autofragment.io

I/O utilities for reading and writing molecular data.

This module provides comprehensive I/O support for molecular file formats:

Readers: - PDB: Protein Data Bank format with CONECT records - MOL2: Tripos MOL2 format with atom types - SDF: MDL Structure Data File (V2000/V3000) - QCSchema: MolSSI standard JSON format - GAMESS, Psi4, Q-Chem, ORCA, NWChem: QC program inputs - VASP: POSCAR/CONTCAR format - CIF: Crystallographic Information File

Writers: - GAMESS: FMO, EFMO, EFP methods - Psi4: Fragment, SAPT methods - Q-Chem: EFP, XSAPT, FRAGMO methods - NWChem, ORCA, Molpro, Turbomole, CFOUR: Fragment calculations - QCSchema: JSON with fragment annotations - XYZ, PDB: With fragment markers

Modules

mmcif	Minimal mmCIF parser for biological partitioning.
output	Output formatting for autofragment results.
readers	Molecular structure file readers for AutoFragment.
writers	Quantum chemistry program output file writers for AutoFragment.
xyz	XYZ file parsing for water clusters.