def run(args=(), params=None, out=None):
if (out is None): out = sys.stdout
if (params is None):
if (len(args) == 0):
raise Usage("pdb_split_chains.py model.pdb")
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
pdb_file_def="split_chains.pdb_file")
params = cmdline.work.extract()
validate_params(params)
params = params.split_chains
if (params.output_dir is None):
params.output_dir = os.getcwd()
if (params.output_base is None):
params.output_base = os.path.basename(
os.path.splitext(params.pdb_file)[0])
from iotbx import file_reader
from iotbx.pdb.hierarchy import new_hierarchy_from_chain
pdb_in = file_reader.any_file(params.pdb_file, force_type="pdb")
pdb_in.check_file_type("pdb")
symm = pdb_in.file_object.crystallographic_section()
hierarchy = pdb_in.file_object.hierarchy
if (len(hierarchy.models()) > 1):
raise Sorry(
"Multi-model PDB files are not supported. You can use " +
"iotbx.pdb.split_models to break the structure into individual model "
+ "files.")
id_counts = {}
outputs = []
for chain in hierarchy.models()[0].chains():
main_conf = chain.conformers()[0]
if (params.exclude_heteroatoms):
if ((not main_conf.is_protein()) and (not main_conf.is_na())):
continue
elif (len(chain.residue_groups()) == 1):
continue
id = chain.id
if (id == " "):
id = "_"
if (id_counts.get(id, 0) > 0):
suffix = "%s-%d" % (id, id_counts[id] + 1)
else:
suffix = id
if (not id in id_counts):
id_counts[id] = 0
id_counts[id] += 1
output_file = os.path.join(params.output_dir,
"%s_%s.pdb" % (params.output_base, suffix))
f = open(output_file, "w")
if (params.preserve_symmetry):
f.write("\n".join(symm))
f.write("\n")
new_hierarchy = new_hierarchy_from_chain(chain)
f.write(new_hierarchy.as_pdb_string())
f.close()
outputs.append(output_file)
print >> out, "Wrote chain '%s' to %s" % (chain.id, output_file)
return outputs
def run (args=(), params=None, out=None) :
if (out is None) : out = sys.stdout
if (params is None) :
if (len(args) == 0) :
raise Usage("pdb_split_chains.py model.pdb")
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
pdb_file_def="split_chains.pdb_file")
params = cmdline.work.extract()
validate_params(params)
params = params.split_chains
if (params.output_dir is None) :
params.output_dir = os.getcwd()
if (params.output_base is None) :
params.output_base = os.path.basename(os.path.splitext(params.pdb_file)[0])
from iotbx import file_reader
from iotbx.pdb.hierarchy import new_hierarchy_from_chain
pdb_in = file_reader.any_file(params.pdb_file, force_type="pdb")
pdb_in.check_file_type("pdb")
symm = pdb_in.file_object.crystallographic_section()
hierarchy = pdb_in.file_object.hierarchy
if (len(hierarchy.models()) > 1) :
raise Sorry("Multi-model PDB files are not supported. You can use "+
"iotbx.pdb.split_models to break the structure into individual model "+
"files.")
id_counts = {}
outputs = []
for chain in hierarchy.models()[0].chains() :
main_conf = chain.conformers()[0]
if (params.exclude_heteroatoms) :
if ((not main_conf.is_protein()) and (not main_conf.is_na())) :
continue
elif (len(chain.residue_groups()) == 1) :
continue
id = chain.id
if (id == " ") :
id = "_"
if (id_counts.get(id, 0) > 0) :
suffix = "%s-%d" % (id, id_counts[id] + 1)
else :
suffix = id
if (not id in id_counts) :
id_counts[id] = 0
id_counts[id] += 1
output_file = os.path.join(params.output_dir, "%s_%s.pdb" %
(params.output_base, suffix))
f = open(output_file, "w")
if (params.preserve_symmetry) :
f.write("\n".join(symm))
f.write("\n")
new_hierarchy = new_hierarchy_from_chain(chain)
f.write(new_hierarchy.as_pdb_string())
f.close()
outputs.append(output_file)
print >> out, "Wrote chain '%s' to %s" % (chain.id, output_file)
return outputs
def my_selection(ph, ch_id, sel_list_extended):
min_iseq = sel_list_extended[0]
new_h = None
for chain in ph.only_model().chains():
if chain.id == ch_id:
if new_h is None:
# append first chain and tweak selections
new_h = new_hierarchy_from_chain(chain)
min_iseq = chain.atoms()[0].i_seq
for i in range(len(sel_list_extended)):
sel_list_extended[i] -= min_iseq
else:
# append extra chain and tweak selection
new_start_iseq = new_h.atoms_size()
old_start_iseq = chain.atoms()[0].i_seq
dif = old_start_iseq - new_start_iseq - min_iseq
new_h.only_model().append_chain(chain.detached_copy())
for i in range(len(sel_list_extended)):
if sel_list_extended[i] >= old_start_iseq - min_iseq:
# new = old - old + new
sel_list_extended[i] -= dif
return new_h.select(flex.size_t(sel_list_extended))
def chain_from_selection(chain, selection): from iotbx.pdb.hierarchy import new_hierarchy_from_chain new_hierarchy = new_hierarchy_from_chain(chain=chain).select(selection)
def chain_from_selection(chain, selection):
from iotbx.pdb.hierarchy import new_hierarchy_from_chain
new_hierarchy = new_hierarchy_from_chain(chain=chain).select(selection)
