deploy: 8468118

_sources/develop/avogadroapp.md.txt

@@ -0,0 +1,42 @@
+(develop-avogadroapp)=
+
+# Avogadro App
+
+The `avogadroapp` project provides a fairly thin set of classes
+around the `avogadrolibs` core. Among other things, it provides
+scripts for bundling the desktop app on MacOS and Windows,
+as well as code to open / save files, load language translations,
+the about dialog, etc.
+
+`aboutdialog`
+: Displays the about dialog, including some versioning
+
+`application`
+: A minimal class mainly to handle `FileOpen` events from the operating system, e.g. to open files on launch
+
+`avogadro`
+: The main command-line program. Mostly handles initialization, including loading translations and the OpenGL context
+
+`backgroundfileformat`
+: Code for opening / saving files in a background thread to retain interactivity
+
+`mainwindow`
+: The main interface class. Handles loading tools, render types, etc. Most changes for `avogadroapp` probably involve this code.
+
+`menubuilder`
+: Code to load and sort the menu items from `avogadroapp` and plugin scripts
+
+`renderingdialog`
+: A settings dialog for various rendering options
+
+`rpclistener`
+: Code to handle [Remote Procedure Calls (RPC)](rpc) from external scripts or programs
+
+`tdxcontroller`
+: Contributed code to handle the 3DConnexion SpaceMouse device.
+
+`tooltipfilter`
+: A workaround to ensure tool buttons have tooltips
+
+`viewfactory`
+: Code to create multiple views on the same molecule

_sources/develop/classlist.md.txt

@@ -6,10 +6,12 @@
 :glob: true
 :maxdepth: 1
 
+avogadroapp
 core
 io
 molequeue
 qtgui
+qtplugins
 rendering
 vtk
 ```

_sources/develop/qtplugins.md.txt

@@ -0,0 +1,109 @@
+(develop-qtplugins)=
+
+# Avogadro::QtPlugins
+
+There are a wide variety of plugins in separate directories, providing
+tools, render types, and commands. Some may provide more than one of these
+for full functionality (e.g., symmetry perception includes both a command and a render type).
+
+What follows is a list of core plugins and brief descriptions. A few plugins are listed in multiple places:
+
+## Tools
+
+- **aligntool** - align molecule to a frame of reference
+- **bondcentrictool** - bond centric manipulation (length, angle, dihedral)
+- **editor** - freehand drawing of atoms and bonds
+- **label** - edit atom labels (also a render type)
+- **manipulator** - move and rotate atoms and selections
+- **measuretool** - measure bond lengths, angles, and dihedrals
+- **navigator** - move the camera view
+- **playertool** - play animations / trajectories
+- **selectiontool** - select atoms individually or in a rectangle
+- **templatetool** - insert ligands, functional groups, and metal geometries
+
+## Render Types
+
+- **ballandstick** - the default ball-and-stick render type
+- **cartoons** - protein backbone and cartoon renderings
+- **closecontacts** - close contacts between atoms
+- **dipole** - dipole moment
+- **force** - forces on atoms (from vibrations or molecular dynamics)
+- **label** - atom and other labels - also a tool
+- **licorice** - stick or licorice rendering
+- **noncovalent** - hydrogen, chalcogen bonds and other non-covalent interactions
+- **meshes** - surfaces, orbitals, etc.
+- **overlayaxes** - reference axes
+- **qtaim** - QTAIM rendering (critical points, etc.), also a command
+- **symmetry** - rendering of symmetry elements, also a command
+- **vanderwaals** - van der Waals spheres
+- **wireframe** - wireframe line rendering
+
+## Main Commands
+
+- **applycolors** - Apply colors to atoms (e.g., by partial charge, etc.)
+- **bonding** - Assign bonds and bond orders, break bonds
+- **coordinateeditor** - Edit, copy and paste atoms and 3D coordinates
+- **copypaste** - Cut, copy and paste commands
+- **crystal** - Commands for handling basic crystal structure properties
+- **focus** - Focus and unfocus the view on a selection
+- **forcefield** - Optimize and run force field calculations, including via scripts
+- **hydrogens** - Add, remove, and adjust hydrogen atoms
+- **insertdna** - Insert DNA fragments
+- **insertfragment** - Insert molecules
+- **lineformatinput** - Insert from SMILES or InChI line formats
+- **molecularproperties** - Molecular property dialogs
+- **openbabel** - Open Babel commands, including file formats, force fields, charges, etc.
+- **propertytables** - Atom, bond, angle, and torsion property spreadsheets
+- **select** - Selection commands
+- **spacegroup** - Handle filling and standardizing the unit cell based on space groups
+- **surfaces** - Generate molecular surfaces and orbitals
+- **symmetry** - Perceive molecular symmetry and symmetrize coordinates
+- **vibrations** - Animate vibrations
+
+## Script Commands
+
+- **commandscripts** - Add menu commands from Python scripts
+- **configurepython** - Configure the Python environment to use for scripts
+- **forcefield** - Optimize and run force field calculations, including via scripts
+- **plugindownloader** - Download and install Python scripts
+- **quantuminput** - Use Python scripts for many quantum chemical input generators (e.g., Orca, Gaussian, Q-Chem, etc.)
+- **scriptcharges** - Assign atomic partial charges using Python scripts (e.g., from `xtb` or `antechamber`)
+- **scriptfileformats** - Import various file formats using Python scripts
+
+## Input Generator Commands
+
+- **apbs** - Input for the APBS program
+- **cp2kinput** - Input for CP2K
+- **gamessinput** - Input for GAMESS-US
+- **lammpsinput** - Input for LAMMPS
+- **openmminput** - Input for OpenMM simulations
+- **quantuminput** - Use Python scripts for many quantum chemical input generators (e.g., Orca, Gaussian, Q-Chem, etc.)
+
+## Import Commands
+
+- **fetchpdb** - Fetch molecules from the Protein Data Bank (PDB)
+- **importpqr** - Import molecules from the Pitt Quantum Repository
+- **networkdatabases** - Fetch molecules by name from the NIH Chemical Resolver
+
+## Export Commands
+
+- **3dmol** - Export the current view for 3dmol.js rendering in a webpage
+- **ply** - Export a 3D PLY format file of the current view
+- **povray** - Export a POV-Ray scene of the current view
+- **svg** - Export a SVG render of the current image
+- **vrml** - Export a VRML / WRL file of the current view
+
+## Plotting Commands
+
+- **spectra** - plot vibrational (IR, Raman), electronic (UV), NMR and other computed spectra
+- **plotpdf** - plot the probability distribution function (PDF)
+- **plotrmsd** - plot RMSD across multiple coordinate sets (e.g., in an MD trajectory)
+- **plotxrd** - plot simulated x-ray diffraction patterns from a crystal structure
+
+## Miscellaneous
+
+- **centroid**
+- **coloropacitymap**
+- **customelements**
+- **resetview**
+- **yaehmop**

_sources/develop/structure.md.txt

@@ -13,17 +13,20 @@ In practice, most functionality and features are provided by `[avogadrolibs](htt
 
 The main project uses various other Open Chemistry modules to function.
 
-[avogadro-i18n](https://github.com/OpenChemistry/)
+[avogadroapp](https://github.com/OpenChemistry/avogadroapp)
+: Code to handle [the desktop app events and interface](develop-avogadroapp)
+
+[avogadro-i18n](https://github.com/OpenChemistry/avogadro-i18n)
 : Language translations and localization handled through [Weblate](https://hosted.weblate.org/engage/avogadro/)
 
-[avogenerators](https://github.com/OpenChemistry/)
+[avogenerators](https://github.com/OpenChemistry/avogenerators)
 : Scripts providing input generator dialogs for various computational packages such as Gaussian, Orca, etc.
 
-[crystals](https://github.com/OpenChemistry/)
+[crystals](https://github.com/OpenChemistry/crystals)
 : Example crystal structures provided through File ⇒ Import ⇒ Crystal
 
 [fragments](https://github.com/OpenChemistry/fragments)
 : Common inorganic ligands and functional groups provided through the Template Tool
 
-[molecules](https://github.com/OpenChemistry/)
+[molecules](https://github.com/OpenChemistry/molecules)
 : Common molecules provided through Build ⇒ Insert ⇒ Molecule

_static/webpack-macros.html

@@ -2,30 +2,23 @@
   AUTO-GENERATED from webpack.config.js, do **NOT** edit by hand.
   These are re-used in layout.html
 -->
-{# Load FontAwesome icons #}
-{% macro head_pre_icons() %}
-  <link href="{{ pathto('_static/vendor/fontawesome/6.5.2/css/all.min.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-  <link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-solid-900.woff2', 1) }}" />
-<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2', 1) }}" />
-<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2', 1) }}" />
-{% endmacro %}
 
 {% macro head_pre_assets() %}
   <!-- Loaded before other Sphinx assets -->
-  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
+  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
 {% endmacro %}
 
 {% macro head_js_preload() %}
+  <!-- So that users can add custom icons -->
+  <script src="{{ pathto('_static/scripts/fontawesome.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=dfe6caa3a7d634c4db9b" />
-<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=dfe6caa3a7d634c4db9b" />
-  <script src="{{ pathto('_static/vendor/fontawesome/6.5.2/js/all.min.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
+  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=26a4bc78f4c0ddb94549" />
+<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=26a4bc78f4c0ddb94549" />
 {% endmacro %}
 
 {% macro body_post() %}
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
-<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
+  <script defer src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
+<script defer src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
 {% endmacro %}