perses

Experiments with expanded ensembles to explore chemical space

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 6 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
2 of 37 committers (5.4%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (18.7%) to scientific vocabulary

Keywords

expanded-ensembles free-energy-perturbation molecular-design molecular-dynamics openmm python relative-free-energy simulation

Last synced: 6 months ago · JSON representation ·

Repository

Experiments with expanded ensembles to explore chemical space

Basic Info

Host: GitHub
Owner: choderalab
License: mit
Language: Python
Default Branch: main
Homepage: http://perses.readthedocs.io
Size: 42.9 MB

Statistics

Stars: 192
Watchers: 20
Forks: 50
Open Issues: 229
Releases: 22

Topics

expanded-ensembles free-energy-perturbation molecular-design molecular-dynamics openmm python relative-free-energy simulation

Created about 11 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

Perses

Experiments with expanded ensemble simulation to explore chemical and mutational space.

License

This software is licensed under the MIT license, a permissive open source license.

Notice

Please be aware that this code is made available in the spirit of open science, but is currently pre-alpha--that is, it is not guaranteed to be completely tested or provide the correct results, and the API can change at any time without warning. If you do use this code, do so at your own risk. We appreciate your input, including raising issues about potential problems with the code, but may not be able to address your issue until other development activities have concluded.

Install

See our installation instructions here.

Quick Start

In a fresh conda environment:

$ conda config --add channels conda-forge openeye $ conda install perses openeye-toolkits

Manifest

perses/ - Package containing code for performing expanded ensemble simulations
examples/ - Contains examples for various systems and methods of simulation
attic/ - some old code that may be useful as part of the new setup
devtools/ - Continuous integration and packaging utilities
notes/ - LaTeX notes deriving acceptance criteria and stochastic approximation methods

Contributors

A complete list of contributors can be found at GitHub Insights.

Major contributors include: * Julie M. Behr * Hannah E. Bruce Macdonald * John D. Chodera * Patrick B. Grinaway * Mike M. Henry * Iván J. Pulido * Jaime Rodríguez-Guerra * Dominic A. Rufa * Ivy Zhang

Cite

Please consider citing: * Software:

Rufa, D. A., Zhang, I., Bruce Macdonald, H. E., Grinaway, P. B., Pulido, I., Henry, M. M., Rodríguez-Guerra, J., Wittmann, M., Albanese, S. K., Glass, W. G., Silveira, A., Schaller, D., Naden, L. N., & Chodera, J. D. (2023). Perses (0.10.3). Zenodo. https://doi.org/10.5281/zenodo.8350218

Protein mutations:

Zhang, I., Rufa, D. A., Pulido, I., Henry, M. M., Rosen, L. E., Hauser, K., Singh, S., & Chodera, J. D. (2023). Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. Journal of chemical theory and computation, 19(15), 4863–4882. https://doi.org/10.1021/acs.jctc.3c00333

Small molecule transformations:

Rufa, D. A., Bruce Macdonald, H. E., Fass, J., Wieder, M., Grinaway, P. B., Roitberg, A. E., Isayev, O., & Chodera, J. D. (2020). Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning / molecular mechanics potentials. In bioRxiv (p. 2020.07.29.227959). https://doi.org/10.1101/2020.07.29.227959

Owner

Name: Chodera lab // Memorial Sloan Kettering Cancer Center
Login: choderalab
Kind: organization
Email: john.chodera@choderalab.org
Location: Memorial Sloan-Kettering Cancer Center, Manhattan, NY

Website: http://choderalab.org
Repositories: 269
Profile: https://github.com/choderalab

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Perses
message: Please cite this software using these metadata.
type: software
authors:
  - given-names: Dominic A.
    family-names: Rufa
    orcid: 'https://orcid.org/0000-0003-0930-9445'
  - given-names: Ivy
    family-names: Zhang
    orcid: 'https://orcid.org/0000-0003-0628-6276'
  - given-names: Hannah E.
    family-names: Bruce Macdonald
    orcid: 'https://orcid.org/0000-0002-5562-6866'
  - given-names: Patrick B.
    family-names: Grinaway
    orcid: 'https://orcid.org/0000-0002-9762-4201'
  - given-names: Iván
    family-names: Pulido
    orcid: 'https://orcid.org/0000-0002-7178-8136'
  - given-names: Mike M.
    family-names: Henry
    orcid: 'https://orcid.org/0000-0002-3870-9993'
  - given-names: Jaime
    family-names: Rodríguez-Guerra
    orcid: 'https://orcid.org/0000-0001-8974-1566'
  - given-names: Matt
    family-names: Wittmann
  - given-names: Steven K.
    family-names: Albanese
    orcid: 'https://orcid.org/0000-0003-0973-5030'
  - given-names: William G.
    family-names: Glass
    orcid: 'https://orcid.org/0000-0002-4099-9280'
  - given-names: Ana
    family-names: Silveira
    orcid: 'https://orcid.org/0000-0002-9419-3397'
  - given-names: David
    family-names: Schaller
    orcid: 'https://orcid.org/0000-0002-1881-4518'
  - given-names: Levi N.
    family-names: Naden
    orcid: 'https://orcid.org/0000-0002-3692-5027'
  - given-names: John D.
    family-names: Chodera
    orcid: 'https://orcid.org/0000-0003-0542-119X'

GitHub Events

Total

Issues event: 1
Watch event: 11
Issue comment event: 6
Push event: 18
Pull request event: 1
Fork event: 1
Create event: 1

Last Year

Issues event: 1
Watch event: 11
Issue comment event: 6
Push event: 18
Pull request event: 1
Fork event: 1
Create event: 1

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 3,285
Total Committers: 37
Avg Commits per committer: 88.784
Development Distribution Score (DDS): 0.785

Past Year

Commits: 75
Committers: 7
Avg Commits per committer: 10.714
Development Distribution Score (DDS): 0.56

Top Committers

Name	Email	Commits
pgrinaway	p**y@g**m	705
Hannah Bruce Macdonald	h**d@c**g	452
pgrinaway	w****o	429
John Chodera (MSKCC)	c**j@m**g	396
John Chodera	j**a@c**g	315
dominicrufa	d**a@g**m	314
Julie Behr	j**r@c**g	154
Mike Henry	1**y@u**m	84
Hannah Bruce Macdonald	4**d@u**m	70
juliebehr	j**r@g**m	66
Ivy Zhang	i**g@w**u	52
Ivy Zhang	3**y@u**m	37
dominicrufa	d**a@c**g	30
Iván Pulido	i**o@p**m	23
Matt Wittmann	m**t@g**m	22
Jaime Rodríguez-Guerra	j**p@u**m	21
Patrick Grinaway	p**y@P**l	20
Jaime RGP	j**e@g**m	14
Patrick Grinaway	p**y@P**e	13
brycestx	b**e@s**m	12
William Glass	w**9@g**m	11
dominicrufa	4**a@u**m	7
Iván Pulido	i**s@u**o	7
Iván Pulido	2**s@u**m	6
steven-albanese	s**1@g**m	6
Chodera	c**j@m**g	3
Dominic Rufa	r**d@l**e	3
Hannah Bruce Macdonald	b**h@l**e	3
Ana Silveira	a**a@h**m	2
Saurav Maheshkar	s**r@g**m	1
and 7 more...

Committer Domains (Top 20 + Academic)

choderalab.org: 5 lilac.hpc.private: 3 lt20.hpc.private: 1 lski1985.mskcc.root.mskcc.org: 1 lu05.hpc.private: 1 lt19.hpc.private: 1 mski1776.mskcc.root.mskcc.org: 1 unal.edu.co: 1 silicontx.com: 1 patricks-mbp-2.fios-router.home: 1 wustl.edu: 1 mskcc.org: 1

Issues and Pull Requests

Last synced: over 2 years ago

All Time

Total issues: 74
Total pull requests: 65
Average time to close issues: 6 months
Average time to close pull requests: 5 months
Total issue authors: 13
Total pull request authors: 10
Average comments per issue: 2.41
Average comments per pull request: 4.32
Merged pull requests: 42
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 66
Pull requests: 52
Average time to close issues: 2 months
Average time to close pull requests: about 1 month
Issue authors: 12
Pull request authors: 9
Average comments per issue: 1.98
Average comments per pull request: 3.35
Merged pull requests: 41
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ijpulidos (21)
jchodera (17)
mikemhenry (8)
zhang-ivy (7)
IAlibay (3)
JenkeScheen (3)
sukritsingh (3)
SZhang66 (2)
slochower (2)
arjun-nufc (2)
viktorbelay (1)
hannahbrucemacdonald (1)
jthorton (1)
richardjgowers (1)
dominicrufa (1)

Pull Request Authors

mikemhenry (30)
ijpulidos (14)
zhang-ivy (9)
dotsdl (3)
dominicrufa (2)
jchodera (2)
craabreu (1)
SauravMaheshkar (1)
dwhswenson (1)
kntkb (1)

Top Labels

Issue Labels

priority: high (18) enhancement :sparkles: (11) potential bug :thinking: :bug: (10) priority: low (9) effort: low (9) tests (8) effort: medium (4) bug :bug: (4) help wanted :raised_hand: (2) optimization (2) analysis (2) feature (2) priority: medium (2) benchmarking (1) cleanup (1) blocked (1) question (1)

Pull Request Labels

tests (2) priority: low (2) do not merge (2) bug :bug: (1) documentation :bookmark_tabs: (1) enhancement :sparkles: (1) priority: high (1)

Packages

Total packages: 1
Total downloads: unknown

Total dependent packages: 0
Total dependent repositories: 3
Total versions: 9

conda-forge.org: perses

Experiments with expanded ensemble simulation to explore chemical and mutational space

Homepage: https://github.com/choderalab/perses
License: MIT
Latest release: 0.10.1
published over 3 years ago

Versions: 9
Dependent Packages: 0
Dependent Repositories: 3

Rankings

Dependent repos count: 18.0%

Forks count: 28.2%

Stargazers count: 30.9%

Average: 32.2%

Dependent packages count: 51.6%

Last synced: 6 months ago

Dependencies

.github/workflows/CI.yaml actions

actions/checkout v2 composite
codecov/codecov-action v1 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/rc-check.yaml actions

actions/checkout v2 composite
benc-uk/workflow-dispatch v1 composite
dwhswenson/conda-rc-check main composite

.github/workflows/rc-test.yaml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/self-hosted-gpu-test.yml actions

actions/checkout v2 composite
aws-actions/configure-aws-credentials v1 composite
codecov/codecov-action v1 composite
conda-incubator/setup-miniconda v2 composite
machulav/ec2-github-runner main composite

docs/environment.yml conda

numba
numpy
numpydoc
python
setuptools
sphinx <5

perses

Science Score: 77.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Perses

License

Notice

Install

Quick Start

Manifest

Contributors

Cite

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

conda-forge.org: perses

Rankings

Dependencies