CGRtools

CGRTools

Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach.

Basic operations:

Read/write/convert formats: MDL .RDF (RXN) and .SDF (MOL), .MRV, SMILES, INCHI (Linux and Windows), .XYZ, .PDB
Standardize molecules and reactions and valid structures checker.
Duplicate searching.
Tetrahedron, Allene and CIS-TRANS stereo checking.
Produce CGRs.
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.

Full documentation can be found here

INSTALL

Highly recommended to use python 3.8+. Python 3.6 and 3.7 deprecated.

Linux Debian based

Install python3.8, virtualenv and git:

sudo apt install python3.8 python3.8-dev git python3-virtualenv

Create new environment and activate it:

virtualenv -p python3.8 venv
source venv/bin/activate

Mac

Install python3.8 and git using brew:
```
brew install git
brew install python3
```
Install virtualenv:
```
pip install virtualenv
```

Create new environment and activate it:

virtualenv -p python3.8 venv
source venv/bin/activate

Windows

Install python3.8 and git using Chocolatey:
```
choco install git
choco install python3
```
Install virtualenv:
```
pip install virtualenv
```
Create new environment and activate it:
```
virtualenv venv
venv\Scripts\activate
```

General part

stable version available through PyPI:
```
pip install CGRTools
```
Install CGRtools with MRV files parsing support:
```
pip install CGRTools[mrv]
```
Install CGRtools with structures clean2d support (Note: install NodeJS into system, see details):
```
pip install CGRtools[clean2d]
```
Install CGRtools with optimized XYZ parser:
```
pip install CGRtools[jit]
```

If you still have questions, please open issue within github.

PACKAGING

For wheel generation just type next command in source root:

python setup.py bdist_wheel

COPYRIGHT

2014-2022 Timur Madzhidov tmadzhidov@gmail.com product owner, idea and development supervision
2014-2021 Ramil Nugmanov nougmanoff@protonmail.com main developer
2021-2022 Valentina Afonina valiaafo@yandex.ru development and support

CONTRIBUTORS

Dinar Batyrshin batyrshin-dinar@mail.ru
Timur Gimadiev timur.gimadiev@gmail.com
Adelia Fatykhova adelik21979@gmail.com
Tagir Akhmetshin tagirshin@gmail.com
Ravil Mukhametgaleev sonic-mc@mail.ru
Valentina Afonina valiaafo@yandex.ru

CITE THIS

CGRtools: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing. Journal of Chemical Information and Modeling 2019 59 (6), 2516-2521. DOI: 10.1021/acs.jcim.9b00102

Metadata

Release files for CGRtools 4.1.35

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for CGRtools 4.1.35
File	Size	Uploaded	Provenance
CGRtools-4.1.35.tar.gz	1.5 MB	Oct 3, 2022	Without provenance	Details

Built distributions (wheels)

Table of built distributions (wheels) for CGRtools 4.1.35
File	Interpreter	ABI	Platform	Reset
CGRtools-4.1.35-cp310-cp310-win_amd64.whl 924.3 kB Oct 3, 2022 Without provenance	CPython 3.10	CPython 3.10	Windows x86-64	Details
CGRtools-4.1.35-cp310-cp310-macosx_10_9_x86_64.whl 280.9 kB Oct 3, 2022 Without provenance	CPython 3.10	CPython 3.10	macOS 10.9+ x86-64	Details
CGRtools-4.1.35-cp39-cp39-win_amd64.whl 925.1 kB Oct 3, 2022 Without provenance	CPython 3.9	CPython 3.9	Windows x86-64	Details
CGRtools-4.1.35-cp39-cp39-macosx_10_9_x86_64.whl 280.6 kB Oct 3, 2022 Without provenance	CPython 3.9	CPython 3.9	macOS 10.9+ x86-64	Details
CGRtools-4.1.35-cp38-cp38-win_amd64.whl 925.1 kB Oct 3, 2022 Without provenance	CPython 3.8	CPython 3.8	Windows x86-64	Details
CGRtools-4.1.35-cp38-cp38-macosx_10_9_x86_64.whl 281.6 kB Oct 3, 2022 Without provenance	CPython 3.8	CPython 3.8	macOS 10.9+ x86-64	Details
CGRtools-4.1.35-cp37-cp37m-win_amd64.whl 925.1 kB Oct 3, 2022 Without provenance	CPython 3.7	CPython 3.7 pymalloc	Windows x86-64	Details
CGRtools-4.1.35-cp37-cp37m-macosx_10_9_x86_64.whl 281.1 kB Oct 3, 2022 Without provenance	CPython 3.7	CPython 3.7 pymalloc	macOS 10.9+ x86-64	Details

Total release size: 6.3 MB

Release files / CGRtools-4.1.35.tar.gz

Download URL	CGRtools-4.1.35.tar.gz
Size	1.5 MB
Tags	Source
SHA-256 checksum How to use checksums	`907436c0f12af7b8a6b5baadfc62dffd4a29ae1802416fd76ab410d3cf95c340`
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Upload date	Oct 3, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.8.10`

Release files / CGRtools-4.1.35-cp310-cp310-win_amd64.whl

Download URL	CGRtools-4.1.35-cp310-cp310-win_amd64.whl
Size	924.3 kB
Tags	CPython 3.10 Windows x86-64
SHA-256 checksum How to use checksums	`7eea8dfc1939aecb86b17fc7f2e969f0d4c516c2ad9fe29c0640c842030cad67`
BLAKE2b-256 checksum How to use checksums	`f61b44b178ec77fe1c8b0ab36e77ec179bb2619a630c82314260ba74da4eda89`
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Uploaded via	`twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.8.10`

Release files / CGRtools-4.1.35-cp310-cp310-macosx_10_9_x86_64.whl

Download URL	CGRtools-4.1.35-cp310-cp310-macosx_10_9_x86_64.whl
Size	280.9 kB
Tags	CPython 3.10 macOS 10.9+ x86-64
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Uploaded via	`twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.8.10`

Release files / CGRtools-4.1.35-cp39-cp39-win_amd64.whl

Download URL	CGRtools-4.1.35-cp39-cp39-win_amd64.whl
Size	925.1 kB
Tags	CPython 3.9 Windows x86-64
SHA-256 checksum How to use checksums	`9acc26cf90947fd661d605337614f7de8f07770b0f454e446015e6ebfb9e4d69`
BLAKE2b-256 checksum How to use checksums	`e8a56f4ff72e0ba5b663fa5c0dd005cc9c6afa6db534ca799d4d148a2d803527`
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Release files / CGRtools-4.1.35-cp39-cp39-macosx_10_9_x86_64.whl

Download URL	CGRtools-4.1.35-cp39-cp39-macosx_10_9_x86_64.whl
Size	280.6 kB
Tags	CPython 3.9 macOS 10.9+ x86-64
SHA-256 checksum How to use checksums	`5f64df716f8c2b25327654eb8df5a675476db13afac17c818d3920e7472f7745`
BLAKE2b-256 checksum How to use checksums	`bedeb4e058a2189dc5dc36362a8289c1a496cc79e186fff819bcbbe42510cd54`
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Release files / CGRtools-4.1.35-cp38-cp38-win_amd64.whl

Download URL	CGRtools-4.1.35-cp38-cp38-win_amd64.whl
Size	925.1 kB
Tags	CPython 3.8 Windows x86-64
SHA-256 checksum How to use checksums	`5fc7aaafaf9ea08f781de006fe2831279bb407f25adaede65219f602a55155d6`
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Release files / CGRtools-4.1.35-cp38-cp38-macosx_10_9_x86_64.whl

Download URL	CGRtools-4.1.35-cp38-cp38-macosx_10_9_x86_64.whl
Size	281.6 kB
Tags	CPython 3.8 macOS 10.9+ x86-64
SHA-256 checksum How to use checksums	`3d198d1efd58fc183b28caa751c6bbae1ee98e1f27e28c328293a865a639dedd`
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Uploaded via	`twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.8.10`

Release files / CGRtools-4.1.35-cp37-cp37m-win_amd64.whl

Download URL	CGRtools-4.1.35-cp37-cp37m-win_amd64.whl
Size	925.1 kB
Tags	CPython 3.7 CPython 3.7 pymalloc Windows x86-64
SHA-256 checksum How to use checksums	`beff037f20852cbbc6ddb8fe5d047e83d5f520afa20620770757bb862c8e22bf`
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Upload date	Oct 3, 2022
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Release files / CGRtools-4.1.35-cp37-cp37m-macosx_10_9_x86_64.whl

Download URL	CGRtools-4.1.35-cp37-cp37m-macosx_10_9_x86_64.whl
Size	281.1 kB
Tags	CPython 3.7 CPython 3.7 pymalloc macOS 10.9+ x86-64
SHA-256 checksum How to use checksums	`44f90b51ff9a7d62860a42bf6fbcef1dec2a2404eadff4525f944d2465ec0241`
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