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.