Use UCSF Chimera IDLE directly in terminal, no GUI

chimera_cli.py

"""
Experimental wrapper to use Chimera's Python directly from console.

You can `import chimera` with no errors!

Usage
=====
1. Alias your /path/to/chimera/bin/python binary to something more user-friendly, like `chimerapy`.
2. Download these two files and put them together
3. Run `chimerapy -i chimera_cli.py`. (Tip: Realias `chimerapy` to this command).
4. Profit!

Notes
=====
Most of this is taken from Greg Couch, at chimera-users:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html>
"""

import os
import sys

def chimera_env():
    """
    Prepare environment and path
    """
    os.environ['CHIMERA'] = CHIMERA = guess_chimera_path()
    os.environ['CHIMERAPATH'] = CHIMERA
    sys.path.insert(0, os.path.join(CHIMERA, 'share'))
    sys.path.insert(0, os.path.join(CHIMERA, 'bin'))


def chimera_init():
    """
    Trigger Chimera initializers
    """
    import chimeraInit
    basepath = os.path.dirname(os.path.abspath(sys.argv[0]))
    # This is the magic!
    # If a script needs to be executed, Chimera does not launch
    # the in-house command interface! So, just passing a `pass`
    # statement does the trick.
    chimera_pass = os.path.join(basepath, 'pass.py')
    chimeraInit.init(['@jaimergp', '--script', chimera_pass], nogui=True,
                      eventloop=False, exitonquit=False)


def guess_chimera_path():
    # WINDOWS
    if sys.platform.startswith('win'):
        for programfiles in ('PROGRAMFILES', 'PROGRAMFILES(X86)', 'PROGRAMW6432'):
            paths = [os.path.join(os.environ[programfiles], d)
                     for d in os.listdir(os.environ[programfiles])
                     if d.startswith('Chimera')]
            if paths:
                break
        else:
            paths = [raw_input('Chimera could not be found. Please, type its location manually.\n'
                               'It should be something like C:/Program Files/Chimera 1.10.1\n')]

        paths.sort()
        return paths[-1]  # get latest version available, if more than one exists
    else:
        return subprocess.check_output(['chimera', '--root']).decode('utf-8')


if "__main__" == __name__:
    chimera_env()
    chimera_init()

pass.py

pass