from __future__ import annotations
from enum import Enum
from rdkit import Chem
from typing import List
[docs]
class BondProvenance(Enum):
"""
Where does the bond come from. This is used to keep names consistent...
For now original is used in places. The others are interchangeable TBH.
"""
ORIGINAL = 1 # present in original mols
MAIN_NOVEL = 2 # joined (zero-atom linking). Closest
OTHER_NOVEL = 3 # joined (zero-atom linking). Others
LINKER = 4
UNASSIGNED = 5 # likely an error
[docs]
@classmethod
def set_all_bonds(cls, mol: Chem.Mol, provenance_name:str) -> None:
"""
Sets the provenance of all bonds in mol to a category, which is a string from the provenance
:param mol:
:param provenance_name: A string original | main_novel " other_novel | linker
:return:
"""
for bond in mol.GetBonds():
cls.set_bond(bond, provenance_name)
[docs]
@classmethod
def get_bond(cls, bond: Chem.Bond) -> BondProvenance:
if not bond.HasProp('_Provenance'):
return cls.UNASSIGNED
else:
p = bond.GetIntProp('_Provenance')
return cls(p)
[docs]
@classmethod
def get_bonds(cls, bonds: List[Chem.Bond]) -> List[BondProvenance]:
return [cls.get_bond(bond) for bond in bonds]
[docs]
@classmethod
def set_bond(cls, bond: Chem.Bond, provenance_name: str) -> None:
bond.SetIntProp('_Provenance', cls[provenance_name.upper()].value)
[docs]
@classmethod
def set_bonds(cls, bonds: List[Chem.Bond], provenance_name: str) -> None:
for bond in bonds:
cls.set_bond(bond, provenance_name)
[docs]
@classmethod
def has_bond(cls, bond: Chem.Bond) -> bool:
return bond.HasProp('_Provenance')
[docs]
@classmethod
def copy_bond(cls, donor: Chem.Bond, acceptor: Chem.Bond) -> None:
p = cls.get_bond(donor)
acceptor.SetIntProp('_Provenance', p.value)