molecular_qm_util

Utilities for molecular electronic structure calculations with Simstack

Functions and their dependencies

The package is organized into sub-modules named after the third-party library they rely on. The table below documents which package powers which function so you can tell, at a glance, what needs to be installed for a given feature.

Function	Import path	Backend package(s)	What it does
compute_iupac_name	molecular_qm_util.pubchempy_scripts	pubchempy	Looks up the IUPAC name of a Molecule on PubChem (falls back to a molecular formula when no name is found).
smiles_to_molecule_obabel (Open Babel)	molecular_qm_util.obabel_scripts	openbabel (openbabel-wheel), simstack	Converts a SMILES string to a 3D Molecule using Open Babel (adds hydrogens, builds 3D coordinates, MMFF94/UFF minimization). Runs as a SimStack node.
cdx_to_molecule	molecular_qm_util.obabel_scripts	openbabel (openbabel-wheel), simstack	Reads a ChemDraw .cdx file into a Molecule using Open Babel.
molecule_to_smiles / compute_smiles / molecule_to_canonical_smiles	molecular_qm_util.rdkit_scripts	rdkit	Converts a Molecule (3D coordinates) to a canonical SMILES string using RDKit bond perception. The three names are aliases of the same function.
smiles_to_molecule_obabel (RDKit)	molecular_qm_util.rdkit_scripts	rdkit	Converts a SMILES string to a 3D Molecule using RDKit ETKDG embedding.
get_3d	molecular_qm_util.rdkit_scripts	rdkit	Generates a 3D MolBlock from a SMILES string via RDKit ETKDG embedding.
get_rotatable_bonds	molecular_qm_util.rdkit_scripts	rdkit	Finds rotatable bonds (as dihedral atom quadruples) in an RDKit molecule.
rotate_bond_rigidly / get_fragment_atoms	molecular_qm_util.rdkit_scripts	rdkit, numpy	Rigidly rotates a bond to enumerate conformers around a dihedral.

Conversion helpers (molecular_qm_util.util)

Function	Backend package(s)	What it does
rdkit_mol_to_molecule	rdkit, molecular_qm_models	Converts an RDKit Mol (with a conformer) to a SimStack Molecule.
pybel_mol_to_molecule	openbabel (pybel), molecular_qm_models	Converts an Open Babel pybel molecule to a SimStack Molecule.
simstack_molecule_to_rdkit	openbabel (pybel), rdkit, molecular_qm_models	Converts a SimStack Molecule to an RDKit Mol via Open Babel.

Note: every function also uses molecular_qm_models for the Molecule/Atom data model. The openbabel- and rdkit-based helpers are imported lazily in molecular_qm_util/__init__.py, so a missing optional backend does not break importing compute_iupac_name.