Argument parsing bugfix, plus writeout suppression options.

propka/lib.py

@@ -130,12 +130,19 @@ def parse_res_string(res_str):
     return chain, resnum, inscode
 
 
-def loadOptions(*args):
+def loadOptions(*args, **kwargs):
     """
     load the arguments parser with options
+
+    :Keywords:
+        *commandline*
+            if True, read options from standard in; otherwise, read options
+            from args; default True
     """
     from optparse import OptionParser
 
+    commandline = kwargs.pop('commandline', True)
+
     # defining a 'usage' message
     usage = "usage: %prog [options] filename"
 
@@ -193,7 +200,7 @@ def loadOptions(*args):
 
 
     # parsing and returning options and arguments
-    if len(args) == 0:
+    if commandline:
         # command line
         options, args = parser.parse_args()
     else:

propka/molecular_container.py

@@ -11,7 +11,7 @@
 import propka.pdb, propka.version, propka.output, propka.conformation_container, propka.group, propka.lib
 
 class Molecular_container:
-    def __init__(self, input_file, options=None):
+    def __init__(self, input_file, options=None, writeout=True):
         # printing out header before parsing input
         propka.output.printHeader()
 
@@ -61,8 +61,9 @@ def __init__(self, input_file, options=None):
             self.find_covalently_coupled_groups()
 
             # write out the input file
-            filename = self.file.replace(input_file_extension,'.propka_input')
-            propka.pdb.write_input(self, filename)
+            if writeout:
+                filename = self.file.replace(input_file_extension,'.propka_input')
+                propka.pdb.write_input(self, filename)
 
 
         elif input_file_extension == '.propka_input':

propka/run.py

@@ -14,20 +14,25 @@ def main():
         my_molecule.calculate_pka()
         my_molecule.write_pka()
 
-def single(pdbfile, optargs=None):
+def single(pdbfile, optargs=None, writeout=True):
     """Run a single PROPKA calculation using *pdbfile* as input.
 
     Commandline options can be passed as a **list** in *optargs*.
 
+    *writeout* can be set to ``False`` to skip writing results to a file.
+
     .. rubric:: Example
 
     ::
        single("protein.pdb", optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])
     """
     optargs = optargs if optargs is not None else []
-    options, ignored_pdbfiles = propka.lib.loadOptions(*optargs)
+    options, ignored_pdbfiles = propka.lib.loadOptions(*optargs, commandline=False)
 
-    my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
+    my_molecule = propka.molecular_container.Molecular_container(pdbfile, options, writeout=writeout)
     my_molecule.calculate_pka()
-    my_molecule.write_pka()
+
+    if writeout:
+        my_molecule.write_pka()
+
     return my_molecule