cgrtools

CGRs, molecules and reactions manipulation

https://github.com/cimm-kzn/cgrtools

Science Score: 23.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary

Keywords from Contributors

interactive serializer packaging network-simulation shellcodes hacking autograding observability embedded optim

Last synced: 10 months ago · JSON representation

Repository

CGRs, molecules and reactions manipulation

Basic Info

Host: GitHub
Owner: cimm-kzn
License: lgpl-3.0
Language: Python
Default Branch: 4.1
Homepage:
Size: 3.54 MB

Statistics

Stars: 43
Watchers: 3
Forks: 16
Open Issues: 1
Releases: 0

Fork of Python3pkg/CGRtools

Created over 5 years ago · Last pushed over 3 years ago

Metadata Files

Readme License

README.rst

CGRTools
========


.. image:: https://zenodo.org/badge/14690494.svg
   :target: https://zenodo.org/badge/latestdoi/14690494


Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach.

Basic operations:
   - Read/write/convert formats: MDL .RDF (RXN) and .SDF (MOL), .MRV, SMILES, INCHI (Linux and Windows), .XYZ, .PDB
   - Standardize molecules and reactions and valid structures checker.
   - Duplicate searching.
   - Tetrahedron, Allene and CIS-TRANS stereo checking.
   - Produce CGRs.
   - Perform subgraph search.
   - Build/edit molecules and reactions.
   - Produce template based reactions and molecules.
   - Atom-to-atom mapping checker and rule-based fixer.
   - Perform MCS search.
   - 2d coordinates generation (based on `SmilesDrawer `_)
   - 2d/3d depiction.

Full documentation can be found `here `_

INSTALL
=======

Highly recommended to use python 3.8+. Python 3.6 and 3.7 deprecated.


Linux Debian based
------------------
* Install python3.8, virtualenv and git::

    sudo apt install python3.8 python3.8-dev git python3-virtualenv
    
* Create new environment and activate it::

    virtualenv -p python3.8 venv
    source venv/bin/activate

Mac
---
* Install python3.8 and git using `brew `_::

    brew install git
    brew install python3

* Install virtualenv::

    pip install virtualenv

* Create new environment and activate it::

    virtualenv -p python3.8 venv
    source venv/bin/activate
    
Windows
-------
* Install python3.8 and git using `Chocolatey `_::

    choco install git
    choco install python3
    
* Install virtualenv::

    pip install virtualenv

* Create new environment and activate it::

    virtualenv venv
    venv\Scripts\activate

General part
------------

* **stable version available through PyPI**::

    pip install CGRTools

* Install CGRtools with MRV files parsing support::

    pip install CGRTools[mrv]

* Install CGRtools with structures `clean2d` support (Note: install NodeJS into system, see `details `_)::

    pip install CGRtools[clean2d]

* Install CGRtools with optimized XYZ parser::

    pip install CGRtools[jit]


**If you still have questions, please open issue within github.**

PACKAGING
=========

For wheel generation just type next command in source root::

    python setup.py bdist_wheel

COPYRIGHT
=========

* 2014-2022 Timur Madzhidov tmadzhidov@gmail.com product owner, idea and development supervision
* 2014-2021 Ramil Nugmanov nougmanoff@protonmail.com main developer
* 2021-2022 Valentina Afonina valiaafo@yandex.ru development and support

CONTRIBUTORS
============

* Dinar Batyrshin batyrshin-dinar@mail.ru
* Timur Gimadiev timur.gimadiev@gmail.com
* Adelia Fatykhova adelik21979@gmail.com
* Tagir Akhmetshin tagirshin@gmail.com
* Ravil Mukhametgaleev sonic-mc@mail.ru
* Valentina Afonina valiaafo@yandex.ru

CITE THIS
=========

CGRtools: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing.
Journal of Chemical Information and Modeling 2019 59 (6), 2516-2521.
DOI: 10.1021/acs.jcim.9b00102

Owner

Name: KFU ChemoInformatics and Molecular Modeling Laboratory
Login: cimm-kzn
Kind: organization
Location: Kazan, Russia

Website: cimm.site
Repositories: 15
Profile: https://github.com/cimm-kzn

GitHub Events

Total

Watch event: 5
Pull request event: 2
Fork event: 2

Last Year

Watch event: 5
Pull request event: 2
Fork event: 2

Committers

Last synced: over 2 years ago

All Time

Total Commits: 746
Total Committers: 13
Avg Commits per committer: 57.385
Development Distribution Score (DDS): 0.416

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
stsouko	s**o@l**u	436
stsouko	n**f@p**m	220
Динар	4****5	48
TimurGimadiev	t**v@g**m	7
Adelia	a**9@g**m	7
Tagir	t**n@g**m	7
valia	v**a@c**e	5
zarinaIbr	6****r	5
kSibran	3****n	4
dependabot[bot]	4****]	3
ValAAfonina	v**o@y**u	2
Alexander Sizov	5****f	1
phrolycheva	6****a	1

Committer Domains (Top 20 + Academic)

yandex.ru: 1 cimm.site: 1 live.ru: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time

Total issues: 4
Total pull requests: 4
Average time to close issues: 4 months
Average time to close pull requests: 2 minutes
Total issue authors: 3
Total pull request authors: 3
Average comments per issue: 2.0
Average comments per pull request: 0.0
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

Past Year

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

View more stats

Top Authors

Issue Authors

UnixJunkie (2)
AsyaOrlova (1)
dln22 (1)

Pull Request Authors

tagirshin (3)
valiaafo (1)
stsouko (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- pypi 4,348 last-month

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 3
(may contain duplicates)
Total versions: 14
Total maintainers: 1

proxy.golang.org: github.com/cimm-kzn/CGRtools

Documentation: https://pkg.go.dev/github.com/cimm-kzn/CGRtools#section-documentation
License: lgpl-3.0
Latest release: v4.1.35+incompatible
published almost 4 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 11 months ago

proxy.golang.org: github.com/cimm-kzn/cgrtools

Documentation: https://pkg.go.dev/github.com/cimm-kzn/cgrtools#section-documentation
License: lgpl-3.0
Latest release: v4.1.35+incompatible
published almost 4 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 11 months ago

pypi.org: cgrtools

Homepage: https://github.com/cimm-kzn/CGRtools
Documentation: https://cgrtools.readthedocs.io/
License: LGPLv3
Latest release: 4.1.35
published almost 4 years ago

Versions: 12
Dependent Packages: 1
Dependent Repositories: 3
Downloads: 4,348 Last month

Rankings

Dependent repos count: 9.0%

Forks count: 9.6%

Dependent packages count: 10.0%

Average: 10.4%

Downloads: 11.7%

Stargazers count: 11.9%

Maintainers (1)

nougmanoff

Last synced: 10 months ago