chemivec 0.0.1a0

Vectorized cheminformatics library leveraging EPAM Indigo Toolkit

Chemivec

Vectorized Cheminformatics Python library, based on EPAM Indigo toolkit C-API and using NumPy for input/output.

Supported operations:

rxn_subsearch(input, query) - reaction substructure match
    input : reaction SMILES array (numpy, pandas and python list supported)
    query : reaction query SMARTS, ex "C=C>>C-C"

Example usage:

import numpy as np
import chemivec

arr = np.array(['[C:1]=O>>[C:1]O', 'C=O>>CO'])
query = "[C:1]=O>>[C:1]O"
res = chemivec.rxn_subsearch(arr, query=query)
print(res)

# Output: array([ True, False]) 

Multithreading

Multithreading realized by OpenMP library. By default, tries to use maximum available number of cores. Number of cores can be specified as a global option or passed as a parameter.

import chemivec

chemivec.rxn_subsearch(arr, query=query)   # default max available cores
chemivec.set_option("n_jobs", 12)                 # change defaults
chemivec.rxn_subsearch(arr, query=query, n_jobs=8)

Atom-to-atom matching (AAM)

If atom mapping is present in the query, ex [C:1]>>[C:1] chemivec follows the standard DAYLIGHT SMARTS rules declared here https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html (Section 4.6 Reaction Queries)

Install

Download from pip

pip install chemivec

Build from sources

python3 -m twine check wheelhouse/*

Ubuntu

sudo apt install build-essential ninja-build mc wget git libcairo2-dev zlib1g-dev -y git clone https://github.com/alkorolyov/chemivec

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh;chmod +x Mambaforge-Linux-x86_64.sh;bash Mambaforge-Linux-x86_64.sh;export MAMBA_NO_BANNER=1

if conda still not seen then ~/.bashrc is not sourced when you log in using SSH.

You need to source it in your ~/.bash_profile like this:

echo "if [ -f ~/.bashrc ]; then . ~/.bashrc fi" >> ~/.bash_profile

restart shell

conda config --set auto_activate_base false mamba create -n dev mamba activate dev mamba install pip pytest -y pip install .

(optional) to build in cibuildwheel

pip install cibuildwheel sudo apt-get install docker.io -y; sudo groupadd docker; sudo usermod -aG docker $USER sudo reboot now cd chemivec cibuildwheel --platform linux

Windows

mingw64 on windows download stable mingw64 release, extract and add to %Path% https://github.com/brechtsanders/winlibs_mingw/releases/download/11.2.0-10.0.0-msvcrt-r1/winlibs-x86_64-posix-seh-gcc-11.2.0-mingw-w64msvcrt-10.0.0-r1.zip download ninja and also add to %Path% https://github.com/ninja-build/ninja/releases/download/v1.11.1/ninja-win.zip cmake -B build -G "Ninja" -D CMAKE_C_COMPILER=gcc.exe -D CMAKE_CXX_COMPILER=g++.exe . cmake --build build --target _chemivec

MacOS

https://github.com/DrDonk/unlocker https://www.wikigain.com/how-to-install-macos-monterey-on-vmware-on-windows-pc/ https://intoguide.com/install-vmware-tools-on-macos-monterey/ https://href.li/?https://softwareupdate.vmware.com/cds/vmw-desktop/fusion/11.1.0/13668589/packages/com.vmware.fusion.tools.darwin.zip.tar

Misc

To check dependencies of your *.pyd library dumpbin should be run from developer command prompt of VS 2022

dumpbin mylib_c_ext.pyd /DEPENDENTS