 169], "similar": [1, 19, 95, 173, 178, 198, 202], "ideal": [1, 14], "give": [1, 4, 7, 8, 20, 23, 39, 48, 118, 171, 178, 211, 245, 256], "some": [1, 4, 23, 28, 62, 64, 82, 85, 95, 115, 136, 161, 166, 167, 171, 173, 175, 176, 181, 183, 186, 198, 242, 244, 245, 251, 253, 254], "simpl": [1, 23, 31, 32, 36, 39, 40, 50, 62, 82, 176, 188, 198, 205, 237, 248], "exampl": [1, 4, 19, 117, 134, 161, 167, 168, 169, 172, 173, 178, 182, 183, 188, 198, 202, 206, 207, 210, 211, 214, 216, 220, 224, 230, 235, 237, 240, 244, 247, 248], "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, 233, 243], "simplest": 1, "wai": [1, 85, 95, 178, 182, 188, 197, 203, 205, 207, 214, 235, 236], "possibl": [1, 5, 21, 22, 49, 84, 171, 178, 204, 237], "molequeu": [1, 2, 82, 159, 166, 173, 237, 240], "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, 215, 240, 244, 246, 252, 254, 256], "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, 215, 217, 218, 219, 220, 223, 224, 225, 226, 228, 230, 235, 237, 246], "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, 235, 237, 240, 243, 245, 254], "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, 216, 217, 218, 219, 220, 221, 225, 226, 230, 231, 232, 235, 236, 237, 243, 244, 245, 252, 253, 254, 256], "rpc": [1, 65, 68, 161, 240], "server": [1, 4, 61, 65, 66, 68, 92, 166, 228], "json": [1, 45, 62, 65, 75, 82, 83, 100, 113, 161, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 240, 245], "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, 234, 235, 236, 237, 240, 243, 244, 246, 247, 252, 253, 254, 255], "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, 233, 235, 239, 242, 246, 251, 252, 256], "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], "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, 241, 243, 244], "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, 230, 232, 235, 245], "To": [1, 11, 16, 51, 63, 65, 74, 168, 171, 178, 181, 202, 209, 214, 219, 220, 237], "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, 201, 205, 206, 208, 209, 211, 216, 222, 229, 230, 231, 235, 237, 241, 243, 245, 246, 249, 250, 251, 252, 256], "connect": [1, 26, 61, 66, 68, 84, 95, 127, 166, 171, 178, 228, 229, 244], "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, 235, 240, 243, 245], "follow": [1, 5, 19, 62, 82, 92, 142, 167, 168, 169, 170, 171, 172, 173, 176, 178, 185, 188, 213, 214, 237], "done": [1, 13, 24, 37, 39, 65, 117, 123, 133, 159, 163, 169, 171, 218, 231], "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, 231, 240, 241, 243, 244, 245, 246], "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, 229, 237, 241, 245, 251], "act": [1, 95, 171, 237], "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, 229, 237, 252, 254, 255, 256], "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, 243, 244, 245, 252], "receiv": [1, 61, 82, 178], "respons": [1, 3, 61, 87, 95, 123, 170, 171, 245], "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, 237, 240, 242, 243, 245, 246], "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, 241], "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, 215, 218, 230, 235, 236, 240, 241, 244, 245, 254], "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, 215, 218, 231, 244, 251], "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, 235, 240, 241, 242, 244, 245], "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, 245], "appear": [1, 62, 78, 82, 95, 173, 175, 181, 188, 207], "work": [1, 3, 4, 6, 24, 103, 168, 178, 182, 190, 193, 204, 207, 210, 213, 235, 236, 237, 244, 245], "directori": [1, 29, 30, 78, 156, 161, 237, 241], "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], "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, 228, 249], "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, 230, 233, 235, 241], "successfulli": [1, 51, 61, 62, 65, 66, 75, 82, 84, 237, 244], "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, 228], "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, 241, 245], "t": [2, 5, 7, 8, 20, 37, 42, 44, 68, 129, 142, 147, 178, 183, 185, 193, 197, 207, 218, 241, 242, 245], "except": [2, 5, 167, 169, 178, 245], "assert": [2, 178], "product": [2, 197, 254], "never": [2, 169, 178], "crash": [2, 62, 82, 168, 173, 233, 235, 241, 243, 244, 245], "prefer": [2, 49, 62, 82, 134, 167, 171, 173, 192, 205, 207, 212, 244], "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, 229, 230, 231, 232, 233, 235, 236, 237, 238, 240, 241, 242, 243, 244, 245, 248, 253], "librari": [2, 4, 51, 103, 142, 175, 181, 237, 241, 245], "over": [2, 182, 186, 192, 193, 196, 218, 228, 233, 235, 240, 241], "boost": [2, 237], "depend": [2, 3, 105, 171, 181, 198, 207, 218, 237, 240, 246, 253], "In": [2, 6, 27, 62, 82, 84, 168, 171, 173, 178, 182, 185, 200, 204, 214, 221, 229, 235, 237, 238, 246], "11": [2, 31, 178, 182], "17": [2, 36, 237], "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, 215, 226, 230, 235, 237, 245, 254], "necessari": [2, 5, 7, 96, 178, 211, 214, 218], "offer": [2, 3, 95, 173, 178, 204, 236], "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, 235], "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, 244], "final": [2, 61, 95, 168, 171, 190, 197, 245], "minim": [2, 62, 82, 140, 173, 190], "third": [2, 182, 237], "parti": [2, 178, 237], "think": 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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, 229, 230, 235, 241, 248], "myclass": 2, "sourc": [2, 3, 5, 84, 133, 159, 161, 165, 183, 204, 236, 238, 240, 244], "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, 230, 244], "myapihead": 2, "our": [2, 3, 6, 115, 116, 120, 121, 124, 126, 127, 128, 129, 136, 137, 138, 167, 178, 183, 190, 236, 254], "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, 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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, 228, 235, 236, 237, 238, 240, 241, 243, 244, 245, 248, 251, 256], "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, 243, 244, 245, 254], "qtgui": [2, 28, 62, 63, 64, 103, 104, 157, 159, 161], "instead": [2, 39, 75, 167, 168, 169, 244], "being": [2, 5, 15, 24, 27, 48, 84, 90, 91, 104, 120, 124, 157, 158, 198, 218, 220, 225, 237, 253], "wrong": [2, 5, 241], "qdialog": [2, 63, 65, 71], "correct": [2, 5, 49, 62, 82, 123, 126, 173, 190, 237, 245, 251], "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, 201, 204, 207, 209, 211, 228, 231, 232, 235, 236, 237, 240, 242, 243, 244, 245, 246], "chemistri": [2, 3, 4, 5, 204, 229, 231, 232, 236, 237, 240, 253], "nest": [2, 190], "everyth": [2, 206, 210, 217], "insid": [2, 5, 175, 237], "mongochem": [2, 245], "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, 237, 244], "most": [2, 15, 61, 62, 72, 73, 75, 78, 82, 125, 126, 164, 168, 173, 178, 204, 205, 207, 211, 215, 218, 229, 230, 235, 237], "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, 228, 232, 233, 235, 237, 240, 241, 244, 245], "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, 215], "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, 215, 230, 235, 236, 241, 243, 244, 253], "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, 215, 218, 220, 229, 235, 237, 242, 243, 244, 245, 253, 256], "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, 215, 217, 218, 219, 230, 240, 245], "symbol": [2, 19, 23, 39, 40, 72, 73, 159, 160, 173, 200, 221, 243], "avoid": [2, 5, 22, 84, 178, 237, 244, 245, 254], "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, 237, 248, 255], "deriv": [2, 15, 20, 21, 25, 38, 48, 85, 100, 104, 126, 158, 178, 229, 248, 249, 253], "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, 216, 217, 218, 219, 220, 221, 225, 229, 230, 235, 237, 240, 245, 247, 253], "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, 215], "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, 237], "id": [2, 26, 27, 28, 33, 49, 61, 65, 68, 85, 90, 91, 95, 115, 119, 131, 135, 136, 166, 237, 241], "show": [2, 28, 65, 78, 89, 181, 185, 187, 190, 191, 202, 207, 220, 228, 229, 235, 244], "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, 233, 235, 236, 237], "look": [2, 5, 49, 118, 171, 175, 183, 202, 211, 235, 237], "better": [2, 4, 204, 212, 218, 235, 236, 245], "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, 215, 217, 218, 219, 220, 221, 225, 226, 229, 230, 231, 235, 236, 237, 238, 240, 241, 243, 244], "afford": 2, "few": [2, 175, 190, 194, 233, 235, 245], "extra": [2, 62, 82, 168, 173, 182], "byte": [2, 51, 105, 141], "like": [3, 15, 24, 37, 61, 65, 78, 162, 166, 169, 171, 172, 190, 211, 212, 235, 236, 237, 241, 242, 243, 244, 245, 253], "mani": [3, 24, 37, 161, 167, 204, 207, 220, 223, 233, 234, 235, 240, 241, 242, 243, 244, 245], "fundament": 3, "commun": [3, 4, 66, 166, 178], "aim": [3, 229], "develop": [3, 4, 204, 229, 233, 235, 236, 240, 241, 243, 244], "contributor": [3, 233, 240, 241, 242, 243, 244, 245], "alik": [3, 179], "hope": 3, "build": [3, 21, 29, 30, 95, 98, 156, 168, 170, 180, 181, 196, 209, 215, 228, 233, 235, 236, 238, 240, 241, 243, 244, 245, 246, 247, 248, 254, 255], "top": [3, 75, 105, 118, 120, 123, 138, 141, 198, 223, 237, 243], "framework": [3, 235, 244, 245], "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, 237, 252, 254, 256], "veri": [3, 4, 22, 31, 36, 161, 183, 202, 241, 243, 244], "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, 240], "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, 236, 239, 240], "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, 228, 229, 235, 236, 237, 240, 241, 243, 244, 245], "its": [3, 8, 14, 26, 39, 49, 51, 72, 73, 81, 95, 126, 161, 170, 171, 178, 197, 205, 225, 252, 253, 254, 256], "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, 215, 218, 220, 221, 230, 232, 235, 237, 240, 245, 254], "come": [3, 193, 198, 214, 215, 220, 236], "would": [3, 75, 126, 134, 190, 202, 204, 233, 235, 236, 237, 253], "particularli": [3, 215, 233, 234, 241, 243, 244], "googl": [3, 241, 243, 244], "summer": [3, 204, 240, 241, 243, 244], "2007": 3, "2008": 3, "2011": 3, "2016": 3, "2018": 3, "2019": [3, 243], "2021": [3, 240, 241, 242], "2022": [3, 204, 243, 244], "kitwar": [3, 237], "inc": 3, "univers": [3, 204, 215, 218], "pittsburgh": [3, 204], "u": [3, 4, 7, 8, 20, 104, 126, 185, 190, 236, 240, 241, 243, 244], "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, 229, 235, 237, 240, 245], "pettt": 3, "program": [3, 65, 66, 67, 68, 134, 159, 163, 166, 167, 168, 173, 182, 188, 208, 214, 233, 243], "research": [3, 190, 236, 253], "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, 237, 251], "infrastructur": 3, "blue": [3, 18, 23, 140, 142, 159, 160, 165, 197, 198, 217, 220, 230, 235], "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, 205, 210, 229, 234, 235, 243, 245, 249, 251], "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, 228, 235], "structur": [3, 21, 22, 23, 24, 26, 28, 37, 75, 170, 171, 183, 189, 190, 194, 196, 198, 200, 206, 211, 215, 218, 221, 235, 240, 241, 243, 251], "databas": [3, 4, 23, 174, 189, 196, 208, 228], "cmake": [3, 237, 245], "eigen": [3, 5, 28, 37, 107, 118, 134, 237], "softwar": [3, 207, 229], "babel": [3, 162, 169, 202, 235, 240, 243, 244], "And": [3, 167], "cours": [3, 189], "johann": 3, "loschmidt": 3, "amedeo": 3, "made": [4, 6, 7, 23, 26, 81, 100, 178, 179, 196, 197, 198, 202, 203, 208, 210, 211, 215, 226, 240], "who": 4, "want": [4, 7, 168, 185, 189, 190, 197, 200, 202, 212, 213, 221, 223, 229, 230, 236], "back": [4, 7, 83, 159, 160, 205, 211, 240, 241, 243], "great": [4, 236, 237], "place": [4, 5, 39, 49, 72, 73, 171, 173, 178, 183, 198, 206, 207, 211, 218, 223, 225, 236, 237, 249], "start": [4, 5, 24, 26, 92, 116, 120, 180, 181, 182, 189, 190, 205, 216, 218, 219, 222, 227, 232, 236, 241, 245], "fellow": 4, "forum": [4, 6], "question": [4, 236], "level": [4, 62, 75, 82, 173, 237], "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, 228, 229, 231, 233, 237, 248, 253, 256], "find": [4, 14, 22, 29, 30, 41, 51, 78, 84, 95, 99, 156, 170, 171, 180, 202, 214, 216, 231, 235, 236, 244, 250, 253], "experi": 4, "valuabl": 4, "bug": [4, 6, 193, 236, 239], "pleas": [4, 6, 236, 240, 241, 243, 244, 253], "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, 231], "moment": [4, 190, 231], "tracker": [4, 236], "issu": [4, 6, 236, 240, 245], "code": [4, 6, 24, 37, 62, 82, 84, 88, 161, 167, 169, 170, 171, 173, 183, 190, 191, 193, 207, 231, 232, 235, 236, 238, 240, 241, 243, 244, 245], "while": [4, 5, 26, 62, 82, 84, 95, 100, 168, 169, 173, 182, 187, 213, 218, 228, 244], "move": [4, 28, 104, 138, 142, 178, 185, 193, 196, 202, 218, 223, 235, 245, 246], "around": [4, 5, 15, 22, 31, 36, 63, 65, 69, 185, 187, 190, 196, 198, 202, 213, 223, 235, 248, 253], "fit": [4, 5, 28, 51, 104, 123, 157, 178], "particular": [4, 23, 51, 62, 75, 82, 166, 167, 169, 173, 178, 189, 204], "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, 235, 253], "discuss": [4, 6, 168, 207, 236, 240, 241, 243, 244, 253], "idea": [4, 236], "plan": 4, "direct": [4, 18, 41, 62, 82, 115, 118, 119, 120, 121, 124, 128, 136, 142, 159, 165, 173, 178, 193, 219, 237, 243, 246], "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, 228, 229, 232, 235, 236, 237, 240, 245, 248], "both": [4, 15, 26, 51, 63, 64, 161, 167, 169, 172, 173, 175, 176, 187, 214, 236, 256], "python": [4, 92, 99, 161, 168, 171, 174, 175, 216, 236, 237, 239, 241, 243, 244, 245], "script": [4, 63, 64, 75, 83, 92, 99, 100, 162, 172, 214, 236, 240, 241, 242, 244, 245], "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, 236, 246], "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, 243, 244, 245], "edit": [4, 14, 64, 95, 161, 180, 188, 197, 198, 200, 202, 207, 209, 210, 211, 221, 223, 232, 233, 235, 237, 243, 244, 245], "tutori": [4, 180, 181, 198, 207, 235, 236], "site": [4, 235, 236], "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, 228, 230, 233, 235, 244, 245], "lesson": [4, 185, 253], "activ": [4, 24, 70, 75, 86, 87, 88, 89, 96, 100, 103, 104, 214, 235, 237], "teacher": 4, "send": [4, 61, 66, 92, 161, 166, 173, 240], "fragment": [4, 133, 134, 159, 165, 180, 192, 195, 203, 205, 223, 226, 235, 240, 245], "report": [4, 6, 62, 82, 173, 183, 236, 241, 242, 243, 244], "encount": [4, 6, 48, 51, 104], "about": [4, 19, 23, 39, 62, 82, 118, 173, 197, 207, 211, 213, 225, 236, 243, 244], "improv": [4, 6, 233, 235, 239, 242], "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, 236, 244], "donat": 4, "pai": [4, 204, 256], "host": [4, 243, 244, 245], "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, 231, 237, 241, 244, 245, 246, 248], "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, 235, 244, 245, 248, 253], "larg": [5, 7, 51, 181, 185, 186, 189, 190, 202, 235, 237], "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, 229, 231, 235, 240, 241, 242, 243, 244, 245], "enforc": [5, 178], "clang": [5, 244], "tool": [5, 25, 38, 75, 100, 101, 104, 159, 164, 180, 182, 185, 189, 190, 196, 198, 200, 202, 203, 204, 213, 233, 236, 240, 242, 243, 245, 248, 252, 255, 256], "space": [5, 19, 21, 22, 25, 27, 28, 38, 39, 51, 95, 146, 159, 160, 169, 173, 181, 183, 185, 186, 187, 188, 211, 243, 245, 251], "tab": [5, 211, 241, 244], "keep": [5, 26, 51, 65, 67, 95, 103, 105, 213, 237], "less": [5, 12, 17, 23, 28, 95, 207, 230, 235, 254], "than": [5, 7, 12, 17, 23, 26, 28, 51, 62, 82, 95, 166, 178, 186, 235, 241, 251, 254], "80": 5, "charact": [5, 19, 48, 62, 82, 168, 173], "wide": [5, 204, 207, 235], "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, 237, 255, 256], "separ": [5, 142, 168, 173, 178, 229, 234], "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, 228, 232, 235, 237, 240, 245], "nmbr": 5, "singl": [5, 17, 28, 51, 62, 64, 66, 70, 82, 84, 95, 116, 142, 173, 190, 191, 197, 203, 226, 244], "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, 251], "unus": [5, 15, 24, 37], "ones": 5, "incorrect": [5, 241, 244, 245], "f": [5, 24, 37, 70, 87, 107, 121, 134, 136, 138, 157, 159, 160, 169, 178, 215, 241], "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, 243], "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, 244, 254], "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, 235, 241, 245], "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, 230, 232, 240], "curli": 5, "blah": [5, 62, 82, 176], "explod": 5, "5": [5, 14, 39, 41, 62, 82, 95, 159, 160, 176, 185, 222, 237, 244, 245, 246, 248, 255, 256], "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, 242], "between": [5, 14, 22, 23, 26, 28, 41, 42, 43, 84, 85, 95, 166, 171, 172, 181, 182, 198, 207, 213, 218, 224, 245, 251, 253, 256], "x": [5, 19, 21, 22, 27, 28, 123, 169, 172, 173, 182, 198, 205, 207, 211, 217, 219, 235, 237, 245, 254], "mystr": 5, "y": [5, 19, 22, 28, 118, 123, 169, 173, 198, 205, 207, 211, 217, 219, 237], "whoah": 5, "surround": [5, 230], "binari": [5, 237, 244], "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, 244], "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, 229, 235, 240, 251, 252, 254], "size": [5, 7, 18, 20, 26, 27, 43, 51, 84, 115, 117, 120, 134, 136, 142, 159, 160, 165, 181, 182, 198, 211, 240, 245, 251], "left": [5, 51, 62, 82, 105, 118, 137, 141, 142, 173, 200, 202, 203, 205, 211, 217, 218, 220, 221, 226, 237], "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, 215, 237, 246, 256], "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, 232, 235, 242, 244, 250], "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, 243, 244], "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, 202], "endl": 5, "bar": [5, 207, 211, 223, 225, 231], "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, 215, 218, 219, 221, 224, 225, 226, 229, 235, 236, 237, 244, 253], "complex": [5, 126, 235, 245], "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, 215, 223, 251], "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, 233, 237, 245], "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, 199, 200, 205, 209, 215, 221, 235, 241, 244, 248], "cover": [5, 168, 204, 228], "b": [5, 19, 21, 26, 28, 41, 47, 53, 59, 85, 91, 95, 105, 140, 159, 160, 169, 173, 178, 191, 243, 245, 251], "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, 240], "express": [5, 62, 82, 173, 178, 254], "intent": 5, "clearer": 5, "label": [5, 12, 19, 28, 62, 82, 95, 107, 138, 159, 160, 164, 168, 170, 173, 176, 178, 199, 213, 235, 240, 241, 243, 245], "column": [5, 21, 41, 67, 86, 98], "everi": [5, 26, 28, 178, 228], "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, 237], "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, 242], "omiss": 5, "anoth": [5, 39, 51, 169, 183, 188, 198, 200, 203, 221, 235, 256], "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, 240, 241, 243], "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, 231, 235, 245], "drawdefault": 5, "shorter": 5, "insert": [5, 7, 28, 62, 82, 159, 160, 168, 176, 180, 181, 185, 189, 190, 191, 192, 195, 209, 223, 235, 240, 241, 243, 245, 246], "comma": [5, 167, 169], "broken": 5, "begin": [5, 7, 43, 84, 95, 105, 130, 141, 144, 159, 160, 165, 200, 203, 220, 221, 230, 232], "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, 235, 249, 254, 256], "currentposit": 5, "offset": [5, 84, 134, 159, 164], "reimplement": [5, 64, 104], "put": [5, 235, 245], "discourag": 5, "prefix": [5, 12, 17, 62, 78, 82, 172, 175, 176, 237], "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, 240], "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, 229, 230, 235, 236, 240, 243, 244, 245], "As": [5, 6, 166, 168, 189, 198, 209, 217, 224, 228, 237, 240, 243], "feel": [5, 236], "free": [5, 51, 104, 168, 173, 178, 204, 236, 237], "bad": 5, "local": [6, 62, 74, 82, 84, 168, 173, 175, 176, 236, 240, 243, 245], "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, 235, 236, 244], "weblat": [6, 240, 241, 242, 243, 244, 245], "autom": [6, 49, 175, 235, 243, 244], "task": [6, 215, 235], "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, 229, 231, 232, 235, 240, 244, 245], "time": [6, 51, 62, 82, 92, 95, 104, 117, 126, 161, 178, 181, 186, 190, 245], "freez": [6, 28], "least": [6, 75, 95, 212, 224, 230, 235, 244], "week": 6, "advanc": [6, 62, 82, 173, 236, 237], "releas": [6, 51, 117, 134, 142, 159, 165, 175, 204, 233, 237, 238, 239], "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, 240, 243, 245], "semant": 7, "effect": [7, 118, 178, 214, 246, 251], "share": [7, 12, 17, 26, 36, 175, 178, 179, 235, 237], "without": [7, 26, 49, 51, 65, 68, 161, 178, 202, 204, 207, 208, 233, 237, 241], "expos": 7, "access": [7, 18, 51, 64, 66, 67, 83, 103, 117, 134, 142, 169, 178, 193, 198, 208, 244], "amount": [7, 185, 207], "non": [7, 8, 23, 28, 62, 82, 95, 126, 169, 171, 173, 178, 240, 241, 244, 245], "trigger": [7, 104, 171], "detach": [7, 134, 159, 160, 209, 243], "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, 233, 235, 237, 238, 239, 240, 245, 246, 247, 252, 253, 254, 255, 256], "perform": [7, 13, 15, 21, 42, 51, 63, 84, 95, 104, 134, 168, 170, 171, 178, 182, 188, 202, 207, 212, 235, 237, 239, 246, 256], "deep": [7, 230, 237], "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, 236], "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, 215], "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, 246], "inputiter": [7, 44], "last": [7, 22, 44, 62, 68, 82, 92, 206, 241], "note": [7, 24, 28, 62, 82, 118, 128, 134, 142, 166, 169, 173, 175, 176, 183, 185, 186, 187, 190, 198, 202, 204, 237, 239, 246, 249, 250, 256], "detachwithcopi": [7, 159, 160], "explicitli": [7, 166], "implicitli": 7, "ensur": [7, 21, 28, 62, 66, 82, 85, 95, 123, 132, 173, 207, 237, 240, 245], "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, 235, 243, 244], "val": 7, "push_back": [7, 159, 160], "v": [7, 39, 41, 42, 43, 127, 128, 134, 176, 178, 193, 237, 245, 247, 254], "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, 245], "delet": [7, 49, 51, 69, 95, 104, 124, 126, 133, 157, 168, 182, 200, 205, 211, 221, 241, 243, 245, 249], "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, 237, 245], "pop": [7, 170, 188, 194, 196, 197, 207, 208, 210, 211, 230], "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, 245], "figur": [8, 73, 213, 251], "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, 231, 237], "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, 233, 235], "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, 230, 246, 253], "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, 223, 224, 225, 226, 227, 228, 230, 232, 233, 235, 240, 241, 243, 244, 245, 248, 254, 256], "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, 240], "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, 235, 236, 248], "moleculetyp": [12, 17, 90, 91, 159, 160, 164], "compil": [12, 133, 134, 159, 165, 237], "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, 235, 244], "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, 248, 253], "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, 240, 241, 245], "setformalcharg": [12, 28, 95, 159, 160, 164], "sign": [12, 28, 95, 134, 237, 243], "charg": [12, 28, 62, 82, 95, 173, 174, 175, 207, 215, 230, 235, 241, 243, 244, 245, 246, 256], "formal": [12, 28, 95, 243, 245], "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, 199, 207, 209, 230, 235, 240, 241, 243, 244, 245], "setlay": [12, 28, 95, 159, 160, 164], "layer": [12, 28, 85, 95, 159, 160, 164, 241, 242, 243, 244, 245], "invalid": [12, 17, 28, 39, 48, 68, 85, 90, 91, 95, 131, 159, 165, 241], "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, 240], "increment": [12, 17], "self": [12, 17, 244], "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, 240, 244, 245, 250, 251, 256], "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, 199, 200, 201, 202, 205, 208, 209, 211, 213, 214, 215, 217, 219, 220, 221, 222, 223, 224, 228, 230, 231, 232, 240, 241, 242, 243, 244, 245, 246], "setforcevector": [12, 28, 95, 159, 160, 164], "forc": [12, 28, 85, 95, 139, 161, 174, 175, 190, 199, 209, 213, 215, 216, 232, 237, 245, 250, 252, 253, 254, 256], "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, 244, 245], "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, 237, 240, 244, 253], "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, 249, 254], "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, 241], "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, 244], "been": [13, 28, 49, 51, 66, 68, 75, 95, 96, 132, 134, 171, 178, 185, 188, 197, 198, 200, 207, 208, 211, 215, 218, 221, 224, 230, 231, 232, 235, 237], "previous": [13, 207, 208, 211, 224], "cach": [13, 51, 62, 66, 82, 92, 175, 244, 245], "There": [13, 62, 81, 82, 173, 191, 192, 193, 203, 211, 226, 236, 237], "correspond": [13, 15, 24, 28, 61, 62, 82, 95, 173, 175, 176, 178, 182, 214, 218, 246], "reset": [13, 48, 51, 62, 82, 90, 91, 92, 96, 104, 118, 123, 157, 159, 160, 163, 164, 185, 209, 219, 223, 224, 225, 240, 241], "typer": 13, "state": [13, 48, 51, 61, 62, 65, 68, 82, 90, 91, 95, 96, 125, 158, 176, 178, 241], "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, 228, 229, 240, 242, 243, 244, 245], "setup": [13, 61, 169, 209, 214, 243], "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, 229, 230, 245], "m_molecul": [13, 15, 95, 159, 160, 164], "popul": [13, 15, 21, 25, 51, 95], "spglib": [14, 39, 95, 183, 240], "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, 235, 241, 245], "unit": [14, 19, 21, 23, 28, 39, 41, 62, 82, 95, 173, 176, 180, 181, 184, 187, 188, 190, 193, 209, 211, 241, 245, 251], "cell": [14, 19, 21, 28, 39, 41, 95, 173, 180, 181, 184, 185, 188, 190, 193, 209, 211, 241, 245, 251], "exist": [14, 22, 26, 28, 43, 51, 65, 67, 85, 95, 102, 126, 134, 168, 172, 173, 218, 233, 241], "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, 235, 240, 245], "cartesian": [14, 19, 21, 24, 37, 39, 41, 95, 169, 173, 182, 183, 186, 187, 198, 209], "toler": [14, 28, 39, 95, 183, 186, 244], "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, 233, 241, 244], "conventionalizecel": [14, 95, 159, 160, 164], "refin": [14, 215], "convention": [14, 95], "symmetr": [14, 95, 159, 160, 187, 235], "basi": [15, 24, 25, 28, 37, 38, 62, 82, 107, 108, 173, 178, 207, 245], "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, 215], "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, 215, 224, 229, 230, 232, 235, 244, 246, 256], "electrontyp": [15, 24, 25, 37, 159, 160], "electron": [15, 23, 24, 25, 28, 38, 207, 229, 230, 244], "pair": [15, 24, 25, 26, 27, 28, 34, 37, 62, 82, 85, 95, 116, 159, 160, 173, 175, 176, 207, 229, 235, 244], "alpha": [15, 24, 25, 41, 140, 142, 159, 160, 165, 169, 240, 244], "beta": [15, 24, 25, 41, 159, 160, 169, 233], "cannot": [15, 21, 29, 30, 49, 51, 68, 156, 178, 235], "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, 236, 237, 240, 253], "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, 216, 218, 227, 229, 233, 235, 236, 244, 245, 248, 253], "orbit": [15, 24, 25, 37, 38, 107, 159, 160, 161, 180, 198, 209, 227, 235, 241, 252, 255], "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, 245], "lumo": [15, 159, 160], "m_electron": [15, 159, 160], "total": [15, 28, 61, 245], "close": [15, 48, 51, 64, 70, 159, 162, 178, 209, 213, 230, 231, 241, 243, 244, 251], "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, 215, 218, 221, 222, 223, 224, 226, 229, 242, 243, 244, 245, 250, 251, 252, 253, 254, 255, 256], "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, 229, 240, 241, 242, 243, 245], "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, 215, 229, 231, 232, 244, 245], "necessarili": 15, "m_name": [15, 22, 159, 160], "usual": [15, 171, 237], "standard": [15, 62, 70, 82, 90, 91, 92, 95, 117, 134, 158, 166, 167, 168, 169, 171, 172, 173, 178, 198, 208, 241, 245], "m_theorynam": [15, 159, 160], "theori": [15, 62, 82, 173, 178, 199, 209, 245, 248], "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, 215, 221, 237, 256], "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], "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, 244], "rang": [18, 21, 62, 82, 124, 126, 128, 134, 140, 142, 167, 169, 173, 176, 207, 235, 244], "intens": [18, 28, 244], "red": [18, 140, 142, 159, 160, 165, 198, 217, 230, 235], "green": [18, 140, 142, 159, 160, 165, 198, 217], "memori": [18, 24, 51, 95, 134, 243], "3": [18, 27, 62, 82, 84, 127, 128, 134, 140, 142, 159, 160, 167, 169, 176, 182, 186, 190, 200, 209, 212, 213, 222, 237, 240, 246, 247, 253, 254, 255], "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, 241, 244], "directli": [18, 49, 67, 167, 178, 189, 191, 195, 229], "opengl": [18, 123, 132, 161, 237, 243, 244, 245], "conveni": [18, 28, 43, 48, 49, 51, 66, 67, 85, 161, 205, 210, 245], "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, 230], "emphasi": 18, "effici": [18, 210, 241], "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, 237, 245], "align": [19, 21, 132, 140, 173, 180, 181, 182, 185, 190, 191, 209, 222, 245], "see": [19, 28, 51, 62, 64, 78, 82, 85, 95, 105, 134, 142, 161, 168, 172, 173, 183, 186, 187, 190, 191, 207, 229], "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, 244, 245, 251], "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, 215, 218, 223, 236, 243], "z": [19, 22, 28, 169, 173, 181, 185, 190, 191, 198, 205, 207, 211, 217, 219, 240], "6": [19, 21, 27, 62, 74, 82, 84, 123, 158, 159, 160, 167, 169, 171, 173, 190, 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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, 237, 241], "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, 245], "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, 241], "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": 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Avogadro::Core::CoordinateBlockGenerator": [[19, "class-avogadro-core-coordinateblockgenerator"]], "Class Avogadro::Core::ArraySet": [[8, "class-avogadro-core-arrayset"]], "Thanks": [[3, "thanks"], [204, "thanks"]], "Code": [[3, "code"]], "Funding": [[3, "funding"]], "Other Projects": [[3, "other-projects"]], "Coding Style (C++)": [[5, "coding-style-c"]], "Indentation": [[5, "indentation"]], "Line Width": [[5, "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::Array": [[7, "class-avogadro-core-array"]], "Class Avogadro::Core::Elements": [[23, "class-avogadro-core-elements"]], "Class Avogadro::Core::Color3f": [[18, "class-avogadro-core-color3f"]], "Class Avogadro::Core::CrystalTools": [[21, "class-avogadro-core-crystaltools"]], "Translations": [[6, "translations"]], "Current Status": [[6, "current-status"]], "Credits": [[6, "credits"], [240, "credits"], [244, "credits"], [243, "credits"], [245, "credits"], [242, "credits"], [241, "credits"]], "Contribute": [[4, "contribute"]], "How to Help": [[4, "how-to-help"]], "Class Avogadro::Core::CoordinateSet": [[20, "class-avogadro-core-coordinateset"]], "Class Avogadro::Core::AtomTyper": [[13, "class-avogadro-core-atomtyper"]], "Class Avogadro::Core::Cube": [[22, "class-avogadro-core-cube"]], "Class Avogadro::Core::ArraySet::Holder": [[9, "class-avogadro-core-arrayset-holder"]], "Class Avogadro::MoleQueue::MoleQueueDialog": [[65, "class-avogadro-molequeue-molequeuedialog"]], "Class Avogadro::MoleQueue::MoleQueueManager": [[66, "class-avogadro-molequeue-molequeuemanager"]], "Class Avogadro::Io::PdbFormat": [[57, "class-avogadro-io-pdbformat"]], "Class Avogadro::QtGui::BackgroundFileFormat": [[69, "class-avogadro-qtgui-backgroundfileformat"]], "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::Io::MdlFormat": [[55, "class-avogadro-io-mdlformat"]], "Class Avogadro::Io::LammpsTrajectoryFormat": [[53, "class-avogadro-io-lammpstrajectoryformat"]], "Class Avogadro::MoleQueue::InputGeneratorDialog": [[63, "class-avogadro-molequeue-inputgeneratordialog"]], "Class Avogadro::Io::GromacsFormat": [[50, "class-avogadro-io-gromacsformat"]], "Class Avogadro::MoleQueue::MoleQueueWidget": [[68, "class-avogadro-molequeue-molequeuewidget"]], "Class Avogadro::Io::Hdf5DataFormat": [[51, "class-avogadro-io-hdf5dataformat"]], "Class Avogadro::Io::PoscarFormat": [[58, "class-avogadro-io-poscarformat"]], "Class Avogadro::Io::LammpsDataFormat": [[52, "class-avogadro-io-lammpsdataformat"]], "Class Avogadro::Io::MMTFFormat": [[54, "class-avogadro-io-mmtfformat"]], "Class Avogadro::MoleQueue::BatchJob": [[61, "class-avogadro-molequeue-batchjob"]], "Class Avogadro::MoleQueue::MoleQueueQueueListModel": [[67, "class-avogadro-molequeue-molequeuequeuelistmodel"]], "Class Avogadro::Io::TrrFormat": [[59, "class-avogadro-io-trrformat"]], "Class Avogadro::Io::XyzFormat": [[60, "class-avogadro-io-xyzformat"]], "Class Avogadro::Io::OutcarFormat": [[56, "class-avogadro-io-outcarformat"]], "Class Avogadro::QtGui::ElementTranslator": [[74, "class-avogadro-qtgui-elementtranslator"]], "Class Avogadro::QtGui::ElementItem": [[73, "class-avogadro-qtgui-elementitem"]], "Class Avogadro::QtGui::ContainerWidget": [[70, "class-avogadro-qtgui-containerwidget"]], "Class Avogadro::QtGui::ElementDetail": [[72, "class-avogadro-qtgui-elementdetail"]], "Class Avogadro::QtGui::CustomElementDialog": [[71, "class-avogadro-qtgui-customelementdialog"]], "Hydrogen Clusters": [[251, "hydrogen-clusters"]], "Task": [[251, "task"], [250, "task"], [252, "task"], [255, "task"], [256, "task"], [254, "task"], [248, "task"], [247, "task"]], "Solution": [[251, "solution"], [252, "solution"], [255, "solution"], [256, "solution"], [254, "solution"], [249, "solution"], [246, "solution"]], "Issues": [[251, "issues"]], "See also": [[251, "see-also"], [250, "see-also"], [252, "see-also"], [255, "see-also"], [256, "see-also"], [254, "see-also"], [248, "see-also"], [247, "see-also"]], "Sources": [[251, "sources"], [252, "sources"], [256, "sources"]], "HCN dipole": [[250, "hcn-dipole"]], "Hydrogen Molecule": [[252, "hydrogen-molecule"]], "Organic Hybridization": [[255, "organic-hybridization"]], "Further reading": [[255, "further-reading"], [254, "further-reading"], [248, "further-reading"], [246, "further-reading"]], "Water": [[256, "water"]], "Markovnikov\u2019s Rule": [[254, "markovnikovs-rule"]], "Teach": [[253, "teach"]], "Class Avogadro::QtGui::Molecule": [[85, "class-avogadro-qtgui-molecule"]], "Class Avogadro::QtGui::PythonScript": [[92, "class-avogadro-qtgui-pythonscript"]], "Class Avogadro::QtGui::InterfaceScript": [[82, "class-avogadro-qtgui-interfacescript"]], "Class Avogadro::QtGui::PersistentAtom": [[90, "class-avogadro-qtgui-persistentatom"]], "Class Avogadro::QtGui::MeshGenerator": [[84, "class-avogadro-qtgui-meshgenerator"]], "Class Avogadro::QtGui::ScenePluginModel": [[98, "class-avogadro-qtgui-scenepluginmodel"]], "Class Avogadro::QtGui::RWAtom": [[93, "class-avogadro-qtgui-rwatom"]], "Class Avogadro::QtGui::ScriptLoader": [[99, "class-avogadro-qtgui-scriptloader"]], "Class Avogadro::QtGui::MultiViewWidget": [[87, "class-avogadro-qtgui-multiviewwidget"]], "Class Avogadro::QtGui::GenericHighlighter": [[79, "class-avogadro-qtgui-generichighlighter"]], "Class Avogadro::QtGui::PeriodicTableView": [[89, "class-avogadro-qtgui-periodictableview"]], "Class Avogadro::QtGui::MoleculeModel": [[86, "class-avogadro-qtgui-moleculemodel"]], "Class Avogadro::QtGui::PeriodicTableScene": [[88, "class-avogadro-qtgui-periodictablescene"]], "Class Avogadro::QtGui::PersistentBond": [[91, "class-avogadro-qtgui-persistentbond"]], "Class Avogadro::QtGui::RWBond": [[94, "class-avogadro-qtgui-rwbond"]], "Class Avogadro::QtGui::ScenePluginFactory": [[97, "class-avogadro-qtgui-scenepluginfactory"]], "Class Avogadro::QtGui::GenericHighlighter::Rule": [[80, "class-avogadro-qtgui-generichighlighter-rule"]], "Class Avogadro::QtGui::InterfaceWidget": [[83, "class-avogadro-qtgui-interfacewidget"]], "Class Avogadro::QtGui::ExtensionPlugin": [[75, "class-avogadro-qtgui-extensionplugin"]], "Class Avogadro::QtGui::RWMolecule": [[95, "class-avogadro-qtgui-rwmolecule"]], "Class Avogadro::QtGui::ExtensionPluginFactory": [[76, "class-avogadro-qtgui-extensionpluginfactory"]], "Class Avogadro::QtGui::ScenePlugin": [[96, "class-avogadro-qtgui-sceneplugin"]], "Class Avogadro::QtGui::FileFormatDialog": [[78, "class-avogadro-qtgui-fileformatdialog"]], "Class Avogadro::QtGui::FileBrowseWidget": [[77, "class-avogadro-qtgui-filebrowsewidget"]], "Class Avogadro::QtGui::HydrogenTools": [[81, "class-avogadro-qtgui-hydrogentools"]], "Drawing Molecules": [[200, "drawing-molecules"]], "Creating Carbon Dioxide": [[200, "creating-carbon-dioxide"]], "Making Selections": [[203, "making-selections"]], "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"]], "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"]], "Geometry Constraints": [[213, "geometry-constraints"]], "Example": [[213, "example"]], "Optimizations": [[213, "optimizations"]], "Example cont.": [[213, "example-cont"]], "Align Tool": [[217, "align-tool"]], "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"]], "Introduction to Molecular Mechanics": [[215, "introduction-to-molecular-mechanics"]], "UFF": [[215, "uff"]], "MMFF94(s)": [[215, "mmff94-s"]], "GAFF": [[215, "gaff"]], "Auto-Rotate Tool": [[219, "auto-rotate-tool"]], "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"]], "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"]], "Draw Tool": [[221, "draw-tool"]], "1. Creating a Molecule": [[221, "creating-a-molecule"]], "2.": [[221, "id1"]], "3.": [[221, "id2"]], "4.": [[221, "id3"]], "5.": [[221, "id4"]], "6.": [[221, "id5"]], "7.": [[221, "id6"]], "8.": [[221, "id7"]], "9.": [[221, "id8"]], "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"]], "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"]], "Auto-Optimize Tool": [[218, "auto-optimize-tool"]], "Force Fields & Algorithms": [[218, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[218, "fixing-ignoring-selections"]], "Tools": [[222, "tools"], [222, null]], "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"]], "Menus": [[209, "menus"], [209, null]], "Manipulate Tool": [[223, "manipulate-tool"]], "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"]], "Getting Started": [[201, "getting-started"], [201, null]], "Introduction": [[202, "introduction"]], "Opening a File": [[202, "opening-a-file"]], "Navigation": [[202, "navigation"]], "Measure Tool": [[224, "measure-tool"]], "Optimizing Geometry": [[216, "optimizing-geometry"]], "Optimization": [[216, null]], "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"]], "Class Avogadro::Core::NameAtomTyper": [[32, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::Molecule": [[28, "class-avogadro-core-molecule"]], "Class Avogadro::Core::ResidueData": [[34, "class-avogadro-core-residuedata"]], "Class Avogadro::Core::VariantMap": [[43, "class-avogadro-core-variantmap"]], "Class Avogadro::Core::SlaterSetTools": [[38, "class-avogadro-core-slatersettools"]], "Class Avogadro::Core::GaussianSetTools": [[25, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::SlaterSet": [[37, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::Variant": [[42, "class-avogadro-core-variant"]], "Class Avogadro::Core::RingPerceiver": [[35, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::Mesh": [[27, "class-avogadro-core-mesh"]], "Class Avogadro::Core::SpaceGroups": [[39, "class-avogadro-core-spacegroups"]], "Class Avogadro::Core::SymbolAtomTyper": [[40, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Io::CjsonFormat": [[45, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Io::FileFormatManager": [[49, "class-avogadro-io-fileformatmanager"]], "Class Avogadro::Core::Mutex": [[31, "class-avogadro-core-mutex"]], "Class Avogadro::Core::UnitCell": [[41, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::MoleculeSerializer": [[30, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Io::DcdFormat": [[47, "class-avogadro-io-dcdformat"]], "Class Avogadro::Io::CmlFormat": [[46, "class-avogadro-io-cmlformat"]], "Class Avogadro::Io::FileFormat": [[48, "class-avogadro-io-fileformat"]], "Class Avogadro::Core::MoleculeDeserializer": [[29, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::Residue": [[33, "class-avogadro-core-residue"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[44, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Core::Graph": [[26, "class-avogadro-core-graph"]], "Class Avogadro::Core::SharedMutex": [[36, "class-avogadro-core-sharedmutex"]], "1,3-diaxial interactions": [[249, "diaxial-interactions"]], "Tasks": [[249, "tasks"], [246, "tasks"]], "Using QTAIM (Atoms in Molecules) Analysis": [[229, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[229, "start-with-a-wfn-file"]], "Release Notes v1.94.0": [[240, "release-notes-v1-94-0"]], "Features": [[240, "features"], [236, "features"]], "\ud83d\udc1b Bug Fixes": [[240, "bug-fixes"], [244, "bug-fixes"], [243, "bug-fixes"], [245, "bug-fixes"], [242, "bug-fixes"], [241, "bug-fixes"]], "\ud83d\udc0d Python Improvements": [[240, "python-improvements"]], "\ud83e\uddf0 Maintenance": [[240, "maintenance"], [244, "maintenance"], [243, "maintenance"], [245, "maintenance"], [242, "maintenance"], [241, "maintenance"]], "Viewing Vibrations": [[232, "viewing-vibrations"]], "Tutorials": [[227, "tutorials"], [227, null]], "What\u2019s New in Avogadro 2": [[233, "whats-new-in-avogadro-2"]], "Major New Features": [[235, "major-new-features"]], "Speed and Stability": [[235, "speed-and-stability"]], "Rendering": [[235, "rendering"]], "New real-time shadows and depth effects": [[235, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[235, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[235, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[235, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[235, "layers"]], "Symmetry Properties": [[235, "symmetry-properties"]], "Template Tool": [[235, "template-tool"]], "Solvent Accessible and Solvent Excluded Surfaces": [[235, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[235, "flexible-electrostatics-models"]], "New Analysis Tools": [[235, "new-analysis-tools"]], "Python Commands / Plugins": [[235, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[235, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[235, "new-and-updated-interfaces-to-external-programs"]], "Release Notes v1.97.0": [[244, "release-notes-v1-97-0"]], "Highlights (tldr)": [[244, "highlights-tldr"], [245, "highlights-tldr"]], "\u2728 Features": [[244, "features"], [243, "features"], [245, "features"], [242, "features"], [241, "features"]], "\ud83d\ude80 Performance Improvements": [[244, "performance-improvements"], [245, "performance-improvements"]], "\ud83d\udcda Translations": [[244, "translations"], [243, "translations"], [245, "translations"], [242, "translations"], [241, "translations"]], "Building Source Code": [[237, "building-source-code"]], "Cloning Repositories": [[237, "cloning-repositories"]], "Updating": [[237, "updating"]], "Prerequisites": [[237, "prerequisites"]], "Debian-based Distribution or Ubuntu": [[237, "debian-based-distribution-or-ubuntu"]], "Building": [[237, "building"]], "Finding Qt, Windows Generators": [[237, "finding-qt-windows-generators"]], "Normal Development": [[237, "normal-development"]], "Build Tree Layout": [[237, "build-tree-layout"]], "Running Executables": [[237, "running-executables"]], "Building Packages": [[237, "building-packages"]], "Install": [[238, "install"], [236, "install"]], "Interface Changes": [[234, "interface-changes"]], "Release Notes v1.96.0": [[243, "release-notes-v1-96-0"]], "Changes": [[243, "changes"], [241, "changes"]], "\ud83d\ude80 Performance Fixes": [[243, "performance-fixes"]], "Navigate Tool": [[225, "navigate-tool"]], "Selection Tool": [[226, "selection-tool"]], "Viewing Electrostatic Potential Maps": [[230, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[230, "changing-surface-settings"]], "Release Notes v1.98.0": [[245, "release-notes-v1-98-0"]], "Basic VSEPR": [[248, "basic-vsepr"]], "Release Notes v1.95.1": [[242, "release-notes-v1-95-1"]], "Resources": [[236, "resources"]], "Connecting with the Avogadro community": [[236, "connecting-with-the-avogadro-community"]], "Naming a Molecule": [[228, "naming-a-molecule"]], "Alkene Isomers": [[247, "alkene-isomers"]], "Acid-Base Properties of Amino Acids": [[246, "acid-base-properties-of-amino-acids"]], "Viewing Molecular Orbitals": [[231, "viewing-molecular-orbitals"]], "Configure": [[231, "configure"]], "Version History": [[239, "version-history"], [239, null]], "Release Notes v1.95.0": [[241, "release-notes-v1-95-0"]], "Building Materials": [[184, "building-materials"], [184, null]], "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"]], "Making a Crystal Surface Slab": [[181, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[181, "import-the-appropriate-crystal-structure"]], "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 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"]], "Importing Molecules by Name": [[194, "importing-molecules-by-name"]], "Building with SMILES": [[192, "building-with-smiles"]], "VTK Classes": [[177, "vtk-classes"]], "Building Molecules": [[195, "building-molecules"], [195, null]], "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 a Peptide": [[189, "building-a-peptide"]], "Table of contents": [[180, "table-of-contents"]], "Display Types": [[199, "display-types"], [199, null]], "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"]], "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"]], "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 DNA or RNA": [[191, "building-dna-or-rna"]], "Building Carbon Nanotubes": [[190, "building-carbon-nanotubes"]], "Building a Polymer Unit Cell": [[182, "building-a-polymer-unit-cell"]], "Reducing Crystals to a Primitive Unit Cell": [[186, "reducing-crystals-to-a-primitive-unit-cell"]], "Scaling Crystal Cell Volume": [[187, "scaling-crystal-cell-volume"]], "Insert Molecular Fragments": [[196, "insert-molecular-fragments"]], "Perceiving Crystall Symmetry": [[183, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[183, "open-a-crystal-file"]], "Building a Supercell": [[188, "building-a-supercell"]], "Creating a Surface": [[188, "creating-a-surface"]], "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"]], "QtGui Classes": [[164, "qtgui-classes"]], "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::TypeTraits< int >": [[151, "class-avogadro-typetraits-int"]], "Class Avogadro::TypeTraits< unsigned int >": [[154, "class-avogadro-typetraits-unsigned-int"]], "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"]], "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"]], "Class Avogadro::TypeTraits< unsigned char >": [[153, "class-avogadro-typetraits-unsigned-char"]], "Class vtkAvogadroActor": [[158, "class-vtkavogadroactor"]], "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"]], "IO Classes": [[162, "io-classes"]], "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::VtkPlot": [[156, "class-avogadro-vtk-vtkplot"]], "Class Avogadro::TypeTraits< short >": [[152, "class-avogadro-typetraits-short"]], "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"]], "MoleQueue Classes": [[163, "molequeue-classes"]], "Class List": [[159, "class-list"]], "Core Classes": [[160, "core-classes"]], "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::TypeTraits< unsigned short >": [[155, "class-avogadro-typetraits-unsigned-short"]], "Rendering Classes": [[165, "rendering-classes"]], "Class Avogadro::Rendering::POVRayVisitor": [[130, "class-avogadro-rendering-povrayvisitor"]], "Class Avogadro::Rendering::GroupNode": [[126, "class-avogadro-rendering-groupnode"]], "Class Avogadro::Rendering::Shader": [[133, "class-avogadro-rendering-shader"]], "Class Avogadro::Rendering::LineStripGeometry": [[127, "class-avogadro-rendering-linestripgeometry"]], "Class Avogadro::TypeTraits": [[147, "class-avogadro-typetraits"]], "Class Avogadro::Rendering::TextRenderStrategy": [[141, "class-avogadro-rendering-textrenderstrategy"]], "Class Avogadro::Rendering::Sphere": [[135, "class-avogadro-rendering-sphere"]], "Class Avogadro::Rendering::TextLabel2D": [[137, "class-avogadro-rendering-textlabel2d"]], "Class Avogadro::TypeTraits< char >": [[148, "class-avogadro-typetraits-char"]], "Class Avogadro::Rendering::VolumeGeometry": [[146, "class-avogadro-rendering-volumegeometry"]], "Class Avogadro::Rendering::SphereGeometry": [[136, "class-avogadro-rendering-spheregeometry"]], "Class Avogadro::Rendering::Visitor": [[145, "class-avogadro-rendering-visitor"]], "Class Avogadro::Rendering::TextProperties": [[140, "class-avogadro-rendering-textproperties"]], "Class Avogadro::Rendering::GeometryVisitor": [[125, "class-avogadro-rendering-geometryvisitor"]], "Class Avogadro::Rendering::TextLabel3D": [[138, "class-avogadro-rendering-textlabel3d"]], "Class Avogadro::Rendering::Node": [[129, "class-avogadro-rendering-node"]], "Class Avogadro::Rendering::TextLabelBase": [[139, "class-avogadro-rendering-textlabelbase"]], "Class Avogadro::Rendering::ShaderProgram": [[134, "class-avogadro-rendering-shaderprogram"]], "Class Avogadro::Rendering::VRMLVisitor": [[144, "class-avogadro-rendering-vrmlvisitor"]], "Class Avogadro::Rendering::Texture2D": [[142, "class-avogadro-rendering-texture2d"]], "Class Avogadro::Rendering::MeshGeometry": [[128, "class-avogadro-rendering-meshgeometry"]], "Class Avogadro::Rendering::Primitive": [[131, "class-avogadro-rendering-primitive"]], "Class Avogadro::Rendering::TransformNode": [[143, "class-avogadro-rendering-transformnode"]], "Class Avogadro::TypeTraits< double >": [[149, "class-avogadro-typetraits-double"]], "Class Avogadro::Rendering::Scene": [[132, "class-avogadro-rendering-scene"]], "Class Avogadro::Rendering::Cylinder": [[119, "class-avogadro-rendering-cylinder"]], "Class Avogadro::Rendering::GLRenderVisitor": [[122, "class-avogadro-rendering-glrendervisitor"]], "Class Avogadro::Rendering::GeometryNode": [[124, "class-avogadro-rendering-geometrynode"]], "Class Avogadro::QtGui::ToolPlugin": [[100, "class-avogadro-qtgui-toolplugin"]], "Class Avogadro::QtOpenGL::QtTextRenderStrategy": [[105, "class-avogadro-qtopengl-qttextrenderstrategy"]], "Class Avogadro::Rendering::Camera": [[118, "class-avogadro-rendering-camera"]], "Class Avogadro::QuantumIO::MopacAux": [[112, "class-avogadro-quantumio-mopacaux"]], "Class Avogadro::QuantumIO::MoldenFile": [[111, "class-avogadro-quantumio-moldenfile"]], "Class Avogadro::QuantumIO::GUKBasisSet": [[107, "class-avogadro-quantumio-gukbasisset"]], "Class Avogadro::QuantumIO::GaussianFchk": [[110, "class-avogadro-quantumio-gaussianfchk"]], "Class Avogadro::Rendering::BufferObject": [[117, "class-avogadro-rendering-bufferobject"]], "Class Avogadro::QtOpenGL::ActiveObjects": [[103, "class-avogadro-qtopengl-activeobjects"]], "Class Avogadro::Rendering::CylinderGeometry": [[120, "class-avogadro-rendering-cylindergeometry"]], "Class Avogadro::QuantumIO::NWChemLog": [[114, "class-avogadro-quantumio-nwchemlog"]], "Class Avogadro::Rendering::ArrowGeometry": [[116, "class-avogadro-rendering-arrowgeometry"]], "Class Avogadro::QuantumIO::GAMESSUSOutput": [[106, "class-avogadro-quantumio-gamessusoutput"]], "Class Avogadro::Rendering::Drawable": [[121, "class-avogadro-rendering-drawable"]], "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry": [[115, 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"docs/display-types/coloring-molecules.md", "docs/display-types/display-types.md", "docs/display-types/index.md", "docs/getting-started/drawing-molecules.md", "docs/getting-started/index.md", "docs/getting-started/introduction.md", "docs/getting-started/making-selections.md", "docs/index.md", "docs/menus/build-menu.md", "docs/menus/edit-menu.md", "docs/menus/extensions-menu.md", "docs/menus/file-menu.md", "docs/menus/index.md", "docs/menus/select-menu.md", "docs/menus/view-menu.md", "docs/optimizing-geometry/conformers.md", "docs/optimizing-geometry/constraints.md", "docs/optimizing-geometry/enabling-ff.md", "docs/optimizing-geometry/force-fields.md", "docs/optimizing-geometry/index.md", "docs/tools/align-tool.md", "docs/tools/auto-optimize-tool.md", "docs/tools/auto-rotate-tool.md", "docs/tools/bond-centric-manipulate-tool.md", "docs/tools/draw-tool.md", "docs/tools/index.md", "docs/tools/manipulate-tool.md", "docs/tools/measure-tool.md", "docs/tools/navigate-tool.md", "docs/tools/selection-tool.md", "docs/tutorials/index.md", "docs/tutorials/naming-a-molecule.md", "docs/tutorials/using-qtaim-and-wfn.md", "docs/tutorials/viewing-electrostatic-potential.md", "docs/tutorials/viewing-molecular-orbitals.md", "docs/tutorials/viewing-vibrations.md", "docs/whats-new-in-avogadro-2/index.md", "docs/whats-new-in-avogadro-2/interface-changes.md", "docs/whats-new-in-avogadro-2/major-new-features.md", "index.md", "install/build.md", "install/index.md", "install/versions/index.md", "install/versions/v194.md", "install/versions/v195.md", "install/versions/v1951.md", "install/versions/v196.md", "install/versions/v197.md", "install/versions/v198.md", "teach/acid_base.md", "teach/alkene_isomers.md", "teach/basic_vsepr.md", "teach/diaxial_interactions.md", "teach/hcn_dipole.md", "teach/hydrogen_clusters.md", "teach/hydrogen_molecule.md", "teach/index.md", "teach/markovnikovs_rule.md", "teach/organic_hybridization.md", "teach/water.md"], "titles": ["Contributing Code", "Documenting Code", "Coding Conventions (C++)", "Thanks", "Contribute", "Coding Style (C++)", "Translations", "Class Avogadro::Core::Array", "Class Avogadro::Core::ArraySet", "Class Avogadro::Core::ArraySet::Holder", "Class Avogadro::Core::ArraySet::PlaceHolder", "Class Avogadro::Core::Atom", "Class Avogadro::Core::AtomTemplate", "Class Avogadro::Core::AtomTyper", "Class Avogadro::Core::AvoSpglib", "Class Avogadro::Core::BasisSet", "Class Avogadro::Core::Bond", "Class Avogadro::Core::BondTemplate", "Class Avogadro::Core::Color3f", "Class Avogadro::Core::CoordinateBlockGenerator", "Class Avogadro::Core::CoordinateSet", "Class Avogadro::Core::CrystalTools", "Class Avogadro::Core::Cube", "Class Avogadro::Core::Elements", "Class Avogadro::Core::GaussianSet", "Class Avogadro::Core::GaussianSetTools", "Class Avogadro::Core::Graph", "Class Avogadro::Core::Mesh", "Class Avogadro::Core::Molecule", "Class Avogadro::Core::MoleculeDeserializer", "Class Avogadro::Core::MoleculeSerializer", "Class Avogadro::Core::Mutex", "Class Avogadro::Core::NameAtomTyper", "Class Avogadro::Core::Residue", "Class Avogadro::Core::ResidueData", "Class Avogadro::Core::RingPerceiver", "Class Avogadro::Core::SharedMutex", "Class Avogadro::Core::SlaterSet", "Class Avogadro::Core::SlaterSetTools", "Class Avogadro::Core::SpaceGroups", "Class Avogadro::Core::SymbolAtomTyper", "Class Avogadro::Core::UnitCell", "Class Avogadro::Core::Variant", "Class Avogadro::Core::VariantMap", "Class Avogadro::Core::internal::ArrayRefContainer", "Class Avogadro::Io::CjsonFormat", "Class Avogadro::Io::CmlFormat", "Class Avogadro::Io::DcdFormat", "Class Avogadro::Io::FileFormat", "Class Avogadro::Io::FileFormatManager", "Class Avogadro::Io::GromacsFormat", "Class Avogadro::Io::Hdf5DataFormat", "Class Avogadro::Io::LammpsDataFormat", "Class Avogadro::Io::LammpsTrajectoryFormat", "Class Avogadro::Io::MMTFFormat", "Class Avogadro::Io::MdlFormat", "Class Avogadro::Io::OutcarFormat", "Class Avogadro::Io::PdbFormat", "Class Avogadro::Io::PoscarFormat", "Class Avogadro::Io::TrrFormat", "Class Avogadro::Io::XyzFormat", "Class Avogadro::MoleQueue::BatchJob", "Class Avogadro::MoleQueue::InputGenerator", "Class Avogadro::MoleQueue::InputGeneratorDialog", "Class Avogadro::MoleQueue::InputGeneratorWidget", "Class Avogadro::MoleQueue::MoleQueueDialog", "Class Avogadro::MoleQueue::MoleQueueManager", "Class Avogadro::MoleQueue::MoleQueueQueueListModel", "Class Avogadro::MoleQueue::MoleQueueWidget", "Class Avogadro::QtGui::BackgroundFileFormat", "Class Avogadro::QtGui::ContainerWidget", "Class Avogadro::QtGui::CustomElementDialog", "Class Avogadro::QtGui::ElementDetail", "Class Avogadro::QtGui::ElementItem", "Class Avogadro::QtGui::ElementTranslator", "Class Avogadro::QtGui::ExtensionPlugin", "Class Avogadro::QtGui::ExtensionPluginFactory", "Class Avogadro::QtGui::FileBrowseWidget", "Class Avogadro::QtGui::FileFormatDialog", "Class Avogadro::QtGui::GenericHighlighter", "Class Avogadro::QtGui::GenericHighlighter::Rule", "Class Avogadro::QtGui::HydrogenTools", "Class Avogadro::QtGui::InterfaceScript", "Class Avogadro::QtGui::InterfaceWidget", "Class Avogadro::QtGui::MeshGenerator", "Class Avogadro::QtGui::Molecule", "Class Avogadro::QtGui::MoleculeModel", "Class Avogadro::QtGui::MultiViewWidget", "Class Avogadro::QtGui::PeriodicTableScene", "Class Avogadro::QtGui::PeriodicTableView", "Class Avogadro::QtGui::PersistentAtom", "Class Avogadro::QtGui::PersistentBond", "Class Avogadro::QtGui::PythonScript", "Class Avogadro::QtGui::RWAtom", "Class Avogadro::QtGui::RWBond", "Class Avogadro::QtGui::RWMolecule", "Class Avogadro::QtGui::ScenePlugin", "Class Avogadro::QtGui::ScenePluginFactory", "Class Avogadro::QtGui::ScenePluginModel", "Class Avogadro::QtGui::ScriptLoader", "Class Avogadro::QtGui::ToolPlugin", "Class Avogadro::QtGui::ToolPluginFactory", "Class Avogadro::QtGui::ViewFactory", "Class Avogadro::QtOpenGL::ActiveObjects", "Class Avogadro::QtOpenGL::GLWidget", "Class Avogadro::QtOpenGL::QtTextRenderStrategy", "Class Avogadro::QuantumIO::GAMESSUSOutput", "Class Avogadro::QuantumIO::GUKBasisSet", "Class Avogadro::QuantumIO::GamessukOut", "Class Avogadro::QuantumIO::GaussianCube", "Class Avogadro::QuantumIO::GaussianFchk", "Class Avogadro::QuantumIO::MoldenFile", "Class Avogadro::QuantumIO::MopacAux", "Class Avogadro::QuantumIO::NWChemJson", "Class Avogadro::QuantumIO::NWChemLog", "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry", "Class Avogadro::Rendering::ArrowGeometry", "Class Avogadro::Rendering::BufferObject", "Class Avogadro::Rendering::Camera", "Class Avogadro::Rendering::Cylinder", "Class Avogadro::Rendering::CylinderGeometry", "Class Avogadro::Rendering::Drawable", "Class 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", "Introduction to Molecular Mechanics", "Optimizing Geometry", "Align Tool", "Auto-Optimize Tool", "Auto-Rotate Tool", "Bond-Centric Manipulate Tool", "Draw Tool", "Tools", "Manipulate Tool", "Measure Tool", "Navigate Tool", "Selection Tool", "Tutorials", "Naming a Molecule", "Using QTAIM (Atoms in Molecules) Analysis", "Viewing Electrostatic Potential 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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, 215, 217, 218, 220, 221, 224, 225, 227, 228, 233, 235, 236, 237, 240, 241, 243, 244, 245, 246, 248, 250, 251, 252, 253, 254, 255, 256], "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, 215, 218, 221, 233, 235, 240, 241, 242, 243, 244, 245], "javadoc": 1, "thei": [1, 2, 4, 6, 13, 51, 62, 64, 82, 84, 115, 136, 173, 175, 176, 178, 185, 189, 215, 218, 237], "go": [1, 5, 75, 81, 100, 191, 193, 197, 213, 214, 218, 223, 237], "next": [1, 62, 82, 139, 169, 176, 182, 197, 212, 230, 233, 235], "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, 205, 209, 213, 215, 220, 221, 223, 229, 231, 233, 236, 237, 241, 242, 248, 251], "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, 237, 241, 245, 252], "minimum": [1, 22, 28, 41, 49, 62, 82, 84, 176, 178, 212, 245], "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, 235, 245], "two": [1, 15, 26, 75, 84, 142, 166, 167, 171, 182, 186, 202, 211, 213, 217, 240, 241, 243, 244, 245, 250, 254, 256], "sentenc": 1, "explain": 1, "what": [1, 28, 43, 85, 95, 180, 197, 207, 211, 225], "intend": [1, 23, 51, 172, 178, 253], "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, 215, 217, 218, 220, 221, 223, 224, 225, 226, 228, 230, 231, 233, 235, 236, 237, 241, 242, 243, 244, 245, 248, 251, 252, 253, 254, 256], "goe": [1, 5, 62, 82, 173, 237], "here": [1, 62, 81, 82, 166, 170, 171, 176, 178, 181, 182, 183, 185, 186, 187, 188, 190, 191, 207, 213, 229, 253, 254], "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, 215, 226, 235, 237, 240, 241, 242, 243, 244, 245, 246, 249, 256], "path": [1, 48, 51, 62, 63, 64, 72, 73, 75, 78, 82, 83, 92, 99, 166, 168, 170, 173, 175, 176, 216, 235, 237, 241, 243, 244, 245], "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, 236, 237, 241, 242, 243, 244, 245], "appropri": [1, 5, 11, 16, 51, 62, 74, 82, 168, 170, 173, 176, 202, 237, 243], "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, 229, 237, 244, 245, 246], "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, 215, 219, 225, 234, 235, 245, 253], "altern": [1, 169], "similar": [1, 19, 95, 173, 178, 198, 202], "ideal": [1, 14], "give": [1, 4, 7, 8, 20, 23, 39, 48, 118, 171, 178, 211, 245, 256], "some": [1, 4, 23, 28, 62, 64, 82, 85, 95, 115, 136, 161, 166, 167, 171, 173, 175, 176, 181, 183, 186, 198, 242, 244, 245, 251, 253, 254], "simpl": [1, 23, 31, 32, 36, 39, 40, 50, 62, 82, 176, 188, 198, 205, 237, 248], "exampl": [1, 4, 19, 117, 134, 161, 167, 168, 169, 172, 173, 178, 182, 183, 188, 198, 202, 206, 207, 210, 211, 214, 216, 220, 224, 230, 235, 237, 240, 244, 247, 248], "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, 233, 243], "simplest": 1, "wai": [1, 85, 95, 178, 182, 188, 197, 203, 205, 207, 214, 235, 236], "possibl": [1, 5, 21, 22, 49, 84, 171, 178, 204, 237], "molequeu": [1, 2, 82, 159, 166, 173, 237, 240], "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, 215, 240, 244, 246, 252, 254, 256], "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, 215, 217, 218, 219, 220, 223, 224, 225, 226, 228, 230, 235, 237, 246], "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, 235, 237, 240, 243, 245, 254], "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, 216, 217, 218, 219, 220, 221, 225, 226, 230, 231, 232, 235, 236, 237, 243, 244, 245, 252, 253, 254, 256], "rpc": [1, 65, 68, 161, 240], "server": [1, 4, 61, 65, 66, 68, 92, 166, 228], "json": [1, 45, 62, 65, 75, 82, 83, 100, 113, 161, 166, 167, 168, 169, 170, 171, 172, 173, 175, 176, 240, 245], "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, 234, 235, 236, 237, 240, 243, 244, 246, 247, 252, 253, 254, 255], "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, 233, 235, 239, 242, 246, 251, 252, 256], "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], "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, 241, 243, 244], "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, 230, 232, 235, 245], "To": [1, 11, 16, 51, 63, 65, 74, 168, 171, 178, 181, 202, 209, 214, 219, 220, 237], "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, 201, 205, 206, 208, 209, 211, 216, 222, 229, 230, 231, 235, 237, 241, 243, 245, 246, 249, 250, 251, 252, 256], "connect": [1, 26, 61, 66, 68, 84, 95, 127, 166, 171, 178, 228, 229, 244], "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, 235, 240, 243, 245], "follow": [1, 5, 19, 62, 82, 92, 142, 167, 168, 169, 170, 171, 172, 173, 176, 178, 185, 188, 213, 214, 237], "done": [1, 13, 24, 37, 39, 65, 117, 123, 133, 159, 163, 169, 171, 218, 231], "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, 231, 240, 241, 243, 244, 245, 246], "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, 229, 237, 241, 245, 251], "act": [1, 95, 171, 237], "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, 229, 237, 252, 254, 255, 256], "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, 243, 244, 245, 252], "receiv": [1, 61, 82, 178], "respons": [1, 3, 61, 87, 95, 123, 170, 171, 245], "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, 237, 240, 242, 243, 245, 246], "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, 241], "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, 215, 218, 230, 235, 236, 240, 241, 244, 245, 254], "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, 215, 218, 231, 244, 251], "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, 235, 240, 241, 242, 244, 245], "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, 245], "appear": [1, 62, 78, 82, 95, 173, 175, 181, 188, 207], "work": [1, 3, 4, 6, 24, 103, 168, 178, 182, 190, 193, 204, 207, 210, 213, 235, 236, 237, 244, 245], "directori": [1, 29, 30, 78, 156, 161, 237, 241], "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], "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, 228, 249], "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, 230, 233, 235, 241], "successfulli": [1, 51, 61, 62, 65, 66, 75, 82, 84, 237, 244], "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, 228], "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, 241, 245], "t": [2, 5, 7, 8, 20, 37, 42, 44, 68, 129, 142, 147, 178, 183, 185, 193, 197, 207, 218, 241, 242, 245], "except": [2, 5, 167, 169, 178, 245], "assert": [2, 178], "product": [2, 197, 254], "never": [2, 169, 178], "crash": [2, 62, 82, 168, 173, 233, 235, 241, 243, 244, 245], "prefer": [2, 49, 62, 82, 134, 167, 171, 173, 192, 205, 207, 212, 244], "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, 229, 230, 231, 232, 233, 235, 236, 237, 238, 240, 241, 242, 243, 244, 245, 248, 253], "librari": [2, 4, 51, 103, 142, 175, 181, 237, 241, 245], "over": [2, 182, 186, 192, 193, 196, 218, 228, 233, 235, 240, 241], "boost": [2, 237], "depend": [2, 3, 105, 171, 181, 198, 207, 218, 237, 240, 246, 253], "In": [2, 6, 27, 62, 82, 84, 168, 171, 173, 178, 182, 185, 200, 204, 214, 221, 229, 235, 237, 238, 246], "11": [2, 31, 178, 182], "17": [2, 36, 237], "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, 215, 226, 230, 235, 237, 245, 254], "necessari": [2, 5, 7, 96, 178, 211, 214, 218], "offer": [2, 3, 95, 173, 178, 204, 236], "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, 235], "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, 244], "final": [2, 61, 95, 168, 171, 190, 197, 245], "minim": [2, 62, 82, 140, 173, 190], "third": [2, 182, 237], "parti": [2, 178, 237], "think": 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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, 229, 230, 235, 241, 248], "myclass": 2, "sourc": [2, 3, 5, 84, 133, 159, 161, 165, 183, 204, 236, 238, 240, 244], "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, 230, 244], "myapihead": 2, "our": [2, 3, 6, 115, 116, 120, 121, 124, 126, 127, 128, 129, 136, 137, 138, 167, 178, 183, 190, 236, 254], "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, 230, 232, 233, 235, 236, 240, 241, 243, 245, 246, 248, 249, 250, 251, 253, 254, 255, 256], "differ": [2, 4, 22, 28, 42, 43, 85, 99, 176, 178, 180, 199, 200, 214, 215, 221, 229, 235, 246, 251, 252, 253], "modul": [2, 170, 175, 214, 235, 237], "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, 232], "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, 237, 240, 245, 246, 248], "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, 228, 235, 236, 237, 238, 240, 241, 243, 244, 245, 248, 251, 256], "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, 243, 244, 245, 254], "qtgui": [2, 28, 62, 63, 64, 103, 104, 157, 159, 161], "instead": [2, 39, 75, 167, 168, 169, 244], "being": [2, 5, 15, 24, 27, 48, 84, 90, 91, 104, 120, 124, 157, 158, 198, 218, 220, 225, 237, 253], "wrong": [2, 5, 241], "qdialog": [2, 63, 65, 71], "correct": [2, 5, 49, 62, 82, 123, 126, 173, 190, 237, 245, 251], "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, 201, 204, 207, 209, 211, 228, 231, 232, 235, 236, 237, 240, 242, 243, 244, 245, 246], "chemistri": [2, 3, 4, 5, 204, 229, 231, 232, 236, 237, 240, 253], "nest": [2, 190], "everyth": [2, 206, 210, 217], "insid": [2, 5, 175, 237], "mongochem": [2, 245], "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, 237, 244], "most": [2, 15, 61, 62, 72, 73, 75, 78, 82, 125, 126, 164, 168, 173, 178, 204, 205, 207, 211, 215, 218, 229, 230, 235, 237], "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, 228, 232, 233, 235, 237, 240, 241, 244, 245], "doesn": [2, 193, 197, 218], "slot": 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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, 237, 248, 255], "deriv": [2, 15, 20, 21, 25, 38, 48, 85, 100, 104, 126, 158, 178, 229, 248, 249, 253], "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, 216, 217, 218, 219, 220, 221, 225, 229, 230, 235, 237, 240, 245, 247, 253], "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, 215], "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, 237], "id": [2, 26, 27, 28, 33, 49, 61, 65, 68, 85, 90, 91, 95, 115, 119, 131, 135, 136, 166, 237, 241], "show": [2, 28, 65, 78, 89, 181, 185, 187, 190, 191, 202, 207, 220, 228, 229, 235, 244], "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, 233, 235, 236, 237], "look": [2, 5, 49, 118, 170, 171, 175, 183, 202, 211, 235, 237], "better": [2, 4, 204, 212, 218, 235, 236, 245], "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, 215, 217, 218, 219, 220, 221, 225, 226, 229, 230, 231, 235, 236, 237, 238, 240, 241, 243, 244], "afford": 2, "few": [2, 175, 190, 194, 233, 235, 245], "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, 235, 236, 237, 241, 242, 243, 244, 245, 253], "mani": [3, 24, 37, 161, 167, 204, 207, 220, 223, 233, 234, 235, 240, 241, 242, 243, 244, 245], "fundament": 3, "commun": [3, 4, 66, 166, 178], "aim": [3, 229], "develop": [3, 4, 204, 229, 233, 235, 236, 240, 241, 243, 244], "contributor": [3, 233, 240, 241, 242, 243, 244, 245], "alik": [3, 179], "hope": 3, "build": [3, 21, 29, 30, 95, 98, 156, 168, 170, 180, 181, 196, 209, 215, 228, 233, 235, 236, 238, 240, 241, 243, 244, 245, 246, 247, 248, 254, 255], "top": [3, 75, 105, 118, 120, 123, 138, 141, 198, 223, 237, 243], "framework": [3, 235, 244, 245], "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, 237, 252, 254, 256], "veri": [3, 4, 22, 31, 36, 161, 183, 202, 241, 243, 244], "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, 240], "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, 236, 239, 240], "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, 228, 229, 235, 236, 237, 240, 241, 243, 244, 245], "its": [3, 8, 14, 26, 39, 49, 51, 72, 73, 81, 95, 126, 161, 170, 171, 178, 197, 205, 225, 252, 253, 254, 256], "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, 215, 218, 220, 221, 230, 232, 235, 237, 240, 245, 254], "come": [3, 193, 198, 214, 215, 220, 236], "would": [3, 75, 126, 134, 190, 202, 204, 233, 235, 236, 237, 253], "particularli": [3, 215, 233, 234, 241, 243, 244], "googl": [3, 241, 243, 244], "summer": [3, 204, 240, 241, 243, 244], "2007": 3, "2008": 3, "2011": 3, "2016": 3, "2018": 3, "2019": [3, 243], "2021": [3, 240, 241, 242], "2022": [3, 204, 243, 244], "kitwar": [3, 237], "inc": 3, "univers": [3, 204, 215, 218], "pittsburgh": [3, 204], "u": [3, 4, 7, 8, 20, 104, 126, 185, 190, 236, 240, 241, 243, 244], "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, 229, 235, 237, 240, 245], "pettt": 3, "program": [3, 65, 66, 67, 68, 134, 159, 163, 166, 167, 168, 173, 182, 188, 208, 214, 233, 243], "research": [3, 190, 236, 253], "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, 237, 251], "infrastructur": 3, "blue": [3, 18, 23, 140, 142, 159, 160, 165, 197, 198, 217, 220, 230, 235], "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, 205, 210, 229, 234, 235, 243, 245, 249, 251], "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, 228, 235], "structur": [3, 21, 22, 23, 24, 26, 28, 37, 75, 170, 171, 183, 189, 190, 194, 196, 198, 200, 206, 211, 215, 218, 221, 235, 240, 241, 243, 251], "databas": [3, 4, 23, 174, 189, 196, 208, 228], "cmake": [3, 237, 245], "eigen": [3, 5, 28, 37, 107, 118, 134, 237], "softwar": [3, 207, 229], "babel": [3, 162, 169, 202, 235, 240, 243, 244], "And": [3, 167], "cours": [3, 189], "johann": 3, "loschmidt": 3, "amedeo": 3, "made": [4, 6, 7, 23, 26, 81, 100, 178, 179, 196, 197, 198, 202, 203, 208, 210, 211, 215, 226, 240], "who": 4, "want": [4, 7, 168, 185, 189, 190, 197, 200, 202, 212, 213, 221, 223, 229, 230, 236], "back": [4, 7, 83, 159, 160, 205, 211, 240, 241, 243], "great": [4, 236, 237], "place": [4, 5, 39, 49, 72, 73, 171, 173, 178, 183, 198, 206, 207, 211, 218, 223, 225, 236, 237, 249], "start": [4, 5, 24, 26, 92, 116, 120, 180, 181, 182, 189, 190, 205, 216, 218, 219, 222, 227, 232, 236, 241, 245], "fellow": 4, "forum": [4, 6], "question": [4, 236], "level": [4, 62, 75, 82, 173, 237], "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, 228, 229, 231, 233, 237, 248, 253, 256], "find": [4, 14, 22, 29, 30, 41, 51, 78, 84, 95, 99, 156, 170, 171, 180, 202, 214, 216, 231, 235, 236, 244, 250, 253], "experi": 4, "valuabl": 4, "bug": [4, 6, 193, 236, 239], "pleas": [4, 6, 236, 240, 241, 243, 244, 253], "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, 231], "moment": [4, 190, 231], "tracker": [4, 236], "issu": [4, 6, 236, 240, 245], "code": [4, 6, 24, 37, 62, 82, 84, 88, 161, 167, 169, 170, 171, 173, 183, 190, 191, 193, 207, 231, 232, 235, 236, 238, 240, 241, 243, 244, 245], "while": [4, 5, 26, 62, 82, 84, 95, 100, 168, 169, 173, 182, 187, 213, 218, 228, 244], "move": [4, 28, 104, 138, 142, 178, 185, 193, 196, 202, 218, 223, 235, 245, 246], "around": [4, 5, 15, 22, 31, 36, 63, 65, 69, 185, 187, 190, 196, 198, 202, 213, 223, 235, 248, 253], "fit": [4, 5, 28, 51, 104, 123, 157, 178], "particular": [4, 23, 51, 62, 75, 82, 166, 167, 169, 173, 178, 189, 204], "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, 235, 253], "discuss": [4, 6, 168, 207, 236, 240, 241, 243, 244, 253], "idea": [4, 236], "plan": 4, "direct": [4, 18, 41, 62, 82, 115, 118, 119, 120, 121, 124, 128, 136, 142, 159, 165, 173, 178, 193, 219, 237, 243, 246], "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, 228, 229, 232, 235, 236, 237, 240, 245, 248], "both": [4, 15, 26, 51, 63, 64, 161, 167, 169, 172, 173, 175, 176, 187, 214, 236, 256], "python": [4, 92, 99, 161, 168, 171, 174, 175, 216, 236, 237, 239, 241, 243, 244, 245], "script": [4, 63, 64, 75, 83, 92, 99, 100, 162, 172, 214, 236, 240, 241, 242, 244, 245], "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, 236, 246], "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, 243, 244, 245], "edit": [4, 14, 64, 95, 161, 180, 188, 197, 198, 200, 202, 207, 209, 210, 211, 221, 223, 232, 233, 235, 237, 243, 244, 245], "tutori": [4, 180, 181, 198, 207, 235, 236], "site": [4, 235, 236], "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, 228, 230, 233, 235, 244, 245], "lesson": [4, 185, 253], "activ": [4, 24, 70, 75, 86, 87, 88, 89, 96, 100, 103, 104, 214, 235, 237], "teacher": 4, "send": [4, 61, 66, 92, 161, 166, 173, 240], "fragment": [4, 133, 134, 159, 165, 180, 192, 195, 203, 205, 223, 226, 235, 240, 245], "report": [4, 6, 62, 82, 173, 183, 236, 241, 242, 243, 244], "encount": [4, 6, 48, 51, 104], "about": [4, 19, 23, 39, 62, 82, 118, 173, 197, 207, 211, 213, 225, 236, 243, 244], "improv": [4, 6, 233, 235, 239, 242], "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, 236, 244], "donat": 4, "pai": [4, 204, 256], "host": [4, 243, 244, 245], "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, 231, 237, 241, 244, 245, 246, 248], "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, 235, 244, 245, 248, 253], "larg": [5, 7, 51, 181, 185, 186, 189, 190, 202, 235, 237], "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, 229, 231, 235, 240, 241, 242, 243, 244, 245], "enforc": [5, 178], "clang": [5, 244], "tool": [5, 25, 38, 75, 100, 101, 104, 159, 164, 180, 182, 185, 189, 190, 196, 198, 200, 202, 203, 204, 213, 233, 236, 240, 242, 243, 245, 248, 252, 255, 256], "space": [5, 19, 21, 22, 25, 27, 28, 38, 39, 51, 95, 146, 159, 160, 169, 173, 181, 183, 185, 186, 187, 188, 211, 243, 245, 251], "tab": [5, 211, 241, 244], "keep": [5, 26, 51, 65, 67, 95, 103, 105, 213, 237], "less": [5, 12, 17, 23, 28, 95, 207, 230, 235, 254], "than": [5, 7, 12, 17, 23, 26, 28, 51, 62, 82, 95, 166, 178, 186, 235, 241, 251, 254], "80": 5, "charact": [5, 19, 48, 62, 82, 168, 173], "wide": [5, 204, 207, 235], "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, 237, 255, 256], "separ": [5, 142, 168, 173, 178, 229, 234], "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, 228, 232, 235, 237, 240, 245], "nmbr": 5, "singl": [5, 17, 28, 51, 62, 64, 66, 70, 82, 84, 95, 116, 142, 173, 190, 191, 197, 203, 226, 244], "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, 251], "unus": [5, 15, 24, 37], "ones": 5, "incorrect": [5, 241, 244, 245], "f": [5, 24, 37, 70, 87, 107, 121, 134, 136, 138, 157, 159, 160, 169, 178, 215, 241], "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, 243], "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, 244, 254], "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, 235, 241, 245], "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, 230, 232, 240], "curli": 5, "blah": [5, 62, 82, 176], "explod": 5, "5": [5, 14, 39, 41, 62, 82, 95, 159, 160, 176, 185, 222, 237, 244, 245, 246, 248, 255, 256], "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, 242], "between": [5, 14, 22, 23, 26, 28, 41, 42, 43, 84, 85, 95, 166, 171, 172, 181, 182, 198, 207, 213, 218, 224, 245, 251, 253, 256], "x": [5, 19, 21, 22, 27, 28, 123, 169, 172, 173, 182, 198, 205, 207, 211, 217, 219, 235, 237, 245, 254], "mystr": 5, "y": [5, 19, 22, 28, 118, 123, 169, 173, 198, 205, 207, 211, 217, 219, 237], "whoah": 5, "surround": [5, 230], "binari": [5, 237, 244], "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, 244], "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, 229, 235, 240, 251, 252, 254], "size": [5, 7, 18, 20, 26, 27, 43, 51, 84, 115, 117, 120, 134, 136, 142, 159, 160, 165, 181, 182, 198, 211, 240, 245, 251], "left": [5, 51, 62, 82, 105, 118, 137, 141, 142, 173, 200, 202, 203, 205, 211, 217, 218, 220, 221, 226, 237], "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, 215, 237, 246, 256], "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, 232, 235, 242, 244, 250], "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, 243, 244], "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, 202], "endl": 5, "bar": [5, 207, 211, 223, 225, 231], "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, 215, 218, 219, 221, 224, 225, 226, 229, 235, 236, 237, 244, 253], "complex": [5, 126, 235, 245], "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, 215, 223, 251], "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, 233, 237, 245], "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, 199, 200, 205, 209, 215, 221, 235, 241, 244, 248], "cover": [5, 168, 204, 228], "b": [5, 19, 21, 26, 28, 41, 47, 53, 59, 85, 91, 95, 105, 140, 159, 160, 169, 173, 178, 191, 243, 245, 251], "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, 240], "express": [5, 62, 82, 173, 178, 254], "intent": 5, "clearer": 5, "label": [5, 12, 19, 28, 62, 82, 95, 107, 138, 159, 160, 164, 168, 170, 173, 176, 178, 199, 213, 235, 240, 241, 243, 245], "column": [5, 21, 41, 67, 86, 98], "everi": [5, 26, 28, 178, 228], "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, 237], "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, 242], "omiss": 5, "anoth": [5, 39, 51, 169, 183, 188, 198, 200, 203, 221, 235, 256], "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, 240, 241, 243], "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, 231, 235, 245], "drawdefault": 5, "shorter": 5, "insert": [5, 7, 28, 62, 82, 159, 160, 168, 176, 180, 181, 185, 189, 190, 191, 192, 195, 209, 223, 235, 240, 241, 243, 245, 246], "comma": [5, 167, 169], "broken": 5, "begin": [5, 7, 43, 84, 95, 105, 130, 141, 144, 159, 160, 165, 200, 203, 220, 221, 230, 232], "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, 235, 249, 254, 256], "currentposit": 5, "offset": [5, 84, 134, 159, 164], "reimplement": [5, 64, 104], "put": [5, 235, 245], "discourag": 5, "prefix": [5, 12, 17, 62, 78, 82, 172, 175, 176, 237], "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, 240], "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, 229, 230, 235, 236, 240, 243, 244, 245], "As": [5, 6, 166, 168, 189, 198, 209, 217, 224, 228, 237, 240, 243], "feel": [5, 236], "free": [5, 51, 104, 168, 173, 178, 204, 236, 237], "bad": 5, "local": [6, 62, 74, 82, 84, 168, 173, 175, 176, 236, 240, 243, 245], "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, 235, 236, 244], "weblat": [6, 240, 241, 242, 243, 244, 245], "autom": [6, 49, 175, 235, 243, 244], "task": [6, 215, 235], "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, 229, 231, 232, 235, 240, 244, 245], "time": [6, 51, 62, 82, 92, 95, 104, 117, 126, 161, 178, 181, 186, 190, 245], "freez": [6, 28], "least": [6, 75, 95, 212, 224, 230, 235, 244], "week": 6, "advanc": [6, 62, 82, 173, 236, 237], "releas": [6, 51, 117, 134, 142, 159, 165, 175, 204, 233, 237, 238, 239], "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, 240, 243, 245], "semant": 7, "effect": [7, 118, 178, 214, 246, 251], "share": [7, 12, 17, 26, 36, 175, 178, 179, 235, 237], "without": [7, 26, 49, 51, 65, 68, 161, 178, 202, 204, 207, 208, 233, 237, 241], "expos": 7, "access": [7, 18, 51, 64, 66, 67, 83, 103, 117, 134, 142, 169, 178, 193, 198, 208, 244], "amount": [7, 185, 207], "non": [7, 8, 23, 28, 62, 82, 95, 126, 169, 171, 173, 178, 240, 241, 244, 245], "trigger": [7, 104, 171], "detach": [7, 134, 159, 160, 209, 243], "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, 233, 235, 237, 238, 239, 240, 245, 246, 247, 252, 253, 254, 255, 256], "perform": [7, 13, 15, 21, 42, 51, 63, 84, 95, 104, 134, 168, 170, 171, 178, 182, 188, 202, 207, 212, 235, 237, 239, 246, 256], "deep": [7, 230, 237], "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, 236], "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, 215], "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, 246], "inputiter": [7, 44], "last": [7, 22, 44, 62, 68, 82, 92, 206, 241], "note": [7, 24, 28, 62, 82, 118, 128, 134, 142, 166, 169, 173, 175, 176, 183, 185, 186, 187, 190, 198, 202, 204, 237, 239, 246, 249, 250, 256], "detachwithcopi": [7, 159, 160], "explicitli": [7, 166], "implicitli": 7, "ensur": [7, 21, 28, 62, 66, 82, 85, 95, 123, 132, 173, 207, 237, 240, 245], "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, 235, 243, 244], "val": 7, "push_back": [7, 159, 160], "v": [7, 39, 41, 42, 43, 127, 128, 134, 176, 178, 193, 237, 245, 247, 254], "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, 245], "delet": [7, 49, 51, 69, 95, 104, 124, 126, 133, 157, 168, 182, 200, 205, 211, 221, 241, 243, 245, 249], "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, 237, 245], "pop": [7, 170, 188, 194, 196, 197, 207, 208, 210, 211, 230], "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, 245], "figur": [8, 73, 213, 251], "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, 231, 237], "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, 233, 235], "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, 230, 246, 253], "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, 223, 224, 225, 226, 227, 228, 230, 232, 233, 235, 240, 241, 243, 244, 245, 248, 254, 256], "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, 240], "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, 235, 236, 248], "moleculetyp": [12, 17, 90, 91, 159, 160, 164], "compil": [12, 133, 134, 159, 165, 237], "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, 235, 244], "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, 248, 253], "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, 240, 241, 245], "setformalcharg": [12, 28, 95, 159, 160, 164], "sign": [12, 28, 95, 134, 237, 243], "charg": [12, 28, 62, 82, 95, 173, 174, 175, 207, 215, 230, 235, 241, 243, 244, 245, 246, 256], "formal": [12, 28, 95, 243, 245], "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, 199, 207, 209, 230, 235, 240, 241, 243, 244, 245], "setlay": [12, 28, 95, 159, 160, 164], "layer": [12, 28, 85, 95, 159, 160, 164, 241, 242, 243, 244, 245], "invalid": [12, 17, 28, 39, 48, 68, 85, 90, 91, 95, 131, 159, 165, 241], "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, 240], "increment": [12, 17], "self": [12, 17, 244], "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, 240, 244, 245, 250, 251, 256], "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, 199, 200, 201, 202, 205, 208, 209, 211, 213, 214, 215, 217, 219, 220, 221, 222, 223, 224, 228, 230, 231, 232, 240, 241, 242, 243, 244, 245, 246], "setforcevector": [12, 28, 95, 159, 160, 164], "forc": [12, 28, 85, 95, 139, 161, 174, 175, 190, 199, 209, 213, 215, 216, 232, 237, 245, 250, 252, 253, 254, 256], "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, 244, 245], "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, 237, 240, 244, 253], "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, 249, 254], "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, 241], "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, 244], "been": [13, 28, 49, 51, 66, 68, 75, 95, 96, 132, 134, 171, 178, 185, 188, 197, 198, 200, 207, 208, 211, 215, 218, 221, 224, 230, 231, 232, 235, 237], "previous": [13, 207, 208, 211, 224], "cach": [13, 51, 62, 66, 82, 92, 175, 244, 245], "There": [13, 62, 81, 82, 173, 191, 192, 193, 203, 211, 226, 236, 237], "correspond": [13, 15, 24, 28, 61, 62, 82, 95, 173, 175, 176, 178, 182, 214, 218, 246], "reset": [13, 48, 51, 62, 82, 90, 91, 92, 96, 104, 118, 123, 157, 159, 160, 163, 164, 185, 209, 219, 223, 224, 225, 240, 241], "typer": 13, "state": [13, 48, 51, 61, 62, 65, 68, 82, 90, 91, 95, 96, 125, 158, 176, 178, 241], "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, 228, 229, 240, 242, 243, 244, 245], "setup": [13, 61, 169, 209, 214, 243], "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, 229, 230, 245], "m_molecul": [13, 15, 95, 159, 160, 164], "popul": [13, 15, 21, 25, 51, 95], "spglib": [14, 39, 95, 183, 240], "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, 235, 241, 245], "unit": [14, 19, 21, 23, 28, 39, 41, 62, 82, 95, 173, 176, 180, 181, 184, 187, 188, 190, 193, 209, 211, 241, 245, 251], "cell": [14, 19, 21, 28, 39, 41, 95, 173, 180, 181, 184, 185, 188, 190, 193, 209, 211, 241, 245, 251], "exist": [14, 22, 26, 28, 43, 51, 65, 67, 85, 95, 102, 126, 134, 168, 172, 173, 218, 233, 241], "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, 235, 240, 245], "cartesian": [14, 19, 21, 24, 37, 39, 41, 95, 169, 173, 182, 183, 186, 187, 198, 209], "toler": [14, 28, 39, 95, 183, 186, 244], "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, 233, 241, 244], "conventionalizecel": [14, 95, 159, 160, 164], "refin": [14, 215], "convention": [14, 95], "symmetr": [14, 95, 159, 160, 187, 235], "basi": [15, 24, 25, 28, 37, 38, 62, 82, 107, 108, 173, 178, 207, 245], "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, 215], "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, 215, 224, 229, 230, 232, 235, 244, 246, 256], "electrontyp": [15, 24, 25, 37, 159, 160], "electron": [15, 23, 24, 25, 28, 38, 207, 229, 230, 244], "pair": [15, 24, 25, 26, 27, 28, 34, 37, 62, 82, 85, 95, 116, 159, 160, 173, 175, 176, 207, 229, 235, 244], "alpha": [15, 24, 25, 41, 140, 142, 159, 160, 165, 169, 240, 244], "beta": [15, 24, 25, 41, 159, 160, 169, 233], "cannot": [15, 21, 29, 30, 49, 51, 68, 156, 178, 235], "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, 236, 237, 240, 253], "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, 216, 218, 227, 229, 233, 235, 236, 244, 245, 248, 253], "orbit": [15, 24, 25, 37, 38, 107, 159, 160, 161, 180, 198, 209, 227, 235, 241, 252, 255], "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, 245], "lumo": [15, 159, 160], "m_electron": [15, 159, 160], "total": [15, 28, 61, 245], "close": [15, 48, 51, 64, 70, 159, 162, 178, 209, 213, 230, 231, 241, 243, 244, 251], "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, 215, 218, 221, 222, 223, 224, 226, 229, 242, 243, 244, 245, 250, 251, 252, 253, 254, 255, 256], "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, 229, 240, 241, 242, 243, 245], "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, 215, 229, 231, 232, 244, 245], "necessarili": 15, "m_name": [15, 22, 159, 160], "usual": [15, 171, 237], "standard": [15, 62, 70, 82, 90, 91, 92, 95, 117, 134, 158, 166, 167, 168, 169, 171, 172, 173, 178, 198, 208, 241, 245], "m_theorynam": [15, 159, 160], "theori": [15, 62, 82, 173, 178, 199, 209, 245, 248], "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, 215, 221, 237, 256], "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], "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, 244], "rang": [18, 21, 62, 82, 124, 126, 128, 134, 140, 142, 167, 169, 173, 176, 207, 235, 244], "intens": [18, 28, 244], "red": [18, 140, 142, 159, 160, 165, 198, 217, 230, 235], "green": [18, 140, 142, 159, 160, 165, 198, 217], "memori": [18, 24, 51, 95, 134, 243], "3": [18, 27, 62, 82, 84, 127, 128, 134, 140, 142, 159, 160, 167, 169, 176, 182, 186, 190, 200, 209, 212, 213, 222, 237, 240, 246, 247, 253, 254, 255], "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, 241, 244], "directli": [18, 49, 67, 167, 178, 189, 191, 195, 229], "opengl": [18, 123, 132, 161, 237, 243, 244, 245], "conveni": [18, 28, 43, 48, 49, 51, 66, 67, 85, 161, 205, 210, 245], "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, 230], "emphasi": 18, "effici": [18, 210, 241], "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, 237, 245], "align": [19, 21, 132, 140, 173, 180, 181, 182, 185, 190, 191, 209, 222, 245], "see": [19, 28, 51, 62, 64, 78, 82, 85, 95, 105, 134, 142, 161, 168, 172, 173, 183, 186, 187, 190, 191, 207, 229], "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, 244, 245, 251], "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, 215, 218, 223, 236, 243], "z": [19, 22, 28, 169, 173, 181, 185, 190, 191, 198, 205, 207, 211, 217, 219, 240], "6": [19, 21, 27, 62, 74, 82, 84, 123, 158, 159, 160, 167, 169, 171, 173, 190, 213, 222, 237, 245, 248, 254], "carbon": [19, 23, 28, 74, 170, 171, 173, 175, 180, 185, 201, 205, 220, 221, 225, 253, 254, 255], "l": [19, 119, 178, 237], "c1": [19, 245], "gamess": [19, 107, 173, 207, 244, 245], "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, 231, 233, 254], "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, 230, 231, 235, 237], "liter": [19, 62, 82, 173], "optim": [19, 28, 62, 82, 169, 173, 176, 180, 182, 190, 200, 209, 215, 221, 235, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 254, 255, 256], "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, 237, 241], "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, 245], "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, 241], "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, 215, 235], "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, 216, 217, 218, 230, 235, 241], "bitwis": [21, 49, 65, 140], "variou": [21, 24, 37, 62, 82, 168, 173, 197, 198, 207, 208, 210, 230, 232, 235, 236, 237, 243], "none": [21, 22, 24, 28, 39, 48, 49, 61, 78, 102, 126, 133, 134, 159, 160, 162, 163, 165, 209, 243], "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, 231, 232, 240, 245, 248], "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, 235, 240, 245, 251], "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, 215, 220], "trig": 21, "sinc": [21, 51, 167, 169, 171, 175, 176, 183, 186, 189, 193, 228, 235, 251], "fragil": 21, "neg": [21, 81, 235], "angl": [21, 41, 118, 200, 207, 211, 213, 221, 222, 224, 243, 244, 245, 255, 256], "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, 228, 231, 236, 237, 240, 241, 242, 243, 244], "http": [21, 51, 84, 172, 175, 178, 190, 193, 194, 207, 237, 240, 241, 243, 244], "xtalopt": [21, 166], "openmolecul": 21, "net": [21, 198, 246], "misc": 21, "rotatetostdorient": 21, "pdf": 21, "setvolum": [21, 159, 160], "real": [21, 41, 42, 169, 245], "newvolum": [21, 95], "isotrop": 21, "scale": [21, 95, 118, 159, 165, 180, 184, 219, 225, 244], "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, 242], "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, 240], "stabl": [21, 27, 159, 160], "comput": [21, 118, 167, 202, 204, 207, 211, 218, 235, 236], "acta": 21, "crystallographica": 21, "foundat": 21, "crystallographi": [21, 181, 188, 193], "2003": 21, "60": 21, "modifi": [21, 27, 28, 49, 64, 81, 85, 95, 104, 118, 157, 159, 164, 168, 170, 171, 178, 188, 202, 209, 228, 235, 236], "extend": [21, 161, 174, 236, 240, 248], "isnigglireduc": [21, 159, 160], "alreadi": [21, 39, 66, 85, 95, 107, 172, 188, 200, 214, 221, 245], "gruber": 21, "cryst": 21, "1973": 21, "29": 21, "4": [21, 84, 105, 128, 140, 141, 159, 160, 166, 169, 179, 181, 186, 190, 212, 218, 222, 235, 247, 248, 254], "433": 21, "440": [21, 240], "buildsupercel": [21, 95, 159, 160, 164], "supercel": [21, 95, 180, 181, 184, 186], "expand": [21, 65, 68, 187, 188, 211], "upon": [21, 95, 126, 178], "zero": [21, 23, 28, 62, 79, 82, 95, 118, 169, 173, 176, 219, 245], "setcellmatrix": [21, 41, 159, 160], "matrix3": [21, 41, 95], "newcellcolmatrix": 21, "ignor": [21, 28, 62, 82, 95, 96, 104, 142, 159, 164, 173, 175, 209, 213, 237, 244], "fractionalcoordin": [21, 159, 160], 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"dummi": [23, 240], "atomicnumberfromsymbol": [23, 159, 160], "xx": [23, 168], "guessatomicnumb": [23, 159, 160], "str": [23, 139], "attempt": [23, 31, 36, 51, 66, 125, 129, 134, 237], "slower": [23, 218], "reliabl": [23, 248], "atomicnumberfrom": 23, "best": [23, 28, 169, 207, 215, 236, 237], "radiusvdw": [23, 159, 160], "van": [23, 181, 199, 207, 235], "der": [23, 181, 199, 207, 235], "waal": [23, 181, 199, 207, 235], "radiu": [23, 28, 115, 119, 120, 125, 132, 135, 136, 138, 139, 159, 160, 165, 235, 240], "radiuscoval": [23, 159, 160], "coval": [23, 81, 244], "valenceelectron": [23, 159, 160], "valenc": [23, 81, 200, 205, 221, 245], "basisset": [24, 25, 28, 37, 107, 159, 160], "gaussian": [24, 182, 209, 232, 240, 243, 245], "qm": [24, 62, 82, 173, 235], "transpar": [24, 37, 240, 241, 244, 245], "quantum": [24, 37, 168, 199, 209, 229, 231, 232, 235, 251], "mechan": [24, 37, 90, 91, 180, 209, 213, 216, 218, 229, 251, 254], "certain": [24, 28, 37, 95, 178, 207], "hierarchi": [24, 37], 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[256, "task"], [254, "task"], [252, "task"], [248, "task"], [247, "task"]], "Solution": [[251, "solution"], [255, "solution"], [256, "solution"], [254, "solution"], [252, "solution"], [246, "solution"], [249, "solution"]], "Issues": [[251, "issues"]], "See also": [[251, "see-also"], [250, "see-also"], [255, "see-also"], [256, "see-also"], [254, "see-also"], [252, "see-also"], [248, "see-also"], [247, "see-also"]], "Sources": [[251, "sources"], [256, "sources"], [252, "sources"]], "HCN dipole": [[250, "hcn-dipole"]], "Teach": [[253, "teach"]], "Organic Hybridization": [[255, "organic-hybridization"]], "Further reading": [[255, "further-reading"], [254, "further-reading"], [246, "further-reading"], [248, "further-reading"]], "Water": [[256, "water"]], "Markovnikov\u2019s Rule": [[254, "markovnikovs-rule"]], "Hydrogen Molecule": [[252, "hydrogen-molecule"]], "Class Avogadro::QtGui::GenericHighlighter::Rule": [[80, "class-avogadro-qtgui-generichighlighter-rule"]], "Class Avogadro::QtGui::MultiViewWidget": [[87, "class-avogadro-qtgui-multiviewwidget"]], "Class Avogadro::QtGui::PersistentBond": [[91, "class-avogadro-qtgui-persistentbond"]], "Class Avogadro::QtGui::RWMolecule": [[95, "class-avogadro-qtgui-rwmolecule"]], "Class Avogadro::QtGui::ScenePluginModel": [[98, "class-avogadro-qtgui-scenepluginmodel"]], "Class Avogadro::QtGui::PeriodicTableScene": [[88, "class-avogadro-qtgui-periodictablescene"]], "Class Avogadro::QtGui::RWAtom": [[93, "class-avogadro-qtgui-rwatom"]], "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::MeshGenerator": [[84, "class-avogadro-qtgui-meshgenerator"]], "Class Avogadro::QtGui::RWBond": [[94, "class-avogadro-qtgui-rwbond"]], "Class Avogadro::QtGui::ExtensionPluginFactory": [[76, "class-avogadro-qtgui-extensionpluginfactory"]], "Class Avogadro::QtGui::ExtensionPlugin": [[75, "class-avogadro-qtgui-extensionplugin"]], "Class Avogadro::QtGui::ScriptLoader": [[99, "class-avogadro-qtgui-scriptloader"]], "Class Avogadro::QtGui::PersistentAtom": [[90, "class-avogadro-qtgui-persistentatom"]], "Class Avogadro::QtGui::MoleculeModel": [[86, "class-avogadro-qtgui-moleculemodel"]], "Class Avogadro::QtGui::InterfaceScript": [[82, "class-avogadro-qtgui-interfacescript"]], "Class Avogadro::QtGui::GenericHighlighter": [[79, "class-avogadro-qtgui-generichighlighter"]], "Class Avogadro::QtGui::FileFormatDialog": [[78, "class-avogadro-qtgui-fileformatdialog"]], "Class Avogadro::QtGui::Molecule": [[85, "class-avogadro-qtgui-molecule"]], "Class Avogadro::QtGui::HydrogenTools": [[81, "class-avogadro-qtgui-hydrogentools"]], "Class Avogadro::QtGui::PeriodicTableView": [[89, "class-avogadro-qtgui-periodictableview"]], "Class Avogadro::QtGui::ScenePlugin": [[96, "class-avogadro-qtgui-sceneplugin"]], "Class Avogadro::QtGui::FileBrowseWidget": [[77, "class-avogadro-qtgui-filebrowsewidget"]], "Getting Started": [[201, "getting-started"], [201, null]], "Auto-Optimize Tool": [[218, "auto-optimize-tool"]], "Force Fields & Algorithms": [[218, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[218, "fixing-ignoring-selections"]], "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"]], "Drawing Molecules": [[200, "drawing-molecules"]], "Creating Carbon Dioxide": [[200, "creating-carbon-dioxide"]], "Draw Tool": [[221, "draw-tool"]], "1. Creating a Molecule": [[221, "creating-a-molecule"]], "2.": [[221, "id1"]], "3.": [[221, "id2"]], "4.": [[221, "id3"]], "5.": [[221, "id4"]], "6.": [[221, "id5"]], "7.": [[221, "id6"]], "8.": [[221, "id7"]], "9.": [[221, "id8"]], "Align Tool": [[217, "align-tool"]], "Auto-Rotate Tool": [[219, "auto-rotate-tool"]], "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"]], "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"]], "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"]], "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"]], "Menus": [[209, "menus"], [209, null]], "Optimizing Geometry": [[216, "optimizing-geometry"]], "Optimization": [[216, 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"]], "Geometry Constraints": [[213, "geometry-constraints"]], "Example": [[213, "example"]], "Optimizations": [[213, "optimizations"]], "Example cont.": [[213, "example-cont"]], "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"]], "Manipulate Tool": [[223, "manipulate-tool"]], "Select Menu": [[210, "select-menu"]], "Select All": [[210, "select-all"], [206, "select-all"]], "Select None": [[210, "select-none"], [206, "select-none"]], "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"]], "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"]], "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"]], "Introduction": [[202, "introduction"]], "Opening a File": [[202, "opening-a-file"]], "Navigation": [[202, "navigation"]], "Tools": [[222, "tools"], [222, null]], "Introduction to Molecular Mechanics": [[215, "introduction-to-molecular-mechanics"]], "UFF": [[215, "uff"]], "MMFF94(s)": [[215, "mmff94-s"]], "GAFF": [[215, "gaff"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[44, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Core::SymbolAtomTyper": [[40, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::MoleculeSerializer": [[30, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Core::NameAtomTyper": [[32, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Io::CmlFormat": [[46, "class-avogadro-io-cmlformat"]], "Class Avogadro::Core::ResidueData": [[34, "class-avogadro-core-residuedata"]], "Class Avogadro::Io::FileFormat": [[48, "class-avogadro-io-fileformat"]], "Class Avogadro::Core::RingPerceiver": [[35, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::Residue": [[33, "class-avogadro-core-residue"]], "Class Avogadro::Io::FileFormatManager": [[49, "class-avogadro-io-fileformatmanager"]], "Class Avogadro::Core::SlaterSetTools": [[38, "class-avogadro-core-slatersettools"]], "Class Avogadro::Core::SpaceGroups": [[39, "class-avogadro-core-spacegroups"]], "Class Avogadro::Io::CjsonFormat": [[45, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Core::Graph": [[26, "class-avogadro-core-graph"]], "Class Avogadro::Core::Variant": [[42, "class-avogadro-core-variant"]], "Class Avogadro::Core::UnitCell": [[41, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::MoleculeDeserializer": [[29, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::Mutex": [[31, "class-avogadro-core-mutex"]], "Class Avogadro::Io::DcdFormat": [[47, "class-avogadro-io-dcdformat"]], "Class Avogadro::Core::SharedMutex": [[36, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::VariantMap": [[43, "class-avogadro-core-variantmap"]], "Class Avogadro::Core::SlaterSet": [[37, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::Mesh": [[27, "class-avogadro-core-mesh"]], "Class Avogadro::Core::GaussianSetTools": [[25, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::Molecule": [[28, "class-avogadro-core-molecule"]], "Install": [[236, "install"], [238, "install"]], "Features": [[236, "features"], [240, "features"]], "Resources": [[236, "resources"]], "Connecting with the Avogadro community": [[236, "connecting-with-the-avogadro-community"]], "Viewing Molecular Orbitals": [[231, "viewing-molecular-orbitals"]], "Configure": [[231, "configure"]], "What\u2019s New in Avogadro 2": [[233, "whats-new-in-avogadro-2"]], "Interface Changes": [[234, "interface-changes"]], "Tutorials": [[227, "tutorials"], [227, null]], "Acid-Base Properties of Amino Acids": [[246, "acid-base-properties-of-amino-acids"]], "Tasks": [[246, "tasks"], [249, "tasks"]], "1,3-diaxial interactions": [[249, "diaxial-interactions"]], "Navigate Tool": [[225, "navigate-tool"]], "Naming a Molecule": [[228, "naming-a-molecule"]], "Release Notes v1.95.0": [[241, "release-notes-v1-95-0"]], "Changes": [[241, "changes"], [243, "changes"]], "\u2728 Features": [[241, "features"], [242, "features"], [244, "features"], [245, "features"], [243, "features"]], "\ud83d\udc1b Bug Fixes": [[241, "bug-fixes"], [240, "bug-fixes"], [242, "bug-fixes"], [244, "bug-fixes"], [245, "bug-fixes"], [243, "bug-fixes"]], "\ud83e\uddf0 Maintenance": [[241, "maintenance"], [240, "maintenance"], [242, "maintenance"], [244, "maintenance"], [245, "maintenance"], [243, "maintenance"]], "\ud83d\udcda Translations": [[241, "translations"], [242, "translations"], [244, "translations"], [245, "translations"], [243, "translations"]], "Major New Features": [[235, "major-new-features"]], "Speed and Stability": [[235, "speed-and-stability"]], "Rendering": [[235, "rendering"]], "New real-time shadows and depth effects": [[235, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[235, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[235, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[235, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[235, "layers"]], "Symmetry Properties": [[235, "symmetry-properties"]], "Template Tool": [[235, "template-tool"]], "Solvent Accessible and Solvent Excluded Surfaces": [[235, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[235, "flexible-electrostatics-models"]], "New Analysis Tools": [[235, "new-analysis-tools"]], "Python Commands / Plugins": [[235, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[235, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[235, "new-and-updated-interfaces-to-external-programs"]], "Version History": [[239, "version-history"], [239, null]], "Release Notes v1.94.0": [[240, "release-notes-v1-94-0"]], "\ud83d\udc0d Python Improvements": [[240, "python-improvements"]], "Using QTAIM (Atoms in Molecules) Analysis": [[229, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[229, "start-with-a-wfn-file"]], "Viewing Vibrations": [[232, "viewing-vibrations"]], "Viewing Electrostatic Potential Maps": [[230, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[230, "changing-surface-settings"]], "Basic VSEPR": [[248, "basic-vsepr"]], "Release Notes v1.95.1": [[242, "release-notes-v1-95-1"]], "Release Notes v1.97.0": [[244, "release-notes-v1-97-0"]], "Highlights (tldr)": [[244, "highlights-tldr"], [245, "highlights-tldr"]], "\ud83d\ude80 Performance Improvements": [[244, "performance-improvements"], [245, "performance-improvements"]], "Release Notes v1.98.0": [[245, "release-notes-v1-98-0"]], "Alkene Isomers": [[247, "alkene-isomers"]], "Building Source Code": [[237, "building-source-code"]], "Cloning Repositories": [[237, "cloning-repositories"]], "Updating": [[237, "updating"]], "Prerequisites": [[237, "prerequisites"]], "Debian-based Distribution or Ubuntu": [[237, "debian-based-distribution-or-ubuntu"]], "Building": [[237, "building"]], "Finding Qt, Windows Generators": [[237, "finding-qt-windows-generators"]], "Normal Development": [[237, "normal-development"]], "Build Tree Layout": [[237, "build-tree-layout"]], "Running Executables": [[237, "running-executables"]], "Building Packages": [[237, "building-packages"]], "Release Notes v1.96.0": [[243, "release-notes-v1-96-0"]], "\ud83d\ude80 Performance Fixes": [[243, "performance-fixes"]], "Selection Tool": [[226, "selection-tool"]], "Display Types": [[199, "display-types"], [199, null]], "Building Carbon Nanotubes": [[190, "building-carbon-nanotubes"]], "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"]], "VTK Classes": [[177, "vtk-classes"]], "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"]], "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"]], "Reducing Crystals to a Primitive Unit Cell": [[186, "reducing-crystals-to-a-primitive-unit-cell"]], "Perceiving Crystall Symmetry": [[183, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[183, "open-a-crystal-file"]], "Insert Molecular Fragments": [[196, "insert-molecular-fragments"]], "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 a Supercell": [[188, "building-a-supercell"]], "Creating a Surface": [[188, "creating-a-surface"]], "Building DNA or RNA": [[191, "building-dna-or-rna"]], "Building Molecules": [[195, "building-molecules"], [195, null]], "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"]], "Building with SMILES": [[192, "building-with-smiles"]], "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 a Peptide": [[189, "building-a-peptide"]], "Building a Polymer Unit Cell": [[182, "building-a-polymer-unit-cell"]], "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"]], "Importing Molecules by Name": [[194, "importing-molecules-by-name"]], "Building Materials": [[184, "building-materials"], [184, null]], "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"]], "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< int >": [[151, "class-avogadro-typetraits-int"]], "Class Avogadro::TypeTraits< unsigned short >": [[155, "class-avogadro-typetraits-unsigned-short"]], "Rendering Classes": [[165, "rendering-classes"]], "Class Avogadro::TypeTraits< unsigned char >": [[153, "class-avogadro-typetraits-unsigned-char"]], "QtGui Classes": [[164, "qtgui-classes"]], "Core Classes": [[160, "core-classes"]], "Class Avogadro::TypeTraits< short >": [[152, "class-avogadro-typetraits-short"]], "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"]], "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"]], "Avogadro Remote Procedure Call (RPC)": [[166, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[166, "rpc-protocol"]], "Methods": [[166, "methods"]], "Script Plugins": [[174, "script-plugins"], [161, "script-plugins"]], "MoleQueue Classes": [[163, "molequeue-classes"]], "Class Avogadro::TypeTraits< unsigned int >": [[154, "class-avogadro-typetraits-unsigned-int"]], "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"]], "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"]], "Develop": [[161, "develop"]], "External Scripting": [[161, "external-scripting"]], "Libraries": [[161, "libraries"]], "Main Classes": [[161, "main-classes"]], "IO Classes": [[162, "io-classes"]], "Class List": [[159, "class-list"]], "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::VTK::vtkGLWidget": [[157, "class-avogadro-vtk-vtkglwidget"]], 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