Add eps keyword argument to P_cif and getParser.

Support setting of the coordinates-resolution eps when constructing
the CIF parser object.

Author: pavoljuhas

diffpy/Structure/Parsers/P_cif.py

@@ -234,13 +234,18 @@ def _get_atom_setters(cifloop):
     # normal methods
     ########################################################################
 
-    def __init__(self):
+    def __init__(self, eps=None):
+        """Initialize the parser for CIF structure files.
+
+        eps  -- fractional coordinates cutoff for duplicate positions.
+                When None use the default for ExpandAsymmetricUnit.
+        """
         StructureParser.__init__(self)
         self.format = "cif"
         self.ciffile = None
         self.stru = None
         self.spacegroup = None
-        self.eps = None
+        self.eps = eps
         self.eau = None
         self.asymmetric_unit = None
         self.labelindex = {}
@@ -722,7 +727,12 @@ def restoreParserOutput(self):
         return
 
 
-def getParser():
-    return P_cif()
+def getParser(eps=None):
+    """Return new parser object for CIF structure format.
+
+    eps  -- fractional coordinates cutoff for duplicate positions.
+            When None use the default for ExpandAsymmetricUnit.
+    """
+    return P_cif(eps=eps)
 
 # End of file

diffpy/Structure/Parsers/__init__.py

@@ -35,8 +35,11 @@
 from diffpy.Structure.Parsers.structureparser import StructureParser
 from diffpy.Structure.Parsers.parser_index_mod import parser_index
 
-def getParser(format):
+def getParser(format, **kw):
     """Return Parser instance for a given structure format.
+
+    kw   -- keyword arguments passed to the Parser init function.
+
     Raises StructureFormatError exception when format is not defined.
     """
     if format not in parser_index:
@@ -46,7 +49,7 @@ def getParser(format):
     pm = None
     import_cmd = 'from diffpy.Structure.Parsers import %s as pm' % pmod
     exec(import_cmd)
-    return pm.getParser()
+    return pm.getParser(**kw)
 
 def inputFormats():
     """Return list of implemented input structure formats"""

diffpy/Structure/tests/TestP_cif.py

@@ -20,6 +20,7 @@
 
 from diffpy.Structure.tests.testutils import datafile
 from diffpy.Structure.Parsers.P_cif import P_cif, leading_float, getSymOp
+from diffpy.Structure.Parsers import getParser
 from diffpy.Structure import Structure
 from diffpy.Structure import StructureFormatError
 
@@ -232,6 +233,19 @@ def test_eps(self):
         self.assertEqual(4, len(grph2))
         return
 
+    def test_getParser(self):
+        """Test passing of eps keyword argument by getParser function.
+        """
+        pcif = getParser('cif', eps=1e-6)
+        grph = pcif.parseFile(self.graphiteciffile)
+        self.assertEqual(8, len(grph))
+        self.assertTrue(all(a.label.startswith('C1') for a in grph[:2]))
+        self.assertTrue(all(a.label.startswith('C2') for a in grph[2:]))
+        pcif2 = getParser('cif')
+        grph2 = pcif2.parseFile(self.graphiteciffile)
+        self.assertEqual(4, len(grph2))
+        return
+
     ########################################################################
     # helpers
     ########################################################################