def run(args):
if (len(args) != 1):
raise RuntimeError("Please specify one pdb file name.")
model_filename = args[0]
pdb_inp = iotbx.pdb.input(file_name=model_filename)
model = mmtbx.model.manager(model_input=pdb_inp)
model.composition().show(log=sys.stdout)
pdb_hierarchy = model.get_hierarchy()
print('\nLoop over hierarchy:')
for model in pdb_hierarchy.models():
for chain in model.chains():
print('Chain: ', chain.id)
for rg in chain.residue_groups():
print(' Resnumber: ', rg.resid())
for ag in rg.atom_groups():
if (ag.resname in aa_resnames):
print(' Resname: %s, Altloc: %s' %
(ag.resname, ag.altloc))
for atom in ag.atoms():
if (atom.name not in ala_atom_names):
print(' %s' % atom.name)
ag.remove_atom(atom=atom)
#print(help(pdb_hierarchy.write_pdb_file))
pdb_hierarchy.write_pdb_file(file_name='polyala.pdb')
def run(args):
if (len(args) != 1):
raise RuntimeError("Please specify one model file name.")
model_filename = args[0]
pdb_inp = iotbx.pdb.input(file_name=model_filename)
model = mmtbx.model.manager(model_input=pdb_inp)
composition_obj = model.composition()
#print(help(composition_obj))
model.composition().show(log=sys.stdout)
def run(args):
if (len(args) != 1):
raise RuntimeError("Please specify one pdb file name.")
model_filename = args[0]
pdb_inp = iotbx.pdb.input(file_name=model_filename)
model = mmtbx.model.manager(model_input=pdb_inp)
model.composition().show(log=sys.stdout)
pdb_hierarchy = model.get_hierarchy()
print('\nLoop over hierarchy:')
for model in pdb_hierarchy.models():
for chain in model.chains():
print('Chain: ', chain.id)
for rg in chain.residue_groups():
pass # Add your code here
def run(args):
if (len(args) != 1):
raise RuntimeError("Please specify one pdb file name.")
model_filename = args[0]
pdb_inp = iotbx.pdb.input(file_name=model_filename)
model = mmtbx.model.manager(model_input=pdb_inp)
model.composition().show(log=sys.stdout)
pdb_hierarchy = model.get_hierarchy()
n_amino_acid_residues = 0
n_other_residues = 0
n_atoms_removed = 0
for model in pdb_hierarchy.models():
for chain in model.chains():
for rg in chain.residue_groups():
if rg_has_amino_acid(rg):
n_amino_acid_residues += 1
for ag in rg.atom_groups():
for atom in ag.atoms():
if (atom.name not in ala_atom_names):
ag.remove_atom(atom=atom)
n_atoms_removed += 1
else:
n_other_residues += 1
print("\nNumber of amino acid residues:", n_amino_acid_residues)
print("Number of other residues:", n_other_residues)
print("Number of atoms removed:", n_atoms_removed)
if (n_atoms_removed != 0):
output_pdb = os.path.splitext(
model_filename)[0] + "_truncated_to_ala.pdb"
print("Writing file: ", output_pdb)
pdb_hierarchy.write_pdb_file(
file_name=output_pdb, crystal_symmetry=pdb_inp.crystal_symmetry())
def get_composition(self, run_map_box=True):
make_sub_header('Get composition', out=self.logger)
self.save_json()
success = True
for p, fn in zip(('', 'r_'),
[self.json_data['pdb_file_updated'], self.json_data['pdb_file_refined']]):
if not fn: continue
pdb_inp = iotbx.pdb.input(file_name = fn)
try:
model = mmtbx.model.manager(
model_input = pdb_inp,
log = null_out())
except Exception as e:
msg = traceback.format_exc()
step = 'Model class without restraints from initial pdb '
print(msg, file=self.logger)
self.write_log(step=step, msg=msg)
self.json_data['success_composition'] = False
self.save_json()
return
ph = model.get_hierarchy()
# Overall composition
if (p == ''):
model_comp = model.composition()
model_comp.show(log=self.logger)
composition = model_comp.result()
self.json_data['n_atoms'] = composition.n_atoms
self.json_data['n_residues'] = composition.n_protein
self.json_data['n_chains'] = composition.n_chains
self.json_data['n_water'] = composition.n_water
self.json_data['n_nucleotide'] = composition.n_nucleotide
self.json_data['n_other'] = composition.n_other
self.json_data['n_hd'] = composition.n_hd
self.json_data['fraction_hd'] = composition.n_hd/composition.n_atoms
self.json_data['composition_keys'] = composition.other_cnts.keys()
self.json_data['n_alt_conf'] = ph.overall_counts().n_alt_conf
#
# ADPs
try:
adp_result = model.adp_statistics().result()
except Exception as e:
msg = traceback.format_exc()
step = 'ADP statistics.'
print(msg, file=self.logger)
self.write_log(step=step, msg=msg)
self.json_data['success_composition'] = False
self.save_json()
return
adp_overall = adp_result.overall
adp_protein = adp_result.protein
adp_other = adp_result.other
if adp_protein is not None:
self.json_data[p+'b_min_protein'] = adp_protein.min
self.json_data[p+'b_max_protein'] = adp_protein.max
self.json_data[p+'b_mean_protein'] = adp_protein.mean
if adp_other is not None:
self.json_data[p+'b_min_other'] = adp_other.min
self.json_data[p+'b_max_other'] = adp_other.max
self.json_data[p+'b_mean_other'] = adp_other.mean
self.json_data[p+'n_iso'] = adp_overall.n_iso
self.json_data[p+'n_aniso'] = adp_overall.n_aniso
#occupancy
occ_stats = model.occupancy_statistics().result()
self.json_data[p+'occ_zero'] = occ_stats.zero_count
self.json_data[p+'occ_equal_to_1'] = occ_stats.equal_to_1_count
self.json_data[p+'occ_between_0_and_1'] = occ_stats.between_0_and_1_count
self.json_data[p+'occ_negative'] = occ_stats.negative
if (p == ''):
self.pickle_data.adp_hist = adp_result.histogram
elif (p == 'r_'):
self.pickle_data.r_adp_hist = adp_result.histogram
# get boxed map
if (p == '' and run_map_box):
print('\nRunning phenix.map_box...', file=self.logger)
pdb_file = self.json_data['pdb_file_updated']
map_file = self.json_data['map_file']
cmds = [
"phenix.map_box",
pdb_file,
map_file,
'resolution=%s' % self.resolution,
'mask_atoms=True',
">& map_box.log"
]
cmd = " ".join(cmds)
print(cmd, file=self.logger)
msg = ''
try:
easy_run.call(cmd)
except Exception as e:
success = False
msg = traceback.format_exc()
map_boxed_fn = os.path.join(self.dest_dir, self.prefix + '_box.ccp4')
if os.path.isfile(map_boxed_fn):
self.json_data['map_boxed'] = map_boxed_fn
else:
success = False
msg = 'No output file from map_box'
self.json_data['success_composition'] = success