alchemistry-flamel 0.3.1

A command line interface (CLI) to alchemlyb.

Flamel

The aim of the project is to develop a command line interface (CLI) to alchemlyb, the well-tested and actively developed library for alchemical free energy calculations. It is supposed to become the successor of the now unsupported alchemical-analysis script.

Installation

The package containing flamel is called alchemistry-flamel. The latest release can be installed with pip or alternatively, install from source. Both methods are explained below.

pip

flamel is available from the Python Package index (PyPi) under the name alchemistry-flamel and can be installed with

pip install alchemistry-flamel

The installed package makes the flamel script available.

From sources

Clone the flamel repository https://github.com/alchemistry/flamel and install with pip

git clone [e-mail]:alchemistry/flamel.git
pip install flamel/

Uninstalling

If you want to remove flamel after having it installed with pip, run

pip uninstall alchemistry-flamel

to delete flamel and its associated files.

Usage

The analysis can be invoked with the following command

flamel -a GROMACS -d dhdl_data -f 10 -g -i 50 -j result.csv -m TI,BAR,MBAR -n dE -o out_data -p dhdl -q xvg -r 3 -s 50 -t 298 -v  -w

Run flamel -h to see the full description of the options.

Output

This script is a wrapper around the ABFE workflow in alchemlyb. The script will generate the output from ABFE workflow, including O_MBAR.pdf, dF_t.pdf, dF_state.pdf, dF_t.pdf, dhdl_TI.pdf.

The script will also generate the result.csv and result.p, which is a pandas DataFrame summarising the results. ::

                  TI  TI_Error    BAR  BAR_Error   MBAR  MBAR_Error
States 0 -- 1  0.962     0.007  0.956      0.007  0.964       0.006
       1 -- 2  0.567     0.006  0.558      0.006  0.558       0.004
       2 -- 3  0.264     0.005  0.258      0.005  0.254       0.004
       3 -- 4  0.035     0.004  0.035      0.004  0.030       0.003
Stages fep     1.828     0.014  1.806      0.016  1.807       0.014
       TOTAL   1.828     0.014  1.806      0.011  1.807       0.014

Name

In the tradition to associate free energy estimations with alchemistry it's named after Nicolas Flamel

Copyright

Copyright (c) 2022, the AUTHORS.

Acknowledgements

@harlor started flamel as a replacement for the original alchemical-analyis.py script.

Project template based on the Computational Molecular Science Python Cookiecutter version 1.1.