def testCanSCNTBond(self):
truepatterns = [
'ASFD', 'HRKD', 'LMNE', 'DEDE', 'ADAE',
[
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Glutamic_Acid',
'L-Alanine'
]
]
falsepatterns = [
'AAAA', 'ADAA', 'SYTA', 'IEWPVIWPV',
[
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
]
]
badpatterns = [
'CBCB', ['L-Notexistene', 'D-Fakene', 'L-Notexistene', 'D-Fakene']
]
for pattern in truepatterns:
self.assertTrue(
sg.can_scntbond(pattern) != False
and sg.can_scntbond(pattern) != None,
'%s cannot SCNT bond' % pattern)
for pattern in falsepatterns:
self.assertTrue(
sg.can_scntbond(pattern) == False,
'%s can SCNT bond' % pattern)
for pattern in badpatterns:
self.assertRaises(sg.UndefinedAminoError, sg.can_scntbond, pattern)
def testConstrainedPeptide(self):
testdic = {
('CAAC', 'SSCXXC'):
'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS1)C(=O)O',
('CACAC', 'SSXXCXC'):
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS1)C(=O)O',
('CWCCWC', 'SSXXCXXC'):
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)N[C@@]([H])(CS3)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)N[C@@]([H])(CS3)C(=O)O',
('CAAC', 'HT'):
'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS)C(=O)1',
('CACAC', 'HT'):
'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS)C(=O)1',
('CWCCWC', 'HT'):
'N3[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)N[C@@]([H])(CS)C(=O)3',
('KPVEE', 'SCNXXXZ'):
'N[C@@]([H])(CCCCN2)C(=O)N1[C@@]([H])(CCC1)C(=O)N[C@@]([H])(C(C)C)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)N[C@@]([H])(CCC2(=O))C(=O)O',
('SHRDK', 'SCEXXZX'):
'N[C@@]([H])(CO2)C(=O)N[C@@]([H])(CC1=CN=C-N1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CC2(=O))C(=O)N[C@@]([H])(CCCCN)C(=O)O',
('AELMK', 'SCXZXXN'):
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CCC1(=O))C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCSC)C(=O)N[C@@]([H])(CCCCN1)C(=O)O',
('SKYTE', 'SCXNXXX'):
'N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCCN2)C(=O)N[C@@]([H])(Cc1ccc(O)cc1)C(=O)N[C@@]([H])(C(O)C)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)2',
('QGCAE', 'SCXXXXZ'):
'N1[C@@]([H])(CCC(=O)N)C(=O)NCC(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'
}
for (seq, bond_def), smi in testdic.items():
self.assertTrue(sg.constrained_peptide_smiles(seq,bond_def)[2]==smi, \
'Wrong smiles for %s: is %s should be %s' % \
(seq, sg.constrained_peptide_smiles(seq,bond_def)[2], smi))
def testCanSSBond(self):
truepatterns = [
'CAAC', 'CCCC', 'HFHFCHCHHHC',
['L-Cysteine', 'L-Alanine', 'L-Glutamine', 'L-Cysteine'],
[
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
]
]
falsepatterns = [
'CACA', 'HDET',
['L-Cysteine', 'L-Threonine', 'L-Cysteine', 'L-Tryptophan'],
['L-Asparagine', 'Glycine', 'L-Alanine', 'L-Histidine'],
[
'L-Arginine', 'L-Glutamic_Acid', 'L-Proline',
'L-Glutamic_Acid', 'L-Proline'
]
]
badpatterns = ['CBC', ['L-Notexistene', 'D-Fakene']]
for pattern in truepatterns:
self.assertTrue(sg.can_ssbond(pattern) !=
False and sg.can_ssbond(pattern) != None, \
'%s cannot ssbond' % pattern)
for pattern in falsepatterns:
self.assertTrue(sg.can_ssbond(pattern) == False, \
'%s can ssbond' % pattern)
for pattern in badpatterns:
self.assertRaises(sg.UndefinedAminoError, sg.can_ssbond, pattern)
def testGenAllMatchingPeptides(self):
testpatterns = ['CXXXC','SSSX','DXDX', \
'YYXYXX', ['L-Cysteine','X','X'],['L-Glutamic_Acid','X','X']]
for pattern in testpatterns:
library = list(sg.gen_all_matching_peptides(pattern))
num_peps = len(library)
self.assertTrue( num_peps== len(sg.aminodata)**pattern.count('X'),
'Incorrect combinations')
#Check for duplicates - sets can't contain duplicates, so...
peps = []
for pep in sg.gen_all_matching_peptides(pattern):
#Lists not hashable, so create string representation
peps.append('-'.join([str(num) for num in pep]))
self.assertTrue(len(set(peps)) == num_peps, 'Duplicate peptides')
bad_patterns = ['12345', '^$%']
bad_type = [23, 450]
for pattern in bad_patterns:
test = sg.gen_all_matching_peptides(pattern)
self.assertRaises(sg.UndefinedAminoError, test.next)
for pattern in bad_type:
test = sg.gen_all_matching_peptides(pattern)
self.assertRaises(TypeError, test.next)
def testAddAmino(self): lib_len = len(sg.print_included_aminos()) for amino in ['D-Lysine', 'L-Ornithine', 'D-Glutamic_Acid']: sg.add_amino(amino) lib_len += 1 self.assertTrue(len(sg.print_included_aminos()) == lib_len ) for not_amino in ['ASDDF', 'lysine', '2']: self.assertRaises(sg.UndefinedAminoError, sg.add_amino, not_amino)
def testAddAmino(self):
lib_len = len(sg.print_included_aminos())
for amino in ['D-Lysine', 'L-Ornithine', 'D-Glutamic_Acid']:
sg.add_amino(amino)
lib_len += 1
self.assertTrue(len(sg.print_included_aminos()) == lib_len)
for not_amino in ['ASDDF', 'lysine', '2']:
self.assertRaises(sg.UndefinedAminoError, sg.add_amino, not_amino)
def testRemoveAmino(self): lib_len = len(sg.print_included_aminos()) for amino in ['D-Lysine', 'L-Ornithine', 'D-Glutamic_Acid']: sg.remove_amino(amino) lib_len-=1 self.assertTrue(len(sg.print_included_aminos()) == (lib_len)) for amino in ['D-Glutamine','D-Serine']: self.assertRaises(sg.UndefinedAminoError, sg.remove_amino, amino)
def testRemoveAmino(self):
lib_len = len(sg.print_included_aminos())
for amino in ['D-Lysine', 'L-Ornithine', 'D-Glutamic_Acid']:
sg.remove_amino(amino)
lib_len -= 1
self.assertTrue(len(sg.print_included_aminos()) == (lib_len))
for amino in ['D-Glutamine', 'D-Serine']:
self.assertRaises(sg.UndefinedAminoError, sg.remove_amino, amino)
def testPepPositions(self):
teststrings = []
for k in range(3, 10):
resis = random.sample(sg.return_available_residues(), k)
random.shuffle(resis)
teststrings.append(''.join(resis))
for seq in teststrings:
locs = sg.pep_positions(seq)
smi = sg.linear_peptide_smiles(seq)
for loc in locs:
self.assertTrue(smi[loc] == 'N', \
'Seq %s loc %s in locs %s is %s' % (seq, loc, locs, smi[loc]))
def testPepPositions(self):
teststrings = []
for k in range(3,10):
resis = random.sample(sg.return_available_residues(),k)
random.shuffle(resis)
teststrings.append(''.join(resis))
for seq in teststrings:
locs = sg.pep_positions(seq)
smi = sg.linear_peptide_smiles(seq)
for loc in locs:
self.assertTrue(smi[loc] == 'N', \
'Seq %s loc %s in locs %s is %s' % (seq, loc, locs, smi[loc]))
def testCanHTBond(self): truepatterns = ['CAAFC', 'FCCCC','HFHFCHCHHHC', ['L-Cysteine','L-Leucine','L-Arginine','L-Cysteine','L-Alanine'], ['L-Cysteine','L-Serine','L-Arginine','L-Cysteine','L-Alanine']] falsepatterns = ['CACA','HDET', 'FG', ['L-Phenylalanine','L-Glutamine'],['L-Isoleucine','L-Asparagine']] badpatterns = ['CBC', ['L-Notexistene','D-Fakene']] for pattern in truepatterns: self.assertTrue(sg.can_htbond(pattern) != False and sg.can_htbond(pattern) != None) for pattern in falsepatterns: self.assertTrue(sg.can_htbond(pattern) == False)
def testGenAllPosPeptides(self):
for num in range(2,5):
library = list(sg.gen_all_pos_peptides(num))
num_peps = len(library)
num_no_dups = len(set(library))
self.assertTrue(num_peps == len(sg.aminodata)**num,
'Incorrect combinations... ')
#Check for duplicates - sets can't contain duplicates, so...
self.assertTrue(num_no_dups == num_peps,'Duplicate Peptides')
bad_iterator = sg.gen_all_pos_peptides('3a')
self.assertRaises(TypeError, bad_iterator.next)
def testGenAllPosPeptides(self):
for num in range(2, 5):
library = list(sg.gen_all_pos_peptides(num))
num_peps = len(library)
num_no_dups = len(set(library))
self.assertTrue(num_peps == len(sg.aminodata)**num,
'Incorrect combinations... ')
#Check for duplicates - sets can't contain duplicates, so...
self.assertTrue(num_no_dups == num_peps, 'Duplicate Peptides')
bad_iterator = sg.gen_all_pos_peptides('3a')
self.assertRaises(TypeError, bad_iterator.next)
def testLinearPeptideSmiles(self):
testdic = {
'AAAA':'N[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)\
N[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)O',
'AGAG':'N[C@@]([H])(C)C(=O)NCC(=O)N[C@@]([H])(C)C(=O)NCC(=O)O',
'PQE':'N1[C@@]([H])(CCC1)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])\
(CCC(=O)O)C(=O)O',
'CNVR':'N[C@@]([H])(CS)C(=O)N[C@@]([H])(C(=O)N)C(=O)\
N[C@@]([H])(C(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)O'
}
for seq, smi in testdic.items():
self.assertTrue(sg.linear_peptide_smiles(seq)==smi, \
'Wrong smiles for %s: saw %s, should be %s'\
% (seq,sg.linear_peptide_smiles(seq),smi ))
def testCanSCCTbond(self): #Can bond K,S,Y,T uniquely truepatterns = ['KHRK','SMNS','YQGC','TYEN'] falsepatterns = ['FLWK','GRCNS','FLWANPY','RFACGT'] badpatterns = ['CBCBC', ['L-Notexistene','D-Fakene', 'L-Notexistene','D-Fakene']] for pattern in truepatterns: self.assertTrue( sg.can_scctbond(pattern) != False and sg.can_scctbond(pattern) != None, '%s cannot SCCT bond' % pattern) for pattern in falsepatterns: self.assertTrue(sg.can_scctbond(pattern) == False, '%s can SCCT bond' % pattern) for pattern in badpatterns: self.assertRaises(sg.UndefinedAminoError, sg.can_scctbond, pattern)
def testBondCounter(self):
testdic = {
'N1[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])\
(C)C(=O)N[C@@]([H])(C)C(=O)1':1,
'N[C@@]([H])(C)C(=O)NCC(=O)N[C@@]([H])(C)C(=O)NCC(=O)O':0,
'N9[C@@]([H])(CCC9)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])\
(CCC(=O)O)C(=O)O':9,
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(C(=O)N)C(=O)N[C@@]([H])\
(C(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)O':0,
'N[C@@]([H])(CS5)C(=O)N[C@@]([H])(C(=O)N)C(=O)N[C@@]([H])(C(C)C)C(=O)\
N[C@@]([H])(CS5)C(=O)O':5
}
for smi, bondcount in testdic.items():
self.assertTrue(sg.bond_counter(smi)==bondcount,\
'Bondcounter: %s should be %s' % (sg.bond_counter(smi),bondcount))
def testCanSCSCBond(self): #Can bond K,S,T to D,E truepatterns = ['KAAD','DAAK','SASGE'] falsepatterns = ['KQGQG','A'] badpatterns = ['CBCB', ['L-Notexistene','D-Fakene', 'L-Notexistene','D-Fakene']] for pattern in truepatterns: self.assertTrue( sg.can_scscbond(pattern) != False and sg.can_scscbond(pattern) != None, '%s cannot SCSC bond' % pattern) for pattern in falsepatterns: self.assertTrue(sg.can_scscbond(pattern) == False, '%s can SCSC bond' % pattern) for pattern in badpatterns: self.assertRaises(sg.UndefinedAminoError, sg.can_scscbond, pattern)
def testWhatConstraints(self):
tests = [('CAAC',['SSCXXC']), ('AAGAA',['HT']),
(['L-Cysteine','L-Serine','L-Arginine','L-Cysteine','L-Alanine'],
['SSCXXCX','HT','SCXEXXX']) ]
for seq, constraints in tests:
self.assertTrue(sg.what_constraints(seq)==constraints)
def testCountConstraintTypes(self):
input = [
('ASDF','','N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)O'),
('QFDSA', 'HT', 'N2[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)2'),
('QFDSA', '', 'N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)O'),
('CRQSC', 'SSCXXXC', 'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS1)C(=O)O'),
('CRQSC', 'HT', 'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)1'),
('CRQSC', '', 'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)O'),
('DSCCK', 'HT', 'N1[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'),
('DSCCK', 'SCXEXXX', 'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'),
('DSCCK', 'SCZXXXN', 'N[C@@]([H])(CC1(=O))C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN1)C(=O)O'),
('DSCCK', '', 'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)O'),
(['L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine', 'L-Alanine'], 'SSCXXCX', 'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)O'),
(['L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine', 'L-Alanine'], 'HT', 'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)1'),
(['L-Cysteine','L-Leucine','L-Arginine','L-Cysteine','L-Alanine'], '', 'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'HT', 'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXEXXX', 'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXXXXZ', 'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXEXXZ', 'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'],'','N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)O')]
count_dict = {'linear':6, 'SS':2, 'HT':5, 'SCSC':2, 'SCCT':2, 'SCNT':1}
test_count_dict = sg.count_constraint_types(input)
self.assertTrue(count_dict == test_count_dict, 'true %s test %s' % (count_dict, test_count_dict))
def testCanSCNTBond(self): truepatterns = ['ASFD','HRKD','LMNE','DEDE','ADAE', ['L-Cysteine','L-Leucine','L-Arginine','L-Glutamic_Acid','L-Alanine']] falsepatterns = ['AAAA','ADAA','SYTA','IEWPVIWPV', ['L-Cysteine','L-Leucine','L-Arginine','L-Cysteine','L-Alanine']] badpatterns = ['CBCB', ['L-Notexistene','D-Fakene', 'L-Notexistene','D-Fakene']] for pattern in truepatterns: self.assertTrue( sg.can_scntbond(pattern) !=False and sg.can_scntbond(pattern) != None,'%s cannot SCNT bond' % pattern) for pattern in falsepatterns: self.assertTrue(sg.can_scntbond(pattern) == False, '%s can SCNT bond' % pattern) for pattern in badpatterns: self.assertRaises(sg.UndefinedAminoError, sg.can_scntbond, pattern)
def testStructsFromSeqs(self):
#gen_structs_from_seqs(sequences, ssbond=False,htbond=False,scctbond=False,
#scntbond=False,scscbond=False,linear=False):
seqs = ['ASDF','QFDSA','CRQSC','DSCCK',
['L-Cysteine','L-Leucine','L-Arginine','L-Cysteine','L-Alanine'],
['L-Alanine','L-Serine','L-Arginine','L-Cysteine','L-Glutamic_Acid']]
results = [
('ASDF','','N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)O'),
('QFDSA', 'HT', 'N2[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)2'),
('QFDSA', '', 'N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)O'),
('CRQSC', 'SSCXXXC', 'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS1)C(=O)O'),
('CRQSC', 'HT', 'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)1'),
('CRQSC', '', 'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)O'),
('DSCCK', 'HT', 'N1[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'),
('DSCCK', 'SCXEXXX', 'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'),
('DSCCK', 'SCZXXXN', 'N[C@@]([H])(CC1(=O))C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN1)C(=O)O'),
('DSCCK', '', 'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)O'),
(['L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine', 'L-Alanine'], 'SSCXXCX', 'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)O'),
(['L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine', 'L-Alanine'], 'HT', 'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)1'),
(['L-Cysteine','L-Leucine','L-Arginine','L-Cysteine','L-Alanine'], '', 'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'HT', 'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXEXXX', 'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXXXXZ', 'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXEXXZ', 'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'],'','N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)O')]
trial = sg.gen_structs_from_seqs(seqs, ssbond=True, htbond=True,
scctbond=True, scntbond=True, scscbond=True, linear=True)
for a, b in zip(results, trial):
self.assertTrue(a == b, ' real %s trial %s' % (a, b))
def testReturnSmiles(self):
#test letter and 3 letter codes
testdic = {'A':'N[C@@]([H])(C)C(=O)O','W':\
'N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)O',\
'Val':'N[C@@]([H])(C(C)C)C(=O)O',\
'Gln':'N[C@@]([H])(CCC(=O)N)C(=O)O'}
for code, smi in testdic.items():
self.assertTrue(sg.return_smiles(code) == smi)
def testReturnSmiles(self):
#test letter and 3 letter codes
testdic = {'A':'N[C@@]([H])(C)C(=O)O','W':\
'N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)O',\
'Val':'N[C@@]([H])(C(C)C)C(=O)O',\
'Gln':'N[C@@]([H])(CCC(=O)N)C(=O)O'}
for code, smi in testdic.items():
self.assertTrue(sg.return_smiles(code)==smi)
def testCanSSBond(self): truepatterns = ['CAAC', 'CCCC','HFHFCHCHHHC', ['L-Cysteine','L-Alanine','L-Glutamine','L-Cysteine'], ['L-Cysteine','L-Leucine','L-Arginine','L-Cysteine','L-Alanine']] falsepatterns = ['CACA','HDET', ['L-Cysteine','L-Threonine','L-Cysteine','L-Tryptophan'], ['L-Asparagine','Glycine','L-Alanine','L-Histidine'], ['L-Arginine','L-Glutamic_Acid','L-Proline','L-Glutamic_Acid','L-Proline']] badpatterns = ['CBC', ['L-Notexistene','D-Fakene']] for pattern in truepatterns: self.assertTrue(sg.can_ssbond(pattern) != False and sg.can_ssbond(pattern) != None, \ '%s cannot ssbond' % pattern) for pattern in falsepatterns: self.assertTrue(sg.can_ssbond(pattern) == False, \ '%s can ssbond' % pattern) for pattern in badpatterns: self.assertRaises(sg.UndefinedAminoError, sg.can_ssbond, pattern)
def testConstrainedPeptide(self):
testdic = {
('CAAC','SSCXXC'):'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS1)C(=O)O',
('CACAC','SSXXCXC'):'N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS1)C(=O)O',
('CWCCWC','SSXXCXXC'):'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)N[C@@]([H])(CS3)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)N[C@@]([H])(CS3)C(=O)O',
('CAAC','HT'):'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS)C(=O)1',
('CACAC','HT'):'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CS)C(=O)1',
('CWCCWC','HT'):'N3[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)N[C@@]([H])(CS)C(=O)3',
('KPVEE','SCNXXXZ'):'N[C@@]([H])(CCCCN2)C(=O)N1[C@@]([H])(CCC1)C(=O)N[C@@]([H])(C(C)C)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)N[C@@]([H])(CCC2(=O))C(=O)O',
('SHRDK','SCEXXZX'):'N[C@@]([H])(CO2)C(=O)N[C@@]([H])(CC1=CN=C-N1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CC2(=O))C(=O)N[C@@]([H])(CCCCN)C(=O)O',
('AELMK','SCXZXXN'):'N[C@@]([H])(C)C(=O)N[C@@]([H])(CCC1(=O))C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCSC)C(=O)N[C@@]([H])(CCCCN1)C(=O)O',
('SKYTE','SCXNXXX'):'N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCCN2)C(=O)N[C@@]([H])(Cc1ccc(O)cc1)C(=O)N[C@@]([H])(C(O)C)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)2',
('QGCAE','SCXXXXZ'):'N1[C@@]([H])(CCC(=O)N)C(=O)NCC(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'
}
for (seq, bond_def), smi in testdic.items():
self.assertTrue(sg.constrained_peptide_smiles(seq,bond_def)[2]==smi, \
'Wrong smiles for %s: is %s should be %s' % \
(seq, sg.constrained_peptide_smiles(seq,bond_def)[2], smi))
def testCanSCSCBond(self):
#Can bond K,S,T to D,E
truepatterns = ['KAAD', 'DAAK', 'SASGE']
falsepatterns = ['KQGQG', 'A']
badpatterns = [
'CBCB', ['L-Notexistene', 'D-Fakene', 'L-Notexistene', 'D-Fakene']
]
for pattern in truepatterns:
self.assertTrue(
sg.can_scscbond(pattern) != False
and sg.can_scscbond(pattern) != None,
'%s cannot SCSC bond' % pattern)
for pattern in falsepatterns:
self.assertTrue(
sg.can_scscbond(pattern) == False,
'%s can SCSC bond' % pattern)
for pattern in badpatterns:
self.assertRaises(sg.UndefinedAminoError, sg.can_scscbond, pattern)
def smiles(self):
"""The peptide SMILES string."""
assert self.constraint_type in ['HT', 'SS', '']
if self.constraint_type == 'SS':
sequence, constraint_type = self._get_disulphide_seq_const()
else:
sequence, constraint_type = self.sequence, self.constraint_type
_, _, smiles = sg.constrained_peptide_smiles(sequence, constraint_type)
return smiles
def testWhatConstraints(self):
tests = [('CAAC', ['SSCXXC']), ('AAGAA', ['HT']),
([
'L-Cysteine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], ['SSCXXCX', 'HT', 'SCXEXXX'])]
for seq, constraints in tests:
self.assertTrue(sg.what_constraints(seq) == constraints)
def testLinearPeptideSmiles(self):
testdic = {
'AAAA':
'N[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)\
N[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)O',
'AGAG':
'N[C@@]([H])(C)C(=O)NCC(=O)N[C@@]([H])(C)C(=O)NCC(=O)O',
'PQE':
'N1[C@@]([H])(CCC1)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])\
(CCC(=O)O)C(=O)O',
'CNVR':
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(C(=O)N)C(=O)\
N[C@@]([H])(C(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)O'
}
for seq, smi in testdic.items():
self.assertTrue(sg.linear_peptide_smiles(seq)==smi, \
'Wrong smiles for %s: saw %s, should be %s'\
% (seq,sg.linear_peptide_smiles(seq),smi ))
def testCanSCCTbond(self):
#Can bond K,S,Y,T uniquely
truepatterns = ['KHRK', 'SMNS', 'YQGC', 'TYEN']
falsepatterns = ['FLWK', 'GRCNS', 'FLWANPY', 'RFACGT']
badpatterns = [
'CBCBC',
['L-Notexistene', 'D-Fakene', 'L-Notexistene', 'D-Fakene']
]
for pattern in truepatterns:
self.assertTrue(
sg.can_scctbond(pattern) != False
and sg.can_scctbond(pattern) != None,
'%s cannot SCCT bond' % pattern)
for pattern in falsepatterns:
self.assertTrue(
sg.can_scctbond(pattern) == False,
'%s can SCCT bond' % pattern)
for pattern in badpatterns:
self.assertRaises(sg.UndefinedAminoError, sg.can_scctbond, pattern)
def testBondCounter(self):
testdic = {
'N1[C@@]([H])(C)C(=O)N[C@@]([H])(C)C(=O)N[C@@]([H])\
(C)C(=O)N[C@@]([H])(C)C(=O)1':
1,
'N[C@@]([H])(C)C(=O)NCC(=O)N[C@@]([H])(C)C(=O)NCC(=O)O':
0,
'N9[C@@]([H])(CCC9)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])\
(CCC(=O)O)C(=O)O':
9,
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(C(=O)N)C(=O)N[C@@]([H])\
(C(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)O':
0,
'N[C@@]([H])(CS5)C(=O)N[C@@]([H])(C(=O)N)C(=O)N[C@@]([H])(C(C)C)C(=O)\
N[C@@]([H])(CS5)C(=O)O':
5
}
for smi, bondcount in testdic.items():
self.assertTrue(sg.bond_counter(smi)==bondcount,\
'Bondcounter: %s should be %s' % (sg.bond_counter(smi),bondcount))
def testGetConstraintType(self):
tests = [('HT', 'HT'), ('SSCXXC', 'SS'), ('SSXCXXC', 'SS'),
('SCZXXE', 'SCSC'), ('SCEXXXX', 'SCCT'), ('SCXNXXX', 'SCCT'),
('SCXXXZX', 'SCNT')]
errors = ['SCZXXD', 'SSZXXD', 'SCCXXC', 'SCCXXZ']
for bond_def, constraint_type in tests:
self.assertTrue(
sg.get_constraint_type(bond_def) == constraint_type)
for bond_def in errors:
self.assertRaises(sg.BondSpecError, sg.get_constraint_type,
bond_def)
def testCanHTBond(self):
truepatterns = [
'CAAFC', 'FCCCC', 'HFHFCHCHHHC',
[
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
],
[
'L-Cysteine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
]
]
falsepatterns = [
'CACA', 'HDET', 'FG', ['L-Phenylalanine', 'L-Glutamine'],
['L-Isoleucine', 'L-Asparagine']
]
badpatterns = ['CBC', ['L-Notexistene', 'D-Fakene']]
for pattern in truepatterns:
self.assertTrue(
sg.can_htbond(pattern) != False
and sg.can_htbond(pattern) != None)
for pattern in falsepatterns:
self.assertTrue(sg.can_htbond(pattern) == False)
def testGenAllMatchingPeptides(self):
testpatterns = ['CXXXC','SSSX','DXDX', \
'YYXYXX', ['L-Cysteine','X','X'],['L-Glutamic_Acid','X','X']]
for pattern in testpatterns:
library = list(sg.gen_all_matching_peptides(pattern))
num_peps = len(library)
self.assertTrue(num_peps == len(sg.aminodata)**pattern.count('X'),
'Incorrect combinations')
#Check for duplicates - sets can't contain duplicates, so...
peps = []
for pep in sg.gen_all_matching_peptides(pattern):
#Lists not hashable, so create string representation
peps.append('-'.join([str(num) for num in pep]))
self.assertTrue(len(set(peps)) == num_peps, 'Duplicate peptides')
bad_patterns = ['12345', '^$%']
bad_type = [23, 450]
for pattern in bad_patterns:
test = sg.gen_all_matching_peptides(pattern)
self.assertRaises(sg.UndefinedAminoError, test.next)
for pattern in bad_type:
test = sg.gen_all_matching_peptides(pattern)
self.assertRaises(TypeError, test.next)
def testGetConstraintType(self):
tests = [
('HT','HT'),
('SSCXXC','SS'),
('SSXCXXC','SS'),
('SCZXXE', 'SCSC'),
('SCEXXXX','SCCT'),
('SCXNXXX','SCCT'),
('SCXXXZX','SCNT')]
errors = ['SCZXXD', 'SSZXXD', 'SCCXXC', 'SCCXXZ']
for bond_def, constraint_type in tests:
self.assertTrue(sg.get_constraint_type(bond_def) == constraint_type)
for bond_def in errors:
self.assertRaises(sg.BondSpecError, sg.get_constraint_type, bond_def)
def testPropertytoName(self):
conversions = {'L-Serine':('Letter', 'S'), 'L-Glutamine':('Code','Gln'),
'L-Isoleucine':('SMILES', 'N[C@@]([H])(C(CC)C)C(=O)O')}
bad_properties = [('Notreal', 'Z'),('Notapropery', 10000000)]
bad_conversions = [('Letter', 'Z'), ('Code', 'QQQ')]
for name, test in conversions.items():
self.assertTrue(sg.property_to_name(*test) == name)
for property, value in bad_properties:
self.assertRaises(sg.UndefinedPropertyError, sg.property_to_name,\
*(property, value))
for property, values in bad_conversions:
self.assertRaises(sg.UndefinedAminoError, sg.property_to_name, \
*(property, value))
def testFilteredOutput(self):
input = [
('ASDF','','N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)O'),
('QFDSA', 'HT', 'N2[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)2'),
('QFDSA', '', 'N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)O'),
('CRQSC', 'SSCXXXC', 'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS1)C(=O)O'),
('CRQSC', 'HT', 'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)1'),
('CRQSC', '', 'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)O'),
('DSCCK', 'HT', 'N1[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'),
('DSCCK', 'SCXEXXX', 'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'),
('DSCCK', 'SCZXXXN', 'N[C@@]([H])(CC1(=O))C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN1)C(=O)O'),
('DSCCK', '', 'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)O'),
(['L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine', 'L-Alanine'], 'SSCXXCX', 'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)O'),
(['L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine', 'L-Alanine'], 'HT', 'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)1'),
(['L-Cysteine','L-Leucine','L-Arginine','L-Cysteine','L-Alanine'], '', 'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'HT', 'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXEXXX', 'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXXXXZ', 'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'], 'SCXEXXZ', 'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'),
(['L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine', 'L-Glutamic_Acid'],'','N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)O')]
over_four_resis = [
('ASDF','','N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)O')]
def trialfunc_one(seq):
if len(seq) > 4:
return False
else:
return True
def trialfunc_two(result):
if len(result[0]) > 4:
return False
else:
return True
for func in [trialfunc_one, trialfunc_two]:
if func is trialfunc_one:
key = 0
else:
key=None
filtered_results = sg.filtered_output(input, func, key)
for output, test_case in zip(filtered_results, over_four_resis):
self.assertTrue(output == test_case, 'output %s test %s' % (output, test_case))
def testPropertytoName(self):
conversions = {
'L-Serine': ('Letter', 'S'),
'L-Glutamine': ('Code', 'Gln'),
'L-Isoleucine': ('SMILES', 'N[C@@]([H])(C(CC)C)C(=O)O')
}
bad_properties = [('Notreal', 'Z'), ('Notapropery', 10000000)]
bad_conversions = [('Letter', 'Z'), ('Code', 'QQQ')]
for name, test in conversions.items():
self.assertTrue(sg.property_to_name(*test) == name)
for property, value in bad_properties:
self.assertRaises(sg.UndefinedPropertyError, sg.property_to_name,\
*(property, value))
for property, values in bad_conversions:
self.assertRaises(sg.UndefinedAminoError, sg.property_to_name, \
*(property, value))
def testCountConstraintTypes(self):
input = [
('ASDF', '',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)O'
),
('QFDSA', 'HT',
'N2[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)2'
),
('QFDSA', '',
'N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)O'
),
('CRQSC', 'SSCXXXC',
'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS1)C(=O)O'
),
('CRQSC', 'HT',
'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)1'
),
('CRQSC', '',
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)O'
),
('DSCCK', 'HT',
'N1[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'
),
('DSCCK', 'SCXEXXX',
'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'
),
('DSCCK', 'SCZXXXN',
'N[C@@]([H])(CC1(=O))C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN1)C(=O)O'
),
('DSCCK', '',
'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)O'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], 'SSCXXCX',
'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)O'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], 'HT',
'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)1'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], '',
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'HT',
'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXEXXX',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXXXXZ',
'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXEXXZ',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], '',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)O'
)
]
count_dict = {
'linear': 6,
'SS': 2,
'HT': 5,
'SCSC': 2,
'SCCT': 2,
'SCNT': 1
}
test_count_dict = sg.count_constraint_types(input)
self.assertTrue(count_dict == test_count_dict,
'true %s test %s' % (count_dict, test_count_dict))
def testFilteredOutput(self):
input = [
('ASDF', '',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)O'
),
('QFDSA', 'HT',
'N2[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)2'
),
('QFDSA', '',
'N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)O'
),
('CRQSC', 'SSCXXXC',
'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS1)C(=O)O'
),
('CRQSC', 'HT',
'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)1'
),
('CRQSC', '',
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)O'
),
('DSCCK', 'HT',
'N1[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'
),
('DSCCK', 'SCXEXXX',
'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'
),
('DSCCK', 'SCZXXXN',
'N[C@@]([H])(CC1(=O))C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN1)C(=O)O'
),
('DSCCK', '',
'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)O'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], 'SSCXXCX',
'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)O'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], 'HT',
'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)1'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], '',
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'HT',
'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXEXXX',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXXXXZ',
'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXEXXZ',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], '',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)O'
)
]
over_four_resis = [(
'ASDF', '',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)O'
)]
def trialfunc_one(seq):
if len(seq) > 4:
return False
else:
return True
def trialfunc_two(result):
if len(result[0]) > 4:
return False
else:
return True
for func in [trialfunc_one, trialfunc_two]:
if func is trialfunc_one:
key = 0
else:
key = None
filtered_results = sg.filtered_output(input, func, key)
for output, test_case in zip(filtered_results, over_four_resis):
self.assertTrue(output == test_case,
'output %s test %s' % (output, test_case))
def testStructsFromSeqs(self):
#gen_structs_from_seqs(sequences, ssbond=False,htbond=False,scctbond=False,
#scntbond=False,scscbond=False,linear=False):
seqs = [
'ASDF', 'QFDSA', 'CRQSC', 'DSCCK',
[
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
],
[
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
]
]
results = [
('ASDF', '',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)O'
),
('QFDSA', 'HT',
'N2[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)2'
),
('QFDSA', '',
'N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(Cc1ccccc1)C(=O)N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(C)C(=O)O'
),
('CRQSC', 'SSCXXXC',
'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS1)C(=O)O'
),
('CRQSC', 'HT',
'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)1'
),
('CRQSC', '',
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CCC(=O)N)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)O'
),
('DSCCK', 'HT',
'N1[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'
),
('DSCCK', 'SCXEXXX',
'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)1'
),
('DSCCK', 'SCZXXXN',
'N[C@@]([H])(CC1(=O))C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN1)C(=O)O'
),
('DSCCK', '',
'N[C@@]([H])(CC(=O)O)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCCCN)C(=O)O'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], 'SSCXXCX',
'N[C@@]([H])(CS1)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS1)C(=O)N[C@@]([H])(C)C(=O)O'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], 'HT',
'N1[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)1'
),
([
'L-Cysteine', 'L-Leucine', 'L-Arginine', 'L-Cysteine',
'L-Alanine'
], '',
'N[C@@]([H])(CS)C(=O)N[C@@]([H])(CC(C)C)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(C)C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'HT',
'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXEXXX',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)1'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXXXXZ',
'N1[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], 'SCXEXXZ',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO1)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC1(=O))C(=O)O'
),
([
'L-Alanine', 'L-Serine', 'L-Arginine', 'L-Cysteine',
'L-Glutamic_Acid'
], '',
'N[C@@]([H])(C)C(=O)N[C@@]([H])(CO)C(=O)N[C@@]([H])(CCCNC(=N)N)C(=O)N[C@@]([H])(CS)C(=O)N[C@@]([H])(CCC(=O)O)C(=O)O'
)
]
trial = sg.gen_structs_from_seqs(seqs,
ssbond=True,
htbond=True,
scctbond=True,
scntbond=True,
scscbond=True,
linear=True)
for a, b in zip(results, trial):
self.assertTrue(a == b, ' real %s trial %s' % (a, b))
