def test_software(self):
"""Test Software class"""
s1 = ihm.Software(name='foo',
version='1.0',
classification='1',
description='2',
location='3')
s2 = ihm.Software(name='foo',
version='2.0',
classification='4',
description='5',
location='6')
s3 = ihm.Software(name='foo',
version='1.0',
classification='7',
description='8',
location='9')
s4 = ihm.Software(name='bar',
version='1.0',
classification='a',
description='b',
location='c')
# Should compare equal iff name and version both match
self.assertEqual(s1, s3)
self.assertEqual(hash(s1), hash(s3))
self.assertNotEqual(s1, s2)
self.assertNotEqual(s1, s4)
def test_all_citations(self):
"""Test _all_citations() method"""
class MockObject(object):
pass
c1 = ihm.Citation(title='Test paper',
journal='J Mol Biol',
volume=45,
page_range=(1, 20),
year=2016,
authors=['Smith A', 'Jones B'],
doi='10.2345/S1384107697000225',
pmid='1234')
c2 = ihm.Citation(title='Test paper',
journal='J Mol Biol',
volume=45,
page_range=(1, 20),
year=2016,
authors=['Smith A', 'Jones B'],
doi='1.2.3.4',
pmid='1234')
c3 = ihm.Citation(title='Test paper2',
journal='J Mol Biol2',
volume=46,
page_range=(1, 20),
year=2017,
authors=['Smith A', 'Jones B'],
doi='5.6.7.8',
pmid='5678')
rsr1 = MockObject() # Not a 3dem restraint
rsr2 = MockObject() # 3dem but with no provided citation
rsr2.fitting_method_citation_id = None
rsr3 = MockObject()
rsr2.fitting_method_citation_id = c1
s1 = ihm.Software(name='test',
classification='test code',
description='Some test program',
version=1,
location='http://test.org')
s2 = ihm.Software(name='test',
classification='test code',
description='Some test program',
version=1,
location='http://test.org',
citation=c3)
s = ihm.System()
s.restraints.extend((rsr1, rsr2, rsr3))
s.citations.extend((c2, c2))
s.software.extend((s1, s2))
# duplicates should be filtered globally
self.assertEqual(list(s._all_citations()), [c2, c3, c1])
def test_all_software(self):
"""Test _all_software() method"""
class MockObject(object):
pass
s1 = ihm.Software(name='test',
classification='test code',
description='Some test program',
version=1,
location='http://test.org')
s2 = ihm.Software(name='foo',
classification='test code',
description='Other test program',
location='http://test2.org')
sm1 = MockObject()
sm1.software = None
sm2 = MockObject()
sm2.software = s1
s = ihm.System()
s.orphan_starting_models.extend((sm1, sm2))
s.software.extend((s2, s2))
step1 = MockObject()
step2 = MockObject()
step1.software = None
step2.software = s2
protocol1 = MockObject()
protocol1.steps = [step1, step2]
analysis1 = MockObject()
astep1 = MockObject()
astep1.software = s2
analysis1.steps = [astep1]
protocol1.analyses = [analysis1]
s.orphan_protocols.append(protocol1)
r1 = MockObject()
r2 = MockObject()
r3 = MockObject()
r2.software = None
r3.software = s1
s.restraints.extend((r1, r2, r3))
# duplicates are kept
self.assertEqual(list(s._all_software()), [s2, s2, s1, s2, s2, s1])
def _parse_phyre_model(self, fh, first_line, local_file, filename, ret):
# Model generated by Phyre2
s = ihm.Software(
name='Phyre2', classification='protein homology modeling',
description='Protein Homology/analogY Recognition '
'Engine V 2.0',
version='2.0', location='http://www.sbg.bio.ic.ac.uk/~phyre2/')
ret['software'].append(s)
self._handle_comparative_model(local_file, filename, ret)
def _parse_modeller_model(self, fh, first_line, local_file, filename, ret):
version, date = first_line[38:].rstrip('\r\n').split(' ', 1)
s = ihm.Software(name='MODELLER',
classification='comparative modeling',
description='Comparative modeling by satisfaction '
'of spatial restraints, build ' + date,
location='https://salilab.org/modeller/',
version=version)
ret['software'].append(s)
self._handle_comparative_model(local_file, filename, ret)
def _parse_swiss_model(self, fh, first_line, local_file, filename, ret):
# Model generated by SWISS-MODEL
meta = _get_swiss_model_metadata(filename)
s = ihm.Software(
name='SWISS-MODEL',
classification='protein homology modeling',
description='SWISS-MODEL: homology modelling of protein '
'structures and complexes, using %s engine' %
meta.get('info', {}).get('ENGIN', 'unknown'),
version=meta.get('info', {}).get('VERSN', ihm.unknown),
location='https://swissmodel.expasy.org/')
ret['software'].append(s)
comp_model_ds = dataset.ComparativeModelDataset(local_file)
ret['dataset'] = comp_model_ds
ret['templates'] = self._add_swiss_model_templates(
local_file, meta, comp_model_ds, ret)
