CIMtools

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

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