Molecule generation

A significant amount of functionality wraps the rdkit package, the main library for doing cheminformatics in Python. For all molecule interactions, we go back and forth between the native rdkit objects and SMILES/SMARTS strings.

• Exhaustive isotopologue generation in SMILES

>>> from astrochem_ml.smiles import isotopes
# exhaustively enumerate all possible combinations isotopologues
# user can set the threshold for natural abundance and whether
# to include hydrogens
>>> isotopes.generate_all_isos("c1ccccc1", explicit_h=False)
['c1[13cH]c[13cH][13cH][13cH]1', ... 'c1ccccc1', '[13cH]1[13cH][13cH][13cH][13cH][13cH]1','c1c[13cH][13cH][13cH]c1']

• Functional group substitutions

Replace substructures with other ones in a tree data structure!

>>> from astrochem_ml.smiles import MoleculeGenerator
# randomly grow out possible structures starting from benzene,
# and iteratively replace structures with other functional groups
>>> benzene = MoleculeGenerator("c1ccccc1", substructs=["c", "cC#N", "cC=O", "cN"])
>>> benzene.grow_tree(50)
100%|██████████████████████████████████████████████████████████████████| 50/50 [00:00<00:00, 237.44it/s]
>>> print(benzene)
c1ccccc1
├── Nc1ccccc1
├── N#Cc1ccccc1
└── O=Cc1ccccc1
├── Nc1ccccc1C=O
│   └── N#Cc1ccccc1C=O
├── Nc1cccc(C=O)c1
│   ├── Nc1cccc(C=O)c1N
│   │   ├── Nc1c(C=O)ccc(C=O)c1N
│   │   ├── Nc1cc(C=O)cc(C=O)c1N
...

This provides a high level interface to view every structure generated, and from which parent.