MOL2 (Tripos structure)¶
Coordinate reader |
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Coordinate writer |
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Topology parser |
The Tripos molecule structure format (MOL2) is a commonly used format. It is used, for instance, by the DOCK docking code.
Warning
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" )
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 @<TRIPOS>MOLECULE benzene 12 12 1 0 0 SMALL NO_CHARGES @<TRIPOS>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 @<TRIPOS>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 @<TRIPOS>SUBSTRUCTURE 1 BENZENE 1 PERM 0 **** **** 0 ROOT