#!/usr/bin/env ccp4-python
"""Module to run phaser on a model"""
__author__ = "Adam Simpkin"
__date__ = "02 May 2017"
__version__ = "1.0"
import os
import shutil
from pyjob import cexec
[docs]class Phaser(object):
"""Class to run PHASER
Attributes
----------
enant : bool
Specify whether to try enantimorphic space groups
f : str
The column label for F
hklin : str
Path to the input hkl file
hklout : str
Path to the output hkl file
logfile : str
Path to the output log file
pdbin : str
Path to the input pdb file
pdbout : str
Path to the output pdb file
sigf : str
The column label for SIGF
solvent : int float
The estimated solvent content of the crystal
work_dir : str
Path to the working directory were you want PHASER to run
Examples
--------
>>> from simbad.mr.phaser_mr import Phaser
>>> phaser = Phaser('<enant>', '<hklin>', '<hklout>', '<i>', '<logfile>', '<nmol>', '<pdbin>', '<pdbout>', '<sigi>',
>>> '<solvent>', '<timeout>', '<workdir>')
>>> phaser.run()
Files relating to the PHASER run will be contained within the work_dir however the location of the output hkl, pdb
and logfile can be specified.
"""
def __init__(self, enant, hklin, hklout, i, logfile, nmol, pdbin, pdbout, sigi, solvent, timeout, work_dir):
self._enant = None
self._i = None
self._hklin = None
self._hklout = None
self._logfile = None
self._nmol = None
self._pdbout = None
self._pdbout = None
self._sigi = None
self._solvent = None
self._timeout = None
self._work_dir = None
self.enant = enant
self.i = i
self.hklin = hklin
self.hklout = hklout
self.logfile = logfile
self._nmol = nmol
self.pdbin = pdbin
self.pdbout = pdbout
self.sigi = sigi
self.solvent = solvent
self.timeout = timeout
self.work_dir = work_dir
@property
def enant(self):
"""Whether to check for enantimophic space groups"""
return self._enant
@enant.setter
def enant(self, enant):
"""Define whether to check for enantiomorphic space groups"""
self._enant = enant
@property
def i(self):
"""The I label from the input hkl"""
return self._i
@i.setter
def i(self, i):
"""Define the I label from the input hkl"""
self._i = i
@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 nmol(self):
"""The number of molecules to look for"""
return self._nmol
@nmol.setter
def nmol(self, nmol):
"""Define the number of molecules to look for"""
self._nmol = nmol
@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 sigi(self):
"""The SIGI label from the input hkl"""
return self._sigi
@sigi.setter
def sigi(self, sigi):
"""Define the SIGI label from the input hkl"""
self._sigi = sigi
@property
def solvent(self):
"""The estimated solvent content of the crystal"""
return self._solvent
@solvent.setter
def solvent(self, solvent):
"""Define the estimated solvent content of the crystal"""
self._solvent = solvent
@property
def timeout(self):
"""The time in minutes before phaser is killed"""
return self._timeout
@timeout.setter
def timeout(self, timeout):
"""Define the time in minutes before phaser should be killed"""
self._timeout = timeout
[docs] def run(self):
"""Function to run molecular replacement using PHASER
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 PHASER 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)
# Copy hklin and pdbin to working dire for efficient running of PHASER
hklin = os.path.join(self.work_dir, os.path.basename(self.hklin))
shutil.copyfile(self.hklin, hklin)
pdbin = os.path.join(self.work_dir, os.path.basename(self.pdbin))
shutil.copyfile(self.pdbin, pdbin)
if self.enant:
sgalternative = "ALL"
else:
sgalternative = "HAND"
if self.timeout == 0:
kill_command = ""
else:
kill_command = "KILL TIME {0}".format(self.timeout)
key = """#---PHASER COMMAND SCRIPT GENERATED BY SIMBAD---
MODE MR_AUTO
ROOT "phaser_mr_output"'
{0}
#---DEFINE DATA---
HKLIN {1}
LABIN I={2} SIGI={3}
SGALTERNATIVE SELECT {4}
#---DEFINE ENSEMBLES---
ENSEMBLE ensemble1 &
PDB "{5}" RMS 0.6
#---DEFINE COMPOSITION---
COMPOSITION BY SOLVENT
COMPOSITION PERCENTAGE {6}
#---SEARCH PARAMETERS---
SEARCH ENSEMBLE ensemble1 NUMBER {7}"""
key = key.format(kill_command, hklin, self.i, self.sigi, sgalternative, pdbin, self.solvent, self.nmol)
Phaser.phaser(self.logfile, key)
# Move the output hkl file to specified filename
if os.path.isfile(os.path.join(self.work_dir, 'phaser_mr_output.1.mtz')):
shutil.move(os.path.join(self.work_dir, 'phaser_mr_output.1.mtz'), self.hklout)
# Move output pdb file to specified filename
if os.path.isfile(os.path.join(self.work_dir, 'phaser_mr_output.1.pdb')):
shutil.move(os.path.join(self.work_dir, 'phaser_mr_output.1.pdb'), self.pdbout)
# Return to original working directory
os.chdir(current_work_dir)
# Delete any files copied across
if os.path.isfile(os.path.join(self.work_dir, os.path.basename(self.hklin))):
os.remove(os.path.join(self.work_dir, os.path.basename(self.hklin)))
if os.path.isfile(os.path.join(self.work_dir, os.path.basename(self.pdbin))):
os.remove(os.path.join(self.work_dir, os.path.basename(self.pdbin)))
[docs] @staticmethod
def phaser(logfile, key):
"""Function to run molecular replacement using PHASER
Parameters
----------
logfile : str
Path to the output log file
key : str
PHASER keywords
Returns
-------
file
Output hkl file
file
Output pdb file
file
Output log file
"""
cmd = ["phaser"]
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 MR using PHASER', prefix_chars="-")
group = parser.add_argument_group()
group.add_argument('-enant', type=bool,
help="Try enantimorph space groups <True/False>")
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('-i', type=str,
help="The column label for I")
group.add_argument('-logfile', type=str,
help="Path to the ouput log file")
group.add_argument('-nmol', type=int,
help="The predicted number of molecules to build")
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('-sigi', type=str,
help="The column label for SIGI")
group.add_argument('-solvent',
help="The estimated solvent content of the crystal")
group.add_argument('-timeout', type=int,
help="The time in mins before phaser will kill a job")
group.add_argument('-work_dir', type=str,
help="Path to the working directory")
args = parser.parse_args()
phaser = Phaser(args.enant, args.hklin, args.hklout, args.i, args.logfile, args.nmol,
args.pdbin, args.pdbout, args.sigi, args.solvent, args.timeout, args.work_dir)
phaser.run()
