Python StructGen示例

示例#1

 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)

示例#2

 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))

示例#3

 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)

示例#4

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#5

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#6

    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)

示例#7

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#8

    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)

示例#9

 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]))

示例#10

文件： StructGen_test.py 项目： fergaljd/cyclops

	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]))

示例#11

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#12

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#13

    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)

示例#14

文件： StructGen_test.py 项目： fergaljd/cyclops

	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 ))

示例#15

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#16

文件： StructGen_test.py 项目： fergaljd/cyclops

	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))

示例#17

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#18

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#19

文件： StructGen_test.py 项目： fergaljd/cyclops

	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))

示例#20

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#21

文件： StructGen_test.py 项目： fergaljd/cyclops

	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))

示例#22

 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)

示例#23

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#24

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#25

文件： StructGen_test.py 项目： fergaljd/cyclops

	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))

示例#26

 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)

示例#27

文件： sequence.py 项目： fergaljd/pep_ga

 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

示例#28

    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)

示例#29

    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 ))

示例#30

 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)

示例#31

    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))

示例#32

    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)

示例#33

 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)

示例#34

    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)

示例#35

文件： StructGen_test.py 项目： fergaljd/cyclops

	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)

示例#36

文件： StructGen_test.py 项目： fergaljd/cyclops

	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))

示例#37

文件： StructGen_test.py 项目： fergaljd/cyclops

	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))

示例#38

    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))

示例#39

    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))

示例#40

    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))

示例#41

    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))