def test_process_part2(self):
"""
check results of calls to removeNeighbors, filterBasedOnAngs,
removeBadAts...
"""
hb_builder = HydrogenBondBuilder()
hb_builder.check_babel_types(self.mol.allAtoms)
result = hb_builder.buildD(self.mol.allAtoms, hb_builder.paramDict)
hAts = result['hAts']
acceptorAts = result['acceptorAts']
dist = hb_builder.paramDict['distCutoff']
atDict = hb_builder.distSelector.select(hAts, acceptorAts, dist)
self.assertEqual(len(atDict), 40)
atDict = hb_builder.removeNeighbors(atDict)
self.assertEqual(len(atDict), 30)
donor2Ats = result['donor2Ats']
donor3Ats = result['donor3Ats']
acceptor2Ats = result['acceptor2Ats']
acceptor3Ats = result['acceptor3Ats']
badAtDict = hb_builder.filterBasedOnAngs(atDict, donor2Ats, donor3Ats,
acceptor2Ats, acceptor3Ats, hb_builder.paramDict)
self.assertEqual(len(badAtDict), 30)
atDict = hb_builder.removeBadAts(atDict, badAtDict)
self.assertEqual(len(atDict), 28)
def test_process_part2(self):
"""
check results of calls to removeNeighbors, filterBasedOnAngs,
removeBadAts...
"""
hb_builder = HydrogenBondBuilder()
hb_builder.check_babel_types(self.mol.allAtoms)
result = hb_builder.buildD(self.mol.allAtoms, hb_builder.paramDict)
hAts = result['hAts']
acceptorAts = result['acceptorAts']
dist = hb_builder.paramDict['distCutoff']
atDict = hb_builder.distSelector.select(hAts, acceptorAts, dist)
self.assertEqual(len(atDict), 40)
atDict = hb_builder.removeNeighbors(atDict)
self.assertEqual(len(atDict), 30)
donor2Ats = result['donor2Ats']
donor3Ats = result['donor3Ats']
acceptor2Ats = result['acceptor2Ats']
acceptor3Ats = result['acceptor3Ats']
badAtDict = hb_builder.filterBasedOnAngs(atDict, donor2Ats, donor3Ats,
acceptor2Ats, acceptor3Ats,
hb_builder.paramDict)
self.assertEqual(len(badAtDict), 30)
atDict = hb_builder.removeBadAts(atDict, badAtDict)
self.assertEqual(len(atDict), 28)
def test_buildD(self):
"""
test buildD: donor3Ats, acceptor3Ats, acceptor2Ats, donor2Ats
"""
hb_builder = HydrogenBondBuilder()
hb_builder.check_babel_types(self.mol.allAtoms)
result = hb_builder.buildD(self.mol.allAtoms, hb_builder.paramDict)
#result_keys = ['donor3Ats', 'acceptor3Ats', 'acceptor2Ats', 'donor2Ats']
result_keys = [
'donor3Ats', 'acceptor3Ats', 'hAts', 'acceptorAts', 'acceptor2Ats',
'donor2Ats'
]
d = {}
d['donor3Ats'] = [
'N', 'OG1', 'OG1', 'SG', 'SG', 'OG', 'OG', 'SG', 'OG1', 'SG',
'OG1', 'OH', 'OG1', 'SG', 'OG1', 'SG', 'OH'
]
d['acceptor3Ats'] = [
'OG1', 'OG1', 'SG', 'SG', 'OG', 'OG', 'SG', 'OG1', 'SG', 'OG1',
'OH', 'OG1', 'SG', 'OG1', 'SG', 'OH'
]
d['hAts'] = [
'HN1', 'HN2', 'HN3', 'HG1', 'HN', 'HG1', 'HN', 'HN', 'HN', 'HG',
'HN', 'HN', 'HN', 'HN', 'HE', 'HH11', 'HH12', 'HH21', 'HH22', 'HN',
'HG', 'HN', 'HD21', 'HD22', 'HN', 'HN', 'HD21', 'HD22', 'HN', 'HN',
'HN', 'HE', 'HH11', 'HH12', 'HH21', 'HH22', 'HN', 'HN', 'HN',
'HG1', 'HN', 'HN', 'HN', 'HN', 'HN', 'HN', 'HG1', 'HN', 'HH', 'HN',
'HG1', 'HN', 'HN', 'HN', 'HN', 'HN', 'HN', 'HN', 'HN', 'HG1', 'HN',
'HN', 'HN', 'HN', 'HH', 'HN', 'HN', 'HD21', 'HD22'
]
d['donor2Ats'] = [
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'NE', 'NH1', 'NH2', 'N',
'N', 'ND2', 'N', 'N', 'ND2', 'N', 'N', 'N', 'NE', 'NH1', 'NH2',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'ND2'
]
d['acceptor2Ats'] = [
'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD1',
'O', 'O', 'OD1', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O',
'OE1', 'OE2', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O',
'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD1', 'OD2',
'O', 'O', 'O', 'OD1', 'OXT'
]
#acceptorAts = acceptor2Ats + acceptor3Ats
d['acceptorAts'] = [
'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD1',
'O', 'O', 'OD1', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O',
'OE1', 'OE2', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O',
'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD1', 'OD2',
'O', 'O', 'O', 'OD1', 'OXT', 'OG1', 'OG1', 'SG', 'SG', 'OG', 'OG',
'SG', 'OG1', 'SG', 'OG1', 'OH', 'OG1', 'SG', 'OG1', 'SG', 'OH'
]
for k in result_keys:
#print 'testing ', k, ': '
if result[k] is not None and len(result[k]):
self.assertEqual(result[k].name, d[k])
else:
self.assertEqual(result[k], d[k])
def test_process_part1(self):
"""
check hAts and acceptorAts from buildD
"""
hb_builder = HydrogenBondBuilder()
hb_builder.check_babel_types(self.mol.allAtoms)
result = hb_builder.buildD(self.mol.allAtoms, hb_builder.paramDict)
hAts = result['hAts']
self.assertEqual(len(hAts), 69)
acceptorAts = result['acceptorAts']
self.assertEqual(len(acceptorAts), 70)
def test_process_part1(self):
"""
check hAts and acceptorAts from buildD
"""
hb_builder = HydrogenBondBuilder()
hb_builder.check_babel_types(self.mol.allAtoms)
result = hb_builder.buildD(self.mol.allAtoms, hb_builder.paramDict)
hAts = result['hAts']
self.assertEqual(len(hAts), 69)
acceptorAts = result['acceptorAts']
self.assertEqual(len(acceptorAts), 70)
def test_buildHbonds_babelTypes(self):
"""
test assigning babel_types
"""
hb_builder = HydrogenBondBuilder()
hb_builder.check_babel_types(self.mol.allAtoms)
d = {}
for a in self.mol.allAtoms:
d[a.babel_type] = 1
all_types= d.keys()
all_types.sort()
#print "all_types=", all_types
#note: these are polar only hydrogens so no type 'HC'
canned_list = ['C+', 'C2', 'C3', 'Cac', 'H', 'N3+',
'Nam', 'Ng+', 'O-', 'O2', 'O3', 'S3']
for k, v in zip(all_types, canned_list):
self.assertEqual(k,v)
def test_buildHbonds_babelTypes(self):
"""
test assigning babel_types
"""
hb_builder = HydrogenBondBuilder()
hb_builder.check_babel_types(self.mol.allAtoms)
d = {}
for a in self.mol.allAtoms:
d[a.babel_type] = 1
all_types = d.keys()
all_types.sort()
#print "all_types=", all_types
#note: these are polar only hydrogens so no type 'HC'
canned_list = [
'C+', 'C2', 'C3', 'Cac', 'H', 'N3+', 'Nam', 'Ng+', 'O-', 'O2',
'O3', 'S3'
]
for k, v in zip(all_types, canned_list):
self.assertEqual(k, v)
def test_buildD(self):
"""
test buildD: donor3Ats, acceptor3Ats, acceptor2Ats, donor2Ats
"""
hb_builder = HydrogenBondBuilder()
hb_builder.check_babel_types(self.mol.allAtoms)
result = hb_builder.buildD(self.mol.allAtoms, hb_builder.paramDict)
#result_keys = ['donor3Ats', 'acceptor3Ats', 'acceptor2Ats', 'donor2Ats']
result_keys = ['donor3Ats', 'acceptor3Ats', 'hAts', 'acceptorAts', 'acceptor2Ats', 'donor2Ats']
d = {}
d['donor3Ats'] = ['N', 'OG1', 'OG1', 'SG', 'SG', 'OG', 'OG', 'SG', 'OG1', 'SG', 'OG1', 'OH', 'OG1', 'SG', 'OG1', 'SG', 'OH']
d['acceptor3Ats'] = ['OG1', 'OG1', 'SG', 'SG', 'OG', 'OG', 'SG', 'OG1', 'SG', 'OG1', 'OH', 'OG1', 'SG', 'OG1', 'SG', 'OH']
d['hAts'] = ['HN1', 'HN2', 'HN3', 'HG1', 'HN', 'HG1', 'HN', 'HN', 'HN', 'HG', 'HN', 'HN', 'HN', 'HN', 'HE', 'HH11', 'HH12', 'HH21', 'HH22', 'HN', 'HG', 'HN', 'HD21', 'HD22', 'HN', 'HN', 'HD21', 'HD22', 'HN', 'HN', 'HN', 'HE', 'HH11', 'HH12', 'HH21', 'HH22', 'HN', 'HN', 'HN', 'HG1', 'HN', 'HN', 'HN', 'HN', 'HN', 'HN', 'HG1', 'HN', 'HH', 'HN', 'HG1', 'HN', 'HN', 'HN', 'HN', 'HN', 'HN', 'HN', 'HN', 'HG1', 'HN', 'HN', 'HN', 'HN', 'HH', 'HN', 'HN', 'HD21', 'HD22']
d['donor2Ats'] = ['N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'NE', 'NH1', 'NH2', 'N', 'N', 'ND2', 'N', 'N', 'ND2', 'N', 'N', 'N', 'NE', 'NH1', 'NH2', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'ND2']
d['acceptor2Ats'] = ['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD1', 'O', 'O', 'OD1', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OE1', 'OE2', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD1', 'OD2', 'O', 'O', 'O', 'OD1', 'OXT']
#acceptorAts = acceptor2Ats + acceptor3Ats
d['acceptorAts'] = ['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD1', 'O', 'O', 'OD1', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OE1', 'OE2', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD1', 'OD2', 'O', 'O', 'O', 'OD1', 'OXT', 'OG1', 'OG1', 'SG', 'SG', 'OG', 'OG', 'SG', 'OG1', 'SG', 'OG1', 'OH', 'OG1', 'SG', 'OG1', 'SG', 'OH']
for k in result_keys:
#print 'testing ', k, ': '
if result[k] is not None and len(result[k]):
self.assertEqual(result[k].name, d[k])
else:
self.assertEqual(result[k], d[k])
