.. -*- coding: utf-8 -*- .. _MOL2-format: ======================================= MOL2 (Tripos structure) ======================================= .. include:: classes/MOL2.txt The Tripos_ molecule structure format (MOL2_) is a commonly used format. It is used, for instance, by the DOCK_ docking code. .. _MOL2: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf .. _Tripos: http://www.tripos.com/ .. _DOCK: http://dock.compbio.ucsf.edu/ .. warning:: :class:`~MDAnalysis.coordinates.MOL2.MOL2Writer` can only be used to write out previously loaded MOL2 files. For example, if you're trying to convert a PDB file to MOL2, you should use other tools such as rdkit_. Here is an example how to use rdkit_ to convert a PDB to MOL:: from rdkit import Chem mol = Chem.MolFromPDBFile("molecule.pdb", removeHs=False) Chem.MolToMolFile(mol, "molecule.mol" ) .. _rdkit: http://www.rdkit.org/docs/GettingStartedInPython.html MOL2 specification ================== * Example file:: # Name: benzene # Creating user name: tom # Creation time: Wed Dec 28 00:18:30 1988 # Modifying user name: tom # Modification time: Wed Dec 28 00:18:30 1988 @MOLECULE benzene 12 12 1 0 0 SMALL NO_CHARGES @ATOM 1 C1 1.207 2.091 0.000 C.ar 1 BENZENE 0.000 2 C2 2.414 1.394 0.000 C.ar 1 BENZENE 0.000 3 C3 2.414 0.000 0.000 C.ar 1 BENZENE 0.000 4 C4 1.207 -0.697 0.000 C.ar 1 BENZENE 0.000 5 C5 0.000 0.000 0.000 C.ar 1 BENZENE 0.000 6 C6 0.000 1.394 0.000 C.ar 1 BENZENE 0.000 7 H1 1.207 3.175 0.000 H 1 BENZENE 0.000 8 H2 3.353 1.936 0.000 H 1 BENZENE 0.000 9 H3 3.353 -0.542 0.000 H 1 BENZENE 0.000 10 H4 1.207 -1.781 0.000 H 1 BENZENE 0.000 11 H5 -0.939 -0.542 0.000 H 1 BENZENE 0.000 12 H6 -0.939 1.936 0.000 H 1 BENZENE 0.000 @BOND 1 1 2 ar 2 1 6 ar 3 2 3 ar 4 3 4 ar 5 4 5 ar 6 5 6 ar 7 1 7 1 8 2 8 1 9 3 9 1 10 4 10 1 11 5 11 1 12 6 12 1 @SUBSTRUCTURE 1 BENZENE 1 PERM 0 **** **** 0 ROOT