rdk-amber 0.1.0

Map AMBER/GAFF atom types to elements and load AMBER-style mol2 files into RDKit.

rdk-amber

Small utilities for bridging AMBER force-field conventions and RDKit:

1. A mapping between AMBER / GAFF atom types and chemical elements.
2. A loader that reads an AMBER-style mol2 file (GAFF/AMBER atom types in the type column) into an rdkit.Chem.Mol.

RDKit's own MolFromMol2File expects SYBYL atom types (C.3, N.ar, …). AmberTools (antechamber, tleap) instead writes GAFF/AMBER atom types (c3, na, …) in that column, which RDKit cannot interpret. This package parses such files directly.

Install

pip install -e .

Requires rdkit (install via conda/pip).

Usage

Atom type → element

from rdk_amber import element_from_amber_type

element_from_amber_type("c3")    # 'C'
element_from_amber_type("ho")    # 'H'
element_from_amber_type("Na+")   # 'Na'
element_from_amber_type("Xx")    # None  (unknown)
element_from_amber_type("Xx", strict=True)   # raises UnknownAtomTypeError

The full table is exposed as rdk_amber.AMBER_ATOM_TYPE_TO_ELEMENT. Types not in the table fall back to a prefix heuristic (e.g. c99 → C).

Load an AMBER mol2

from rdk_amber import load_amber_mol2

mol = load_amber_mol2("ligand.mol2")          # sanitized RDKit Mol, with 3D coords
mol = load_amber_mol2("ligand.mol2", remove_hs=True)

Or use the class for more control / multi-molecule files:

from rdk_amber import AmberMol2Loader

loader = AmberMol2Loader.from_file("ligand.mol2")
loader.num_molecules        # number of @<TRIPOS>MOLECULE records
loader.names                # their names
mol  = loader.to_rdkit(index=0, sanitize=True)
mols = loader.to_rdkit_all()

Each atom keeps the original AMBER data as properties:

property	meaning
_AmberAtomType	the GAFF/AMBER atom type (c3, ca, …)
_TriposAtomName	the atom name column
_TriposResidueName	the substructure / residue name
_TriposPartialCharge	the mol2 partial charge (double)

Notes

• Bond orders are read from the @<TRIPOS>BOND section. ar → aromatic, am → single, 1/2/3 → single/double/triple.
• If sanitization fails (unusual force-field valences), pass sanitize=False to obtain the unsanitized molecule.
• Partial charges are stored as properties; formal charges are not inferred.

Tests

pytest

rdk-amber