developer.align_mapping module

A helper program to add SMILEIDX to mapping files.

This program align MD molecules from the Universe to an rdkit molecule created by SMILES. Can be used with a care to semi-manualy curate mapping files, SMILES, and add the alignments for only heavy atoms. Further should be converted into a mature CI/CD script.

developer.align_mapping.mk_universe_compact(s: System) → Universe

Make universe based on just TPR and GRO records

developer.align_mapping.get_1mol_selstr(comp_name: str, mol_obj: Molecule) → str

Return selection string for a single molecule

developer.align_mapping.get_brutto_formula(eorder: str, agrp: AtomGroup, charge: float = 0) → str

Get brutto formula (according to element order) of neutralized form

developer.align_mapping.compare_neutralized(a: Mol, b: Mol)

Compare neutralized forms of molecules

developer.align_mapping.find_uname(x, atom_name, res_name) → str

developer.align_mapping.main()