Metadata-Version: 1.1
Name: pychimera
Version: 0.1.0b0
Summary: Use UCSF Chimera Python API in a standard Python 2.7 interpreter.
Home-page: https://github.com/insilichem/pychimera
Author: Jaime Rodríguez-Guerra
Author-email: jaime.rogue@gmail.com
License: LGPL
Download-URL: https://github.com/insilichem/pychimera/tarball/v0.1.0-beta
Description: PyChimera
        =========
        
        Use [UCSF Chimera](https://www.cgl.ucsf.edu/chimera/) packages in any Python 2.7 interpreter 
        
        With PyChimera you can...
        
        * Enable `import chimera` in interactive coding sessions (console, notebooks) __outside Chimera__. 
        Just call `enable_chimera()`. _Careful! Call it prior to other code or you'll lose your previous work._
        * You can also launch Chimera-preenabled IPython sessions or Notebooks with `pychimera ipython` and 
        `pychimera notebook` respectively.
        * Run scripts depending on chimera __from CLI__ with either `pychimera` or `python -m chimera`. This 
        includes modules (`-m` flag) and strings (`-c` flag).
        
        I hope it's useful! Feedback is appreciated!
        
        Installation
        ------------
        First, if you haven't already, install [latest UCSF Chimera](http://www.cgl.ucsf.edu/chimera/download.html).
        
        Then, install PyChimera via pip, conda or setup.py:
        
            pip install pychimera
            conda install -c insilichem pychimera
            git clone https://github.com/insilichem/pychimera.git && python pychimera/setup.py install
        
        Usage
        -----
        Run `pychimera -h` for quick help.
        
        To start an interactive Python session:
        
            pychimera                  # standalone
            pychimera -i some_file.py  # with some file
            pychimera -im module       # with a Python module
            pychimera -ic "string"     # with a command
            pychimera ipython          # launch IPython interpreter
            pychimera notebook         # launch IPython notebook
        
        To launch a module that uses Chimera internally:
        
            pychimera -m this
        
        To execute any Python statement:
        
            pychimera -c 'import chimera'
        
        To execute one or more scripts:
        
            pychimera script.py [script_2.py ...]
        
        
        For developers
        --------------
        PyChimera provides access to Chimera's modules from any Python 2.x interpreter. This is achieved
        in two steps:
        
        1. `patch_environ()` patches environment variables with proper paths (packages and libraries).
        Since the original `sys.path` is exported to `PYTHONPATH`, you can use all your virtualenv/conda
        packages with Chimera. This call restarts Python to inject a new `os.environ` with `os.execve`.
        
        2. `load_chimera()` initializes Chimera. This is done through their own routines (`chimeraInit`).
        
        However, you may call the alias function `enable_chimera()` without worrying on the steps.
        
        PyChimera also offers its interface through python `-m`. Add `-i` for interactive mode:
        
            python -[i]m pychimera [-m another_module | -c "string" | script.py | ipython | notebook]
        
        You can also try to launch it from IPython, but some things may not work. Anyway, these two commands
        have the same effect:
        
            pychimera ipython [notebook]
            ipython -m pychimera [notebook]
        
        If you want to run a script with IPython and then inspect the results (`-i` flag), your best bet is
        to run `pychimera ipython` and then call `%run path/to/file.py` inside the interpreter.
        
        Notes
        -----
        Obviously, you need to install Chimera in your computer. PyChimera will do its best to find the
        installation path automagically in the standard locations. If somehow it doesn't succeed,
        you can always set an environment variable called `CHIMERADIR` in your `.bashrc`, or similar.
        
            export CHIMERADIR="~/.local/UCSF-Chimera"
        
        Chimera bundles its own distribution of some popular packages, like numpy, and those are loaded before
        your env packages for compatibility reasons. Be warned if you use specific versions for your project,
        because you can face strange bugs if you don't take this into account.
        
        Acknowledgments
        ---------------
        Largely based on ideas by [Greg Couch at chimera-users](http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html).
Platform: any
Classifier: Programming Language :: Python :: 2.7
Classifier: Development Status :: 3 - Alpha
Classifier: Natural Language :: English
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Chemistry
