def test_all_chem_descriptors(self):
"""Test _all_chem_descriptors() method"""
class MockObject(object):
pass
d1 = ihm.ChemDescriptor("d1")
d2 = ihm.ChemDescriptor("d2")
d3 = ihm.ChemDescriptor("d3")
d4 = ihm.ChemDescriptor("d4")
s = ihm.System()
f = ihm.flr.FLRData()
s.flr_data.append(f)
r1 = MockObject()
r2 = MockObject()
r2.linker = None
r3 = MockObject()
r2.linker = d3
s.restraints.extend((r1, r2))
r2.feature = None
s.orphan_chem_descriptors.extend((d1, d2, d1))
# FLR chemical descriptors
conj = ihm.flr.PolyProbeConjugate(sample_probe=None,
chem_descriptor=d4,
ambiguous_stoichiometry=False)
f.poly_probe_conjugates.append(conj)
# duplicates should not be filtered
self.assertEqual(list(s._all_chem_descriptors()), [d1, d2, d1, d3, d4])
def test_chem_descriptor(self):
"""Test ChemDescriptor class"""
d1 = ihm.ChemDescriptor('EDC', chemical_name='test-EDC',
chem_comp_id='test-chem-comp',
common_name='test-common-EDC', smiles='CCN=C=NCCCN(C)C')
self.assertEqual(d1.auth_name, 'EDC')
self.assertEqual(d1.chem_comp_id, 'test-chem-comp')
self.assertEqual(d1.chemical_name, 'test-EDC')
self.assertEqual(d1.common_name, 'test-common-EDC')
self.assertEqual(d1.smiles, 'CCN=C=NCCCN(C)C')
self.assertIsNone(d1.inchi)
self.assertIsNone(d1.inchi_key)
"""Chemical descriptors of commonly-used cross-linkers.
Each of these is an instance of the :class:`ihm.ChemDescriptor` class,
and so can be used anywhere these objects are required, generally for
:class:`ihm.restraint.CrossLinkRestraint`.
"""
import ihm
dss = ihm.ChemDescriptor('DSS', chemical_name='disuccinimidyl suberate',
smiles='C1CC(=O)N(C1=O)OC(=O)CCCCCCC(=O)ON2C(=O)CCC2=O',
inchi='1S/C16H20N2O8/c19-11-7-8-12(20)17(11)25-15(23)5-'
'3-1-2-4-6-16(24)26-18-13(21)9-10-14(18)22/h1-10H2',
inchi_key='ZWIBGKZDAWNIFC-UHFFFAOYSA-N')
dsg = ihm.ChemDescriptor('DSG', chemical_name='disuccinimidyl glutarate',
smiles='C1CC(=O)N(C1=O)OC(=O)CCCC(=O)ON2C(=O)CCC2=O',
inchi='1S/C13H14N2O8/c16-8-4-5-9(17)14(8)22-12(20)2-1-3-'
'13(21)23-15-10(18)6-7-11(15)19/h1-7H2',
inchi_key='LNQHREYHFRFJAU-UHFFFAOYSA-N')
bs3 = ihm.ChemDescriptor('BS3', chemical_name='bissulfosuccinimidyl suberate',
smiles='C1C(C(=O)N(C1=O)OC(=O)CCCCCCC(=O)ON2C(=O)CC(C2=O)S(=O)'
'(=O)O)S(=O)(=O)O',
inchi='1S/C16H20N2O14S2/c19-11-7-9(33(25,26)27)15(23)17(11)31'
'-13(21)5-3-1-2-4-6-14(22)32-18-12(20)8-10(16(18)24)'
'34(28,29)30/h9-10H,1-8H2,(H,25,26,27)(H,28,29,30)',
inchi_key='VYLDEYYOISNGST-UHFFFAOYSA-N')
dsso = ihm.ChemDescriptor('DSSO', chemical_name='disuccinimidyl sulfoxide',
smiles='O=C(CCS(CCC(ON1C(CCC1=O)=O)=O)=O)ON2C(CCC2=O)=O',
"""Chemical descriptors of commonly-used cross-linkers.
Each of these is an instance of the :class:`ihm.ChemDescriptor` class,
and so can be used anywhere these objects are required, generally for
:class:`ihm.restraint.CrossLinkRestraint`.
"""
import ihm
dss = ihm.ChemDescriptor(
'DSS',
chemical_name='disuccinimidyl suberate',
smiles='C1CC(=O)N(C1=O)OC(=O)CCCCCCC(=O)ON2C(=O)CCC2=O',
inchi='1S/C16H20N2O8/c19-11-7-8-12(20)17(11)25-15(23)5-'
'3-1-2-4-6-16(24)26-18-13(21)9-10-14(18)22/h1-10H2',
inchi_key='ZWIBGKZDAWNIFC-UHFFFAOYSA-N')
bs3 = ihm.ChemDescriptor(
'BS3',
chemical_name='bissulfosuccinimidyl suberate',
smiles='C1C(C(=O)N(C1=O)OC(=O)CCCCCCC(=O)ON2C(=O)CC(C2=O)S(=O)'
'(=O)O)S(=O)(=O)O',
inchi='1S/C16H20N2O14S2/c19-11-7-9(33(25,26)27)15(23)17(11)31'
'-13(21)5-3-1-2-4-6-14(22)32-18-12(20)8-10(16(18)24)'
'34(28,29)30/h9-10H,1-8H2,(H,25,26,27)(H,28,29,30)',
inchi_key='VYLDEYYOISNGST-UHFFFAOYSA-N')
dsso = ihm.ChemDescriptor(
'DSSO',
chemical_name='disuccinimidyl sulfoxide',
smiles='O=C(CCS(CCC(ON1C(CCC1=O)=O)=O)=O)ON2C(CCC2=O)=O',
