Metadata-Version: 2.1
Name: alchemistry-flamel
Version: 0.3.1
Summary: A command line interface (CLI) to alchemlyb.
Author-email: alchemistry <william@zhiyiwu.me>
License: BSD-3-Clause
Project-URL: Source, https://github.com/alchemistry/flamel/
Project-URL: Documentation, https://github.com/alchemistry/flamel/blob/master/README.md
Project-URL: Issue Tracker, https://github.com/alchemistry/flamel/issues
Project-URL: Discussions, https://github.com/alchemistry/flamel/discussions
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows 
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: AUTHORS
Requires-Dist: alchemlyb (>=1.0)
Requires-Dist: importlib-resources ; python_version < "3.12"
Provides-Extra: test
Requires-Dist: pytest (>=6.1.2) ; extra == 'test'
Requires-Dist: pytest-runner ; extra == 'test'
Requires-Dist: pytest-mock ; extra == 'test'

# Flamel

[//]: # (Badges)
[![GitHub Actions Build Status](https://github.com/alchemistry/flamel/workflows/CI/badge.svg)](https://github.com/alchemistry/flamel/actions?query=workflow%3ACI)
[![codecov](https://codecov.io/gh/alchemistry/flamel/branch/master/graph/badge.svg?token=NvoYnT9NSb)](https://codecov.io/gh/alchemistry/flamel)

The aim of the project is to develop a **command line interface (CLI) to 
[alchemlyb](https://github.com/alchemistry/alchemlyb)**, the well-tested and 
actively developed library for alchemical free energy calculations. It is 
supposed to [become the successor](https://github.com/alchemistry/alchemlyb/wiki/Roadmap#librarify-alchemical-analysis-functionality) 
of the now unsupported [alchemical-analysis](https://github.com/MobleyLab/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
```shell
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`
```shell
git clone git@github.com:alchemistry/flamel.git
pip install flamel/
```

### Uninstalling
If you want to remove *flamel* after having it installed with `pip`,
run
```shell
pip uninstall alchemistry-flamel
```
to delete `flamel` and its associated files.


## Usage

The analysis can be invoked with the following command

```shell
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](https://alchemlyb.readthedocs.io/en/latest/workflows/alchemlyb.workflows.ABFE.html#alchemlyb.workflows.ABFE) 
workflow in [alchemlyb](https://github.com/alchemistry/alchemlyb). 
The script will generate the output from ABFE workflow, including 
[O_MBAR.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#overlap-matrix-of-the-mbar),
[dF_t.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#df-states-plots-between-different-estimators),
[dF_state.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#overlap-matrix-of-the-mbar),
[dF_t.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#forward-and-backward-convergence),
[dhdl_TI.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#dhdl-plot-of-the-ti).

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](https://en.wikipedia.org/wiki/Nicolas_Flamel)

## Copyright

Copyright (c) 2022, the [AUTHORS](./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](https://github.com/molssi/cookiecutter-cms) version 1.1.

