Skip to content

Commit

Permalink
Add (partial) support for non-zero sequence offset
Browse files Browse the repository at this point in the history 
Map IMP residue indices to IHM when creating model
representation and coordinates (we will likely also
need to map residue indices elsewhere, e.g. when
handling crosslinks).
  • Loading branch information
@benmwebb
benmwebb committed Sep 16, 2023
1 parent c2c78a7 commit 1a62715
Show file tree
Hide file tree
Showing 3 changed files with 42 additions and 26 deletions.
33 changes: 20 additions & 13 deletions modules/mmcif/pyext/src/data.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -195,10 +195,6 @@ def add(self, chain, entity, offset):
entity.description = \
component.name.split("@")[0].split(".")[0]
self._all_components.append(component)
if offset != 0:
raise ValueError(
"Non-zero chain sequence offsets are not "
"currently handled")
asym = ihm.AsymUnit(entity, name, id=asym_id,
auth_seq_id_map=offset)
self.system.asym_units.append(asym)
Expand All @@ -210,6 +206,12 @@ def add(self, chain, entity, offset):
raise ValueError("Two chains have the same ID (%s) but "
"different sequences - rename one of the "
"chains" % component.asym_unit.id)
if component.asym_unit.auth_seq_id_map != offset:
raise ValueError(
"Two chains have the same ID (%s) but different offsets "
"(%d, %d) - this is not supported"
% (component.asym_unit.id,
component.asym_unit.auth_seq_id_map, offset))
return component

def get_all(self):
Expand All @@ -222,8 +224,10 @@ class _RepSegmentFactory(object):
particles with the same representation"""
def __init__(self, asym):
self.asym = asym
# Offset from IHM to IMP numbering
self.offset = asym.auth_seq_id_map
self.particles = []
self.residue_range = () # inclusive range
self.imp_residue_range = () # inclusive range, using IMP numbering

def add(self, particle, starting_model):
"""Add a new particle to the last segment (and return None).
Expand All @@ -234,7 +238,7 @@ def add(self, particle, starting_model):

def start_new_segment():
self.particles = [particle]
self.residue_range = resrange
self.imp_residue_range = resrange
self.rigid_body = rigid_body
self.is_res = is_res
self.is_atom = is_atom
Expand All @@ -245,12 +249,12 @@ def start_new_segment():
elif (type(particle) == type(self.particles[0]) # noqa: E721
and is_res == self.is_res
and is_atom == self.is_atom
and resrange[0] <= self.residue_range[1] + 1
and resrange[0] <= self.imp_residue_range[1] + 1
and starting_model == self.starting_model
and self._same_rigid_body(rigid_body)):
# Continue an existing segment
self.particles.append(particle)
self.residue_range = (self.residue_range[0], resrange[1])
self.imp_residue_range = (self.imp_residue_range[0], resrange[1])
else:
# Make a new segment
seg = self.get_last()
Expand All @@ -260,7 +264,9 @@ def start_new_segment():
def get_last(self):
"""Return the last segment, or None"""
if self.particles:
asym = self.asym(*self.residue_range)
# Convert residue_range from IMP to IHM
asym = self.asym(self.imp_residue_range[0] - self.offset,
self.imp_residue_range[1] - self.offset)
if self.is_atom:
return ihm.representation.AtomicSegment(
asym_unit=asym, rigid=self.rigid_body is not None,
Expand Down Expand Up @@ -773,17 +779,18 @@ def matches_asym(s):
if matches_asym(s.asym_unit)],
self._system, self._datasets)
segfactory = _RepSegmentFactory(asym)
offset = asym.auth_seq_id_map
for p in ps:
starting_model = smf.find(p)
seg = segfactory.add(p, starting_model)
if seg:
self._representation.append(seg)
self._add_atom_or_sphere(p, asym)
self._add_atom_or_sphere(p, asym, offset)
last = segfactory.get_last()
if last:
self._representation.append(last)

def _add_atom_or_sphere(self, p, asym):
def _add_atom_or_sphere(self, p, asym, offset):
if isinstance(p, IMP.atom.Atom):
residue = IMP.atom.get_residue(p)
xyz = IMP.core.XYZ(p).get_coordinates()
Expand All @@ -794,7 +801,7 @@ def _add_atom_or_sphere(self, p, asym):
if het:
atom_name = atom_name[4:]
self._atoms.append(ihm.model.Atom(
asym_unit=asym, seq_id=residue.get_index(),
asym_unit=asym, seq_id=residue.get_index() - offset,
atom_id=atom_name, type_symbol=element,
x=xyz[0], y=xyz[1], z=xyz[2], het=het,
biso=p.get_temperature_factor(),
Expand All @@ -809,7 +816,7 @@ def _add_atom_or_sphere(self, p, asym):
xyzr = IMP.core.XYZR(p)
xyz = xyzr.get_coordinates()
self._spheres.append(ihm.model.Sphere(
asym_unit=asym, seq_id_range=(sbegin, send),
asym_unit=asym, seq_id_range=(sbegin - offset, send - offset),
x=xyz[0], y=xyz[1], z=xyz[2], radius=xyzr.get_radius()))

def get_structure_particles(self, h):
Expand Down
9 changes: 6 additions & 3 deletions modules/mmcif/test/test_convert.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -428,21 +428,24 @@ def test_model_creation(self):
self.add_chains(m, top)
c = IMP.mmcif.Convert()
chain0 = top.get_child(0).get_child(0)
self.assertTrue(IMP.atom.Chain.get_is_setup(chain0))
# Test that IMP residue numbering (11-14) maps to IHM (1-4)
IMP.atom.Chain(chain0).set_sequence_offset(10)
residue = IMP.atom.Residue.setup_particle(IMP.Particle(m),
IMP.atom.ALA, 1)
IMP.atom.ALA, 11)
IMP.core.XYZR.setup_particle(
residue, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(1, 2, 3), 4))
IMP.atom.Mass.setup_particle(residue, 1.0)
chain0.add_child(residue)
residue = IMP.atom.Residue.setup_particle(IMP.Particle(m),
IMP.atom.HIS, 2)
IMP.atom.HIS, 12)
atom = IMP.atom.Atom.setup_particle(IMP.Particle(m),
IMP.atom.AT_CA)
IMP.core.XYZR.setup_particle(
atom, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(5, 6, 7), 8))
residue.add_child(atom)
chain0.add_child(residue)
frag = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [3, 4])
frag = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [13, 14])
chain0.add_child(frag)
IMP.core.XYZR.setup_particle(
frag, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(9, 10, 11), 12))
Expand Down
26 changes: 16 additions & 10 deletions modules/mmcif/test/test_data.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -141,8 +141,9 @@ def test_component_mapper_non_zero_offset(self):
cm = IMP.mmcif.data._ComponentMapper(system)
entity1 = ihm.Entity("ANC")
chain1 = make_chain(m, "A", "A")
# Non-zero offsets are not currently handled
self.assertRaises(ValueError, cm.add, chain1, entity1, 100)
cm.add(chain1, entity1, 100)
# Cannot add the same chain but with a different offset
self.assertRaises(ValueError, cm.add, chain1, entity1, 200)

def test_component_mapper_get_all(self):
"""Test ComponentMapper get_all()"""
Expand All @@ -160,13 +161,17 @@ def test_component_mapper_get_all(self):

def test_representation_same_rigid_body(self):
"""Test RepSegmentFactory._same_rigid_body()"""
class MockComp(object):
auth_seq_id_map = 0

m = IMP.Model()
xyz1 = IMP.core.XYZ.setup_particle(IMP.Particle(m),
IMP.algebra.Vector3D(1,1,1))
xyz2 = IMP.core.XYZ.setup_particle(IMP.Particle(m),
IMP.algebra.Vector3D(2,2,2))
rigid1 = IMP.core.RigidBody.setup_particle(IMP.Particle(m), [xyz1])
r = IMP.mmcif.data._RepSegmentFactory('mockcomp')
mockcomp = MockComp()
r = IMP.mmcif.data._RepSegmentFactory(mockcomp)
r.rigid_body = None
self.assertTrue(r._same_rigid_body(None))
self.assertFalse(r._same_rigid_body(rigid1))
Expand Down Expand Up @@ -354,38 +359,39 @@ def test_coordinate_handler_add_chain(self):
"""Test CoordinateHandler.add_chain()"""
s = ihm.System()
ent = ihm.Entity('ACGT')
asym = ihm.AsymUnit(ent)
# Check that IMP residue numbering (11-18) maps to IHM (1-8)
asym = ihm.AsymUnit(ent, auth_seq_id_map=10)
m = IMP.Model()
top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
# Two flexible residues
residue = IMP.atom.Residue.setup_particle(IMP.Particle(m),
IMP.atom.ALA, 1)
IMP.atom.ALA, 11)
add_attrs(residue)
top.add_child(residue)
residue = IMP.atom.Residue.setup_particle(IMP.Particle(m),
IMP.atom.ALA, 2)
IMP.atom.ALA, 12)
add_attrs(residue)
top.add_child(residue)
# One rigid residue
residue = IMP.atom.Residue.setup_particle(IMP.Particle(m),
IMP.atom.ALA, 3)
IMP.atom.ALA, 13)
add_attrs(residue)
rigid1 = IMP.core.RigidBody.setup_particle(IMP.Particle(m), [residue])
top.add_child(residue)
# One residue with atomic representation
residue = IMP.atom.Residue.setup_particle(IMP.Particle(m),
IMP.atom.ALA, 4)
IMP.atom.ALA, 14)
for att in (IMP.atom.AT_CA, IMP.atom.AT_O):
atom = IMP.atom.Atom.setup_particle(IMP.Particle(m), att)
IMP.core.XYZR.setup_particle(
atom, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(1, 2, 3), 4))
residue.add_child(atom)
top.add_child(residue)
# Two beads each spanning two residues
frag = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [5, 6])
frag = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [15, 16])
add_attrs(frag)
top.add_child(frag)
frag = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [7, 8])
frag = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [17, 18])
add_attrs(frag)
top.add_child(frag)
ch = IMP.mmcif.data._CoordinateHandler(s, None)
Expand Down

0 comments on commit 1a62715

Please sign in to comment.