def add_hydrogens(self):
# Not used and not working anymore.
self.whole_pdb_h = self.get_intermediate_result_hierarchy()
cs = self.model.crystal_symmetry()
pdb_str, changed = check_and_add_hydrogen(
pdb_hierarchy=self.whole_pdb_h,
file_name=None,
nuclear=False,
keep_hydrogens=False,
verbose=False,
model_number=0,
n_hydrogen_cut_off=0,
time_limit=120,
allow_multiple_models=True,
crystal_symmetry=self.cs,
do_flips=True,
log=self.log)
self.whole_pdb_h = iotbx.pdb.input(lines=pdb_str, source_info=None).construct_hierarchy()
# we need to renew everythig here: grm, whole model, xrs!
self.whole_xrs = self.working_pdb_h.extract_xray_structure(crystal_symmetry=cs)
self.get_grm()
# self.get_filtered_ncs_group_list()
# temp workaround, do something here to handle NCS cases
self.working_pdb_h = self.whole_pdb_h
self.working_xrs = self.working_pdb_h.extract_xray_structure(crystal_symmetry=cs)
self.working_grm = self.whole_grm
def add_hydrogens(self, model, nuclear=False):
from mmtbx.validation.clashscore import check_and_add_hydrogen
hierarchy = model.get_hierarchy()
reduce_str, check = check_and_add_hydrogen(pdb_hierarchy=hierarchy,
file_name=None,
nuclear=nuclear,
keep_hydrogens=True,
verbose=False,
model_number=0,
n_hydrogen_cut_off=0,
time_limit=120,
allow_multiple_models=True,
crystal_symmetry=None,
do_flips=False,
log=None)
#There should be a check here for whether Reduce completed
return reduce_str
def test_file_with_unknown_pair_type():
'''
Verify that ready_set can fix issues with unknown_pair_type
'''
model = obtain_model(raw_records = unknown_pairs_pdb_str,
stop_for_unknowns = False)
ph = model.get_hierarchy()
pdb_with_h, h_were_added = mvc.check_and_add_hydrogen(
pdb_hierarchy = ph,
allow_multiple_models = False,
crystal_symmetry = model.crystal_symmetry(),
log = null_out())
sorry = None
try:
model = obtain_model(raw_records=pdb_with_h)
except Sorry as e:
sorry = e
assert(sorry is not None)
def test_identifying_and_addition_of_hydrogen(self):
""" test identifying and addition of hydrogen """
has_reduce = libtbx.env.has_module(name="reduce")
if has_reduce:
pdb_inp = iotbx.pdb.input(file_name=self.file_name)
pdb_hierarchy = pdb_inp.construct_hierarchy()
elements = pdb_hierarchy.atoms().extract_element()
h_count_0 = elements.count(' H') + elements.count(' D')
new_pdb_str, _ = check_and_add_hydrogen(file_name=self.file_name,
verbose=False)
pdb_inp = iotbx.pdb.input(source_info=None, lines=new_pdb_str)
pdb_hierarchy = pdb_inp.construct_hierarchy()
elements = pdb_hierarchy.atoms().extract_element()
h_count_1 = elements.count(' H') + elements.count(' D')
self.assertEqual(h_count_0, 0)
self.assertTrue(h_count_1 > 0)
else:
# Skip test if reduce is not present
pass
def test_identifying_and_addition_of_hydrogen(self):
""" test identifying and addition of hydrogen """
has_reduce = libtbx.env.has_module(name="reduce")
if has_reduce:
pdb_inp = iotbx.pdb.input(file_name=self.file_name)
pdb_hierarchy = pdb_inp.construct_hierarchy()
elements = pdb_hierarchy.atoms().extract_element()
h_count_0 = elements.count(' H') + elements.count(' D')
new_pdb_str,_ = check_and_add_hydrogen(
file_name=self.file_name,
verbose=False)
pdb_inp = iotbx.pdb.input(source_info=None, lines=new_pdb_str)
pdb_hierarchy = pdb_inp.construct_hierarchy()
elements = pdb_hierarchy.atoms().extract_element()
h_count_1 = elements.count(' H') + elements.count(' D')
self.assertEqual(h_count_0,0)
self.assertTrue(h_count_1>0)
else:
# Skip test if reduce is not present
pass
def run(args, out=None):
"""
Calculates number of non-bonded atoms overlaps in a model
prints to log:
When verbose=True the function print detailed results to log
When verbose=False it will print:
nb_overlaps_macro_molecule,
nb_overlaps_due_to_sym_op,
nb_overlaps_all
Args:
args (list): list of options.
model=input_file input PDB file
cif=input_file input CIF file for additional model information
keep_hydrogens=True keep input hydrogen files (otherwise regenerate)
nuclear=False use nuclear x-H distances and vdW radii
verbose=True verbose text output
time_limit=120 Time limit (sec) for Reduce optimization
show_overlap_type=all what type of overlaps to show
show_normalized_nbo=False Show non-bonded overlaps per 1000 atoms
substitute_non_crystallographic_unit_cell_if_necessary=false
fix CRYST1 records if needed
out : where to wrote the output to.
Returns:
nb_overlaps (obj): Object containing overlap and overlap per thousand
atoms information
"""
if not out: out = sys.stdout
if not args:
print >> out, usage_string
return None
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="model",
cif_file_def="cif",
usage_string=usage_string)
params = cmdline.work.extract()
if (params.model is None):
raise Usage(usage_string)
pdb_file_name = [x for x in args if x.endswith('.pdb')]
cif_file_name = [x for x in args if x.endswith('.cif')]
assert pdb_file_name
pdb_file_name = pdb_file_name[0]
if not params.skip_hydrogen_test:
pdb_with_h, h_were_added = mvc.check_and_add_hydrogen(
file_name=pdb_file_name,
model_number=0,
nuclear=params.nuclear,
verbose=params.verbose,
time_limit=params.time_limit,
keep_hydrogens=params.keep_hydrogens,
allow_multiple_models=False,
log=out)
if h_were_added:
pdb_file_name = pdb_file_name.replace('.pdb', '_with_h.pdb')
open(pdb_file_name, 'w').write(pdb_with_h)
files = [pdb_file_name]
if cif_file_name:
files += cif_file_name
pdb_processed_file = pdb_inter.run(
args=files,
assume_hydrogens_all_missing=False,
hard_minimum_nonbonded_distance=0.0,
nonbonded_distance_threshold=None,
substitute_non_crystallographic_unit_cell_if_necessary=params.
substitute_non_crystallographic_unit_cell_if_necessary,
log=null_out())
# test that CRYST1 records are ok
sps = pdb_processed_file.all_chain_proxies.special_position_settings
if not sps:
msg = 'None valid CRSYT1 records.\n'
msg += 'Consider running mmtbx.nonbonded_overlaps with the option:\n'
msg += 'substitute_non_crystallographic_unit_cell_if_necessary=true'
raise Sorry(msg)
grm = pdb_processed_file.geometry_restraints_manager()
xrs = pdb_processed_file.xray_structure()
sites_cart = xrs.sites_cart()
site_labels = xrs.scatterers().extract_labels()
hd_sel = xrs.hd_selection()
macro_mol_sel = nbo.get_macro_mol_sel(pdb_processed_file)
nb_overlaps = nbo.info(geometry_restraints_manager=grm,
macro_molecule_selection=macro_mol_sel,
sites_cart=sites_cart,
site_labels=site_labels,
hd_sel=hd_sel)
if params.verbose:
nb_overlaps.show(log=out,
nbo_type=params.show_overlap_type,
normalized_nbo=params.show_normalized_nbo)
else:
all = nb_overlaps.result.nb_overlaps_all
macro_molecule = nb_overlaps.result.nb_overlaps_macro_molecule
sym = nb_overlaps.result.nb_overlaps_due_to_sym_op
out_list = map(lambda x: str(round(x, 2)), [macro_molecule, sym, all])
print >> out, ', '.join(out_list)
return nb_overlaps
def run (args, out=None) :
"""
Calculates number of non-bonded atoms overlaps in a model
prints to log:
When verbose=True the function print detailed results to log
When verbose=False it will print:
nb_overlaps_macro_molecule,
nb_overlaps_due_to_sym_op,
nb_overlaps_all
Args:
args (list): list of options.
model=input_file input PDB file
cif=input_file input CIF file for additional model information
keep_hydrogens=True keep input hydrogen files (otherwise regenerate)
nuclear=False use nuclear x-H distances and vdW radii
verbose=True verbose text output
time_limit=120 Time limit (sec) for Reduce optimization
show_overlap_type=all what type of overlaps to show
show_normalized_nbo=False Show non-bonded overlaps per 1000 atoms
substitute_non_crystallographic_unit_cell_if_necessary=false
fix CRYST1 records if needed
out : where to wrote the output to.
Returns:
nb_overlaps (obj): Object containing overlap and overlap per thousand
atoms information
"""
if not out: out = sys.stdout
if not args:
print >> out,usage_string
return None
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="model",
cif_file_def="cif",
usage_string=usage_string)
params = cmdline.work.extract()
if (params.model is None) :
raise Usage(usage_string)
pdb_file_name = [x for x in args if x.endswith('.pdb')]
cif_file_name = [x for x in args if x.endswith('.cif')]
assert pdb_file_name
pdb_file_name = pdb_file_name[0]
if not params.skip_hydrogen_test:
pdb_with_h, h_were_added = mvc.check_and_add_hydrogen(
file_name=pdb_file_name,
model_number=0,
nuclear=params.nuclear,
verbose=params.verbose,
time_limit=params.time_limit,
keep_hydrogens=params.keep_hydrogens,
allow_multiple_models=False,
log=out)
if h_were_added:
pdb_file_name = pdb_file_name.replace('.pdb','_with_h.pdb')
open(pdb_file_name,'w').write(pdb_with_h)
files = [pdb_file_name]
if cif_file_name:
files += cif_file_name
pdb_processed_file = pdb_inter.run(
args=files,
assume_hydrogens_all_missing=False,
hard_minimum_nonbonded_distance=0.0,
nonbonded_distance_threshold=None,
substitute_non_crystallographic_unit_cell_if_necessary=
params.substitute_non_crystallographic_unit_cell_if_necessary,
log=null_out() )
# test that CRYST1 records are ok
sps = pdb_processed_file.all_chain_proxies.special_position_settings
if not sps:
msg = 'None valid CRSYT1 records.\n'
msg += 'Consider running phenix.clashscore with the option:\n'
msg += 'substitute_non_crystallographic_unit_cell_if_necessary=true'
raise Sorry(msg)
grm = pdb_processed_file.geometry_restraints_manager()
xrs = pdb_processed_file.xray_structure()
sites_cart = xrs.sites_cart()
site_labels = xrs.scatterers().extract_labels()
hd_sel = xrs.hd_selection()
macro_mol_sel = nbo.get_macro_mol_sel(pdb_processed_file)
nb_overlaps = nbo.info(
geometry_restraints_manager=grm,
macro_molecule_selection=macro_mol_sel,
sites_cart=sites_cart,
site_labels=site_labels,
hd_sel=hd_sel)
if params.verbose:
nb_overlaps.show(
log=out,
nbo_type=params.show_overlap_type,
normalized_nbo=params.show_normalized_nbo)
else:
all = nb_overlaps.result.nb_overlaps_all
macro_molecule = nb_overlaps.result.nb_overlaps_macro_molecule
sym = nb_overlaps.result.nb_overlaps_due_to_sym_op
out_list = map(lambda x: str(round(x,2)),[macro_molecule,sym,all])
print >> out,', '.join(out_list)
return nb_overlaps
