Macs in Chemistry

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An automated framework for NMR chemical shift calculations of small organic molecules

 

A recent paper in Journal of Cheminformatics describes An automated framework for NMR chemical shift calculations of small organic molecules DOI.

As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties—specifically NMR chemical shifts in this manuscript—via the open source, high-performance computational chemistry software, NWChem.

Isicle is available from GitHub https://github.com/pnnl/isicle or can be installed using Conda (with required dependencies

conda create -n isicle -c bioconda -c openbabel -c rdkit -c ambermd python=3.6.1 openbabel rdkit ambertools snakemake numpy pandas yaml statsmodels

In addition, ensure the following third-party software is installed and added to your PATH:

cxcalc (license required from ChemAxon, Marvin)
NWChem http://www.nwchem-sw.org/index.php/Download.

ISiCLE is implemented using the Snakemake workflow management system, enabling scalability, portability, provenance, fault tolerance, and automatic job restarting. Snakemake provides a readable Python-based workflow definition language and execution environment that scales, without modification, from single-core workstations to compute clusters through as-available job queuing based on a task dependency graph.

There is more details on Snakemake here.

I've added Isicle to the Spectroscopy Page.


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