diff --git a/pyext/src/mmcif.py b/pyext/src/mmcif.py
index 25651769..519ba8b4 100644
--- a/pyext/src/mmcif.py
+++ b/pyext/src/mmcif.py
@@ -38,6 +38,7 @@
import ihm.representation
import ihm.geometry
import ihm.cross_linkers
+import ihm.reference
def _assign_id(obj, seen_objs, obj_by_id):
@@ -1082,7 +1083,7 @@ def _get_alphabet(self, alphabet):
else:
raise TypeError("Don't know how to handle %s" % alphabet)
- def add(self, component_name, sequence, offset, alphabet):
+ def add(self, component_name, sequence, offset, alphabet, uniprot):
def entity_seq(sequence):
# Map X to UNK
if 'X' in sequence:
@@ -1095,7 +1096,8 @@ def entity_seq(sequence):
d = component_name.split("@")[0].split(".")[0]
entity = Entity(entity_seq(sequence), description=d,
pmi_offset=offset,
- alphabet=self._get_alphabet(alphabet))
+ alphabet=self._get_alphabet(alphabet),
+ uniprot=uniprot)
self.system.entities.append(entity)
self._sequence_dict[sequence] = entity
self[component_name] = self._sequence_dict[sequence]
@@ -1198,11 +1200,18 @@ class Entity(ihm.Entity):
removed). The actual offset (which is the integer to be added to the
IHM numbering to get PMI numbering, or equivalently the number of
not-represented N-terminal residues in the PMI sequence) is
- available in the `pmi_offset` member."""
- def __init__(self, sequence, pmi_offset, *args, **keys):
+ available in the `pmi_offset` member.
+
+ If a UniProt accession was provided for the sequence (either when
+ State.create_molecule() was called, or in the FASTA alignment file
+ header) then that is available in the `uniprot` member, and can be
+ added to the IHM system with the add_uniprot_reference method.
+ """
+ def __init__(self, sequence, pmi_offset, uniprot, *args, **keys):
# Offset between PMI numbering and IHM; <pmi_#> = <ihm_#> + pmi_offset
# (pmi_offset is also the number of N-terminal gaps in the FASTA file)
self.pmi_offset = pmi_offset
+ self.uniprot = uniprot
super().__init__(sequence, *args, **keys)
def pmi_residue(self, res_id):
@@ -1214,6 +1223,24 @@ def pmi_range(self, res_id_begin, res_id_end):
off = self.pmi_offset
return self(res_id_begin - off, res_id_end - off)
+ def add_uniprot_reference(self):
+ """Add UniProt accession (if available) to the IHM system.
+ If a UniProt accession was provided for the sequence (either when
+ State.create_molecule() was called, or in the FASTA alignment file
+ header), then look this up at the UniProt web site (requires
+ network access) to get full information, and add it to the IHM
+ system. The resulting reference object is returned. If the IMP
+ and UniProt sequences are not identical, then this object may
+ need to be modified by specifying an alignment and/or
+ single-point mutations.
+ """
+ if self.uniprot:
+ print('Adding UniProt accession %s reference for entity %s'
+ % (self.uniprot, self.description))
+ ref = ihm.reference.UniProtSequence.from_accession(self.uniprot)
+ self.references.append(ref)
+ return ref
+
class AsymUnit(ihm.AsymUnit):
"""A single asymmetric unit in the system. This roughly corresponds to
@@ -1397,7 +1424,7 @@ def create_component(self, state, name, modeled, asym_name=None):
self.all_modeled_components.append(name)
def add_component_sequence(self, state, name, seq, asym_name=None,
- alphabet=None):
+ alphabet=None, uniprot=None):
if asym_name is None:
asym_name = name
@@ -1409,7 +1436,7 @@ def add_component_sequence(self, state, name, seq, asym_name=None,
# Offset is always zero to start with; this may be modified
# later in finalize_build() if any non-modeled N-terminal
# residues are removed
- self.entities.add(name, seq, 0, alphabet)
+ self.entities.add(name, seq, 0, alphabet, uniprot)
if asym_name in self.asym_units:
if self.asym_units[asym_name] is None:
# Set up a new asymmetric unit for this component
diff --git a/pyext/src/topology/__init__.py b/pyext/src/topology/__init__.py
index 80c24b2f..2ced305e 100644
--- a/pyext/src/topology/__init__.py
+++ b/pyext/src/topology/__init__.py
@@ -809,7 +809,8 @@ def _build_protocol_output(self):
asym_name=self._name_with_copy)
po.add_component_sequence(state, name, self.sequence,
asym_name=self._name_with_copy,
- alphabet=self.alphabet)
+ alphabet=self.alphabet,
+ uniprot=self.uniprot)
def _finalize_build(self):
# For clones, pass the representation of the original molecule
diff --git a/test/test_mmcif.py b/test/test_mmcif.py
index 31a755fd..94f55501 100644
--- a/test/test_mmcif.py
+++ b/test/test_mmcif.py
@@ -315,21 +315,43 @@ def test_cif_entities(self):
"""Test _EntityMapper class"""
system = ihm.System()
c = IMP.pmi.mmcif._EntityMapper(system)
- c.add('foo', 'MELS', 0, alphabet=None)
- c.add('bar', 'SELM', 0, alphabet=IMP.pmi.alphabets.amino_acid)
- c.add('foo_2', 'MELS', 0, alphabet=None)
+ c.add('foo', 'MELS', 0, alphabet=None, uniprot=None)
+ c.add('bar', 'SELM', 0, alphabet=IMP.pmi.alphabets.amino_acid,
+ uniprot='baracc')
+ c.add('foo_2', 'MELS', 0, alphabet=None, uniprot=None)
self.assertRaises(TypeError, c.add, 'baz', 'MELSXX', 0,
- alphabet='garbage')
+ alphabet='garbage', uniprot=None)
self.assertEqual(len(system.entities), 2)
self.assertIs(c['foo'], c['foo_2'])
self.assertIsNot(c['foo'], c['bar'])
a = system.entities
self.assertEqual(len(a), 2)
self.assertEqual(a[0].description, 'foo')
+ self.assertIsNone(a[0].uniprot)
self.assertEqual(''.join(x.code for x in a[0].sequence), 'MELS')
self.assertEqual(a[1].description, 'bar')
+ self.assertEqual(a[1].uniprot, 'baracc')
self.assertEqual(''.join(x.code for x in a[1].sequence), 'SELM')
+ def test_entity_add_uniprot_reference(self):
+ """Test Entity.add_uniprot_reference()"""
+ system = ihm.System()
+ c = IMP.pmi.mmcif._EntityMapper(system)
+ c.add('foo', 'MELS', 0, alphabet=None, uniprot=None)
+ c.add('bar', 'SELM', 0, alphabet=None, uniprot='baracc')
+ # Mock out UniProtSequence.from_accession
+ orig = ihm.reference.UniProtSequence.from_accession
+ def mock_from_acc(acc):
+ return "mock+" + acc
+ try:
+ ihm.reference.UniProtSequence.from_accession = mock_from_acc
+ ref = c['foo'].add_uniprot_reference()
+ self.assertIsNone(ref)
+ ref = c['bar'].add_uniprot_reference()
+ self.assertEqual(ref, 'mock+baracc')
+ finally:
+ ihm.reference.UniProtSequence.from_accession = orig
+
def test_all_datasets_all_group(self):
"""Test AllDatasets.get_all_group()"""
s = ihm.System()