refactor and fix tests (NO_JIRA)

Author: jasonccole

scripts/refcodes_with_properties/entry_property_calculator.py

@@ -101,8 +101,7 @@ def helptext():
     def __call__(self, entry):
         try:
             molecule = entry.crystal.molecule
-            return len([x for x in molecule.atoms if x.atomic_number in self.allowed_atomic_numbers]) == len(
-                molecule.atoms)
+            return len([x for x in molecule.atoms if x.atomic_number in self.allowed_atomic_numbers]) == len(molecule.atoms)
         except TypeError:
             return False
 
@@ -126,17 +125,16 @@ def __call__(self, entry):
         try:
             molecule = entry.crystal.molecule
 
-            contains = {}
+            contains = set()
             for x in molecule.atoms:
-                if not contains.has_key(x.atomic_number):
-                    contains[x.atomic_number] = 0
-                contains[x.atomic_number] = contains[x.atomic_number] + 1
+                contains.add(x.atomic_number)
+
             for x in self.must_have_atomic_numbers:
-                if not contains.has_key(x):
+                if x not in contains:
                     return False
 
             return True
-        except:
+        except TypeError:
             return False
 
 
@@ -196,7 +194,7 @@ def helptext():
     def value(self, entry):
         try:
             return entry.crystal.molecule.all_atoms_have_sites
-        except:
+        except TypeError:
             return False
 
 
@@ -453,160 +451,3 @@ def parse_control_file(lines):
                 cls = _filter_classes[parts[0].strip()]
                 evaluator.add_filter(cls(parts[1]))
     return evaluator
-
-
-import unittest
-
-
-class TestFiltering(unittest.TestCase):
-
-    def setUp(self):
-
-        self.reader = ccdc.io.EntryReader('CSD')
-        self.aabhtz = self.reader.entry("AABHTZ")
-        self.aacani_ten = self.reader.entry("AACANI10")
-        self.aadamc = self.reader.entry("AADAMC")
-        self.aadrib = self.reader.entry("AADRIB")
-        self.abadis = self.reader.entry("ABADIS")
-
-    def test_organic_filter(self):
-
-        test_file = """
-organic : 1
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-
-        self.assertTrue(evaluator.evaluate(self.aabhtz))
-
-        self.assertFalse(evaluator.evaluate(self.aacani_ten))
-
-    def test_component_filter(self):
-        test_file = """
-component range : 0 1
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-
-        self.assertTrue(evaluator.evaluate(self.aabhtz))
-
-        self.assertFalse(evaluator.evaluate(self.aacani_ten))
-
-    def test_donor_count_filter(self):
-        test_file = """
-donor count : 2 2
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-
-        self.assertFalse(evaluator.evaluate(self.aabhtz))
-
-        self.assertTrue(evaluator.evaluate(self.aadamc))
-
-        test_file = """
-donor count : 0 3
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-
-        self.assertTrue(evaluator.evaluate(self.aabhtz))
-        self.assertTrue(evaluator.evaluate(self.aadamc))
-
-    def test_acceptor_count_filter(self):
-        test_file = """
-acceptor count : 7 7
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-
-        # regards Cl as an acceptor ...
-        self.assertTrue(evaluator.evaluate(self.aabhtz))
-
-        self.assertTrue(evaluator.evaluate(self.aacani_ten))
-
-    def test_zprime(self):
-        test_file = """
-zprime range : 0.99 1.01
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-        self.assertTrue(evaluator.evaluate(self.aabhtz))
-        self.assertFalse(evaluator.evaluate(self.aadrib))
-
-    def test_atomic_numbers(self):
-        test_file = """
-allowed atomic numbers : 1 6 7 8
-must have atomic numbers : 1 6 7 8
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-        self.assertFalse(evaluator.evaluate(self.aabhtz))
-        self.assertFalse(evaluator.evaluate(self.aadrib))
-
-        test_file = """
-must have atomic numbers : 1 6 7 8
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-        self.assertTrue(evaluator.evaluate(self.aabhtz))
-        self.assertFalse(evaluator.evaluate(self.aadrib))
-
-    def test_rotatable_bond_count(self):
-        test_file = """
-rotatable bond count : 0 3
-"""
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-        self.assertTrue(evaluator.evaluate(self.abadis))
-
-    def test_multiple(self):
-        test_file = """
-
-# An example control file
-#
-#
-# only include organic structures as output
-organic : 1
-# specify a range of donors
-donor count     : 0 10
-# specify a range of acceptors
-acceptor count :    5 5
-# rotatable bond count range
-rotatable bond count : 3 7
-# number of atoms to allow through
-atom count : 0 100
-# only include structures containing Hydrogen, Carbon, Nitrogen or Oxygen and nothing else
-allowed atomic numbers : 1 6 7 8
-# only include structures containing all of these elements (i.e.) Hydrogen, Carbon, Nitrogen or Oxygen
-must have atomic numbers : 1 6 7 8
-# Ensure Z-prime is one
-zprime range : 0.99 1.01
-# Ensure only one component in the structure
-component range : 2 2
-# Dont include disordered structures
-disordered : 0
-# Specify an R-factor range
-rfactor range : 0.1 5
-#
-
-
-"""
-
-        lines = test_file.split('\n')
-        evaluator = parse_control_file(lines)
-
-        counter = 0
-        hits = []
-
-        test_entries = ['AABHTZ', 'ABAQEB', 'ABELEY', 'ADAQOM', 'ADARAA', 'ADARAZ', 'ADUWIG', 'AFEREK']
-        for id in test_entries:
-            e = self.reader.entry(id)
-
-            if evaluator.evaluate(e):
-                hits.append(e.identifier)
-
-        self.assertEquals(['ABAQEB', 'ABELEY', 'ADAQOM', 'ADUWIG', 'AFEREK'], hits)
-
-
-if __name__ == "__main__":
-    unittest.main()

scripts/refcodes_with_properties/test_entry_property_calculator.py

@@ -98,7 +98,7 @@ def test_atomic_numbers(self):
 
     def test_rotatable_bond_count(self):
         test_file = """
-rotatable bond count : 0 3
+rotatable bond count : 0 4
 """
         lines = test_file.split('\n')
         evaluator = parse_control_file(lines)
@@ -150,4 +150,4 @@ def test_multiple(self):
             if evaluator.evaluate(e):
                 hits.append(e.identifier)
 
-        self.assertEquals(['ABAQEB', 'ABELEY', 'ADAQOM', 'ADUWIG', 'AFEREK'], hits)
+        self.assertEqual(['ABAQEB', 'ABELEY', 'ADAQOM', 'ADUWIG', 'AFEREK'], hits)