Removed functions to run molrep/refmac and phaser from mr_util

simbad/util/mr_util.py

@@ -679,68 +679,6 @@ def matthews_coef(self, cell_parameters, space_group):
         os.remove(logfile)
 
         return solvent_content
-
-
-    def molrep(self, model, logfile):
-        """Function to run molecular replacement using MOLREP"""
-
-        cmd = ["molrep"
-               "-f", self.mtz,
-               "-m", os.path.join(self.model_dir, '{0}.pdb'.format(model.pdb_code))]
-        command_line = os.linesep.join(map(str, cmd))
-
-        simbad_util.run_job(command_line, logfile, key='')
-        return
-
-    def phaser(self, model, logfile):
-        """Function to run molecular replacement using PHASER"""
-
-        cmd = "phaser"
-
-        if self.enam:
-            sgalternative = "ALL"
-        else:
-            sgalternative = "HAND"
-
-        key = """#---PHASER COMMAND SCRIPT GENERATED BY SIMBAD---
-MODE MR_AUTO
-ROOT "{0}_mr_output"'
-#---DEFINE DATA---
-HKLIN {1}
-LABIN F={2} SIGF={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 1""".format(model.pdb_code, 
-                                             self.mtz, 
-                                             self.f, self.sigf, 
-                                             sgalternative, 
-                                             os.path.join(self.model_dir, '{0}.pdb'.format(model.pdb_code)), 
-                                             self.solvent)
-
-        simbad_util.run_job(cmd, logfile, key)
-
-        return
-
-    def refmac(self, xyzin, xyzout, hklout, ncyc, logfile):
-        """Function to run refinement using REFMAC"""
-
-        cmd = ['refmac5',
-               'hklin', self.mtz,
-               'hklout', hklout, 
-               'xyzin', xyzin,
-               'xyzout', xyzout]
-        command_line = os.linesep.join(map(str, cmd))
-
-        key = "ncyc = {0}".format(ncyc)
-
-        simbad_util.run_job(command_line, logfile, key)
-        return
 
     def summarize(self, csv_file="mr_results.csv"):
         """Summarize the search results