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.IX Title "FreeContact 3pm"
.TH FreeContact 3pm "2016-03-11" "perl v5.24.1" "User Contributed Perl Documentation"
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.nh
.SH "NAME"
FreeContact \- fast protein contact predictor
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use FreeContact;
\&
\&  open(EXAMPLE, \*(Aq<\*(Aq, \*(Aq/usr/share/doc/libfreecontact\-perl/examples/demo_1000.aln\*(Aq) || confess($!);
\&  my @aln = <EXAMPLE>; chomp(@aln); close(EXAMPLE);
\&
\&  my $contacts = FreeContact::Predictor\->new()\->run(ali => \e@aln);
\&
\&  my $predictor = FreeContact::Predictor\->new();
\&  my %parset = FreeContact::get_ps_evfold();
\&  my $contacts = $predictor\->run(ali => \e@aln, %parset, num_threads => 1);
\&
\&  my $predictor = FreeContact::Predictor\->new();
\&  my($aliw, $wtot) = $predictor\->get_seq_weights(ali => \e@aln, num_threads => 1);
\&  my $contacts = $predictor\->run_with_seq_weights(ali => \e@aln, aliw => $aliw, wtot => $wtot, num_threads => 1);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
FreeContact is a protein residue contact predictor optimized for speed.
Its input is a multiple sequence alignment. FreeContact can function as an
accelerated drop-in for the published contact predictors
EVfold-mfDCA of \s-1DS.\s0 Marks (2011) and
\&\s-1PSICOV\s0 of D. Jones (2011).
FreeContact is accelerated by a combination of vector instructions, multiple
threads, and faster implementation of key parts.
Depending on the alignment, 10\-fold or higher speedups are possible.
.PP
A sufficiently large alignment is required for meaningful results.
As a minimum, an alignment with an effective (after-weighting) sequence count
bigger than the length of the query sequence should be used. Alignments with
tens of thousands of (effective) sequences are considered good input.
.PP
\&\fIjackhmmer\fR\|(1) from the hmmer package, or \fIhhblits\fR\|(1) from hhsuite
can be used to generate the alignments, for example.
.SH "FreeContact"
.IX Header "FreeContact"
.SS "\s-1EXPORT_OK\s0"
.IX Subsection "EXPORT_OK"
.IP "\fIget_ps_evfold()\fR" 4
.IX Item "get_ps_evfold()"
Get parameters for EVfold-mfDCA operating mode.
.IP "\fIget_ps_psicov()\fR" 4
.IX Item "get_ps_psicov()"
Get parameters for \s-1PSICOV \s0'improved results' operating mode.
.IP "\fIget_ps_psicov_sd()\fR" 4
.IX Item "get_ps_psicov_sd()"
Get parameters for \s-1PSICOV \s0'sensible default' operating mode. This is much faster than 'improved results' for a
slight loss of precision.
.Sp
These \fIget_ps_()\fR functions return a hash of arguments (clustpc => \fInum\fR,...,rho => \fInum\fR) that can be used
with \fIget_seq_weights()\fR, \fIrun()\fR or \fIrun_with_seq_weights()\fR. The arguments correspond to the published parametrization of the
respective method.
.SH "FreeContact::Predictor"
.IX Header "FreeContact::Predictor"
.SS "Constructor"
.IX Subsection "Constructor"
.IP "new( dbg => bool )" 4
.IX Item "new( dbg => bool )"
Creates an \*(L"FreeContact::Predictor\*(R".
.SS "Methods"
.IX Subsection "Methods"
.IP "\fIget_seq_weights()\fR" 4
.IX Item "get_seq_weights()"
Defaults for the arguments are obtained with \fIget_ps_evfold()\fR.
.IP "run(ali => \fI[]\fR, clustpc => dbl, density => dbl, gapth => dbl, mincontsep => uint, pseudocnt => dbl, pscnt_weight => dbl, estimate_ivcov => bool, shrink_lambda => dbl, cov20 => bool, apply_gapth => bool, rho => dbl, [veczw => bool], [num_threads => int], [icme_timeout => int], [timing => \fI{}\fR])" 4
.IX Item "run(ali => [], clustpc => dbl, density => dbl, gapth => dbl, mincontsep => uint, pseudocnt => dbl, pscnt_weight => dbl, estimate_ivcov => bool, shrink_lambda => dbl, cov20 => bool, apply_gapth => bool, rho => dbl, [veczw => bool], [num_threads => int], [icme_timeout => int], [timing => {}])"
Defaults for the arguments are obtained with \fIget_ps_evfold()\fR.
.RS 4
.IP "ali" 4
.IX Item "ali"
Reference to array holding alignment rows as strings. The first
row must hold the query, with no gaps.
.IP "clustpc" 4
.IX Item "clustpc"
BLOSUM-style clustering similarity threshold [0\-1].
.IP "icme_timeout" 4
.IX Item "icme_timeout"
Inverse covariance matrix estimation timeout in seconds. Default: 1800.
.Sp
The estimation sometimes gets stuck. If the timeout is reached, the \fIrun()\fR
method dies with \*(L"Caught FreeContact timeout exception: ...\*(R". You can catch
this exception and handle it as needed, e.g. by setting a higher \fBrho\fR value.
.IP "num_threads" 4
.IX Item "num_threads"
Number of OpenMP threads to use. If unset, all CPUs are used.
.IP "timing" 4
.IX Item "timing"
If given, this hash reference is filled with data containing wall clock
timing results in seconds:
.Sp
.Vb 8
\&  {
\&    num_threads =>  NUM,
\&    seqw =>         NUM,
\&    pairfreq =>     NUM,
\&    shrink =>       NUM,
\&    inv =>          NUM,
\&    all =>          NUM
\&  }
.Ve
.RE
.RS 4
.Sp
\&\fIrun()\fR returns a hash reference of contact prediction results:
.Sp
.Vb 11
\&  {
\&    fro => [  # identifier of scoring scheme
\&      [
\&        I,    # 0\-based index of amino acid i
\&        J,    # 0\-based index of amino acid j
\&        SCORE # contact score
\&      ], ...
\&    ],
\&    MI => ...,
\&    l1norm => ...
\&  }
.Ve
.Sp
Use 'fro' scores with EVfold.
.RE
.SH "AUTHOR"
.IX Header "AUTHOR"
Laszlo Kajan, <lkajan@rostlab.org>
.SH "COPYRIGHT AND LICENSE"
.IX Header "COPYRIGHT AND LICENSE"
Copyright (C) 2013 by Laszlo Kajan
.PP
This program is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.