Library for processing molecules and reactions in python way

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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

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    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

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    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.

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    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)
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