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Using External Programs within OpenStructure¶
It is often very useful to use external programs to do a specific task. In principle, this can be done by writing out files from OpenStructure and manually running an external program, however, for convenience, this can also be done directly from within OpenStructure using Python commands.
This tutorial will give you some hints how to do this for a new external program. The process basically consists of four steps:
Locating the Executable¶
There is a helper function available to locate files, and especially executables:
As an example, we would like to obtain the full path of the msms executable (a program to calculate molecular surfaces):
from ost import settings exe_path = settings.Locate('msms', search_paths=['/opt/app','/home/app'], env_name='MSMS', search_system_paths=True) print exe_path
Prepare All Files¶
The preparation of the necessary files is very dependent on the external program. Often it is useful to generate a temporary directory or file. For this, the Python module tempfile is very handy.
An example how to generate a temporary directory, open a file in this directory and write the position and radius of all atoms into this file is shown here:
import tempfile import os # generate a temporary directory tmp_dir_name = tempfile.mkdtemp() print 'temporary directory:',tmp_dir_name # generate and open a file in the temp directory tmp_file_name = os.path.join(tmp_dir_name,"entity") tmp_file_handle = open(tmp_file_name, 'w') print 'temporary file:',tmp_file_handle # write position and radius of all atoms to file for a in entity.GetAtomList(): position = a.GetPos() tmp_file_handle.write('%8.3f %8.3f %8.3f %4.2f\n' % (position, position, position, a.GetProp().radius)) # close the file tmp_file_handle.close()
Execute the External Program¶
The external program can be executed from python using the python module subprocess.
To run the external program msms from the above example, with the temporary file generated before, we can use the following:
import subprocess # set the command to execute command = "%s -if %s -of %s" % (exe_path, tmp_file_name, tmp_file_name) print 'command:',command # run the executable with the command proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE) stdout_value, stderr_value = proc.communicate() # check for successful completion of msms if proc.returncode != 0: print "WARNING: msms error\n", stdout_value raise subprocess.CalledProcessError(proc.returncode, command) # print everything written to the command line (stdout) print stdout_value
Read Generated Output¶
The last step includes reading of generated files (like in the case of msms) and/or processing of the generated command line output.
Here we first print the command line output and then load the generated msms surface and print the number of vertex points:
# print everything written to the command line (stdout) print stdout_value # read msms surface from file surface = io.LoadSurface(tmp_file_name, "msms") print 'number of vertices:',len(surface.GetVertexIDList())
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