Created a class to run refmac

simbad/util/refmac_util.py

@@ -0,0 +1,176 @@
+"""Module to run refmac on a model"""
+
+import os
+import simbad_util
+
+__author__ = "Adam Simpkin"
+__date__ = "02 May 2017"
+__version__ = "0.1"
+
+
+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
+    ncyc : int float
+        The number of cycles of refinement to perform [default : 30]
+
+    Examples
+    --------
+    >>> from simbad.util.refmac_util 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
+
+    def run(self, ncyc=30):
+        """Function to run refinement using REFMAC
+
+        Parameters
+        ----------
+        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
+        """
+
+        key = "ncyc {0}".format(ncyc)
+
+        self.refmac(self.hklin, self.hklout, self.pdbin, self.pdbout, self.logfile, key)
+        return
+
+    @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]
+        command_line = os.linesep.join(map(str, cmd))
+
+        simbad_util.run_job(command_line, logfile, key)
+        return