alchemlyb

alchemlyb: the simple alchemistry library - Published in JOSS (2024)

https://github.com/alchemistry/alchemlyb

Keywords

free-energy library molecular-dynamics python science

Scientific Fields

Mathematics Computer Science - 84% confidence

Artificial Intelligence and Machine Learning Computer Science - 83% confidence

Last synced: 4 months ago · JSON representation ·

Repository

the simple alchemistry library

Basic Info

Host: GitHub
Owner: alchemistry
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://alchemlyb.readthedocs.io
Size: 2.3 MB

Statistics

Stars: 219
Watchers: 14
Forks: 54
Open Issues: 26
Releases: 22

Topics

free-energy library molecular-dynamics python science

Created over 9 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation Authors

alchemlyb: the simple alchemistry library

alchemlyb makes alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack. It includes:

Parsers for extracting raw data from output files of common molecular dynamics engines such as GROMACS, AMBER, NAMD and other simulation codes.
Subsamplers for obtaining uncorrelated samples from timeseries data (including extracting independent, equilibrated samples Chodera2016 as implemented in the pymbar package).
Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) Shirts2008 and BAR (from pymbar) and thermodynamic integration (TI).

How to Cite

If you use this software in your research, please cite it as follows:

Wu, Z., Dotson, D. L., Alibay, I., Allen, B. K., Barhaghi, M. S., Hénin, J., Joseph, T. T.,
Kenney, I. M., Lee, H., Li, H., Lim, V., Liu, S., Marson, D., Merz, P. T., Schlaich, A.,
Mobley, D., Shirts, M. R., Beckstein, O. (2024).
alchemlyb: the simple alchemistry library.
Journal of Open Source Software, 9(101), 6934.
https://doi.org/10.21105/joss.06934

Documentation

The documentation is hosted on Read the Docs.

Installation

Install via pip from PyPi (alchemlyb):

bash pip install alchemlyb

or as a conda package from the conda-forge (alchemlyb) channel:

bash conda install -c conda-forge alchemlyb

Update with pip:

bash pip install --update alchemlyb

or with conda run:

bash conda update -c conda-forge alchemlyb

to get the latest released version.

Getting involved

Contributions of all kinds are very welcome.

If you have questions or want to discuss alchemlyb please post in the alchemlyb Discussions.

If you have bug reports or feature requests then please get in touch with us through the Issue Tracker.

We also welcome code contributions: have a look at our Developer Guide. Open an issue with the proposed fix or change in the Issue Tracker and submit a pull request against the alchemistry/alchemlyb GitHub repository.

References

Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics 129, 124105.
Chodera, J.D. (2016). A Simple Method for Automated Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation 12, 1799–1805.

Owner

Name: alchemistry.org
Login: alchemistry
Kind: organization

Website: http://alchemistry.org
Repositories: 8
Profile: https://github.com/alchemistry

Advancing alchemical free energy calculations for small molecule design

JOSS Publication

alchemlyb: the simple alchemistry library

Published

September 26, 2024

DOI

10.21105/joss.06934

Volume 9, Issue 101, Page 6934

Authors

Zhiyi Wu

Exscientia plc, Schroedinger Building, Oxford, United Kingdom

David L. Dotson

Department of Physics, Arizona State University, Tempe, Arizona, United States of America, Datryllic LLC, Phoenix, Arizona, United States of America (present affiliation)

Irfan Alibay

Open Free Energy, Open Molecular Software Foundation, Davis, California, United States

Bryce K. Allen

Differentiated Therapeutics, San Diego, CA

Mohammad Soroush Barhaghi

Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan, United States of America

Jérôme Hénin

Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France

Thomas T. Joseph

Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

Ian M. Kenney

Department of Physics, Arizona State University, Tempe, Arizona, United States of America

Hyungro Lee

Pacific Northwest National Laboratory, Richland, Washington, United States of America

Haoxi Li

UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States of America

Victoria Lim

Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, Irvine, California, United States of America

Shuai Liu

Silicon Therapeutics LLC, Boston, United States of America

Domenico Marson

Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy

Pascal T. Merz

PM Scientific Consulting, Basel, Switzerland

Alexander Schlaich

Stuttgart Center for Simulation Science (SC SimTech) & Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany

David Mobley

Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, Irvine, California, United States of America

Michael R. Shirts

University of Colorado Boulder, Boulder, Colorado, United States of America

Oliver Beckstein

Department of Physics, Arizona State University, Tempe, Arizona, United States of America, Center for Biological Physics, Arizona State University, Tempe, AZ, United States of America

Editor

Sarath Menon

Citation (CITATION.cff)

# -*- coding: utf-8 -*-
# This CITATION.cff file was initially generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: 'alchemlyb: the simple alchemistry library'
message: >-
  If you use this software, please cite it using the
  preferred citation (JOSS DOI 10.21105/joss.06934) together
  with any other references.
type: software
authors:
  - email: david@datryllic.com
    given-names: David L.
    family-names: Dotson
    orcid: 'https://orcid.org/0000-0001-5879-2942'
    affiliation: Datryllic LLC
  - given-names: Ian M.
    family-names: Kenney
    orcid: 'https://orcid.org/0000-0002-9749-8866'
    affiliation: Kenney Consulting, LLC    
  - given-names: Oliver
    family-names: Beckstein
    email: obeckste@asu.edu
    affiliation: Arizona State University
    orcid: 'https://orcid.org/0000-0003-1340-0831'
  - given-names: Shuai
    family-names: Liu
    orcid: 'https://orcid.org/0000-0002-8632-633X'
    affiliation: Silicon Therapeutics LLC
  - given-names: Travis
    family-names: Jensen
  - given-names: Bryce
    family-names: Allen
    orcid: 'https://orcid.org/0000-0002-0804-8127'
    affiliation: Differentiated Therapeutics
  - given-names: Dominik
    family-names: Wille
    affiliation: Freie Universität Berlin
  - given-names: Victoria
    family-names: Lim
    orcid: 'https://orcid.org/0000-0003-4030-9312'
    affiliation: University of California Irvine
  - given-names: Hyungro
    family-names: Lee
    orcid: 'https://orcid.org/0000-0002-4221-7094'
    affiliation: Pacific Northwest National Laboratory
  - given-names: Mohammad Soroush
    family-names: Barhaghi
    orcid: 'https://orcid.org/0000-0001-8226-7347'
    affiliation: Wayne State University
  - given-names: Zhiyi
    family-names: Wu
    affiliation: Exscientia plc
    orcid: 'https://orcid.org/0000-0002-7615-7851'
    email: william@zhiyiwu.me
  - given-names: Wei-Tse
    family-names: Hsu
    orcid: https://orcid.org/0000-0001-6167-5480
    affiliation: University of Colorado Boulder    
  - given-names: Alexander
    family-names: Schlaich
    orcid: 'https://orcid.org/0000-0002-4250-363X'
    affiliation: University of Stuttgart
  - given-names: Jérôme
    family-names: Hénin
    orcid: 'https://orcid.org/0000-0003-2540-4098'
    affiliation: CNRS
  - given-names: Thomas T.
    family-names: Joseph
    orcid: 'https://orcid.org/0000-0003-1323-3244'
    affiliation: University of Pennsylvania
  - given-names: Irfan
    family-names: Alibay
    orcid: 'https://orcid.org/0000-0001-5787-9130'
    affiliation: Open Molecular Software Foundation
  - given-names: Pascal T.
    family-names: Merz
    affiliation: PM Scientific Consulting
    orcid: 'https://orcid.org/0000-0002-7045-8725'
  - given-names: Domenico
    family-names: Marson
    orcid: 'https://orcid.org/0000-0003-1839-9868'
    affiliation: University of Trieste
  - given-names: Shujie
    family-names: Fan
    orcid: 'https://orcid.org/0000-0002-0271-2760'
    affiliation: Arizona State University
  - given-names: Jan
    family-names: Janssen
    affiliation: Max-Planck-Institut for Sustainable Materials
    orcid: 'https://orcid.org/0000-0001-9948-7119'
  - given-names: Haoxi
    family-names: Li
    orcid: 'https://orcid.org/0009-0004-8369-1042'
    affiliation: University of North Carolina
  - given-names: Helmut
    family-names: Carter
    orcid: https://orcid.org/0000-0003-0273-4107    
    affiliation: City University of New York
  - given-names: David
    family-names: Mobley
    orcid: 'https://orcid.org/0000-0002-1083-5533'
    affiliation: University of California Irvine    
  - given-names: Michael R.
    family-names: Shirts
    orcid: 'https://orcid.org/0000-0003-3249-1097'
    affiliation: University of Colorado Boulder
  - given-names: Jennifer A.
    family-names: Clark
    orcid: https://orcid.org/0000-0003-4897-5651
    affiliation: National Institute of Standards and Technology
identifiers:
  - type: swh
    value: 'swh:1:dir:4cd266754be413312ee7ef3f1f7fbe05b38192cf'
    description: >-
      The Software Heritage identifier for the top level
      directory of the repository.
repository-code: 'https://github.com/alchemistry/alchemlyb'
url: 'https://alchemlyb.readthedocs.io'
abstract: >-
  alchemlyb is an open-source Python software package for
  the analysis of alchemical free energy calculations. Its
  functionality contains individual composable building
  blocks for all aspects of a full typical free energy
  analysis workflow, starting with the extraction of raw
  data from the output of diverse molecular simulation
  packages, moving on to data preprocessing tasks such as
  decorrelation of time series, using various estimators to
  derive free energy estimates from simulation samples, and
  finally providing quality analysis tools for data
  convergence checking and visualization. alchemlyb also
  contains high-level end-to-end workflows that combine
  multiple building blocks into a user-friendly analysis
  pipeline from the initial data input stage to the final
  results.
keywords:
  - Python
  - free energy
  - molecular dynamics
  - alchemistry
license: BSD-3-Clause
preferred-citation:
  title: 'alchemlyb: the simple alchemistry library'
  authors:
    - given-names: Zhiyi
      family-names: Wu
      affiliation: Exscientia plc
      orcid: 'https://orcid.org/0000-0002-7615-7851'
      email: william@zhiyiwu.me  
    - given-names: David L.
      family-names: Dotson
      orcid: 'https://orcid.org/0000-0001-5879-2942'
      affiliation: Arizona State University
    - given-names: Irfan
      family-names: Alibay
      orcid: 'https://orcid.org/0000-0001-5787-9130'
      affiliation: Open Molecular Software Foundation
    - given-names: Bryce
      family-names: Allen
      orcid: 'https://orcid.org/0000-0002-0804-8127'
      affiliation: Differentiated Therapeutics
    - given-names: Mohammad Soroush
      family-names: Barhaghi
      orcid: 'https://orcid.org/0000-0001-8226-7347'
      affiliation: Wayne State University
    - given-names: Jérôme
      family-names: Hénin
      orcid: 'https://orcid.org/0000-0003-2540-4098'
      affiliation: CNRS
    - given-names: Thomas T.
      family-names: Joseph
      orcid: 'https://orcid.org/0000-0003-1323-3244'
      affiliation: University of Pennsylvania      
    - given-names: Ian M.
      family-names: Kenney
      orcid: 'https://orcid.org/0000-0002-9749-8866'
      affiliation: Arizona State University
    - given-names: Hyungro
      family-names: Lee
      orcid: 'https://orcid.org/0000-0002-4221-7094'
      affiliation: Pacific Northwest National Laboratory
    - given-names: Haoxi
      family-names: Li
      orcid: 'https://orcid.org/0009-0004-8369-1042'
      affiliation: University of North Carolina      
    - given-names: Victoria
      family-names: Lim
      orcid: 'https://orcid.org/0000-0003-4030-9312'
      affiliation: University of California Irvine      
    - given-names: Shuai
      family-names: Liu
      orcid: 'https://orcid.org/0000-0002-8632-633X'
      affiliation: Silicon Therapeutics LLC
    - given-names: Domenico
      family-names: Marson
      orcid: 'https://orcid.org/0000-0003-1839-9868'
      affiliation: University of Trieste
    - given-names: Pascal T.
      family-names: Merz
      affiliation: PM Scientific Consulting
      orcid: 'https://orcid.org/0000-0002-7045-8725'      
    - given-names: Alexander
      family-names: Schlaich
      orcid: 'https://orcid.org/0000-0002-4250-363X'
      affiliation: University of Stuttgart
    - given-names: David
      family-names: Mobley
      orcid: 'https://orcid.org/0000-0002-1083-5533'
      affiliation: University of California Irvine
    - given-names: Michael R.
      family-names: Shirts
      orcid: 'https://orcid.org/0000-0003-3249-1097'
      affiliation: University of Colorado Boulder
    - given-names: Oliver
      family-names: Beckstein
      email: obeckste@asu.edu
      affiliation: Arizona State University
      orcid: 'https://orcid.org/0000-0003-1340-0831'
  type: 'article'
  year: 2024
  journal: 'Journal of Open Source Software'
  doi: '10.21105/joss.06934'
  pages: '6934'
  volume: '9'
  number: '101'
references:
  - title: Statistically optimal analysis of samples from multiple equilibrium states
    authors:
      - family-names: Shirts
        given-names: Michael R
      - family-names: Chodera
        given-names: John D
    type: 'article'
    pages: '124105'
    year: '2008'
    journal: Journal of Chemical Physics
    doi: '10.1063/1.2978177'
  - title: A Simple Method for Automated Equilibration Detection in Molecular Simulations
    authors:
      - family-names: Chodera
        given-names: John D.
    type: 'article'
    pages: '1799–1805'
    year: '2016'
    journal: 'Journal of Chemical Theory and Computation'
    doi: '10.1021/acs.jctc.5b00784'

GitHub Events

Total

Issues event: 13
Watch event: 19
Delete event: 3
Issue comment event: 29
Push event: 24
Pull request review comment event: 41
Pull request review event: 42
Pull request event: 14
Fork event: 3
Create event: 3

Last Year

Issues event: 13
Watch event: 19
Delete event: 3
Issue comment event: 29
Push event: 24
Pull request review comment event: 41
Pull request review event: 42
Pull request event: 14
Fork event: 3
Create event: 3

Committers

Last synced: 5 months ago

All Time

Total Commits: 358
Total Committers: 24
Avg Commits per committer: 14.917
Development Distribution Score (DDS): 0.712

Past Year

Commits: 30
Committers: 6
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
Oliver Beckstein	o**t@g**m	103
David Dotson	d**l@g**m	92
Zhiyi Wu	z**u@e**i	81
harlor	h**r@w**e	24
Domenico Marson	d**7@g**m	11
Ian Kenney	i**y@a**u	8
shuai	s**5@g**m	7
Hyungro Lee	h**e@g**m	6
trje3733	t**3@c**u	6
Jennifer A Clark	j**3@g**m	4
Victoria Lim	l**a@g**m	3
brycestx	b**e@s**m	1
Alexander Schlaich	s**h@i**e	1
Irfan Alibay	I****y	1
Isaac Spackman	8****n	1
Jérôme Hénin	h**j@g**m	1
Mohammad Soroush Barhaghi	f**4@w**u	1
Pascal Merz	p**z@m**m	1
Tom Joseph	t****h	1
Wei-Tse Hsu	w****1	1
Yuxuan Zhuang	y**g@s**u	1
evidencebp	i**t@g**m	1
helmut carter	7****r	1
hl2500	4****0	1

Committer Domains (Top 20 + Academic)

stanford.edu: 1 me.com: 1 wayne.edu: 1 icp.uni-stuttgart.de: 1 silicontx.com: 1 colorado.edu: 1 asu.edu: 1 exscientia.ai: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 106
Total pull requests: 111
Average time to close issues: 8 months
Average time to close pull requests: 26 days
Total issue authors: 29
Total pull request authors: 18
Average comments per issue: 3.77
Average comments per pull request: 3.57
Merged pull requests: 102
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 22
Pull requests: 22
Average time to close issues: 19 days
Average time to close pull requests: 11 days
Issue authors: 10
Pull request authors: 6
Average comments per issue: 1.64
Average comments per pull request: 2.73
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

orbeckst (34)
xiki-tempula (29)
DrDomenicoMarson (11)
ianmkenney (4)
jaclark5 (3)
davidlmobley (2)
DDGmichigan (2)
dotsdl (2)
schuhmc (1)
josiahbones (1)
evidencebp (1)
ECNUwangjn (1)
danielguion (1)
9527567 (1)
fr-0zt (1)

Pull Request Authors

xiki-tempula (75)
orbeckst (26)
DrDomenicoMarson (10)
jaclark5 (10)
jhenin (4)
dotsdl (4)
evidencebp (4)
helmutcarter (2)
msoroush (2)
IAlibay (2)
yuxuanzhuang (2)
ptmerz (2)
spackman (2)
hl2500 (2)
brycestx (2)

Top Labels

Issue Labels

docs (13) paper (11) CI (11) AMBER (11) release (10) estimators (10) bug (9) parsers (8) help wanted (8) testing (8) enhancement (7) preprocessors (5) logging (4) installation (4) question (3) workflows (3) wontfix (3) NAMD (1) convergence (1) visualisation (1) GROMACS (1) persistence (1)

Pull Request Labels

docs (5) paper (4) enhancement (4) parsers (3) preprocessors (3) estimators (2) release (1) LAMMPS (1)

Packages

Total packages: 2
Total downloads:
- pypi 87,384 last-month
Total docker downloads: 93

Total dependent packages: 3
(may contain duplicates)
Total dependent repositories: 9
(may contain duplicates)
Total versions: 26
Total maintainers: 3

pypi.org: alchemlyb

the simple alchemistry library

Homepage: https://github.com/alchemistry/alchemlyb
Documentation: https://alchemlyb.readthedocs.io/
License: BSD
Latest release: 2.4.1
published over 1 year ago

Versions: 23
Dependent Packages: 3
Dependent Repositories: 8
Downloads: 87,384 Last month
Docker Downloads: 93

Rankings

Dependent packages count: 2.4%

Docker downloads count: 3.4%

Dependent repos count: 5.2%

Average: 6.1%

Downloads: 13.4%

Maintainers (3)

dotsdl Oliver.Beckstein wuzhiyi

Last synced: 4 months ago

conda-forge.org: alchemlyb

alchemlyb is an open-source Python software package for the analysis of alchemical free energy calculations. Its functionality contains individual composable building blocks for all aspects of a full typical free energy analysis workflow, starting with the extraction of raw data from the output of diverse molecular simulation packages, moving on to data preprocessing tasks such as decorrelation of time series, using various estimators to derive free energy estimates from simulation samples, and finally providing quality analysis tools for data convergence checking and visualization. alchemlyb also contains high-level end-to-end workflows that combine multiple building blocks into a user-friendly analysis pipeline from the initial data input stage to the final results.

Homepage: https://github.com/alchemistry/alchemlyb
License: BSD-3-Clause
Latest release: 1.0.0
published about 3 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 1

Rankings

Dependent repos count: 24.3%

Forks count: 27.6%

Stargazers count: 30.3%

Average: 33.5%

Dependent packages count: 51.6%

Last synced: 4 months ago

alchemlyb

Science Score: 100.0%

Keywords

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

alchemlyb: the simple alchemistry library

How to Cite

Documentation

Installation

Getting involved

References

Owner

JOSS Publication

alchemlyb: the simple alchemistry library

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

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All Time

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pypi.org: alchemlyb

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conda-forge.org: alchemlyb

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