Chimera2 Programming Manual¶
This manual covers programming APIs for the Chimera Core, tools and libraries. They are implemented in Python with routines that need to run fast implemented in C++. This code is free for non-commercial use, see the license for details.
User documentation for the Chimera application is in the User's Manual
.
- Python Modules
- atomic: Atomic structures
- cli: Application command line support
- Functions for User Commands
- configfile: Application saved settings support
- data_events: Support for bulk tracking of data changes
- geometry: Points and coordinate systems
- graphics: Rendering using OpenGL
- gui: Main Chimera 2 user interface
- history: Application history support
- io: Manage file formats that can be opened and exported
- logger: Application log support
- map: Density maps
- models: Displayed data
- molsurf: Compute molecular surfaces
- orderedset: An ordered set
- pdbio: PDB input/output
- safesave: Safely write files
- serialize: Support serialization of “simple” types
- session: Application session support
- settings: Save/access tool interface values
- surface: Triangulated surface calculations
- tasks: Task creation and monitoring
- tools: Manage running tool instances
- toolshed: Manage installed and available tools
- triggerset: Support for managing triggers and handlers
- utils: Generically useful stuff that doesn’t fit elsewhere
- Python Classes
Atom
- a molecule atomAtomicStructure
- molecular dataAtoms
- a collection of atomsBond
- a molecule bondCamera
- position the scene is rendered fromChain
- a polymer chainCommand
- user commandDrawing
- 3-d graphical objectGrid_Data
- density map dataLighting
- lighting paramtersLog
- text command logMaterial
- material reflectivity parametersModel
- Displayed data with id numberMolecularSurface
- molecular surfacesPlace
- position and orientation in spaceResidue
- a molecule residueSession
- application stateSettings
- save tool preferencesToolInfo
- information about an available toolToolInstance
- running toolsToolshed
- manages tool updatesTriggerSet
- event notificationsView
- graphics windowVolume
- density map
Indices and tables¶
License¶
Non-Commercial Software License Agreement
Copright © 2015 by the Regents of the University of California. All Rights Reserved.