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 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 test_code_must_be_valid(self):
pdb = Pdb()
with self.assertRaises(ValueError):
pdb.code = "1xxxx"
with self.assertRaises(ValueError):
pdb.code = "1xx"
def test_code_must_be_str(self):
pdb = Pdb()
with self.assertRaises(TypeError):
pdb.code = 100
def test_can_update_code(self):
pdb = Pdb()
pdb._code = "1xxx"
pdb.code = "2yyy"
self.assertEqual(pdb._code, "2yyy")
def test_code(pdb_3heg: Pdb):
assert pdb_3heg.code() == '3HEG'