safep

Tools for Analyzing and Debugging (SA)FEP calculations. See also the SAFEP Tutorial: https://github.com/jhenin/SAFEP_tutorial/tree/main Documentation: https://safep-alchemy.readthedocs.io/en/latest/

https://github.com/branniganlab/safep

Science Score: 44.0%

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

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (8.9%) to scientific vocabulary

Keywords

free-energy-perturbation molecular-dynamics-simulation safep

Last synced: 9 months ago · JSON representation ·

Repository

Tools for Analyzing and Debugging (SA)FEP calculations. See also the SAFEP Tutorial: https://github.com/jhenin/SAFEP_tutorial/tree/main Documentation: https://safep-alchemy.readthedocs.io/en/latest/

Basic Info

Host: GitHub
Owner: BranniganLab
License: gpl-3.0
Language: Jupyter Notebook
Default Branch: main
Homepage:
Size: 90.9 MB

Statistics

Stars: 6
Watchers: 5
Forks: 1
Open Issues: 23
Releases: 3

Topics

free-energy-perturbation molecular-dynamics-simulation safep

Created almost 5 years ago · Last pushed 10 months ago

Metadata Files

Readme License Citation

README.md

SAFEP

See detailed documentation here: https://safep-alchemy.readthedocs.io/en/latest/

SAFEP-related scripts and tools

These scripts and notebooks are broadly applicable to FEP analysis.

Sample Notebooks:

AlternativeParser_nBAR uses less RAM to read large fepout files. Rarely useful unless each fepout file is extremely large.
BAREstimatorBasic: General use FEP analysis. Includes cumulative dG estimates, error estimates, and measures of convergence.
BAREstimatorExpanded: Extendend functionality including bootstrapped error estimates, kernel estimation of dL distributions, and more.
BatchBasic: Like BAREstimator_Basic but designed for multiple replicas of the same calculation.

Installation:

Clone this repository
Enter the repository directory
Run pip install .

Run pip install git+https://github.com/BranniganLab/safep.git

Owner

Name: Brannigan Lab
Login: BranniganLab
Kind: organization

Repositories: 4
Profile: https://github.com/BranniganLab

Citation (citation.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Hénin"
  given-names: "Jérôme"
- family-names: "Santiago"
  given-names: "Ezry"
- family-names: "Joseph"
  given-names: "Tom"
- family-names: "Brannigan"
  given-names: "Grace"

title: "safep"
version: 0.1.0
date-released: 2022-01-15
url: "https://github.com/BranniganLab/safep"

GitHub Events

Total

Create event: 4
Release event: 1
Issues event: 8
Watch event: 1
Delete event: 4
Issue comment event: 4
Push event: 16
Pull request review comment event: 31
Pull request review event: 35
Pull request event: 7

Last Year

Create event: 4
Release event: 1
Issues event: 8
Watch event: 1
Delete event: 4
Issue comment event: 4
Push event: 16
Pull request review comment event: 31
Pull request review event: 35
Pull request event: 7

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 2
Total pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: about 1 month
Total issue authors: 2
Total pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: about 1 month
Issue authors: 2
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

EzryStIago (8)
jhenin (5)
ttjoseph (1)

Pull Request Authors

EzryStIago (10)
jhenin (1)

Top Labels

Issue Labels

enhancement (8) bug (3) housekeeping (2)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 11 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 2
Total maintainers: 1

pypi.org: safep

Tools for Analyzing and Debugging (SA)FEP calculations

Homepage: https://github.com/BranniganLab/safep
Documentation: https://safep.readthedocs.io/
License: GNU General Public License v3 or later (GPLv3+)
Latest release: 0.1.4
published 10 months ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 11 Last month

Rankings

Dependent packages count: 9.6%

Average: 36.5%

Dependent repos count: 63.4%

Maintainers (1)

Ezry