def exercise_model_only():
from mmtbx.building import extend_sidechains
import iotbx.pdb.hierarchy
import mmtbx.monomer_library
pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""
ATOM 65 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N
ATOM 66 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C
ATOM 67 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C
ATOM 68 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O
ATOM 69 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C
ATOM 70 CG LYS A 7 4.345 7.215 0.830 1.00 33.58 C
ATOM 71 CD LYS A 7 3.213 7.570 -0.123 1.00 41.39 C
ATOM 72 CE LYS A 7 2.976 6.471 -1.165 1.00 48.81 C
""")
extend_sidechains.extend_protein_model(
pdb_hierarchy=pdb_in.hierarchy,
mon_lib_srv=mmtbx.monomer_library.server.server())
assert (pdb_in.hierarchy.as_pdb_string() == """\
ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N
ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C
ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C
ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O
ATOM 5 CB LYS A 7 3.980 6.048 1.757 1.00 23.56 C
ATOM 6 CG LYS A 7 4.366 7.205 0.850 1.00 33.58 C
ATOM 7 CD LYS A 7 3.241 7.559 -0.109 1.00 41.39 C
ATOM 8 CE LYS A 7 3.011 6.457 -1.129 1.00 48.81 C
ATOM 9 NZ LYS A 7 1.911 6.790 -2.075 1.00 26.71 N
TER
""")
def exercise_model_only () :
from mmtbx.building import extend_sidechains
import iotbx.pdb.hierarchy
pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""
ATOM 65 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N
ATOM 66 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C
ATOM 67 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C
ATOM 68 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O
ATOM 69 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C
ATOM 70 CG LYS A 7 4.345 7.215 0.830 1.00 33.58 C
ATOM 71 CD LYS A 7 3.213 7.570 -0.123 1.00 41.39 C
ATOM 72 CE LYS A 7 2.976 6.471 -1.165 1.00 48.81 C
""")
extend_sidechains.extend_protein_model(
pdb_hierarchy=pdb_in.hierarchy,
modify_segids=False,
log=null_out())
assert (pdb_in.hierarchy.as_pdb_string() == """\
ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N
ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C
ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C
ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O
ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C
ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C
ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C
ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C
ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N
TER
""")
def exercise_model_only():
from mmtbx.building import extend_sidechains
import iotbx.pdb.hierarchy
pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""
ATOM 65 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N
ATOM 66 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C
ATOM 67 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C
ATOM 68 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O
ATOM 69 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C
ATOM 70 CG LYS A 7 4.345 7.215 0.830 1.00 33.58 C
ATOM 71 CD LYS A 7 3.213 7.570 -0.123 1.00 41.39 C
ATOM 72 CE LYS A 7 2.976 6.471 -1.165 1.00 48.81 C
""")
extend_sidechains.extend_protein_model(pdb_hierarchy=pdb_in.hierarchy,
modify_segids=False,
log=null_out())
assert (pdb_in.hierarchy.as_pdb_string() == """\
ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N
ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C
ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C
ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O
ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C
ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C
ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C
ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C
ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N
TER
""")
def exercise_do_not_move_if_complete():
pdb_inp = iotbx.pdb.input(source_info=None,
lines=pdb_str_do_no_move_if_complete)
pdb_h = pdb_inp.construct_hierarchy()
xyz1 = pdb_h.atoms().extract_xyz()
pdb_h_completed = pdb_h.deep_copy()
extend_sidechains.extend_protein_model(pdb_hierarchy=pdb_h_completed,
mon_lib_srv=mon_lib_srv,
add_hydrogens=False)
xyz2 = pdb_h_completed.atoms().extract_xyz()
assert approx_equal(flex.max(flex.sqrt((xyz1 - xyz2).dot())), 0.0)
def exercise_extend_sidechains(pdb_str_bad, pdb_str_good, i, Sorry_msg, add_h):
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_bad)
pdb_h = pdb_inp.construct_hierarchy()
pdb_h.write_pdb_file(file_name="m_in_%d.pdb" % i)
pdb_h_bad = pdb_h.deep_copy()
e = None
try:
extend_sidechains.extend_protein_model(pdb_hierarchy=pdb_h,
mon_lib_srv=mon_lib_srv,
add_hydrogens=add_h)
except Exception, e:
pass
def complete_model(pdb_hierarchy):
fraction_of_nonH_incomplete = None
try:
number_of_residues = len(list(pdb_hierarchy.residue_groups()))
n_changed = extend_sidechains.extend_protein_model(pdb_hierarchy,
mon_lib_server,
add_hydrogens=False)
fraction_of_nonH_incomplete = n_changed * 100. / number_of_residues
except KeyboardInterrupt:
raise
except Exception, e:
fraction_of_nonH_incomplete = None
def exercise_extend_sidechains(pdb_str_bad, pdb_str_good, i, Sorry_msg, add_h):
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_bad)
pdb_h = pdb_inp.construct_hierarchy()
pdb_h.write_pdb_file(file_name="m_in_%d.pdb" % i)
pdb_h_bad = pdb_h.deep_copy()
e = None
try:
extend_sidechains.extend_protein_model(pdb_hierarchy=pdb_h,
mon_lib_srv=mon_lib_srv,
add_hydrogens=add_h)
except Exception as e:
if (Sorry_msg is not None):
assert str(e).find(Sorry_msg) > -1
return
#
pdb_h.write_pdb_file(file_name="m_completed_%d.pdb" % i)
pdb_h_result = pdb_h.deep_copy()
#
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_good)
pdb_h_answer = pdb_inp.construct_hierarchy()
pdb_h_answer.write_pdb_file(file_name="m_good_%d.pdb" % i)
#
check(answer=pdb_h_answer, result=pdb_h_result, bad=pdb_h_bad)
def complete_pdb_hierarchy(
hierarchy,
geometry_restraints_manager,
use_capping_hydrogens=False,
append_to_end_of_model=False,
pdb_filename=None,
pdb_inp=None,
original_pdb_filename=None,
verbose=False,
debug=False,
):
for ag in hierarchy.atom_groups():
if get_class(ag.resname) in ['common_rna_dna']:
raise Sorry('')
from mmtbx.building import extend_sidechains
params = None
original_hierarchy = None
if use_capping_hydrogens:
params = hierarchy_utils.get_pdb_interpretation_params()
params.link_distance_cutoff = 1.8 # avoid linking across a single missing AA
if original_pdb_filename:
original_pdb_inp = iotbx.pdb.input(original_pdb_filename)
original_hierarchy = original_pdb_inp.construct_hierarchy()
if debug:
output = hierarchy_utils.write_hierarchy(
pdb_filename,
pdb_inp,
hierarchy,
'temp1',
)
#
# assume model is heavy-atom complete
#
if not use_capping_hydrogens:
if debug:
ppf = hierarchy_utils.get_processed_pdb(pdb_filename=output)
else:
raw_records = hierarchy_utils.get_raw_records(pdb_inp, hierarchy)
ppf = hierarchy_utils.get_processed_pdb(
raw_records=raw_records,
params=params,
)
sites_cart = hierarchy.atoms().extract_xyz()
ppf.all_chain_proxies.pdb_hierarchy.atoms().set_xyz(sites_cart)
n_changed = extend_sidechains.extend_protein_model(
ppf.all_chain_proxies.pdb_hierarchy,
mon_lib_server,
add_hydrogens=False,
)
if debug:
print 'number of side chains changed', n_changed
output = hierarchy_utils.write_hierarchy(
pdb_filename,
pdb_inp,
ppf.all_chain_proxies.pdb_hierarchy,
'temp2',
)
#
# need to use Reduce/ReadySet! to add hydrogens
#
if not use_capping_hydrogens:
output = hierarchy_utils.write_hierarchy(
pdb_filename,
pdb_inp,
ppf.all_chain_proxies.pdb_hierarchy,
'readyset_input',
)
hierarchy = hierarchy_utils.add_hydrogens_using_ReadySet(output)
#
# remove side chain acid hydrogens - maybe not required since recent changes
#
if debug:
ppf = hierarchy_utils.get_processed_pdb(
pdb_filename=output,
params=params,
)
else:
raw_records = hierarchy_utils.get_raw_records(pdb_inp, hierarchy)
ppf = hierarchy_utils.get_processed_pdb(
raw_records=raw_records,
params=params,
)
sites_cart = hierarchy.atoms().extract_xyz()
ppf.all_chain_proxies.pdb_hierarchy.atoms().set_xyz(sites_cart)
remove_acid_side_chain_hydrogens(ppf.all_chain_proxies.pdb_hierarchy)
#
# add hydrogens in special cases
# eg ETA
# eg N - H, H2
#
if debug:
ppf = hierarchy_utils.get_processed_pdb(
pdb_filename=output,
params=params,
)
else:
hierarchy = ppf.all_chain_proxies.pdb_hierarchy
raw_records = hierarchy_utils.get_raw_records(pdb_inp, hierarchy)
ppf = hierarchy_utils.get_processed_pdb(
raw_records=raw_records,
params=params,
)
sites_cart = hierarchy.atoms().extract_xyz()
ppf.all_chain_proxies.pdb_hierarchy.atoms().set_xyz(sites_cart)
special_case_hydrogens(
ppf.all_chain_proxies.pdb_hierarchy,
ppf.geometry_restraints_manager(),
#use_capping_hydrogens=use_capping_hydrogens,
#append_to_end_of_model=append_to_end_of_model,
#original_hierarchy=original_hierarchy,
verbose=verbose,
)
#
# add terminals atoms including hydrogens and OXT - more docs here...
#
if debug:
output = hierarchy_utils.write_hierarchy(
pdb_filename,
pdb_inp,
ppf.all_chain_proxies.pdb_hierarchy,
'temp3',
)
ppf = hierarchy_utils.get_processed_pdb(
pdb_filename=output,
params=params,
)
else:
hierarchy = ppf.all_chain_proxies.pdb_hierarchy
raw_records = hierarchy_utils.get_raw_records(pdb_inp, hierarchy)
ppf = hierarchy_utils.get_processed_pdb(
raw_records=raw_records,
params=params,
)
sites_cart = hierarchy.atoms().extract_xyz()
ppf.all_chain_proxies.pdb_hierarchy.atoms().set_xyz(sites_cart)
add_terminal_hydrogens(
ppf.all_chain_proxies.pdb_hierarchy,
ppf.geometry_restraints_manager(),
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
original_hierarchy=original_hierarchy,
verbose=verbose,
) # in place
ppf.all_chain_proxies.pdb_hierarchy.atoms(
).set_chemical_element_simple_if_necessary()
ppf.all_chain_proxies.pdb_hierarchy.sort_atoms_in_place()
#display_hierarchy_atoms(ppf.all_chain_proxies.pdb_hierarchy)
#ppf.all_chain_proxies.pdb_hierarchy.atoms_reset_serial()
#ppf.all_chain_proxies.pdb_hierarchy.atoms().reset_i_seq()
return ppf
def complete_pdb_hierarchy(
hierarchy,
geometry_restraints_manager,
use_capping_hydrogens=False,
append_to_end_of_model=False,
pdb_filename=None,
pdb_inp=None,
original_pdb_filename=None,
verbose=False,
debug=False,
):
"""Complete PDB hierarchy with hydrogen atoms as needed
This needs to move to Phenix with better functionality
Args:
hierarchy (hierarchy): Starting model
geometry_restraints_manager (GRM): Starting restraints
use_capping_hydrogens (bool, optional): Capping or not
append_to_end_of_model (bool, optional): Added atoms go to end of atom list
pdb_filename (None, optional): Description
pdb_inp (None, optional): Description
original_pdb_filename (None, optional): Description
verbose (bool, optional): Description
debug (bool, optional): Description
Returns:
TYPE: Description
Raises:
Sorry: Description
"""
for ag in hierarchy.atom_groups():
if get_class(ag.resname) in ['common_rna_dna']:
raise Sorry('Nucleotides are not currently supported. e.g. %s' %
ag.resname)
from mmtbx.building import extend_sidechains
original_hierarchy = None
params = hierarchy_utils.get_pdb_interpretation_params()
params.restraints_library.cdl = False
if use_capping_hydrogens:
params.link_distance_cutoff = 1.8 # avoid linking across a single missing AA
if original_pdb_filename:
original_pdb_inp = iotbx.pdb.input(original_pdb_filename)
original_hierarchy = original_pdb_inp.construct_hierarchy()
if debug:
output = hierarchy_utils.write_hierarchy(
pdb_filename,
pdb_inp,
hierarchy,
'temp1',
)
#
# assume model is heavy-atom complete
#
if not use_capping_hydrogens:
if debug:
ppf = hierarchy_utils.get_processed_pdb(pdb_filename=output)
else:
raw_records = hierarchy_utils.get_raw_records(pdb_inp, hierarchy)
ppf = hierarchy_utils.get_processed_pdb(
raw_records=raw_records,
params=params,
)
sites_cart = hierarchy.atoms().extract_xyz()
ppf.all_chain_proxies.pdb_hierarchy.atoms().set_xyz(sites_cart)
n_changed = extend_sidechains.extend_protein_model(
ppf.all_chain_proxies.pdb_hierarchy,
mon_lib_server,
add_hydrogens=False,
)
if debug:
print('number of side chains changed', n_changed)
output = hierarchy_utils.write_hierarchy(
pdb_filename,
pdb_inp,
ppf.all_chain_proxies.pdb_hierarchy,
'temp2',
)
#
# need to use Reduce/ReadySet! to add hydrogens
#
if not use_capping_hydrogens:
output = hierarchy_utils.write_hierarchy(
pdb_filename,
pdb_inp,
ppf.all_chain_proxies.pdb_hierarchy,
'readyset_input',
)
hierarchy = hierarchy_utils.add_hydrogens_using_ReadySet(output)
#
# remove side chain acid hydrogens - maybe not required since recent changes
#
if debug:
ppf = hierarchy_utils.get_processed_pdb(
pdb_filename=output,
params=params,
)
else:
raw_records = hierarchy_utils.get_raw_records(pdb_inp, hierarchy)
ppf = hierarchy_utils.get_processed_pdb(
raw_records=raw_records,
params=params,
)
sites_cart = hierarchy.atoms().extract_xyz()
ppf.all_chain_proxies.pdb_hierarchy.atoms().set_xyz(sites_cart)
remove_acid_side_chain_hydrogens(ppf.all_chain_proxies.pdb_hierarchy)
#
# add hydrogens in special cases
# eg ETA
# eg N - H, H2
#
if debug:
ppf = hierarchy_utils.get_processed_pdb(
pdb_filename=output,
params=params,
)
else:
hierarchy = ppf.all_chain_proxies.pdb_hierarchy
raw_records = hierarchy_utils.get_raw_records(pdb_inp, hierarchy)
ppf = hierarchy_utils.get_processed_pdb(
raw_records=raw_records,
params=params,
)
sites_cart = hierarchy.atoms().extract_xyz()
ppf.all_chain_proxies.pdb_hierarchy.atoms().set_xyz(sites_cart)
special_case_hydrogens(
ppf.all_chain_proxies.pdb_hierarchy,
ppf.geometry_restraints_manager(),
#use_capping_hydrogens=use_capping_hydrogens,
#append_to_end_of_model=append_to_end_of_model,
#original_hierarchy=original_hierarchy,
verbose=verbose,
)
#
# add terminals atoms including hydrogens and OXT - more docs here...
#
if debug:
output = hierarchy_utils.write_hierarchy(
pdb_filename,
pdb_inp,
ppf.all_chain_proxies.pdb_hierarchy,
'temp3',
)
ppf = hierarchy_utils.get_processed_pdb(
pdb_filename=output,
params=params,
)
else:
hierarchy = ppf.all_chain_proxies.pdb_hierarchy
raw_records = hierarchy_utils.get_raw_records(pdb_inp, hierarchy)
ppf = hierarchy_utils.get_processed_pdb(
raw_records=raw_records,
params=params,
)
sites_cart = hierarchy.atoms().extract_xyz()
ppf.all_chain_proxies.pdb_hierarchy.atoms().set_xyz(sites_cart)
#
# moved to mmtbx.ligands
#
add_terminal_hydrogens(
ppf.all_chain_proxies.pdb_hierarchy,
ppf.geometry_restraints_manager(),
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
original_hierarchy=original_hierarchy,
verbose=verbose,
) # in place
ppf.all_chain_proxies.pdb_hierarchy.atoms(
).set_chemical_element_simple_if_necessary()
ppf.all_chain_proxies.pdb_hierarchy.sort_atoms_in_place()
#display_hierarchy_atoms(ppf.all_chain_proxies.pdb_hierarchy)
#ppf.all_chain_proxies.pdb_hierarchy.atoms_reset_serial()
#ppf.all_chain_proxies.pdb_hierarchy.atoms().reset_i_seq()
return ppf