def write_pdb_file(self, prefix):
from iotbx.pdb.misc_records_output import link_record_output
link_records = link_record_output(self.processed_pdb_file.all_chain_proxies)
broadcast(m=prefix, log = self.log)
self.pdb_hierarchy.adopt_xray_structure(self.xray_structure)
ofn = self.params.output_file_name_prefix
directory = self.params.directory
suffix = "_" + self._pdb_suffix + ".pdb"
if(ofn is None):
pfn = os.path.basename(self.pdb_file_names[0])
ind = max(0,pfn.rfind("."))
ofn = pfn+suffix if ind==0 else pfn[:ind]+suffix
else: ofn = self.params.output_file_name_prefix+".pdb"
if (self.use_directory_prefix) and (directory is not None) :
ofn = os.path.join(directory, ofn)
print >> self.log, " output file name:", ofn
print >> self.log, self.min_max_mean_shift()
print >> self.log, self.min_max_mean_shift()
cs = None
if self.output_crystal_symmetry:
cs = self.xray_structure.crystal_symmetry()
write_whole_pdb_file(
file_name=ofn,
processed_pdb_file=self.processed_pdb_file,
pdb_hierarchy=self.pdb_hierarchy,
crystal_symmetry=cs,
link_records=link_records,
)
if(self.states_collector):
self.states_collector.write(
file_name=ofn[:].replace(".pdb","_all_states.pdb"))
self.output_file_name = os.path.abspath(ofn)
def write(self, pdb_output_file_name="", crystal_symmetry=None):
""" (string) -> text file
Writes the modified protein, with the added chains, obtained by the
BIOMT/MTRIX reconstruction, to a text file in a pdb format.
self.assembled_multimer is the modified pdb object with the added chains
Argumets:
pdb_output_file_name -- string. 'name.pdb'
if no pdn_output_file_name is given pdb_output_file_name=file_name
>>> v = multimer('name.pdb','ba')
>>> v.write('new_name.pdb')
Write a file 'new_name.pdb' to the current directory
>>> v.write(v.pdb_input_file_name)
Write a file 'copy_name.pdb' to the current directory
"""
input_file_name = os.path.basename(self.pdb_input_file_name)
if pdb_output_file_name == "":
pdb_output_file_name = input_file_name
# Avoid writing over the original file
if pdb_output_file_name == input_file_name:
# if file name of output is the same as the input, add 'copy_' in front of the name
self.pdb_output_file_name = self.transform_type + "_" + input_file_name
else:
self.pdb_output_file_name = pdb_output_file_name
# we need to add crystal symmetry to the new file since it is
# sometimes needed when calculating the R-work factor (r_factor_calc.py)
if not crystal_symmetry and os.path.isfile(self.pdb_input_file_name):
crystal_symmetry = crystal_symmetry_from_any.extract_from(self.pdb_input_file_name)
# using the function to write whole pdb file
pdb.write_whole_pdb_file(
file_name=self.pdb_output_file_name,
pdb_hierarchy=self.assembled_multimer,
crystal_symmetry=crystal_symmetry,
)
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)
pdb_h = pdb_input.construct_hierarchy(sort_atoms=True)
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.pdb"
if hasattr(pdb_input, "extract_secondary_structure"):
ss_annotation = pdb_input.extract_secondary_structure()
write_whole_pdb_file(
file_name=out_fn,
output_file=None,
processed_pdb_file=None,
pdb_hierarchy=pdb_h,
crystal_symmetry=pdb_input.crystal_symmetry(),
ss_annotation=ss_annotation,
atoms_reset_serial_first_value=None,
link_records=None)
else:
# This was a mmcif file, so outputting mmcif
pdb_h.write_mmcif_file(
file_name = out_fn,
crystal_symmetry=pdb_input.crystal_symmetry(),
)
def write_pdb_file(self, prefix):
from iotbx.pdb.misc_records_output import link_record_output
link_records = link_record_output(self.processed_pdb_file.all_chain_proxies)
broadcast(m=prefix, log = self.log)
self.pdb_hierarchy.adopt_xray_structure(self.xray_structure)
ofn = self.params.output_file_name_prefix
directory = self.params.directory
suffix = "_" + self._pdb_suffix + ".pdb"
if(ofn is None):
pfn = os.path.basename(self.pdb_file_names[0])
ind = max(0,pfn.rfind("."))
ofn = pfn+suffix if ind==0 else pfn[:ind]+suffix
else: ofn = self.params.output_file_name_prefix+".pdb"
if (self.use_directory_prefix) and (directory is not None) :
ofn = os.path.join(directory, ofn)
print >> self.log, " output file name:", ofn
print >> self.log, self.min_max_mean_shift()
print >> self.log, self.min_max_mean_shift()
cs = None
if self.output_crystal_symmetry:
cs = self.xray_structure.crystal_symmetry()
write_whole_pdb_file(
file_name=ofn,
processed_pdb_file=self.processed_pdb_file,
pdb_hierarchy=self.pdb_hierarchy,
crystal_symmetry=cs,
link_records=link_records,
)
if(self.states_collector):
self.states_collector.write(
file_name=ofn[:].replace(".pdb","_all_states.pdb"))
self.output_file_name = os.path.abspath(ofn)
def run(args, command_name=libtbx.env.dispatcher_name):
parser = argparse.ArgumentParser(
prog=command_name,
usage='%s pdb_file "atom_selection" [...]' % command_name)
parser.add_argument("file_name",
nargs=1,
help="File name of the model file")
parser.add_argument(
"inselections",
help="Atom selection strings",
nargs='+',
)
parser.add_argument("--write-pdb-file",
action="store",
help="write selected atoms to new PDB file",
default=None)
parser.add_argument(
"--cryst1-replacement-buffer-layer",
action="store",
type=float,
help="replace CRYST1 with pseudo unit cell covering the selected"
" atoms plus a surrounding buffer layer",
default=None)
co = parser.parse_args(args)
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=co.file_name[0],
log=sys.stdout)
print
acp = processed_pdb_file.all_chain_proxies
selection_cache = acp.pdb_hierarchy.atom_selection_cache()
atoms = acp.pdb_atoms
all_bsel = flex.bool(atoms.size(), False)
for selection_string in co.inselections:
print selection_string
isel = acp.iselection(string=selection_string, cache=selection_cache)
all_bsel.set_selected(isel, True)
if (not co.write_pdb_file):
print " %d atom%s selected" % plural_s(isel.size())
for atom in atoms.select(isel):
print " %s" % atom.format_atom_record()
print
if (co.write_pdb_file):
print "Writing file:", show_string(co.write_pdb_file)
sel_hierarchy = acp.pdb_hierarchy.select(all_bsel)
if (co.cryst1_replacement_buffer_layer is None):
crystal_symmetry = acp.special_position_settings
else:
import cctbx.crystal
crystal_symmetry = cctbx.crystal.non_crystallographic_symmetry(
sites_cart=sel_hierarchy.atoms().extract_xyz(),
buffer_layer=co.cryst1_replacement_buffer_layer)
write_whole_pdb_file(file_name=co.write_pdb_file,
processed_pdb_file=processed_pdb_file,
pdb_hierarchy=sel_hierarchy,
crystal_symmetry=crystal_symmetry)
print
def run(args, out=sys.stdout, replace_stderr=True):
log = mmtbx.utils.set_log(args, out=out, replace_stderr=replace_stderr)
broadcast(m="phenix.pdbtools tools for PDB model manipulations.", log=log)
if(len(args)==0):
master_params().show(out = log)
return None
inputs = get_inputs(args=args, log=log, master_params=master_params())
### get i/o file names
ofn = inputs.params.output.file_name
output_format = inputs.params.output.format
ifn = inputs.pdb_file_names
if(ofn is None):
if output_format == "pdb": ext = "pdb"
elif output_format == "mmcif": ext = "cif"
if(len(ifn)==1): ofn = os.path.basename(ifn[0]) + "_modified."+ext
elif(len(ifn)>1): ofn = os.path.basename(ifn[0]) + "_et_al_modified"+ext
else:
pdbout = os.path.basename(inputs.pdb_file_names[0])
ofn = pdbout+"_modified."+ext
# Show parameters
broadcast(m="Complete set of parameters", log=log)
master_params().format(inputs.params).show(out = log)
print >> log
# Run calcs
broadcast(m="Performing manipulations", log=log)
task_obj = mmtbx.pdbtools.modify(
xray_structure = inputs.xray_structure,
params = inputs.params.modify,
pdb_hierarchy = inputs.pdb_hierarchy,
log = log)
results = task_obj.get_results()
#
broadcast(m="Writing output model", log=log)
print >> log, "Output model file name: ", ofn
if(inputs.fake_crystal_symmetry):
crystal_symmetry = None
else:
crystal_symmetry = results.crystal_symmetry
if output_format == "pdb":
write_whole_pdb_file(
file_name = ofn,
pdb_hierarchy = results.pdb_hierarchy,
ss_annotation = inputs.pdb_inp.extract_secondary_structure(),
crystal_symmetry = crystal_symmetry,
append_end = True,
atoms_reset_serial_first_value = 1)
elif output_format =="mmcif":
write_whole_cif_file(
file_name = ofn,
pdb_hierarchy = results.pdb_hierarchy,
ss_annotation = inputs.pdb_inp.extract_secondary_structure(),
crystal_symmetry = crystal_symmetry)
broadcast(m="All done.", log=log)
return None
def run(args):
log = sys.stdout
if len(args) == 0:
format_usage_message(log)
return
inputs = mmtbx.utils.process_command_line_args(args=args,
master_params=master_params())
work_params = inputs.params.extract()
inputs.params.show(prefix=" ", out=log)
pdb_file_names = list(inputs.pdb_file_names)
if work_params.file_name is not None:
pdb_file_names += work_params.file_name
if len(pdb_file_names) == 0:
raise Sorry("No PDB file specified")
work_params.model_idealization.enabled=True
# work_params.model_idealization.file_name_before_regularization="before.pdb"
pdb_combined = iotbx.pdb.combine_unique_pdb_files(file_names=pdb_file_names)
pdb_input = iotbx.pdb.input(source_info=None,
lines=flex.std_string(pdb_combined.raw_records))
pdb_h = pdb_input.construct_hierarchy()
# couple checks if combined pdb_h is ok
o_c = pdb_h.overall_counts()
o_c.raise_duplicate_atom_labels_if_necessary()
o_c.raise_residue_groups_with_multiple_resnames_using_same_altloc_if_necessary()
o_c.raise_chains_with_mix_of_proper_and_improper_alt_conf_if_necessary()
o_c.raise_improper_alt_conf_if_necessary()
ann = ioss.annotation.from_phil(
phil_helices=work_params.secondary_structure.protein.helix,
phil_sheets=work_params.secondary_structure.protein.sheet,
pdb_hierarchy=pdb_h)
if ann.get_n_helices() + ann.get_n_sheets() == 0:
ann = pdb_input.extract_secondary_structure()
if ann is None or ann.get_n_helices() + ann.get_n_sheets() == 0:
raise Sorry("No secondary structure annotations found.")
ssb.substitute_ss(
real_h=pdb_h,
xray_structure=pdb_input.xray_structure_simple(),
ss_annotation=ann,
params=work_params.model_idealization,
cif_objects=inputs.cif_objects,
verbose=True,
log=log,
)
# Write resulting pdb file.
write_whole_pdb_file(
file_name="%s_idealized.pdb" % os.path.basename(pdb_file_names[0]),
pdb_hierarchy=pdb_h,
crystal_symmetry=pdb_input.crystal_symmetry(),
ss_annotation=ann)
print >> log, "All done."
def shift_and_write_result(self, hierarchy, fname_suffix, grm=None):
cs_to_write = self.cs if self.shift_vector is None else None
pdb_h_shifted = hierarchy.deep_copy()
pdb_h_shifted.reset_atom_i_seqs()
if self.shift_vector is not None:
atoms = pdb_h_shifted.atoms()
sites_cart = atoms.extract_xyz()
atoms.set_xyz(new_xyz=sites_cart-self.shift_vector)
write_whole_pdb_file(
file_name="%s_%s_nosh.pdb" % (self.params.output_prefix, fname_suffix),
pdb_hierarchy=hierarchy,
crystal_symmetry=self.cs,
ss_annotation=self.ann)
write_whole_pdb_file(
file_name="%s_%s.pdb" % (self.params.output_prefix, fname_suffix),
pdb_hierarchy=pdb_h_shifted,
crystal_symmetry=cs_to_write,
ss_annotation=self.original_ann)
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()
pdb_h = pdb_input.construct_hierarchy()
info = pdb_h.flip_symmetric_amino_acids()
print info
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 hasattr(pdb_input, "extract_secondary_structure"):
ss_annotation = pdb_input.extract_secondary_structure()
write_whole_pdb_file(
file_name=out_fn,
output_file=None,
processed_pdb_file=None,
pdb_hierarchy=pdb_h,
crystal_symmetry=pdb_input.crystal_symmetry(),
ss_annotation=ss_annotation,
atoms_reset_serial_first_value=None,
link_records=None)
else:
# This was a mmcif file, so outputting mmcif
pdb_h.write_mmcif_file(
file_name = out_fn,
crystal_symmetry=pdb_input.crystal_symmetry(),
)
def write(self,pdb_output_file_name='',crystal_symmetry=None):
''' (string) -> text file
Writes the modified protein, with the added chains, obtained by the
BIOMT/MTRIX reconstruction, to a text file in a pdb format.
self.assembled_multimer is the modified pdb object with the added chains
Argumets:
pdb_output_file_name -- string. 'name.pdb'
if no pdn_output_file_name is given pdb_output_file_name=file_name
>>> v = multimer('name.pdb','ba')
>>> v.write('new_name.pdb')
Write a file 'new_name.pdb' to the current directory
>>> v.write(v.pdb_input_file_name)
Write a file 'copy_name.pdb' to the current directory
'''
input_file_name = os.path.basename(self.pdb_input_file_name)
if pdb_output_file_name == '':
pdb_output_file_name = input_file_name
# Avoid writing over the original file
if pdb_output_file_name == input_file_name:
# if file name of output is the same as the input, add 'copy_' in front of the name
self.pdb_output_file_name = self.transform_type + '_' + input_file_name
else:
self.pdb_output_file_name = pdb_output_file_name
# we need to add crystal symmetry to the new file since it is
# sometimes needed when calculating the R-work factor (r_factor_calc.py)
if not crystal_symmetry and os.path.isfile(self.pdb_input_file_name):
crystal_symmetry = crystal_symmetry_from_any.extract_from(
self.pdb_input_file_name)
# using the function to write whole pdb file
pdb.write_whole_pdb_file(
file_name=self.pdb_output_file_name,
pdb_hierarchy=self.assembled_multimer,
crystal_symmetry=crystal_symmetry,
ss_annotation=self.new_annotation)
def run(args, command_name=libtbx.env.dispatcher_name):
if (len(args) == 0): args = ["--help"]
command_line = (option_parser(
usage='%s pdb_file "atom_selection" [...]' % command_name)
.option(None, "--write_pdb_file",
action="store",
type="string",
default=None,
help="write selected atoms to new PDB file",
metavar="FILE")
.option(None, "--cryst1_replacement_buffer_layer",
action="store",
type="float",
default=None,
help="replace CRYST1 with pseudo unit cell covering the selected"
" atoms plus a surrounding buffer layer",
metavar="WIDTH")
).process(args=args, min_nargs=2)
co = command_line.options
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=command_line.args[0],
log=sys.stdout)
print
acp = processed_pdb_file.all_chain_proxies
hierarchy=acp.pdb_hierarchy
asc=hierarchy.atom_selection_cache()
sel=asc.selection(string = "chain 'A' and resid 1 through 8 and icode ' '")
h1=hierarchy.select(sel) # keep original hierarchy too
print h1.as_pdb_string()
selection_cache = acp.pdb_hierarchy.atom_selection_cache()
atoms = acp.pdb_atoms
all_bsel = flex.bool(atoms.size(), False)
for selection_string in command_line.args[1:]:
print selection_string
isel = acp.iselection(string=selection_string, cache=selection_cache)
all_bsel.set_selected(isel, True)
if (not co.write_pdb_file):
print " %d atom%s selected" % plural_s(isel.size())
for atom in atoms.select(isel):
print " %s" % atom.format_atom_record()
print
if (co.write_pdb_file):
print "Writing file:", show_string(co.write_pdb_file)
sel_hierarchy = acp.pdb_hierarchy.select(all_bsel)
if (co.cryst1_replacement_buffer_layer is None):
crystal_symmetry = acp.special_position_settings
else:
import cctbx.crystal
crystal_symmetry = cctbx.crystal.non_crystallographic_symmetry(
sites_cart=sel_hierarchy.atoms().extract_xyz(),
buffer_layer=co.cryst1_replacement_buffer_layer)
write_whole_pdb_file(
file_name=co.write_pdb_file,
processed_pdb_file=processed_pdb_file,
pdb_hierarchy=sel_hierarchy,
crystal_symmetry=crystal_symmetry)
print
def __init__(self,
pdb_input,
cif_objects=None,
params=None,
log=sys.stdout,
verbose=True):
t_0 = time()
self.pdb_input = pdb_input
self.cif_objects = cif_objects
self.params = params
self.log = log
self.verbose = verbose
self.rmsd_from_start = None
self.init_model_statistics = None
self.after_ss_idealization = None
self.after_loop_idealization = None
self.after_rotamer_fixing = None
self.final_model_statistics = None
self.reference_map = None
self.whole_grm = None
self.master_grm = None
self.working_grm = None
self.mon_lib_srv = None
self.ener_lib = None
self.rotamer_manager = None
self.rama_manager = rama_eval()
self.original_hierarchy = None # original pdb_h, without any processing
self.original_boxed_hierarchy = None # original and boxed (if needed)
self.whole_pdb_h = None # boxed with processing (AC trimming, H trimming,...)
self.master_pdb_h = None # master copy in case of NCS
self.working_pdb_h = None # one to use for fixing (master_pdb_h or working_pdb_h)
# various checks, shifts, trims
self.cs = self.pdb_input.crystal_symmetry()
# check self.cs (copy-paste from secondary_sturcure_restraints)
corrupted_cs = False
if self.cs is not None:
if [self.cs.unit_cell(), self.cs.space_group()].count(None) > 0:
corrupted_cs = True
self.cs = None
elif self.cs.unit_cell().volume() < 10:
corrupted_cs = True
self.cs = None
self.original_hierarchy = self.pdb_input.construct_hierarchy()
# couple checks if pdb_h is ok
o_c = self.original_hierarchy.overall_counts()
o_c.raise_duplicate_atom_labels_if_necessary()
o_c.raise_residue_groups_with_multiple_resnames_using_same_altloc_if_necessary()
o_c.raise_chains_with_mix_of_proper_and_improper_alt_conf_if_necessary()
o_c.raise_improper_alt_conf_if_necessary()
if len(self.original_hierarchy.models()) > 1:
raise Sorry("Multi model files are not supported")
ca_only_present = False
for c in self.original_hierarchy.only_model().chains():
if c.is_ca_only():
ca_only_present = True
if ca_only_present:
raise Sorry("Don't support models with chains containing only CA atoms.")
self.original_boxed_hierarchy = self.original_hierarchy.deep_copy()
self.original_boxed_hierarchy.reset_atom_i_seqs()
self.shift_vector = None
if self.cs is None:
if corrupted_cs:
print >> self.log, "Symmetry information is corrupted, "
else:
print >> self.log, "Symmetry information was not found, "
print >> self.log, "putting molecule in P1 box."
self.log.flush()
from cctbx import uctbx
atoms = self.original_boxed_hierarchy.atoms()
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=atoms.extract_xyz(),
buffer_layer=3)
atoms.set_xyz(new_xyz=box.sites_cart)
self.cs = box.crystal_symmetry()
self.shift_vector = box.shift_vector
# self.original_boxed_hierarchy.write_pdb_file(file_name="original_boxed_h.pdb")
if self.shift_vector is not None:
write_whole_pdb_file(
file_name="%s_boxed.pdb" % self.params.output_prefix,
pdb_hierarchy=self.original_boxed_hierarchy,
crystal_symmetry=self.cs,
ss_annotation=self.pdb_input.extract_secondary_structure())
asc = self.original_boxed_hierarchy.atom_selection_cache()
if self.params.trim_alternative_conformations:
sel = asc.selection("altloc ' '")
self.whole_pdb_h = self.original_boxed_hierarchy.select(sel).deep_copy()
print >> self.log, "Atoms in original/working model: %d/%d" % (
self.original_boxed_hierarchy.atoms_size(), self.whole_pdb_h.atoms_size())
else:
self.whole_pdb_h = self.original_boxed_hierarchy.deep_copy()
# self.whole_pdb_h.reset_atom_i_seqs()
# Trimming hydrogens
# Many intermediate variables are needed due to strange behavior of
# selections described in
# iotbx/pdb/tst_hierarchy.py:exercise_selection_and_deep_copy()
asc2 = self.whole_pdb_h.atom_selection_cache()
h_sel = asc2.selection("not (element H or element D)")
temp_h = self.whole_pdb_h.select(h_sel)
self.whole_pdb_h = temp_h.deep_copy()
self.whole_pdb_h.reset_atom_i_seqs()
self.init_model_statistics = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=self.whole_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
self.time_for_init = time()-t_0
def __init__(self,
model, # shifted, with shift_manager
map_data = None, # shifted map_data
params=None,
log=sys.stdout,
verbose=True):
t_0 = time()
self.model = model
# self.cif_objects = cif_objects
self.params = params
self.log = log
self.verbose = verbose
# self.shift_manager = self.model.get_shift_manager()
self.rmsd_from_start = None
self.init_model_statistics = None
self.init_gm_model_statistics = None
self.after_ss_idealization = None
self.after_loop_idealization = None
self.after_rotamer_fixing = None
self.final_model_statistics = None
self.user_supplied_map = map_data
self.reference_map = None # Whole map for all NCS copies
self.master_map = None # Map for only one NCS copy, or == reference_map if no NCS
self.init_ref_map = None # separate map for initial GM. Should be tighter than the 2 above
self.whole_grm = None
self.master_grm = None
self.working_grm = None
params_line = grand_master_phil_str
params = iotbx.phil.parse(
input_string=params_line, process_includes=True).extract()
params.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
params.pdb_interpretation.peptide_link.ramachandran_restraints = True
params.pdb_interpretation.peptide_link.oldfield.weight_scale=3
params.pdb_interpretation.peptide_link.oldfield.plot_cutoff=0.03
params.pdb_interpretation.peptide_link.apply_peptide_plane = True
if self.params.loop_idealization.make_all_trans:
params.pdb_interpretation.peptide_link.apply_all_trans = True
params.pdb_interpretation.nonbonded_weight = 10000
params.pdb_interpretation.c_beta_restraints=True
params.pdb_interpretation.max_reasonable_bond_distance = None
params.pdb_interpretation.ncs_search.enabled = True
params.pdb_interpretation.ncs_search.chain_max_rmsd=4.0
params.pdb_interpretation.ncs_search.chain_similarity_threshold=0.99
params.pdb_interpretation.ncs_search.residue_match_radius=999.0
params.pdb_interpretation.restraints_library.rdl = True
params.pdb_interpretation.secondary_structure = self.params.secondary_structure
self.model.set_pdb_interpretation_params(params)
self.original_hierarchy = self.model.get_hierarchy().deep_copy() # original pdb_h, without any processing
self.original_boxed_hierarchy = None # original and boxed (if needed)
self.filtered_ncs_restr_group_list = []
self.init_ss_annotation = self.model.get_ss_annotation()
# various checks, shifts, trims
self.cs = self.original_cs = self.model.crystal_symmetry()
if self.model.get_shift_manager() is not None:
self.cs = self.model.get_shift_manager().box_crystal_symmetry
# check self.cs (copy-paste from secondary_sturcure_restraints)
corrupted_cs = False
if self.cs is not None:
if [self.cs.unit_cell(), self.cs.space_group()].count(None) > 0:
corrupted_cs = True
self.cs = None
elif self.cs.unit_cell().volume() < 10:
corrupted_cs = True
self.cs = None
# couple checks if pdb_h is ok
o_c = self.original_hierarchy.overall_counts()
o_c.raise_duplicate_atom_labels_if_necessary()
o_c.raise_residue_groups_with_multiple_resnames_using_same_altloc_if_necessary()
o_c.raise_chains_with_mix_of_proper_and_improper_alt_conf_if_necessary()
o_c.raise_improper_alt_conf_if_necessary()
if len(self.original_hierarchy.models()) > 1:
raise Sorry("Multi model files are not supported")
ca_only_present = False
for c in self.original_hierarchy.only_model().chains():
if c.is_ca_only():
ca_only_present = True
if ca_only_present:
raise Sorry("Don't support models with chains containing only CA atoms.")
self.original_boxed_hierarchy = self.model.get_hierarchy().deep_copy()
self.shift_vector = None
if self.cs is None:
assert self.model.get_shift_manager() is None
# should it happen here?
if corrupted_cs:
print >> self.log, "Symmetry information is corrupted, "
else:
print >> self.log, "Symmetry information was not found, "
print >> self.log, "putting molecule in P1 box."
self.log.flush()
from cctbx import uctbx
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=self.model.get_sites_cart(),
buffer_layer=3)
self.model.set_sites_cart(sites_cart=box.sites_cart)
self.original_boxed_hierarchy = self.model.get_hierarchy().deep_copy()
self.cs = box.crystal_symmetry()
self.model.set_crystal_symmetry(self.cs)
self.shift_vector = box.shift_vector
if self.shift_vector is not None and self.params.debug:
write_whole_pdb_file(
file_name="%s_boxed.pdb" % self.params.output_prefix,
pdb_hierarchy=self.model.get_hierarchy(),
crystal_symmetry=self.model.crystal_symmetry(),
ss_annotation=self.init_ss_annotation)
if self.params.trim_alternative_conformations:
self.model.remove_alternative_conformations(always_keep_one_conformer=True)
self.model = self.model.remove_hydrogens()
self.time_for_init = time()-t_0
def run(args, command_name=libtbx.env.dispatcher_name):
if (len(args) == 0): args = ["--help"]
command_line = (option_parser(
usage='%s pdb_file "atom_selection" [...]' % command_name).option(
None,
"--write_pdb_file",
action="store",
type="string",
default=None,
help="write selected atoms to new PDB file",
metavar="FILE"
).option(
None,
"--cryst1_replacement_buffer_layer",
action="store",
type="float",
default=None,
help="replace CRYST1 with pseudo unit cell covering the selected"
" atoms plus a surrounding buffer layer",
metavar="WIDTH")).process(args=args, min_nargs=2)
co = command_line.options
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=command_line.args[0],
log=sys.stdout)
print
acp = processed_pdb_file.all_chain_proxies
hierarchy = acp.pdb_hierarchy
asc = hierarchy.atom_selection_cache()
sel = asc.selection(string="chain 'A' and resid 1 through 8 and icode ' '")
h1 = hierarchy.select(sel) # keep original hierarchy too
print h1.as_pdb_string()
selection_cache = acp.pdb_hierarchy.atom_selection_cache()
atoms = acp.pdb_atoms
all_bsel = flex.bool(atoms.size(), False)
for selection_string in command_line.args[1:]:
print selection_string
isel = acp.iselection(string=selection_string, cache=selection_cache)
all_bsel.set_selected(isel, True)
if (not co.write_pdb_file):
print " %d atom%s selected" % plural_s(isel.size())
for atom in atoms.select(isel):
print " %s" % atom.format_atom_record()
print
if (co.write_pdb_file):
print "Writing file:", show_string(co.write_pdb_file)
sel_hierarchy = acp.pdb_hierarchy.select(all_bsel)
if (co.cryst1_replacement_buffer_layer is None):
crystal_symmetry = acp.special_position_settings
else:
import cctbx.crystal
crystal_symmetry = cctbx.crystal.non_crystallographic_symmetry(
sites_cart=sel_hierarchy.atoms().extract_xyz(),
buffer_layer=co.cryst1_replacement_buffer_layer)
write_whole_pdb_file(file_name=co.write_pdb_file,
processed_pdb_file=processed_pdb_file,
pdb_hierarchy=sel_hierarchy,
crystal_symmetry=crystal_symmetry)
print