#!/usr/bin/env ccp4-python
"""Module to run REFMAC on a model"""
__author__ = "Adam Simpkin"
__date__ = "02 May 2017"
__version__ = "1.0"
import os
from pyjob import cexec
[docs]class Refmac(object):
"""Class to run refmac
Attributes
----------
hklin : str
Path to the input hkl file
hklout : str
Path to the output hkl file
pdbin : str
Path to the input pdb file
pdbout : str
Path to the output pdb file
logfile : str
Path to the output logfile
key : str
REFMAC key words
work_dir : str
Path to the working directory were you want REFMAC to run
ncyc : int float
The number of cycles of refinement to perform [default : 30]
Examples
--------
>>> from simbad.mr.refmac_refine import Refmac
>>> refmac = Refmac('<hklin>', '<hklout>', '<logfile>', '<pdbin>', '<pdbout>', '<work_dir>')
>>> refmac.run('<ncyc>')
Files relating to the REFMAC run will be contained within the work_dir however the location of the output hkl, pdb
and logfile can be specified.
"""
def __init__(self, hklin, hklout, logfile, pdbin, pdbout, work_dir):
self._hklin = None
self._hklout = None
self._logfile = None
self._pdbout = None
self._pdbout = None
self._work_dir = None
self.hklin = hklin
self.hklout = hklout
self.logfile = logfile
self.pdbin = pdbin
self.pdbout = pdbout
self.work_dir = work_dir
@property
def hklin(self):
"""The input hkl file"""
return self._hklin
@hklin.setter
def hklin(self, hklin):
"""Define the input hkl file"""
self._hklin = hklin
@property
def hklout(self):
"""The output hkl file"""
return self._hklout
@hklout.setter
def hklout(self, hklout):
"""Define the output hkl file"""
self._hklout = hklout
@property
def logfile(self):
"""The logfile output"""
return self._logfile
@logfile.setter
def logfile(self, logfile):
"""Define the output logfile"""
self._logfile = logfile
@property
def pdbin(self):
"""The input pdb file"""
return self._pdbin
@pdbin.setter
def pdbin(self, pdbin):
"""Define the input pdb file"""
self._pdbin = pdbin
@property
def pdbout(self):
"""The output pdb file"""
return self._pdbout
@pdbout.setter
def pdbout(self, pdbout):
"""Define the output pdb file"""
self._pdbout = pdbout
@property
def work_dir(self):
"""The path to the working directory"""
return self._work_dir
@work_dir.setter
def work_dir(self, work_dir):
"""Define the working directory"""
self._work_dir = work_dir
[docs] def run(self, type, ncyc=30):
"""Function to run refinement using REFMAC
Parameters
----------
type : str
The type of refinement to run
ncyc : int float
The number of cycles of refinement to perform [default : 30]
Returns
-------
file
Output hkl file
file
Output pdb file
file
Output log file
"""
# Make a note of the current working directory
current_work_dir = os.getcwd()
# Change to the REFMAC working directory
if os.path.exists(self.work_dir):
os.chdir(self.work_dir)
else:
os.makedirs(self.work_dir)
os.chdir(self.work_dir)
if type == 'jelly_body':
key = "ncyc 100" + os.linesep + "ridg dist sigm 0.02"
else:
key = "ncyc {0}".format(ncyc)
Refmac.refmac(self.hklin, self.hklout, self.pdbin, self.pdbout, self.logfile, key)
# Return to original working directory
os.chdir(current_work_dir)
[docs] @staticmethod
def refmac(hklin, hklout, pdbin, pdbout, logfile, key):
"""Function to run refinement using REFMAC
Parameters
----------
hklin : str
Path to the input hkl file
hklout : str
Path to the output hkl file
pdbin : str
Path to the input pdb file
pdbout : str
Path to the output pdb file
logfile : str
Path to the output logfile
key : str
REFMAC key words
Returns
-------
file
Output hkl file
file
Output pdb file
file
Output log file
"""
cmd = ['refmac5', 'hklin', hklin, 'hklout', hklout,
'xyzin', pdbin, 'xyzout', pdbout]
stdout = cexec(cmd, stdin=key)
with open(logfile, 'w') as f_out:
f_out.write(stdout)
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description='Runs refinement using REFMAC', prefix_chars="-")
group = parser.add_argument_group()
group.add_argument('-hklin', type=str,
help="Path the input hkl file")
group.add_argument('-hklout', type=str,
help="Path the output hkl file")
group.add_argument('-logfile', type=str,
help="Path to the ouput log file")
group.add_argument('-ncyc', type=int, default=30,
help="Number of cycles of refinement to run")
group.add_argument('-pdbin', type=str,
help="Path to the input pdb file")
group.add_argument('-pdbout', type=str,
help="Path to the output pdb file")
group.add_argument('-refinement_type', type=str, default='jelly_body',
help="The type of refinement to run")
group.add_argument('-work_dir', type=str,
help="Path to the working directory")
args = parser.parse_args()
refmac = Refmac(args.hklin, args.hklout, args.logfile, args.pdbin, args.pdbout, args.work_dir)
refmac.run(args.refinement_type, args.ncyc)
