populate drugs structure property table

[sgosline]

need to add drug structure/fingerprints.

[jjacobson95]

This is pretty straight forward with python rdkit. Just need to know how detailed we want the fingerprints to be

from rdkit import Chem
from rdkit.Chem import AllChem
def smiles_to_fingerprint(smiles):
    mol = Chem.MolFromSmiles(smiles)
    fingerprint = AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=1024)  # update these parameters
    fingerprint_array = np.array(fingerprint)
    return fingerprint_array

[sgosline]

also need to add mordred descriptors

[jjacobson95]

@sgosline What are your thoughts on changing the schema for Drug Descriptor to have three columns, improve_drug_id, fingerprint, and mordred?

Also what should these files be called? "{dataset}_drug_descriptor.tsv"? or "{dataset}_structures.tsv"?

Current Schema:

  Drug:
    description: List of chemicals/drugs used in the data package. Each identifer corresponds to a distinct structure.
    slots:
      - improve_drug_id
    attributes:
      chem_name:
        description: Name of drug
      canSMILES:
        description: Canonical SMILE string
      isoSMILES:
        description: Isomeric SMILE string
      InChIKey:
        description: InChIKey
      formula:
        description: Chemical formula
      weight:
        description: Molecular weight
        range: float
      pubchem_id:
        description: PubChem Identifier for this drug, can be many.
        range: int
  Drug Descriptor:
    description: Computational summary of drug chemical properties
    slots:
      - improve_drug_id
    attributes:
      structural_descriptor:
        description: string name describing structural descriptor
      descriptor_value:
        range: any
        description: value representing descriptor value

[sgosline]

There are currently 1800 different mordred descriptors - creating an entry for each drug will be time consuming and space intensive. We need a use case/algorithm to motivate this further.

[sgosline]

Here is the script to intrgrate: https://github.com/adpartin/mol-features/blob/master/src/gen_mol_fea.py