def print_stats(self, prefix='') -> None:
"""
Prints statistics to stdout
Args:
prefix: Text prefix to prepend to printed data
"""
stats = self.get_stats()
self.print_model_stats(prefix)
self.print_chain_stats(prefix)
print('{} Num. residues: {}'.format(prefix, stats['num_res']))
print('{} Num. residues with ins. codes: {}'.format(
prefix, stats['res_insc']))
print('{} Num. HETATM residues: {}'.format(prefix,
stats['res_hetats']))
print('{} Num. ligands or modified residues: {}'.format(
prefix, stats['res_ligands']))
print('{} Num. water mol.: {}'.format(prefix, stats['num_wat']))
print('{} Num. atoms: {}'.format(prefix, stats['num_ats']))
if stats['ca_only']:
print('Possible CA-Only structure')
if self.hetatm[mu.MODRES]:
print('Modified residues found')
for res in self.hetatm[mu.MODRES]:
print(mu.residue_id(res))
if self.hetatm[mu.METAL]:
print('Metal/Ion residues found')
for res in self.hetatm[mu.METAL]:
print(mu.residue_id(res))
if self.hetatm[mu.ORGANIC]:
print('Small mol ligands found')
for res in self.hetatm[mu.ORGANIC]:
print(mu.residue_id(res))
def add_hydrogens(self, ion_res_list, remove_h: bool = True):
"""
Add hydrogens considering selections in ion_res_list
Args:
**r_at_list**: dict as Bio.PDB.Residue: Tauromeric Option
**remove_h**: Remove Hydrogen atom before adding new ones
"""
add_h_rules = self.data_library.get_add_h_rules()
for res in self.all_residues:
if mu.is_hetatm(res):
continue
if remove_h:
mu.remove_H_from_r(res, verbose=False)
if res not in self.prev_residue:
prev_residue = None
else:
prev_residue = self.prev_residue[res]
error_msg = mu.add_hydrogens_backbone(res, prev_residue)
if error_msg:
print(error_msg, mu.residue_id(res))
rcode = res.get_resname()
if rcode == 'GLY':
continue
if rcode not in add_h_rules:
print(NotAValidResidueError(rcode).message)
continue
if res in ion_res_list:
if rcode != ion_res_list[res]:
print('Replacing {} by {}'.format(mu.residue_id(res),
ion_res_list[res]))
error_msg = mu.add_hydrogens_side(
res, self.res_library, ion_res_list[res],
add_h_rules[rcode][ion_res_list[res]])
res.resname = ion_res_list[res]
else:
error_msg = mu.add_hydrogens_side(res, self.res_library, rcode,
add_h_rules[rcode])
if error_msg:
print(error_msg, mu.residue_id(res))
self.residue_renumbering()
self.atom_renumbering()
self.modified = True
def fix_backbone_O_atoms(self, r_at: Tuple[Residue,
Sequence[str]]) -> bool:
"""Adding missing backbone atoms not affecting main-chain like O and OXT
Args:
**r_at**: tuple as [Bio.PDB.Residue, [list of atom ids]]
"""
res, at_list = r_at
print(mu.residue_id(res))
if 'C' not in res:
raise NotEnoughAtomsError
if len(at_list) == 2 or at_list == ['O']:
if 'CA' not in res or 'N' not in res or 'C' not in res:
raise NotEnoughAtomsError
print(" Adding new atom O")
mu.add_new_atom_to_residue(res, 'O', mu.build_coords_O(res))
if 'OXT' in at_list:
if 'CA' not in res or 'C' not in res or 'O' not in res:
raise NotEnoughAtomsError
print(" Adding new atom OXT")
mu.add_new_atom_to_residue(
res, 'OXT',
mu.build_coords_SP2(mu.OINTERNALS[0], res['C'], res['CA'],
res['O']))
self.atom_renumbering()
self.modified = True
return True
def merge_structure(self, new_st: Structure, mod_id: str, ch_id: str,
brk_list: Union[Sequence[Atom],
Sequence[Sequence[Atom]]],
offset: int) -> Union[str, List[str]]:
spimp = Superimposer()
fixed_ats = [
atm for atm in self.st[mod_id][ch_id].get_atoms() if atm.id == 'CA'
]
moving_ats = []
for atm in fixed_ats:
moving_ats.append(new_st[0][' '][atm.get_parent().id[1] - offset +
1]['CA'])
spimp.set_atoms(fixed_ats, moving_ats)
spimp.apply(new_st.get_atoms())
list_res = self.st[mod_id][ch_id].get_list()
fixed_gaps = []
for i in range(0,
len(self.sequence_data.data[ch_id]['pdb'][mod_id]) - 1):
gap_start = self.sequence_data.data[ch_id]['pdb'][mod_id][
i].features[0].location.end
gap_end = self.sequence_data.data[ch_id]['pdb'][mod_id][
i + 1].features[0].location.start
if [
self.st[mod_id][ch_id][gap_start],
self.st[mod_id][ch_id][gap_end]
] not in brk_list:
continue
pos = 0
while pos < len(list_res) and self.st[mod_id][ch_id].child_list[
pos].id[1] != gap_start:
pos += 1
self.remove_residue(self.st[mod_id][ch_id][gap_start],
update_int=False)
self.remove_residue(self.st[mod_id][ch_id][gap_end],
update_int=False)
for nres in range(gap_start, gap_end + 1):
res = new_st[0][' '][nres - offset + 1].copy()
res.id = (' ', nres, ' ')
self.st[mod_id][ch_id].insert(pos, res)
pos += 1
print("Adding " + mu.residue_id(res))
fixed_gaps.append('{}{}-{}{}/{}'.format(ch_id, gap_start, ch_id,
gap_end, mod_id + 1))
print()
return fixed_gaps
def fix_side_chain(self, r_at: Tuple[Residue, Sequence[str]]) -> None:
"""
Fix missing side chain atoms in given residue. Triggers **modified** flag
Args:
**r_at**: tuple as [Bio.PDB.Residue, [list of atom ids]]
"""
print(mu.residue_id(r_at[0]))
for at_id in r_at[1]:
print(" Adding new atom " + at_id)
if at_id == 'CB':
coords = mu.build_coords_CB(r_at[0])
else:
coords = mu.build_coords_from_lib(r_at[0], self.res_library,
r_at[0].get_resname(), at_id)
mu.add_new_atom_to_residue(r_at[0], at_id, coords)
self.atom_renumbering()
self.modified = True
def apply(self, mut_map, res_lib, remove_h):
""" Perform the individual mutations on the set. """
mutated_res = []
for mut in self.mutations:
res = mut['resobj']
#struc[mut['model']][mut['chain']][mut['residue']]
rname = res.get_resname().replace(' ', '')
# Deleting H
if remove_h == 'mut':
mu.remove_H_from_r(res, verbose=True)
# checking side chain
side_atoms = []
bck_atoms = []
for atm in res.get_atoms():
if atm.id in mut_map[rname]['side_atoms']:
side_atoms.append(atm.id)
else:
bck_atoms.append(atm.id)
for at_id in ['N', 'CA', 'C']:
if at_id not in bck_atoms:
sys.exit('#ERROR: Backbone atoms missing for {}, aborting'.
format(mu.residue_id(res)))
missing_ats = [
at_id for at_id in mut_map[rname]['side_atoms']
if at_id not in side_atoms
]
print("Replacing " + mu.residue_id(res) + " into " + self.new_id)
in_rules = []
extra_adds = []
# Renaming ats
if MOV in mut_map[rname][self.new_id]:
for rule in mut_map[rname][self.new_id][MOV]:
old_at, new_at = rule.split("-")
print(' Renaming {} to {}'.format(old_at, new_at))
if old_at in side_atoms:
mu.rename_atom(res, old_at, new_at)
else:
print('#WARNING: atom {} missing in {}'.format(
old_at, mu.residue_id(res)))
extra_adds.append(new_at)
in_rules.append(old_at)
# Deleting atoms
if DEL in mut_map[rname][self.new_id]:
for at_id in mut_map[rname][self.new_id][DEL]:
print(' Deleting {}'.format(at_id))
if at_id in side_atoms:
mu.delete_atom(res, at_id)
else:
print('#WARNING: atom {} already missing in {}'.format(
at_id, mu.residue_id(res)))
in_rules.append(at_id)
# Adding atoms (new_id required as r.resname is still the original)
# Adding missing atoms that keep name
for at_id in mut_map[rname]['side_atoms']:
if at_id not in in_rules and at_id in missing_ats:
print(' Adding missing atom {}'.format(at_id))
mu.build_atom(res, at_id, res_lib, self.new_id)
for at_id in extra_adds:
print(' Adding new atom {}'.format(at_id))
mu.build_atom(res, at_id, res_lib, self.new_id)
if ADD in mut_map[rname][self.new_id]:
for at_id in mut_map[rname][self.new_id][ADD]:
print(' Adding new atom {}'.format(at_id))
mu.build_atom(res, at_id, res_lib, self.new_id)
#Renaming residue
res.resname = self.new_id
mutated_res.append(res)
print("")
return mutated_res