the simple alchemistry library

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for dotsdl from gravatar.com dotsdl Avatar for Oliver.Beckstein from gravatar.com Oliver.Beckstein Avatar for wuzhiyi from gravatar.com wuzhiyi

Unverified details

These details have not been verified by PyPI
Meta
Classifiers

Project description

Zenodo DOI Documentation Build Status Code coverage

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

  1. Parsers for extracting raw data from output files of common molecular dynamics engines such as GROMACS, AMBER, NAMD and other simulation codes.

  2. Subsamplers for obtaining uncorrelated samples from timeseries data.

  3. Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) [Shirts2008] and thermodynamic integration (TI).

In particular, it uses internally the excellent pymbar library for performing MBAR and extracting independent, equilibrated samples [Chodera2016].

[Shirts2008]

Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics 129, 124105.

[Chodera2016]

Chodera, J.D. (2016). A Simple Method for Automated Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation 12, 1799–1805.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for dotsdl from gravatar.com dotsdl Avatar for Oliver.Beckstein from gravatar.com Oliver.Beckstein Avatar for wuzhiyi from gravatar.com wuzhiyi

Unverified details

These details have not been verified by PyPI
Meta
Classifiers

Release history Release notifications | RSS feed

2.4.1

2.4.1rc1 pre-release

2.4.0

2.3.2

2.3.1

2.3.0

2.2.0

2.1.0

2.0.1

2.0.0

1.0.1

1.0.0

0.7.0

0.6.0

0.5.1

0.5.0

This version

0.4.2

0.4.1

0.4.0

0.3.1

0.3.0

0.1.0

0.1.0a0 pre-release

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

alchemlyb-0.4.2.tar.gz (47.5 kB view details)

Uploaded Source

Built Distribution

alchemlyb-0.4.2-py2.py3-none-any.whl (45.0 kB view details)

Uploaded Python 2 Python 3

File details

Details for the file alchemlyb-0.4.2.tar.gz.

File metadata

  • Download URL: alchemlyb-0.4.2.tar.gz
  • Upload date:
  • Size: 47.5 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.4.1 importlib_metadata/4.4.0 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.0 CPython/3.6.13

File hashes

Hashes for alchemlyb-0.4.2.tar.gz
Algorithm Hash digest
SHA256 e0403642267e6d5c353fa8fe72adc73f7180d6cf0837b2a9653da23630f9e400
MD5 27d17e3b8dd250099332e6482640adc1
BLAKE2b-256 1d6a38df8d8dde657c7c25bbc79c55e637f59bbcc6110f91d823ff7fd19ae2c7

See more details on using hashes here.

File details

Details for the file alchemlyb-0.4.2-py2.py3-none-any.whl.

File metadata

  • Download URL: alchemlyb-0.4.2-py2.py3-none-any.whl
  • Upload date:
  • Size: 45.0 kB
  • Tags: Python 2, Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.4.1 importlib_metadata/4.4.0 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.0 CPython/3.6.13

File hashes

Hashes for alchemlyb-0.4.2-py2.py3-none-any.whl
Algorithm Hash digest
SHA256 ad2a49ec0c5dc8c8a7dc56f3eb6f20b942b973d35146bd8fbb1ea47c66e7c7d6
MD5 418846fdb83922a0c633cfc932351b77
BLAKE2b-256 8fe9b822f710930a2b6dd463ce9c76ab703440759a12b9a6f0dbabd480b9c892

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page