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
1 maintainer
Metadata
1 maintainer
Release files for cgrtools-stable 4.2.13
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
Total release size: 11.6 MB
Release files / cgrtools_stable-4.2.13-cp312-cp312-win_amd64.whl
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| Tags | CPython 3.12 Windows x86-64 |
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Release files / cgrtools_stable-4.2.13-cp312-cp312-win32.whl
| Download URL | cgrtools_stable-4.2.13-cp312-cp312-win32.whl |
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Release files / cgrtools_stable-4.2.13-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Release files / cgrtools_stable-4.2.13-cp312-cp312-macosx_11_0_arm64.whl
| Download URL | cgrtools_stable-4.2.13-cp312-cp312-macosx_11_0_arm64.whl |
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Release files / cgrtools_stable-4.2.13-cp311-cp311-win_amd64.whl
| Download URL | cgrtools_stable-4.2.13-cp311-cp311-win_amd64.whl |
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Release files / cgrtools_stable-4.2.13-cp311-cp311-win32.whl
| Download URL | cgrtools_stable-4.2.13-cp311-cp311-win32.whl |
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| Size | 927.6 kB |
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Release files / cgrtools_stable-4.2.13-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | cgrtools_stable-4.2.13-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 1.1 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
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Release files / cgrtools_stable-4.2.13-cp311-cp311-macosx_11_0_arm64.whl
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Release files / cgrtools_stable-4.2.13-cp310-cp310-win_amd64.whl
| Download URL | cgrtools_stable-4.2.13-cp310-cp310-win_amd64.whl |
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Release files / cgrtools_stable-4.2.13-cp310-cp310-win32.whl
| Download URL | cgrtools_stable-4.2.13-cp310-cp310-win32.whl |
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| Size | 927.5 kB |
| Tags | CPython 3.10 Windows x86-32 |
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Release files / cgrtools_stable-4.2.13-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | cgrtools_stable-4.2.13-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 1.1 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
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Release files / cgrtools_stable-4.2.13-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | cgrtools_stable-4.2.13-cp310-cp310-macosx_11_0_arm64.whl |
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| Size | 943.6 kB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
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