def test_auth_seq_id_dict(self):
"""Test auth_seq_id dict map from seq_id"""
e = ihm.Entity('AHCDAH')
a = ihm.AsymUnit(e, auth_seq_id_map={1: 0, 2: 4})
self.assertEqual(a._get_auth_seq_id(1), 0)
self.assertEqual(a._get_auth_seq_id(2), 4)
self.assertEqual(a._get_auth_seq_id(3), 3)
def test_auth_seq_id_list(self):
"""Test auth_seq_id list map from seq_id"""
e = ihm.Entity('AHCDAH')
a = ihm.AsymUnit(e, auth_seq_id_map=[None, 0, 4])
self.assertEqual(a._get_auth_seq_id(1), 0)
self.assertEqual(a._get_auth_seq_id(2), 4)
self.assertEqual(a._get_auth_seq_id(3), 3)
def make_representation(system, cccp):
"""Using one of the output RMFs as a guide, create the IHM representation
(i.e. the subunits in the system and how residues are represented
as beads)."""
fname = os.path.join('..', 'final_models_1x_Spc29',
'cluster_without_Spc29',
'cluster2.1/top_scoring_model.rmf')
seqs = IMP.pmi.topology.Sequences(
os.path.join('..', '..', 'inputs', 'shared_inputs', 'seqs.fasta'))
ccdatasets = _get_starting_coiled_coil_datasets()
# Mapping from RMF names of subunits to ihm.Entity objects
entities_by_name = {}
# Map from localization density filename to list of asym ranges
density_map = {}
rep = ihm.representation.Representation()
m = IMP.Model()
rh = RMF.open_rmf_file_read_only(fname)
hs = IMP.rmf.create_hierarchies(rh, m)
for h in hs:
name = h.get_name()
entity_name = 'GFP' if name.endswith('GFP') else name
if entity_name not in entities_by_name:
e = ihm.Entity(seqs[entity_name], description=entity_name)
system.entities.append(e)
entities_by_name[entity_name] = e
asym = ihm.AsymUnit(entities_by_name[entity_name], details=name)
system.asym_units.append(asym)
_add_asym_representation(h, asym, rep, ccdatasets, cccp)
_add_density_map(h, asym, density_map)
system.orphan_representations.append(rep)
return entities_by_name, rep, density_map
def test_auth_seq_id_list(self):
"""Test auth_seq_id list map from seq_id"""
e = ihm.Entity('AHCDAH')
a = ihm.AsymUnit(e, auth_seq_id_map=[None, 0, 4])
self.assertEqual(a._get_auth_seq_id_ins_code(1), (0, None))
self.assertEqual(a._get_auth_seq_id_ins_code(2), (4, None))
self.assertEqual(a._get_auth_seq_id_ins_code(3), (3, None))
def test_auth_seq_id_dict(self):
"""Test auth_seq_id dict map from seq_id"""
e = ihm.Entity('AHCDAH')
a = ihm.AsymUnit(e, auth_seq_id_map={1: 0, 2: (4, 'A')})
self.assertEqual(a._get_auth_seq_id_ins_code(1), (0, None))
self.assertEqual(a._get_auth_seq_id_ins_code(2), (4, 'A'))
self.assertEqual(a._get_auth_seq_id_ins_code(3), (3, None))
def test_asym_segment(self):
"""Test AsymUnitSegment class"""
e = ihm.Entity('AHCDAH')
a = ihm.AsymUnit(e)
seg = a.segment('AH--CD', 1, 4)
self.assertEqual(seg.gapped_sequence, 'AH--CD')
self.assertEqual(seg.seq_id_range, (1, 4))
def test_asym_unit_residue(self):
"""Test Residue derived from an AsymUnit"""
e = ihm.Entity('AHCDAH')
a = ihm.AsymUnit(e, auth_seq_id_map=5)
r = a.residue(3)
self.assertIsNone(r.entity)
self.assertEqual(r.asym, a)
self.assertEqual(r.seq_id, 3)
self.assertEqual(r.auth_seq_id, 8)
def test_atom_asym(self):
"""Test Atom class built from an AsymUnit"""
e = ihm.Entity('AHCDAH')
asym = ihm.AsymUnit(e)
a = asym.residue(3).atom('CA')
self.assertEqual(a.id, 'CA')
self.assertEqual(a.residue.seq_id, 3)
self.assertIsNone(a.entity)
self.assertEqual(a.asym, asym)
self.assertEqual(a.seq_id, 3)
def test_asym_range(self):
"""Test AsymUnitRange class"""
e = ihm.Entity('AHCDAH')
heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
a = ihm.AsymUnit(e)
aheme = ihm.AsymUnit(heme)
a._id = 42
self.assertEqual(a.seq_id_range, (1, 6))
# seq_id is not defined for nonpolymers
self.assertEqual(aheme.seq_id_range, (None, None))
r = a(3, 4)
self.assertEqual(r.seq_id_range, (3, 4))
self.assertEqual(r._id, 42)
self.assertEqual(r.entity, e)
# Cannot create ranges for nonpolymeric entities
self.assertRaises(TypeError, aheme.__call__, 1, 1)
samer = a(3, 4)
otherr = a(2, 4)
self.assertEqual(r, samer)
self.assertEqual(hash(r), hash(samer))
self.assertNotEqual(r, otherr)
self.assertNotEqual(r, a) # asym_range != asym
self.assertNotEqual(r, e(3, 4)) # asym_range != entity_range
self.assertNotEqual(r, e) # asym_range != entity
def _get_seq_id_range_all_templates(self):
"""Get the seq_id range covered by all templates in this starting
model, as an AsymUnit or AsymUnitRange object. Where there are
multiple templates, consolidate them; template info is given in
starting_comparative_models."""
def get_seq_id_range(template, full):
# The template may cover more than the current starting model
rng = template.seq_id_range
return (max(rng[0] + self.offset,
full[0]), min(rng[1] + self.offset, full[1]))
if self.templates:
full = self.asym_unit.seq_id_range
rng = get_seq_id_range(self.templates[0], full)
for template in self.templates[1:]:
this_rng = get_seq_id_range(template, full)
rng = (min(rng[0], this_rng[0]), max(rng[1], this_rng[1]))
return ihm.AsymUnit(self.asym_unit.entity)(*rng)
else:
return self.asym_unit
def test_all_entity_ranges(self):
"""Test _all_entity_ranges() method"""
class MockObject(object):
pass
s = ihm.System()
e1 = ihm.Entity('AHCD', description='foo')
a1 = ihm.AsymUnit(e1)
s.entities.append(e1)
s.asym_units.append(a1)
e1rng = e1(1, 3)
a1rng = a1(1, 2)
sm1 = MockObject()
sm1.asym_unit = e1rng
s.orphan_starting_models.append(sm1)
rep = ihm.representation.Representation()
seg1 = ihm.representation.Segment()
seg1.starting_model = None
seg1.asym_unit = a1
rep.append(seg1)
s.orphan_representations.append(rep)
asmb1 = ihm.Assembly([e1, a1])
s.orphan_assemblies.append(asmb1)
ensemble = MockObject()
density = MockObject()
density.asym_unit = a1rng
ensemble.densities = [density]
s.ensembles.append(ensemble)
# duplicates should not be filtered
self.assertEqual(list(s._all_entity_ranges()),
[e1rng, a1, e1, a1, a1rng])
def test_auth_seq_id_offset(self):
"""Test auth_seq_id offset from seq_id"""
e = ihm.Entity('AHCDAH')
a = ihm.AsymUnit(e, auth_seq_id_map=5)
self.assertEqual(a._get_auth_seq_id(1), 6)
m = ihm.dataset.EMMicrographsDataset(ihm.location.EMPIARLocation('EMPIAR-123'))
em_dataset.parents.append(m)
# Next, define the entities for each unique sequence in the system
# (here represented as polyalanines):
entityA = ihm.Entity('AAA', description='Subunit A')
entityB = ihm.Entity('AAAAAA', description='Subunit B')
system.entities.extend((entityA, entityB))
# Next, we define asymmetric units for everything we modeled.
# These roughly correspond to chains in a traditional PDB file. Multiple
# asymmetric units may map to the same entity (for example if there are
# several copies of a given protein). Parts of the system that were seen in
# an experiment but were not modeled are represented as entities to which no
# asymmetric units map.
asymA = ihm.AsymUnit(entityA, details='Subunit A')
asymB = ihm.AsymUnit(entityB, details='Subunit B')
system.asym_units.extend((asymA, asymB))
# Next, we group asymmetric units (and/or entities) into assemblies.
# Here, we'll define an assembly of everything that we modeled, plus
# two subassemblies (of the subunits) that the SAXS data applies to:
modeled_assembly = ihm.Assembly((asymA, asymB), name='Modeled assembly')
assemblyA = ihm.Assembly((asymA, ), name='Subunit A')
assemblyB = ihm.Assembly((asymB, ), name='Subunit B')
# Define how the system was represented. Multiple representations of the
# system are possible, and can overlap. Here we'll say we represent A
# atomically as a rigid body and B as 3 flexible coarse-grained spheres:
rep = ihm.representation.Representation([
ihm.representation.AtomicSegment(asymA, rigid=True),
# A ligand entity (in this case, heme)
heme = ihm.NonPolymerChemComp("HEM",
name='PROTOPORPHYRIN IX CONTAINING FE',
formula='C34 H32 Fe N4 O4')
entity_heme = ihm.Entity([heme], description='Heme')
# Water
entity_h2o = ihm.Entity([ihm.WaterChemComp()], description='Water')
system.entities.extend(
(entity_protein, entity_rna, entity_dna, entity_heme, entity_h2o))
# Next, we define asymmetric units for everything we modeled.
# Here, we have a single instance of each protein, RNA and DNA, two hemes,
# plus crystal waters
asym_protein = ihm.AsymUnit(entity_protein, details='Subunit A')
asym_rna = ihm.AsymUnit(entity_rna, details='RNA chain')
asym_dna = ihm.AsymUnit(entity_dna, details='DNA chain')
asym_heme1 = ihm.AsymUnit(entity_heme, details='First heme')
asym_heme2 = ihm.AsymUnit(entity_heme, details='Second heme')
asym_h2o = ihm.AsymUnit(entity_h2o, details='Crystal waters')
system.asym_units.extend(
(asym_protein, asym_rna, asym_dna, asym_heme1, asym_heme2, asym_h2o))
# todo: show handling of multiple waters
# Once the system is complete, we can write it out to an mmCIF file:
with open('output.cif', 'w') as fh:
ihm.dumper.write(fh, [system])