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Transition Metal Oxidation State documentation

  • Getting Started
  • User Guide
  • API Documentation
  • Developer Guide
  • Getting Started
  • User Guide
  • API Documentation
  • Developer Guide

Section Navigation

  • build_rdmol
    • add_obvious_bonds
    • assess_atoms
    • copy_atom_coords
    • determine_bonds_mda
    • determine_bonds_openbabel
    • determine_bonds_rdkit
    • determine_connectivity
    • get_atom_charge
    • qcelemental_to_rdkit
    • update_atom_bond_props
    • update_formal_charges
    • xyz_to_rdkit
  • geometry
    • get_coordinates
    • get_distance
    • get_geometry_from_mol
    • get_geometry_from_xyz
  • graph_mapping
    • find_atom_mapping
    • find_molecular_rings
    • get_atom_environment
    • implicit_hydrogen_atom_mapping
    • mol_to_graph
    • validate_mapping
  • reference_values
  • tmos
    • assert_same_ring
    • check_ligand_exception
    • cleave_mol_from_index
    • compare_fingerprint
    • compute_centroid_excluding
    • correct_ferrocene
    • detect_additional_bonds
    • determine_bonds
    • find_metal_index
    • find_missing_coords
    • fix_missing_coords
    • get_ligand_attributes
    • get_tm_attributes
    • mol_from_smiles
    • mol_to_smiles
    • prepare_complex
    • reform_metal_complex
    • sanitize_complex
    • sanitize_ligand
    • sanitize_molecule
    • wipe_molecule
  • utils
    • first_traceback
    • get_molecular_formula
    • molecular_formula_to_dict
    • save_to_json
    • view3D
  • API Documentation

API Documentation#

tmos.build_rdmol

Functions for building RDKit molecules.

tmos.geometry

tmos.graph_mapping

Turn RDKit molecules into graphical representations, then perform comparisons and analyses.

tmos.reference_values

Reference dictionaries of interest.

tmos.tmos

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

tmos.utils

General utilities

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