[med-svn] [pscoils] 03/05: New upstream version 1.0+20120128
Andreas Tille
tille at debian.org
Tue Dec 26 21:57:33 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pscoils.
commit c3f8432af0a3a84285b62fd7443a329176715ac6
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 26 22:56:01 2017 +0100
New upstream version 1.0+20120128
---
LICENSE.TXT | 674 ++++++++++++++++++++++++++++++++++++++++++++++
__init__.py | 0
debian/changelog | 5 -
debian/compat | 1 -
debian/control | 19 --
debian/copyright | 28 --
debian/docs | 1 -
debian/rules | 11 -
debian/source/format | 1 -
debian/watch | 4 -
doc/doc.aux | 29 ++
doc/doc.dvi | Bin 0 -> 10816 bytes
doc/doc.log | 124 +++++++++
doc/doc.pdf | Bin 0 -> 66265 bytes
doc/doc.tex | 181 +++++++++++++
doc/doc.tex.bak | 168 ++++++++++++
pscoils/psCoils.py | 345 ++++++++++++++++++++++++
setup.py | 18 ++
test/CEBA_BOVIN.seq | 2 +
test/ferritin.Coils | 66 +++++
test/ferritin.PCoils | 66 +++++
test/ferritin.PSCoils | 66 +++++
test/ferritin.PredCoils | 66 +++++
test/ferritin.PredPCoils | 66 +++++
test/ferritin.PredPSCoils | 66 +++++
test/ferritin.cc | 67 +++++
test/ferritin.fasta | 2 +
test/ferritin.prof | 68 +++++
test/test.sh | 11 +
29 files changed, 2085 insertions(+), 70 deletions(-)
diff --git a/LICENSE.TXT b/LICENSE.TXT
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/LICENSE.TXT
@@ -0,0 +1,674 @@
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+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/__init__.py b/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 0990298..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,5 +0,0 @@
-pscoils (1.0+20120128-1) UNRELEASED; urgency=low
-
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
-
- -- Piero Fariselli <piero.fariselli at unibo.it> Sun, 29 Jan 2012 10:42:19 +0100
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index f599e28..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-10
diff --git a/debian/control b/debian/control
deleted file mode 100644
index d2e16e9..0000000
--- a/debian/control
+++ /dev/null
@@ -1,19 +0,0 @@
-Source: pscoils
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Piero Fariselli <piero.fariselli at unibo.it>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 10),
- python
-Standards-Version: 3.9.8
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/pscoils/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/pscoils/trunk/
-Homepage: http://www.biocomp.unibo.it/piero/PS-COILS/
-
-Package: pscoils
-Architecture: all
-Depends: ${misc:Depends},
- ${python:Depends}
-Description: coiled-coil predictor
- This is a python version of COILS program that takes advantage
- of both evolutionary and signle sequence information.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 82eceba..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,28 +0,0 @@
-Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: pscoils
-Source: http://www.biocomp.unibo.it/piero/PS-COILS/download
-
-Files: *
-Copyright: 2012 Piero Fariselli <piero.fariselli at unibo.it>
-License: GPL-2.0+
-
-Files: debian/*
-Copyright: 2012 Piero Fariselli <piero.fariselli at unibo.it>
-License: GPL-2.0+
-
-License: GPL-2.0+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --git a/debian/docs b/debian/docs
deleted file mode 100644
index 2c94003..0000000
--- a/debian/docs
+++ /dev/null
@@ -1 +0,0 @@
-LICENSE.TXT
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 07661fe..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/make -f
-
-# Uncomment this to turn on verbose mode.
-export DH_VERBOSE=1
-
-%:
- dh $@ --with python2
-
-#override_dh_auto_test:
- #any unit test can go here
-
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index e0fc178..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,4 +0,0 @@
-version=4
-
-http://www.biocomp.unibo.it/piero/PS-COILS/download/pscoils-([\d.+]+)\.orig\.tar\.gz
-
diff --git a/doc/doc.aux b/doc/doc.aux
new file mode 100644
index 0000000..83b3b52
--- /dev/null
+++ b/doc/doc.aux
@@ -0,0 +1,29 @@
+\relax
+\citation{Lupas}
+\citation{pcoils}
+\citation{Lupas}
+\citation{comparison}
+\citation{Lupas}
+\select at language{english}
+\@writefile{toc}{\select at language{english}}
+\@writefile{lof}{\select at language{english}}
+\@writefile{lot}{\select at language{english}}
+\@writefile{toc}{\contentsline {section}{\numberline {1}PSCOILS program}{1}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Background}{1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}COILS}{1}}
+\citation{Lupas}
+\citation{pcoils}
+\newlabel{eq:prodcoils}{{4}{2}}
+\newlabel{eq:fcoils}{{5}{2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}PCOILS}{2}}
+\newlabel{eq:prodpcoils}{{6}{2}}
+\newlabel{eq:fpcoils}{{7}{2}}
+\citation{pcoils}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3}PSCOILS}{3}}
+\newlabel{eq:prodpscoils}{{8}{3}}
+\newlabel{eq:fpscoils}{{9}{3}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}PSCOILS usage}{3}}
+\bibcite{Lupas}{1}
+\bibcite{pcoils}{2}
+\bibcite{comparison}{3}
+\@writefile{toc}{\contentsline {section}{\numberline {4}Availability}{4}}
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+h, portuges, romanian, russian, serbian, slovak, slovene, spanish, swedish, tur
+kish, ukrainian, nohyphenation, loaded.
+(/usr/share/texmf-tetex/tex/latex/base/article.cls
+Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
+(/usr/share/texmf-tetex/tex/latex/base/size11.clo
+File: size11.clo 2004/02/16 v1.4f Standard LaTeX file (size option)
+)
+\c at part=\count79
+\c at section=\count80
+\c at subsection=\count81
+\c at subsubsection=\count82
+\c at paragraph=\count83
+\c at subparagraph=\count84
+\c at figure=\count85
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+\bibindent=\dimen102
+)
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+Package: babel 2004/11/20 v3.8d The Babel package
+
+(/usr/share/texmf-tetex/tex/generic/babel/english.ldf
+Language: english 2004/06/14 v3.3o English support from the babel system
+
+(/usr/share/texmf-tetex/tex/generic/babel/babel.def
+File: babel.def 2004/11/20 v3.8d Babel common definitions
+\babel at savecnt=\count87
+\U at D=\dimen103
+)
+\l at british = a dialect from \language\l at english
+\l at UKenglish = a dialect from \language\l at english
+\l at canadian = a dialect from \language\l at american
+\l at australian = a dialect from \language\l at british
+\l at newzealand = a dialect from \language\l at british
+)) (./doc.aux)
+\openout1 = `doc.aux'.
+
+LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 10.
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+
+Overfull \hbox (13.94177pt too wide) in paragraph at lines 23--25
+\OT1/cmr/m/n/10.95 Here we sum-ma-rize the ba-sic al-go-rithms be-hind COILS, P
+COILS and PSCOILS
+ []
+
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+
+] [2]
+Overfull \hbox (2.16733pt too wide) in paragraph at lines 123--123
+[]\OT1/cmtt/m/n/10.95 This program is distributed in the hope that it will be u
+seful,[]
+ []
+
+
+Overfull \hbox (7.91602pt too wide) in paragraph at lines 134--134
+[] \OT1/cmtt/m/n/10.95 -l T/F # print prediction labels when set T (default) i
+f P>0.5[]
+ []
+
+
+Overfull \hbox (65.4029pt too wide) in paragraph at lines 134--134
+[] \OT1/cmtt/m/n/10.95 -L [0.0,1.0] lambda value. It will be used only if both
+-f and -p are set[]
+ []
+
+[3]
+Overfull \hbox (25.16208pt too wide) in paragraph at lines 157--157
+[] \OT1/cmtt/m/n/10.95 Pos A Hep Score Prob Gcc Gg Pred (Loop=L Coi
+ledcoil=C)[]
+ []
+
+
+Overfull \hbox (96.97939pt too wide) in paragraph at lines 165--167
+\OT1/cmr/m/n/10.95 PSCOILS is avail-able as stand-alone python pro-gram at http
+://www.biocomp.unibo.it/piero/PS-
+ []
+
+Missing character: There is no � in font cmr10!
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+[4] [5] (./doc.aux) )
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+Output written on doc.dvi (5 pages, 10816 bytes).
diff --git a/doc/doc.pdf b/doc/doc.pdf
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@@ -0,0 +1,181 @@
+\documentclass[11pt,english]{article}
+
+\usepackage[english]{babel}
+
+
+
+\title{PS-COILS}
+
+\author{Piero Fariselli}
+\begin{document}
+
+\maketitle
+
+\section{PSCOILS program}
+
+PSCOILS is a simple evolution of COILS \cite{Lupas} and PCOILS \cite{pcoils} programs.
+It uses the same parameters that were developed for COILS and exploits both sequence and
+evolutionary information (in the form of sequence profiles). For the details of the
+parameter construction please see \cite{Lupas,comparison}.
+
+\section{Background}
+
+Here we summarize the basic algorithms behind COILS, PCOILS and PSCOILS in order to
+highlight the basic differences.
+
+\subsection{COILS}
+The coils program is based on scoring tables $S^h(a)$ that are used to compute the probability score
+for each segment of a protein sequence (see \cite{Lupas}), and some parameters that
+define Gaussian probabilities. Then the main parameters are:
+\begin{itemize}
+\item $ \mu_{cc}, \mu_{g}$ the average scoring values of the coiled-coil and globular protein sets;
+\item $ \sigma_{cc}, \sigma_{g}$ the standard deviation of the scoring values for the
+ coiled-coil and globular protein sets;
+\item $ S^h(a)=$ the score for the residue type $a$ in the heptad position $h$ (from 1 to 7).
+\end{itemize}
+So that the probability of a coiled-coil segment of length $W$ starting at position $i$ in
+a given sequence is computed as
+\begin{equation}
+Pr_i=\frac{G_{cc}}{G_{cc}+c\cdot G_{g}}
+\end{equation}
+where $c$ is the bias for the most abundant globular class ($g$) and
+$G_{cc}$ and $G_{g}$ are defined as
+\begin{equation}
+G_{cc}=\frac{1}{\surd{2}\sigma_{cc}}e^{-\frac{(x_i-\mu_{cc})^2}{\sigma_{cc}^2}}
+\end{equation}
+\begin{equation}
+G_{g}=\frac{1}{\surd{2}\sigma_{g}}e^{-\frac{(x_i-\mu_{g})^2}{\sigma_{g}^2}}
+\end{equation}
+
+The score $x_i$ is computed using the matrix $S^h(a)$ (\cite{Lupas}) along the segment $W$ starting
+at position $i$ as
+\begin{equation}
+x_i=(\prod_{h=1}^W f(a_{i+h},h)^{e_h})^{1/N}
+\label{eq:prodcoils}
+\end{equation}
+where $e_h$ is the exponential weight of the position $h$ (if not weighted is simply $e_h=1$) and
+$N$ is the normalization factor $N=\sum_{h=1}^W e_h$.
+The function $f$ is in the case of COILS program is simply
+\begin{equation}
+f(a_{i+h},h)=S^h(a_{i+h})
+\label{eq:fcoils}
+\end{equation}
+where $S^h(a_{i+h})$ is the element of the COILS scoring table
+accounting for the residue type $a_{i+h}$ in the $h^{th}$ heptad position.
+
+\subsection{PCOILS}
+
+For sake of clarity we have to mention that this is {\em our implementation} of PCOILS, and we cannot
+guarantee that the original PCOILS program works in the same way, since the authors
+does not show the explicit algorithm \cite{pcoils}. However, in case of our PCOILS, all the
+machinery described above still remains untouched, with the exception of function $f$
+(Eq. \ref{eq:fcoils}). Since we are dealing with evolutionary information
+computed from a given multiple alignment, instead of the single-sequence $s$
+we work with the profile $P_k(a)$, that represents the frequency of residue $a$ in position $k$ of
+the alignment.
+In this case the PCOILS score is still defined by an equation similar to Eq.\ref{eq:prodcoils},
+but with the new function:
+\begin{equation}
+x_i=(\prod_{h=1}^W f(S,P,h)^{e_h})^{1/N}
+\label{eq:prodpcoils}
+\end{equation}
+and
+\begin{equation}
+f(S,P,h)=<S^h,P_{i+h}>=\sum_{a \in \{Residues\}} S^h(a)\cdot P_{i+h}(a)
+\label{eq:fpcoils}
+\end{equation}
+
+\subsection{PSCOILS}
+PSCOILS combines the sequence and the profile information using a linear
+weighting scheme, namely $\lambda COILS + (1-\lambda)PCOILS$ with $\lambda$
+in the range of $[0,1]$ the only variation with respect to the previous algorithm
+is again the $f$ equation (\ref{eq:fcoils} and \ref{eq:fpcoils}). We then have
+as before
+\begin{equation}
+x_i=(\prod_{h=1}^W f(S,P,h,\lambda)^{e_h})^{1/N}
+\label{eq:prodpscoils}
+\end{equation}
+and
+\begin{equation}
+f(S,P,h,\lambda)=\lambda S^h(a_{i+h}) + (1-\lambda) <S^h,P_{i+h}>
+\label{eq:fpscoils}
+\end{equation}
+where the meaning of $S^h(a_{i+h})$ and $<S^h,P_{i+h}>$ are the same as in
+\ref{eq:fcoils} and \ref{eq:fpcoils}, respectively.
+No attempt have been made to optimize $\lambda$ but in the current stage it has
+been set to $1/2$. In this case the sequence and the profile are equally weighted.
+
+
+\section{PSCOILS usage}
+
+The program {\tt psCoils.py} is written in {\bf python} and it is distributed under the
+{\em GPL License},
+\begin{verbatim}
+psCoils.py is free software and can be redistributed and/or
+modified under the terms of the GNU General Public License as
+published by the Free Software Foundation.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+\end{verbatim}
+{\tt psCoils.py} incorporates both COILS and our version of PCOILS, since the original one
+\cite{pcoils} were not explicitly described.
+Just typing the program name {\tt psCoils.py} on the standard output will appear
+\begin{verbatim}
+USAGE: ./psCoils.py -f fasta -p profile [options]
+Options:
+ -W 14/21/28 # one of the possible windows (default 21)
+ -w w/uw # weight or unweight default=uw
+ -l T/F # print prediction labels when set T (default) if P>0.5
+ -L [0.0,1.0] lambda value. It will be used only if both -f and -p are set
+\end{verbatim}
+The parameters are the standard one defined for COILS, such as:
+\begin{itemize}
+\item {\tt -W}: the input window that is set to 21 as default;
+\item {\tt -w}: can set the heptad weighted {\tt w}, or unweighted {\tt uw} periodicity
+\item {\tt -l}: set the label printing in the output options (unless -l F is set)
+\item {\tt -L}: this set the linear weighting scheme between sequence and profile, according to
+ $\lambda$ Sequence +(1-$\lambda$) Profile.
+\end{itemize}
+{\tt psCoils.py} can be used as COILS, PCOILS or PSCOILS depending on the different
+input provided, such as:
+\begin{itemize}
+\item As {\bf COILS}: use only {\tt -f fasta} option.
+\item As {\bf PCOILS}: use only {\tt -p profile} option.
+\item As {\bf PSCOILS}: use both {\tt -f fasta -p profile} options.
+\end{itemize}
+A typical output is
+\begin{verbatim}
+ Pos A Hep Score Prob Gcc Gg Pred (Loop=L Coiledcoil=C)
+ 1 C a 0.480 0.000 0.000 0.927 L
+ 2 M a 0.804 0.000 0.001 4.596 L
+ 3 S b 0.804 0.000 0.001 4.596 L
+..
+\end{verbatim}
+where {\tt Pos} is the sequence position, {\tt A} contains the residue sequence
+(only an {\tt x} if PCOILS is used), {\tt Prob} is the computed probability as
+described above, {\tt Gcc} and {\tt Gg} are Gaussian values obtained as described above
+and {\tt Pred} is the label associated at {\tt Prob} if its value is greater of $0.5$.
+
+\section{Availability}
+
+PSCOILS is available as stand-alone python program at http://www.biocomp.unibo.it/piero/PS-COILS/download/
+or as python package as part of the {\tt plone4bio} effort at http://www.plone4bio.org.
+
+\begin{thebibliography}{99}
+
+\bibitem{Lupas} Lupas AN, Van Dyke M and Stock J. (1991) ``Predicting coiled coils from protein
+ sequences''. $Science$, 252, 1162-1164.
+
+\bibitem{pcoils} Gruber M, Soding J and Lupas AN (2005) ``REPPER-repeats and their periodicities
+in fibrous proteins'', {\em Nucleic Acids Res.} 33:239–243.
+
+\bibitem{comparison} Gruber M, Soding J and Lupas AN (2006)
+``Comparative analysis of coiled-coil prediction methods''. {\em J Struct Biol}, 155:140-145.
+
+\end{thebibliography}
+
+\end{document}
diff --git a/doc/doc.tex.bak b/doc/doc.tex.bak
new file mode 100644
index 0000000..100686f
--- /dev/null
+++ b/doc/doc.tex.bak
@@ -0,0 +1,168 @@
+\documentclass[11pt,english]{article}
+
+\usepackage[english]{babel}
+
+
+
+\title{PS-COILS}
+
+\author{Piero Fariselli}
+\begin{document}
+
+\maketitle
+
+\section{PSCOILS program}
+
+PSCOILS is a simple evolution of COILS \cite{Lupas} and PCOILS \cite{pcoils} programs.
+It uses the same parameters that were developed for COILS and exploits both sequence and
+evolutionary information (in the form of sequence profiles). For the details of the
+parameter construction plese see \cite{Lupas,comparison}.
+
+\section{Background}
+
+Here we summarize the basic algorithms behind COILS, PCOILS and PSCOILS in order to
+understand the basic differences.
+
+\subsection{COILS}
+The coils program is based on scoring tables $S^h(a)$ that are used to compute the probability score
+for each segment of a protein sequence (see \cite{Lupas}), and some paramters that
+define gaussian probabilities. Then the main parameters are:
+\begin{itemize}
+\item $ \mu_{cc}, \mu_{g}$ the average values of the coiled-coil and globular protein sets;
+\item $ \sigma_{cc}, \sigma_{g}$ the standard deviation of the coiled-coil and globular protein sets;
+\item $ S^h(a)=$ the score for the residue type $a$ in the heptad position $h$ (from 1 to 7).
+\end{itemize}
+So that the probability of a coiled-coil segment of length $W$ starting at position $i$ in sequence
+is given by
+\begin{equation}
+Pr_i=\frac{G_{cc}}{G_{cc}+c\cdot G_{g}}
+\end{equation}
+where $c$ is the bias for the most abundant globular class ($g$) and
+$G_{cc}$ and $G_{g}$ are defined as
+\begin{equation}
+G_{cc}=\frac{1}{\surd{2}\sigma_{cc}}e^{-\frac{(x_i-\mu_{cc})^2}{\sigma_{cc}^2}}
+\end{equation}
+\begin{equation}
+G_{g}=\frac{1}{\surd{2}\sigma_{g}}e^{-\frac{(x_i-\mu_{g})^2}{\sigma_{g}^2}}
+\end{equation}
+
+The score $x_i$ is computed using the matrix $S^h(a)$ (\cite{Lupas}) along the segment $W$ starting
+at position $i$ as
+\begin{equation}
+x_i=(\prod_{h=1}^W f(a_{i+h},h)^{e_h})^{1/N}
+\label{eq:prodcoils}
+\end{equation}
+where $e_h$ is the exponential weight of the position $h$ (if not weighted is simply $e_h=1$) and
+$N$ is the normalization factor $N=\sum_{h=1}^W e_h$.
+The function $f$ is in the case of COILS program is simply
+\begin{equation}
+f(a_{i+h},h)=S^h(a_{i+h})
+\label{eq:fcoils}
+\end{equation}
+
+\subsection{PCOILS}
+
+In case of PCOILS, all the machinery described above still remains untouched, with the exception
+of function $f$ (\ref{eq:fcoils}). Since we are using a profile matrix, instead of the sequence $s$
+we are dealing with $P_k(a)$, that is the frequency of residue $a$ in position $k$ of the alignment.
+In this case the PCOILS score is still defined by an equation similar to Eq.\ref{eq:prodcoils},
+but with the new function:
+\begin{equation}
+x_i=(\prod_{h=1}^W f(S,P,h)^{e_h})^{1/N}
+\label{eq:prodpcoils}
+\end{equation}
+and
+\begin{equation}
+f(S,P,h)=<S^h,P_{i+h}>=\sum_{a=residues} S^h(a)\cdot P_{i+h}(a)
+\label{eq:fpcoils}
+\end{equation}
+
+\subsection{PSCOILS}
+PSCOILS combines the sequence and the profile information using a linear
+weighting scheme, namely $\lambda COILS + (1-\lambda)PCOILS$ with $\lambda$
+in the range of $[0,1]$ the only variation with respect to the previous algorithm
+is again the $f$ equation (\ref{eq:fcoils} and \ref{eq:fpcoils}). We then have
+as before
+\begin{equation}
+x_i=(\prod_{h=1}^W f(S,P,h,\lambda)^{e_h})^{1/N}
+\label{eq:prodpscoils}
+\end{equation}
+and
+\begin{equation}
+f(S,P,h,\lambda)=\lambda S^h(a_{i+h}) + (1-\lambda) <S^h,P_{i+h}>
+\label{eq:fpscoils}
+\end{equation}
+where the meaning of $S^h(a_{i+h})$ and $<S^h,P_{i+h}>$ are the same as in
+\ref{eq:fcoils} and \ref{eq:fpcoils}, respectively.
+No attempt have been made to optimize $\lambda$ but in the actual stage it has
+been set to $1/2$. In this case the sequence and the profile are equally weighted.
+
+
+\section{PSCOILS usage}
+
+The program {\tt psCoils.py} is written in {\bf python} and it is distrubuted under the
+{\em GPL License},
+\begin{verbatim}
+psCoils.py is free software and can be redistributed and/or
+modified under the terms of the GNU General Public License as
+published by the Free Software Foundation.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+\end{verbatim}
+{\tt psCoils.py} incorporetes both COILS and our version of PCOILS, since the original one
+\cite{pcoils} were not explicitly described.
+Just typing the program name {\tt psCoils.py} on the standard output will appear
+\begin{verbatim}
+USAGE: ./psCoils.py -f fasta -p profile [options]
+Options:
+ -W 14/21/28 #deafult 21 one of the possible window
+ -w w/uw # weight or unweight default=uw
+ -l T/F # print prediction labels when set T (default) if P>0.5
+ -L [0.0,1.0] lambda value. It will be used only if both -f and -p are set
+\end{verbatim}
+The parameters are the standard one defined for COILS, such as:
+\begin{itemize}
+\item {\tt -W}: the input vindow that is set to 21 as default;
+\item {\tt -w}: can set the heptad weighted {\tt w}, or unweighted {\tt uw} periodicity
+\item {\tt -l}: set the label printing in the output options (unless -l F is set)
+\item {\tt -L}: this set the linear weighting scheme between sequence and profile, according to
+ $\lambda$ Sequence +(1-$\lambda$) Profile.
+\end{itemize}
+{\tt psCoils.py} can be used as COILS, PCOILS or PSCOILS depending on the different
+input provided, such as:
+\begin{itemize}
+\item As {\bf COILS}: use only {\tt -f fasta} option.
+\item As {\bf PCOILS}: use only {\tt -p profile} option.
+\item As {\bf PSCOILS}: use both {\tt -f fasta -p profile} options.
+\end{itemize}
+A typical output is
+\begin{verbatim}
+ Pos A Hep Score Prob Gcc Gg Pred (Loop=L Coiledcoil=C)
+ 1 C a 0.480 0.000 0.000 0.927 L
+ 2 M a 0.804 0.000 0.001 4.596 L
+ 3 S b 0.804 0.000 0.001 4.596 L
+..
+\end{verbatim}
+where {\tt Pos} is the sequence position, {\tt A} contains the residue sequence
+(only an {\tt x} if PCOILS is used), {\tt Prob} is the computed probability as
+described above, {\tt Gcc} and {\tt Gg} are gaussian values obtained as descibed above
+and {\tt Pred} is the label associated at {\tt Prob} if its value is greater of $0.5$.
+
+\begin{thebibliography}{99}
+
+\bibitem{Lupas} Lupas AN, Van Dyke M and Stock J. (1991) ``Predicting coiled coils from protein
+ sequences''. $Science$, 252, 1162-1164.
+
+\bibitem{pcoils} Gruber M, Soding J and Lupas AN (2005) ``REPPER-repeats and their periodicities
+in fibrous proteins'', {\em Nucleic Acids Res.} 33:239–243.
+
+\bibitem{comparison} Gruber M, Soding J and Lupas AN (2006)
+``Comparative analysis of coiled-coil prediction methods''. {\em J Struct Biol}, 155:140-145.
+
+\end{thebibliography}
+
+\end{document}
diff --git a/pscoils/psCoils.py b/pscoils/psCoils.py
new file mode 100755
index 0000000..2b6e5e3
--- /dev/null
+++ b/pscoils/psCoils.py
@@ -0,0 +1,345 @@
+#!/usr/bin/env python
+'''
+ Copyright (C) 2007 Piero Fariselli
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ psCoils.py Copyright (C) 2007 Piero Fariselli
+ contacts: Piero Fariselli
+ e-mail: piero at biocomp.unibo.it, piero.fariselli at unibo.it
+ Dept. of Biology
+ University of Bologna
+ via Irnerio 42
+ 40126 Bologna
+ Italy
+ This program comes with ABSOLUTELY NO WARRANTY; for details type psCoils.py.
+ This is free software, and you are welcome to redistribute it
+ under the condition of preserving this text
+'''
+
+# Iports
+
+import sys
+import getopt
+import math
+import string
+
+AAs="ACDEFGHIKLMNPQRSTVWY"
+NewMat='''L 2.998 0.269 0.367 3.852 0.510 0.514 0.562
+I 2.408 0.261 0.345 0.931 0.402 0.440 0.289
+V 1.525 0.479 0.350 0.887 0.286 0.350 0.362
+M 2.161 0.605 0.442 1.441 0.607 0.457 0.570
+F 0.490 0.075 0.391 0.639 0.125 0.081 0.038
+Y 1.319 0.064 0.081 1.526 0.204 0.118 0.096
+G 0.084 0.215 0.432 0.111 0.153 0.367 0.125
+A 1.283 1.364 1.077 2.219 0.490 1.265 0.903
+K 1.233 2.194 1.817 0.611 2.095 1.686 2.027
+R 1.014 1.476 1.771 0.114 1.667 2.006 1.844
+H 0.590 0.646 0.584 0.842 0.307 0.611 0.396
+E 0.281 3.351 2.998 0.789 4.868 2.735 3.812
+D 0.068 2.103 1.646 0.182 0.664 1.581 1.401
+Q 0.311 2.290 2.330 0.811 2.596 2.155 2.585
+N 1.231 1.683 2.157 0.197 1.653 2.430 2.065
+S 0.332 0.753 0.930 0.424 0.734 0.801 0.518
+T 0.197 0.543 0.647 0.680 0.905 0.643 0.808
+C 0.918 0.002 0.385 0.440 0.138 0.432 0.079
+W 0.066 0.064 0.065 0.747 0.006 0.115 0.014
+P 0.004 0.108 0.018 0.006 0.010 0.004 0.007'''
+Parameters='''w 14 1.89 0.30 1.04 0.27 20
+w 21 1.79 0.24 0.92 0.22 25
+w 28 1.74 0.20 0.86 0.18 30
+uw 14 1.82 0.28 0.95 0.26 20
+uw 21 1.74 0.23 0.86 0.21 25
+uw 28 1.69 0.18 0.80 0.18 30'''
+
+class Params:
+ ''' define the Coils parameters '''
+ def __init__(self,weighted='w',window=21):
+ ''' initialize the parameters '''
+ self.pow=[1.0]*7
+ if weighted.lower() not in ['w','uw']:
+ self.weight='uw'
+ else:
+ self.weight=weighted.lower()
+ if self.weight=='w':
+ self.pow[0]=self.pow[3]=2.5
+ if window not in [14,21,28]:
+ self.win=21
+ else:
+ self.win=window
+ self.m_cc,self.sd_cc,self.m_g,self.sd_g,self.sc,self.mat=_initData(self.win,self.weight)
+
+
+def _initData(window,weighted):
+ ''' _initData builds the parameters starting from string '''
+ from string import atof, atoi
+ s=NewMat
+ sl=s.split('\n')
+ d={}
+ for e in sl:
+ v=e.split()
+ for k in range(len(v[1:])):
+ d[(v[0],k)]=atof(v[1:][k])
+ s=Parameters
+ sl=s.split('\n')
+ for e in sl:
+ v=e.split()
+ if (v[0] == weighted) and (atoi(v[1])==window):
+ vec=[]
+ for n in v[2:]:
+ vec.append(atof(n))
+ return vec+[d]
+
+
+
+#
+#
+#---------------------------------#
+def readProf(fname,aaOrder='VLIMFWYGAPSTCHRKQEND'):
+ ''' readProf(fname,aaOrder) returns a dictionary profile prof[(pos,aa)]'''
+ try:
+ lines=open(fname,'r').readlines()
+ except:
+ sys.stderr.write('cannot open file '+fname+'\n')
+ sys.exit()
+ prof={}
+ i=0
+ while lines[i].find("#")>=0 and i <len(lines):
+ pos=lines[i].find("ALPHABET=")
+ if pos>0:
+ v=lines[i][pos+len("ALPHABET="):].split()
+ aaOrder=''.join(v[:20])
+
+ i+=1
+ if i >= len(lines):
+ sys.stderr.write('Error in '+fname+'\n')
+ sys.exit()
+ pos=0
+ while i<len(lines):
+ v=lines[i].split()
+ for j in range(len(aaOrder)):
+ prof[(pos,aaOrder[j])]=string.atof(v[j])/100.0
+ # prof[(pos,aaOrder[j])]=string.atoi(v[j])
+ pos+=1
+ i+=1
+ return prof,pos
+
+#---------------------------------#
+
+
+#----------- readFasta files
+def readFasta(fname):
+ ''' readFasta(fname) returns a dictionary
+ '''
+ try:
+ lines=open(fname,'r').readlines()
+ except:
+ sys.stderr.write('cannot open file '+fname+'\n')
+ sys.exit()
+ seqs={}
+ name=''
+ seq=''
+ for line in lines:
+ if line[0]=='>': # assuming fasta file
+ if name != '':
+ seqs[name]=seq
+ seq=''
+ name=line[1:].strip()
+ else:
+ seq+=''.join(line.split())
+ if name != '':
+ seqs[name]=seq
+ return seqs
+#---------------------------------#
+
+#---------------------------------#
+def coilProb(cScore,params):
+ ''' coilProb(curScore,params) returns coiled-coils probability dependin on params'''
+ t1=1/params.sd_cc
+ t2=(cScore-params.m_cc)/params.sd_cc
+ t4=t2*t2
+ Gcc=t1*math.exp(-0.5*t4)
+ t1=1/params.sd_g
+ t2=(cScore-params.m_g)/params.sd_g
+ t4=t2*t2
+ Gg=t1*math.exp(-0.5*t4)
+ return Gg,Gcc,Gcc/(params.sc*Gg + Gcc )
+#---------------------------------#
+
+#---------------------------------#
+def seqScore(mat,seq,sPos,hept_pos):
+ ''' seqScore(mat,aa,pos) comoputes the sequenc based score'''
+ try:
+ retVal=mat[(seq[sPos],hept_pos)]
+ except:
+ retVal=1
+ return retVal
+#---------------------------------#
+
+
+#---------------------------------#
+def profScore(mat,prof,sPos,hept_pos):
+ ''' profScore(mat,aa,pos) comoputes the sequenc based score'''
+ sum=0.0
+ for aa in AAs:
+ prof[(sPos,aa)]
+ mat[(aa,hept_pos)]
+ sum+=prof[(sPos,aa)]*mat[(aa,hept_pos)]
+ return sum
+#---------------------------------#
+
+
+#---------------------------------#
+def pred_coil(seq,seqLen,params,fScore):
+ ''' pred_coil(seq,seqLen,params,fScore) returns the coiled coil prediction of sequence seq'''
+ hept_pos=['a','b','c','d','e','f','g']
+ score=[0.0]*seqLen
+ prob=[0.0]*seqLen
+ gcc=[0.0]*seqLen
+ gg=[0.0]*seqLen
+ hept_seq=['x']*seqLen
+ for i in range(seqLen-params.win+1):
+ this_score=1.0
+ actual_win=0.0
+ for j in range(min(params.win,seqLen-i)):
+ pos=j%7
+ actual_win+=params.pow[pos]
+ this_score*=math.pow( fScore(params.mat,seq,i+j,pos), params.pow[pos] )
+ if actual_win > 0:
+ this_score=math.pow(this_score,1/actual_win)
+ else:
+ this_score=0.0
+ for j in range(min(params.win,seqLen-i)):
+ pos=j%7
+ if this_score > score[i+j]:
+ score[i+j]=this_score
+ hept_seq[i+j]=hept_pos[pos]
+ for i in range(seqLen):
+ gg[i],gcc[i],prob[i]= coilProb(score[i],params)
+ return gg,gcc,prob,hept_seq,score
+
+
+#---------------------------------#
+def pred_coil2(seq,prof,params,ws=0.5):
+ ''' pred_coil2(seq,prof,params,ws=0.5) returns the coiled coil prediction of sequence seq'''
+ hept_pos=['a','b','c','d','e','f','g']
+ seqLen=len(seq)
+ score=[0.0]*seqLen
+ prob=[0.0]*seqLen
+ gcc=[0.0]*seqLen
+ gg=[0.0]*seqLen
+ hept_seq=['x']*seqLen
+ for i in range(seqLen-params.win+1):
+ this_score=1.0
+ actual_win=0.0
+ for j in range(min(params.win,seqLen-i)):
+ pos=j%7
+ actual_win+=params.pow[pos]
+ avScore=(1-ws)*profScore(params.mat,prof,i+j,pos)+ws*seqScore(params.mat,seq,i+j,pos)
+ this_score*=math.pow( avScore , params.pow[pos] )
+ if actual_win > 0:
+ this_score=math.pow(this_score,1/actual_win)
+ else:
+ this_score=0.0
+ for j in range(min(params.win,seqLen-i)):
+ pos=j%7
+ if this_score > score[i+j]:
+ score[i+j]=this_score
+ hept_seq[i+j]=hept_pos[pos]
+ for i in range(seqLen):
+ gg[i],gcc[i],prob[i]= coilProb(score[i],params)
+ return gg,gcc,prob,hept_seq,score
+
+#---------------------------------#
+#---------------------------------#
+def printCoil(seq,seqLen,hept_seq,score,P,Gcc,Gg,labels='T'):
+ ''' '''
+ ccLab="C"
+ loopLab="L"
+ if labels !='T' :
+ for i in range(seqLen):
+ #print "%4d %c %c %7.3f %7.3f (%7.3f %7.3f)" % (i+1,seq[i],hept_seq[i],score[i],P[i],Gcc[i],Gg[i])
+ print "%4d %c %c %7.3f %7.3f %7.3f %7.3f" % (i+1,seq[i],hept_seq[i],score[i],P[i],Gcc[i],Gg[i])
+ else:
+ print " Pos A Hep Score Prob Gcc Gg Pred (Loop=L Coiledcoil=C)"
+ for i in range(seqLen):
+ if P[i] > 0.5:
+ clabel=ccLab
+ else:
+ clabel=loopLab
+ print "%4d %c %c %7.3f %7.3f %7.3f %7.3f %s" % (i+1,seq[i],hept_seq[i],score[i],P[i],Gcc[i],Gg[i],clabel)
+ return
+#---------------------------------#
+#---------------------------------#
+def usage(prog):
+ ''' '''
+ print "USAGE: ",prog, "-f fasta -p profile [options]"
+ print "Options:"
+ print " -W 14/21/28 # one of the possible windows (default 21)"
+ print " -w w/uw # weight or unweight default=uw"
+ print " -l T/F # print prediction labels when set T (default) if P>0.5"
+ print " -L [0.0,1.0] lambda value. It will be used only if both -f and -p are set "
+ return
+#---------------------------------#
+
+if __name__=='__main__':
+ try:
+ opts, args = getopt.getopt(sys.argv[1:], "f:p:w:W:l:L:")
+ except:
+ usage(sys.argv[0])
+ sys.exit(2)
+ weight='un'
+ labels='T'
+ wlambda=0.5
+ win=21
+ modefasta=modeprofile=False
+ if not opts:
+ usage(sys.argv[0])
+ sys.exit(2)
+ for o,a in opts:
+ if o == '-f':
+ seqs=readFasta(a)
+ modefasta=True
+ elif o == '-p':
+ prof,profLen=readProf(a)
+ modeprofile=True
+ elif o == '-L':
+ wlambda=string.atof(a)
+ elif o == '-l':
+ labels=a
+ elif o == '-w':
+ weight=a
+ elif o == '-W':
+ try:
+ win=string.atoi(a)
+ except:
+ usage(sys.argv[0])
+ sys.exit(2)
+ else:
+ usage(sys.argv[0])
+ sys.exit(2)
+ params=Params(weight,win)
+ if modeprofile and modefasta:
+ #use both
+ for name in seqs.keys(): # WARNING We assume only one sequence!!!
+ gg,gcc,prob,hept_seq,score=pred_coil2(seqs[name],prof,params,wlambda)
+ printCoil(seqs[name],len(seqs[name]),hept_seq,score,prob,gcc,gg,labels)
+ elif modefasta:
+ for name in seqs.keys():
+# print "> ",name
+ gg,gcc,prob,hept_seq,score=pred_coil(seqs[name],len(seqs[name]),params,seqScore)
+ printCoil(seqs[name],len(seqs[name]),hept_seq,score,prob,gcc,gg,labels)
+ elif modeprofile:
+ gg,gcc,prob,hept_seq,score=pred_coil(prof,profLen,params,profScore)
+ printCoil('x'*profLen,profLen,hept_seq,score,prob,gcc,gg,labels)
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..3d23b2d
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,18 @@
+from distutils.core import setup
+import sys, os
+
+version = '1.0'
+
+setup(name='pscoil',
+ version=version,
+ description="Predictor of Coiled-coils based on evolutionary ans sequnce information",
+ long_description="""\
+Long description here ...""",
+ classifiers=[], # Get strings from http://pypi.python.org/pypi?%3Aaction=list_classifiers
+ keywords='Bio-Informatics',
+ author='Piero Fariselli',
+ author_email='piero at biocomp.unibo.it',
+ url='http://www.biocomp.unibo.it/piero',
+ license='GPLv2',
+ scripts=['pscoils/psCoils.py']
+ )
diff --git a/test/CEBA_BOVIN.seq b/test/CEBA_BOVIN.seq
new file mode 100644
index 0000000..596fdb0
--- /dev/null
+++ b/test/CEBA_BOVIN.seq
@@ -0,0 +1,2 @@
+> CEBA_BOVIN
+MESADFYEAEPRPPMSSHLQSPPHAPSSAAFGFPRGAGPSQPPAPPAAPEPLGGICEHETSIDISAYIDPAAFNDEFLADLFQHSRQQEKAKAAAAPAGGGNDFDYPGAPVGPGGAVMPGGTHGPPPGYGCAAAGYLDSRLEPLYERVGAPALRPLVIKQEPREEDEAKQLALAGLFPYQPPPPPPPPNSHPPPAHLAAPHLQFQIAHCGQTTMHLQPGHPTPPPTPVPSPHPAPALGAAGLPGPGGALKGLVATHPDLRAGGGGGGKAKKSVDKNSNEYRVRRERNNIAVRKSRDKAKQRNVETQQKVLELTSDNDRLRKRVEQLSRELDTLRGIFRQLPESSLVKAMGNCA
diff --git a/test/ferritin.Coils b/test/ferritin.Coils
new file mode 100644
index 0000000..5cc818e
--- /dev/null
+++ b/test/ferritin.Coils
@@ -0,0 +1,66 @@
+ 1 C a 0.480 0.000 0.000 0.927
+ 2 M a 0.804 0.000 0.001 4.596
+ 3 S b 0.804 0.000 0.001 4.596
+ 4 P a 1.126 0.002 0.123 2.134
+ 5 D b 1.126 0.002 0.123 2.134
+ 6 Q c 1.126 0.002 0.123 2.134
+ 7 W d 1.126 0.002 0.123 2.134
+ 8 D e 1.126 0.002 0.123 2.134
+ 9 K a 1.233 0.015 0.384 0.981
+ 10 E b 1.233 0.015 0.384 0.981
+ 11 A c 1.233 0.015 0.384 0.981
+ 12 A d 1.233 0.015 0.384 0.981
+ 13 Q e 1.233 0.015 0.384 0.981
+ 14 Y f 1.233 0.015 0.384 0.981
+ 15 D g 1.233 0.015 0.384 0.981
+ 16 A a 1.233 0.015 0.384 0.981
+ 17 H b 1.233 0.015 0.384 0.981
+ 18 A c 1.233 0.015 0.384 0.981
+ 19 Q d 1.233 0.015 0.384 0.981
+ 20 E e 1.233 0.015 0.384 0.981
+ 21 F f 1.233 0.015 0.384 0.981
+ 22 E g 1.233 0.015 0.384 0.981
+ 23 K a 1.233 0.015 0.384 0.981
+ 24 K b 1.233 0.015 0.384 0.981
+ 25 S c 1.233 0.015 0.384 0.981
+ 26 H d 1.233 0.015 0.384 0.981
+ 27 R e 1.233 0.015 0.384 0.981
+ 28 N f 1.233 0.015 0.384 0.981
+ 29 N g 1.233 0.015 0.384 0.981
+ 30 G f 1.098 0.001 0.088 2.507
+ 31 T g 1.098 0.001 0.088 2.507
+ 32 P e 0.932 0.000 0.009 4.488
+ 33 E a 0.934 0.000 0.009 4.475
+ 34 A a 1.352 0.121 1.049 0.306
+ 35 D b 1.352 0.121 1.049 0.306
+ 36 Q c 1.352 0.121 1.049 0.306
+ 37 Y d 1.352 0.121 1.049 0.306
+ 38 R e 1.352 0.121 1.049 0.306
+ 39 H f 1.352 0.121 1.049 0.306
+ 40 M g 1.352 0.121 1.049 0.306
+ 41 A a 1.380 0.187 1.278 0.222
+ 42 S b 1.380 0.187 1.278 0.222
+ 43 Q c 1.380 0.187 1.278 0.222
+ 44 Y d 1.380 0.187 1.278 0.222
+ 45 Q e 1.380 0.187 1.278 0.222
+ 46 A f 1.380 0.187 1.278 0.222
+ 47 M g 1.380 0.187 1.278 0.222
+ 48 A a 1.380 0.187 1.278 0.222
+ 49 Q b 1.380 0.187 1.278 0.222
+ 50 K c 1.380 0.187 1.278 0.222
+ 51 L d 1.380 0.187 1.278 0.222
+ 52 K e 1.380 0.187 1.278 0.222
+ 53 A f 1.380 0.187 1.278 0.222
+ 54 I g 1.380 0.187 1.278 0.222
+ 55 A a 1.380 0.187 1.278 0.222
+ 56 N b 1.380 0.187 1.278 0.222
+ 57 Q c 1.380 0.187 1.278 0.222
+ 58 L d 1.380 0.187 1.278 0.222
+ 59 K e 1.380 0.187 1.278 0.222
+ 60 K f 1.380 0.187 1.278 0.222
+ 61 G g 1.380 0.187 1.278 0.222
+ 62 S e 1.336 0.092 0.929 0.365
+ 63 E f 1.336 0.092 0.929 0.365
+ 64 T g 1.336 0.092 0.929 0.365
+ 65 C g 0.948 0.000 0.012 4.365
+ 66 R g 0.858 0.000 0.003 4.762
diff --git a/test/ferritin.PCoils b/test/ferritin.PCoils
new file mode 100644
index 0000000..2df27e5
--- /dev/null
+++ b/test/ferritin.PCoils
@@ -0,0 +1,66 @@
+ 1 x a 0.656 0.000 0.000 2.969
+ 2 x a 0.820 0.000 0.001 4.678
+ 3 x b 0.820 0.000 0.001 4.678
+ 4 x a 1.090 0.001 0.080 2.612
+ 5 x b 1.090 0.001 0.080 2.612
+ 6 x c 1.090 0.001 0.080 2.612
+ 7 x a 1.255 0.023 0.469 0.814
+ 8 x b 1.255 0.023 0.469 0.814
+ 9 x a 1.525 0.779 2.806 0.032
+ 10 x b 1.525 0.779 2.806 0.032
+ 11 x c 1.525 0.779 2.806 0.032
+ 12 x d 1.525 0.779 2.806 0.032
+ 13 x e 1.525 0.779 2.806 0.032
+ 14 x f 1.525 0.779 2.806 0.032
+ 15 x g 1.525 0.779 2.806 0.032
+ 16 x a 1.525 0.779 2.806 0.032
+ 17 x b 1.525 0.779 2.806 0.032
+ 18 x c 1.525 0.779 2.806 0.032
+ 19 x d 1.525 0.779 2.806 0.032
+ 20 x e 1.525 0.779 2.806 0.032
+ 21 x f 1.525 0.779 2.806 0.032
+ 22 x g 1.525 0.779 2.806 0.032
+ 23 x a 1.525 0.779 2.806 0.032
+ 24 x b 1.525 0.779 2.806 0.032
+ 25 x c 1.525 0.779 2.806 0.032
+ 26 x d 1.525 0.779 2.806 0.032
+ 27 x e 1.525 0.779 2.806 0.032
+ 28 x f 1.525 0.779 2.806 0.032
+ 29 x g 1.525 0.779 2.806 0.032
+ 30 x d 1.388 0.212 1.351 0.201
+ 31 x e 1.388 0.212 1.351 0.201
+ 32 x f 1.388 0.212 1.351 0.201
+ 33 x g 1.388 0.212 1.351 0.201
+ 34 x a 1.533 0.806 2.901 0.028
+ 35 x b 1.533 0.806 2.901 0.028
+ 36 x c 1.533 0.806 2.901 0.028
+ 37 x d 1.533 0.806 2.901 0.028
+ 38 x e 1.533 0.806 2.901 0.028
+ 39 x f 1.533 0.806 2.901 0.028
+ 40 x g 1.533 0.806 2.901 0.028
+ 41 x a 1.533 0.806 2.901 0.028
+ 42 x b 1.533 0.806 2.901 0.028
+ 43 x c 1.533 0.806 2.901 0.028
+ 44 x d 1.533 0.806 2.901 0.028
+ 45 x e 1.533 0.806 2.901 0.028
+ 46 x f 1.533 0.806 2.901 0.028
+ 47 x g 1.533 0.806 2.901 0.028
+ 48 x a 1.533 0.806 2.901 0.028
+ 49 x b 1.533 0.806 2.901 0.028
+ 50 x c 1.533 0.806 2.901 0.028
+ 51 x d 1.533 0.806 2.901 0.028
+ 52 x e 1.533 0.806 2.901 0.028
+ 53 x f 1.533 0.806 2.901 0.028
+ 54 x g 1.533 0.806 2.901 0.028
+ 55 x e 1.516 0.751 2.711 0.036
+ 56 x f 1.516 0.751 2.711 0.036
+ 57 x g 1.516 0.751 2.711 0.036
+ 58 x a 1.516 0.751 2.711 0.036
+ 59 x b 1.516 0.751 2.711 0.036
+ 60 x c 1.516 0.751 2.711 0.036
+ 61 x d 1.516 0.751 2.711 0.036
+ 62 x e 1.516 0.751 2.711 0.036
+ 63 x f 1.516 0.751 2.711 0.036
+ 64 x g 1.516 0.751 2.711 0.036
+ 65 x g 1.092 0.001 0.082 2.585
+ 66 x g 0.934 0.000 0.009 4.473
diff --git a/test/ferritin.PSCoils b/test/ferritin.PSCoils
new file mode 100644
index 0000000..d36eaf1
--- /dev/null
+++ b/test/ferritin.PSCoils
@@ -0,0 +1,66 @@
+ 1 C a 0.610 0.000 0.000 2.347
+ 2 M a 0.852 0.000 0.003 4.758
+ 3 S b 0.852 0.000 0.003 4.758
+ 4 P a 1.137 0.003 0.140 1.996
+ 5 D b 1.137 0.003 0.140 1.996
+ 6 Q c 1.137 0.003 0.140 1.996
+ 7 W a 1.217 0.012 0.328 1.122
+ 8 D b 1.217 0.012 0.328 1.122
+ 9 K a 1.423 0.341 1.686 0.130
+ 10 E b 1.423 0.341 1.686 0.130
+ 11 A c 1.423 0.341 1.686 0.130
+ 12 A d 1.423 0.341 1.686 0.130
+ 13 Q e 1.423 0.341 1.686 0.130
+ 14 Y f 1.423 0.341 1.686 0.130
+ 15 D g 1.423 0.341 1.686 0.130
+ 16 A a 1.423 0.341 1.686 0.130
+ 17 H b 1.423 0.341 1.686 0.130
+ 18 A c 1.423 0.341 1.686 0.130
+ 19 Q d 1.423 0.341 1.686 0.130
+ 20 E e 1.423 0.341 1.686 0.130
+ 21 F f 1.423 0.341 1.686 0.130
+ 22 E g 1.423 0.341 1.686 0.130
+ 23 K a 1.423 0.341 1.686 0.130
+ 24 K b 1.423 0.341 1.686 0.130
+ 25 S c 1.423 0.341 1.686 0.130
+ 26 H d 1.423 0.341 1.686 0.130
+ 27 R e 1.423 0.341 1.686 0.130
+ 28 N f 1.423 0.341 1.686 0.130
+ 29 N g 1.423 0.341 1.686 0.130
+ 30 G d 1.272 0.031 0.548 0.696
+ 31 T e 1.272 0.031 0.548 0.696
+ 32 P f 1.272 0.031 0.548 0.696
+ 33 E g 1.272 0.031 0.548 0.696
+ 34 A a 1.488 0.637 2.387 0.054
+ 35 D b 1.488 0.637 2.387 0.054
+ 36 Q c 1.488 0.637 2.387 0.054
+ 37 Y d 1.488 0.637 2.387 0.054
+ 38 R e 1.488 0.637 2.387 0.054
+ 39 H f 1.488 0.637 2.387 0.054
+ 40 M g 1.488 0.637 2.387 0.054
+ 41 A a 1.488 0.637 2.387 0.054
+ 42 S b 1.488 0.637 2.387 0.054
+ 43 Q c 1.488 0.637 2.387 0.054
+ 44 Y d 1.488 0.637 2.387 0.054
+ 45 Q e 1.488 0.637 2.387 0.054
+ 46 A f 1.488 0.637 2.387 0.054
+ 47 M g 1.488 0.637 2.387 0.054
+ 48 A a 1.488 0.637 2.387 0.054
+ 49 Q b 1.488 0.637 2.387 0.054
+ 50 K c 1.488 0.637 2.387 0.054
+ 51 L d 1.488 0.637 2.387 0.054
+ 52 K e 1.488 0.637 2.387 0.054
+ 53 A f 1.488 0.637 2.387 0.054
+ 54 I g 1.488 0.637 2.387 0.054
+ 55 A e 1.477 0.588 2.262 0.064
+ 56 N f 1.477 0.588 2.262 0.064
+ 57 Q g 1.477 0.588 2.262 0.064
+ 58 L a 1.477 0.588 2.262 0.064
+ 59 K b 1.477 0.588 2.262 0.064
+ 60 K c 1.477 0.588 2.262 0.064
+ 61 G d 1.477 0.588 2.262 0.064
+ 62 S e 1.477 0.588 2.262 0.064
+ 63 E f 1.477 0.588 2.262 0.064
+ 64 T g 1.477 0.588 2.262 0.064
+ 65 C g 1.060 0.001 0.055 3.027
+ 66 R g 0.945 0.000 0.011 4.387
diff --git a/test/ferritin.PredCoils b/test/ferritin.PredCoils
new file mode 100644
index 0000000..5cc818e
--- /dev/null
+++ b/test/ferritin.PredCoils
@@ -0,0 +1,66 @@
+ 1 C a 0.480 0.000 0.000 0.927
+ 2 M a 0.804 0.000 0.001 4.596
+ 3 S b 0.804 0.000 0.001 4.596
+ 4 P a 1.126 0.002 0.123 2.134
+ 5 D b 1.126 0.002 0.123 2.134
+ 6 Q c 1.126 0.002 0.123 2.134
+ 7 W d 1.126 0.002 0.123 2.134
+ 8 D e 1.126 0.002 0.123 2.134
+ 9 K a 1.233 0.015 0.384 0.981
+ 10 E b 1.233 0.015 0.384 0.981
+ 11 A c 1.233 0.015 0.384 0.981
+ 12 A d 1.233 0.015 0.384 0.981
+ 13 Q e 1.233 0.015 0.384 0.981
+ 14 Y f 1.233 0.015 0.384 0.981
+ 15 D g 1.233 0.015 0.384 0.981
+ 16 A a 1.233 0.015 0.384 0.981
+ 17 H b 1.233 0.015 0.384 0.981
+ 18 A c 1.233 0.015 0.384 0.981
+ 19 Q d 1.233 0.015 0.384 0.981
+ 20 E e 1.233 0.015 0.384 0.981
+ 21 F f 1.233 0.015 0.384 0.981
+ 22 E g 1.233 0.015 0.384 0.981
+ 23 K a 1.233 0.015 0.384 0.981
+ 24 K b 1.233 0.015 0.384 0.981
+ 25 S c 1.233 0.015 0.384 0.981
+ 26 H d 1.233 0.015 0.384 0.981
+ 27 R e 1.233 0.015 0.384 0.981
+ 28 N f 1.233 0.015 0.384 0.981
+ 29 N g 1.233 0.015 0.384 0.981
+ 30 G f 1.098 0.001 0.088 2.507
+ 31 T g 1.098 0.001 0.088 2.507
+ 32 P e 0.932 0.000 0.009 4.488
+ 33 E a 0.934 0.000 0.009 4.475
+ 34 A a 1.352 0.121 1.049 0.306
+ 35 D b 1.352 0.121 1.049 0.306
+ 36 Q c 1.352 0.121 1.049 0.306
+ 37 Y d 1.352 0.121 1.049 0.306
+ 38 R e 1.352 0.121 1.049 0.306
+ 39 H f 1.352 0.121 1.049 0.306
+ 40 M g 1.352 0.121 1.049 0.306
+ 41 A a 1.380 0.187 1.278 0.222
+ 42 S b 1.380 0.187 1.278 0.222
+ 43 Q c 1.380 0.187 1.278 0.222
+ 44 Y d 1.380 0.187 1.278 0.222
+ 45 Q e 1.380 0.187 1.278 0.222
+ 46 A f 1.380 0.187 1.278 0.222
+ 47 M g 1.380 0.187 1.278 0.222
+ 48 A a 1.380 0.187 1.278 0.222
+ 49 Q b 1.380 0.187 1.278 0.222
+ 50 K c 1.380 0.187 1.278 0.222
+ 51 L d 1.380 0.187 1.278 0.222
+ 52 K e 1.380 0.187 1.278 0.222
+ 53 A f 1.380 0.187 1.278 0.222
+ 54 I g 1.380 0.187 1.278 0.222
+ 55 A a 1.380 0.187 1.278 0.222
+ 56 N b 1.380 0.187 1.278 0.222
+ 57 Q c 1.380 0.187 1.278 0.222
+ 58 L d 1.380 0.187 1.278 0.222
+ 59 K e 1.380 0.187 1.278 0.222
+ 60 K f 1.380 0.187 1.278 0.222
+ 61 G g 1.380 0.187 1.278 0.222
+ 62 S e 1.336 0.092 0.929 0.365
+ 63 E f 1.336 0.092 0.929 0.365
+ 64 T g 1.336 0.092 0.929 0.365
+ 65 C g 0.948 0.000 0.012 4.365
+ 66 R g 0.858 0.000 0.003 4.762
diff --git a/test/ferritin.PredPCoils b/test/ferritin.PredPCoils
new file mode 100644
index 0000000..2df27e5
--- /dev/null
+++ b/test/ferritin.PredPCoils
@@ -0,0 +1,66 @@
+ 1 x a 0.656 0.000 0.000 2.969
+ 2 x a 0.820 0.000 0.001 4.678
+ 3 x b 0.820 0.000 0.001 4.678
+ 4 x a 1.090 0.001 0.080 2.612
+ 5 x b 1.090 0.001 0.080 2.612
+ 6 x c 1.090 0.001 0.080 2.612
+ 7 x a 1.255 0.023 0.469 0.814
+ 8 x b 1.255 0.023 0.469 0.814
+ 9 x a 1.525 0.779 2.806 0.032
+ 10 x b 1.525 0.779 2.806 0.032
+ 11 x c 1.525 0.779 2.806 0.032
+ 12 x d 1.525 0.779 2.806 0.032
+ 13 x e 1.525 0.779 2.806 0.032
+ 14 x f 1.525 0.779 2.806 0.032
+ 15 x g 1.525 0.779 2.806 0.032
+ 16 x a 1.525 0.779 2.806 0.032
+ 17 x b 1.525 0.779 2.806 0.032
+ 18 x c 1.525 0.779 2.806 0.032
+ 19 x d 1.525 0.779 2.806 0.032
+ 20 x e 1.525 0.779 2.806 0.032
+ 21 x f 1.525 0.779 2.806 0.032
+ 22 x g 1.525 0.779 2.806 0.032
+ 23 x a 1.525 0.779 2.806 0.032
+ 24 x b 1.525 0.779 2.806 0.032
+ 25 x c 1.525 0.779 2.806 0.032
+ 26 x d 1.525 0.779 2.806 0.032
+ 27 x e 1.525 0.779 2.806 0.032
+ 28 x f 1.525 0.779 2.806 0.032
+ 29 x g 1.525 0.779 2.806 0.032
+ 30 x d 1.388 0.212 1.351 0.201
+ 31 x e 1.388 0.212 1.351 0.201
+ 32 x f 1.388 0.212 1.351 0.201
+ 33 x g 1.388 0.212 1.351 0.201
+ 34 x a 1.533 0.806 2.901 0.028
+ 35 x b 1.533 0.806 2.901 0.028
+ 36 x c 1.533 0.806 2.901 0.028
+ 37 x d 1.533 0.806 2.901 0.028
+ 38 x e 1.533 0.806 2.901 0.028
+ 39 x f 1.533 0.806 2.901 0.028
+ 40 x g 1.533 0.806 2.901 0.028
+ 41 x a 1.533 0.806 2.901 0.028
+ 42 x b 1.533 0.806 2.901 0.028
+ 43 x c 1.533 0.806 2.901 0.028
+ 44 x d 1.533 0.806 2.901 0.028
+ 45 x e 1.533 0.806 2.901 0.028
+ 46 x f 1.533 0.806 2.901 0.028
+ 47 x g 1.533 0.806 2.901 0.028
+ 48 x a 1.533 0.806 2.901 0.028
+ 49 x b 1.533 0.806 2.901 0.028
+ 50 x c 1.533 0.806 2.901 0.028
+ 51 x d 1.533 0.806 2.901 0.028
+ 52 x e 1.533 0.806 2.901 0.028
+ 53 x f 1.533 0.806 2.901 0.028
+ 54 x g 1.533 0.806 2.901 0.028
+ 55 x e 1.516 0.751 2.711 0.036
+ 56 x f 1.516 0.751 2.711 0.036
+ 57 x g 1.516 0.751 2.711 0.036
+ 58 x a 1.516 0.751 2.711 0.036
+ 59 x b 1.516 0.751 2.711 0.036
+ 60 x c 1.516 0.751 2.711 0.036
+ 61 x d 1.516 0.751 2.711 0.036
+ 62 x e 1.516 0.751 2.711 0.036
+ 63 x f 1.516 0.751 2.711 0.036
+ 64 x g 1.516 0.751 2.711 0.036
+ 65 x g 1.092 0.001 0.082 2.585
+ 66 x g 0.934 0.000 0.009 4.473
diff --git a/test/ferritin.PredPSCoils b/test/ferritin.PredPSCoils
new file mode 100644
index 0000000..d36eaf1
--- /dev/null
+++ b/test/ferritin.PredPSCoils
@@ -0,0 +1,66 @@
+ 1 C a 0.610 0.000 0.000 2.347
+ 2 M a 0.852 0.000 0.003 4.758
+ 3 S b 0.852 0.000 0.003 4.758
+ 4 P a 1.137 0.003 0.140 1.996
+ 5 D b 1.137 0.003 0.140 1.996
+ 6 Q c 1.137 0.003 0.140 1.996
+ 7 W a 1.217 0.012 0.328 1.122
+ 8 D b 1.217 0.012 0.328 1.122
+ 9 K a 1.423 0.341 1.686 0.130
+ 10 E b 1.423 0.341 1.686 0.130
+ 11 A c 1.423 0.341 1.686 0.130
+ 12 A d 1.423 0.341 1.686 0.130
+ 13 Q e 1.423 0.341 1.686 0.130
+ 14 Y f 1.423 0.341 1.686 0.130
+ 15 D g 1.423 0.341 1.686 0.130
+ 16 A a 1.423 0.341 1.686 0.130
+ 17 H b 1.423 0.341 1.686 0.130
+ 18 A c 1.423 0.341 1.686 0.130
+ 19 Q d 1.423 0.341 1.686 0.130
+ 20 E e 1.423 0.341 1.686 0.130
+ 21 F f 1.423 0.341 1.686 0.130
+ 22 E g 1.423 0.341 1.686 0.130
+ 23 K a 1.423 0.341 1.686 0.130
+ 24 K b 1.423 0.341 1.686 0.130
+ 25 S c 1.423 0.341 1.686 0.130
+ 26 H d 1.423 0.341 1.686 0.130
+ 27 R e 1.423 0.341 1.686 0.130
+ 28 N f 1.423 0.341 1.686 0.130
+ 29 N g 1.423 0.341 1.686 0.130
+ 30 G d 1.272 0.031 0.548 0.696
+ 31 T e 1.272 0.031 0.548 0.696
+ 32 P f 1.272 0.031 0.548 0.696
+ 33 E g 1.272 0.031 0.548 0.696
+ 34 A a 1.488 0.637 2.387 0.054
+ 35 D b 1.488 0.637 2.387 0.054
+ 36 Q c 1.488 0.637 2.387 0.054
+ 37 Y d 1.488 0.637 2.387 0.054
+ 38 R e 1.488 0.637 2.387 0.054
+ 39 H f 1.488 0.637 2.387 0.054
+ 40 M g 1.488 0.637 2.387 0.054
+ 41 A a 1.488 0.637 2.387 0.054
+ 42 S b 1.488 0.637 2.387 0.054
+ 43 Q c 1.488 0.637 2.387 0.054
+ 44 Y d 1.488 0.637 2.387 0.054
+ 45 Q e 1.488 0.637 2.387 0.054
+ 46 A f 1.488 0.637 2.387 0.054
+ 47 M g 1.488 0.637 2.387 0.054
+ 48 A a 1.488 0.637 2.387 0.054
+ 49 Q b 1.488 0.637 2.387 0.054
+ 50 K c 1.488 0.637 2.387 0.054
+ 51 L d 1.488 0.637 2.387 0.054
+ 52 K e 1.488 0.637 2.387 0.054
+ 53 A f 1.488 0.637 2.387 0.054
+ 54 I g 1.488 0.637 2.387 0.054
+ 55 A e 1.477 0.588 2.262 0.064
+ 56 N f 1.477 0.588 2.262 0.064
+ 57 Q g 1.477 0.588 2.262 0.064
+ 58 L a 1.477 0.588 2.262 0.064
+ 59 K b 1.477 0.588 2.262 0.064
+ 60 K c 1.477 0.588 2.262 0.064
+ 61 G d 1.477 0.588 2.262 0.064
+ 62 S e 1.477 0.588 2.262 0.064
+ 63 E f 1.477 0.588 2.262 0.064
+ 64 T g 1.477 0.588 2.262 0.064
+ 65 C g 1.060 0.001 0.055 3.027
+ 66 R g 0.945 0.000 0.011 4.387
diff --git a/test/ferritin.cc b/test/ferritin.cc
new file mode 100644
index 0000000..af5f57d
--- /dev/null
+++ b/test/ferritin.cc
@@ -0,0 +1,67 @@
+ Pos A Hep Score Prob Gcc Gg Pred (Loop=L Coiledcoil=C)
+ 1 C a 0.610 0.000 0.000 2.347 L
+ 2 M a 0.852 0.000 0.003 4.758 L
+ 3 S b 0.852 0.000 0.003 4.758 L
+ 4 P a 1.137 0.003 0.140 1.996 L
+ 5 D b 1.137 0.003 0.140 1.996 L
+ 6 Q c 1.137 0.003 0.140 1.996 L
+ 7 W a 1.217 0.012 0.328 1.122 L
+ 8 D b 1.217 0.012 0.328 1.122 L
+ 9 K a 1.423 0.341 1.686 0.130 L
+ 10 E b 1.423 0.341 1.686 0.130 L
+ 11 A c 1.423 0.341 1.686 0.130 L
+ 12 A d 1.423 0.341 1.686 0.130 L
+ 13 Q e 1.423 0.341 1.686 0.130 L
+ 14 Y f 1.423 0.341 1.686 0.130 L
+ 15 D g 1.423 0.341 1.686 0.130 L
+ 16 A a 1.423 0.341 1.686 0.130 L
+ 17 H b 1.423 0.341 1.686 0.130 L
+ 18 A c 1.423 0.341 1.686 0.130 L
+ 19 Q d 1.423 0.341 1.686 0.130 L
+ 20 E e 1.423 0.341 1.686 0.130 L
+ 21 F f 1.423 0.341 1.686 0.130 L
+ 22 E g 1.423 0.341 1.686 0.130 L
+ 23 K a 1.423 0.341 1.686 0.130 L
+ 24 K b 1.423 0.341 1.686 0.130 L
+ 25 S c 1.423 0.341 1.686 0.130 L
+ 26 H d 1.423 0.341 1.686 0.130 L
+ 27 R e 1.423 0.341 1.686 0.130 L
+ 28 N f 1.423 0.341 1.686 0.130 L
+ 29 N g 1.423 0.341 1.686 0.130 L
+ 30 G d 1.272 0.031 0.548 0.696 L
+ 31 T e 1.272 0.031 0.548 0.696 L
+ 32 P f 1.272 0.031 0.548 0.696 L
+ 33 E g 1.272 0.031 0.548 0.696 L
+ 34 A a 1.488 0.637 2.387 0.054 C
+ 35 D b 1.488 0.637 2.387 0.054 C
+ 36 Q c 1.488 0.637 2.387 0.054 C
+ 37 Y d 1.488 0.637 2.387 0.054 C
+ 38 R e 1.488 0.637 2.387 0.054 C
+ 39 H f 1.488 0.637 2.387 0.054 C
+ 40 M g 1.488 0.637 2.387 0.054 C
+ 41 A a 1.488 0.637 2.387 0.054 C
+ 42 S b 1.488 0.637 2.387 0.054 C
+ 43 Q c 1.488 0.637 2.387 0.054 C
+ 44 Y d 1.488 0.637 2.387 0.054 C
+ 45 Q e 1.488 0.637 2.387 0.054 C
+ 46 A f 1.488 0.637 2.387 0.054 C
+ 47 M g 1.488 0.637 2.387 0.054 C
+ 48 A a 1.488 0.637 2.387 0.054 C
+ 49 Q b 1.488 0.637 2.387 0.054 C
+ 50 K c 1.488 0.637 2.387 0.054 C
+ 51 L d 1.488 0.637 2.387 0.054 C
+ 52 K e 1.488 0.637 2.387 0.054 C
+ 53 A f 1.488 0.637 2.387 0.054 C
+ 54 I g 1.488 0.637 2.387 0.054 C
+ 55 A e 1.477 0.588 2.262 0.064 C
+ 56 N f 1.477 0.588 2.262 0.064 C
+ 57 Q g 1.477 0.588 2.262 0.064 C
+ 58 L a 1.477 0.588 2.262 0.064 C
+ 59 K b 1.477 0.588 2.262 0.064 C
+ 60 K c 1.477 0.588 2.262 0.064 C
+ 61 G d 1.477 0.588 2.262 0.064 C
+ 62 S e 1.477 0.588 2.262 0.064 C
+ 63 E f 1.477 0.588 2.262 0.064 C
+ 64 T g 1.477 0.588 2.262 0.064 C
+ 65 C g 1.060 0.001 0.055 3.027 L
+ 66 R g 0.945 0.000 0.011 4.387 L
diff --git a/test/ferritin.fasta b/test/ferritin.fasta
new file mode 100644
index 0000000..771fc55
--- /dev/null
+++ b/test/ferritin.fasta
@@ -0,0 +1,2 @@
+> ferritin
+CMSPDQWDKEAAQYDAHAQEFEKKSHRNNGTPEADQYRHMASQYQAMAQKLKAIANQLKKGSETCR
diff --git a/test/ferritin.prof b/test/ferritin.prof
new file mode 100644
index 0000000..15ae009
--- /dev/null
+++ b/test/ferritin.prof
@@ -0,0 +1,68 @@
+# The order of the profile is listed after the keyword alphabet= in capital letter
+# ALPHABET=V L I M F W Y G A P S T C H R K Q E N D
+ 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0
+ 0 0 0 33 0 0 0 0 0 0 0 0 0 0 0 0 67 0 0 0
+ 0 0 0 0 67 0 0 0 0 0 33 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 75
+ 0 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 25 0 0 50
+ 0 0 0 0 0 50 50 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 50
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0
+ 0 0 0 0 0 0 0 0 25 0 0 0 0 25 0 0 0 0 0 50
+ 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 0 40 20 0 0
+ 0 0 20 0 0 0 20 40 0 0 0 0 0 0 0 0 20 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 0 0 0 0 60
+ 0 20 0 0 0 0 0 0 20 0 0 0 0 0 20 40 0 0 0 0
+ 0 0 0 0 0 0 0 0 40 0 0 0 0 20 0 0 40 0 0 0
+ 20 20 0 0 0 0 0 0 40 0 20 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 33 0 0 0 0 0 0 0 0 0 17 0 33 17 0 0
+ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 67 0 0
+ 0 0 40 0 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 80 0 0
+ 0 33 0 0 0 0 0 0 0 0 0 0 0 0 17 33 0 17 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 0 17 0 0
+ 0 0 0 0 0 0 0 0 0 0 17 0 0 0 17 17 0 17 0 33
+ 0 33 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 17 0 0
+ 0 33 0 0 0 0 0 0 0 0 0 0 0 0 17 50 0 0 0 0
+ 0 17 0 0 0 0 0 0 0 0 0 33 0 0 17 0 0 17 17 0
+ 0 0 0 0 0 0 0 0 0 0 17 0 0 0 33 0 0 33 17 0
+ 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 17 0 33 0 17
+ 0 33 17 0 0 0 0 0 17 0 0 17 0 0 0 0 0 0 0 17
+ 17 0 0 0 0 0 0 0 0 67 0 0 0 0 0 17 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 17 67 0 0
+ 0 50 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 17 0 67
+ 0 0 0 0 0 0 0 0 17 0 17 17 0 0 0 0 33 17 0 0
+ 0 0 0 0 67 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 33 0 0 0 0 0 33 17 0 17 0 0
+ 0 0 0 0 0 0 0 0 17 0 0 0 0 17 0 50 0 17 0 0
+ 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 50 33 0 0
+ 0 0 0 0 0 0 0 0 83 0 0 0 0 17 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 20 0 0 80 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 40 40 0 0
+ 0 20 0 0 0 0 40 0 0 0 0 0 0 0 0 0 40 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 40 40 0 0
+ 0 0 0 0 0 0 0 20 40 0 0 40 0 0 0 0 0 0 0 0
+ 0 60 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0
+ 20 20 0 0 0 0 0 0 60 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 40 20 0 20
+ 0 40 0 0 0 0 0 0 0 0 0 0 0 0 0 60 0 0 0 0
+ 0 40 0 20 0 0 0 0 0 0 0 0 0 0 40 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 40 20 0 0 20
+ 0 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 0 40 0 20
+ 0 40 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 20 0 40 0 20
+ 0 20 0 0 0 0 0 0 0 0 0 0 0 0 20 0 40 0 20 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 0 40 20 0 0
+ 0 80 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 80 0 0 0 0
+ 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 40 0 0 0 40
+ 0 0 0 20 0 0 0 20 0 0 0 0 0 0 0 0 0 0 20 40
+ 20 0 0 0 0 0 0 0 40 0 20 20 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 80 0 0
+ 0 50 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0
+ 0 50 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0
diff --git a/test/test.sh b/test/test.sh
new file mode 100755
index 0000000..4bc43bd
--- /dev/null
+++ b/test/test.sh
@@ -0,0 +1,11 @@
+
+
+# test Coils
+echo "test Coils"
+psCoils.py -f ./ferritin.fasta -l F > ./ferritin.Coils
+# test PCoils
+echo "test PSCoils"
+psCoils.py -p ./ferritin.prof -l F > ./ferritin.PCoils
+# test PSCoils
+echo "test PSCoils"
+psCoils.py -p ./ferritin.prof -f ./ferritin.fasta -l F > ./ferritin.PSCoils
--
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