CGRtools is a set of tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach, details on Github https://github.com/cimm-kzn/CGRtools. Published in JCIM DOI
- Read /write /convert formats MDL .RDF and .SDF, SMILES, .MRV
- Standardize reactions and valid structures checker.
- Produce CGRs.
- Perfrom subgraph search.
- Build /correct molecules and reactions.
- Produce template based reactions.
stable version are available through PyPI
pip install CGRTools
Install CGRtools library DEV version for features that are not well tested
pip install -U git+https://github.com/cimm-kzn/CGRtools.git@master#egg=CGRtools
There is also a tutorial using Jupyter notebook https://github.com/cimm-kzn/CGRtools/tree/master/tutorial
The Chemfp project started as a way to promote the FPS format for cheminformatics fingerprint exchange and has evolved into a set of command-line tools and a Python library for fingerprint generation and high-performance similarity search. The 10 years of work and research results of the chemfp project have now been described in an excellent publication.
I looked at Chemfp when comparing various options for clustering large datasets and Chemfp was one of the highest performing, and Andrew Dalke was very responsive to questions.
When I wrote the article entitled A few thoughts on scientific software one of the responses I got was that people did not know about the existence of open-source chemistry toolkits so I thought I'd publish a page that hopefully prevent stop people reinventing the wheel. Here are a few open-source cheminformatics toolkits that I'm aware of.
As a follow up I thought I'd put together a list of useful python libraries for data science
As always happy to hear comments or suggestion for additions.
OpenEye have announced the release of OpenEye Toolkits v2018.Oct. These libraries include the usual support for C++, Python, C#, and Java. HIGHLIGHTS:
- Omega TK now includes a method specifically tuned to sample macrocyclic conformational space.
- FastROCS TK is now available in C++ and Java.
- Quacpac TK includes improvements to the tautomer functionality.
Full details are in the Release notes.