A python package for parsing, modifying, and analysis of molecular structure files.
Installation
Easiest way to install is from PyPI:
pip install molparse
Usage
Python Module
MolParse is primarily a python module which can be used interactively, or within (batch) scripts:
Use pydoc to see help on the molparse module, or its methods & classes. E.g. from a shell:
pydoc molparse
pydoc molparse.System
Binaries and command-line programs
moltree
In addition to the python module, an interactive command-line interface is available with the binary moltree. Pass a
PDB or GRO file as follows:
moltree <FILE>
Use the mouse to interact with buttons and CTR-C to exit.
molxvg
Gromacs produces data files in XVG format by default, these can be parsed using the molparse.xvg.parseXVG method from
within a python environment, alternatively a binary exists to access its basic functionality from the command line. Run
the following to open an interactive plotly graph of an xvg:
molxvg [FILE.xvg] -s
Other options can be found by running molxvg --help.
Installation from source
Requirements
Installing ASE
pip install --upgrade --user aseexport PATH=$PATH:~/.local/binto your.bash_profileexport PYTHONPATH=$PYTHONPATH:~/.local/lib/python3.X/site-packagesto your.bash_profileWhere X is your python version.
MPyTools
git clone https://github.com/mwinokan/MPyTools.git- Add
export MPYTOOLS=/path/to/directoryto your.bash_profile - Add
export PYTHONPATH=$PYTHONPATH:$MPYTOOLSto your.bash_profile
MolParse
git clone https://github.com/mwinokan/MolParse.git- Add
export MOLPARSE=/path/to/directoryto your.bash_profile - Add
export PYTHONPATH=$PYTHONPATH:$MOLPARSEto your.bash_profile
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