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
A Randomizer Oracle

Tezos Randomizer Tezod Randomizer "Oracle". It's a smart contract that you can call to get a random number between X and Y (for now). It uses entropy

Asbjorn Enge 19 Sep 13, 2022
These scripts look for non-printable unicode characters in all text files in a source tree

find-unicode-control These scripts look for non-printable unicode characters in all text files in a source tree. find_unicode_control.py should work w

Siddhesh Poyarekar 25 Aug 30, 2022
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
Gradually automate your procedures, one step at a time

Gradualist Gradually automate your procedures, one step at a time Inspired by https://blog.danslimmon.com/2019/07/15/ Features Main Features Converts

Ross Jacobs 8 Jul 24, 2022
Networkx with neo4j back-end

Dump networkx graph into nodes/relations TSV from neo4jnx.tsv import graph_to_tsv g = pklload('indranet_dir_graph.pkl') graph_to_tsv(g, 'docker/nodes.

Benjamin M. Gyori 1 Oct 27, 2021
A utility tool to create .env files

A utility tool to create .env files dump-env takes an .env.template file and some optional environmental variables to create a new .env file from thes

wemake.services 89 Dec 08, 2022
Conveniently measures the time of your loops, contexts and functions.

Conveniently measures the time of your loops, contexts and functions.

Maciej J Mikulski 79 Nov 15, 2022
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
✨ Une calculatrice totalement faite en Python par moi, et en français.

Calculatrice ❗ Une calculatrice totalement faite en Python par moi, et en français. 🔮 Voici une calculatrice qui vous permet de faire vos additions,

MrGabin 3 Jun 06, 2021
Find version automatically based on git tags and commit messages.

GIT-CONVENTIONAL-VERSION Find version automatically based on git tags and commit messages. The tool is very specific in its function, so it is very fl

0 Nov 07, 2021
ticktock is a minimalist library to view Python time performance of Python code.

ticktock is a minimalist library to view Python time performance of Python code.

Victor Benichoux 30 Sep 28, 2022
Implicit hierarchical a posteriori error estimates in FEniCSx

FEniCSx Error Estimation (FEniCSx-EE) Description FEniCSx-EE is an open source library showing how various error estimation strategies can be implemen

Jack S. Hale 1 Dec 08, 2021
A repo for working with and building daos

DAO Mix DAO Mix About How to DAO No Code Tools Getting Started Prerequisites Installation Usage On-Chain Governance Example Off-Chain governance Examp

Brownie Mixes 86 Dec 19, 2022
DiddiParser 2: The DiddiScript parser.

DiddiParser 2 The DiddiScript parser, written in Python. Installation DiddiParser2 can be installed via pip: pip install diddiparser2 Usage DiddiPars

Diego Ramirez 3 Dec 28, 2022
Fraud Multiplication Table Detection in python

Fraud-Multiplication-Table-Detection-in-python In this program, I have detected fraud multiplication table using python without class. Here, I have co

Sachin Vinayak Dabhade 4 Sep 24, 2021
Let's renew the puzzle collection. We'll produce a collection of new puzzles out of the lichess game database.

Let's renew the puzzle collection. We'll produce a collection of new puzzles out of the lichess game database.

Thibault Duplessis 96 Jan 03, 2023
Python lightweight dependency injection library

pythondi pythondi is a lightweight dependency injection library for python Support both sync and async functions Installation pip3 install pythondi Us

Hide 41 Dec 16, 2022
Rabbito is a mini tool to find serialized objects in input values

Rabbito-ObjectFinder Rabbito is a mini tool to find serialized objects in input values What does Rabbito do Rabbito has the main object finding Serial

7 Dec 13, 2021
glip is a module for retrieve ip address like local-ip, global-ip, external-ip as string.

gle_ip_info glip is a module for retrieve ip address like local-ip, global-ip, external-ip as string.

Fatin Shadab 3 Nov 21, 2021
UUID version 7, which are time-sortable (following the Peabody RFC4122 draft)

uuid7 - time-sortable UUIDs This module implements the version 7 UUIDs, proposed by Peabody and Davis in https://www.ietf.org/id/draft-peabody-dispatc

Steve Simmons 22 Dec 20, 2022