Library for processing molecules and reactions in python way

Last update: Dec 01, 2022

Related tags

General Utilities chython

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

2014-2021 Ramil Nugmanov [email protected] main developer

CONTRIBUTORS

Adelia Fatykhova [email protected]
Aleksandr Sizov [email protected]
Dinar Batyrshin [email protected]
Dmitrij Zanadvornykh [email protected]
Ravil Mukhametgaleev [email protected]
Tagir Akhmetshin [email protected]
Timur Gimadiev [email protected]
Zarina Ibragimova

Comments

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:

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
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

ReDoS problem (#226) (17cbf8f)

Changelog

Sourced from loader-utils's changelog.

1.4.2 (2022-11-11)

Bug Fixes

ReDoS problem (#226) (17cbf8f)

Commits

331ad50 chore(release): 1.4.2

17cbf8f fix: ReDoS problem (#226)

See full diff in compare view

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
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

security problem (#220) (4504e34)

Changelog

Sourced from loader-utils's changelog.

1.4.1 (2022-11-07)

Bug Fixes

security problem (#220) (4504e34)

Commits

8f082b3 chore(release): 1.4.1

4504e34 fix: security problem (#220)

See full diff in compare view

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
Bumps minimist from 1.2.5 to 1.2.6.

Commits

7efb22a 1.2.6

ef88b93 security notice for additional prototype pollution issue

c2b9819 isConstructorOrProto adapted from PR

bc8ecee test from prototype pollution PR

See full diff in compare view

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

fix bug


  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.

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

Python Libraries with functions and constants related to electrical engineering.

ElectricPy Electrical-Engineering-for-Python Python Libraries with functions and constants related to electrical engineering. The functions and consta

39 Dec 23, 2022

Just some scripts to export vector tiles to geojson.

Vector tiles to GeoJSON Nowadays modern web maps are usually based on vector tiles. The great thing about vector tiles is, that they are not just imag

77 Jul 26, 2022

Display your calendar on the wallpaper.

wallCal Have your calendar appear as the wallpaper. disclaimer Use at your own risk. Don't blame me if you miss a meeting :-) Some parts of the script

7 Jun 14, 2022

Customized python validations.

A customized python validations.

2 Apr 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

3 Jun 06, 2021

.bvh to .mcfunction file converter.

bvh-to-mcf .bvh file to .mcfunction converter

28 Nov 21, 2022

'ToolBurnt' A Set Of Tools In One Place =}

5 Sep 10, 2022

A functional standard library for Python.

Toolz A set of utility functions for iterators, functions, and dictionaries. See the PyToolz documentation at https://toolz.readthedocs.io LICENSE New

4.1k Dec 30, 2022

A hashtag from string extract python module

3 Aug 10, 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

Pass arguments by reference—in Python!

byref Pass arguments by reference—in Python! byrefis a decorator that allows Python functions to declare reference parameters, with similar semantics

9 Feb 10, 2022

jsoooooooon derulo - Make sure your 'jason derulo' is featured as the first part of your json data

jsonderulo Make sure your 'jason derulo' is featured as the first part of your json data Install: # python pip install jsonderulo poetry add jsonderul

3 Sep 13, 2021

Fuzzy box is a quick program I wrote to fuzz a URL that is in the format https:// url 20characterstring.

What is this? Fuzzy box is a quick program I wrote to fuzz a URL that is in the format https://url/20characterstring.extension. I have redacted th

1 Oct 19, 2021

A collection of tools for biomedical research assay analysis in Python.

waltlabtools A collection of tools for biomedical research assay analysis in Python. Key Features Analysis for assays such as digital ELISA, including

1 Apr 18, 2022

[P]ython [w]rited [B]inary [C]onverter

pwbinaryc [P]ython [w]rited [Binary] [C]onverter You have rights to: Modify the code and use it private (friends are allowed too) Make a page and redi

0 Jun 21, 2022

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

79 Nov 15, 2022

Find dependent python scripts of a python script in a project directory.

2 Dec 05, 2021

More routines for operating on iterables, beyond itertools

More Itertools Python's itertools library is a gem - you can compose elegant solutions for a variety of problems with the functions it provides. In mo

2.9k Jan 06, 2023

Color box that provides various colors‘ rgb decimal code.

colorbox Color box that provides various colors‘ rgb decimal code

1 Dec 07, 2021

Aurin - A quick AUR installer for Arch Linux. Install packages from AUR website in a click.

51 Nov 04, 2022

Library for processing molecules and reactions in python way

Related tags

Overview

Chython [ˈkʌɪθ(ə)n]

INSTALL

TESTS

COPYRIGHT

CONTRIBUTORS

Comments

Pip installation bug

Bump loader-utils from 1.4.1 to 1.4.2 in /clean2d

v1.4.2

1.4.2 (2022-11-11)

Bug Fixes

1.4.2 (2022-11-11)

Bug Fixes

Bump loader-utils from 1.4.0 to 1.4.1 in /clean2d

v1.4.1

1.4.1 (2022-11-07)

Bug Fixes

1.4.1 (2022-11-07)

Bug Fixes

Bump minimist from 1.2.5 to 1.2.6 in /clean2d

allene stereo

Releases(1.48)

1.48(Dec 14, 2022)

What's Changed

1.45(Oct 26, 2022)

What's Changed

1.38(Aug 30, 2022)

1.27(May 30, 2022)

1.23(Apr 21, 2022)

1.22(Apr 15, 2022)

What's Changed

New Contributors

Owner

Python Libraries with functions and constants related to electrical engineering.

Just some scripts to export vector tiles to geojson.

Display your calendar on the wallpaper.

Customized python validations.

✨ Un DNS Resolver totalement fait en Python par moi, et en français

.bvh to .mcfunction file converter.

'ToolBurnt' A Set Of Tools In One Place =}

A functional standard library for Python.

A hashtag from string extract python module

Rabbito is a mini tool to find serialized objects in input values

Pass arguments by reference—in Python!

jsoooooooon derulo - Make sure your 'jason derulo' is featured as the first part of your json data

Fuzzy box is a quick program I wrote to fuzz a URL that is in the format https:// url 20characterstring.

A collection of tools for biomedical research assay analysis in Python.

[P]ython [w]rited [B]inary [C]onverter

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

Find dependent python scripts of a python script in a project directory.

More routines for operating on iterables, beyond itertools

Color box that provides various colors‘ rgb decimal code.

Aurin - A quick AUR installer for Arch Linux. Install packages from AUR website in a click.