Confgen#

aleimi.confgen.confgen(mol: Mol, rdkit_d_RMSD: float, numConfs: int, rdkit_numThreads: float = 0, UFF: bool = False)[source]#

Generate conformers stochastically for mol and filter them out based on geometrical and energetic criterions.

Parameters:

  • mol (Chem.rdchem.Mol) – The RDKit molecule for which the stochastic conformations will be generated.

  • rdkit_d_RMSD (float) – RMSD to filter out redundant conformations, geometric filter.

  • numConfs (int) – Maximum number of conformation to generate

  • rdkit_numThreads (float, optional) – Number of CPUs to use, by default 0 (use all)

  • UFF (bool, optional) – If True a classical mechanical optimization will be performed, by default False

Returns:

  • RDKit molecule with conformations, the hydrogens are always added.

  • Index of conformer to use.

  • List of classic energies if UFF = True, if not, a list of None values with length, number of conformers.

Return type:

tuple

aleimi.confgen.main(suppl: str, numConfs: int = 10, rdkit_d_RMSD: float = 0.2, UFF: bool = False, rdkit_numThreads: int = 0, mopac_keywords: str = 'PM7 precise ef xyz geo-ok t=3h THREADS = 2') → List[str][source]#

Generate conformers stochastically for the supplied molecules and filter them out based on geometrical and energetic criterions.

Parameters:

  • suppl (str) – Path for the molecule file. It could be:.pdb, .mol2, .mol, .sdf, .smi. In case of .smi you can define several SMILES. and for all of them the configuration will be generated. TODO: do the same for sdf files

  • numConfs (int, optional) – Maximum number of conformation to generate, by default 10

  • rdkit_d_RMSD (float, optional) – RMSD to filter out redundant conformations, geometric filter, by default 0.2

  • UFF (bool, optional) – If True a classical mechanical optimization will be performed, by default False

  • rdkit_numThreads (int, optional) – Number of CPUs to use, by default 0 (use all)

  • mopac_keywords (str, optional) – This is head of a .mop file, basically a definition of the sei-empirical job. Check the MOPAC Documentation for more information , by default ‘PM7 precise ef xyz geo-ok t=3h THREADS = 2’

Returns:

List of names of the used molecules

Return type:

List[str]

Raises:

  • ValueError – If in the .smi there are invalid SMILES

  • ValueError – If the extension of molecule is not: .pdb, .mol2, .mol, .sdf or .smi.

  • ValueError – If the molecule was not understood by RDKit

aleimi.confgen.makeimg(mols: List[Mol], **keywords)[source]#

Simple function to create a picture of the input molecules. The file used_mols.png will be createad.

Parameters:

mols (List[Chem.rdchem.Mol]) – list of molecules