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efp_db
templates
.gitignore
CreateNewFragment.py
LICENSE
README
convert2EFP.py
fragrepr.py
gencluster.py
pyEFP.py

README

pyEFP is a library and tools to represent large molecules as a union of small effective fragments.

You can find more information about effective fragments potential in the following publications:

1) Mark S. Gordon, Dmitri G. Fedorov, Spencer R. Pruitt and Lyudmila V. Slipchenko,
"Fragmentation Methods: A Route to Accurate Calculations on Large Systems",
Chem. Rev., 2012, V. 112, Pp. 632-672

2)Ilya A. Kaliman and Lyudmila V. Slipchenko,
"LIBEFP: A New Parallel Implementation of the Effective
Fragment Potential Method as a Portable Software Library",
J. Comp. Chem., 2013, V. 34, Pp. 2284-2292.


The project consists of several files:

pyEFP.py - a library to read, write and store EFP data.

fragrepr.py - a library to subdivide molecule into fragments.

convert2EFP.py - a tool to generate input file for large molecule in GAMESS format.

gencluster.py - a tool to construct a shell of given thickness around the QM part of the system.

CreateNewFragment.py - a tool to calculate new effective fragment and add it to the database