review items (NO_JIRA))

Author: jasonccole

scripts/refcodes_with_properties/EntryPropertyCalculator.py

@@ -15,18 +15,22 @@
 import ccdc.io
 
 _filter_classes = {}
+
+
 def register(cls):
-    ''' Register a filter class to use in the script. 
-    :param cls: the class to register
+    ''' Register a filter class to use in the script.
+    :param cls: the class to register.
     '''
     if cls.name() in _filter_classes:
         raise ValueError(f"a class with the name {cls.name()} is already registered. Use a different name")
 
     _filter_classes[cls.name()] = cls
 
+
 def filter(name):
    return _filter_classes[name]
 
+
 def helptext():
     ''' Get help text
     '''
@@ -41,15 +45,16 @@ class _Filter(object):
 
     @staticmethod
     def name():
-        raise NotImplementedError # override this
+        raise NotImplementedError  # override this
 
     @staticmethod
     def helptext():
-        raise NotImplementedError # override this
+        raise NotImplementedError  # override this
 
     @staticmethod
     def argument_pair():
-        raise NotImplementedError # override this
+        raise NotImplementedError  # override this
+
 
 class _ComparativeFilter(_Filter):
     def __init__(self, args):
@@ -60,7 +65,7 @@ def __init__(self, args):
         self.expected_value = value
 
     def value(self):
-        raise NotImplementedError # override this
+        raise NotImplementedError  # override this
 
     def __call__(self,theobject):
         value = self.value(theobject)
@@ -71,8 +76,8 @@ class _RangeFilter(_Filter):
     def __init__(self, args):
 
         parts = [ p.strip() for p in args.split() ]
-        self.minimum = eval(parts[0])
-        self.maximum = eval(parts[1])
+        self.minimum = float(parts[0])
+        self.maximum = float(parts[1])
 
     def value(self):
         raise NotImplementedError # override this
@@ -81,9 +86,10 @@ def __call__(self,theobject):
         value = self.value(theobject)
         return value >= self.minimum and value <= self.maximum
 
+
 class AllowedAtomicNumbersFilter(_Filter):
     def __init__(self,args):
-        self.allowed_atomic_numbers = [eval(x) for x in args.strip().split()]
+        self.allowed_atomic_numbers = [int(x) for x in args.strip().split()]
 
     @staticmethod
     def name():
@@ -105,7 +111,7 @@ def __call__(self,entry):
 
 class MustContainAtomicNumbersFilter(_Filter):
     def __init__(self,args):
-        self.must_have_atomic_numbers = [eval(x) for x in args.strip().split()]
+        self.must_have_atomic_numbers = [int(x) for x in args.strip().split()]
 
     @staticmethod
     def name():
@@ -132,8 +138,10 @@ def __call__(self,entry):
         except:
             return False
 
+
 register(MustContainAtomicNumbersFilter)
 
+
 class OrganicFilter(_ComparativeFilter):
     def __init__(self, args):
         super(self.__class__,self).__init__(args)
@@ -149,8 +157,10 @@ def helptext():
     def value(self,entry):
         return entry.is_organic
 
+
 register(OrganicFilter)
 
+
 class PolymericFilter(_ComparativeFilter):
     def __init__(self, args):
         super(self.__class__,self).__init__(args)
@@ -166,8 +176,10 @@ def helptext():
     def value(self,entry):
         return entry.is_polymeric
 
+
 register(PolymericFilter)
 
+
 class AllHaveSitesFilter(_ComparativeFilter):
     def __init__(self, args):
         super(self.__class__,self).__init__(args)
@@ -186,8 +198,10 @@ def value(self,entry):
         except:
             return False
 
+
 register(AllHaveSitesFilter)
 
+
 class DisorderedFilter(_ComparativeFilter):
     def __init__(self, args):
 
@@ -204,6 +218,7 @@ def helptext():
     def value(self,entry):
         return entry.has_disorder
 
+
 register(DisorderedFilter)
 
 
@@ -226,8 +241,10 @@ def value(self,entry):
         except TypeError:
             return 0.0
 
+
 register(AtomicWeightFilter)
 
+
 class AtomCountFilter(_RangeFilter):
     def __init__(self,args):
         super(self.__class__,self).__init__(args)
@@ -247,8 +264,10 @@ def value(self,entry):
         except TypeError:
             return 0
 
+
 register(AtomCountFilter)
 
+
 class RotatableBondFilter(_RangeFilter):
     def __init__(self,args):
         super(self.__class__,self).__init__(args)
@@ -268,8 +287,10 @@ def value(self,entry):
         except TypeError:
             return 0
 
+
 register(RotatableBondFilter)
 
+
 class DonorCountFilter(_RangeFilter):
     def __init__(self,args):
         super(self.__class__,self).__init__(args)
@@ -289,8 +310,10 @@ def value(self,entry):
         except TypeError:
             return 0
 
+
 register(DonorCountFilter)
 
+
 class AcceptorCountFilter(_RangeFilter):
     def __init__(self,args):
         super(self.__class__,self).__init__(args)
@@ -310,8 +333,10 @@ def value(self,entry):
         except TypeError:
             return 0
 
+
 register(AcceptorCountFilter)
 
+
 class ComponentCountFilter(_RangeFilter):
     def __init__(self,args):
         super(self.__class__,self).__init__(args)
@@ -330,6 +355,7 @@ def value(self,entry):
         except TypeError:
             return 0
 
+
 register(ComponentCountFilter)
 
 
@@ -348,6 +374,7 @@ def helptext():
     def value(self,entry):
         return entry.crystal.z_prime
 
+
 register(ZPrimeFilter)
 
 
@@ -366,8 +393,10 @@ def helptext():
     def value(self,entry):
         return entry.r_factor
 
+
 register(RfactorFilter)
 
+
 class SpacegroupNumberFilter(_RangeFilter):
     def __init__(self,args):
         super(self.__class__,self).__init__(args)
@@ -383,8 +412,10 @@ def helptext():
     def value(self,entry):
         return entry.crystal.spacegroup_number_and_setting[0]
 
+
 register(SpacegroupNumberFilter)
 
+
 class FilterEvaluation(object):
     def __init__(self):
         self._methods = []
@@ -412,6 +443,7 @@ def values(self,entry):
                     pass
         return values
 
+
 def parse_control_file(lines):
     evaluator = FilterEvaluation()
     for line in lines:
@@ -423,7 +455,6 @@ def parse_control_file(lines):
     return evaluator
 
 
-
 import unittest
 
 class TestFiltering(unittest.TestCase):