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

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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

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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

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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

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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

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