build_rdmol#

tmos.build_rdmol

Description

Functions for building RDKit molecules.

Such functions include:

Utilities to import molecules from one package to RDKit
Determine the connectivity of the molecule from XYZ coordinates using RDKit or OpenBabel
Determining the bond orders of a molecule using RDKit, OpenBabel, or MDAnalysis

Functions

`add_obvious_bonds`	Correct bond order for adjacent atoms with hanging bonds.
`assess_atoms`	Assess an RDKit molecule's atoms to determine which are charged or not fully satisfied.
`copy_atom_coords`	Copy the coordinates of one atom to another
`determine_bonds_mda`	Determine bond orders with MDAnalysis, or None if failed.
`determine_bonds_openbabel`	Determine bond orders with Open Babel, or None if failed.
`determine_bonds_rdkit`	Determine bond orders with RDKit, or None if failed.
`determine_connectivity`	Determine connectivity for molecules, particularly transition metal organometallic complexes.
`get_atom_charge`	Get the effective charge of an atom based on its default valence and total bond orders.
`qcelemental_to_rdkit`	Convert a QCElemental molecule to an RDKit molecule.
`update_atom_bond_props`	Update atom and bond properties of one molecule to match another.
`update_formal_charges`	Update the formal charges of a molecule to align with their implied charge from connectivity.
`xyz_to_rdkit`	Convert a QCElemental molecule to an RDKit molecule.