def add_model(s1, s2):
''' add chains from s2 to existing s1'''
s1 = s1.deep_copy()
s1_ph = s1.get_hierarchy() # working hierarchy
from mmtbx.secondary_structure.find_ss_from_ca import get_chain_ids
existing_chain_ids = get_chain_ids(s1_ph)
for model_mm_2 in s2.get_hierarchy().models()[:1]:
for chain in model_mm_2.chains():
assert chain.id not in existing_chain_ids # duplicate chains in add_model
new_chain = chain.detached_copy()
for model_mm in s1_ph.models()[:1]:
model_mm.append_chain(new_chain)
s1.reset_after_changing_hierarchy()
return s1
def get_chain_id(model, chain_id, log=sys.stdout):
from mmtbx.secondary_structure.find_ss_from_ca import get_chain_ids
chain_ids = get_chain_ids(model.get_hierarchy())
if len(chain_ids) == 1:
chain_id = chain_ids[0]
elif chain_id is not None:
if chain_id in chain_ids:
print("Working on chain '%s' only" % (chain_id), file=log)
else:
raise Sorry("Chain %s is not in the chains present (%s)" %
(chain_id, " ".join(chain_ids)))
else:
chain_id = chain_ids[0]
print("Working on chain '%s' only (skipping other chains: %s)" %
(chain_id, " ".join(chain_ids[1:])),
file=log)
def tst_05():
from mmtbx.validation.chain_comparison import \
extract_unique_part_of_hierarchy as euph
from mmtbx.secondary_structure.find_ss_from_ca import get_chain_ids
print("Testing extraction of unique part and unique matching")
for m in [modela, modelb, modelaa, modelaab, modelaabaab]:
import iotbx.pdb
from cctbx.array_family import flex
model_pdb_inp = iotbx.pdb.input(source_info='model',
lines=flex.split_lines(m))
crystal_symmetry = model_pdb_inp.crystal_symmetry()
model_hierarchy = model_pdb_inp.construct_hierarchy()
print("\nExtraction of unique MODEL with %s residues" %
(model_hierarchy.overall_counts().n_residues))
query_hierarchy = iotbx.pdb.input(
source_info='query',
lines=flex.split_lines(target)).construct_hierarchy()
unique_hierarchy = euph(model_hierarchy, target_ph=query_hierarchy)
print("FINAL chain ids: %s \n" %
(" ".join(get_chain_ids(unique_hierarchy))))
print("OK")