promptbind.utils.post_optim_utils

Functions

compute_RMSD(a, b)
post_optimize_compound_coords(...[, lr, ...])
post_optimize_compound_coords_lbfgs(...[, ...])
post_optimize_loss_function(epoch, x, ...[, ...])
read_molecule(molecule_file[, sanitize, ...])	Load a molecule from a file of format .mol2 or .sdf or .pdbqt or .pdb. :param molecule_file: Path to file for storing a molecule, which can be of format .mol2 or .sdf or .pdbqt or .pdb. :type molecule_file: str :param sanitize: Whether sanitization is performed in initializing RDKit molecule instances. See https://www.rdkit.org/docs/RDKit_Book.html for details of the sanitization. Default to False. :type sanitize: bool :param calc_charges: Whether to add Gasteiger charges via RDKit. Setting this to be True will enforce sanitize to be True. Default to False. :type calc_charges: bool :param remove_hs: Whether to remove hydrogens via RDKit. Note that removing hydrogens can be quite slow for large molecules. Default to False. :type remove_hs: bool :param use_conformation: Whether we need to extract molecular conformation from proteins and ligands. Default to True. :type use_conformation: bool.
write_mol(reference_file, coords, output_file)