Data

Tools

Indexes

Applications

Experiments

Open Source Science

geomm

Mirror of main geomm repository. Simple and stupid library for strictly geometric operations (zero-knowledge of topology) common to computational biology and chemistry. https://adicksonlab.github.io/geomm/

https://github.com/adicksonlab/geomm

Science Score: 46.0%

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
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.3%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Mirror of main geomm repository. Simple and stupid library for strictly geometric operations (zero-knowledge of topology) common to computational biology and chemistry. https://adicksonlab.github.io/geomm/

Basic Info
  • Host: GitHub
  • Owner: ADicksonLab
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 5.25 MB
Statistics
  • Stars: 4
  • Watchers: 4
  • Forks: 1
  • Open Issues: 7
  • Releases: 2
Created about 8 years ago · Last pushed 9 months ago
Metadata Files
Readme License Authors Zenodo

README.org 

* geomm


# badges

#+begin_export html
DOI
#+end_export

# end badges

A simple no-nonsense library for computing common geometry on
macromolecular systems.

This library aims to work completely on numpy arrays and knows nothing
about molecule or system topologies, atom types, or other "real world"
properties.

You only need to provide atom coordinates, atom indices (for molecule,
group, molecule selections etc.), and other parameters for functions.

Thus it aims to be more like numpy or scipy itself than a typical
macromolecular software library, except that the particular routines
and functions are usually found in that context.


** Docs and Info

See the [[file:./info][info]] directory for the documentation and history of the
project. The [[file:./info/README.org][README]] serves as an index. These files are (mostly) in
emacs org-mode and serve as the primary source of documentation. 

Other "rendered" versions may exist and be published. The default
location is at
[[https://salotz.github.io/geomm][adicksonlab.github.io/geomm]]
in HTML rendered with Sphinx.

** COMMENT Maintenance Intent

** Developing

See the [[file:sphinx/source/dev_guide.org][Developers Guide]] for developing.


** Other Info

Current [[https://zenodo.org/badge/latestdoi/125404701][Zenodo DOI]].

Owner

  • Name: ADicksonLab
  • Login: ADicksonLab
  • Kind: organization

GitHub Events

Total
  • Issue comment event: 1
  • Member event: 1
  • Push event: 2
  • Pull request event: 1
  • Create event: 2
Last Year
  • Issue comment event: 1
  • Member event: 1
  • Push event: 2
  • Pull request event: 1
  • Create event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 104
  • Total Committers: 4
  • Avg Commits per committer: 26.0
  • Development Distribution Score (DDS): 0.413
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Samuel Lotz s****z@s****o 61
salotz s****z@s****o 32
Alex Dickson a****d@m****u 8
Nazanin n****n@u****u 3
Committer Domains (Top 20 + Academic)
salotz.info: 2 urmia.bch.msu.edu: 1 msu.edu: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 0
  • Total pull requests: 10
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.2
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 8
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 40 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • dependabot[bot] (8)
  • alexrd (1)
  • kilince (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (8)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 186 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 4
  • Total versions: 12
  • Total maintainers: 2
pypi.org: geomm

A simple no-nonsense library for computing common geometry on macromolecular systems.

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 4
  • Downloads: 186 Last month
Rankings
Dependent repos count: 7.5%
Dependent packages count: 10.1%
Average: 17.4%
Forks count: 22.6%
Stargazers count: 23.1%
Downloads: 23.5%
Maintainers (2)
salotz alexrd
Last synced: 8 months ago

Dependencies

.jubeo/requirements.in pypi
  • coverage *
  • fabric *
  • ghp-import *
  • invoke *
  • jubeo *
  • lxdock *
  • pip-tools *
  • pytest *
  • pytest-runner *
  • versioneer *
.jubeo/requirements.txt pypi
  • attrs ==19.3.0
  • bcrypt ==3.1.7
  • certifi ==2020.4.5.1
  • cffi ==1.14.0
  • chardet ==3.0.4
  • click ==7.1.2
  • colorlog ==2.10.0
  • coverage ==5.1
  • cryptography ==2.9.2
  • fabric ==2.5.0
  • ghp-import ==0.5.5
  • gitdb ==4.0.5
  • gitpython ==3.1.2
  • hyperlink ==19.0.0
  • idna ==2.9
  • invoke ==1.4.1
  • jubeo ==0.0.3a0.dev0
  • lxdock ==0.4.1
  • more-itertools ==8.2.0
  • packaging ==20.3
  • paramiko ==2.7.1
  • pbr ==5.4.5
  • pip-tools ==5.1.2
  • pluggy ==0.13.1
  • py ==1.8.1
  • pycparser ==2.20
  • pylxd ==2.2.10
  • pynacl ==1.3.0
  • pyparsing ==2.4.7
  • pytest ==5.4.2
  • pytest-runner ==5.2
  • python-dateutil ==2.8.1
  • python-dotenv ==0.13.0
  • pyyaml ==3.13
  • requests ==2.23.0
  • requests-toolbelt ==0.9.1
  • requests-unixsocket ==0.2.0
  • six ==1.14.0
  • smmap ==3.0.4
  • toml ==0.10.0
  • urllib3 ==1.25.9
  • versioneer ==0.18
  • voluptuous ==0.11.7
  • wcwidth ==0.1.9
  • ws4py ==0.5.1
.jubeo/tools.requirements.txt pypi
  • pip *
bootstrap.requirements.txt pypi
  • invoke *
envs/base/requirements.in pypi
  • numpy *
  • pint *
  • scipy *
envs/base/requirements.txt pypi
  • numpy ==1.18.1
  • pint ==0.10.1
  • scipy ==1.4.1
envs/dev/requirements.in pypi
  • argcomplete * development
  • coverage * development
  • cython * development
  • fabric * development
  • flake8 * development
  • guzzle_sphinx_theme * development
  • invoke * development
  • ipython * development
  • lizard * development
  • nbsphinx * development
  • notebook * development
  • numpy * development
  • pdbpp * development
  • pip * development
  • pip-tools * development
  • pipdeptree * development
  • pytest * development
  • pytest-benchmark * development
  • pytest-cov * development
  • pytest-datadir * development
  • pytest-profiling * development
  • pytest-runner * development
  • remote-pdb * development
  • sphinx * development
  • sphinxcontrib-napoleon * development
  • tox * development
  • twine * development
  • wheel * development
envs/dev/requirements.txt pypi
  • 137 dependencies
envs/dev/tools.requirements.txt pypi
  • pip * development
envs/test_install/tools.requirements.txt pypi
  • pip * test
info/examples/format_conversion/conversion.requirements.txt pypi
  • mdtraj *
  • openpyxl *
  • pandas *
  • tables *
  • wepy >=1.0.0
requirements.in pypi
  • numpy *
  • pint *
  • scipy *
tools.requirements.txt pypi
  • invoke *
  • pip-tools *
envs/base/self.requirements.txt pypi
envs/dev/self.requirements.txt pypi
pyproject.toml pypi
setup.py pypi