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jasonccolejasonccole
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renmae files, move tests (NO_JIRA)
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3 files changed

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3 files changed

+158
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‎scripts/refcodes_with_properties/EntryPropertyCalculator.py renamed to ‎scripts/refcodes_with_properties/entry_property_calculator.py

File renamed without changes.

‎scripts/refcodes_with_properties/refcodes_with_properties.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@
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import sys
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import os
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import argparse
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import EntryPropertyCalculator
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import entry_property_calculator
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from ccdc import io
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if __name__ == '__main__':
@@ -28,9 +28,9 @@
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parser.add_argument( '-r','--refcode_file', help='input file containing the list of refcodes', default = None )
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parser.add_argument( '-d','--database_file', help='input file containing the list of refcodes', default = None )
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parser.add_argument( '-c','--control_file', help='configuration file containing the desired properties\n\n %s' % (EntryPropertyCalculator.helptext()) )
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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()) )
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parser.add_argument( '-o','--output_file', default = None, help='output CSV file for results\n\n %s' % (EntryPropertyCalculator.helptext()) )
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parser.add_argument( '-c','--control_file', help='configuration file containing the desired properties\n\n %s' % (entry_property_calculator.helptext()) )
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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()) )
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parser.add_argument( '-o','--output_file', default = None, help='output CSV file for results\n\n %s' % (entry_property_calculator.helptext()) )
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args = parser.parse_args()
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@@ -43,7 +43,7 @@
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if args.output_file != None:
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outfile = open(args.output_file, 'wb')
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filterer = EntryPropertyCalculator.parse_control_file(open(control_file,"r").readlines())
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filterer = entry_property_calculator.parse_control_file(open(control_file,"r").readlines())
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reader = None
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if refcode_file:

‎scripts/refcodes_with_properties/test_entry_property_calculator.py

Lines changed: 153 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,153 @@
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import unittest
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from ccdc.io import EntryReader
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from entry_property_calculator import parse_control_file
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class TestFiltering(unittest.TestCase):
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def setUp(self):
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self.reader = EntryReader('CSD')
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self.aabhtz = self.reader.entry("AABHTZ")
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self.aacani_ten = self.reader.entry("AACANI10")
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self.aadamc = self.reader.entry("AADAMC")
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self.aadrib = self.reader.entry("AADRIB")
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self.abadis = self.reader.entry("ABADIS")
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def test_organic_filter(self):
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test_file = """
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organic : 1
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"""
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lines = test_file.split('\n')
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evaluator = parse_control_file(lines)
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self.assertTrue(evaluator.evaluate(self.aabhtz))
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self.assertFalse(evaluator.evaluate(self.aacani_ten))
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def test_component_filter(self):
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test_file = """
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component range : 0 1
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"""
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lines = test_file.split('\n')
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evaluator = parse_control_file(lines)
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self.assertTrue(evaluator.evaluate(self.aabhtz))
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self.assertFalse(evaluator.evaluate(self.aacani_ten))
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def test_donor_count_filter(self):
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test_file = """
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donor count : 2 2
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"""
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lines = test_file.split('\n')
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evaluator = parse_control_file(lines)
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self.assertFalse(evaluator.evaluate(self.aabhtz))
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self.assertTrue(evaluator.evaluate(self.aadamc))
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test_file = """
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donor count : 0 3
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"""
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lines = test_file.split('\n')
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evaluator = parse_control_file(lines)
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self.assertTrue(evaluator.evaluate(self.aabhtz))
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self.assertTrue(evaluator.evaluate(self.aadamc))
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def test_acceptor_count_filter(self):
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test_file = """
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acceptor count : 7 7
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"""
64+
lines = test_file.split('\n')
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evaluator = parse_control_file(lines)
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# regards Cl as an acceptor ...
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self.assertTrue(evaluator.evaluate(self.aabhtz))
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self.assertTrue(evaluator.evaluate(self.aacani_ten))
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def test_zprime(self):
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test_file = """
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zprime range : 0.99 1.01
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"""
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lines = test_file.split('\n')
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evaluator = parse_control_file(lines)
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self.assertTrue(evaluator.evaluate(self.aabhtz))
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self.assertFalse(evaluator.evaluate(self.aadrib))
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def test_atomic_numbers(self):
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test_file = """
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allowed atomic numbers : 1 6 7 8
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must have atomic numbers : 1 6 7 8
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"""
86+
lines = test_file.split('\n')
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evaluator = parse_control_file(lines)
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self.assertFalse(evaluator.evaluate(self.aabhtz))
89+
self.assertFalse(evaluator.evaluate(self.aadrib))
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test_file = """
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must have atomic numbers : 1 6 7 8
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"""
94+
lines = test_file.split('\n')
95+
evaluator = parse_control_file(lines)
96+
self.assertTrue(evaluator.evaluate(self.aabhtz))
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self.assertFalse(evaluator.evaluate(self.aadrib))
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99+
def test_rotatable_bond_count(self):
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test_file = """
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rotatable bond count : 0 3
102+
"""
103+
lines = test_file.split('\n')
104+
evaluator = parse_control_file(lines)
105+
self.assertTrue(evaluator.evaluate(self.abadis))
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107+
def test_multiple(self):
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test_file = """
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# An example control file
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#
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#
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# only include organic structures as output
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organic : 1
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# specify a range of donors
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donor count : 0 10
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# specify a range of acceptors
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acceptor count : 5 5
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# rotatable bond count range
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rotatable bond count : 3 7
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# number of atoms to allow through
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atom count : 0 100
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# only include structures containing Hydrogen, Carbon, Nitrogen or Oxygen and nothing else
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allowed atomic numbers : 1 6 7 8
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# only include structures containing all of these elements (i.e.) Hydrogen, Carbon, Nitrogen or Oxygen
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must have atomic numbers : 1 6 7 8
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# Ensure Z-prime is one
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zprime range : 0.99 1.01
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# Ensure only one component in the structure
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component range : 2 2
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# Dont include disordered structures
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disordered : 0
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# Specify an R-factor range
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rfactor range : 0.1 5
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#
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137+
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"""
139+
140+
lines = test_file.split('\n')
141+
evaluator = parse_control_file(lines)
142+
143+
counter = 0
144+
hits = []
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146+
test_entries = ['AABHTZ', 'ABAQEB', 'ABELEY', 'ADAQOM', 'ADARAA', 'ADARAZ', 'ADUWIG', 'AFEREK']
147+
for id in test_entries:
148+
e = self.reader.entry(id)
149+
150+
if evaluator.evaluate(e):
151+
hits.append(e.identifier)
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153+
self.assertEquals(['ABAQEB', 'ABELEY', 'ADAQOM', 'ADUWIG', 'AFEREK'], hits)

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