Minor changes and refactoring.

- Added helper function for initializing the logger in Qpyl.common
- Added torsion calculations and fixed rmsd in Qpyl.core.qcalc
- Added some newly implemented parameter keywords to Qpyl.core.qdyninp
- Fatal errors due to 'bad' inputs/keywords in Qpyl.core.qdyninp /
  Qpyl.qgeninp / q_genrelax.py / q_genfeps.py can now be bypassed with
  ignore_errors / --ignore_errors

packages/Qpyl/common.py

@@ -28,6 +28,7 @@
 # Some common classes and functions
 
 import math
+import sys
 import os
 import shutil
 import logging
@@ -50,7 +51,40 @@ def format(self, record):
         return logging.Formatter.format(self, record)
 
 
-def raise_or_log(message, exception_class, logger, ignore_errors=False):
+def init_logger(name,
+                level=None,
+                handler=None,
+                formatter=None):
+    """Helper function for initializing the logger.
+
+    Args:
+        name (string):  module name, usually root: 'Qpyl'
+        level (int, optional):  logging level (DEBUG, INFO, WARNING...),
+                                default is INFO
+        handler: (logging.Handler, optional):  default is
+                                               StreamHandler(sys.stdout)
+        formatter: (logging.Formatter, optional): default is
+                                                  SpecialFormatter
+
+    Returns:
+        lg (logging.Logger)
+
+    """
+    lg = logging.getLogger(name)
+    if level == None:
+        level = logging.INFO
+    lg.setLevel(level)
+
+    if handler == None:
+        handler = logging.StreamHandler(sys.stdout)
+    if formatter == None:
+        handler.setFormatter(SpecialFormatter())
+
+    lg.addHandler(handler)
+    return lg
+
+
+def raise_or_log(message, exception_class, logger, ignore_errors):
     """Method used for raising exceptions or writting them to logger instead
 
     This way one can bypass certain exceptions like non-integer charge groups,

packages/Qpyl/core/qcalc.py

@@ -75,10 +75,7 @@ def run(self, qcalc_input_str, workdir=None):
         # "\n" is added to fix the blocking qcalc5 issue 
         stdout, stderr = self.process.communicate(qcalc_input_str + "\n")
 
-        # not sure if this ever happens, but will keep it anyway
-        if stderr:
-            raise QCalcError("QCalc wrote to STDERR: {}".format(stderr))
-
+        # stderr is useless in qcalc5
         return stdout
 
 
@@ -128,7 +125,22 @@ def add_angle(self, atom1, atom2, atom3):
 
         """
         self.actions.append((self.CALC_ANGLE, ["{} {} {}".format(atom1,
-                                                                 atom2)]))
+                                                                 atom2,
+                                                                 atom3)]))
+    def add_torsion(self, atom1, atom2, atom3, atom4):
+        """Add a torsion/torsion_energy calculation.
+
+        Args:
+            atom1 (int): index of atom in topology
+            atom2 (int): index of atom in topology
+            atom3 (int): index of atom in topology
+            atom4 (int): index of atom in topology
+
+        """
+        self.actions.append((self.CALC_TORSION,
+                             ["{} {} {} {}".format(atom1, atom2,
+                                                   atom3, atom4)]))
+
 
     def add_rmsd(self, masks):
         """Add a RMSD calculation.
@@ -139,7 +151,8 @@ def add_rmsd(self, masks):
         """
         if isinstance(masks, basestring):
             masks = [masks,]
-        self.actions.append((self.CALC_RMSD, "rmsd.out", masks + ["."]))
+        # rmsd.out is due to the unfortunate feature added in Q c79ef672400
+        self.actions.append((self.CALC_RMSD, masks + [".",] + ["rmsd.out",]))
 
     def add_residue_nb_mon(self, resid_first, resid_last, masks):
         """Add a residue nonbond monitor calculation.
@@ -254,6 +267,12 @@ def _parse(self):
                 self.results[calc_i] = DataContainer(["Frame", "angle"])
             elif "angle, qangle energy between" in line:
                 self.results[calc_i] = DataContainer(["Frame", "angle"])
+            elif "torsion between" in line:
+                self.results[calc_i] = DataContainer(["Frame", "torsion"])
+            elif "torsion, torsion energy between" in line:
+                self.results[calc_i] = DataContainer(["Frame", "torsion"])
+            elif "torsion, qtorsion energy between" in line:
+                self.results[calc_i] = DataContainer(["Frame", "torsion"])
             elif "nonbond monitor for residues" in line:
                 pass
             else: