CIMtools

ChemoInformatics Modeling tools distributive. Include ISIDA Fragmentor python wrapper and RDtool atom-to-atom mapper python wrapper.

Documentation

https://cimtools.readthedocs.io

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

CONTRIBUTORS

SUPERVISION

Timur Madzhidov tmadzhidov@gmail.com

Subpackages

Tutorial