def run(args, log):
t0 = time.time()
if len(args) == 0:
print_legend_and_usage(log)
return
params = get_inputs(
args=args,
log=log,
master_params=master_params(),
#validated = validated,
)
if (params.verbose):
print("Starting Q|R charge", file=log)
print('version: ', __version__, file=log)
del sys.argv[1:]
cc = charges.charges_class(
params.model_file_name,
ligand_cif_file_names=params.ligand_cif_file_name,
electrons=params.electrons,
verbose=params.verbose,
)
rc = cc.get_total_charge(
list_charges=params.list_charges,
assert_correct_chain_terminii=params.assert_correct_chain_terminii,
)
if (params.verbose):
print('Charge: %s' % rc, file=log)
print("Time: %6.4f" % (time.time() - t0), file=log)
if (params.list_charges):
print('Charges:', file=log)
print(rc, file=log)
print("Time: %6.4f" % (time.time() - t0), file=log)
def run(file_name,
d_min=0.8,
maxnum_residues_in_cluster=3,
filter_non_protein_and_hd=True):
prefix = os.path.basename(file_name)[3:7]
print file_name, prefix
pdb_inp = iotbx.pdb.input(file_name=file_name)
resolution = pdb_inp.resolution()
data_type = pdb_inp.get_experiment_type()
if (resolution is not None and resolution <= d_min):
if (data_type in ["X-RAY DIFFRACTION", "NEUTRON DIFFRACTION"]):
pdb_hierarchy = pdb_inp.construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure()
xray_structure.convert_to_isotropic()
pdb_hierarchy.adopt_xray_structure(xray_structure)
if (filter_non_protein_and_hd):
pdb_hierarchy = keep_protein_only(pdb_hierarchy=pdb_hierarchy)
if (pdb_hierarchy is not None):
if (have_conformers(pdb_hierarchy=pdb_hierarchy)):
pdb_hierarchy.remove_alt_confs(
always_keep_one_conformer=True)
pdb_hierarchy = add_hydrogens_using_ReadySet(
pdb_hierarchy=pdb_hierarchy)
box = box_pdb(pdb_hierarchy=pdb_hierarchy)
fq = fragments(
pdb_hierarchy=box.pdb_hierarchy,
maxnum_residues_in_cluster=maxnum_residues_in_cluster,
debug=True,
crystal_symmetry=box.cs)
print "clusters:", fq.clusters
os.mkdir(prefix)
cntr = 0
for fname in os.listdir(os.getcwd()):
if fname.endswith("_cluster.pdb"):
if check_missing_atom(pdb_filename=fname):
os.remove(fname)
else:
cl_fn = "%s_%d.pdb" % (prefix, cntr)
fo = open(cl_fn, "w")
ph_i = iotbx.pdb.input(
file_name=fname).construct_hierarchy()
ph_i = completion.run(pdb_hierarchy=ph_i,
crystal_symmetry=box.cs,
model_completion=False)
pdb_str = ph_i.as_pdb_string(
crystal_symmetry=box.cs, append_end=True)
pdb_str = validate(pdb_str=pdb_str)
if (pdb_str is None): continue
charge = charges_class(
raw_records=pdb_str).get_total_charge()
fo.write("REMARK charge= %s \n" % str(charge))
fo.write(pdb_str)
fo.close()
cntr += 1
libtbx.easy_run.fully_buffered("mv %s %s" %
(cl_fn, prefix))
libtbx.easy_run.fully_buffered("rm -rf *.pdb ase/")
if not os.listdir(prefix):
os.rmdir(prefix)
print "Empty dir"
def get_charge(fn, assert_correct_chain_terminii=True):
cc=charges_class(fn)
return cc.get_total_charge(
assert_correct_chain_terminii=assert_correct_chain_terminii)