CIMtools
ChemoInformatics Modeling tools distributive. Include ISIDA Fragmentor python wrapper and RDtool atom-to-atom mapper python wrapper.
Documentation
DataSets
CIMtools include datasets of reactional rate constants (SN2, E2, Diels-Alder) and tautomerism equilibriums (Nicklaus dataset).
Has same API as sklearn. See tutorial for example.
from CIMtools.datasets import load_sn2, load_e2, load_da, load_nicklaus_tautomers
INSTALL
Linux Debian based
Install python3.7, virtualenv and git:
sudo apt install python3.7 python3.7-dev git python3-virtualenv
Create new environment and activate it:
virtualenv -p python3.7 venv source venv/bin/activate
Mac
Install python3.7 and git using <https://brew.sh>:
brew install git brew install python3
Install virtualenv:
pip install virtualenv
Create new environment and activate it:
virtualenv -p python3.7 venv source venv/bin/activate
Windows
Install python3.7 and git using <https://chocolatey.org/>:
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 will be available through PyPI:
pip install CIMtools
Install CGRtools library DEV version for features that are not well tested. Git lfs installation required <https://git-lfs.github.com/>:
pip install -U git+https://github.com/cimm-kzn/CIMtools.git@master#egg=CIMtools
If you still have questions, please open issue within github.
SETUP
For ChemAxon standardizer used pyjnius. First of all install JDK (not JRE) OpenJDK or Oracle. Some times it can’t to find java installation properly. Just set environment variables:
JAVA_HOME = '/path/to/dir/which/contain/bin/dir'. for example /usr/lib/jvm/java-11-openjdk-amd64
JVM_PATH = '/path/to/lib/server/libjvm.so'. For example '/usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so'
PACKAGING
For wheel generation just type next command in source root:
python setup.py bdist_wheel
COPYRIGHT
2015-2021 Ramil Nugmanov nougmanoff@protonmail.com
2021-2022 Timur Madzhidov tmadzhidov@gmail.com
2022-2023 Timur Gimadiev timur.gimadiev@gmail.com
CONTRIBUTORS
Ramil Nugmanov - main developer nougmanoff@protonmail.com
Assima Rakhimbekova asima.astana@outlook.com
Tagir Akhmetshin tagirshin@gmail.com
Zarina Ibragimova zarinaIbr12@yandex.ru
SUPERVISION
Timur Madzhidov tmadzhidov@gmail.com