Use pymol as a python library

The explanation will be given in the following environment. Linux: 3.13.0-37-generic #64-Ubuntu

Python 2.7.6

Display the path of the imported module

<module name>.path

>>> import pymol
>>> pymol.__path__
['/usr/lib/python2.7/dist-packages/pymol']

installation of biopython

[hnishi@hn python_pymol]$ sudo apt-get install python-biopython

View module help

help(<module name>)

>>> import Bio
>>> help(Bio)

Use pymol functions from regular python (CUI)

** pymol -c **: open pymol with CUI only

cui_pymol.py

import pymol
pymol.pymol_argv = ['pymol','-c'] 
pymol.finish_launching()
pymol.cmd.fetch("4m61")

Output result

[hnishi@hn python_pymol]$ python cui_pymol.py
 PyMOL(TM) Molecular Graphics System, Version 1.7.0.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

    Created by Warren L. DeLano, Ph.D.

    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".

    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Command mode. No graphics front end.
 PyMOL: normal program termination.

With the option pymol -q, you can hide the version information etc. that appears at the beginning of the log (Quiet).

For options when starting pymol http://pymolwiki.org/index.php/Command_Line_Options reference

Get coordinate information of pymol object (molecule)

** pymol.cmd.iterate_state (\ <state >, \ <selection >, \ <expression >) **: pymol function and object information

iterate_state.py

#!/usr/bin/python2.7 -i

import sys, os

### pymol launching
import pymol
pymol.pymol_argv = ['pymol','-qc'] + sys.argv[1:]
pymol.finish_launching()
cmd = pymol.cmd

### read pdb
r = cmd.fetch("4m61","obj1")
print r
cmd.iterate_state(1, "obj1 and name CA and resi 3 and chai A", "print x,y,z")  #print coordinates

Output result

[hnishi@hn python_pymol]$ python iterate_state.py
obj1
9.97799968719 35.7999992371 20.9699993134

The mystery that there are 4 digits or less even though the value is up to 3 decimal places on the PDB file.

Source cui_pymol.py https://gist.github.com/hnishi/3b9a3247a4bc356e17c7.js

Launch pymol from python (GUI)

gui_pymol.py

#!/usr/bin/env python

# Tell PyMOL we don't want any GUI features.
# It runs PyMol fullscreen stereo, and disables the internal gui.
import __main__
__main__.pymol_argv = [ 'pymol', '-qei' ]  #$ pymol -qei

# Importing the PyMOL module will create the window.
import pymol

# Call the function below before using any PyMOL modules.
pymol.finish_launching()

[hnishi@hn python_pymol]$ python gui_pymol.py The pymol window launches in full screen. The internal GUI function is turned off. Instead, it's light enough to run slimy from the server via x-window.

Show methods and members of objects and modules

dir(<something>)

python2.7

>>> import Bio
>>> print dir(Bio)
['BiopythonDeprecationWarning', 'BiopythonExperimentalWarning', 'BiopythonParserWarning', 'BiopythonWarning', 'MissingExternalDependencyError', 'MissingPythonDependencyError', '__builtins__', '__doc__', '__docformat__', '__file__', '__name__', '__package__', '__path__', '__version__']

on hold

from multiprocessing import Pool a = range(100) a p = Pool()

Link

How to write a pymol script http://qiita.com/hnishi/items/e77b270ad1a6d574d6cc

reference

Use pymol from python http://pymolwiki.org/index.php/Launching_From_a_Script Extract object information in pymol http://www.pymolwiki.org/index.php/Simple_Scripting