tmos

tmos.tmos

Description

Sanitize and generate oxidation state and other properties for transition metal complexes.

This module uses function architectures originally produced in [xyz2mol_tm](jensengroup/xyz2mol_tm). However rather than using the Huckel method an arrow pushing script is produced here with custom checks for ferrocene structures.

Functions

assert_same_ring	Determine whether two atoms are in the same chemical ring
check_ligand_exception	Corrects formal charges and bonds for molecular exceptions.
cleave_mol_from_index	Given an atomic index of an RDKit molecule, cleave the attaching bonds and return the resulting molecules
compare_fingerprint	Compare molecular identity
compute_centroid_excluding	Compute the centroid of a molecule while excluding specified atom indices.
correct_ferrocene	Correct a ferrocene containing molecule to ensure that all hydrogens are included
detect_additional_bonds	Use the coordinates to check if any other bonds could be defined.
determine_bonds	Determine bond orders with OpenBabel, with MDA fallback.
find_metal_index	Find the molecule index for the metal
find_missing_coords	Determine if an RDKit molecule has a relevant geometry
fix_missing_coords	Add coordinates to RDKit molecule with missing coordinates
get_ligand_attributes	Analyze default valence and bonds to determine ligand attributes.
get_tm_attributes	Compute possible oxidation states, formal charges, and electron counts for a transition metal center.
mol_from_smiles	Convert a SMILES string into a RDKit Molecule
mol_to_smiles	Generate SMILES without isomeric information from a RDKit molecule
prepare_complex	Prepare complex removing anomalous substructs, adding additional metal connections, checking for missing coordinates, and possible addition of hydrogens.
reform_metal_complex	Reconnects ligands to a transition metal center to reform a metal complex.
sanitize_complex	Sanitize ligands, determining X-type and L-type, returning a sanitized complex with oxidation state, number of electrons, and metal formal charge.
sanitize_ligand	Delete atoms from a molecule and then redetermine bond orders.
sanitize_molecule	Sanitize TMC molecule by updating formal charges to apparent value based on connectivity and use RDKit sanitization without SANITIZE_SETAROMATICITY or SANITIZE_KEKULIZE.
wipe_molecule	Wipe all bond order and aromatic information from a molecule so that only single bonds remain.