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"Navigation": [[215, "navigation"]], "Navigation Tool": [[251, null]], "Necessary": [[9, "necessary"]], "New": [[222, "new"]], "New View": [[225, "new-view"]], "New Window: Create our Molecule": [[190, "new-window-create-our-molecule"]], "New analysis tools": [[264, "new-analysis-tools"]], "New and updated interfaces to external programs": [[264, "new-and-updated-interfaces-to-external-programs"]], "New cartoon/ribbon styles for proteins": [[264, "new-cartoon-ribbon-styles-for-proteins"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[264, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New real-time shadows and depth effects": [[264, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose-contact\u201d rendering": [[264, "new-close-contact-rendering"]], "Open": [[222, "open"]], "Open Recent": [[222, "open-recent"]], "Open a Crystal File": [[188, "open-a-crystal-file"]], 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clone": [[9, "recursive-clone"]], "Redo": [[220, "redo"]], "Reducing Crystals to a Primitive Unit Cell": [[191, null]], "Referencing Members": [[1, "referencing-members"]], "Remote Teaching": [[302, "remote-teaching"]], "Remove Hydrogens": [[219, "remove-hydrogens"]], "Render Types": [[168, "render-types"]], "Rendering": [[264, "rendering"], [282, "rendering"], [283, "rendering"]], "Rendering / Display": [[289, "rendering-display"], [290, "rendering-display"]], "Requesting Full Structure of Current Molecule": [[65, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md9"], [85, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md23"], [177, "requesting-full-structure-of-current-molecule"]], "Required and optional submodules": [[9, "required-and-optional-submodules"]], "Reset Display Types": [[225, "reset-display-types"]], "Resources": [[265, "resources"]], "Retrieving necessary components": [[175, "retrieving-necessary-components"]], "Returning Data": [[172, "returning-data"]], "Returning Data in a Specific File Format": [[172, "returning-data-in-a-specific-file-format"]], "Revert to Saved": [[222, "revert-to-saved"]], "Ribbon": [[211, "ribbon"]], "Ring": [[211, "ring"]], "Running Gaussian": [[221, "running-gaussian"]], "Running executables": [[9, "running-executables"]], "Sample Input and Output": [[175, "sample-input-and-output"]], "Save": [[222, "save"]], "Save As\u2026": [[222, "save-as"]], "Save vs Export": [[263, "save-vs-export"]], "Saving Files": [[217, null]], "Scaling Crystal Cell Volume": [[192, null]], "Script Commands": [[168, "script-commands"]], "Script Entry Points": [[65, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md0"], [85, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md14"], [172, "script-entry-points"], [177, "script-entry-points"]], "Script Interfaces": [[180, null]], "Script Plugins": [[178, null]], "Script plugins": [[164, "script-plugins"]], "Section 1 \u2013 Definitions.": [[183, 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"Line Width": [[1, "line-width"]], "Linux ": [[9, null], [9, null], [9, null], [9, null], [9, null]], "Locating Display Types": [[211, "locating-display-types"]], "MMFF94(s)": [[230, "mmff94-s"]], "Main Commands": [[168, "main-commands"]], "Main classes": [[164, "main-classes"]], "Major New Features": [[264, null]], "Making Selections": [[216, null]], "Making a Crystal Surface Slab": [[186, null]], "Manipulation Tool": [[249, null]], "Manual clone": [[9, "manual-clone"]], "Markovnikov\u2019s Rule": [[309, null]], "Materials / Nano": [[302, "materials-nano"]], "Measure Tool": [[250, null]], "Menu organization": [[263, "menu-organization"]], "Menus": [[223, null], [223, null]], "Methods": [[170, "methods"]], "Miscellaneous": [[168, "miscellaneous"]], "Molecular Mechanics": [[221, "molecular-mechanics"]], "Molecular Orbitals": [[221, "molecular-orbitals"]], "Namespaces": [[3, "namespaces"]], "Naming a Molecule": [[257, null]], "Nanotube Builder\u2026": [[219, "nanotube-builder"]], "Navigation": [[215, "navigation"]], "Navigation Tool": [[251, null]], "Necessary": [[9, "necessary"]], "New": [[222, "new"]], "New View": [[225, "new-view"]], "New Window: Create our Molecule": [[190, "new-window-create-our-molecule"]], "New analysis tools": [[264, "new-analysis-tools"]], "New and updated interfaces to external programs": [[264, "new-and-updated-interfaces-to-external-programs"]], "New cartoon/ribbon styles for proteins": [[264, "new-cartoon-ribbon-styles-for-proteins"]], "New non-bonded rendering analysis, including hydrogen bonds, halogen bonds, and chalcogen bonds": [[264, "new-non-bonded-rendering-analysis-including-hydrogen-bonds-halogen-bonds-and-chalcogen-bonds"]], "New real-time shadows and depth effects": [[264, "new-real-time-shadows-and-depth-effects"]], "New \u201cclose-contact\u201d rendering": [[264, "new-close-contact-rendering"]], "Open": [[222, "open"]], "Open Recent": [[222, "open-recent"]], "Open a Crystal File": [[188, "open-a-crystal-file"]], 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clone": [[9, "recursive-clone"]], "Redo": [[220, "redo"]], "Reducing Crystals to a Primitive Unit Cell": [[191, null]], "Referencing Members": [[1, "referencing-members"]], "Remote Teaching": [[302, "remote-teaching"]], "Remove Hydrogens": [[219, "remove-hydrogens"]], "Render Types": [[168, "render-types"]], "Rendering": [[264, "rendering"], [282, "rendering"], [283, "rendering"]], "Rendering / Display": [[289, "rendering-display"], [290, "rendering-display"]], "Requesting Full Structure of Current Molecule": [[65, "class_avogadro_1_1_mole_queue_1_1_input_generator_1autotoc_md9"], [85, "class_avogadro_1_1_qt_gui_1_1_interface_script_1autotoc_md23"], [177, "requesting-full-structure-of-current-molecule"]], "Required and optional submodules": [[9, "required-and-optional-submodules"]], "Reset Display Types": [[225, "reset-display-types"]], "Resources": [[265, "resources"]], "Retrieving necessary components": [[175, "retrieving-necessary-components"]], "Returning Data": [[172, 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"Avogadro::QtGui::CustomElementDialog", "Avogadro::QtGui::ElementDetail", "Avogadro::QtGui::ElementItem", "Avogadro::QtGui::ElementTranslator", "Avogadro::QtGui::ExtensionPlugin", "Avogadro::QtGui::ExtensionPluginFactory", "Avogadro::QtGui::FileBrowseWidget", "Avogadro::QtGui::FileFormatDialog", "Avogadro::QtGui::GenericHighlighter", "Avogadro::QtGui::GenericHighlighter::Rule", "Avogadro::QtGui::HydrogenTools", "Avogadro::QtGui::InterfaceScript", "Avogadro::QtGui::InterfaceWidget", "Avogadro::QtGui::MeshGenerator", "Avogadro::QtGui::Molecule", "Avogadro::QtGui::MoleculeModel", "Avogadro::QtGui::MultiViewWidget", "Avogadro::QtGui::PeriodicTableScene", "Avogadro::QtGui::PeriodicTableView", "Avogadro::QtGui::PersistentAtom", "Avogadro::QtGui::PersistentBond", "Avogadro::QtGui::PythonScript", "Avogadro::QtGui::RWAtom", "Avogadro::QtGui::RWBond", "Avogadro::QtGui::RWMolecule", "Avogadro::QtGui::ScenePlugin", "Avogadro::QtGui::ScenePluginFactory", "Avogadro::QtGui::ScenePluginModel", "Avogadro::QtGui::ScriptLoader", "Avogadro::QtGui::ToolPlugin", "Avogadro::QtGui::ToolPluginFactory", "Avogadro::QtGui::ViewFactory", "Avogadro::QtOpenGL::ActiveObjects", "Avogadro::QtOpenGL::GLWidget", "Avogadro::QtOpenGL::QtTextRenderStrategy", "Avogadro::QuantumIO::GAMESSUSOutput", "Avogadro::QuantumIO::GUKBasisSet", "Avogadro::QuantumIO::GamessukOut", "Avogadro::QuantumIO::GaussianCube", "Avogadro::QuantumIO::GaussianFchk", "Avogadro::QuantumIO::MoldenFile", "Avogadro::QuantumIO::MopacAux", "Avogadro::QuantumIO::NWChemJson", "Avogadro::QuantumIO::NWChemLog", "Avogadro::Rendering::AmbientOcclusionSphereGeometry", "Avogadro::Rendering::ArrowGeometry", "Avogadro::Rendering::BufferObject", "Avogadro::Rendering::Camera", "Avogadro::Rendering::Cylinder", "Avogadro::Rendering::CylinderGeometry", "Avogadro::Rendering::Drawable", "Avogadro::Rendering::GLRenderVisitor", "Avogadro::Rendering::GLRenderer", "Avogadro::Rendering::GeometryNode", "Avogadro::Rendering::GeometryVisitor", "Avogadro::Rendering::GroupNode", "Avogadro::Rendering::LineStripGeometry", "Avogadro::Rendering::MeshGeometry", "Avogadro::Rendering::Node", "Avogadro::Rendering::POVRayVisitor", "Avogadro::Rendering::Primitive", "Avogadro::Rendering::Scene", "Avogadro::Rendering::Shader", "Avogadro::Rendering::ShaderProgram", "Avogadro::Rendering::Sphere", "Avogadro::Rendering::SphereGeometry", "Avogadro::Rendering::TextLabel2D", "Avogadro::Rendering::TextLabel3D", "Avogadro::Rendering::TextLabelBase", "Avogadro::Rendering::TextProperties", "Avogadro::Rendering::TextRenderStrategy", "Avogadro::Rendering::Texture2D", "Avogadro::Rendering::TransformNode", "Avogadro::Rendering::VRMLVisitor", "Avogadro::Rendering::Visitor", "Avogadro::Rendering::VolumeGeometry", "Avogadro::TypeTraits", "Avogadro::TypeTraits< char >", "Avogadro::TypeTraits< double >", "Avogadro::TypeTraits< float >", "Avogadro::TypeTraits< int >", "Avogadro::TypeTraits< short >", "Avogadro::TypeTraits< unsigned char >", "Avogadro::TypeTraits< unsigned int >", "Avogadro::TypeTraits< unsigned short >", "Avogadro::VTK::VtkPlot", "Avogadro::VTK::vtkGLWidget", "vtkAvogadroActor", "API Documentation", "Avogadro::Core", "Develop", "Avogadro::IO", "Avogadro::MoleQueue", "Avogadro::QtGui", "Avogadro::QtPlugins", "Avogadro::Rendering", "Avogadro Remote Procedure Call (RPC)", "Charges / Electrostatics", "Command Scripts", "Energy / Force Fields", "Example Plugin Script - Part 1", "Example Plugin Script - Part 2", "File Formats", "Input Generators", "Script Plugins", "Installing Script Plugins", "Script Interfaces", "Project Structure", "Avogadro::VTK", "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", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "Coloring Part of a Molecules", "Display Types", "Different Display Styles", "Extensions", "Drawing Molecules", "Getting Started", "Introduction", "Making Selections", "Saving Files", "Guide", "Build Menu", "Edit Menu", "Extensions Menu", "File Menu", "Menus", "Select Menu", "View Menu", "Finding Conformers of Molecules", "Geometry Constraints", "Enabling additional force fields", "Optimizing Geometry", "Introduction to Molecular Mechanics", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "<no title>", "Language", "Align Tool", "Animation Tool", "Auto-Rotate Tool", "Bond-Centric Manipulation Tool", "Draw Tool", 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