bug fixes and changed default mr_program from phaser to molrep

rigdenlab · May 5, 2017 · bc046bd · bc046bd
1 parent da05222
commit bc046bd
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/simbad/command_line/__init__.py b/simbad/command_line/__init__.py
@@ -105,7 +105,7 @@ def _argparse_mr_options(p):
                     help='Path to file containing keywords for the refinement program')
     sg.add_argument('-amore_exe', type=str, default=os.path.join(os.environ["CCP4"], 'bin', 'amoreCCB2.exe'),
                     help='Path to amore executable')
-    sg.add_argument('-mr_program', type=str, default="phaser",
+    sg.add_argument('-mr_program', type=str, default="molrep",
                     help='Path to the MR program to use. Options: < molrep | phaser >')
     sg.add_argument('-refine_program', type=str, default="refmac5",
                     help='Path to the refinement program to use. Options: < refmac5 >')

diff --git a/simbad/util/simbad_util.py b/simbad/util/simbad_util.py
@@ -116,7 +116,7 @@ def run_job(cmd, logfile=None, directory=None, stdin=None):
     return p.returncode
 
 
-def molecular_weight(self, model):
+def molecular_weight(model):
     """Function to run ``rwcontents`` to get the molecular weight of a model
 
     Parameters
@@ -131,7 +131,7 @@ def molecular_weight(self, model):
 
     """
     cmd = ['rwcontents', 'xyzin', model]
-    logfile = 'rwcontents_{0}.log'.format(self.name)
+    logfile = 'rwcontents.log'.format()
     run_job(cmd, logfile=logfile)
 
     # Exctract molecular weight from log file