Derived Class for Fragmenter

Once you have the fragmentation algorithms such as BRICS, you can get derived class from Fragmenter base class.

Example Use

from fragmentretro.fragmenter import BRICSFragmenter

smiles = "COc1ccc(-n2nccn2)c(C(=O)N2CCC[C@@]2(C)c2nc3c(C)c(Cl)ccc3[nH]2)c1"
fragmenter = BRICSFragmenter(smiles)

# Custom figure size
fragmenter.visualize(figsize=(20, 10), verbose=False, with_indices=True)

Source Code

fragmentretro.fragmenter

Module for fragmenting molecules using BRICS (add other algorithms later).

BRICSFragmenter

Bases: Fragmenter

Source code in src/fragmentretro/fragmenter.py

class BRICSFragmenter(Fragmenter):
    def __init__(self, smiles: str) -> None:
        """
        Initialize with SMILES string.

        Args:
            smiles: SMILES string of molecule to fragment
        """
        super().__init__(smiles)

    def _find_fragmentation_bonds(self, mol: Mol) -> list[BondType]:
        return list(FindBRICSBonds(mol))

    def _break_bonds(self, mol: Mol, bonds: list[BondType]) -> Mol:
        return BreakBRICSBonds(mol, bonds)

__init__(smiles)

Initialize with SMILES string.

Parameters:

Name	Type	Description	Default
smiles	str	SMILES string of molecule to fragment	required

Source code in src/fragmentretro/fragmenter.py

def __init__(self, smiles: str) -> None:
    """
    Initialize with SMILES string.

    Args:
        smiles: SMILES string of molecule to fragment
    """
    super().__init__(smiles)

rBRICSFragmenter

Bases: Fragmenter

Source code in src/fragmentretro/fragmenter.py

class rBRICSFragmenter(Fragmenter):
    def __init__(self, smiles: str) -> None:
        """
        Initialize with SMILES string.

        Args:
            smiles: SMILES string of molecule to fragment
        """
        super().__init__(smiles)

    def _find_fragmentation_bonds(self, mol: Mol) -> list[BondType]:
        return list(find_brics_bonds(mol))  # type: ignore[no-untyped-call]

    def _break_bonds(self, mol: Mol, bonds: list[BondType]) -> Mol:
        return break_r_brics_bonds(mol, bonds)  # type: ignore[no-untyped-call]

__init__(smiles)

Initialize with SMILES string.

Parameters:

Name	Type	Description	Default
smiles	str	SMILES string of molecule to fragment	required

Source code in src/fragmentretro/fragmenter.py

def __init__(self, smiles: str) -> None:
    """
    Initialize with SMILES string.

    Args:
        smiles: SMILES string of molecule to fragment
    """
    super().__init__(smiles)