def run(args):
if len(args) == 0:
show_usage()
return
inp_fn = args[0]
import time
t0 = time.time()
pdb_input = iotbx.pdb.input(file_name=inp_fn,
source_info=None,
raise_sorry_if_format_error=True)
t0 = time.time()
model = mmtbx.model.manager(model_input=pdb_input)
pdb_h = model.get_hierarchy()
info = pdb_h.flip_symmetric_amino_acids()
print(info)
model.set_sites_cart_from_hierarchy()
out_fn_prefix = inp_fn
if inp_fn.endswith(".pdb") or inp_fn.endswith(".cif"):
out_fn_prefix = inp_fn[:-4]
out_fn = out_fn_prefix + "_iupac.pdb"
if model.input_model_format_cif():
out_fn = out_fn_prefix + "_iupac.cif"
txt = model.model_as_mmcif()
else:
out_fn = out_fn_prefix + "_iupac.cif"
txt = model.model_as_pdb()
with open(out_fn, 'w') as f:
f.write(txt)
def run(args, out=sys.stdout):
for file_name in args:
try:
assert os.path.exists(file_name)
print >> out, "Converting %s to mmCIF format." %file_name
pdb_input = iotbx.pdb.pdb_input(file_name=file_name)
model = mmtbx.model.manager(
model_input = pdb_input)
# hierarchy = pdb_input.construct_hierarchy(sort_atoms=False)
hierarchy = model.get_hierarchy()
pdb_atoms = hierarchy.atoms()
pdb_atoms.set_chemical_element_simple_if_necessary()
elements = pdb_atoms.extract_element().strip()
if (not elements.all_ne("")) :
n_missing = elements.count("")
raise RuntimeError("Missing element symbol for %d atoms." % n_missing)
basename = os.path.splitext(os.path.basename(file_name))[0]
txt = model.model_as_mmcif()
with open(basename+".cif", 'w') as f:
f.write(txt)
print >> out, " wrote %s.cif" % basename
# except IOError, e: # debugging variant, to see traceback
except Exception, e:
print >> out, "Error converting %s to mmCIF format:" %file_name
print >> out, " ", str(e)
continue
def run(args):
if len(args) == 0:
show_usage()
return
inp_fn = args[0]
pdb_input = iotbx.pdb.input(
file_name=inp_fn,
source_info=None,
raise_sorry_if_format_error=True)
model = mmtbx.model.manager(
model_input = pdb_input)
out_fn_prefix = inp_fn
if inp_fn.endswith(".pdb") or inp_fn.endswith(".cif"):
out_fn_prefix = inp_fn[:-4]
out_fn = out_fn_prefix + "_sorted"
txt = ""
if model.input_format_was_cif():
out_fn += ".cif"
txt = model.model_as_mmcif()
else:
out_fn += ".pdb"
txt = model.model_as_pdb()
with open(out_fn, 'w') as f:
f.write(txt)
def run(self):
model = self.data_manager.get_model()
self.cif_blocks = list()
# sequence block
print ('Creating mmCIF block for sequence', file=self.logger)
sequence = self.data_manager.get_sequence()
hierarchy = model._pdb_hierarchy
seq_block = hierarchy.as_cif_block_with_sequence(
sequence, crystal_symmetry=model.crystal_symmetry(),
alignment_params=self.params.sequence_alignment)
self.cif_blocks.append(seq_block)
# create additional cif blocks?
# add cif blocks together
print ('Creating complete mmCIF', file=self.logger)
self.cif_model = model.model_as_mmcif(additional_blocks=self.cif_blocks)
# write output file
self.output_file = os.path.splitext(
self.data_manager.get_default_model_name())[0] + '.deposit.cif'
print ('Writing mmCIF', file=self.logger)
print (' Output file = %s' % self.output_file, file=self.logger)
with open(self.output_file, 'wb') as f:
f.write(self.cif_model)
# update data manager for any downstream applications
pdb_input = iotbx.pdb.input(self.output_file)
model = mmtbx.model.manager(model_input=pdb_input, log=self.logger)
self.data_manager.add_model(self.output_file, model)
self.data_manager.set_default_model(self.output_file)
def test_2(): inp = iotbx.pdb.input(source_info=None, lines=pdb_str_0) model = mmtbx.model.manager(model_input=inp) model.expand_with_BIOMT_records() model = shift_and_box_model(model) model.search_for_ncs() model.setup_ncs_constraints_groups(filter_groups=True) assert model.ncs_constraints_present() assert not model.can_be_unique_with_biomt() assert "" == model.model_as_mmcif(try_unique_with_biomt=True)
def test_1():
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_0)
model = mmtbx.model.manager(model_input=inp)
model.expand_with_BIOMT_records()
model = shift_and_box_model(model)
sel = model.selection("chain '0' or chain 'C' or chain 'F' or chain 'I' or chain 'L' or chain 'O' or chain 'R' or chain 'U' or chain 'X'")
model = model.select(sel)
model.search_for_ncs()
model.setup_ncs_constraints_groups(filter_groups=True)
n1 = model.get_number_of_atoms()
assert n1 == 648, n1
assert model.ncs_constraints_present()
nrgl = model.get_ncs_groups()
assert len(nrgl[0].master_iselection) == 72
assert len(nrgl[0].copies) == 8
# nrgl._show()
# print (model.can_be_unique_with_biomt())
cif_txt = model.model_as_mmcif(try_unique_with_biomt=True)
# print (cif_txt)
assert_lines_in_text(cif_txt, """
loop_
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
_pdbx_struct_assembly_gen.asym_id_list
1 (1-9) A""")
assert_lines_in_text(cif_txt, """
loop_
_pdbx_struct_assembly.id
_pdbx_struct_assembly.details
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
1 'Symmetry assembly' ? ? ? """)
assert_lines_in_text(cif_txt, """
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'point symmetry operation' ? ? 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0""")
inp = iotbx.pdb.input(source_info=None, lines=cif_txt)
m2 = mmtbx.model.manager(model_input=inp)
n2_1 = m2.get_number_of_atoms()
assert n2_1 == 72
m2.expand_with_BIOMT_records()
n2_2 = m2.get_number_of_atoms()
# print (n1, n2)
assert n1 == n2_2, "%d, %d" % (n1, n2)
def run(args):
"""
Apply MTRIX records of PDB or equivalent records of mmCIF.
Example:
phenix.pdb.mtrix_reconstruction model.pdb
phenix.pdb.mtrix_reconstruction model.cif
"""
if (len(args) == 0 or "--help" in args or "-h" in args):
print(run.__doc__)
return
file_name = args[0]
pdb_inp = iotbx.pdb.input(file_name=file_name)
model = mmtbx.model.manager(model_input=pdb_inp)
if model.input_model_format_cif():
out_text = model.model_as_mmcif()
ext = ".cif"
else:
out_text = model.model_as_pdb()
ext = ".pdb"
ofn = "%s_MTRIX_expanded%s" % (os.path.splitext(
os.path.basename(file_name))[0], ext)
print("Writing result to %s file." % ofn)
with open(ofn, 'w') as f:
f.write(out_text)
