| Name | alchemistry-flamel JSON |
| Version |
0.3.1
JSON |
| download |
| home_page | |
| Summary | A command line interface (CLI) to alchemlyb. |
| upload_time | 2022-12-06 16:29:45 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | BSD-3-Clause |
| keywords |
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No requirements were recorded.
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# Flamel
[//]: # (Badges)
[](https://github.com/alchemistry/flamel/actions?query=workflow%3ACI)
[](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.
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"description": "# Flamel\n\n[//]: # (Badges)\n[](https://github.com/alchemistry/flamel/actions?query=workflow%3ACI)\n[](https://codecov.io/gh/alchemistry/flamel)\n\nThe aim of the project is to develop a **command line interface (CLI) to \n[alchemlyb](https://github.com/alchemistry/alchemlyb)**, the well-tested and \nactively developed library for alchemical free energy calculations. It is \nsupposed to [become the successor](https://github.com/alchemistry/alchemlyb/wiki/Roadmap#librarify-alchemical-analysis-functionality) \nof the now unsupported [alchemical-analysis](https://github.com/MobleyLab/alchemical-analysis) script.\n\n## Installation\n\nThe package containing `flamel` is called **alchemistry-flamel**. The\nlatest release can be installed with `pip` or alternatively, install\nfrom source. Both methods are explained below.\n\n### `pip`\n*flamel* is available from the Python Package index (PyPi) under the\nname **alchemistry-flamel** and can be installed with\n```shell\npip install alchemistry-flamel\n```\nThe installed package makes the `flamel` script available.\n\n\n### From sources\nClone the *flamel* repository https://github.com/alchemistry/flamel\nand install with `pip`\n```shell\ngit clone git@github.com:alchemistry/flamel.git\npip install flamel/\n```\n\n### Uninstalling\nIf you want to remove *flamel* after having it installed with `pip`,\nrun\n```shell\npip uninstall alchemistry-flamel\n```\nto delete `flamel` and its associated files.\n\n\n## Usage\n\nThe analysis can be invoked with the following command\n\n```shell\nflamel -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\n```\n\nRun ``flamel -h`` to see the full description of the options.\n\n## Output\n\nThis script is a wrapper around the \n[ABFE](https://alchemlyb.readthedocs.io/en/latest/workflows/alchemlyb.workflows.ABFE.html#alchemlyb.workflows.ABFE) \nworkflow in [alchemlyb](https://github.com/alchemistry/alchemlyb). \nThe script will generate the output from ABFE workflow, including \n[O_MBAR.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#overlap-matrix-of-the-mbar),\n[dF_t.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#df-states-plots-between-different-estimators),\n[dF_state.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#overlap-matrix-of-the-mbar),\n[dF_t.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#forward-and-backward-convergence),\n[dhdl_TI.pdf](https://alchemlyb.readthedocs.io/en/latest/visualisation.html#dhdl-plot-of-the-ti).\n\nThe script will also generate the `result.csv` and `result.p`, which is a \npandas DataFrame summarising the results. ::\n\n TI TI_Error BAR BAR_Error MBAR MBAR_Error\n States 0 -- 1 0.962 0.007 0.956 0.007 0.964 0.006\n 1 -- 2 0.567 0.006 0.558 0.006 0.558 0.004\n 2 -- 3 0.264 0.005 0.258 0.005 0.254 0.004\n 3 -- 4 0.035 0.004 0.035 0.004 0.030 0.003\n Stages fep 1.828 0.014 1.806 0.016 1.807 0.014\n TOTAL 1.828 0.014 1.806 0.011 1.807 0.014\n\n## Name\n\nIn the tradition to associate free energy estimations with alchemistry it's \nnamed after [Nicolas Flamel](https://en.wikipedia.org/wiki/Nicolas_Flamel)\n\n## Copyright\n\nCopyright (c) 2022, the [AUTHORS](./AUTHORS).\n\n\n## Acknowledgements\n\n@harlor started *flamel* as a replacement for the original\n`alchemical-analyis.py` script.\n\nProject template based on the [Computational Molecular Science Python\nCookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.\n\n",
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