#!/usr/bin/env ccp4-python
"""
Created on 2 Feb 2015
@author: jmht
"""
import logging
import os
import shutil
import sys
import uuid
from ample.util import ample_util, mtz_util
try:
from mrbump.parsers import parse_shelxe
except ImportError:
mrbumpd = os.path.join(os.environ['CCP4'], "share", "mrbump", "include", "parsers")
sys.path.insert(0, mrbumpd)
import parse_shelxe
logger = logging.getLogger(__name__)
[docs]class MRinfo(object):
"""An object to analyse Molecular Replacement solutions
Attributes
----------
work_dir : str
Path to the working directory
shelxe_exe : str
Path to the SHELXE executable
stem : str
The name for all the SHELXE files
originShift : list
The origin shift of the MR pdb to native as a list of three floats
MPE : float
The Mean Phase Error of the MR pdb to the native pdb
wMPE : float
The weighted Mean Phase Error of the MR pdb to the native pdb
"""
def __init__(self, shelxe_exe, native_pdb, native_mtz, work_dir=None):
"""Intialise from native pdb and mtz so that analyse only requires a MR pdb
Parameters
----------
shelxe_exe : str
Path to the SHELXE executable
native_pdb : str
Path to the native PDB file
native_mtz : str
Path to the native MTZ file
"""
self.work_dir = work_dir or os.getcwd()
self.shelxe_exe = shelxe_exe
self.stem = 'shelxe-input-{}'.format(str(uuid.uuid1()))
self.MPE = None
self.wMPE = None
self.originShift = None
self.mk_native_files(native_pdb, native_mtz)
return
[docs] def mk_native_files(self, native_pdb, native_mtz):
"""Create the files required by SHELXE from the native structure
Parameters
----------
native_pdb : str
Path to the native PDB file
native_mtz : str
Path to the native MTZ file
"""
mtz_util.to_hkl(native_mtz, hkl_file=os.path.join(self.work_dir, self.stem + ".hkl"))
shutil.copyfile(native_pdb, os.path.join(self.work_dir, self.stem + ".ent"))
[docs] def analyse(self, mr_pdb, cleanup=True):
"""Use SHELXE to analyse an MR pdb file to determine the origin shift and phase error
This function sets the ``MPE``, ``wMPE`` and ``originShift`` attributes.
Parameters
----------
mr_pdb : str
Path to the Molecular Replacement PDB file
"""
os.chdir(self.work_dir)
input_pdb = self.stem + ".pda"
shutil.copyfile(mr_pdb, os.path.join(self.work_dir, input_pdb))
cmd = [self.shelxe_exe, input_pdb, '-a0', '-q', '-s0.5', '-o', '-n', '-t0', '-m0', '-x']
logfile = os.path.abspath('shelxe_{}.log'.format(str(uuid.uuid1())))
ret = ample_util.run_command(cmd=cmd, logfile=logfile, directory=None, dolog=False, stdin=None)
if ret != 0:
raise RuntimeError("Error running shelxe - see log: {0}".format(logfile))
sp = parse_shelxe.ShelxeLogParser(logfile)
# Only added in later version of MRBUMP shelxe parser
if hasattr(sp, 'MPE'):
self.MPE = sp.MPE
self.wMPE = sp.wMPE
if isinstance(sp.originShift, list):
self.originShift = [o * -1 for o in sp.originShift]
if cleanup:
for ext in ['.hkl', '.ent', '.pda', '.pdo', '.phs', '.lst', '_trace.ps']:
try:
os.unlink(self.stem + ext)
except:
pass
os.unlink(logfile)
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description='Determine origin using SHELXE', prefix_chars="-")
parser.add_argument('--native_mtz', help='Native MTZ', required=True)
parser.add_argument('--native_pdb', help='Native PDB', required=True)
parser.add_argument('--mr_pdb', help='Molecular Replacement MTZ', required=True)
parser.add_argument('--executable', help="Path to SHELXE executable")
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
executable = None
if args.executable:
executable = args.executable
else:
executable = os.path.join(os.environ['CCP4'], "bin", "shelxe" + ample_util.EXE_EXT)
# Get full paths to all files
native_mtz = os.path.abspath(args.native_mtz)
if not os.path.isfile(native_mtz):
raise RuntimeError("Cannot find input file: {0}".format(native_mtz))
native_pdb = os.path.abspath(args.native_pdb)
if not os.path.isfile(native_pdb):
raise RuntimeError("Cannot find input file: {0}".format(native_pdb))
mr_pdb = os.path.abspath(args.mr_pdb)
if not os.path.isfile(mr_pdb):
raise RuntimeError("Cannot find input file: {0}".format(mr_pdb))
mrinfo = MRinfo(executable, native_pdb, native_mtz)
mrinfo.analyse(mr_pdb)
os.unlink('shelxe-input.hkl')
os.unlink('shelxe-input.ent')
logger.info("Origin shift is: {0}".format(mrinfo.originShift))
logger.info("Phase error is MPE: {0} | wMPE: {1}".format(mrinfo.originShift, mrinfo.MPE, mrinfo.wMPE))
