neurosnap.conformers module

Provides functions and classes related to processing and generating conformers.

neurosnap.conformers.find_LCS(mol)

Find the largest common substructure (LCS) between a set of conformers and aligns all conformers to the LCS.

Parameters:

mol (Mol) – Input RDkit molecule object, must already have conformers present

Return type:

Mol

Returns:

Resultant molecule object with all conformers aligned to the LCS

Raises:

Exception – if no LCS is detected

neurosnap.conformers.generate(input_mol, output_name='unique_conformers', write_multi=False, num_confs=1000, min_method='auto', max_atoms=500)

Generate conformers for an input molecule.

Performs the following actions in order: 1. Generate conformers using ETKDG method 2. Minimize energy of all conformers and remove those below a dynamic threshold 3. Align & create RMSD matrix of all conformers 4. Clusters using Butina method to remove structurally redundant conformers 5. Return most energetically favorable conformers in each cluster

Parameters:

• input_mol (Any) – Input molecule can be a path to a molecule file, a SMILES string, or an instance of rdkit.Chem.rdchem.Mol

• output_name (str) – Output to write SDF files of passing conformers

• write_multi (bool) – If True will write all unique conformers to a single SDF file, if False will write all unique conformers in separate SDF files in output_name

• num_confs (int) – Number of conformers to generate

• min_method (Optional[str]) – Method for minimization, can be either “auto”, “UFF”, “MMFF94”, “MMFF94s”, or None for no minimization

• max_atoms (int) – Maximum number of atoms allowed for the input molecule

Return type:

DataFrame

Returns:

A dataframe with all conformer statistics. Note if energy minimization is disabled or fails then energy column will consist of None values.

neurosnap.conformers.minimize(mol, method='MMFF94', percentile=100.0)

Minimize conformer energy (kcal/mol) using RDkit and filter out conformers based on energy percentile.

Parameters:

• mol (Mol) – RDkit mol object containing the conformers you want to minimize. (rdkit.Chem.rdchem.Mol)

• method (str) – Can be either UFF, MMFF94, or MMFF94s (str)

• percentile (float) – Filters out conformers above a given energy percentile (0 to 100). For example, 10.0 will retain conformers within the lowest 10% energy. (float)

Return type:

Tuple[float, Dict[int, float]]

Returns:

A tuple of the form (mol_filtered, energies) - mol_filtered: Molecule object with filtered conformers. - energies: Dictionary where keys are conformer IDs and values are calculated energies in kcal/mol.