Chirality and 3D structure filters added NO_JIRA

Added option to filter for one specific chirality value, might extend this at some point if anyone requests it.
Added 3D structure bool filter
Added exception when RuntimeError is raised for some space group searches

Author: pmbulit

scripts/refcodes_with_properties/entry_property_calculator.py

@@ -85,6 +85,23 @@ def __call__(self, theobject):
         return value >= self.minimum and value <= self.maximum
 
 
+class _ValueFilter(_Filter):
+    def __init__(self, args):
+        values = [p for p in args.split()]
+        #To do: add option for two values?
+        if values[0] == 'None':
+            self.expected_value = None
+        else:
+            self.expected_value = values[0]
+
+    def value(self, theobject):
+        raise NotImplementedError  # override this
+
+    def __call__(self, theobject):
+        value = self.value(theobject)
+        return value == self.expected_value
+
+
 class AllowedAtomicNumbersFilter(_Filter):
     def __init__(self, args):
         self.allowed_atomic_numbers = [int(atomic_number) for atomic_number in args.strip().split()]
@@ -200,6 +217,25 @@ def value(self, entry):
 register(AllHaveSitesFilter)
 
 
+class Has3DStructure(_ComparativeFilter):
+    def __init__(self, args):
+        super().__init__(args)
+
+    @staticmethod
+    def name():
+        return "has 3D structure"
+
+    @staticmethod
+    def helptext():
+        return "whether 3D coordinates have been determined for the structure"
+
+    def value(self, entry):
+        return entry.has_3d_structure
+
+
+register(Has3DStructure)
+
+
 class DisorderedFilter(_ComparativeFilter):
     def __init__(self, args):
         super().__init__(args)
@@ -413,6 +449,30 @@ def value(self, entry):
 register(SpacegroupNumberFilter)
 
 
+class ChiralityFilter(_ValueFilter):
+    def __init__(self, args):
+        super().__init__(args)
+
+    @staticmethod
+    def name():
+        return "chirality"
+
+    @staticmethod
+    def helptext():
+        return "specify the chirality value to be used as filter"
+
+    def value(self, entry):
+        try:
+            molecule = entry.crystal.molecule
+            chirality = next((atom.chirality for atom in molecule.atoms if atom.is_chiral), None)
+            return chirality
+        except TypeError:
+            return None
+
+
+register(ChiralityFilter)
+
+
 class FilterEvaluation(object):
     def __init__(self):
         self._methods = []
@@ -425,7 +485,7 @@ def evaluate(self, entry):
             try:
                 if not method(entry):
                     return False
-            except TypeError:
+            except (TypeError, RuntimeError):
                 return False
 
         return True

scripts/refcodes_with_properties/refcodes_with_properties.py

@@ -46,7 +46,7 @@
 
     outfile = sys.stdout
     if args.output_file is not None:
-        outfile = open(args.output_file, 'wb')
+        outfile = open(args.output_file, 'w', encoding='utf-8')
 
     filterer = entry_property_calculator.parse_control_file(open(control_file, "r").readlines())