openmol 1.2.2

Convert between popular molecular dynamics data file formats.

OpenMOL

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.

Features

• 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.

Installation

You can install openmol directly from PyPI using pip.

pip install openmol

Usage Examples

AMBER to LAMMPS

Convert 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()

Fix VMD MOL2

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()

Fix DSV mol2 residue names

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()

Current Implementations

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 .

License

GNU General Public License v3.0 (GPLv3.0)