navicatGA.chemistry_smiles

Attributes

lg

logger

Functions

diagnose_mol(mol)

Tries to identify and print to logger whatever was or is wrong with the chemistry_selfies of an rdkit.mol object.

draw_smiles(smiles, root_name)

get_ECFP4(mol)

get_conformer_rmsd(mol)

get_confs_ff(mol[, maxiters])

get_interatomic_distances(conf)

get_structure_ff(mol[, n_confs])

Generates a reasonable set of 3D structures

has_transition_metals(mol)

Returns True if the rdkit.mol object passed as argument has a (transition)-metal atom, False if else.

is_transition_metal(at)

Returns True if the rdkit.Atom object passed as argument is a transition metal, False if else.

prune_mol_conformers(mol, energies_list)

randomize_smiles(mol)

sanitize_multiple_smiles(smiles_list)

Calls sanitize_smiles for every item in a list.

sanitize_smiles(smiles)

Return a canonical smile representation of smi.

set_dative_bonds(mol[, fromAtoms])

Tries to replace bonds with metal atoms by dative bonds, while keeping valence rules enforced. Adapted from G. Landrum.

timed_sanitizer(smiles)

Convert smiles string to rdkit.mol, call exception and return None if it takes more than 10 seconds to run.

Module Contents

Tries to identify and print to logger whatever was or is wrong with the chemistry_selfies of an rdkit.mol object.

Generates a reasonable set of 3D structures using forcefields for a given rdkit.mol object. It will try several 3D generation approaches in rdkit. It will try to sample several conformations and get the minima.

Parameters: :param mol: an rdkit mol object :type mol: rdkit.mol :param n_confs: number of conformations to sample :type n_confs: int

Returns: :return mol_structure: mol with 3D coordinate information set

Returns True if the rdkit.mol object passed as argument has a (transition)-metal atom, False if else.

Returns True if the rdkit.Atom object passed as argument is a transition metal, False if else.

Calls sanitize_smiles for every item in a list.

Parameters: :param smiles_list: list of smile strings to be sanitized.

Returns: :return sanitized_smiles: list of sanitized smile strings or None in case a smiles led to error

Return a canonical smile representation of smi. If there are metals, it will try to fix the bonds as dative.

Parameters: :param smi: smile string to be canonicalized :type smi: str

Returns: :return mol: rdkit mol object, None if exception caught :return smi_canon: canonicalized smile representation of smi, None if exception caught. :return conversion_successful: True if no exception caught, False if exception caught.

Tries to replace bonds with metal atoms by dative bonds, while keeping valence rules enforced. Adapted from G. Landrum.

Convert smiles string to rdkit.mol, call exception and return None if it takes more than 10 seconds to run.