6.13. MOL2 file format — MDAnalysis.coordinates.MOL2
Classes to work with Tripos molecule structure format (MOL2) coordinate and topology files. Used, for instance, by the DOCK docking code.
6.13.1. Example for working with mol2 files
To open a mol2, remove all hydrogens and save as a new file, use the following:
u = Universe("Molecule.mol2")
gr = u.select_atoms("not name H*")
print(len(u.atoms), len(gr))
gr.write("Molecule_noh.mol2")
6.13.2. Classes
- class MDAnalysis.coordinates.MOL2.MOL2Reader(filename, **kwargs)[source]
Reader for MOL2 structure format.
Changed in version 0.11.0: Frames now 0-based instead of 1-based. MOL2 now reuses the same Timestep object for every frame, previously created a new instance of Timestep each frame.
Changed in version 0.20.0: Allows for comments at top of file. Ignores status bit strings
Changed in version 2.0.0: Bonds attribute is not added if no bonds are present in MOL2 file
Changed in version 2.2.0: Read MOL2 files with optional columns omitted.
Read coordinates from filename.
- Parameters
filename (str or NamedStream) – name of the mol2 file or stream
- units = {'length': 'Angstrom', 'time': None}
dict with units of of time and length (and velocity, force, … for formats that support it)
- class MDAnalysis.coordinates.MOL2.MOL2Writer(filename, n_atoms=None, convert_units=True)[source]
mol2 format writer
Write a file in the Tripos molecule structure format (MOL2).
Note
MOL2Writercan only be used to write out previously loaded MOL2 files. If you’re trying to convert, for example, a PDB file to MOL you should use other tools, like 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 writer is currently not available for rdkit master. It requires SYBYL atomtype generation. See page 7 for list of SYBYL atomtypes (http://tripos.com/tripos_resources/fileroot/pdfs/mol2_format2.pdf).
Changed in version 0.11.0: Frames now 0-based instead of 1-based
Create a new MOL2Writer
- Parameters
- units = {'length': 'Angstrom', 'time': None}
dict with units of of time and length (and velocity, force, … for formats that support it)
Notes
The MDAnalysis
MOL2ReaderandMOL2Writeronly handle the MOLECULE, SUBSTRUCTURE, ATOM, and BOND record types. Other records are not currently read or preserved on writing.As the CRYSIN record type is not parsed / written, MOL2 systems always have dimensions set to
Noneand dimensionless MOL2 files are written.
6.13.3. MOL2 format notes
MOL2 Format Specification: (http://www.tripos.com/data/support/mol2.pdf)
Example file (http://www.tripos.com/mol2/mol2_format3.html):
# 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