renmae files, move tests (NO_JIRA)

Author: jasonccole

…th_properties/EntryPropertyCalculator.py …_properties/entry_property_calculator.pyscripts/refcodes_with_properties/EntryPropertyCalculator.py renamed to scripts/refcodes_with_properties/entry_property_calculator.py scripts/refcodes_with_properties/EntryPropertyCalculator.py renamed to scripts/refcodes_with_properties/entry_property_calculator.py

@@ -17,7 +17,7 @@
 import sys
 import os
 import argparse
-import EntryPropertyCalculator
+import entry_property_calculator
 from ccdc import io
 
 if __name__ == '__main__':
@@ -28,9 +28,9 @@
 
     parser.add_argument( '-r','--refcode_file', help='input file containing the list of refcodes', default = None )
     parser.add_argument( '-d','--database_file', help='input file containing the list of refcodes', default = None )
-    parser.add_argument( '-c','--control_file', help='configuration file containing the desired properties\n\n %s' % (EntryPropertyCalculator.helptext()) )
-    parser.add_argument( '-v','--get_values', action="store_true", help='calculate and print descriptor values where possible rather than filter\n\n %s' % (EntryPropertyCalculator.helptext()) )
-    parser.add_argument( '-o','--output_file', default = None, help='output CSV file for results\n\n %s' % (EntryPropertyCalculator.helptext()) )
+    parser.add_argument( '-c','--control_file', help='configuration file containing the desired properties\n\n %s' % (entry_property_calculator.helptext()) )
+    parser.add_argument( '-v','--get_values', action="store_true", help='calculate and print descriptor values where possible rather than filter\n\n %s' % (entry_property_calculator.helptext()) )
+    parser.add_argument( '-o','--output_file', default = None, help='output CSV file for results\n\n %s' % (entry_property_calculator.helptext()) )
 
     args = parser.parse_args()
 
@@ -43,7 +43,7 @@
     if args.output_file != None:
         outfile = open(args.output_file, 'wb')
 
-    filterer = EntryPropertyCalculator.parse_control_file(open(control_file,"r").readlines())
+    filterer = entry_property_calculator.parse_control_file(open(control_file,"r").readlines())
 
     reader = None
     if refcode_file:

scripts/refcodes_with_properties/refcodes_with_properties.py

@@ -0,0 +1,153 @@
+import unittest
+from ccdc.io import EntryReader
+
+from entry_property_calculator import parse_control_file
+
+class TestFiltering(unittest.TestCase):
+
+    def setUp(self):
+
+        self.reader = 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)