pubchempy

Python wrapper for the PubChem PUG REST API.

https://github.com/mcs07/pubchempy

Science Score: 64.0%

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
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
1 of 10 committers (10.0%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (13.7%) to scientific vocabulary

Keywords

cheminformatics chemistry pubchem python

Keywords from Contributors

bioinformatics protein-structure

Last synced: 4 months ago · JSON representation ·

Repository

Python wrapper for the PubChem PUG REST API.

Basic Info

Host: GitHub
Owner: mcs07
License: mit
Language: Python
Default Branch: main
Homepage: http://docs.pubchempy.org
Size: 517 KB

Statistics

Stars: 457
Watchers: 18
Forks: 119
Open Issues: 33
Releases: 5

Topics

cheminformatics chemistry pubchem python

Created almost 13 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog License Citation Codemeta

PubChemPy

PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.

Installation

Install PubChemPy with pip:

shell pip install pubchempy

Or with conda:

shell conda install -c conda-forge pubchempy

For detailed instructions, see the installation guide.

Example usage

Retrieve a compound by its PubChem Compound Identifier (CID) and print its SMILES and IUPAC name:

```pycon

import pubchempy as pcp comp = pcp.Compound.fromcid(1423) print(comp.smiles) CCCCCCCNC1CCCC1CCCCCCC(=O)O print(comp.iupacname) 7-[2-(heptylamino)cyclopentyl]heptanoic acid ```

Search compounds by name and print the SMILES and molecular weight of the first result:

```pycon

results = pcp.getcompounds("Aspirin", "name") print(results[0].smiles) CC(=O)OC1=CC=CC=C1C(=O)O print(results[0].molecularweight) 180.16 ```

Documentation

Full documentation is available at https://docs.pubchempy.org.

This includes a step-by-step guide on how to use PubChemPy, as well as a complete API reference.

Contributing

Feature ideas and bug reports are welcome on the Issue Tracker.
Fork the source code on GitHub, make changes and file a pull request.

License

PubChemPy is licensed under the MIT license.

Owner

Name: Matt Swain
Login: mcs07
Kind: user
Location: New York, NY
Company: @DEShawResearch

Website: https://matt-swain.com
Twitter: mattswain123
Repositories: 76
Profile: https://github.com/mcs07

Developing software for drug discovery

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software in your work, please cite it using the following metadata."
title: "PubChemPy"
type: software
authors:
  - family-names: "Swain"
    given-names: "Matthew"
    orcid: "https://orcid.org/0000-0001-6428-5189"
version: 1.0.4
doi: "10.5281/zenodo.541438"
date-released: "2017-04-11"
repository-code: "https://github.com/mcs07/PubChemPy"
url: "https://pubchempy.org"
repository-artifact: "https://pypi.org/project/PubChemPy/"
license: "MIT"
license-url: "https://spdx.org/licenses/MIT.html"
identifiers:
  - type: doi
    description: Fixed concept DOI for all versions
    value: "10.5281/zenodo.593126"
abstract: Python package for interacting with the PubChem database via the PUG REST API service.
keywords:
  - cheminformatics
  - chemistry
  - API
  - python
  - pubchem
preferred-citation:
  type: software
  title: "PubChemPy"
  authors:
    - family-names: "Swain"
      given-names: "Matthew"
      orcid: "https://orcid.org/0000-0001-6428-5189"
  version: 1.0.4
  date-released: "2017-04-11"
  doi: "10.5281/zenodo.541438"
  url: "https://pubchempy.org"

CodeMeta (codemeta.json)

{
  "@context": "https://w3id.org/codemeta/3.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "http://edamontology.org/topic_2258",
  "author": [
    {
      "id": "https://orcid.org/0000-0001-6428-5189",
      "type": "Person",
      "email": "m.swain@me.com",
      "familyName": "Swain",
      "givenName": "Matthew"
    }
  ],
  "codeRepository": "https://github.com/mcs07/PubChemPy",
  "dateCreated": "2013-01-05",
  "dateModified": "2017-04-11",
  "datePublished": "2014-01-06",
  "description": "Python package for interacting with the PubChem database via the PUG REST API service.",
  "identifier": "https://doi.org/10.5281/zenodo.541438",
  "keywords": [
    "cheminformatics",
    "chemistry",
    "API",
    "python",
    "pubchem"
  ],
  "license": "https://spdx.org/licenses/MIT",
  "name": "PubChemPy",
  "programmingLanguage": "Python",
  "softwareVersion": "1.0.5",
  "continuousIntegration": "https://github.com/mcs07/PubChemPy/actions",
  "readme": "https://github.com/mcs07/PubChemPy/blob/main/README.md",
  "url": "https://docs.pubchempy.org",
  "issueTracker": "https://github.com/mcs07/PubChemPy/issues",
  "relatedLink": [
    "https://pypi.org/project/PubChemPy/",
    "https://docs.pubchempy.org"
  ]
}

GitHub Events

Total

Issues event: 27
Watch event: 55
Delete event: 20
Issue comment event: 53
Push event: 37
Pull request event: 57
Fork event: 12
Create event: 20

Last Year

Issues event: 27
Watch event: 55
Delete event: 20
Issue comment event: 53
Push event: 37
Pull request event: 57
Fork event: 12
Create event: 20

Committers

Last synced: 8 months ago

All Time

Total Commits: 108
Total Committers: 10
Avg Commits per committer: 10.8
Development Distribution Score (DDS): 0.12

Past Year

Commits: 3
Committers: 2
Avg Commits per committer: 1.5
Development Distribution Score (DDS): 0.333

Top Committers

Name	Email	Commits
Matt Swain	m**n@m**m	95
RickardSjogren	r**9@g**m	4
nbehrnd	n****d	2
huei820504	h**4@g**m	1
Luis Oliveira	3****t	1
Leonardo Lazzaro	l**o@d**r	1
Eka A. Kurniawan	e**n@g**m	1
Björn Dahlgren	b**h@g**m	1
zachcp	z**p@r**u	1
zach powers	z**p@r**u	1

Committer Domains (Top 20 + Academic)

rockefeller.edu: 1 rockefeller.du: 1 dc.uba.ar: 1 me.com: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 71
Total pull requests: 60
Average time to close issues: over 1 year
Average time to close pull requests: 9 months
Total issue authors: 68
Total pull request authors: 21
Average comments per issue: 1.54
Average comments per pull request: 0.55
Merged pull requests: 30
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 7
Pull requests: 34
Average time to close issues: about 1 month
Average time to close pull requests: about 4 hours
Issue authors: 7
Pull request authors: 8
Average comments per issue: 2.0
Average comments per pull request: 0.29
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

RickardSjogren (2)
nbehrnd (2)
beyondpie (2)
jtd1g16 (1)
rraadd88 (1)
debanjansen48 (1)
ianlongden (1)
timothymillar (1)
supern8ent (1)
gmboyer (1)
S1mHub (1)
ecojimb (1)
HYUNSEONG-KIM (1)
llazzaro (1)
Yaoyx (1)

Pull Request Authors

mcs07 (24)
nbehrnd (6)
pjknowles (4)
riinbre-bioinfo (2)
khoivan88 (2)
zachcp (2)
HYUNSEONG-KIM (2)
sg-s (2)
mehr-licht (2)
RickardSjogren (2)
WhiteSymmetry (2)
bjodah (1)
bertiewooster (1)
ghost (1)
jalavosus (1)

Top Labels

Issue Labels

question (8) bug (5) documentation (3) enhancement (2) duplicate (1) invalid (1)

Pull Request Labels

bug (4) duplicate (3) documentation (2)

Packages

Total packages: 3
Total downloads:
- pypi 217,319 last-month
Total docker downloads: 250,254

Total dependent packages: 34
(may contain duplicates)
Total dependent repositories: 78
(may contain duplicates)
Total versions: 7
Total maintainers: 2

pypi.org: pubchempy

A simple Python wrapper around the PubChem PUG REST API.

Homepage: https://github.com/mcs07/PubChemPy
Documentation: https://pubchempy.readthedocs.io/
License: MIT
Latest release: 1.0.4
published over 8 years ago

Versions: 5
Dependent Packages: 31
Dependent Repositories: 73
Downloads: 217,319 Last month
Docker Downloads: 250,254

Rankings

Dependent packages count: 0.5%

Docker downloads count: 1.0%

Downloads: 1.6%

Dependent repos count: 1.8%

Average: 2.1%

Stargazers count: 3.5%

Forks count: 4.5%

Maintainers (1)

mcs07

Last synced: 4 months ago

conda-forge.org: pubchempy

Homepage: https://github.com/mcs07/PubChemPy
License: MIT
Latest release: 1.0.4
published about 6 years ago

Versions: 1
Dependent Packages: 2
Dependent Repositories: 5

Rankings

Dependent repos count: 14.8%

Forks count: 18.6%

Average: 18.9%

Dependent packages count: 19.6%

Stargazers count: 22.4%

Last synced: 4 months ago

spack.io: py-pubchempy

Homepage: https://github.com/mcs07/PubChemPy
License: []
Latest release: 1.0.4
published almost 3 years ago

Versions: 1
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 11.4%

Stargazers count: 12.9%

Average: 20.4%

Dependent packages count: 57.3%

Maintainers (1)

meyersbs

Last synced: 4 months ago

Dependencies

requirements/common.txt pypi

pandas >=0.16.2

requirements/dev.txt pypi

Sphinx >=1.3.1 development
bumpversion >=0.5.3 development
coverage >=4.0 development
coveralls >=1.0 development
pytest >=3.0.7 development
sphinx-rtd-theme >=0.1.9 development