PF_HP

Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings).

Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. Hier implementieren wir einen brute-force Algorithmus zur Lösung kurzer Eingabesequenzen (0-1-Bitstrings) für die Proteinfaltung.

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Credits
======
Principle Investigator
--------------------------
Gerrit Leder: protein folding algorithm design and testing, and initial implementation in Eiffel.

Eiffel Consultant
---------------------
Finnian Reilly: Eiffel code optimization and parallel processing adaptation.
www.hex11software.com
finnian at eiffel hyphen loop dot com

Features

parallel computation with command line flag -pf2_mt
defaults to 4 threads can be customized with switch -threads ...
custom 0-1-bitstring with command line flag -sequence ...
serial algorithm with command line flag -pf2
To-Do: Bugfix pf3 and pf3_mt, Implementation w/ directions S, R and L
To-Do: make lib EL void-safe
To-Do: unit-tests on CLI and IDE

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License

GNU General Public License version 2.0 (GPLv2)

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