{ "info": { "author": "Dr. Ramil Nugmanov, Dr. Timur Madzhidov, Valentina Afonina", "author_email": "tmadzhidov@gmail.com", "bugtrack_url": null, "classifiers": [ "Environment :: Plugins", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 3 :: Only", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Information Analysis", "Topic :: Software Development", "Topic :: Software Development :: Libraries", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "CGRTools\n========\n\n\n.. image:: https://zenodo.org/badge/14690494.svg\n :target: https://zenodo.org/badge/latestdoi/14690494\n\n\nTools for processing of reactions based on Condensed Graph of Reaction (CGR) approach.\n\nBasic operations:\n - Read/write/convert formats: MDL .RDF (RXN) and .SDF (MOL), .MRV, SMILES, INCHI (Linux and Windows), .XYZ, .PDB\n - Standardize molecules and reactions and valid structures checker.\n - Duplicate searching.\n - Tetrahedron, Allene and CIS-TRANS stereo checking.\n - Produce CGRs.\n - Perform subgraph search.\n - Build/edit molecules and reactions.\n - Produce template based reactions and molecules.\n - Atom-to-atom mapping checker and rule-based fixer.\n - Perform MCS search.\n - 2d coordinates generation (based on `SmilesDrawer `_)\n - 2d/3d depiction.\n\nFull documentation can be found `here `_\n\nINSTALL\n=======\n\nHighly recommended to use python 3.8+. Python 3.6 and 3.7 deprecated.\n\n\nLinux Debian based\n------------------\n* Install python3.8, virtualenv and git::\n\n sudo apt install python3.8 python3.8-dev git python3-virtualenv\n \n* Create new environment and activate it::\n\n virtualenv -p python3.8 venv\n source venv/bin/activate\n\nMac\n---\n* Install python3.8 and git using `brew `_::\n\n brew install git\n brew install python3\n\n* Install virtualenv::\n\n pip install virtualenv\n\n* Create new environment and activate it::\n\n virtualenv -p python3.8 venv\n source venv/bin/activate\n \nWindows\n-------\n* Install python3.8 and git using `Chocolatey `_::\n\n choco install git\n choco install python3\n \n* Install virtualenv::\n\n pip install virtualenv\n\n* Create new environment and activate it::\n\n virtualenv venv\n venv\\Scripts\\activate\n\nGeneral part\n------------\n\n* **stable version available through PyPI**::\n\n pip install CGRTools\n\n* Install CGRtools with MRV files parsing support::\n\n pip install CGRTools[mrv]\n\n* Install CGRtools with structures `clean2d` support (Note: install NodeJS into system, see `details `_)::\n\n pip install CGRtools[clean2d]\n\n* Install CGRtools with optimized XYZ parser::\n\n pip install CGRtools[jit]\n\n\n**If you still have questions, please open issue within github.**\n\nPACKAGING\n=========\n\nFor wheel generation just type next command in source root::\n\n python setup.py bdist_wheel\n\nCOPYRIGHT\n=========\n\n* 2014-2022 Timur Madzhidov tmadzhidov@gmail.com product owner, idea and development supervision\n* 2014-2021 Ramil Nugmanov nougmanoff@protonmail.com main developer\n* 2021-2022 Valentina Afonina valiaafo@yandex.ru development and support\n\nCONTRIBUTORS\n============\n\n* Dinar Batyrshin batyrshin-dinar@mail.ru\n* Timur Gimadiev timur.gimadiev@gmail.com\n* Adelia Fatykhova adelik21979@gmail.com\n* Tagir Akhmetshin tagirshin@gmail.com\n* Ravil Mukhametgaleev sonic-mc@mail.ru\n* Valentina Afonina valiaafo@yandex.ru\n\nCITE 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