diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
index c7b27fa3..607e458c 100644
Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ
diff --git a/.doctrees/scripts/install.doctree b/.doctrees/scripts/install.doctree
index 3db458b6..9e7ef896 100644
Binary files a/.doctrees/scripts/install.doctree and b/.doctrees/scripts/install.doctree differ
diff --git a/_sources/scripts/install.md.txt b/_sources/scripts/install.md.txt
index 2738282d..a8c35dce 100644
--- a/_sources/scripts/install.md.txt
+++ b/_sources/scripts/install.md.txt
@@ -71,3 +71,15 @@ Required sections:
 
 Note that any files **not** listed in the `commands` list will be ignored by
 Avogadro during launch.
+
+## Adding to the Plugin Directory
+
+When you are ready to add your plugin repository to the download list, create a release and submit a 
+pull request to:
+https://github.com/Avogadro/plugins/blob/master/repositories.txt
+
+Someone will check your plugin and approve the addition to the list of approved repositories. An 
+automated script runs daily to generate the cached information on the plugin repositories, so it may
+not appear immediately.
+
+Suggestions for a more complete plugin repository system are welcome.
diff --git a/scripts/install.html b/scripts/install.html
index e30cd763..d22166fb 100644
--- a/scripts/install.html
+++ b/scripts/install.html
@@ -570,6 +570,16 @@ <h2>Plugin Packages and Repositories<a class="headerlink" href="#plugin-packages
 <p>Note that any files <strong>not</strong> listed in the <code class="docutils literal notranslate"><span class="pre">commands</span></code> list will be ignored by
 Avogadro during launch.</p>
 </section>
+<section id="adding-to-the-plugin-directory">
+<h2>Adding to the Plugin Directory<a class="headerlink" href="#adding-to-the-plugin-directory" title="Link to this heading">#</a></h2>
+<p>When you are ready to add your plugin repository to the download list, create a release and submit a
+pull request to:
+<a class="github reference external" href="https://github.com/Avogadro/plugins/blob/master/repositories.txt">Avogadro/plugins</a></p>
+<p>Someone will check your plugin and approve the addition to the list of approved repositories. An
+automated script runs daily to generate the cached information on the plugin repositories, so it may
+not appear immediately.</p>
+<p>Suggestions for a more complete plugin repository system are welcome.</p>
+</section>
 </section>
 
 
@@ -617,6 +627,7 @@ <h2>Plugin Packages and Repositories<a class="headerlink" href="#plugin-packages
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#directories">Directories</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#plugin-packages-and-repositories">Plugin Packages and Repositories</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#adding-to-the-plugin-directory">Adding to the Plugin Directory</a></li>
 </ul>
   </nav></div>
 
diff --git a/searchindex.js b/searchindex.js
index 178d9dc9..37f6f7bf 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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"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", "scripts/charges.md", "scripts/commands.md", "scripts/energy.md", "scripts/example1.md", "scripts/example2.md", "scripts/formats.md", "scripts/generators.md", "scripts/index.md", "scripts/install.md", "scripts/interface.md"], "titles": ["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 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Classes", "Develop", "IO Classes", "MoleQueue Classes", "QtGui Classes", "Rendering Classes", "Avogadro Remote Procedure Call (RPC)", "VTK Classes", "Contributing Code", "Documenting Code", "Coding Conventions (C++)", "Thanks", "Contribute", "Coding Style (C++)", "Translations", "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", "Optimizing Geometry", "Introduction to Molecular Mechanics", "Align Tool", "Auto-Optimize Tool", "Auto-Rotate Tool", "Bond-Centric Manipulate Tool", "Draw Tool", "Tools", "Manipulate Tool", "Measure Tool", "Navigate Tool", "Selection Tool", "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", "Charges / Electrostatics", "Command Scripts", "Energy / Force Fields", "Example Plugin Script - Part 1", "Example 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220, 226, 230, 234, 237, 240, 241, 243, 244], "filenam": [159, 162, 234, 237, 241, 243], "rutil": 159, "poscar": [159, 173], "note": [159, 173, 175, 176, 177, 180, 188, 192, 194, 226, 228, 237, 241, 243, 244], "infer": 159, "here": [159, 162, 168, 171, 172, 173, 175, 176, 177, 178, 180, 181, 197, 203, 218, 238, 239, 244], "content": [159, 162, 168, 241], "tio2": 159, "n1": 159, "00000000": 159, "n2": 159, "95812000": 159, "n0": 159, "4": [159, 169, 171, 176, 180, 202, 207, 237], "59373000": 159, "nO": 159, "ti": 159, "n4": 159, "ndirect": 159, "30530000": 159, "69470000": 159, "50000000": 159, "19470000": 159, "80530000": 159, "case": [159, 163, 166, 168, 187, 190, 200, 209, 210, 232, 233, 234, 237, 239, 241], "explicitli": 159, "pass": [159, 230, 233, 236, 241], "string": [159, 166, 167, 182, 236, 239, 241], "rather": 159, "than": [159, 166, 168, 176, 224, 230], "re": [161, 165, 179, 180, 181, 187, 229, 234], "interest": [161, 173, 218, 226], "we": [161, 162, 163, 164, 165, 166, 167, 172, 173, 175, 176, 177, 180, 181, 187, 202, 203, 218, 223, 224, 225, 226, 229, 230, 232, 233, 236, 237, 239], "recommend": [161, 226, 231, 241], "understand": [161, 168], "github": [161, 165, 167, 224, 226, 229, 232, 233, 234, 242, 243], "flow": 161, "fork": 161, "repositori": [161, 165, 234, 242], "make": [161, 162, 163, 165, 166, 168, 170, 172, 175, 178, 186, 187, 191, 198, 200, 202, 222, 224, 225, 226, 229, 230, 231, 232, 233, 234, 235, 237, 239], "chang": [161, 168, 170, 172, 177, 190, 194, 196, 198, 199, 201, 206, 209, 210, 214, 224, 226, 228, 234, 239], "git": [161, 226], "version": [161, 168, 175, 183, 194, 207, 224, 226, 233, 234, 243], "control": [161, 175, 181, 192, 226, 238], "financi": [161, 164, 165], "pull": [161, 163, 226, 232, 233], "other": [161, 163, 166, 172, 180, 187, 197, 198, 203, 207, 217, 218, 219, 224, 225, 226, 233, 235, 236, 241], "review": [161, 203], "test": [161, 202, 226, 231, 232, 239], "merg": [161, 167], "main": [161, 179, 241, 243], "have": [161, 162, 165, 166, 168, 172, 175, 182, 183, 187, 197, 201, 203, 207, 213, 220, 222, 223, 226, 229, 230, 232, 233, 239, 241, 244], "sever": [161, 165, 166, 168, 180, 192, 207, 224, 226, 229, 230, 231, 233, 234, 241], "suggest": [161, 165, 222, 225, 229, 230, 232, 233, 236, 242], "far": 161, "style": [161, 162, 163, 170, 194, 241], "convent": [161, 166], "well": [161, 168, 180, 181, 197, 198, 203, 205, 224, 226, 232, 236, 243], "document": [161, 163, 165, 175, 196, 198, 225, 229, 230, 232, 233, 240, 241], "your": [161, 162, 165, 166, 168, 177, 178, 182, 183, 186, 190, 192, 193, 195, 197, 198, 200, 201, 203, 206, 207, 209, 210, 212, 215, 217, 219, 224, 225, 226, 233, 237], "comment": [161, 166, 229, 230, 232, 233, 241], "doxygen": [161, 162], "api": [161, 162, 225], "doc": [161, 229, 239], "which": [161, 165, 168, 172, 175, 176, 177, 192, 200, 217, 218, 224, 226, 230, 234, 235, 236, 237, 238, 239, 240, 241, 243, 244], "ultim": 161, "becom": 161, "websit": [161, 180, 182, 183, 197, 232, 233], "featur": [161, 165, 167, 170, 171, 175, 187, 188, 193, 194, 195, 196, 197, 200, 201, 205, 207, 220, 221, 222, 228], "header": [161, 162, 166, 229, 233], "export": [161, 178, 199, 229, 234], "macro": 161, "privat": [161, 230], "cast": [161, 164, 166, 207, 232], "aesthet": 161, "indent": 161, "line": [161, 172, 182, 209, 224, 233, 234, 235, 236, 237, 238, 239, 240, 241], "width": [161, 233], "declar": [161, 162, 163, 234, 237], "variabl": [161, 203, 226, 238], "whitespac": 161, "brace": 161, "parenthes": 161, "switch": [161, 172, 175, 192, 202, 229, 233, 234], "statement": 161, "break": [161, 239], "inherit": 161, "virtual": 161, "keyword": [161, 197, 221, 241], "referenc": 161, "name": [161, 162, 163, 168, 170, 171, 187, 199, 203, 216, 226, 233, 234, 235, 236, 237, 238, 239, 240, 241, 243, 244], "class": [161, 163, 166, 224, 230, 234, 241], "descript": [161, 165, 232, 235, 237, 240, 241, 243], "javadoc": 162, "thei": [162, 163, 165, 167, 168, 175, 179, 205, 207, 226, 241, 243, 244], "go": [162, 166, 181, 183, 187, 203, 207, 212, 226], "next": [162, 172, 187, 202, 219, 222, 224, 237, 244], "should": [162, 163, 166, 168, 172, 192, 195, 202, 226, 230, 234, 235, 236, 237, 240, 241, 243, 244], "minimum": [162, 168, 202, 234, 244], "brief": [162, 243], "one": [162, 163, 166, 168, 171, 172, 180, 181, 182, 188, 192, 197, 201, 203, 209, 224, 234, 236, 241], "sentenc": 162, "explain": 162, "what": [162, 170, 187, 197, 201, 214], "intend": [162, 168, 240], "purpos": [162, 163, 166, 168, 197, 235], "goe": [162, 166, 226, 241], "void": [162, 166], "dosometh": [162, 166], "overview": [162, 166], "add": [162, 167, 172, 177, 178, 197, 199, 201, 203, 205, 215, 224, 226, 229, 230, 231, 232, 233, 234, 244], "appropri": [162, 166, 192, 226, 232, 236, 238, 241, 244], "point": [162, 166, 175, 195, 201, 206, 218, 226, 233, 234, 235, 238], "out": [162, 168, 172, 173, 192, 194, 203, 205, 208, 214, 223, 234, 244], "altern": [162, 237], "similar": [162, 168, 188, 192, 241], "ideal": 162, "give": [162, 165, 168, 201, 234, 239], "simpl": [162, 178, 188, 195, 226, 244], "demonstr": [162, 188, 200], "simplest": 162, "wai": [162, 168, 172, 178, 187, 193, 195, 197, 224, 225], "possibl": [162, 166, 168, 194, 226, 239], "jsonrpcclient": 162, "client": [162, 168], "rpc": [162, 229], "author": [162, 168, 236, 241, 243], "marcu": [162, 164], "d": [162, 164, 168, 230, 232, 233], "hanwel": [162, 164], "To": [162, 168, 171, 192, 199, 208, 209, 226, 236, 239], "creat": [162, 168, 172, 177, 179, 188, 191, 195, 196, 198, 199, 201, 218, 219, 220, 224, 226, 230, 232, 234, 237, 238, 241, 244], "method": [162, 166, 205, 224, 229, 232, 234, 235, 237, 241], "follow": [162, 166, 168, 175, 178, 203, 226, 235, 236, 237, 238, 239, 240, 241, 244], "done": [162, 207, 220, 237, 239], "connecttoserv": 162, "myrpcserv": 162, "qjsonobject": 162, "emptyrequest": 162, "qlatin1str": 162, "listqueu": 162, "sendrequest": 162, "endcod": 162, "signal": [162, 163], "order": [162, 188, 190, 210, 213, 218, 226, 230, 234, 235, 236, 239, 241, 244], "act": [162, 226, 239], "notif": 162, "error": [162, 168, 232, 233, 234], "receiv": [162, 168], "respons": [162, 164, 234, 238, 239], "public": [162, 163, 166, 230], "qobject": 162, "end": [162, 163, 166, 172, 175, 187, 208, 209], "constructor": 162, "more": [162, 163, 166, 168, 180, 187, 188, 193, 194, 197, 200, 201, 203, 205, 207, 219, 224, 225, 229, 230, 233, 234, 236, 240, 241, 242], "construct": [162, 192, 195], "describ": [162, 168, 235, 237, 240, 241], "paramet": [162, 178, 197, 203, 205, 207, 220, 233, 236, 237], "job": [162, 241], "appear": [162, 171, 178, 197, 241], "work": [162, 164, 165, 167, 168, 172, 180, 183, 194, 197, 200, 203, 224, 225, 226, 233, 234, 236], "specifi": [162, 168, 171, 173, 175, 176, 200, 235, 237, 238, 239, 240, 244], "return": [162, 166, 195, 217, 235, 238, 239], "true": [162, 166, 235, 236, 237, 238, 239, 244], "wa": [162, 176, 178, 187, 192, 194, 219, 222, 224, 230, 241], "successfulli": [162, 226, 233], "fals": [162, 166, 235, 237, 239, 241], "otherwis": [162, 168, 202, 217, 240, 241], "bool": 162, "setinputfil": 162, "const": [162, 163, 166], "qstring": [162, 163], "don": [163, 166, 207, 230, 234], "t": [163, 166, 168, 173, 175, 183, 187, 197, 207, 230, 231, 234], "except": [163, 166, 168, 234, 235, 237], "assert": [163, 168], "product": [163, 187], "never": [163, 168, 237], "crash": [163, 222, 224, 230, 232, 233, 234, 236, 241], "prefer": [163, 182, 195, 197, 202, 233, 235, 239, 241], "solut": 163, "librari": [154, 163, 165, 171, 226, 230, 234, 243], "over": [163, 172, 176, 182, 183, 186, 207, 217, 222, 229, 230], "boost": [163, 226], "depend": [163, 164, 171, 188, 197, 207, 226, 229, 239], "In": [163, 167, 168, 172, 175, 190, 194, 210, 218, 226, 227, 236, 239, 241], "11": [163, 168, 172, 226], "17": 163, "necessari": [163, 166, 168, 201, 207], "offer": [163, 164, 168, 194, 225, 241], "avo_overrid": 163, "avo_fin": 163, "defin": [163, 168, 171, 172, 175, 195, 224, 236, 238, 241], "overrid": [163, 233, 241], "final": [163, 180, 187, 234, 236, 239], "minim": [163, 180, 241], "third": [163, 172, 226], "parti": [163, 168, 226], "think": [163, 225, 235], "carefulli": 163, "befor": [163, 166, 168, 177, 187, 202, 203, 207, 220, 226, 234, 244], "ad": [163, 167, 178, 179, 180, 188, 190, 210, 217, 224, 229, 234, 244], "templat": [163, 167, 230, 234, 241], "sens": 163, "alwai": [163, 166, 168, 202, 230, 232, 233, 242], "form": [163, 168, 187, 203, 205, 230, 232, 233, 235, 236, 237, 240, 241], "project": [163, 165, 166, 172, 175, 196, 199, 225, 226, 230, 234], "someth": [163, 194], "type": [163, 166, 170, 171, 179, 180, 181, 184, 187, 190, 192, 193, 195, 197, 199, 200, 203, 206, 210, 214, 215, 218, 219, 224, 230, 236, 238, 240, 241, 242, 243, 244], "myclass": 163, "special": [163, 168], "first": [163, 172, 177, 192, 197, 200, 219, 233, 236, 237, 241], "myapihead": 163, "our": [163, 164, 167, 168, 173, 180, 225, 235], "differ": [163, 165, 168, 170, 190, 205, 210, 218, 224, 244], "modul": [163, 224, 226, 238, 243], "qtcore": 163, "vector": [163, 172, 173, 221], "stl": 163, "do": [163, 166, 168, 173, 180, 190, 192, 210, 226, 229, 234, 239, 240], "avogadrorenderingexport": 163, "denot": 163, "_p": 163, "camel": [163, 166], "instead": [163, 233, 235, 236, 237], "being": [163, 166, 188, 207, 209, 214, 226], "wrong": [163, 166, 230], "qdialog": 163, "correct": [163, 166, 180, 226, 234, 241], "chemistri": [163, 164, 165, 166, 194, 218, 220, 221, 225, 226, 229], "nest": [163, 180], "everyth": [163, 196, 200, 206], "insid": [163, 166, 226, 243], "mongochem": [163, 234], "contain": [163, 166, 202, 226, 233, 235, 236, 237, 239, 240, 241, 243], "overspecifi": 163, "doesn": [163, 183, 187, 207], "slot": 163, "moc": 163, "often": [163, 173, 205], "littl": 163, "help": [163, 164, 194, 195, 205, 219, 224, 225, 230, 232, 233, 235, 237, 240], "onli": [163, 166, 168, 180, 187, 188, 192, 197, 200, 205, 207, 209, 218, 224, 226, 231, 232, 233, 234, 235, 236, 237, 239, 240, 241], "specif": [163, 172, 187, 197, 200, 203, 205, 206, 207, 208, 219, 229, 234, 239, 240, 241], "symbol": [163, 190, 210, 232, 241], "avoid": [163, 166, 168, 226, 233, 234], "static_cast": 163, "dynamic_cast": 163, "const_cast": 163, "reinterpret_cast": [163, 166], "For": [163, 165, 166, 168, 172, 178, 181, 188, 194, 196, 197, 200, 201, 203, 207, 209, 212, 213, 226, 235, 237, 238, 239, 240, 241, 244], "deriv": [163, 168, 218], "qobject_cast": 163, "enum": 163, "constant": [163, 197], "static": [163, 205], "verbos": 163, "argument": [163, 226, 235, 236, 237, 239, 240, 241], "show": [163, 171, 175, 177, 180, 181, 192, 197, 209, 217, 218, 224, 233], "autocomplet": 163, "It": [163, 184, 192, 194, 198, 222, 224, 225, 226, 236, 238, 239, 241], "look": [163, 166, 173, 192, 201, 224, 226, 239, 243], "better": [163, 165, 194, 202, 207, 224, 225, 234], "poor": 163, "peopl": [163, 194], "guess": 163, "abbrevi": [163, 166], "ambigu": 163, "afford": 163, "few": [163, 180, 184, 222, 224, 234, 243], "extra": [163, 172, 236, 241], "byte": 163, "fundament": 164, "aim": [164, 218], "contributor": [164, 222, 229, 230, 231, 232, 233, 234], "alik": [164, 169], "hope": 164, "build": [164, 170, 171, 186, 199, 205, 217, 222, 224, 225, 227, 229, 230, 232, 233, 234, 236, 238], "top": [164, 188, 212, 226, 232], "framework": [164, 224, 233, 234], "veri": [164, 165, 173, 192, 230, 232, 233], "grate": 164, "shahzad": 164, "ali": 164, "michael": 164, "banck": 164, "ross": 164, "braithwait": 164, "jame": 164, "bunt": 164, "donald": 164, "curti": 164, "naomi": 164, "fox": 164, "geoff": 164, "hutchison": [164, 194, 243], "beno\u00eet": 164, "jacob": 164, "jordan": 164, "mantha": 164, "thoma": [164, 229], "margraf": 164, "carsten": 164, "niehau": 164, "simon": 164, "ochsenreith": 164, "konstantin": 164, "tokarev": 164, "allison": 164, "vacanti": 164, "tim": 164, "vandermeersch": 164, "ha": [164, 165, 168, 175, 177, 178, 181, 183, 187, 188, 190, 192, 195, 197, 198, 205, 207, 209, 210, 219, 221, 224, 226, 229, 234, 239], "come": [164, 183, 188, 205, 209, 225], "would": [164, 180, 192, 194, 222, 224, 225, 226], "particularli": [164, 205, 222, 223, 230, 232, 233], "googl": [164, 230, 232, 233], "summer": [164, 194, 229, 230, 232, 233], "2007": 164, "2008": 164, "2011": 164, "2016": 164, "2018": 164, "2019": [164, 232], "2021": [164, 229, 230, 231], "2022": [164, 194, 232, 233], "kitwar": 164, "inc": 164, "univers": [164, 194, 205, 207], "pittsburgh": [164, 194], "u": [164, 165, 175, 180, 225, 229, 230, 232, 233], "depart": [164, 194], "defens": 164, "dod": 164, "pettt": 164, "research": [164, 180, 225], "corpor": [164, 168], "cottrel": 164, "scholar": 164, "award": 164, "reli": 164, "infrastructur": 164, "blue": [164, 187, 188, 206, 209, 219, 224], "obelisk": 164, "group": [164, 166, 173, 175, 176, 177, 178, 180, 195, 200, 218, 223, 224, 232, 234, 241], "pybind11": 164, "structur": [164, 173, 179, 180, 184, 186, 188, 190, 196, 201, 205, 207, 210, 224, 229, 230, 232, 238, 239], "databas": [164, 165, 179, 186, 198, 217, 242], "cmake": [164, 226, 234], "eigen": [164, 166, 226], "softwar": [164, 197, 218], "And": [164, 235], "cours": [164, 179], "johann": 164, "loschmidt": 164, "amedeo": 164, "made": [165, 167, 168, 169, 186, 187, 188, 192, 193, 198, 200, 201, 205, 215, 229], "who": 165, "want": [165, 175, 179, 180, 187, 190, 192, 202, 203, 210, 212, 218, 219, 225, 236], "back": [165, 195, 201, 229, 230, 232], "great": [165, 225, 226], "place": [165, 166, 168, 173, 188, 196, 197, 201, 207, 212, 214, 225, 226, 239, 241], "start": [165, 166, 170, 171, 172, 179, 180, 195, 207, 208, 221, 225, 230, 234], "fellow": 165, "forum": [165, 167], "question": [165, 225], "level": [165, 226, 241], "post": [165, 203], "mai": [165, 168, 171, 173, 175, 179, 180, 181, 184, 194, 202, 207, 217, 218, 220, 222, 226, 235, 236, 239, 241, 243, 244], "find": [165, 170, 192, 220, 224, 225, 233, 238, 239], "experi": 165, "valuabl": 165, "bug": [165, 167, 183, 225, 228], "pleas": [165, 167, 225, 229, 230, 232, 233], "take": [165, 171, 184, 188, 197, 201, 207, 212, 214, 220, 239], "moment": [165, 180, 220], "tracker": [165, 225], "issu": [165, 167, 225, 229, 234], "code": [165, 167, 173, 180, 181, 183, 197, 220, 221, 224, 225, 227, 229, 230, 232, 233, 234, 235, 237, 238, 239, 241], "while": [165, 166, 172, 177, 203, 207, 217, 233, 236, 237, 241], "move": [165, 168, 175, 183, 186, 192, 207, 212, 224, 234], "around": [165, 166, 175, 177, 180, 186, 188, 192, 203, 212, 224], "fit": [165, 166, 168], "itself": 165, "section": [165, 188, 193, 194, 195, 197, 203, 207, 212, 224, 241, 243], "discuss": [165, 167, 197, 225, 229, 230, 232, 233, 236], "idea": [165, 225], "plan": 165, "direct": [165, 168, 183, 208, 226, 232, 241], "progress": [165, 198], "util": [165, 178, 188, 197, 243], "friend": 165, "cite": 165, "paper": [165, 182, 225], "write": [165, 166, 232, 233, 234, 237, 238, 241], "tutori": [165, 170, 171, 188, 197, 224, 225], "site": [165, 224, 225], "lesson": [165, 175], "activ": [165, 224, 226], "teacher": 165, "fragment": [165, 170, 182, 193, 195, 212, 215, 224, 229, 234], "report": [165, 167, 173, 225, 230, 231, 232, 233, 241], "encount": [165, 167], "about": [165, 187, 194, 197, 201, 203, 214, 225, 232, 233, 241], "improv": [165, 167, 222, 224, 228, 231], "languag": [165, 200, 225, 233, 235, 236, 237, 238, 241], "donat": 165, "pai": [165, 194], "host": [165, 232, 233, 234], "meet": 165, "bounti": 165, "when": [166, 177, 178, 187, 188, 192, 193, 195, 197, 201, 202, 212, 220, 226, 230, 233, 234, 236, 237, 238, 239, 241], "larg": [166, 171, 175, 176, 179, 180, 192, 224, 226], "kde": 166, "enforc": [166, 168], "clang": [166, 233], "tool": [166, 170, 172, 175, 179, 180, 186, 188, 190, 192, 193, 194, 203, 222, 225, 229, 231, 232, 234], "space": [166, 171, 173, 175, 176, 177, 178, 201, 232, 234, 237, 241], "tab": [166, 201, 230, 233], "keep": [166, 203, 226], "less": [166, 197, 219, 224], "80": 166, "charact": [166, 236, 241], "wide": [166, 194, 197, 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"map": 219, "configur": 220, "vibrat": 221, "what": 222, "major": 224, "speed": 224, "stabil": 224, "real": 224, "time": 224, "shadow": 224, "depth": 224, "effect": 224, "contact": 224, "non": 224, "halogen": 224, "chalcogen": 224, "layer": 224, "templat": 224, "access": 224, "exclud": 224, "flexibl": 224, "model": 224, "jupyt": 224, "integr": 224, "extern": 224, "program": 224, "return": 236, "specif": 236, "append": 236}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"Class Avogadro::Core::Array": [[0, "class-avogadro-core-array"]], "Class Avogadro::Core::ArraySet": [[1, "class-avogadro-core-arrayset"]], "Class Avogadro::Core::ArraySet::Holder": [[2, "class-avogadro-core-arrayset-holder"]], "Class Avogadro::Core::ArraySet::PlaceHolder": [[3, "class-avogadro-core-arrayset-placeholder"]], "Class Avogadro::Core::Atom": [[4, "class-avogadro-core-atom"]], "Class Avogadro::Core::AtomTemplate": [[5, "class-avogadro-core-atomtemplate"]], "Class Avogadro::Core::AtomTyper": [[6, "class-avogadro-core-atomtyper"]], "Class Avogadro::Core::AvoSpglib": [[7, "class-avogadro-core-avospglib"]], "Class Avogadro::Core::BasisSet": [[8, "class-avogadro-core-basisset"]], "Class Avogadro::Core::Bond": [[9, "class-avogadro-core-bond"]], "Class Avogadro::Core::BondTemplate": [[10, "class-avogadro-core-bondtemplate"]], "Class Avogadro::Core::Color3f": [[11, "class-avogadro-core-color3f"]], "Class Avogadro::Core::CoordinateBlockGenerator": [[12, "class-avogadro-core-coordinateblockgenerator"]], "Class Avogadro::Core::CoordinateSet": [[13, "class-avogadro-core-coordinateset"]], "Class Avogadro::Core::CrystalTools": [[14, "class-avogadro-core-crystaltools"]], "Class Avogadro::Core::Cube": [[15, "class-avogadro-core-cube"]], "Class Avogadro::Core::Elements": [[16, "class-avogadro-core-elements"]], "Class Avogadro::Core::GaussianSet": [[17, "class-avogadro-core-gaussianset"]], "Class Avogadro::Core::GaussianSetTools": [[18, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::Graph": [[19, "class-avogadro-core-graph"]], "Class Avogadro::Core::Mesh": [[20, "class-avogadro-core-mesh"]], "Class Avogadro::Core::Molecule": [[21, "class-avogadro-core-molecule"]], "Class Avogadro::Core::MoleculeDeserializer": [[22, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::MoleculeSerializer": [[23, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Core::Mutex": [[24, "class-avogadro-core-mutex"]], "Class Avogadro::Core::NameAtomTyper": [[25, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::Residue": [[26, "class-avogadro-core-residue"]], "Class Avogadro::Core::ResidueData": [[27, "class-avogadro-core-residuedata"]], "Class Avogadro::Core::RingPerceiver": [[28, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::SharedMutex": [[29, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::SlaterSet": [[30, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::SlaterSetTools": [[31, "class-avogadro-core-slatersettools"]], "Class Avogadro::Core::SpaceGroups": [[32, "class-avogadro-core-spacegroups"]], "Class Avogadro::Core::SymbolAtomTyper": [[33, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::UnitCell": [[34, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::Variant": [[35, "class-avogadro-core-variant"]], "Class Avogadro::Core::VariantMap": [[36, "class-avogadro-core-variantmap"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[37, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Io::CjsonFormat": [[38, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Io::CmlFormat": [[39, "class-avogadro-io-cmlformat"]], "Class Avogadro::Io::DcdFormat": [[40, "class-avogadro-io-dcdformat"]], "Class Avogadro::Io::FileFormat": [[41, "class-avogadro-io-fileformat"]], "Class Avogadro::Io::FileFormatManager": [[42, "class-avogadro-io-fileformatmanager"]], "Class Avogadro::Io::GromacsFormat": [[43, "class-avogadro-io-gromacsformat"]], "Class Avogadro::Io::Hdf5DataFormat": [[44, "class-avogadro-io-hdf5dataformat"]], "Class Avogadro::Io::LammpsDataFormat": [[45, "class-avogadro-io-lammpsdataformat"]], "Class Avogadro::Io::LammpsTrajectoryFormat": [[46, "class-avogadro-io-lammpstrajectoryformat"]], "Class Avogadro::Io::MMTFFormat": [[47, "class-avogadro-io-mmtfformat"]], "Class Avogadro::Io::MdlFormat": [[48, "class-avogadro-io-mdlformat"]], "Class Avogadro::Io::OutcarFormat": [[49, "class-avogadro-io-outcarformat"]], "Class Avogadro::Io::PdbFormat": [[50, "class-avogadro-io-pdbformat"]], "Class Avogadro::Io::PoscarFormat": [[51, "class-avogadro-io-poscarformat"]], "Class Avogadro::Io::TrrFormat": [[52, "class-avogadro-io-trrformat"]], "Class Avogadro::Io::XyzFormat": [[53, "class-avogadro-io-xyzformat"]], "Class Avogadro::MoleQueue::BatchJob": [[54, "class-avogadro-molequeue-batchjob"]], "Class Avogadro::MoleQueue::InputGenerator": [[55, "class-avogadro-molequeue-inputgenerator"]], "Class Avogadro::MoleQueue::InputGeneratorDialog": [[56, "class-avogadro-molequeue-inputgeneratordialog"]], "Class Avogadro::MoleQueue::InputGeneratorWidget": [[57, "class-avogadro-molequeue-inputgeneratorwidget"]], "Class Avogadro::MoleQueue::MoleQueueDialog": [[58, "class-avogadro-molequeue-molequeuedialog"]], "Class Avogadro::MoleQueue::MoleQueueManager": [[59, "class-avogadro-molequeue-molequeuemanager"]], "Class Avogadro::MoleQueue::MoleQueueQueueListModel": [[60, "class-avogadro-molequeue-molequeuequeuelistmodel"]], "Class Avogadro::MoleQueue::MoleQueueWidget": [[61, "class-avogadro-molequeue-molequeuewidget"]], "Class Avogadro::QtGui::BackgroundFileFormat": [[62, "class-avogadro-qtgui-backgroundfileformat"]], "Class Avogadro::QtGui::ContainerWidget": [[63, "class-avogadro-qtgui-containerwidget"]], "Class Avogadro::QtGui::CustomElementDialog": [[64, "class-avogadro-qtgui-customelementdialog"]], "Class Avogadro::QtGui::ElementDetail": [[65, "class-avogadro-qtgui-elementdetail"]], "Class Avogadro::QtGui::ElementItem": [[66, "class-avogadro-qtgui-elementitem"]], "Class Avogadro::QtGui::ElementTranslator": [[67, "class-avogadro-qtgui-elementtranslator"]], "Class Avogadro::QtGui::ExtensionPlugin": [[68, "class-avogadro-qtgui-extensionplugin"]], "Class Avogadro::QtGui::ExtensionPluginFactory": [[69, "class-avogadro-qtgui-extensionpluginfactory"]], "Class Avogadro::QtGui::FileBrowseWidget": [[70, "class-avogadro-qtgui-filebrowsewidget"]], "Class Avogadro::QtGui::FileFormatDialog": [[71, "class-avogadro-qtgui-fileformatdialog"]], "Class Avogadro::QtGui::GenericHighlighter": [[72, "class-avogadro-qtgui-generichighlighter"]], "Class Avogadro::QtGui::GenericHighlighter::Rule": [[73, "class-avogadro-qtgui-generichighlighter-rule"]], "Class Avogadro::QtGui::HydrogenTools": [[74, "class-avogadro-qtgui-hydrogentools"]], "Class Avogadro::QtGui::InterfaceScript": [[75, "class-avogadro-qtgui-interfacescript"]], "Class Avogadro::QtGui::InterfaceWidget": [[76, "class-avogadro-qtgui-interfacewidget"]], "Class Avogadro::QtGui::MeshGenerator": [[77, "class-avogadro-qtgui-meshgenerator"]], "Class Avogadro::QtGui::Molecule": [[78, "class-avogadro-qtgui-molecule"]], "Class Avogadro::QtGui::MoleculeModel": [[79, "class-avogadro-qtgui-moleculemodel"]], "Class Avogadro::QtGui::MultiViewWidget": [[80, "class-avogadro-qtgui-multiviewwidget"]], "Class Avogadro::QtGui::PeriodicTableScene": [[81, "class-avogadro-qtgui-periodictablescene"]], "Class Avogadro::QtGui::PeriodicTableView": [[82, "class-avogadro-qtgui-periodictableview"]], "Class Avogadro::QtGui::PersistentAtom": [[83, "class-avogadro-qtgui-persistentatom"]], "Class Avogadro::QtGui::PersistentBond": [[84, "class-avogadro-qtgui-persistentbond"]], "Class Avogadro::QtGui::PythonScript": [[85, "class-avogadro-qtgui-pythonscript"]], "Class Avogadro::QtGui::RWAtom": [[86, "class-avogadro-qtgui-rwatom"]], "Class Avogadro::QtGui::RWBond": [[87, "class-avogadro-qtgui-rwbond"]], "Class Avogadro::QtGui::RWMolecule": [[88, "class-avogadro-qtgui-rwmolecule"]], "Class Avogadro::QtGui::ScenePlugin": [[89, "class-avogadro-qtgui-sceneplugin"]], "Class Avogadro::QtGui::ScenePluginFactory": [[90, "class-avogadro-qtgui-scenepluginfactory"]], "Class Avogadro::QtGui::ScenePluginModel": [[91, "class-avogadro-qtgui-scenepluginmodel"]], "Class Avogadro::QtGui::ScriptLoader": [[92, "class-avogadro-qtgui-scriptloader"]], "Class Avogadro::QtGui::ToolPlugin": [[93, "class-avogadro-qtgui-toolplugin"]], "Class Avogadro::QtGui::ToolPluginFactory": [[94, "class-avogadro-qtgui-toolpluginfactory"]], "Class Avogadro::QtGui::ViewFactory": [[95, "class-avogadro-qtgui-viewfactory"]], "Class Avogadro::QtOpenGL::ActiveObjects": [[96, "class-avogadro-qtopengl-activeobjects"]], "Class Avogadro::QtOpenGL::GLWidget": [[97, "class-avogadro-qtopengl-glwidget"]], "Class Avogadro::QtOpenGL::QtTextRenderStrategy": [[98, "class-avogadro-qtopengl-qttextrenderstrategy"]], "Class Avogadro::QuantumIO::GAMESSUSOutput": [[99, "class-avogadro-quantumio-gamessusoutput"]], "Class Avogadro::QuantumIO::GUKBasisSet": [[100, "class-avogadro-quantumio-gukbasisset"]], "Class Avogadro::QuantumIO::GamessukOut": [[101, "class-avogadro-quantumio-gamessukout"]], "Class Avogadro::QuantumIO::GaussianCube": [[102, "class-avogadro-quantumio-gaussiancube"]], "Class Avogadro::QuantumIO::GaussianFchk": [[103, "class-avogadro-quantumio-gaussianfchk"]], "Class Avogadro::QuantumIO::MoldenFile": [[104, "class-avogadro-quantumio-moldenfile"]], "Class Avogadro::QuantumIO::MopacAux": [[105, "class-avogadro-quantumio-mopacaux"]], "Class Avogadro::QuantumIO::NWChemJson": [[106, "class-avogadro-quantumio-nwchemjson"]], "Class Avogadro::QuantumIO::NWChemLog": [[107, "class-avogadro-quantumio-nwchemlog"]], "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry": [[108, "class-avogadro-rendering-ambientocclusionspheregeometry"]], "Class Avogadro::Rendering::ArrowGeometry": [[109, "class-avogadro-rendering-arrowgeometry"]], "Class Avogadro::Rendering::BufferObject": [[110, "class-avogadro-rendering-bufferobject"]], "Class Avogadro::Rendering::Camera": [[111, "class-avogadro-rendering-camera"]], "Class Avogadro::Rendering::Cylinder": [[112, "class-avogadro-rendering-cylinder"]], "Class Avogadro::Rendering::CylinderGeometry": [[113, "class-avogadro-rendering-cylindergeometry"]], "Class Avogadro::Rendering::Drawable": [[114, "class-avogadro-rendering-drawable"]], "Class Avogadro::Rendering::GLRenderVisitor": [[115, "class-avogadro-rendering-glrendervisitor"]], "Class Avogadro::Rendering::GLRenderer": [[116, "class-avogadro-rendering-glrenderer"]], "Class Avogadro::Rendering::GeometryNode": [[117, "class-avogadro-rendering-geometrynode"]], "Class Avogadro::Rendering::GeometryVisitor": [[118, "class-avogadro-rendering-geometryvisitor"]], "Class Avogadro::Rendering::GroupNode": [[119, "class-avogadro-rendering-groupnode"]], "Class Avogadro::Rendering::LineStripGeometry": [[120, "class-avogadro-rendering-linestripgeometry"]], "Class Avogadro::Rendering::MeshGeometry": [[121, "class-avogadro-rendering-meshgeometry"]], "Class Avogadro::Rendering::Node": [[122, "class-avogadro-rendering-node"]], "Class Avogadro::Rendering::POVRayVisitor": [[123, "class-avogadro-rendering-povrayvisitor"]], "Class Avogadro::Rendering::Primitive": [[124, "class-avogadro-rendering-primitive"]], "Class Avogadro::Rendering::Scene": [[125, "class-avogadro-rendering-scene"]], "Class Avogadro::Rendering::Shader": [[126, "class-avogadro-rendering-shader"]], "Class Avogadro::Rendering::ShaderProgram": [[127, "class-avogadro-rendering-shaderprogram"]], "Class Avogadro::Rendering::Sphere": [[128, "class-avogadro-rendering-sphere"]], "Class Avogadro::Rendering::SphereGeometry": [[129, "class-avogadro-rendering-spheregeometry"]], "Class Avogadro::Rendering::TextLabel2D": [[130, "class-avogadro-rendering-textlabel2d"]], "Class Avogadro::Rendering::TextLabel3D": [[131, "class-avogadro-rendering-textlabel3d"]], "Class Avogadro::Rendering::TextLabelBase": [[132, "class-avogadro-rendering-textlabelbase"]], "Class Avogadro::Rendering::TextProperties": [[133, "class-avogadro-rendering-textproperties"]], "Class Avogadro::Rendering::TextRenderStrategy": [[134, "class-avogadro-rendering-textrenderstrategy"]], "Class Avogadro::Rendering::Texture2D": [[135, "class-avogadro-rendering-texture2d"]], "Class Avogadro::Rendering::TransformNode": [[136, "class-avogadro-rendering-transformnode"]], "Class Avogadro::Rendering::VRMLVisitor": [[137, "class-avogadro-rendering-vrmlvisitor"]], "Class Avogadro::Rendering::Visitor": [[138, "class-avogadro-rendering-visitor"]], "Class Avogadro::Rendering::VolumeGeometry": [[139, "class-avogadro-rendering-volumegeometry"]], "Class Avogadro::TypeTraits": [[140, "class-avogadro-typetraits"]], "Class Avogadro::TypeTraits< char >": [[141, "class-avogadro-typetraits-char"]], "Class Avogadro::TypeTraits< double >": [[142, "class-avogadro-typetraits-double"]], "Class Avogadro::TypeTraits< float >": [[143, "class-avogadro-typetraits-float"]], "Class Avogadro::TypeTraits< int >": [[144, "class-avogadro-typetraits-int"]], "Class Avogadro::TypeTraits< short >": [[145, "class-avogadro-typetraits-short"]], "Class Avogadro::TypeTraits< unsigned char >": [[146, "class-avogadro-typetraits-unsigned-char"]], "Class Avogadro::TypeTraits< unsigned int >": [[147, "class-avogadro-typetraits-unsigned-int"]], "Class Avogadro::TypeTraits< unsigned short >": [[148, "class-avogadro-typetraits-unsigned-short"]], "Class Avogadro::VTK::VtkPlot": [[149, "class-avogadro-vtk-vtkplot"]], "Class Avogadro::VTK::vtkGLWidget": [[150, "class-avogadro-vtk-vtkglwidget"]], "Class vtkAvogadroActor": [[151, "class-vtkavogadroactor"]], "Class list": [[152, "class-list"]], "Core Classes": [[153, "core-classes"]], "Develop": [[154, "develop"]], "Main Classes": [[154, "main-classes"]], "IO Classes": [[155, "io-classes"]], "MoleQueue Classes": [[156, "molequeue-classes"]], "QtGui Classes": [[157, "qtgui-classes"]], "Rendering Classes": [[158, "rendering-classes"]], "Avogadro Remote Procedure Call (RPC)": [[159, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[159, "rpc-protocol"]], "Methods": [[159, "methods"]], "VTK Classes": [[160, "vtk-classes"]], "Contributing Code": [[161, "contributing-code"], [161, null]], "Documenting Code": [[162, "documenting-code"]], "Class Descriptions": [[162, "class-descriptions"]], "Function Descriptions": [[162, "function-descriptions"]], "Coding Conventions (C++)": [[163, "coding-conventions-c"]], "C++ Features": [[163, "c-features"]], "Including Headers": [[163, "including-headers"]], "Export Macro Headers": [[163, "export-macro-headers"]], "Private Headers": [[163, "private-headers"]], "Qt Headers": [[163, "qt-headers"]], "Namespaces": [[163, "namespaces"]], "Casting": [[163, "casting"]], "Aesthetics": [[163, "aesthetics"]], "Thanks": [[164, "thanks"], [194, "thanks"]], "Code": [[164, "code"]], "Funding": [[164, "funding"]], "Other Projects": [[164, "other-projects"]], "Contribute": [[165, "contribute"]], "How to Help": [[165, "how-to-help"]], "Coding Style (C++)": [[166, "coding-style-c"]], "Indentation": [[166, "indentation"]], "Line Width": [[166, "line-width"]], "Declaring Variables": [[166, "declaring-variables"]], "Whitespace": [[166, "whitespace"]], "Braces": [[166, "braces"]], "Parentheses": [[166, "parentheses"]], "Switch Statements": [[166, "switch-statements"]], "Line Breaks": [[166, "line-breaks"]], "Inheritance and the \u201cvirtual\u201d Keyword": [[166, "inheritance-and-the-virtual-keyword"]], "Referencing Members": [[166, "referencing-members"]], "File Naming": [[166, "file-naming"]], "Breaking Rules": [[166, "breaking-rules"]], "Translations": [[167, "translations"]], "Current Status": [[167, "current-status"]], "Credits": [[167, "credits"], [229, "credits"], [230, "credits"], [231, "credits"], [232, "credits"], [233, "credits"], [234, "credits"]], "License": [[168, "license"]], "Creative Commons Attribution-ShareAlike 4.0 International": [[168, "creative-commons-attribution-sharealike-4-0-international"]], "Using Creative Commons Public Licenses": [[168, "using-creative-commons-public-licenses"]], "Creative Commons Attribution-ShareAlike 4.0 International Public License": [[168, "creative-commons-attribution-sharealike-4-0-international-public-license"]], "Section 1 \u2013 Definitions.": [[168, "section-1-definitions"]], "Section 2 \u2013 Scope.": [[168, "section-2-scope"]], "Section 3 \u2013 License Conditions.": [[168, "section-3-license-conditions"]], "Section 4 \u2013 Sui Generis Database Rights.": [[168, "section-4-sui-generis-database-rights"]], "Section 5 \u2013 Disclaimer of Warranties and Limitation of Liability.": [[168, "section-5-disclaimer-of-warranties-and-limitation-of-liability"]], "Section 6 \u2013 Term and Termination.": [[168, "section-6-term-and-termination"]], "Section 7 \u2013 Other Terms and Conditions.": [[168, "section-7-other-terms-and-conditions"]], "Section 8 \u2013 Interpretation.": [[168, "section-8-interpretation"]], "Avogadro: Molecular Editor and Visualization": [[169, "avogadro-molecular-editor-and-visualization"], [194, "avogadro-molecular-editor-and-visualization"]], "Table of contents": [[170, "table-of-contents"]], "Making a Crystal Surface Slab": [[171, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[171, "import-the-appropriate-crystal-structure"]], "Building a Polymer Unit Cell": [[172, "building-a-polymer-unit-cell"]], "Perceiving Crystall Symmetry": [[173, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[173, "open-a-crystal-file"]], "Building Materials": [[174, "building-materials"]], "Building Molecule-Surface Interactions": [[175, "building-molecule-surface-interactions"]], "Start with a generated Crystal Surface": [[175, "start-with-a-generated-crystal-surface"]], "New Window: Create our Molecule": [[175, "new-window-create-our-molecule"]], "Reducing Crystals to a Primitive Unit Cell": [[176, "reducing-crystals-to-a-primitive-unit-cell"]], "Scaling Crystal Cell Volume": [[177, "scaling-crystal-cell-volume"]], "Building a Supercell": [[178, "building-a-supercell"]], "Creating a Surface": [[178, "creating-a-surface"]], "Building a Peptide": [[179, "building-a-peptide"]], "Building Carbon Nanotubes": [[180, "building-carbon-nanotubes"]], "Building DNA or RNA": [[181, "building-dna-or-rna"]], "Building with SMILES": [[182, "building-with-smiles"]], "Importing from the Protein Data Bank (PDB)": [[183, "importing-from-the-protein-data-bank-pdb"]], "Importing Directly": [[183, "importing-directly"]], "Reading a Downloaded PDB file": [[183, "reading-a-downloaded-pdb-file"]], "Importing Molecules by Name": [[184, "importing-molecules-by-name"]], "Building Molecules": [[185, "building-molecules"]], "Insert Molecular Fragments": [[186, "insert-molecular-fragments"]], "Coloring Part of a Molecules": [[187, "coloring-part-of-a-molecules"]], "Hemoglobin": [[187, "hemoglobin"]], "Select by Residue": [[187, "select-by-residue"]], "Select by Element": [[187, "select-by-element"]], "Different Display Styles": [[188, "different-display-styles"]], "Locating Display Types": [[188, "locating-display-types"]], "Axes": [[188, "axes"]], "Ball and Stick": [[188, "ball-and-stick"]], "Cartoon": [[188, "cartoon"]], "Dipole": [[188, "dipole"]], "Force": [[188, "force"]], "Hydrogen Bond": [[188, "hydrogen-bond"]], "Label": [[188, "label"]], "Polygon": [[188, "polygon"]], "QTAIM (Quantum Theory of Atoms in Molecules)": [[188, "qtaim-quantum-theory-of-atoms-in-molecules"], [197, "qtaim-quantum-theory-of-atoms-in-molecules"]], "Ribbon": [[188, "ribbon"]], "Ring": [[188, "ring"]], "Stick": [[188, "stick"]], "Surfaces": [[188, "surfaces"]], "Van der Waals Spheres": [[188, "van-der-waals-spheres"]], "Wireframe": [[188, "wireframe"]], "Display Types": [[189, "display-types"]], "Drawing Molecules": [[190, "drawing-molecules"]], "Creating Carbon Dioxide": [[190, "creating-carbon-dioxide"]], "Getting Started": [[191, "getting-started"], [191, null]], "Introduction": [[192, "introduction"]], "Opening a File": [[192, "opening-a-file"]], "Navigation": [[192, "navigation"]], "Making Selections": [[193, "making-selections"]], "User Guide": [[194, "user-guide"]], "Avogadro 2": [[194, "avogadro-2"]], "Build Menu": [[195, "build-menu"]], "Cartesian Editor\u2026": [[195, "cartesian-editor"]], "1. Sort by\u2026": [[195, "sort-by"]], "2. Unit of Measure": [[195, "unit-of-measure"]], "3. Editing & Modifying Data": [[195, "editing-modifying-data"]], "Change H to Methyl": [[195, "change-h-to-methyl"]], "Add Hydrogens": [[195, "add-hydrogens"]], "Add Hydrogens for pH\u2026": [[195, "add-hydrogens-for-ph"]], "Remove Hydrogens": [[195, "remove-hydrogens"]], "Insert": [[195, "insert"]], "Invert Chirality": [[195, "invert-chirality"]], "Super Cell Builder\u2026": [[195, "super-cell-builder"]], "Nanotube Builder\u2026": [[195, "nanotube-builder"]], "Edit Menu": [[196, "edit-menu"]], "Undo": [[196, "undo"]], "Redo": [[196, "redo"]], "Cut": [[196, "cut"]], "Copy": [[196, "copy"]], "Copy As": [[196, "copy-as"]], "Paste": [[196, "paste"]], "Clear": [[196, "clear"]], "Select All": [[196, "select-all"], [200, "select-all"]], "Select None": [[196, "select-none"], [200, "select-none"]], "Extension Menu": [[197, "extension-menu"]], "Animation": [[197, "animation"]], "Optimize Geometry": [[197, "optimize-geometry"]], "Molecular Mechanics": [[197, "molecular-mechanics"]], "Setup Force Field\u2026": [[197, "setup-force-field"]], "Calculate Energy": [[197, "calculate-energy"]], "Conformer Search": [[197, "conformer-search"]], "Constraints": [[197, "constraints"], [203, "constraints"]], "Ignore Selection": [[197, "ignore-selection"]], "Fix Selected Atoms": [[197, "fix-selected-atoms"]], "Avogadro Extensions\u2013Plugins": [[197, "avogadro-extensionsplugins"]], "General \u201cHow To\u201d for Plugins": [[197, "general-how-to-for-plugins"]], "Running Gaussian": [[197, "running-gaussian"]], "Molecular Orbitals": [[197, "molecular-orbitals"]], "Spectra\u2026": [[197, "spectra"]], "Create Surfaces\u2026": [[197, "create-surfaces"]], "File Menu": [[198, "file-menu"]], "New": [[198, "new"]], "Open": [[198, "open"]], "Open Recent": [[198, "open-recent"]], "Close": [[198, "close"]], "Save": [[198, "save"]], "Save As\u2026": [[198, "save-as"]], "Revert to Saved": [[198, "revert-to-saved"]], "Import": [[198, "import"]], "Export": [[198, "export"]], "Menus": [[199, "menus"], [199, null]], "Select Menu": [[200, "select-menu"]], "Invert Selection": [[200, "invert-selection"]], "Select SMARTS\u2026": [[200, "select-smarts"]], "Select by Element\u2026": [[200, "select-by-element"]], "Select by Residue\u2026": [[200, "select-by-residue"]], "Select Solvent": [[200, "select-solvent"]], "Add Name Selection\u2026": [[200, "add-name-selection"]], "View Menu": [[201, "view-menu"]], "New View": [[201, "new-view"]], "Duplicate View": [[201, "duplicate-view"]], "Detach View": [[201, "detach-view"]], "Close View": [[201, "close-view"]], "Center": [[201, "center"]], "Align View to Axes": [[201, "align-view-to-axes"]], "Full Screen": [[201, "full-screen"]], "Reset Display Types": [[201, "reset-display-types"]], "Set Background Color\u2026": [[201, "set-background-color"]], "Projection": [[201, "projection"]], "Display Axes": [[201, "display-axes"]], "Debug Information": [[201, "debug-information"]], "Use Quick Render": [[201, "use-quick-render"]], "All Molecules in File\u2026": [[201, "all-molecules-in-file"]], "Crystal View Options\u2026": [[201, "crystal-view-options"]], "Properties": [[201, "properties"]], "Finding Conformers of Molecules": [[202, "finding-conformers-of-molecules"]], "Start with your molecule of interest": [[202, "start-with-your-molecule-of-interest"]], "Optimize the geometry": [[202, "optimize-the-geometry"]], "Change the force field options": [[202, "change-the-force-field-options"]], "Set the conformer search options": [[202, "set-the-conformer-search-options"]], "Pick a search method and start the search": [[202, "pick-a-search-method-and-start-the-search"]], "Geometry Constraints": [[203, "geometry-constraints"]], "Example": [[203, "example"]], "Optimizations": [[203, "optimizations"]], "Example cont.": [[203, "example-cont"]], "Optimizing Geometry": [[204, "optimizing-geometry"]], "Introduction to Molecular Mechanics": [[205, "introduction-to-molecular-mechanics"]], "UFF": [[205, "uff"]], "MMFF94(s)": [[205, "mmff94-s"]], "GAFF": [[205, "gaff"]], "Align Tool": [[206, "align-tool"]], "Auto-Optimize Tool": [[207, "auto-optimize-tool"]], "Force Fields & Algorithms": [[207, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[207, "fixing-ignoring-selections"]], "Auto-Rotate Tool": [[208, "auto-rotate-tool"]], "Bond-Centric Manipulate Tool": [[209, "bond-centric-manipulate-tool"]], "Starting with the basics:": [[209, "starting-with-the-basics"]], "Adjusting Bonds and Torsion Angles": [[209, "adjusting-bonds-and-torsion-angles"]], "Draw Tool": [[210, "draw-tool"]], "1. Creating a Molecule": [[210, "creating-a-molecule"]], "2.": [[210, "id1"]], "3.": [[210, "id2"]], "4.": [[210, "id3"]], "5.": [[210, "id4"]], "6.": [[210, "id5"]], "7.": [[210, "id6"]], "8.": [[210, "id7"]], "9.": [[210, "id8"]], "Tools": [[211, "tools"]], "Manipulate Tool": [[212, "manipulate-tool"]], "Measure Tool": [[213, "measure-tool"]], "Navigate Tool": [[214, "navigate-tool"]], "Selection Tool": [[215, "selection-tool"]], "Tutorials": [[216, "tutorials"], [216, null]], "Naming a Molecule": [[217, "naming-a-molecule"]], "Using QTAIM (Atoms in Molecules) Analysis": [[218, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[218, "start-with-a-wfn-file"]], "Viewing Electrostatic Potential Maps": [[219, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[219, "changing-surface-settings"]], "Viewing Molecular Orbitals": [[220, "viewing-molecular-orbitals"]], "Configure": [[220, "configure"]], "Viewing Vibrations": [[221, "viewing-vibrations"]], "What\u2019s New in Avogadro 2": [[222, "whats-new-in-avogadro-2"]], "Interface Changes": [[223, "interface-changes"]], "Major New Features": [[224, "major-new-features"]], "Speed and Stability": [[224, "speed-and-stability"]], "Rendering": [[224, "rendering"]], "New real-time shadows and depth effects": [[224, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[224, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[224, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[224, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[224, "layers"]], "Symmetry Properties": [[224, "symmetry-properties"]], "Template Tool": [[224, "template-tool"]], "Solvent Accessible and Solvent Excluded Surfaces": [[224, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[224, "flexible-electrostatics-models"]], "New Analysis Tools": [[224, "new-analysis-tools"]], "Python Commands / Plugins": [[224, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[224, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[224, "new-and-updated-interfaces-to-external-programs"]], "Install": [[225, "install"], [227, "install"]], "Features": [[225, "features"], [229, "features"]], "Resources": [[225, "resources"]], "Connecting with the Avogadro community": [[225, "connecting-with-the-avogadro-community"]], "Building Source Code": [[226, "building-source-code"]], "Cloning Repositories": [[226, "cloning-repositories"]], "Updating": [[226, "updating"]], "Prerequisites": [[226, "prerequisites"]], "Building": [[226, "building"]], "Finding Qt, Windows Generators": [[226, "finding-qt-windows-generators"]], "Normal Development": [[226, "normal-development"]], "Build Tree Layout": [[226, "build-tree-layout"]], "Running Executables": [[226, "running-executables"]], "Building Packages": [[226, "building-packages"]], "Version History": [[228, "version-history"], [228, null]], "Release Notes v1.94.0": [[229, "release-notes-v1-94-0"]], "\ud83d\udc1b Bug Fixes": [[229, "bug-fixes"], [230, "bug-fixes"], [231, "bug-fixes"], [232, "bug-fixes"], [233, "bug-fixes"], [234, "bug-fixes"]], "\ud83d\udc0d Python Improvements": [[229, "python-improvements"]], "\ud83e\uddf0 Maintenance": [[229, "maintenance"], [230, "maintenance"], [231, "maintenance"], [232, "maintenance"], [233, "maintenance"], [234, "maintenance"]], "Release Notes v1.95.0": [[230, "release-notes-v1-95-0"]], "Changes": [[230, "changes"], [232, "changes"]], "\u2728 Features": [[230, "features"], [231, "features"], [232, "features"], [233, "features"], [234, "features"]], "\ud83d\udcda Translations": [[230, "translations"], [231, "translations"], [232, "translations"], [233, "translations"], [234, "translations"]], "Release Notes v1.95.1": [[231, "release-notes-v1-95-1"]], "Release Notes v1.96.0": [[232, "release-notes-v1-96-0"]], "\ud83d\ude80 Performance Fixes": [[232, "performance-fixes"]], "Release Notes v1.97.0": [[233, "release-notes-v1-97-0"]], "Highlights (tldr)": [[233, "highlights-tldr"], [234, "highlights-tldr"]], "\ud83d\ude80 Performance Improvements": [[233, "performance-improvements"], [234, "performance-improvements"]], "Release Notes v1.98.0": [[234, "release-notes-v1-98-0"]], "Charges / Electrostatics": [[235, "charges-electrostatics"]], "Identify the Script with --metadata": [[235, "identify-the-script-with-metadata"], [237, "identify-the-script-with-metadata"]], "Calculating Atomic Partial Charges with --charge": [[235, "calculating-atomic-partial-charges-with-charge"]], "Generating Electrostatic Potentials with --potential": [[235, "generating-electrostatic-potentials-with-potential"]], "Command Scripts": [[236, "command-scripts"]], "Script Entry Points": [[236, "script-entry-points"], [241, "script-entry-points"]], "Specifying UI options with \u2013print-options": [[236, "specifying-ui-options-with-print-options"]], "Returning Data": [[236, "returning-data"]], "Returning Data in a Specific File Format": [[236, "returning-data-in-a-specific-file-format"]], "Appending New Atoms and Bonds": [[236, "appending-new-atoms-and-bonds"]], "Bonding New Atoms": [[236, "bonding-new-atoms"]], "Selected Atoms": [[236, "selected-atoms"]], "Debugging": [[236, "debugging"], [241, "debugging"]], "Energy / Force Fields": [[237, "energy-force-fields"]], "Calculating Energies and Gradients": [[237, "calculating-energies-and-gradients"]], "Unit Cells, Total Charge, and Spin Multiplicity": [[237, "unit-cells-total-charge-and-spin-multiplicity"]], "Lattice Vectors and Fractional Coordinates": [[237, "lattice-vectors-and-fractional-coordinates"]], "Example Plugin Script - Part 1": [[238, "example-plugin-script-part-1"]], "The Main function:": [[238, "the-main-function"]], "Input Arguments": [[238, "input-arguments"]], "getOptions() Function": [[238, "getoptions-function"]], "Example Plugin Script - Part 2": [[239, "example-plugin-script-part-2"]], "Providing Input to Run Command": [[239, "providing-input-to-run-command"]], "runCommand() Function": [[239, "runcommand-function"]], "Operation Function": [[239, "operation-function"]], "Retrieving necessary components": [[239, "retrieving-necessary-components"]], "Support for Selection": [[239, "support-for-selection"]], "Sample Input and Output": [[239, "sample-input-and-output"]], "File Formats": [[240, "file-formats"]], "Identify the Format with --metadata": [[240, "identify-the-format-with-metadata"]], "Reading a format with --read": [[240, "reading-a-format-with-read"]], "Writing a format with --write": [[240, "writing-a-format-with-write"]], "Input Generators": [[241, "input-generators"]], "Specifying parameters with --print-options": [[241, "specifying-parameters-with-print-options"]], "Special Parameters": [[241, "special-parameters"]], "Syntax Highlighting": [[241, "syntax-highlighting"]], "Requesting Full Structure of Current Molecule": [[241, "requesting-full-structure-of-current-molecule"]], "Handling User Selections: --generate-input": [[241, "handling-user-selections-generate-input"]], "Automatic Generation of Geometry": [[241, "automatic-generation-of-geometry"]], "Coordinate Blocks": [[241, "coordinate-blocks"]], "Error Handling": [[241, "error-handling"]], "Script Plugins": [[242, "script-plugins"]], "Installing Script Plugins": [[243, "installing-script-plugins"]], "Directories": [[243, "directories"]], "Plugin Packages and Repositories": [[243, "plugin-packages-and-repositories"]], "Script Interfaces": [[244, "script-interfaces"]], "Fixed String Lists (Pop-up menus)": [[244, "fixed-string-lists-pop-up-menus"]], "Short Free-Form Text Parameters": [[244, "short-free-form-text-parameters"]], "Existing files": 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"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", "scripts/charges.md", "scripts/commands.md", "scripts/energy.md", "scripts/example1.md", "scripts/example2.md", "scripts/formats.md", "scripts/generators.md", "scripts/index.md", "scripts/install.md", "scripts/interface.md"], "titles": ["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&lt; char &gt;", "Class Avogadro::TypeTraits&lt; double &gt;", "Class Avogadro::TypeTraits&lt; float &gt;", "Class Avogadro::TypeTraits&lt; int &gt;", "Class Avogadro::TypeTraits&lt; short &gt;", "Class Avogadro::TypeTraits&lt; unsigned char &gt;", "Class Avogadro::TypeTraits&lt; unsigned int &gt;", "Class Avogadro::TypeTraits&lt; unsigned short &gt;", "Class Avogadro::VTK::VtkPlot", "Class Avogadro::VTK::vtkGLWidget", "Class vtkAvogadroActor", "Class list", "Core Classes", "Develop", "IO Classes", "MoleQueue Classes", "QtGui Classes", "Rendering Classes", "Avogadro Remote Procedure Call (RPC)", "VTK Classes", "Contributing Code", "Documenting Code", "Coding Conventions (C++)", "Thanks", "Contribute", "Coding Style (C++)", "Translations", "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", "Optimizing Geometry", "Introduction to Molecular Mechanics", "Align Tool", "Auto-Optimize Tool", "Auto-Rotate Tool", "Bond-Centric Manipulate Tool", "Draw Tool", "Tools", "Manipulate Tool", "Measure Tool", "Navigate Tool", "Selection Tool", "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", "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"], "terms": {"core": [152, 154, 162, 163, 164, 222, 232, 241], "avogadro": [152, 153, 154, 155, 156, 157, 158, 160, 161, 163, 164, 165, 167, 170, 171, 172, 175, 176, 177, 179, 180, 181, 182, 183, 184, 186, 188, 190, 192, 193, 195, 198, 199, 203, 205, 207, 210, 213, 217, 218, 219, 221, 223, 224, 226, 227, 229, 230, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244], "arrai": [152, 153, 235, 237, 240, 241, 244], "arrayset": [152, 153], "holder": [152, 153, 168], "placehold": [152, 153], "atom": [152, 153, 154, 170, 171, 172, 173, 175, 178, 187, 190, 193, 195, 199, 200, 201, 202, 203, 206, 207, 208, 209, 210, 212, 213, 214, 215, 217, 219, 221, 222, 224, 229, 230, 232, 233, 234, 237, 238, 239, 241], "atomtempl": [152, 153], "atomtyp": [152, 153], "avospglib": [152, 153], "basisset": [152, 153], "bond": [152, 153, 154, 170, 172, 178, 180, 190, 193, 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203, 207, 210, 218, 219, 224, 225, 229, 232, 233, 234, 235, 236, 237, 240, 241], "mani": [154, 164, 194, 197, 209, 212, 222, 223, 224, 229, 230, 231, 232, 233, 234, 235], "exampl": [154, 162, 165, 168, 172, 173, 178, 188, 192, 196, 197, 200, 201, 209, 213, 219, 224, 226, 229, 233, 235, 236, 237, 240, 241], "found": [154, 188, 193, 194, 195, 196, 197, 200, 215, 217, 220, 225, 226, 229, 230, 231, 232, 233, 238, 241], "qtplugin": 154, "subdirectori": [154, 226, 243], "handl": [155, 156, 157, 224, 229, 234, 235, 236, 237, 240], "": [155, 159, 163, 168, 170, 173, 180, 190, 195, 197, 201, 203, 206, 207, 208, 209, 210, 214, 218, 219, 224, 226, 229, 234, 236, 237, 238, 240, 241], "nativ": [155, 229], "input": [155, 162, 170, 172, 182, 197, 224, 229, 230, 231, 233, 234, 235, 236, 237, 240, 242, 243, 244], "output": [155, 156, 196, 203, 205, 218, 220, 221, 233, 234, 235, 236, 237, 240, 241], "beyond": [155, 175, 237], "babel": [155, 164, 192, 224, 229, 232, 233, 237], "load": [155, 159, 197, 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233, 241], "program": [156, 159, 164, 172, 178, 198, 222, 232, 235, 236, 241], "complet": [156, 162, 175, 235, 236, 243], "basic": [157, 159, 190, 196, 233], "oper": [157, 166, 172, 236, 238, 240], "gui": [157, 226, 236, 241, 244], "qt": [157, 161, 162, 164, 166, 229, 233, 234], "object": [157, 187, 203, 229, 235, 236, 237, 240, 241], "most": [157, 163, 168, 194, 195, 197, 201, 205, 207, 218, 219, 224, 226, 236, 241], "through": [157, 164, 165, 166, 167, 168, 171, 172, 176, 177, 178, 181, 182, 187, 188, 190, 192, 197, 198, 200, 207, 210, 218, 224, 226, 229, 234, 237, 239, 242, 243], "2": [159, 162, 166, 170, 172, 175, 180, 183, 190, 199, 202, 213, 223, 224, 225, 226, 229, 232, 233, 237, 241, 244], "commun": [159, 164, 165, 168], "between": [159, 166, 171, 172, 188, 197, 203, 207, 213, 234, 239, 240], "standard": [159, 168, 188, 198, 230, 234, 235, 236, 237, 239, 240, 241], "messag": [159, 229, 233, 234, 241], "e": [159, 163, 166, 168, 171, 175, 180, 182, 183, 190, 202, 210, 217, 221, 222, 224, 226, 229, 230, 233, 234, 235, 236, 237, 240, 241, 243, 244], "0": [159, 162, 166, 169, 172, 175, 183, 194, 207, 222, 224, 227, 228, 231, 235, 237, 239, 241, 243, 244], "xtalopt": 159, "socket": 159, "connect": [159, 162, 168, 217, 218, 233, 239], "server": [159, 162, 165, 217], "send": [159, 165, 229, 241], "g": [159, 166, 168, 171, 180, 182, 183, 190, 202, 210, 217, 221, 224, 226, 229, 234, 235, 236, 237, 240, 241, 243, 244], "data": [159, 166, 170, 196, 199, 200, 218, 224, 229, 235, 239, 240], "As": [159, 166, 167, 179, 188, 199, 206, 213, 217, 226, 229, 232, 236], "part": [159, 161, 168, 170, 197, 223, 224, 229, 230, 232, 233, 236, 241], "syntax": [159, 244], "so": [159, 164, 168, 173, 180, 186, 187, 188, 197, 207, 226, 239, 241, 243], "jsonrpc": 159, "id": [159, 163, 226, 230], "idnum": 159, "uniqu": [159, 235, 237, 240, 241], "number": [159, 164, 166, 175, 181, 188, 190, 192, 195, 197, 202, 203, 207, 210, 226, 235, 237, 239, 241, 243, 244], "32768": 159, "particular": 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163, 164, 165, 166, 167, 172, 173, 175, 176, 177, 180, 181, 187, 202, 203, 218, 223, 224, 225, 226, 229, 230, 232, 233, 236, 237, 239], "recommend": [161, 226, 231, 241], "understand": [161, 168], "github": [161, 165, 167, 224, 226, 229, 232, 233, 234, 242, 243], "flow": 161, "fork": 161, "repositori": [161, 165, 234, 242], "make": [161, 162, 163, 165, 166, 168, 170, 172, 175, 178, 186, 187, 191, 198, 200, 202, 222, 224, 225, 226, 229, 230, 231, 232, 233, 234, 235, 237, 239], "chang": [161, 168, 170, 172, 177, 190, 194, 196, 198, 199, 201, 206, 209, 210, 214, 224, 226, 228, 234, 239], "git": [161, 226], "version": [161, 168, 175, 183, 194, 207, 224, 226, 233, 234, 243], "control": [161, 175, 181, 192, 226, 238], "financi": [161, 164, 165], "pull": [161, 163, 226, 232, 233, 243], "other": [161, 163, 166, 172, 180, 187, 197, 198, 203, 207, 217, 218, 219, 224, 225, 226, 233, 235, 236, 241], "review": [161, 203], "test": [161, 202, 226, 231, 232, 239], "merg": [161, 167], "main": [161, 179, 241, 243], "have": [161, 162, 165, 166, 168, 172, 175, 182, 183, 187, 197, 201, 203, 207, 213, 220, 222, 223, 226, 229, 230, 232, 233, 239, 241, 244], "sever": [161, 165, 166, 168, 180, 192, 207, 224, 226, 229, 230, 231, 233, 234, 241], "suggest": [161, 165, 222, 225, 229, 230, 232, 233, 236, 242, 243], "far": 161, "style": [161, 162, 163, 170, 194, 241], "convent": [161, 166], "well": [161, 168, 180, 181, 197, 198, 203, 205, 224, 226, 232, 236, 243], "document": [161, 163, 165, 175, 196, 198, 225, 229, 230, 232, 233, 240, 241], "your": [161, 162, 165, 166, 168, 177, 178, 182, 183, 186, 190, 192, 193, 195, 197, 198, 200, 201, 203, 206, 207, 209, 210, 212, 215, 217, 219, 224, 225, 226, 233, 237, 243], "comment": [161, 166, 229, 230, 232, 233, 241], "doxygen": [161, 162], "api": [161, 162, 225], "doc": [161, 229, 239], "which": [161, 165, 168, 172, 175, 176, 177, 192, 200, 217, 218, 224, 226, 230, 234, 235, 236, 237, 238, 239, 240, 241, 243, 244], "ultim": 161, "becom": 161, "websit": [161, 180, 182, 183, 197, 232, 233], "featur": [161, 165, 167, 170, 171, 175, 187, 188, 193, 194, 195, 196, 197, 200, 201, 205, 207, 220, 221, 222, 228], "header": [161, 162, 166, 229, 233], "export": [161, 178, 199, 229, 234], "macro": 161, "privat": [161, 230], "cast": [161, 164, 166, 207, 232], "aesthet": 161, "indent": 161, "line": [161, 172, 182, 209, 224, 233, 234, 235, 236, 237, 238, 239, 240, 241], "width": [161, 233], "declar": [161, 162, 163, 234, 237], "variabl": [161, 203, 226, 238], "whitespac": 161, "brace": 161, "parenthes": 161, "switch": [161, 172, 175, 192, 202, 229, 233, 234], "statement": 161, "break": [161, 239], "inherit": 161, "virtual": 161, "keyword": [161, 197, 221, 241], "referenc": 161, "name": [161, 162, 163, 168, 170, 171, 187, 199, 203, 216, 226, 233, 234, 235, 236, 237, 238, 239, 240, 241, 243, 244], "class": [161, 163, 166, 224, 230, 234, 241], "descript": [161, 165, 232, 235, 237, 240, 241, 243], "javadoc": 162, "thei": [162, 163, 165, 167, 168, 175, 179, 205, 207, 226, 241, 243, 244], "go": [162, 166, 181, 183, 187, 203, 207, 212, 226], "next": [162, 172, 187, 202, 219, 222, 224, 237, 244], "should": [162, 163, 166, 168, 172, 192, 195, 202, 226, 230, 234, 235, 236, 237, 240, 241, 243, 244], "minimum": [162, 168, 202, 234, 244], "brief": [162, 243], "one": [162, 163, 166, 168, 171, 172, 180, 181, 182, 188, 192, 197, 201, 203, 209, 224, 234, 236, 241], "sentenc": 162, "explain": 162, "what": [162, 170, 187, 197, 201, 214], "intend": [162, 168, 240], "purpos": [162, 163, 166, 168, 197, 235], "goe": [162, 166, 226, 241], "void": [162, 166], "dosometh": [162, 166], "overview": [162, 166], "add": [162, 167, 172, 177, 178, 197, 199, 201, 203, 205, 215, 224, 226, 229, 230, 231, 232, 233, 234, 243, 244], "appropri": [162, 166, 192, 226, 232, 236, 238, 241, 244], "point": [162, 166, 175, 195, 201, 206, 218, 226, 233, 234, 235, 238], "out": [162, 168, 172, 173, 192, 194, 203, 205, 208, 214, 223, 234, 244], "altern": [162, 237], 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[162, 163], "order": [162, 188, 190, 210, 213, 218, 226, 230, 234, 235, 236, 239, 241, 244], "act": [162, 226, 239], "notif": 162, "error": [162, 168, 232, 233, 234], "receiv": [162, 168], "respons": [162, 164, 234, 238, 239], "public": [162, 163, 166, 230], "qobject": 162, "end": [162, 163, 166, 172, 175, 187, 208, 209], "constructor": 162, "more": [162, 163, 166, 168, 180, 187, 188, 193, 194, 197, 200, 201, 203, 205, 207, 219, 224, 225, 229, 230, 233, 234, 236, 240, 241, 242, 243], "construct": [162, 192, 195], "describ": [162, 168, 235, 237, 240, 241], "paramet": [162, 178, 197, 203, 205, 207, 220, 233, 236, 237], "job": [162, 241], "appear": [162, 171, 178, 197, 241, 243], "work": [162, 164, 165, 167, 168, 172, 180, 183, 194, 197, 200, 203, 224, 225, 226, 233, 234, 236], "specifi": [162, 168, 171, 173, 175, 176, 200, 235, 237, 238, 239, 240, 244], "return": [162, 166, 195, 217, 235, 238, 239], "true": [162, 166, 235, 236, 237, 238, 239, 244], "wa": [162, 176, 178, 187, 192, 194, 219, 222, 224, 230, 241], "successfulli": [162, 226, 233], "fals": [162, 166, 235, 237, 239, 241], "otherwis": [162, 168, 202, 217, 240, 241], "bool": 162, "setinputfil": 162, "const": [162, 163, 166], "qstring": [162, 163], "don": [163, 166, 207, 230, 234], "t": [163, 166, 168, 173, 175, 183, 187, 197, 207, 230, 231, 234], "except": [163, 166, 168, 234, 235, 237], "assert": [163, 168], "product": [163, 187], "never": [163, 168, 237], "crash": [163, 222, 224, 230, 232, 233, 234, 236, 241], "prefer": [163, 182, 195, 197, 202, 233, 235, 239, 241], "solut": 163, "librari": [154, 163, 165, 171, 226, 230, 234, 243], "over": [163, 172, 176, 182, 183, 186, 207, 217, 222, 229, 230], "boost": [163, 226], "depend": [163, 164, 171, 188, 197, 207, 226, 229, 239], "In": [163, 167, 168, 172, 175, 190, 194, 210, 218, 226, 227, 236, 239, 241], "11": [163, 168, 172, 226], "17": 163, "necessari": [163, 166, 168, 201, 207], "offer": [163, 164, 168, 194, 225, 241], "avo_overrid": 163, "avo_fin": 163, 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218, 224, 226, 231, 232, 233, 234, 235, 236, 237, 239, 240, 241], "specif": [163, 172, 187, 197, 200, 203, 205, 206, 207, 208, 219, 229, 234, 239, 240, 241], "symbol": [163, 190, 210, 232, 241], "avoid": [163, 166, 168, 226, 233, 234], "static_cast": 163, "dynamic_cast": 163, "const_cast": 163, "reinterpret_cast": [163, 166], "For": [163, 165, 166, 168, 172, 178, 181, 188, 194, 196, 197, 200, 201, 203, 207, 209, 212, 213, 226, 235, 237, 238, 239, 240, 241, 244], "deriv": [163, 168, 218], "qobject_cast": 163, "enum": 163, "constant": [163, 197], "static": [163, 205], "verbos": 163, "argument": [163, 226, 235, 236, 237, 239, 240, 241], "show": [163, 171, 175, 177, 180, 181, 192, 197, 209, 217, 218, 224, 233], "autocomplet": 163, "It": [163, 184, 192, 194, 198, 222, 224, 225, 226, 236, 238, 239, 241], "look": [163, 166, 173, 192, 201, 224, 226, 239, 243], "better": [163, 165, 194, 202, 207, 224, 225, 234], "poor": 163, "peopl": [163, 194], "guess": 163, "abbrevi": [163, 166], "ambigu": 163, "afford": 163, "few": [163, 180, 184, 222, 224, 234, 243], "extra": [163, 172, 236, 241], "byte": 163, "fundament": 164, "aim": [164, 218], "contributor": [164, 222, 229, 230, 231, 232, 233, 234], "alik": [164, 169], "hope": 164, "build": [164, 170, 171, 186, 199, 205, 217, 222, 224, 225, 227, 229, 230, 232, 233, 234, 236, 238], "top": [164, 188, 212, 226, 232], "framework": [164, 224, 233, 234], "veri": [164, 165, 173, 192, 230, 232, 233], "grate": 164, "shahzad": 164, "ali": 164, "michael": 164, "banck": 164, "ross": 164, "braithwait": 164, "jame": 164, "bunt": 164, "donald": 164, "curti": 164, "naomi": 164, "fox": 164, "geoff": 164, "hutchison": [164, 194, 243], "beno\u00eet": 164, "jacob": 164, "jordan": 164, "mantha": 164, "thoma": [164, 229], "margraf": 164, "carsten": 164, "niehau": 164, "simon": 164, "ochsenreith": 164, "konstantin": 164, "tokarev": 164, "allison": 164, "vacanti": 164, "tim": 164, "vandermeersch": 164, "ha": [164, 165, 168, 175, 177, 178, 181, 183, 187, 188, 190, 192, 195, 197, 198, 205, 207, 209, 210, 219, 221, 224, 226, 229, 234, 239], "come": [164, 183, 188, 205, 209, 225], "would": [164, 180, 192, 194, 222, 224, 225, 226], "particularli": [164, 205, 222, 223, 230, 232, 233], "googl": [164, 230, 232, 233], "summer": [164, 194, 229, 230, 232, 233], "2007": 164, "2008": 164, "2011": 164, "2016": 164, "2018": 164, "2019": [164, 232], "2021": [164, 229, 230, 231], "2022": [164, 194, 232, 233], "kitwar": 164, "inc": 164, "univers": [164, 194, 205, 207], "pittsburgh": [164, 194], "u": [164, 165, 175, 180, 225, 229, 230, 232, 233], "depart": [164, 194], "defens": 164, "dod": 164, "pettt": 164, "research": [164, 180, 225], "corpor": [164, 168], "cottrel": 164, "scholar": 164, "award": 164, "reli": 164, "infrastructur": 164, "blue": [164, 187, 188, 206, 209, 219, 224], "obelisk": 164, "group": [164, 166, 173, 175, 176, 177, 178, 180, 195, 200, 218, 223, 224, 232, 234, 241], "pybind11": 164, "structur": [164, 173, 179, 180, 184, 186, 188, 190, 196, 201, 205, 207, 210, 224, 229, 230, 232, 238, 239], "databas": [164, 165, 179, 186, 198, 217, 242], "cmake": [164, 226, 234], "eigen": [164, 166, 226], "softwar": [164, 197, 218], "And": [164, 235], "cours": [164, 179], "johann": 164, "loschmidt": 164, "amedeo": 164, "made": [165, 167, 168, 169, 186, 187, 188, 192, 193, 198, 200, 201, 205, 215, 229], "who": 165, "want": [165, 175, 179, 180, 187, 190, 192, 202, 203, 210, 212, 218, 219, 225, 236], "back": [165, 195, 201, 229, 230, 232], "great": [165, 225, 226], "place": [165, 166, 168, 173, 188, 196, 197, 201, 207, 212, 214, 225, 226, 239, 241], "start": [165, 166, 170, 171, 172, 179, 180, 195, 207, 208, 221, 225, 230, 234], "fellow": 165, "forum": [165, 167], "question": [165, 225], "level": [165, 226, 241], "post": [165, 203], "mai": [165, 168, 171, 173, 175, 179, 180, 181, 184, 194, 202, 207, 217, 218, 220, 222, 226, 235, 236, 239, 241, 243, 244], "find": [165, 170, 192, 220, 224, 225, 233, 238, 239], "experi": 165, "valuabl": 165, "bug": [165, 167, 183, 225, 228], "pleas": [165, 167, 225, 229, 230, 232, 233], "take": [165, 171, 184, 188, 197, 201, 207, 212, 214, 220, 239], "moment": [165, 180, 220], "tracker": [165, 225], "issu": [165, 167, 225, 229, 234], "code": [165, 167, 173, 180, 181, 183, 197, 220, 221, 224, 225, 227, 229, 230, 232, 233, 234, 235, 237, 238, 239, 241], "while": [165, 166, 172, 177, 203, 207, 217, 233, 236, 237, 241], "move": [165, 168, 175, 183, 186, 192, 207, 212, 224, 234], "around": [165, 166, 175, 177, 180, 186, 188, 192, 203, 212, 224], "fit": [165, 166, 168], "itself": 165, "section": [165, 188, 193, 194, 195, 197, 203, 207, 212, 224, 241, 243], "discuss": [165, 167, 197, 225, 229, 230, 232, 233, 236], "idea": [165, 225], "plan": 165, "direct": [165, 168, 183, 208, 226, 232, 241], "progress": [165, 198], "util": [165, 178, 188, 197, 243], "friend": 165, "cite": 165, "paper": [165, 182, 225], "write": [165, 166, 232, 233, 234, 237, 238, 241], "tutori": [165, 170, 171, 188, 197, 224, 225], "site": [165, 224, 225], "lesson": [165, 175], "activ": [165, 224, 226], "teacher": 165, "fragment": [165, 170, 182, 193, 195, 212, 215, 224, 229, 234], "report": [165, 167, 173, 225, 230, 231, 232, 233, 241], "encount": [165, 167], "about": [165, 187, 194, 197, 201, 203, 214, 225, 232, 233, 241], "improv": [165, 167, 222, 224, 228, 231], "languag": [165, 200, 225, 233, 235, 236, 237, 238, 241], "donat": 165, "pai": [165, 194], "host": [165, 232, 233, 234], "meet": 165, "bounti": 165, "when": [166, 177, 178, 187, 188, 192, 193, 195, 197, 201, 202, 212, 220, 226, 230, 233, 234, 236, 237, 238, 239, 241, 243], "larg": [166, 171, 175, 176, 179, 180, 192, 224, 226], "kde": 166, "enforc": [166, 168], "clang": [166, 233], "tool": [166, 170, 172, 175, 179, 180, 186, 188, 190, 192, 193, 194, 203, 222, 225, 229, 231, 232, 234], "space": [166, 171, 173, 175, 176, 177, 178, 201, 232, 234, 237, 241], "tab": [166, 201, 230, 233], "keep": [166, 203, 226], "less": [166, 197, 219, 224], "80": 166, "charact": [166, 236, 241], "wide": [166, 194, 197, 224], "separ": [166, 168, 218, 223, 236, 241], "nmbr": 166, "singl": [166, 180, 181, 187, 193, 215, 233, 241], "fine": [166, 241], "counter": 166, "temporari": [166, 237], "obviou": 166, "wait": 166, "until": [166, 195, 207], "unus": 166, "ones": 166, "incorrect": [166, 230, 233, 234], "f": [166, 168, 205, 230, 237], "lower": [166, 201], "letter": [166, 181, 232], "word": 166, "acronym": 166, "cntr": 166, "std": 166, "rawxml": 166, "list_delimit": 166, "center": [166, 175, 179, 180, 181, 187, 188, 199, 215, 224, 230, 234], "listdelimit": 166, "upper": 166, "m_": 166, "blank": [166, 201, 244], "togeth": [166, 243], "after": [166, 171, 175, 176, 177, 178, 180, 184, 186, 187, 190, 195, 197, 198, 203, 210, 212, 219, 221, 229, 236, 237, 244], "curli": 166, "blah": [166, 244], "explod": 166, "5": [166, 175, 226, 233, 234, 244], "pointer": 166, "refer": [166, 168, 203, 206, 207, 231, 238], "x": [166, 172, 188, 195, 197, 201, 206, 208, 224, 234, 237, 240, 241], "mystr": 166, "y": [166, 188, 195, 197, 201, 206, 208, 237, 241], "whoah": 166, "surround": [166, 219], "binari": [166, 226, 233], "No": [166, 168, 233, 235], "memoryblock": 166, "malloc": 166, "size": [166, 171, 172, 188, 201, 229, 234], "left": [166, 190, 192, 193, 195, 201, 206, 207, 209, 210, 215, 226, 241], "normal": [166, 177, 192, 241], "same": [166, 168, 187, 201, 205, 226, 235], "foo": 166, "run": [166, 192, 199, 221, 224, 231, 233, 235, 236, 237, 238, 240, 243], "myfun": 166, "cout": 166, "suppli": [166, 168, 192, 235, 236, 237], "endl": 166, "bar": [166, 197, 201, 212, 214, 220], "bodi": 166, "condit": [166, 180], "complex": [166, 224, 234], "42": 166, "var": [166, 238], "parent": 166, "doe": [166, 168, 176, 197, 205, 212, 235, 236, 237], "wrap": 166, "isvalid": 166, "agooddai": 166, "els": 166, "block": [166, 236, 244], "cover": [166, 194, 217, 236], "b": [166, 168, 181, 232, 234, 237, 241], "empti": [166, 177, 229, 236], "express": [166, 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Avogadro::Core::ArraySet": [[1, "class-avogadro-core-arrayset"]], "Class Avogadro::Core::ArraySet::Holder": [[2, "class-avogadro-core-arrayset-holder"]], "Class Avogadro::Core::ArraySet::PlaceHolder": [[3, "class-avogadro-core-arrayset-placeholder"]], "Class Avogadro::Core::Atom": [[4, "class-avogadro-core-atom"]], "Class Avogadro::Core::AtomTemplate": [[5, "class-avogadro-core-atomtemplate"]], "Class Avogadro::Core::AtomTyper": [[6, "class-avogadro-core-atomtyper"]], "Class Avogadro::Core::AvoSpglib": [[7, "class-avogadro-core-avospglib"]], "Class Avogadro::Core::BasisSet": [[8, "class-avogadro-core-basisset"]], "Class Avogadro::Core::Bond": [[9, "class-avogadro-core-bond"]], "Class Avogadro::Core::BondTemplate": [[10, "class-avogadro-core-bondtemplate"]], "Class Avogadro::Core::Color3f": [[11, "class-avogadro-core-color3f"]], "Class Avogadro::Core::CoordinateBlockGenerator": [[12, "class-avogadro-core-coordinateblockgenerator"]], "Class Avogadro::Core::CoordinateSet": [[13, "class-avogadro-core-coordinateset"]], "Class Avogadro::Core::CrystalTools": [[14, "class-avogadro-core-crystaltools"]], "Class Avogadro::Core::Cube": [[15, "class-avogadro-core-cube"]], "Class Avogadro::Core::Elements": [[16, "class-avogadro-core-elements"]], "Class Avogadro::Core::GaussianSet": [[17, "class-avogadro-core-gaussianset"]], "Class Avogadro::Core::GaussianSetTools": [[18, "class-avogadro-core-gaussiansettools"]], "Class Avogadro::Core::Graph": [[19, "class-avogadro-core-graph"]], "Class Avogadro::Core::Mesh": [[20, "class-avogadro-core-mesh"]], "Class Avogadro::Core::Molecule": [[21, "class-avogadro-core-molecule"]], "Class Avogadro::Core::MoleculeDeserializer": [[22, "class-avogadro-core-moleculedeserializer"]], "Class Avogadro::Core::MoleculeSerializer": [[23, "class-avogadro-core-moleculeserializer"]], "Class Avogadro::Core::Mutex": [[24, "class-avogadro-core-mutex"]], "Class Avogadro::Core::NameAtomTyper": [[25, "class-avogadro-core-nameatomtyper"]], "Class Avogadro::Core::Residue": [[26, "class-avogadro-core-residue"]], "Class Avogadro::Core::ResidueData": [[27, "class-avogadro-core-residuedata"]], "Class Avogadro::Core::RingPerceiver": [[28, "class-avogadro-core-ringperceiver"]], "Class Avogadro::Core::SharedMutex": [[29, "class-avogadro-core-sharedmutex"]], "Class Avogadro::Core::SlaterSet": [[30, "class-avogadro-core-slaterset"]], "Class Avogadro::Core::SlaterSetTools": [[31, "class-avogadro-core-slatersettools"]], "Class Avogadro::Core::SpaceGroups": [[32, "class-avogadro-core-spacegroups"]], "Class Avogadro::Core::SymbolAtomTyper": [[33, "class-avogadro-core-symbolatomtyper"]], "Class Avogadro::Core::UnitCell": [[34, "class-avogadro-core-unitcell"]], "Class Avogadro::Core::Variant": [[35, "class-avogadro-core-variant"]], "Class Avogadro::Core::VariantMap": [[36, "class-avogadro-core-variantmap"]], "Class Avogadro::Core::internal::ArrayRefContainer": [[37, "class-avogadro-core-internal-arrayrefcontainer"]], "Class Avogadro::Io::CjsonFormat": [[38, "class-avogadro-io-cjsonformat"]], "Class Avogadro::Io::CmlFormat": [[39, "class-avogadro-io-cmlformat"]], "Class Avogadro::Io::DcdFormat": [[40, "class-avogadro-io-dcdformat"]], "Class Avogadro::Io::FileFormat": [[41, "class-avogadro-io-fileformat"]], "Class Avogadro::Io::FileFormatManager": [[42, "class-avogadro-io-fileformatmanager"]], "Class Avogadro::Io::GromacsFormat": [[43, "class-avogadro-io-gromacsformat"]], "Class Avogadro::Io::Hdf5DataFormat": [[44, "class-avogadro-io-hdf5dataformat"]], "Class Avogadro::Io::LammpsDataFormat": [[45, "class-avogadro-io-lammpsdataformat"]], "Class Avogadro::Io::LammpsTrajectoryFormat": [[46, "class-avogadro-io-lammpstrajectoryformat"]], "Class Avogadro::Io::MMTFFormat": [[47, "class-avogadro-io-mmtfformat"]], "Class Avogadro::Io::MdlFormat": [[48, "class-avogadro-io-mdlformat"]], "Class Avogadro::Io::OutcarFormat": [[49, "class-avogadro-io-outcarformat"]], "Class Avogadro::Io::PdbFormat": [[50, 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Avogadro::MoleQueue::MoleQueueWidget": [[61, "class-avogadro-molequeue-molequeuewidget"]], "Class Avogadro::QtGui::BackgroundFileFormat": [[62, "class-avogadro-qtgui-backgroundfileformat"]], "Class Avogadro::QtGui::ContainerWidget": [[63, "class-avogadro-qtgui-containerwidget"]], "Class Avogadro::QtGui::CustomElementDialog": [[64, "class-avogadro-qtgui-customelementdialog"]], "Class Avogadro::QtGui::ElementDetail": [[65, "class-avogadro-qtgui-elementdetail"]], "Class Avogadro::QtGui::ElementItem": [[66, "class-avogadro-qtgui-elementitem"]], "Class Avogadro::QtGui::ElementTranslator": [[67, "class-avogadro-qtgui-elementtranslator"]], "Class Avogadro::QtGui::ExtensionPlugin": [[68, "class-avogadro-qtgui-extensionplugin"]], "Class Avogadro::QtGui::ExtensionPluginFactory": [[69, "class-avogadro-qtgui-extensionpluginfactory"]], "Class Avogadro::QtGui::FileBrowseWidget": [[70, "class-avogadro-qtgui-filebrowsewidget"]], "Class Avogadro::QtGui::FileFormatDialog": [[71, "class-avogadro-qtgui-fileformatdialog"]], "Class Avogadro::QtGui::GenericHighlighter": [[72, "class-avogadro-qtgui-generichighlighter"]], "Class Avogadro::QtGui::GenericHighlighter::Rule": [[73, "class-avogadro-qtgui-generichighlighter-rule"]], "Class Avogadro::QtGui::HydrogenTools": [[74, "class-avogadro-qtgui-hydrogentools"]], "Class Avogadro::QtGui::InterfaceScript": [[75, "class-avogadro-qtgui-interfacescript"]], "Class Avogadro::QtGui::InterfaceWidget": [[76, "class-avogadro-qtgui-interfacewidget"]], "Class Avogadro::QtGui::MeshGenerator": [[77, "class-avogadro-qtgui-meshgenerator"]], "Class Avogadro::QtGui::Molecule": [[78, "class-avogadro-qtgui-molecule"]], "Class Avogadro::QtGui::MoleculeModel": [[79, "class-avogadro-qtgui-moleculemodel"]], "Class Avogadro::QtGui::MultiViewWidget": [[80, "class-avogadro-qtgui-multiviewwidget"]], "Class Avogadro::QtGui::PeriodicTableScene": [[81, "class-avogadro-qtgui-periodictablescene"]], "Class Avogadro::QtGui::PeriodicTableView": [[82, "class-avogadro-qtgui-periodictableview"]], "Class Avogadro::QtGui::PersistentAtom": [[83, "class-avogadro-qtgui-persistentatom"]], "Class Avogadro::QtGui::PersistentBond": [[84, "class-avogadro-qtgui-persistentbond"]], "Class Avogadro::QtGui::PythonScript": [[85, "class-avogadro-qtgui-pythonscript"]], "Class Avogadro::QtGui::RWAtom": [[86, "class-avogadro-qtgui-rwatom"]], "Class Avogadro::QtGui::RWBond": [[87, "class-avogadro-qtgui-rwbond"]], "Class Avogadro::QtGui::RWMolecule": [[88, "class-avogadro-qtgui-rwmolecule"]], "Class Avogadro::QtGui::ScenePlugin": [[89, "class-avogadro-qtgui-sceneplugin"]], "Class Avogadro::QtGui::ScenePluginFactory": [[90, "class-avogadro-qtgui-scenepluginfactory"]], "Class Avogadro::QtGui::ScenePluginModel": [[91, "class-avogadro-qtgui-scenepluginmodel"]], "Class Avogadro::QtGui::ScriptLoader": [[92, "class-avogadro-qtgui-scriptloader"]], "Class Avogadro::QtGui::ToolPlugin": [[93, "class-avogadro-qtgui-toolplugin"]], "Class Avogadro::QtGui::ToolPluginFactory": [[94, "class-avogadro-qtgui-toolpluginfactory"]], "Class Avogadro::QtGui::ViewFactory": [[95, "class-avogadro-qtgui-viewfactory"]], "Class Avogadro::QtOpenGL::ActiveObjects": [[96, "class-avogadro-qtopengl-activeobjects"]], "Class Avogadro::QtOpenGL::GLWidget": [[97, "class-avogadro-qtopengl-glwidget"]], "Class Avogadro::QtOpenGL::QtTextRenderStrategy": [[98, "class-avogadro-qtopengl-qttextrenderstrategy"]], "Class Avogadro::QuantumIO::GAMESSUSOutput": [[99, "class-avogadro-quantumio-gamessusoutput"]], "Class Avogadro::QuantumIO::GUKBasisSet": [[100, "class-avogadro-quantumio-gukbasisset"]], "Class Avogadro::QuantumIO::GamessukOut": [[101, "class-avogadro-quantumio-gamessukout"]], "Class Avogadro::QuantumIO::GaussianCube": [[102, "class-avogadro-quantumio-gaussiancube"]], "Class Avogadro::QuantumIO::GaussianFchk": [[103, "class-avogadro-quantumio-gaussianfchk"]], "Class Avogadro::QuantumIO::MoldenFile": [[104, "class-avogadro-quantumio-moldenfile"]], "Class Avogadro::QuantumIO::MopacAux": [[105, "class-avogadro-quantumio-mopacaux"]], "Class Avogadro::QuantumIO::NWChemJson": [[106, "class-avogadro-quantumio-nwchemjson"]], "Class Avogadro::QuantumIO::NWChemLog": [[107, "class-avogadro-quantumio-nwchemlog"]], "Class Avogadro::Rendering::AmbientOcclusionSphereGeometry": [[108, "class-avogadro-rendering-ambientocclusionspheregeometry"]], "Class Avogadro::Rendering::ArrowGeometry": [[109, "class-avogadro-rendering-arrowgeometry"]], "Class Avogadro::Rendering::BufferObject": [[110, "class-avogadro-rendering-bufferobject"]], "Class Avogadro::Rendering::Camera": [[111, "class-avogadro-rendering-camera"]], "Class Avogadro::Rendering::Cylinder": [[112, "class-avogadro-rendering-cylinder"]], "Class Avogadro::Rendering::CylinderGeometry": [[113, "class-avogadro-rendering-cylindergeometry"]], "Class Avogadro::Rendering::Drawable": [[114, "class-avogadro-rendering-drawable"]], "Class Avogadro::Rendering::GLRenderVisitor": [[115, "class-avogadro-rendering-glrendervisitor"]], "Class Avogadro::Rendering::GLRenderer": [[116, "class-avogadro-rendering-glrenderer"]], "Class Avogadro::Rendering::GeometryNode": [[117, "class-avogadro-rendering-geometrynode"]], "Class Avogadro::Rendering::GeometryVisitor": [[118, "class-avogadro-rendering-geometryvisitor"]], "Class Avogadro::Rendering::GroupNode": [[119, "class-avogadro-rendering-groupnode"]], "Class Avogadro::Rendering::LineStripGeometry": [[120, "class-avogadro-rendering-linestripgeometry"]], "Class Avogadro::Rendering::MeshGeometry": [[121, "class-avogadro-rendering-meshgeometry"]], "Class Avogadro::Rendering::Node": [[122, "class-avogadro-rendering-node"]], "Class Avogadro::Rendering::POVRayVisitor": [[123, "class-avogadro-rendering-povrayvisitor"]], "Class Avogadro::Rendering::Primitive": [[124, "class-avogadro-rendering-primitive"]], "Class Avogadro::Rendering::Scene": [[125, "class-avogadro-rendering-scene"]], "Class Avogadro::Rendering::Shader": [[126, "class-avogadro-rendering-shader"]], "Class Avogadro::Rendering::ShaderProgram": [[127, "class-avogadro-rendering-shaderprogram"]], "Class Avogadro::Rendering::Sphere": [[128, "class-avogadro-rendering-sphere"]], "Class Avogadro::Rendering::SphereGeometry": [[129, "class-avogadro-rendering-spheregeometry"]], "Class Avogadro::Rendering::TextLabel2D": [[130, "class-avogadro-rendering-textlabel2d"]], "Class Avogadro::Rendering::TextLabel3D": [[131, "class-avogadro-rendering-textlabel3d"]], "Class Avogadro::Rendering::TextLabelBase": [[132, "class-avogadro-rendering-textlabelbase"]], "Class Avogadro::Rendering::TextProperties": [[133, "class-avogadro-rendering-textproperties"]], "Class Avogadro::Rendering::TextRenderStrategy": [[134, "class-avogadro-rendering-textrenderstrategy"]], "Class Avogadro::Rendering::Texture2D": [[135, "class-avogadro-rendering-texture2d"]], "Class Avogadro::Rendering::TransformNode": [[136, "class-avogadro-rendering-transformnode"]], "Class Avogadro::Rendering::VRMLVisitor": [[137, "class-avogadro-rendering-vrmlvisitor"]], "Class Avogadro::Rendering::Visitor": [[138, "class-avogadro-rendering-visitor"]], "Class Avogadro::Rendering::VolumeGeometry": [[139, "class-avogadro-rendering-volumegeometry"]], "Class Avogadro::TypeTraits": [[140, "class-avogadro-typetraits"]], "Class Avogadro::TypeTraits< char >": [[141, "class-avogadro-typetraits-char"]], "Class Avogadro::TypeTraits< double >": [[142, "class-avogadro-typetraits-double"]], "Class Avogadro::TypeTraits< float >": [[143, "class-avogadro-typetraits-float"]], "Class Avogadro::TypeTraits< int >": [[144, "class-avogadro-typetraits-int"]], "Class Avogadro::TypeTraits< short >": [[145, "class-avogadro-typetraits-short"]], "Class Avogadro::TypeTraits< unsigned char >": [[146, "class-avogadro-typetraits-unsigned-char"]], "Class Avogadro::TypeTraits< unsigned int >": [[147, "class-avogadro-typetraits-unsigned-int"]], "Class Avogadro::TypeTraits< unsigned short >": [[148, "class-avogadro-typetraits-unsigned-short"]], "Class Avogadro::VTK::VtkPlot": [[149, "class-avogadro-vtk-vtkplot"]], "Class Avogadro::VTK::vtkGLWidget": [[150, "class-avogadro-vtk-vtkglwidget"]], "Class vtkAvogadroActor": [[151, "class-vtkavogadroactor"]], "Class list": [[152, "class-list"]], "Core Classes": [[153, "core-classes"]], "Develop": [[154, "develop"]], "Main Classes": [[154, "main-classes"]], "IO Classes": [[155, "io-classes"]], "MoleQueue Classes": [[156, "molequeue-classes"]], "QtGui Classes": [[157, "qtgui-classes"]], "Rendering Classes": [[158, "rendering-classes"]], "Avogadro Remote Procedure Call (RPC)": [[159, "avogadro-remote-procedure-call-rpc"]], "RPC Protocol": [[159, "rpc-protocol"]], "Methods": [[159, "methods"]], "VTK Classes": [[160, "vtk-classes"]], "Contributing Code": [[161, "contributing-code"], [161, null]], "Documenting Code": [[162, "documenting-code"]], "Class Descriptions": [[162, "class-descriptions"]], "Function Descriptions": [[162, "function-descriptions"]], "Coding Conventions (C++)": [[163, "coding-conventions-c"]], "C++ Features": [[163, "c-features"]], "Including Headers": [[163, "including-headers"]], "Export Macro Headers": [[163, "export-macro-headers"]], "Private Headers": [[163, "private-headers"]], "Qt Headers": [[163, "qt-headers"]], "Namespaces": [[163, "namespaces"]], "Casting": [[163, "casting"]], "Aesthetics": [[163, "aesthetics"]], "Thanks": [[164, "thanks"], [194, "thanks"]], "Code": [[164, "code"]], "Funding": [[164, "funding"]], "Other Projects": [[164, "other-projects"]], "Contribute": [[165, "contribute"]], "How to Help": [[165, "how-to-help"]], "Coding Style (C++)": [[166, "coding-style-c"]], "Indentation": [[166, "indentation"]], "Line Width": [[166, "line-width"]], "Declaring Variables": [[166, "declaring-variables"]], "Whitespace": [[166, "whitespace"]], "Braces": [[166, "braces"]], "Parentheses": [[166, "parentheses"]], "Switch Statements": [[166, "switch-statements"]], "Line Breaks": [[166, "line-breaks"]], "Inheritance and the \u201cvirtual\u201d Keyword": [[166, "inheritance-and-the-virtual-keyword"]], "Referencing Members": [[166, "referencing-members"]], "File Naming": [[166, "file-naming"]], "Breaking Rules": [[166, "breaking-rules"]], "Translations": [[167, "translations"]], "Current Status": [[167, "current-status"]], "Credits": [[167, "credits"], [229, "credits"], [230, "credits"], [231, "credits"], [232, "credits"], [233, "credits"], [234, "credits"]], "License": [[168, "license"]], "Creative Commons Attribution-ShareAlike 4.0 International": [[168, "creative-commons-attribution-sharealike-4-0-international"]], "Using Creative Commons Public Licenses": [[168, "using-creative-commons-public-licenses"]], "Creative Commons Attribution-ShareAlike 4.0 International Public License": [[168, "creative-commons-attribution-sharealike-4-0-international-public-license"]], "Section 1 \u2013 Definitions.": [[168, "section-1-definitions"]], "Section 2 \u2013 Scope.": [[168, "section-2-scope"]], "Section 3 \u2013 License Conditions.": [[168, "section-3-license-conditions"]], "Section 4 \u2013 Sui Generis Database Rights.": [[168, "section-4-sui-generis-database-rights"]], "Section 5 \u2013 Disclaimer of Warranties and Limitation of Liability.": [[168, "section-5-disclaimer-of-warranties-and-limitation-of-liability"]], "Section 6 \u2013 Term and Termination.": [[168, "section-6-term-and-termination"]], "Section 7 \u2013 Other Terms and Conditions.": [[168, "section-7-other-terms-and-conditions"]], "Section 8 \u2013 Interpretation.": [[168, "section-8-interpretation"]], "Avogadro: Molecular Editor and Visualization": [[169, "avogadro-molecular-editor-and-visualization"], [194, "avogadro-molecular-editor-and-visualization"]], "Table of contents": [[170, "table-of-contents"]], "Making a Crystal Surface Slab": [[171, "making-a-crystal-surface-slab"]], "Import the appropriate crystal structure.": [[171, "import-the-appropriate-crystal-structure"]], "Building a Polymer Unit Cell": [[172, "building-a-polymer-unit-cell"]], "Perceiving Crystall Symmetry": [[173, "perceiving-crystall-symmetry"]], "Open a Crystal File": [[173, "open-a-crystal-file"]], "Building Materials": [[174, "building-materials"]], "Building Molecule-Surface Interactions": [[175, "building-molecule-surface-interactions"]], "Start with a generated Crystal Surface": [[175, "start-with-a-generated-crystal-surface"]], "New Window: Create our Molecule": [[175, "new-window-create-our-molecule"]], "Reducing Crystals to a Primitive Unit Cell": [[176, "reducing-crystals-to-a-primitive-unit-cell"]], "Scaling Crystal Cell Volume": [[177, "scaling-crystal-cell-volume"]], "Building a Supercell": [[178, "building-a-supercell"]], "Creating a Surface": [[178, "creating-a-surface"]], "Building a Peptide": [[179, "building-a-peptide"]], "Building Carbon Nanotubes": [[180, "building-carbon-nanotubes"]], "Building DNA or RNA": [[181, "building-dna-or-rna"]], "Building with SMILES": [[182, "building-with-smiles"]], "Importing from the Protein Data Bank (PDB)": [[183, "importing-from-the-protein-data-bank-pdb"]], "Importing Directly": [[183, "importing-directly"]], "Reading a Downloaded PDB file": [[183, "reading-a-downloaded-pdb-file"]], "Importing Molecules by Name": [[184, "importing-molecules-by-name"]], "Building Molecules": [[185, "building-molecules"]], "Insert Molecular Fragments": [[186, "insert-molecular-fragments"]], "Coloring Part of a Molecules": [[187, "coloring-part-of-a-molecules"]], "Hemoglobin": [[187, "hemoglobin"]], "Select by Residue": [[187, "select-by-residue"]], "Select by Element": [[187, "select-by-element"]], "Different Display Styles": [[188, "different-display-styles"]], "Locating Display Types": [[188, "locating-display-types"]], "Axes": [[188, "axes"]], "Ball and Stick": [[188, "ball-and-stick"]], "Cartoon": [[188, "cartoon"]], "Dipole": [[188, "dipole"]], "Force": [[188, "force"]], "Hydrogen Bond": [[188, "hydrogen-bond"]], "Label": [[188, "label"]], "Polygon": [[188, "polygon"]], "QTAIM (Quantum Theory of Atoms in Molecules)": [[188, "qtaim-quantum-theory-of-atoms-in-molecules"], [197, "qtaim-quantum-theory-of-atoms-in-molecules"]], "Ribbon": [[188, "ribbon"]], "Ring": [[188, "ring"]], "Stick": [[188, "stick"]], "Surfaces": [[188, "surfaces"]], "Van der Waals Spheres": [[188, "van-der-waals-spheres"]], "Wireframe": [[188, "wireframe"]], "Display Types": [[189, "display-types"]], "Drawing Molecules": [[190, "drawing-molecules"]], "Creating Carbon Dioxide": [[190, "creating-carbon-dioxide"]], "Getting Started": [[191, "getting-started"], [191, null]], "Introduction": [[192, "introduction"]], "Opening a File": [[192, "opening-a-file"]], "Navigation": [[192, "navigation"]], "Making Selections": [[193, "making-selections"]], "User Guide": [[194, "user-guide"]], "Avogadro 2": [[194, "avogadro-2"]], "Build Menu": [[195, "build-menu"]], "Cartesian Editor\u2026": [[195, "cartesian-editor"]], "1. Sort by\u2026": [[195, "sort-by"]], "2. Unit of Measure": [[195, "unit-of-measure"]], "3. Editing & Modifying Data": [[195, "editing-modifying-data"]], "Change H to Methyl": [[195, "change-h-to-methyl"]], "Add Hydrogens": [[195, "add-hydrogens"]], "Add Hydrogens for pH\u2026": [[195, "add-hydrogens-for-ph"]], "Remove Hydrogens": [[195, "remove-hydrogens"]], "Insert": [[195, "insert"]], "Invert Chirality": [[195, "invert-chirality"]], "Super Cell Builder\u2026": [[195, "super-cell-builder"]], "Nanotube Builder\u2026": [[195, "nanotube-builder"]], "Edit Menu": [[196, "edit-menu"]], "Undo": [[196, "undo"]], "Redo": [[196, "redo"]], "Cut": [[196, "cut"]], "Copy": [[196, "copy"]], "Copy As": [[196, "copy-as"]], "Paste": [[196, "paste"]], "Clear": [[196, "clear"]], "Select All": [[196, "select-all"], [200, "select-all"]], "Select None": [[196, "select-none"], [200, "select-none"]], "Extension Menu": [[197, "extension-menu"]], "Animation": [[197, "animation"]], "Optimize Geometry": [[197, "optimize-geometry"]], "Molecular Mechanics": [[197, "molecular-mechanics"]], "Setup Force Field\u2026": [[197, "setup-force-field"]], "Calculate Energy": [[197, "calculate-energy"]], "Conformer Search": [[197, "conformer-search"]], "Constraints": [[197, "constraints"], [203, "constraints"]], "Ignore Selection": [[197, "ignore-selection"]], "Fix Selected Atoms": [[197, "fix-selected-atoms"]], "Avogadro Extensions\u2013Plugins": [[197, "avogadro-extensionsplugins"]], "General \u201cHow To\u201d for Plugins": [[197, "general-how-to-for-plugins"]], "Running Gaussian": [[197, "running-gaussian"]], "Molecular Orbitals": [[197, "molecular-orbitals"]], "Spectra\u2026": [[197, "spectra"]], "Create Surfaces\u2026": [[197, "create-surfaces"]], "File Menu": [[198, "file-menu"]], "New": [[198, "new"]], "Open": [[198, "open"]], "Open Recent": [[198, "open-recent"]], "Close": [[198, "close"]], "Save": [[198, "save"]], "Save As\u2026": [[198, "save-as"]], "Revert to Saved": [[198, "revert-to-saved"]], "Import": [[198, "import"]], "Export": [[198, "export"]], "Menus": [[199, "menus"], [199, null]], "Select Menu": [[200, "select-menu"]], "Invert Selection": [[200, "invert-selection"]], "Select SMARTS\u2026": [[200, "select-smarts"]], "Select by Element\u2026": [[200, "select-by-element"]], "Select by Residue\u2026": [[200, "select-by-residue"]], "Select Solvent": [[200, "select-solvent"]], "Add Name Selection\u2026": [[200, "add-name-selection"]], "View Menu": [[201, "view-menu"]], "New View": [[201, "new-view"]], "Duplicate View": [[201, "duplicate-view"]], "Detach View": [[201, "detach-view"]], "Close View": [[201, "close-view"]], "Center": [[201, "center"]], "Align View to Axes": [[201, "align-view-to-axes"]], "Full Screen": [[201, "full-screen"]], "Reset Display Types": [[201, "reset-display-types"]], "Set Background Color\u2026": [[201, "set-background-color"]], "Projection": [[201, "projection"]], "Display Axes": [[201, "display-axes"]], "Debug Information": [[201, "debug-information"]], "Use Quick Render": [[201, "use-quick-render"]], "All Molecules in File\u2026": [[201, "all-molecules-in-file"]], "Crystal View Options\u2026": [[201, "crystal-view-options"]], "Properties": [[201, "properties"]], "Finding Conformers of Molecules": [[202, "finding-conformers-of-molecules"]], "Start with your molecule of interest": [[202, "start-with-your-molecule-of-interest"]], "Optimize the geometry": [[202, "optimize-the-geometry"]], "Change the force field options": [[202, "change-the-force-field-options"]], "Set the conformer search options": [[202, "set-the-conformer-search-options"]], "Pick a search method and start the search": [[202, "pick-a-search-method-and-start-the-search"]], "Geometry Constraints": [[203, "geometry-constraints"]], "Example": [[203, "example"]], "Optimizations": [[203, "optimizations"]], "Example cont.": [[203, "example-cont"]], "Optimizing Geometry": [[204, "optimizing-geometry"]], "Introduction to Molecular Mechanics": [[205, "introduction-to-molecular-mechanics"]], "UFF": [[205, "uff"]], "MMFF94(s)": [[205, "mmff94-s"]], "GAFF": [[205, "gaff"]], "Align Tool": [[206, "align-tool"]], "Auto-Optimize Tool": [[207, "auto-optimize-tool"]], "Force Fields & Algorithms": [[207, "force-fields-algorithms"]], "Fixing & Ignoring Selections": [[207, "fixing-ignoring-selections"]], "Auto-Rotate Tool": [[208, "auto-rotate-tool"]], "Bond-Centric Manipulate Tool": [[209, "bond-centric-manipulate-tool"]], "Starting with the basics:": [[209, "starting-with-the-basics"]], "Adjusting Bonds and Torsion Angles": [[209, "adjusting-bonds-and-torsion-angles"]], "Draw Tool": [[210, "draw-tool"]], "1. Creating a Molecule": [[210, "creating-a-molecule"]], "2.": [[210, "id1"]], "3.": [[210, "id2"]], "4.": [[210, "id3"]], "5.": [[210, "id4"]], "6.": [[210, "id5"]], "7.": [[210, "id6"]], "8.": [[210, "id7"]], "9.": [[210, "id8"]], "Tools": [[211, "tools"]], "Manipulate Tool": [[212, "manipulate-tool"]], "Measure Tool": [[213, "measure-tool"]], "Navigate Tool": [[214, "navigate-tool"]], "Selection Tool": [[215, "selection-tool"]], "Tutorials": [[216, "tutorials"], [216, null]], "Naming a Molecule": [[217, "naming-a-molecule"]], "Using QTAIM (Atoms in Molecules) Analysis": [[218, "using-qtaim-atoms-in-molecules-analysis"]], "Start with a WFN File": [[218, "start-with-a-wfn-file"]], "Viewing Electrostatic Potential Maps": [[219, "viewing-electrostatic-potential-maps"]], "Changing Surface Settings": [[219, "changing-surface-settings"]], "Viewing Molecular Orbitals": [[220, "viewing-molecular-orbitals"]], "Configure": [[220, "configure"]], "Viewing Vibrations": [[221, "viewing-vibrations"]], "What\u2019s New in Avogadro 2": [[222, "whats-new-in-avogadro-2"]], "Interface Changes": [[223, "interface-changes"]], "Major New Features": [[224, "major-new-features"]], "Speed and Stability": [[224, "speed-and-stability"]], "Rendering": [[224, "rendering"]], "New real-time shadows and depth effects": [[224, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose contact\u201d rendering": [[224, "new-close-contact-rendering"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[224, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New cartoon / ribbon styles for proteins": [[224, "new-cartoon-ribbon-styles-for-proteins"]], "Layers": [[224, "layers"]], "Symmetry Properties": [[224, "symmetry-properties"]], "Template Tool": [[224, "template-tool"]], "Solvent Accessible and Solvent Excluded Surfaces": [[224, "solvent-accessible-and-solvent-excluded-surfaces"]], "Flexible Electrostatics Models": [[224, "flexible-electrostatics-models"]], "New Analysis Tools": [[224, "new-analysis-tools"]], "Python Commands / Plugins": [[224, "python-commands-plugins"]], "Python Scripting and Jupyter Integration": [[224, "python-scripting-and-jupyter-integration"]], "New and updated interfaces to external programs": [[224, "new-and-updated-interfaces-to-external-programs"]], "Install": [[225, "install"], [227, "install"]], "Features": [[225, "features"], [229, "features"]], "Resources": [[225, "resources"]], "Connecting with the Avogadro community": [[225, "connecting-with-the-avogadro-community"]], "Building Source Code": [[226, "building-source-code"]], "Cloning Repositories": [[226, "cloning-repositories"]], "Updating": [[226, "updating"]], "Prerequisites": [[226, "prerequisites"]], "Building": [[226, "building"]], "Finding Qt, Windows Generators": [[226, "finding-qt-windows-generators"]], "Normal Development": [[226, "normal-development"]], "Build Tree Layout": [[226, "build-tree-layout"]], "Running Executables": [[226, "running-executables"]], "Building Packages": [[226, "building-packages"]], "Version History": [[228, "version-history"], [228, null]], "Release Notes v1.94.0": [[229, "release-notes-v1-94-0"]], "\ud83d\udc1b Bug Fixes": [[229, "bug-fixes"], [230, "bug-fixes"], [231, "bug-fixes"], [232, "bug-fixes"], [233, "bug-fixes"], [234, "bug-fixes"]], "\ud83d\udc0d Python Improvements": [[229, "python-improvements"]], "\ud83e\uddf0 Maintenance": [[229, "maintenance"], [230, "maintenance"], [231, "maintenance"], [232, "maintenance"], [233, "maintenance"], [234, "maintenance"]], "Release Notes v1.95.0": [[230, "release-notes-v1-95-0"]], "Changes": [[230, "changes"], [232, "changes"]], "\u2728 Features": [[230, "features"], [231, "features"], [232, "features"], [233, "features"], [234, "features"]], "\ud83d\udcda Translations": [[230, "translations"], [231, "translations"], [232, "translations"], [233, "translations"], [234, "translations"]], "Release Notes v1.95.1": [[231, "release-notes-v1-95-1"]], "Release Notes v1.96.0": [[232, "release-notes-v1-96-0"]], "\ud83d\ude80 Performance Fixes": [[232, "performance-fixes"]], "Release Notes v1.97.0": [[233, "release-notes-v1-97-0"]], "Highlights (tldr)": [[233, "highlights-tldr"], [234, "highlights-tldr"]], "\ud83d\ude80 Performance Improvements": [[233, "performance-improvements"], [234, "performance-improvements"]], "Release Notes v1.98.0": [[234, "release-notes-v1-98-0"]], "Charges / Electrostatics": [[235, "charges-electrostatics"]], "Identify the Script with --metadata": [[235, "identify-the-script-with-metadata"], [237, "identify-the-script-with-metadata"]], "Calculating Atomic Partial Charges with --charge": [[235, "calculating-atomic-partial-charges-with-charge"]], "Generating Electrostatic Potentials with --potential": [[235, "generating-electrostatic-potentials-with-potential"]], "Command Scripts": [[236, "command-scripts"]], "Script Entry Points": [[236, "script-entry-points"], [241, "script-entry-points"]], "Specifying UI options with \u2013print-options": [[236, "specifying-ui-options-with-print-options"]], "Returning Data": [[236, "returning-data"]], "Returning Data in a Specific File Format": [[236, "returning-data-in-a-specific-file-format"]], "Appending New Atoms and Bonds": [[236, "appending-new-atoms-and-bonds"]], "Bonding New Atoms": [[236, "bonding-new-atoms"]], "Selected Atoms": [[236, "selected-atoms"]], "Debugging": [[236, "debugging"], [241, "debugging"]], "Energy / Force Fields": [[237, "energy-force-fields"]], "Calculating Energies and Gradients": [[237, "calculating-energies-and-gradients"]], "Unit Cells, Total Charge, and Spin Multiplicity": [[237, "unit-cells-total-charge-and-spin-multiplicity"]], "Lattice Vectors and Fractional Coordinates": [[237, "lattice-vectors-and-fractional-coordinates"]], "Example Plugin Script - Part 1": [[238, "example-plugin-script-part-1"]], "The Main function:": [[238, "the-main-function"]], "Input Arguments": [[238, "input-arguments"]], "getOptions() Function": [[238, "getoptions-function"]], "Example Plugin Script - Part 2": [[239, "example-plugin-script-part-2"]], "Providing Input to Run Command": [[239, "providing-input-to-run-command"]], "runCommand() Function": [[239, "runcommand-function"]], "Operation Function": [[239, "operation-function"]], "Retrieving necessary components": [[239, "retrieving-necessary-components"]], "Support for Selection": [[239, "support-for-selection"]], "Sample Input and Output": [[239, "sample-input-and-output"]], "File Formats": [[240, "file-formats"]], "Identify the Format with --metadata": [[240, "identify-the-format-with-metadata"]], "Reading a format with --read": [[240, "reading-a-format-with-read"]], "Writing a format with --write": [[240, "writing-a-format-with-write"]], "Input Generators": [[241, "input-generators"]], "Specifying parameters with --print-options": [[241, "specifying-parameters-with-print-options"]], "Special Parameters": [[241, "special-parameters"]], "Syntax Highlighting": [[241, "syntax-highlighting"]], "Requesting Full Structure of Current Molecule": [[241, "requesting-full-structure-of-current-molecule"]], "Handling User Selections: --generate-input": [[241, "handling-user-selections-generate-input"]], "Automatic Generation of Geometry": [[241, "automatic-generation-of-geometry"]], "Coordinate Blocks": [[241, "coordinate-blocks"]], "Error Handling": [[241, "error-handling"]], "Script Plugins": [[242, "script-plugins"]], "Installing Script Plugins": [[243, "installing-script-plugins"]], "Directories": [[243, "directories"]], "Plugin Packages and Repositories": [[243, "plugin-packages-and-repositories"]], "Adding to the Plugin Directory": [[243, "adding-to-the-plugin-directory"]], "Script Interfaces": [[244, "script-interfaces"]], "Fixed String Lists (Pop-up menus)": [[244, "fixed-string-lists-pop-up-menus"]], "Short Free-Form Text Parameters": [[244, "short-free-form-text-parameters"]], "Existing files": [[244, "existing-files"]], "Integer Values": [[244, "integer-values"]], "Floating-point values": [[244, "floating-point-values"]], "Boolean Parameters": [[244, "boolean-parameters"]]}, "indexentries": {}})
\ No newline at end of file