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MolParse

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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>

moltree

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

moltree

Other options can be found by running molxvg --help.

Installation from source

Requirements

  • ASE
  • MPyTools

Installing ASE

  • pip install --upgrade --user ase
  • export PATH=$PATH:~/.local/bin to your .bash_profile
  • export PYTHONPATH=$PYTHONPATH:~/.local/lib/python3.X/site-packages to your .bash_profile Where X is your python version.

MPyTools

  • git clone https://github.com/mwinokan/MPyTools.git
  • Add export MPYTOOLS=/path/to/directory to your .bash_profile
  • Add export PYTHONPATH=$PYTHONPATH:$MPYTOOLS to your .bash_profile

MolParse

  • git clone https://github.com/mwinokan/MolParse.git
  • Add export MOLPARSE=/path/to/directory to your .bash_profile
  • Add export PYTHONPATH=$PYTHONPATH:$MOLPARSE to your .bash_profile