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Open Source Science

https://github.com/tunneling-group/aqua-duct

https://github.com/tunneling-group/aqua-duct

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: TUNNELING-GROUP
  • License: gpl-3.0
  • Language: Python
  • Default Branch: brave-new-branch
  • Size: 267 MB
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 1
  • Open Issues: 11
  • Releases: 0
Created almost 8 years ago · Last pushed 12 months ago
Metadata Files
Readme License

README.md

AQUA-DUCT

Aqua-Duct a new tool facilitating analysis of the flow of solvent molecules in molecular dynamic simulations.

Visit our homepage at aquaduct.pl.

Overview

Aqua-Duct comprises of several applications build on top of aquaduct Python module:

  1. valve - performs most of core calculations including tracing of molecules.
  2. kraken - performs additional analysis of results.
  3. pond - calculates pockets, hotspots, and energy profiles.

Aqua-Duct comes also with simple GUI interface - valveconfig - allowing to setup calculations in a convenient way.

Availability

Aqua-Duct is licensed under GNU GPL v3 license <https://www.gnu.org/licenses/gpl-3.0.en.html>.

Source code is available at github.com/TUNNELING-GROUP/aqua-duct.

Summary of the most important changes is available in our changelog.

Installation

Aqua-Duct can be easily installed via PyPi:

pip install aquaduct

Detailed instructions on Aqua-Duct installation are available at aquaduct.pl/installation.

To start using Aqua-Duct type:

valve.py --help

Installing in Python3.9 with requirements.txt

You can also install Aqua-Duct using the requirements.txt file in a Python 3.9:

sh pip install -r requirements.txt

This will install all necessary dependencies for Aqua-Duct.

NOTE:

Using a virtual environment is recommended to manage dependencies and avoid conflicts with other Python packages.

Troubleshooting

If you encounter any problems with installation do not hesitate to contact us at info@aquaduct.pl. We are REALLY willing to help!

You can also contact us at github.com/TUNNELING-GROUP/aqua-duct.

Documentation

Documentation can be found on our homepage aquaduct.pl/documentation.

The most recent documentation is also available at TUNNELING-GROUP.github.io/aqua-duct.

GitHub Events

Total
  • Issues event: 5
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 3
  • Member event: 5
  • Push event: 24
  • Pull request event: 7
  • Create event: 13
Last Year
  • Issues event: 5
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 3
  • Member event: 5
  • Push event: 24
  • Pull request event: 7
  • Create event: 13

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 1,151
  • Total Committers: 11
  • Avg Commits per committer: 104.636
  • Development Distribution Score (DDS): 0.492
Top Committers
Name Email Commits
Tomasz Magdziarz t****m@w****l 585
Tomasz Magdziarz t****z@t****l 332
Michał Banas b****r@g****m 169
ptero g****d@o****l 28
Michał s****3@g****m 11
robert r****t@r****x 10
agataraczynska a****3@g****m 8
yourKara k****a@a****c 3
b4naser G****K 2
robert r****t@g****m 2
ADMIN u****r@t****x 1
Committer Domains (Top 20 + Academic)
airmail.cc: 1 o2.pl: 1 tunnelinggroup.pl: 1 wp.pl: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 10
  • Total pull requests: 5
  • Average time to close issues: about 23 hours
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 6
  • Pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 3
View more stats
Top Authors
Issue Authors
  • tljm (6)
  • rubinanoor9 (1)
  • djami97 (1)
  • WXYWD (1)
  • pruethemann (1)
Pull Request Authors
  • dependabot[bot] (5)
  • tljm (2)
  • 0xBytefuzz (2)
Top Labels
Issue Labels
bug (1) enhancement (1) need investigation (1)
Pull Request Labels
dependencies (5) python (5)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 124 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 22
  • Total maintainers: 2
pypi.org: aquaduct

Tracing molecules in MD simulation

  • Versions: 22
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 124 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.6%
Average: 23.9%
Stargazers count: 27.8%
Forks count: 29.8%
Downloads: 30.1%
Maintainers (2)
tljm TunnelingGroup
Last synced: 11 months ago

Dependencies

src/setup.py pypi
  • MDAnalysis *
  • numpy >=1.10.0
  • scikit-learn >=0.16.0
  • scipy >=0.17.1
Pipfile pypi
  • GridDataFormats ==1.0.2
  • MDAnalysis ==2.7.0
  • aquaduct ==1.0.11
  • cftime ==1.6.4
  • contourpy ==1.2.1
  • cycler ==0.12.1
  • fasteners ==0.19
  • fonttools ==4.54.1
  • importlib_resources ==6.4.5
  • joblib ==1.1.1
  • kiwisolver ==1.4.7
  • matplotlib ==3.8.4
  • mda-xdrlib ==0.2.0
  • mmtf-python ==1.1.3
  • mrcfile ==1.5.3
  • msgpack ==1.1.0
  • netCDF4 ==1.5.8
  • numpy ==1.22.4
  • packaging ==24.1
  • pillow ==10.4.0
  • pyparsing ==3.1.4
  • python-dateutil ==2.9.0.post0
  • scikit-learn ==1.1.1
  • scipy ==1.7.1
  • six ==1.16.0
  • threadpoolctl ==3.5.0
  • tqdm ==4.66.5
  • zipp ==3.20.2
requirements.txt pypi
  • GridDataFormats ==1.0.2
  • MDAnalysis ==2.7.0
  • aquaduct ==1.0.11
  • cftime ==1.6.4
  • contourpy ==1.2.1
  • cycler ==0.12.1
  • fasteners ==0.19
  • fonttools ==4.54.1
  • importlib_resources ==6.4.5
  • joblib ==1.1.1
  • kiwisolver ==1.4.7
  • matplotlib ==3.8.4
  • mda-xdrlib ==0.2.0
  • mmtf-python ==1.1.3
  • mrcfile ==1.5.3
  • msgpack ==1.1.0
  • netCDF4 ==1.5.8
  • numpy ==1.22.4
  • packaging ==24.1
  • pillow ==10.4.0
  • pyparsing ==3.1.4
  • python-dateutil ==2.9.0.post0
  • scikit-learn ==1.1.1
  • scipy ==1.7.1
  • six ==1.16.0
  • threadpoolctl ==3.5.0
  • tqdm ==4.66.5
  • zipp ==3.20.2