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')
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
s = ihm.System()
s.restraints.extend((rsr1, rsr2, rsr3))
s.citations.extend((c2, c2))
# duplicates should be filtered globally
self.assertEqual(list(s._all_citations()), [c2, c1])
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_citation(self):
"""Test Citation class"""
s = 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')
self.assertEqual(s.title, 'Test paper')
def mock_from_pubmed(cls, pubmed_id):
return ihm.Citation(
pmid=30190596,
title='Architecture of Pol II(G) and molecular mechanism of '
'transcription regulation by Gdown1.',
journal='Nat Struct Mol Biol', volume=25, page_range=(859,867),
year=2018, doi='10.1038/s41594-018-0118-5', authors=[
'Jishage M', 'Yu X', 'Shi Y', 'Ganesan SJ', 'Chen WY',
'Sali A', 'Chait BT', 'Asturias FJ', 'Roeder RG'])
def mock_from_pubmed(cls, pubmed_id):
return ihm.Citation(
pmid=32719457,
title='Structural basis of CD4 downregulation by HIV-1 Nef',
journal='Nat Struct Mol Biol',
volume=None,
page_range=None,
year=2020,
doi='10.1038/s41594-020-0463-z',
authors=[
'Kwon Y', 'Kaake RM', 'Echeverria I', 'Suarez M',
'Karimian Shamsabadi M', 'Stoneham C', 'Ramirez PW', 'Kress J',
'Singh R', 'Sali A', 'Krogan N,'
'Guatelli J', 'Jia X'
])
"""Citations for some commonly-used software packages.
Each of these is an instance of the :class:`ihm.Citation` class,
and so can be used anywhere these objects are required, generally for
:class:`ihm.Software`.
"""
import ihm
imp = ihm.Citation(
pmid='22272186',
title='Putting the pieces together: integrative modeling platform '
'software for structure determination of macromolecular assemblies',
journal='PLoS Biol',
volume=10,
page_range='e1001244',
year=2012,
authors=[
'Russel D', 'Lasker K', 'Webb B', 'Velázquez-Muriel J', 'Tjioe E',
'Schneidman-Duhovny D', 'Peterson B', 'Sali A'
],
doi='10.1371/journal.pbio.1001244')
pmi = ihm.Citation(
pmid='31396911',
title='Modeling Biological Complexes Using Integrative Modeling Platform.',
journal='Methods Mol Biol',
volume=2022,
page_range=(353, 377),
year=2019,
authors=[