Library for processing molecules and reactions in python way

Related tags

General Utilitieschython
Overview

Chython [ˈkʌɪθ(ə)n]

Library for processing molecules and reactions in python way.

Features:
  • Read/write/convert formats: MDL .RDF (.RXN) and .SDF (.MOL), .MRV, SMILES, INCHI (inchi-trust library), .XYZ, .PDB
  • Standardize molecules and reactions and valid structures checker
  • Supported python-magic
  • Tetrahedron, Allene and CIS-TRANS stereo supporting
  • 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
  • Produce CGRs (Condensed Graph of Reaction)

Full documentation can be found here.

Chython is fork of CGRtools.

INSTALL

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

Note: for using clean2d install NodeJS into system.

  • stable version available through PyPI:

    pip install chython

  • Install chython library DEV version for features that are not well tested:

    pip install -U git+https://github.com/chython/[email protected]#egg=chython

TESTS

Run unit tests:

git clone https://github.com/chython/chython.git && cd chython  # skip if already got sources
pip install -e .
pytest --pyargs chython

COPYRIGHT

CONTRIBUTORS

Comments
  • Pip installation bug

    Pip installation bug

    I tried to install the package via pip (not the DEV version) and encountered an error related to setuptools. The error looks like this: setuptools bug

    I found that downgrading setuptools to version 41 solves problem. And it really worked out.

    opened by tagirshin 1
  • Bump loader-utils from 1.4.1 to 1.4.2 in /clean2d

    Bump loader-utils from 1.4.1 to 1.4.2 in /clean2d

    Bumps loader-utils from 1.4.1 to 1.4.2.

    Release notes

    Sourced from loader-utils's releases.

    v1.4.2

    1.4.2 (2022-11-11)

    Bug Fixes

    Changelog

    Sourced from loader-utils's changelog.

    1.4.2 (2022-11-11)

    Bug Fixes

    Commits

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    • @dependabot use these labels will set the current labels as the default for future PRs for this repo and language
    • @dependabot use these reviewers will set the current reviewers as the default for future PRs for this repo and language
    • @dependabot use these assignees will set the current assignees as the default for future PRs for this repo and language
    • @dependabot use this milestone will set the current milestone as the default for future PRs for this repo and language

    You can disable automated security fix PRs for this repo from the Security Alerts page.

    dependencies 
    opened by dependabot[bot] 0
  • Bump loader-utils from 1.4.0 to 1.4.1 in /clean2d

    Bump loader-utils from 1.4.0 to 1.4.1 in /clean2d

    Bumps loader-utils from 1.4.0 to 1.4.1.

    Release notes

    Sourced from loader-utils's releases.

    v1.4.1

    1.4.1 (2022-11-07)

    Bug Fixes

    Changelog

    Sourced from loader-utils's changelog.

    1.4.1 (2022-11-07)

    Bug Fixes

    Commits

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    • @dependabot use these labels will set the current labels as the default for future PRs for this repo and language
    • @dependabot use these reviewers will set the current reviewers as the default for future PRs for this repo and language
    • @dependabot use these assignees will set the current assignees as the default for future PRs for this repo and language
    • @dependabot use this milestone will set the current milestone as the default for future PRs for this repo and language

    You can disable automated security fix PRs for this repo from the Security Alerts page.

    dependencies 
    opened by dependabot[bot] 0
  • Bump minimist from 1.2.5 to 1.2.6 in /clean2d

    Bump minimist from 1.2.5 to 1.2.6 in /clean2d

    Bumps minimist from 1.2.5 to 1.2.6.

    Commits

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    • @dependabot use these labels will set the current labels as the default for future PRs for this repo and language
    • @dependabot use these reviewers will set the current reviewers as the default for future PRs for this repo and language
    • @dependabot use these assignees will set the current assignees as the default for future PRs for this repo and language
    • @dependabot use this milestone will set the current milestone as the default for future PRs for this repo and language

    You can disable automated security fix PRs for this repo from the Security Alerts page.

    dependencies 
    opened by dependabot[bot] 0
  • allene stereo

    allene stereo

    fix bug image

    
  Mrv2115 01212215432D          

 10 10  0  0  0  0            999 V2000
   -7.6610    0.9215    0.0000 C   0  0  0  0  0  0  0  0  0  6  0  0
   -7.2485    1.6360    0.0000 C   0  0  0  0  0  0  0  0  0  8  0  0
   -6.4732    1.9181    0.0000 C   0  0  0  0  0  0  0  0  0 10  0  0
   -5.8542    1.4128    0.0000 C   0  0  1  0  0  0  0  0  0 12  0  0
   -5.2855    0.9215    0.0000 C   0  0  0  0  0  0  0  0  0 11  0  0
   -5.4287    0.1090    0.0000 C   0  0  0  0  0  0  0  0  0  9  0  0
   -6.0607   -0.4213    0.0000 C   0  0  0  0  0  0  0  0  0  7  0  0
   -6.8857   -0.4213    0.0000 C   0  0  0  0  0  0  0  0  0  5  0  0
   -7.5177    0.1090    0.0000 C   0  0  0  0  0  0  0  0  0  4  0  0
   -6.4732    2.7431    0.0000 H   0  0  0  0  0  0  0  0  0 13  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  3 10  1  1  0  0  0
M  END
    opened by stsouko 0
Releases(1.48)

  • 1.48(Dec 14, 2022)

    What's Changed

    • Kekule fixed for invalid pyridine complexes
    • Automatic clean2d on depiction. useful for smiles-parsed structures.
    • Depiction customization

    Full Changelog: https://github.com/chython/chython/compare/1.45...1.48

    Source code(tar.gz)
    Source code(zip)

  • 1.45(Oct 26, 2022)

    What's Changed

    • molecules bytes pack V2
    • reactor enumerator now supports lists of atoms in product
    • smiles parser fix
    • smarts parser improved (globally unique masked atoms)
    • heuristic mapper fixed
    • thiele fixed
    • small bugfixes

    Full Changelog: https://github.com/chython/chython/compare/1.38...1.45

    Source code(tar.gz)
    Source code(zip)

  • 1.38(Aug 30, 2022)

    • parsers better logging added.
    • thiele and kekule fixed.
    • pandas adhoc fix for better representation of molecules in df. chython.utils.patch_pandas
    • remove_reagents method now support AAM-less detection.
    • Reactor call api changed.
    • new smiles formatting key: !z - disable charges information.
    • small bugs.

    Full Changelog: https://github.com/chython/chython/compare/1.27...1.38

    Source code(tar.gz)
    Source code(zip)

  • 1.27(May 30, 2022)

    • Fixed rule-based AAM fixer.
    • Improved clean2d
    • standardize now can keep tautomers.
    • remove_acids molecule standardization method added.
    • split_metal_salts molecule standardization implemented.
    • SDF metadata writer now follow specification
    • Reactor improved.
    • Groups deprotection transformers for common groups implemented.
    • utils.svg2png renderer added.

    Full Changelog: https://github.com/chython/chython/compare/1.23...1.27

    Source code(tar.gz)
    Source code(zip)

  • 1.23(Apr 21, 2022)

    SMARTS parser added!

    There are a few limitations:

    stereo ignored only D, a, h, r, and !R atom primitives supported. bond order list and not bond supported. [not]ring bond supported. Only with explicit bonds. not bond and order list supported. mapping, charge, and isotopes supported. list of elements supported. A - treats as any element. A primitive (aliphatic) ignored. M - treats as any metal. <&> logic operator unsupported. <;> logic operator is mandatory except for charge, isotope, and stereo marks. used CXSMARTS extension for radical, hybridization (SP3, SP2, SP1, and Aromatic coded as 3, 2, 1, and 4), and heteroatoms (not C or H) count coding

    For example:

        [C;r5,r6;a]-;!@[C;h0,h1] |atomProp:1.hyb.24:1.het.0|

    Aromatic C member of 5 or 6 atoms ring connected with non-ring single bond to aromatic or SP2 C with 0 or 1 hydrogen without heteroatomic neighbors. Left molecules matches.

    image

    • Tutorial updated.
    • Fixed Reactor stereo. Now patch without stereo doesn't override matched molecule stereo.
    • SMARTS generator fixed.

    Full Changelog: https://github.com/chython/chython/compare/1.22...1.23

    Source code(tar.gz)
    Source code(zip)

  • 1.22(Apr 15, 2022)

    What's Changed

    • Atom-to-Atom mapping for reactions.
    • SMILES parser refactored and fixed. CXSMILES support was added for fragments and radicals.
    • SMILES generator refactored. CXSMILES support was added for fragments and radicals.
    • Isomorphism speedup with cython.
    • Stereo processing speedup.
    • QueryContainer now supports bond in ring attribute. SMARTS now daylight compatible. CXSMARTS notation used for radicals, hybridizations, and heteroatoms attrs.
    • chython.utils.GridDepict and chython.utils.RetroDepict for lists of molecules and rooted tree of molecules (e.g. retro-synthetic tree)
    • Tautomerism refactored. Use mol.enumerate_tautomers() for generating.
    • Protonated and deprotonated structures enumeration added mol.enumerate_charged_forms()
    • Bug fixes.

    New Contributors

    • @TimurGimadiev

    Full Changelog: https://github.com/chython/chython/commits/1.22

    Source code(tar.gz)
    Source code(zip)
Owner
GitHub Repository
An awesome tool to save articles from RSS feed to Pocket automatically.

RSS2Pocket An awesome tool to save articles from RSS feed to Pocket automatically. About the Project I used to use IFTTT to save articles from RSS fee

Hank Liao 10 Nov 12, 2022
An OData v4 query parser and transpiler for Python

odata-query is a library that parses OData v4 filter strings, and can convert them to other forms such as Django Queries, SQLAlchemy Queries, or just plain SQL.

Gorilla 39 Jan 05, 2023
🚧Useful shortcuts for simple task on windows

Windows Manager A tool containg useful utilities for performing simple shortcut tasks on Windows 10 OS. Features Lit Up - Turns up screen brightness t

Olawale Oyeyipo 0 Mar 24, 2022
Homebase Name Changer for Fortnite: Save the World.

Homebase Name Changer This program allows you to change the Homebase name in Fortnite: Save the World. How to use it? After starting the HomebaseNameC

PRO100KatYT 7 May 21, 2022
Similar looking domain detection using python fuzzywuzzy

Major cause of phishing and BEC incident is similar looking domain, if you detect it early, you can prevent incidents early, python fuzzywuzzy module let you do that

2 Nov 07, 2021
A fixture that allows runtime xfail

pytest-runtime-xfail pytest plugin, providing a runtime_xfail fixture, which is callable as runtime_xfail(), to allow runtime decisions to mark a test

Brian Okken 4 Apr 06, 2022
A simple and easy to use collection of random python functions.

A simple and easy to use collection of random python functions.

Diwan Mohamed Faheer 1 Nov 17, 2021
A Program that generates and checks Stripe keys 24x7.

A Program that generates and checks Stripe keys 24x7. This was made only for Educational Purposes, I'm not responsible for the damages cause by you

iNaveen 18 Dec 17, 2022
Export watched content from Tautulli to the Letterboxd CSV Import Format

Export watched content from Tautulli to the Letterboxd CSV Import Format

Evan J 5 Aug 31, 2022
Python implementation of Gorilla time series compression

Gorilla Time Series Compression This is an implementation (with some adaptations) of the compression algorithm described in section 4.1 (Time series c

Ghiles Meddour 19 Jan 01, 2023
This python program will display all SSID usernames and SSID passwords you once connected to your laptop

Windows-Wifi-password-extractor This python program will display all SSID usernames and SSID passwords you once connected to your laptop How to run th

Bhaskar Pal 3 Apr 26, 2022
Python script to get some stats on nodes in a Blender material nodetree

Python script to get some stats on nodes in a Blender material nodetree. It counts the nodes, the node types and the max deep level for group nodes.

Alek Mugnozzo 2 Sep 03, 2022
Python code to divide big numbers

divide-big-num Python code to divide big numbers

VuMinhNgoc 1 Oct 15, 2021
A tool for testing improper put method vulnerability

Putter-CUP A tool for testing improper put method vulnerability Usage :- python3 put.py -f live-subs.txt Result :- The result in txt file "result.txt"

Zahir Tariq 6 Aug 06, 2021
A python tool give n number of inputs and parallelly you will get a output by separetely

http-status-finder Hello Everyone!! This is kavisurya, In this tool you can give n number of inputs and parallelly you will get a output by separetely

KAVISURYA V 3 Dec 05, 2021
Toolkit for collecting and applying templates of prompting instances

PromptSource Toolkit for collecting and applying templates of prompting instances. WIP Setup Download the repo Navigate to root directory of the repo

BigScience Workshop 1k Jan 05, 2023
Handy Tool to check the availability of onion site and to extract the title of submitted onion links.

This tool helps is to quickly investigate a huge set of onion sites based by checking its availability which helps to filter out the inactive sites and collect the site title that might helps us to c

Balaji 13 Nov 25, 2022
Writing Alfred copy/paste scripts in Python

Writing Alfred copy/paste scripts in Python This repository shows how to create Alfred scripts in Python. It assumes that you using pyenv for Python v

Will Fitzgerald 2 Oct 26, 2021
A simple toolchain for moving Remarkable highlights to Readwise

A simple toolchain for moving Remarkable highlights to Readwise

zach wick 20 Dec 20, 2022
✨ Un générateur de lien raccourcis en fonction d'un lien totalement fait en Python par moi, et en français.

Shorter Link ❗ Un générateur de lien raccourcis en fonction d'un lien totalement fait en Python par moi, et en français. Dépendences : pip install pys

MrGabin 3 Jun 06, 2021