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* amphihelix, version 0.2.2  *
* Onur Erbilgin, Kerfeld Lab *
* http://www.kerfeldlab.org  *
*   oerbilgin@berkeley.edu   *
*     onuruno.e@gmail.com    *
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COMPATIBLE OPERATING SYSTEMS:
(have been tested in these OS)
---Mac OS X 10.6+
---Windows 7

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BASIC INFORMATION:

The purpose of this script is for the batch calculation of the 
amphipathicity, or hydrophobic moment (HM), of alpha helices.

If you publish any work resulting from the use of this script, please 
reference the Kerfeld lab website: http://www.kerfeldlab.org

This script must be run from the command line. 
The usage of the script is:
$ amphihelix <input_file.txt> <output_file.txt>

For Mac OS X users: You will probably have to change permissions to allow execution of the script:
$ chmod 777 amphihelix_0.2.2_osx

The input file should be in FASTA format.
---The script is not case-sensitive.
---Gaps in the sequence are removed before calculating HM:
	example: PEPTI-DE --> PEPTIDE
---Only the 20 standard amino acid single letter codes are allowed:
	A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V
	Any other letter in the input peptide will cause that peptide
	to not have its HM calculated, and this will be noted in the 
	'Notes' column of the output file, along with what the offending
	peptide(s) is/are.	

The output file will be tab delimited, and include the sequence name
(the FASTA header; what is after the '>'), the peptide for which the
HM was calculated for (i.e. after removing gaps), the calculated HM,
and any notes (if gaps were removed or if invalid characters were
found).

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METHODS AND REFERENCES:

The equation used to calculate the HM is from the heliquest help site:
http://heliquest.ipmc.cnrs.fr/HelpProcedure.htm

That equation is a derivation from the equation published in 1982:
Eisenberg, D., Weiss, R.M., and Terwilliger, T.C. (1982) The helical 
hydrophobic moment: a measure of the amphiphilicity of a helix. 
Nature 299: 371-374

The hydrophobicity values of each amino acid were from:
Fauchère, J., and Pliska, V. 1983. Hydrophobic parameters {pi} of 
amino-acid side chains from the partitioning of N-acetyl-amino-acid 
amides. Eur. J. Med. Chem. 8: 369–375

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Extra information for those of you with too much time:

The original script was written in Python 3.3

For ease of distribution, PyInstaller 2.1 was used to package the 
script into a single executable file. However, PyInstaller 2.1 
was not yet compatible with Python3, so 3to2 was used to convert 
the Python3 syntax to Python2 syntax. 
PyInstaller homepage: https://github.com/pyinstaller/pyinstaller/wiki
3to2 homepage: http://www.startcodon.com/wordpress/category/3to2/

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Written by Onur Erbilgin
December 8, 2014