docs added and bug fix for matthews_coef function in mr_util

docs/api/command_line.rst

@@ -0,0 +1,13 @@
+Command line subpackage
+=======================
+
+.. automodule:: simbad.command_line
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. toctree::
+   :glob:
+
+   generated/simbad.command_line.*
+

docs/api/generated/simbad.command_line.rst

@@ -12,6 +12,7 @@ Submodules
 .. toctree::
 
    simbad.command_line.simbad_contaminant
+   simbad.command_line.simbad_create_lattice_db
    simbad.command_line.simbad_lattice
    simbad.command_line.simbad_main
 

docs/api/generated/simbad.command_line.simbad_create_lattice_db.rst

@@ -0,0 +1,7 @@
+simbad.command_line.simbad_create_lattice_db module
+===================================================
+
+.. automodule:: simbad.command_line.simbad_create_lattice_db
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/generated/simbad.parsers.molrep_parser.rst

@@ -0,0 +1,7 @@
+simbad.parsers.molrep_parser module
+===================================
+
+.. automodule:: simbad.parsers.molrep_parser
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/generated/simbad.parsers.phaser_parser.rst

@@ -0,0 +1,7 @@
+simbad.parsers.phaser_parser module
+===================================
+
+.. automodule:: simbad.parsers.phaser_parser
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/generated/simbad.parsers.refmac_parser.rst

@@ -0,0 +1,7 @@
+simbad.parsers.refmac_parser module
+===================================
+
+.. automodule:: simbad.parsers.refmac_parser
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/generated/simbad.parsers.rst

@@ -11,5 +11,7 @@ Submodules
 
 .. toctree::
 
-   simbad.parsers.database_parser
+   simbad.parsers.molrep_parser
+   simbad.parsers.phaser_parser
+   simbad.parsers.refmac_parser
 

docs/api/generated/simbad.rst

@@ -23,5 +23,5 @@ Submodules
 .. toctree::
 
    simbad.constants
-   simbad.main
+   simbad.version
 

docs/api/generated/simbad.util.molrep_util.rst

@@ -0,0 +1,7 @@
+simbad.util.molrep_util module
+==============================
+
+.. automodule:: simbad.util.molrep_util
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/generated/simbad.util.phaser_util.rst

@@ -0,0 +1,7 @@
+simbad.util.phaser_util module
+==============================
+
+.. automodule:: simbad.util.phaser_util
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/generated/simbad.util.pyrvapi_results.rst

@@ -0,0 +1,7 @@
+simbad.util.pyrvapi_results module
+==================================
+
+.. automodule:: simbad.util.pyrvapi_results
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/generated/simbad.util.refmac_util.rst

@@ -0,0 +1,7 @@
+simbad.util.refmac_util module
+==============================
+
+.. automodule:: simbad.util.refmac_util
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/generated/simbad.util.rst

@@ -12,16 +12,15 @@ Submodules
 .. toctree::
 
    simbad.util.anomalous_util
-   simbad.util.argparse_util
    simbad.util.clusterize
-   simbad.util.config_util
    simbad.util.exit_util
-   simbad.util.logging_util
+   simbad.util.molrep_util
    simbad.util.mr_util
    simbad.util.mtz_util
-   simbad.util.options_processor
+   simbad.util.phaser_util
+   simbad.util.pyrvapi_results
+   simbad.util.refmac_util
    simbad.util.simbad_util
-   simbad.util.version
    simbad.util.worker
    simbad.util.workers_util
 

docs/api/generated/simbad.version.rst

@@ -0,0 +1,7 @@
+simbad.version module
+=====================
+
+.. automodule:: simbad.version
+    :members:
+    :undoc-members:
+    :show-inheritance:

simbad/rotsearch/amore_search.py

@@ -420,7 +420,7 @@ def matthews_coef(self, model, cell_parameters, space_group, min_solvent_content
         """
 
         # Get the molecular weight of the input model
-        molecular_weight = self.rwcontents(model)
+        molecular_weight = simbad_util.molecular_weight(model)
 
         cmd = ["matthews_coef"]
         key = """CELL {0}
@@ -498,42 +498,6 @@ def rotfun(self, logs_dir, shres, intrad, pklim, npic, rotastep):
         logfile = os.path.join(self.work_dir, logs_dir, '{0}.log'.format(self.name))
         simbad_util.run_job(cmd, logfile=logfile, stdin=key)
 
-    def rwcontents(self, model):
-        """Function to run ``rwcontents`` to get the molecular weight of a model
-
-        Parameters
-        ----------
-        model : str
-            Path to input model
-
-        Returns
-        -------
-        float
-            Molecular weight of input model
-        """
-
-        cmd = ['rwcontents',
-               'xyzin', model]
-
-        logfile = 'rwcontents_{0}.log'.format(self.name)
-        simbad_util.run_job(cmd, logfile=logfile)
-
-        # Exctract molecular weight from log file
-        molecular_weight = None
-        with open(logfile, 'r') as f:
-            for line in f:
-                if line.startswith(" Molecular Weight of protein"):
-                    molecular_weight = float(line.split()[-1])
-        if not molecular_weight:
-            msg = "Cannot find Molecular weight in logfile {0}".format(logfile)
-            logger.debug(msg)
-            raise RuntimeError(msg)
-
-        # Clean up
-        os.remove(logfile)
-
-        return molecular_weight
-
     def sortfun(self):
         """A function to prepare files for amore rotation function
 

simbad/util/mr_util.py

@@ -335,14 +335,13 @@ def get_mtz_info(self, mtz):
             The predicted solvent content of the protein
         """
         # Extract crystal data from input mtz
-        self._cell_parameters, self._resolution, self._space_group = mtz_util.crystal_data(mtz)
+        self._space_group, _, self._cell_parameters = mtz_util.crystal_data(mtz)
 
         # Extract column labels from input mtz
         self._f, self._sigf, self._dano, self._sigdano, self._free = mtz_util.get_labels(mtz)
 
         # Get solvent content
         self._solvent = self.matthews_coef(self._cell_parameters, self._space_group)
-        return
 
     def multiprocessing(self, results, time_out=60, nproc=2):
         """Code to run MR and refinement in parallel
@@ -511,26 +510,25 @@ def matthews_coef(self, cell_parameters, space_group):
             solvent content of the protein
 
         """
-
         cmd = ["matthews_coef"]
         key = """CELL {0}
-symm {1}
-auto""".format(cell_parameters,
-               space_group)
+        symm {1}
+        auto""".format(cell_parameters,
+                       space_group)
 
         logfile = 'matt_coef.log'
         ret = simbad_util.run_job(cmd, logfile=logfile, stdin=key)
-        if ret != 0:
-            msg = "matthews_coef exited with non-zero return code. Log is {0}".format(logfile)
+        if ret and ret != 0:
+            msg = "matthews_coef exited with non-zero return code ({0}). Log is {1}".format(ret, logfile)
             logger.critical(msg)
             raise RuntimeError(msg)
 
         # Determine if the model can fit in the unit cell
         solvent_content = 0.5
-        with open(logfile, 'r') as f:
-            for line in f:
-                if line.startswith('  1'):
-                    solvent_content = (float(line.split()[2]) / 100)
+        for line in open(logfile, 'r'):
+            if line.startswith('  1'):
+                solvent_content = (float(line.split()[2]) / 100)
+                break
 
         os.remove(logfile)
         return solvent_content

simbad/util/mtz_util.py

@@ -17,8 +17,6 @@
 logger.setLevel(logging.DEBUG)
 
 
-
-
 # TODO: Get rid of this function completely
 def set_crystal_data(optd):
     """Set crystallographic parameters from mtz file"""

simbad/util/simbad_util.py

@@ -116,6 +116,39 @@ def run_job(cmd, logfile=None, directory=None, stdin=None):
     return p.returncode
 
 
+def molecular_weight(self, model):
+    """Function to run ``rwcontents`` to get the molecular weight of a model
+
+    Parameters
+    ----------
+    model : str
+       Path to input model
+
+    Returns
+    -------
+    float
+       Molecular weight of input model
+
+    """
+    cmd = ['rwcontents', 'xyzin', model]
+    logfile = 'rwcontents_{0}.log'.format(self.name)
+    run_job(cmd, logfile=logfile)
+
+    # Exctract molecular weight from log file
+    molecular_weight = None
+    with open(logfile, 'r') as f:
+        for line in f:
+            if line.startswith(" Molecular Weight of protein"):
+                molecular_weight = float(line.split()[-1])
+    if not molecular_weight:
+        msg = "Cannot find Molecular weight in logfile {0}".format(logfile)
+        logger.debug(msg)
+        raise RuntimeError(msg)
+
+    os.remove(logfile)
+    return molecular_weight
+
+
 def tmp_file_name(delete=True, directory=None, suffix=""):
     """Return a filename for a temporary file