def set_assembly(self, fn_pdb, names):
"""
Sets an assembly from a single PDB file. The function assumes that
the components of the assembly are the chains of the PDB file.
@param fn_pdb PDB with the file for the assembly
@param names Names for each of the components (chains)
of the assembly
"""
self.assembly = representation.create_assembly_from_pdb(self.model, fn_pdb, names)
self.components_rbs = representation.create_rigid_bodies(self.assembly)
self.not_optimized_rbs = []
def write_pdb_for_reference_frames(fn_pdbs, refs_texts, fn_output):
"""
Read the PDB files, apply reference frames to them, and write a pdb
"""
model = IMP.kernel.Model()
assembly = representation.create_assembly(model, fn_pdbs)
rbs = representation.create_rigid_bodies(assembly)
for t, rb in zip(refs_texts, rbs):
r = TextToReferenceFrame(t).get_reference_frame()
rb.set_reference_frame(r)
atom.write_pdb(assembly, fn_output)
def write_pdb_for_reference_frames(fn_pdbs, refs_texts, fn_output):
"""
Read the PDB files, apply reference frames to them, and write a pdb
"""
model = IMP.kernel.Model()
assembly = representation.create_assembly(model, fn_pdbs)
rbs = representation.create_rigid_bodies(assembly)
for t, rb in zip(refs_texts, rbs):
r = TextToReferenceFrame(t).get_reference_frame()
rb.set_reference_frame(r)
atom.write_pdb(assembly, fn_output)
def set_assembly_components(self, fn_pdbs, names):
"""
Sets the components of an assembly, each one given as a separate
PDB file.
@param fn_pdbs List with the names of the pdb files
@param names List with the names of the components of the assembly.
"""
if len(fn_pdbs) != len(names):
raise ValueError("Each PDB file needs a name")
self.names = names
self.assembly = representation.create_assembly(self.model, fn_pdbs, names)
self.components_rbs = representation.create_rigid_bodies(self.assembly)
self.not_optimized_rbs = []
def set_assembly(self, fn_pdb, names):
"""
Sets an assembly from a single PDB file. The function assumes that
the components of the assembly are the chains of the PDB file.
@param fn_pdb PDB with the file for the assembly
@param names Names for each of the components (chains)
of the assembly
"""
self.assembly = representation.create_assembly_from_pdb(self.model,
fn_pdb,
names)
self.components_rbs = representation.create_rigid_bodies(self.assembly)
self.not_optimized_rbs = []
def set_assembly_components(self, fn_pdbs, names):
"""
Sets the components of an assembly, each one given as a separate
PDB file.
@param fn_pdbs List with the names of the pdb files
@param names List with the names of the components of the assembly.
"""
if len(fn_pdbs) != len(names):
raise ValueError("Each PDB file needs a name")
self.names = names
self.assembly = representation.create_assembly(self.model, fn_pdbs,
names)
self.components_rbs = representation.create_rigid_bodies(self.assembly)
self.not_optimized_rbs = []
def set_native_assembly_for_benchmark(self, params):
"""
Sets the native model for benchmark, by reading the native
structure and set the rigid bodies.
"""
self.measure_models = True
self.native_model = IMP.Model()
if hasattr(params.benchmark, "fn_pdb_native"):
self.native_assembly = \
representation.create_assembly_from_pdb(self.native_model,
params.benchmark.fn_pdb_native, params.names)
elif hasattr(params.benchmark, "fn_pdbs_native"):
self.native_assembly = \
representation.create_assembly(self.native_model,
params.benchmark.fn_pdbs_native, params.names)
else:
raise ValueError("set_native_assembly_for_benchmark: Requested "
"to set a native assembly for benchmark but did not provide "
"its pdb, or the pdbs of the components")
self.native_rbs = representation.create_rigid_bodies(
self.native_assembly)
anchor_assembly(self.native_rbs, params.anchor)
def set_native_assembly_for_benchmark(self, params):
"""
Sets the native model for benchmark, by reading the native
structure and set the rigid bodies.
"""
self.measure_models = True
self.native_model = IMP.Model()
if hasattr(params.benchmark, "fn_pdb_native"):
self.native_assembly = \
representation.create_assembly_from_pdb(self.native_model,
params.benchmark.fn_pdb_native, params.names)
elif hasattr(params.benchmark, "fn_pdbs_native"):
self.native_assembly = \
representation.create_assembly(self.native_model,
params.benchmark.fn_pdbs_native, params.names)
else:
raise ValueError("set_native_assembly_for_benchmark: Requested "
"to set a native assembly for benchmark but did not provide "
"its pdb, or the pdbs of the components")
self.native_rbs = representation.create_rigid_bodies(
self.native_assembly)
anchor_assembly(self.native_rbs, params.anchor)