def test_001(pdb_str):
'''
Check keyword n_terminal_charge:
NH3 on resseq 1, first residue in chain, or no NH3 at all
'''
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
# initial model
model_initial = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
#
# place H atoms: NH3 at resseq 1 only
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(model=model_initial)
reduce_add_h_obj.run()
model_h_added = reduce_add_h_obj.get_model()
#
hd_sel_h_added = model_h_added.get_hd_selection()
ph_h_added = model_h_added.get_hierarchy()
h_atoms_added = ph_h_added.select(hd_sel_h_added).atoms()
h_names_added = list(h_atoms_added.extract_name())
assert (h_names_added.count(' H1 ') == 1)
assert (h_names_added.count(' H2 ') == 1)
assert (h_names_added.count(' H3 ') == 1)
#
# place H atoms: NH3 at first residue in chain
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(
model=model_initial, n_terminal_charge='first_in_chain')
reduce_add_h_obj.run()
model_h_added = reduce_add_h_obj.get_model()
#
hd_sel_h_added = model_h_added.get_hd_selection()
ph_h_added = model_h_added.get_hierarchy()
h_atoms_added = ph_h_added.select(hd_sel_h_added).atoms()
h_names_added = list(h_atoms_added.extract_name())
assert (h_names_added.count(' H1 ') == 3)
assert (h_names_added.count(' H2 ') == 3)
assert (h_names_added.count(' H3 ') == 3)
#
# place H atoms: no NH3
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(
model=model_initial, n_terminal_charge='no_charge')
reduce_add_h_obj.run()
model_h_added = reduce_add_h_obj.get_model()
#
hd_sel_h_added = model_h_added.get_hd_selection()
ph_h_added = model_h_added.get_hierarchy()
h_atoms_added = ph_h_added.select(hd_sel_h_added).atoms()
h_names_added = list(h_atoms_added.extract_name())
assert (h_names_added.count(' H1 ') == 0)
assert (h_names_added.count(' H2 ') == 0)
assert (h_names_added.count(' H3 ') == 0)
def run(self):
self.model = self.data_manager.get_model()
#
make_sub_header('Add H atoms', out=self.logger)
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(
model=self.model,
use_neutron_distances=self.params.use_neutron_distances,
n_terminal_charge=self.params.n_terminal_charge)
#import line_profiler
#lp = line_profiler.LineProfiler(reduce_add_h_obj.run)
#lp.enable()
reduce_add_h_obj.run()
#lp.disable()
#lp.print_stats()
self.model = reduce_add_h_obj.get_model()
reduce_add_h_obj.show(log=self.logger)
#
make_sub_header('Optimize H atoms', out=self.logger)
self.model = reduce_hydrogen.optimize(model=self.model)
#
if (self.params.output.file_name_prefix is not None):
base = self.params.output.file_name_prefix
else:
fp = self.data_manager.get_default_model_name()
base = os.path.splitext(os.path.basename(fp))[0]
of = open("%s_hydrogenate.pdb" % base, "w")
of.write(self.model.model_as_pdb())
of.close()
def compare_models(pdb_str, contains=None, not_contains=None):
'''
Function to compare model with new H to the known answer (pdb_str)
'''
#
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
model_initial = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
ph_initial = model_initial.get_hierarchy()
hd_sel_initial = model_initial.get_hd_selection()
h_atoms_initial = ph_initial.select(hd_sel_initial).atoms()
h_names_initial = list(h_atoms_initial.extract_name())
# number of H in pdb string (right answer)
number_h_expected = hd_sel_initial.count(True)
# get model obj without H atoms
model_without_h = model_initial.select(~hd_sel_initial)
# make sure model without H indeed has no H atoms
hd_sel_without_h = model_without_h.get_hd_selection()
assert (hd_sel_without_h is not None)
assert (hd_sel_without_h.count(True) == 0)
#model_h_added = reduce.add(model = model_without_h)
# place H atoms
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(model=model_without_h)
reduce_add_h_obj.run()
model_h_added = reduce_add_h_obj.get_model()
hd_sel_h_added = model_h_added.get_hd_selection()
ph_h_added = model_h_added.get_hierarchy()
assert ph_initial.is_similar_hierarchy(other=ph_h_added)
number_h_added = hd_sel_h_added.count(True)
assert (number_h_expected == number_h_added)
h_atoms_added = ph_h_added.select(hd_sel_h_added).atoms()
h_names_added = list(h_atoms_added.extract_name())
if not_contains:
assert (not_contains not in h_names_added)
if contains:
assert (contains in h_names_added)
sc_h_initial = model_initial.select(hd_sel_initial).get_sites_cart()
sc_h_added = model_h_added.select(hd_sel_h_added).get_sites_cart()
d1 = {
h_names_initial[i]: sc_h_initial[i]
for i in range(len(h_names_initial))
}
d2 = {h_names_added[i]: sc_h_added[i] for i in range(len(h_names_added))}
# check that coordinates are correct
for name, sc in d2.items():
assert (name in d1)
assert approx_equal(sc, d1[name], 0.01)
def compare_models(pdb_str, contains=None, not_contains=None):
#
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
# initial model
model_initial = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
hd_sel_initial = model_initial.get_hd_selection()
number_h_expected = hd_sel_initial.count(True)
ph_initial = model_initial.get_hierarchy()
h_atoms_initial = ph_initial.select(hd_sel_initial).atoms()
h_names_initial = list(h_atoms_initial.extract_name())
# remove H atoms
model_without_h = model_initial.select(~hd_sel_initial)
hd_sel_without_h = model_without_h.get_hd_selection()
assert (hd_sel_without_h is not None)
assert (hd_sel_without_h.count(True) == 0)
# place H atoms again
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(model=model_without_h)
reduce_add_h_obj.run()
#
model_h_added = reduce_add_h_obj.get_model()
hd_sel_h_added = model_h_added.get_hd_selection()
ph_h_added = model_h_added.get_hierarchy()
h_atoms_added = ph_h_added.select(hd_sel_h_added).atoms()
h_names_added = list(h_atoms_added.extract_name())
number_h_added = hd_sel_h_added.count(True)
#f = open("bla_intermediate.pdb","w")
#f.write(model_h_added.model_as_pdb())
#f.close()
assert ph_initial.is_similar_hierarchy(other=ph_h_added)
assert (number_h_expected == number_h_added)
if not_contains:
assert (not_contains not in h_names_added)
if contains:
assert (contains in h_names_added)
sc_h_initial = model_initial.select(hd_sel_initial).get_sites_cart()
sc_h_added = model_h_added.select(hd_sel_h_added).get_sites_cart()
d1 = {
h_names_initial[i]: sc_h_initial[i]
for i in range(len(h_names_initial))
}
d2 = {h_names_added[i]: sc_h_added[i] for i in range(len(h_names_added))}
for name, sc in d2.items():
assert (name in d1)
assert approx_equal(sc, d1[name], 0.01), name
def test_000(pdb_str):
'''
Make sure reduce does not crash for single_atom_residue models
'''
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
# initial model (has no H atoms)
model_initial = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
number_h_expected = model_initial.get_hd_selection().count(True)
assert (number_h_expected == 0)
# place H atoms
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(model=model_initial)
reduce_add_h_obj.run()
# We don't expect H atoms to be placed
# (not enough restraints for single atom residues)
model_h_added = reduce_add_h_obj.get_model()
number_h_placed = model_h_added.get_hd_selection().count(True)
assert (number_h_placed == 0)
def run(self):
# String describing the run that will be output to the specified file.
outString = 'reduce2 v.{}, run {}\n'.format(version, datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
for a in sys.argv:
outString += ' {}'.format(a)
outString += '\n'
make_sub_header('Loading Model', out=self.logger)
# Get our model.
self.model = self.data_manager.get_model()
# Fix up bogus unit cell when it occurs by checking crystal symmetry.
cs = self.model.crystal_symmetry()
if (cs is None) or (cs.unit_cell() is None):
self.model = shift_and_box_model(model = self.model)
if self.params.approach == 'add':
# Add Hydrogens to the model
make_sub_header('Adding Hydrogens', out=self.logger)
startAdd = work_clock()
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(
model = self.model,
n_terminal_charge=self.params.n_terminal_charge,
stop_for_unknowns=True
)
reduce_add_h_obj.run()
self.model = reduce_add_h_obj.get_model()
doneAdd = work_clock()
# Interpret the model after shifting and adding Hydrogens to it so that
# all of the needed fields are filled in when we use them below.
# @todo Remove this once place_hydrogens() does all the interpretation we need.
make_sub_header('Interpreting Hydrogenated Model', out=self.logger)
startInt = work_clock()
self.model.get_hierarchy().sort_atoms_in_place()
self.model.get_hierarchy().atoms().reset_serial()
p = mmtbx.model.manager.get_default_pdb_interpretation_params()
p.pdb_interpretation.allow_polymer_cross_special_position=True
p.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
p.pdb_interpretation.use_neutron_distances = self.params.use_neutron_distances
p.pdb_interpretation.proceed_with_excessive_length_bonds=True
#p.pdb_interpretation.sort_atoms=True
self.model.process(make_restraints=True, pdb_interpretation_params=p) # make restraints
doneInt = work_clock()
make_sub_header('Optimizing', out=self.logger)
startOpt = work_clock()
Optimizers.probePhil = self.params.probe
opt = Optimizers.FastOptimizer(self.params.add_flip_movers, self.model, probeRadius=0.25,
altID=self.params.alt_id, preferenceMagnitude=self.params.preference_magnitude)
doneOpt = work_clock()
outString += opt.getInfo()
outString += 'Time to Add Hydrogen = '+str(doneAdd-startAdd)+'\n'
outString += 'Time to Interpret = '+str(doneInt-startInt)+'\n'
outString += 'Time to Optimize = '+str(doneOpt-startOpt)+'\n'
else: # Removing Hydrogens from the model rather than adding them.
make_sub_header('Removing Hydrogens', out=self.logger)
sel = self.model.selection("element H")
for a in self.model.get_atoms():
if sel[a.i_seq]:
a.parent().remove_atom(a)
# Re-process the model because we have removed some atoms that were previously
# bonded. Don't make restraints during the reprocessing.
# We had to do this to keep from crashing on a call to pair_proxies when generating
# mmCIF files, so we always do it for safety.
self.model.process(make_restraints=False, pdb_interpretation_params=p)
make_sub_header('Writing output', out=self.logger)
# Write the description output to the specified file.
of = open(self.params.output.description_file_name,"w")
of.write(outString)
of.close()
# Determine whether to write a PDB or CIF file and write the appropriate text output.
# Then determine the output file name and write it there.
if str(self.params.output.suffix).lower() == "pdb":
txt = self.model.model_as_pdb()
suffix = ".pdb"
else:
txt = self.model.model_as_mmcif()
suffix = ".cif"
if self.params.output.model_file_base_name is not None:
base = self.params.output.model_file_base_name
else:
file_name = self.data_manager.get_model_names()[0]
base = os.path.splitext(os.path.basename(file_name))[0] + "_reduced"
fullname = base+suffix
with open(fullname, 'w') as f:
f.write(txt)
print('Wrote',fullname,'and',self.params.output.description_file_name, file = self.logger)
# Report profiling info if we've been asked to in the Phil parameters
if self.params.profile:
print('Profile results:')
import pstats
profile_params = {'sort_by': 'time', 'num_entries': 20}
self._pr.disable()
ps = pstats.Stats(self._pr).sort_stats(profile_params['sort_by'])
ps.print_stats(profile_params['num_entries'])