def fill_serial_numbers(pdb: Pdb):
"""The reduce program can add hydrogens to ligands, those hydrogens will have no atom serial numbers
RDKit will give parse error on a PDB block with atoms without an atom serial number.
This method adds serial ids and bonds those hydrogens to their heavy atom based on it's name
Args:
pdb: The pdb to fill serial ids in
"""
model = pdb.model()
max_serial_number = max(
[a.atom_id() for a in model.atoms() if a.atom_id()])
for mol in model.molecules(generic=True):
for a in mol.atoms(element='H'):
if a.atom_id() != 0:
continue
max_serial_number += 1
# a.atom_id() is not a setter, so set it using private prop
a._id = max_serial_number
hgrp = a.name()[1]
bonded = False
for heavy in mol.atoms(exclude='H'):
oname = heavy.name()
if len(oname) > 1 and oname[1] == hgrp:
logger.info('Binding {0}:{1} with {2}:{3}'.format(
a.atom_id(), a.name(), heavy.atom_id(), heavy.name()))
heavy.bond(a)
bonded = True
if not bonded:
logger.warning('Unable to bind {0}:{1} to heavy atom'.format(
a.atom_id(), a.name()))
def remove_unwanted_molecules(pdb: Pdb):
"""Remove unwanted molecules from model
Cleans pdb by removing molecules which:
* Have name in UNWANTED_HETEROS list
* Is out side LIGAND_MAX_MASS..LIGAND_MIN_MASS mass range
* Have name already processed (aka removes duplicates)
Removing is done in-place.
Args:
pdb: Atomium PDB entry containing possible unwanted molecules
"""
unique_names = set()
model = pdb.model()
for mol in sorted(model.molecules(generic=True),
key=lambda m: m.molecule_id()):
is_unwanted = mol.name() in UNWANTED_HETEROS
in_mass_range = LIGAND_MIN_MASS < mol.mass() < LIGAND_MAX_MASS
seen_before = mol.name() in unique_names
if is_unwanted or not in_mass_range or seen_before:
model.remove_molecule(mol)
else:
unique_names.add(mol.name())
def ligands(pdb: Pdb, ligand_expo: Dict[str, Mol]) -> List[Ligand]:
"""Ligands of a pdb
Args:
pdb: The pdb
ligand_expo: Dictionary with molecules of ligand expo
Raises:
NoLigands: When PDB has no ligands
Returns:
List of ligands, ordered by name
"""
model = pdb.model()
ligs = {}
for amol in model.molecules(generic=True):
amol_id = amol.molecule_id()
# Workaround for atomium 0.8 as to handle molecules with resID 0
# NOTE: was fixed in 0.11.1, but other changes break kripo
if amol_id[1:]=="":
amol._id = amol_id + '0'
amol_id = amol.molecule_id()
lig_id = pdb.code().lower() + '_' + amol.name() + '_1_' + amol_id[0] + '_' + amol_id[1:]
try:
lig = ligand_expo[lig_id]
plig = protonate_molecule(lig)
ligs[lig_id] = Ligand(amol, plig)
except KeyError:
logger.warning('Unable to find {0} in ligand expo db, skipping'.format(lig_id))
pass
if not ligs:
raise NoLigands()
return sorted(ligs.values(), key=lambda l: l.name())
def ligands(pdb: Pdb, ligand_expo: Dict[str, Mol]) -> List[Ligand]:
"""Ligands of a pdb
Args:
pdb: The pdb
ligand_expo: Dictionary with molecules of ligand expo
Raises:
NoLigands: When PDB has no ligands
Returns:
List of ligands, ordered by name
"""
model = pdb.model()
ligs = {}
for amol in model.molecules(generic=True):
amol_id = amol.molecule_id()
lig_id = pdb.code().lower() + '_' + amol.name(
) + '_1_' + amol_id[0] + '_' + amol_id[1:]
try:
lig = ligand_expo[lig_id]
plig = protonate_molecule(lig)
ligs[lig_id] = Ligand(amol, plig)
except KeyError:
logger.warning(
'Unable to find {0} in ligand expo db, skipping'.format(
lig_id))
pass
if not ligs:
raise NoLigands()
return sorted(ligs.values(), key=lambda l: l.name())
def remove_non_contacting_molecules(pdb: Pdb):
"""Remove unwanted molecules from model
Cleans pdb by removing molecules which:
* Is more then MAX_CONTACT_DISTANCE away from protein
Removing is done in-place.
Args:
pdb: Atomium PDB entry containing possible unwanted molecules
"""
model = pdb.model()
for mol in sorted(model.molecules(generic=True), key=lambda m: m.molecule_id()):
in_contact_with_protein = ligand_contacts_protein(mol, model)
if not in_contact_with_protein:
try:
model.remove_molecule(mol)
except KeyError:
# in 1efr was unable to delete atom with key 22969, ignore error
pass
