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