Library for processing molecules and reactions in python way

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)
Simple code to generate a password for your account!

Password-Generator Simple code to generate a password for your account! Password Generator for passwords for your accounts or anything else! This code

DEEM 1 Jun 05, 2022
python package for generating typescript grpc-web stubs from protobuf files.

grpc-web-proto-compile NOTE: This package has been superseded by romnn/proto-compile, which provides the same functionality but offers a lot more flex

Roman Dahm 0 Sep 05, 2021
A sys-botbase client for remote control automation of Nintendo Switch consoles. Based on SysBot.NET, written in python.

SysBot.py A sys-botbase client for remote control automation of Nintendo Switch consoles. Based on SysBot.NET, written in python. Setup: Download the

7 Dec 16, 2022
Dependency injection lib for Python 3.8+

PyDI Dependency injection lib for python How to use To define the classes that should be injected and stored as bean use decorator @component @compone

Nikita Antropov 2 Nov 09, 2021
A python module to update the console without flashing.

A python module to update the console without flashing.

Matthias 112 Dec 19, 2022
Tools for binary data on cassette

Micro Manchester Tape Storage Tools for storing binary data on cassette Includes: Python script for encoding Arduino sketch for decoding Eagle CAD fil

Zack Nelson 28 Dec 25, 2022
A color library based on pokemons colors!

pokepalette A simple pokemon color chooser " This repo is based on CDWimmer/PokePalette and was originated from this tweet. If you don't remember your

Thomas Capelle 5 Aug 30, 2021
JavaScript-style async programming for Python.

promisio JavaScript-style async programming for Python. Examples Create a promise-based async function using the promisify decorator. It works on both

Miguel Grinberg 191 Dec 30, 2022
Finds price floor for every single attribute in a given collection

Solana Solanart Scanner Enjoy the Free Code Steps to run Download VS Code

Dalton Nisbett 19 Oct 20, 2022
✨ Un DNS Resolver totalement fait en Python par moi, et en français

DNS Resolver ❗ Un DNS Resolver totalement fait en Python par moi, et en français. 🔮 Grâce a une adresse (url) vous pourrez avoir l'ip ainsi que le DN

MrGabin 3 Jun 06, 2021
Extends the pyranges module with operations on joined genomic intervals

tiedpyranges Extends the pyranges module with operations on joined genomic intervals (e.g. exons of same transcript) Install with: pip install tiedpyr

Marco Mariotti 4 Aug 05, 2022
HeadHunter parser

HHparser Description Program for finding work at HeadHunter service Features Find job Parse vacancies Dependencies python pip geckodriver firefox Inst

memphisboy 1 Oct 30, 2021
PyGMT - A Python interface for the Generic Mapping Tools

PyGMT A Python interface for the Generic Mapping Tools Documentation (development version) | Contact | Try Online Why PyGMT? A beautiful map is worth

The Generic Mapping Tools (GMT) 564 Dec 28, 2022
A collection of utility functions to prototype geometry processing research in python

gpytoolbox This repo is a work in progress and contains general utility functions I have needed to code while trying to work on geometry process resea

Silvia Sellán 73 Jan 06, 2023
An okayish python script to generate a random Euler circuit with given number of vertices and edges.

Euler-Circuit-Test-Case-Generator An okayish python script to generate a random Euler circuit with given number of vertices and edges. Executing the S

Alen Antony 1 Nov 13, 2021
pydsinternals - A Python native library containing necessary classes, functions and structures to interact with Windows Active Directory.

pydsinternals - Directory Services Internals Library A Python native library containing necessary classes, functions and structures to interact with W

Podalirius 36 Dec 14, 2022
Easy compression and extraction for any compression or archival format.

Tzar: Tar, Zip, Anything Really Easy compression and extraction for any compression or archival format. Usage/Examples tzar compress large-dir compres

DanielVZ 37 Nov 02, 2022
Format Norminette Output!

Format Norminette Output!

7 Apr 19, 2022
Helper script to bootstrap a Python environment with the tools required to build and install packages.

python-bootstrap Helper script to bootstrap a Python environment with the tools required to build and install packages. Usage $ python -m bootstrap.bu

Filipe Laíns 7 Oct 06, 2022
Install, run, and update apps without root and only in your home directory

Qube Apps Install, run, and update apps in the private storage of a Qube. Build and install in Qubes Get the code: git clone https://github.com/micahf

Micah Lee 26 Dec 27, 2022