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_format_was_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):
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(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_format_was_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)