| Name | openmol JSON |
| Version |
1.2.2
JSON |
| download |
| home_page | |
| Summary | Convert between popular molecular dynamics data file formats. |
| upload_time | 2024-02-25 05:56:04 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.0 |
| license | |
| keywords |
research
simulation
development
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# 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](https://pypi.org/project/openmol) using `pip`.
```sh
pip install openmol
```
## Usage Examples
### AMBER to LAMMPS
Convert AMBER **prmtop** and **restart** files to a LAMMPS **data** file.
```python
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.
```python
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.
```python
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](https://github.com/akhlakm/OpenMOL).
```sh
git clone https://github.com/akhlakm/OpenMOL
cd OpenMOL
pip install -e .
```
## License
GNU General Public License v3.0 (GPLv3.0)
Raw data
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