Toolkit Overview

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About

The Simmate Toolkit serves as an alternative to RDkit, OpenEye-Toolkit, and other Python packages for cheminformatics.

Our toolkit is the product of...

• Incorporating features from other toolkits (e.g., wrapping an RDkit function)
• Creating more Pythonic and user-friendly APIs
• Adding optional integrations with databases and workflows

Our toolkit is "batteries-included", meaning it includes many features typically used in large projects. As a result, it requires a larger installation (i.e., more dependencies). However, this also means that larger projects can benefit significantly from using our toolkit instead of building features from scratch with toolkits like RDkit.

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Preview

To understand how the Simmate Toolkit simplifies tasks, consider this script. The script...

1. Reads an SDF file containing multiple molecules
2. Removes all molecules with more than 3 stereocenters, more than 30 heavy atoms, and containing sodium (Na)
3. Generates a list of InChI keys from the final set

This script is less intuitive and less Pythonic for other toolkits, but it's straightforward and clean with Simmate:

simmate-toolkitrdkitoe-toolkit

from simmate.toolkit import Molecule

# STEP 1
molecules = Molecule.from_sdf_file("example.sdf")

# STEP 2
molecules_filtered = []
for molecule in molecules:
    if molecule.num_stereocenters > 3:
        continue
    if molecule.num_atoms_heavy > 30:
        continue
    if "Na" in molecule.elements:
        continue
    molecules_filtered.append(molecule)

# STEP 3
inchi_keys = [m.to_inchi_key() for m in molecules_filtered]

from rdkit import Chem
from rdkit.Chem import FindMolChiralCenters, Descriptors

# STEP 1
molecules = []
with Chem.SDMolSupplier("example.sdf") as supplier:
for molecule in supplier:
    if mol is None:
        continue
    molecules.append(molecule)

# STEP 2
molecules_filtered = []
for molecule in molecules:

    chiral_centers = FindMolChiralCenters(
        molecule,
        force=True,
        includeUnassigned=True,
        useLegacyImplementation=False,
    )
    if len(chiral_centers) > 3:
        continue

    nheavy = Descriptors.HeavyAtomCount(molecule)
    if nheavy > 30:
        continue

    has_na = False  # false until proven otherwise
    for atom in molecule.GetAtoms():
        if atom.GetSymbol() == "Na":
            has_na = True
            break
    if has_na:
        continue

    molecules_filtered.append(molecule)

# STEP 3
inchi_keys = [Chem.MolToInchiKey(m) for m in molecules_filtered]

from openeye import oechem
from openeye import oeiupac

# STEP 1
molecules = []
with oechem.oemolistream("example.sdf") as ifs:
    for mol in ifs.GetOEMols():
        if mol is None:
            continue
        molecules.append(mol)

# STEP 2
molecules_filtered = []
for mol in molecules:

    stereo_count = sum(1 for atom in mol.GetAtoms() if atom.IsChiral())
    if stereo_count > 3:
        continue

    heavy_atom_count = sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() > 1)
    if heavy_atom_count > 30:
        continue

    has_na = any(atom.GetAtomicNum() == 11 for atom in mol.GetAtoms())
    if has_na:
        continue

    molecules_filtered.append(mol)

# STEP 3
inchi_keys = [oeiupac.OECreateInChIKey(m) for m in molecules_filtered]

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