import os
from pyjob import cexec
from swamp.parsers import RefmacParser
from swamp.wrappers.wrapper import Wrapper
[docs]class wRefmac(Wrapper):
"""Refmac5 wrapper
:param str workdir: working directory where refmac will be executed
:param str pdbin: pdb filename with the placed search model
:param str mtzin: target's mtz filename
:param str make_hydr: mset MAKE_HYDR (default: 'N')
:param str weight_matrix: set WEIGHT MATRIX stdin value for jelly body refinement (default: '0.01')
:param str ridg_dist_sigm: set RIDG DIST SIGM stdin value for jelly body refinement (default: '0.02')
:param str ncyc: number of refinement cycles (default: '100')
:param str phased_mtz: target's mtz filename containing phases (default: None)
:param bool silent_start: if True, the logger will not display the start banner (default False)
:param `~swamp.logger.swamplogger.SwampLogger` logger: logging interface for the wrapper (default None)
:ivar str rfree: calculated Rfree after refinement
:ivar str rfactor: calculated Rfactor after refinement
:ivar tuple rfactor_delta: a tuple with the intial and final Rfactor
:ivar tuple rfree_delta: a tuple with the intial and final Rfree
:ivar tuple bondlenght_delta: a tuple with the intial and final Bond length
:ivar tuple bondangle_delta: a tuple with the intial and final Bond angle
:ivar tuple chirvol_delta: a tuple with the intial and final Chirvol
:ivar str ovarall_CC: overall correlation coefficient between phases at \
:py:attr:`~swamp.wrappers.wrefmac.wRefmac.phased_mtz` and the refined search model
:ivar str local_CC: local correlation coefficient between phases at \
:py:attr:`~swamp.wrappers.wrefmac.wRefmac.phased_mtz` and the refined search model
:example:
>>> from swamp.wrappers import wRefmac
>>> my_refmac = wRefmac('<workdir>', '<pdbin>', '<mtzin>')
>>> my_refmac.run()
>>> my_refmac.make_logfile()
"""
def __init__(self, workdir, pdbin, mtzin, make_hydr='N', weight_matrix="0.01", ncyc="100", ridg_dist_sigm="0.02",
logger=None, phased_mtz=None, silent_start=False):
super(wRefmac, self).__init__(logger=logger, workdir=workdir, silent_start=silent_start)
self.rfactor = "NA"
self.rfree = "NA"
self.rfactor_delta = ("NA", "NA")
self.rfree_delta = ("NA", "NA")
self.bondlenght_delta = ("NA", "NA")
self.bondangle_delta = ("NA", "NA")
self.chirvol_delta = ("NA", "NA")
self.local_CC = "NA"
self.overall_CC = "NA"
self.make_hydr = make_hydr
self.ridg_dist_sigm = ridg_dist_sigm
self.weight_matrix = weight_matrix
self.ncyc = ncyc
self.pdbin = pdbin
self.mtzin = mtzin
self.phased_mtz = phased_mtz
@property
def wrapper_name(self):
"""The name of this `~swamp.wrapper.wrapper.Wrapper` child class (refmac)"""
return "refmac5"
@property
def cmd(self):
"""Command to be executed on the shell"""
return [self.source, 'hklin', self.mtzin, 'hklout', self.mtzout, 'xyzin', self.pdbin, 'xyzout', self.pdbout]
@property
def summary_results(self):
"""String representation of a summary of the obtained figures of merit"""
return "Refmac results: Rfactor - %s Rfree - %s Local CC - %s Overall CC - %s" \
"" % (self.rfactor, self.rfree, self.local_CC, self.overall_CC)
@property
def keywords(self):
"""Keywords tos be passed to refmac5 through the stdin"""
return "RIDG DIST SIGM %s" % self.ridg_dist_sigm + os.linesep + "MAKE HYDR %s" % \
self.make_hydr + os.linesep + "WEIGHT MATRIX %s" % self.weight_matrix \
+ os.linesep + "NCYC %s" % self.ncyc + os.linesep + "END"
[docs] def get_scores(self, logfile=None):
"""Parse the logfile and extract scores after refinement using a \
:py:obj:`~swamp.parsers.refmacparser.RefmacParser` instance
:param None logfile: Not in use (default None)
"""
parser = RefmacParser(self.logcontents, logger=self.logger)
parser.parse()
# If there was an error
if parser.error:
self.error = True
self.logger.warning('Previous detected while parsing refmac output!')
return
self.rfactor, self.rfree, self.rfactor_delta, self.rfree_delta, self.bondlenght_delta, \
self.bondangle_delta, self.chirvol_delta = parser.summary
# If everything is ok so far, get the CC
if self.phased_mtz is not None:
self.local_CC, self.overall_CC = self.get_cc(os.path.join(self.workdir, "phenix"), self.phased_mtz,
self.pdbout)
def _run(self):
"""Run :py:attr:`~swamp.wrappers.wrefmac.wRefmac.cmd` in the shell"""
if not self.silent_start:
self.logger.info(self.wrapper_header)
self.logger.info('Running %s cycles of refinement' % self.ncyc)
self.make_workdir()
tmp_dir = os.getcwd()
os.chdir(self.workdir)
self.logger.debug(" ".join(self.cmd))
self.logcontents = cexec(self.cmd, stdin=self.keywords, permit_nonzero=True)
self.get_scores()
if not self.error and (not os.path.isfile(self.pdbout) or not os.path.isfile(self.mtzout)):
self.logger.error("refmac output pdb/mtz missing!")
self.error = True
self.logger.info(self.summary_results)
os.chdir(tmp_dir)
