OpenMOL is a Python package to convert between popular molecular dynamics data file formats. It exposes a pythonic way to easily manipulate MOL2 and LAMMPS data files.
- Convert AMBER PARM7 and restart files into LAMMPS data files.
- Read, manipulate and write MOL2 files.
- Save data files into portable openmol json format without losing any properties.
- Build complex mol2 systems using Discovery Studio and import into tleap.
- Extensible.
You can install openmol directly from PyPI using pip.
pip install openmolConvert AMBER prmtop and restart files to a LAMMPS data file.
from openmol import amber_parm7 as amber
from openmol import lammps_full as lammps
# read amber parm files
p = amber.read('system.prmtop', 'system.rst7')
# calculate necessary lammps items and write
p = lammps.build(p)
lmp = lammps.Writer(p, 'system.data')
lmp.write()The SUBSTRUCTURE section of the MOL2 files created by VMD are not always properly formated. Use the following to fix the format.
from openmol import tripos_mol2 as mol2
# read vmd output mol2 file
p = mol2.read('vmd_saved.mol2')
# calculate necessary mol2 residue info
p = mol2.build(p)
# write the fixed mol2 file
mol2.Writer(p, 'fixed_vmd_saved.mol2').write()Discovery Studio Visualizer generated MOL2 files can contain digits as suffixes in the residue names. Update the residue names for all atoms as below.
from openmol import tripos_mol2 as mol2
p = mol2.read('dsv_output.mol2')
# set all atom's resname to FeO
for i, atom in enumerate(p.atom_name):
p.atom_resname[i] = 'FeO'
p = mol2.build(p)
# write the fixed mol2 file
mol2.Writer(p, 'fixed_dsv_output.mol2').write()| Parser | Reader | Writer |
|---|---|---|
| Amber | Yes | x |
| LAMMPS | x | Yes |
| MOL2 | Yes | Yes |
Contributions welcome!
For the latest development version you can clone the Git repository.
git clone https://github.com/akhlakm/OpenMOL
cd OpenMOL
pip install -e .GNU General Public License v3.0 (GPLv3.0)