hprof trace results
hprof trace results
(Note: the following figures do not include allocations considered negligible
enough not to appear in hprof's heap statistics.)
TOTALS AT END |
Bytes |
Objects |
Live |
$live_bytes |
$live_objects |
Allocated |
$alloc_bytes |
$alloc_objects |
EOF
print_allocation_table('heap_live', 'Live Data', 3, $live_bytes);
print_allocation_table('heap_alloc', 'Allocated Data', 5, $alloc_bytes);
print_cpu_table();
print <
EOF
exit 0;
sub print_allocation_table
{
my ($anchor, $sort_name, $i, $total) = @_;
print <Heap Allocation Sites (Ordered by $sort_name)
Rank |
Percent |
Live |
Allocated |
Class Name |
Stack Trace |
Self |
Accum |
Bytes |
Objects |
Bytes |
Objects |
EOF
my $rank = 1;
my $cum = 0.0;
foreach my $site (sort { $b->[$i] <=> $a->[$i] } @allocations)
{
my (undef, undef, undef, $lbytes, $lobj, $abytes, $aobj, $trace, $class) = @$site;
my $percent = $site->[$i] * 100 / $total;
$cum += $percent;
my $percent_str = sprintf('%.2f', $percent);
my $cum_str = sprintf('%.2f', $cum);
my $stack = build_stack_trace($trace);
print <
$rank |
$percent_str% |
$cum_str% |
$lbytes |
$lobj |
$abytes |
$aobj |
$class |
$stack |
EOF
$rank++;
}
print <
EOF
}
sub print_cpu_table
{
print <CPU Samples
Rank |
Self |
Cumulative |
Count |
Method |
Stack Trace |
EOF
foreach my $site (@samples)
{
my ($rank, $percent, $cum, $count, $trace, $method) = @$site;
my $stack = build_stack_trace($trace);
print <
$rank |
$percent |
$cum |
$count |
$method |
$stack |
EOF
}
print <
EOF
}
sub build_stack_trace
{
my ($trace) = @_;
my $stack = join '
', @{$traces[$trace]};
$stack =~ s/ / /g;
return $stack;
}
MBA2/bin/profile 0100755 0000765 0000024 00000000240 10066206447 013375 0 ustar janvitek staff #! /bin/sh
time java -Xmx1079m -Xrunhprof:heap=sites,cpu=samples,file=${HPROFOUT:-java.hprof.txt} -classpath lib/concurrent.jar:lib/Jama-1.0.1.jar:. Main "$@"
MBA2/bin/r 0100755 0000765 0000024 00000010516 10066403776 012211 0 ustar janvitek staff #1
nohup ./doIt -dataset=observedData/zdomain.mba -maxMissings=3 -maxWindowSize=300000 -alpha=.025 -beta=.025
#2
nohup ./doIt -dataset=observedData/csp.mba -maxMissings=1 -maxWindowSize=300000 -alpha=.025 -beta=.025
#3
nohup ./doIt \
-dataset=observedData/ns1.mba -maxMissings=6 -maxWindowSize=300000 -alpha=.025 -beta=.025
#4
nohup ./doIt -dataset=observedData/rnasewt.mba -maxMissings=5 -maxWindowSize=300000 -alpha=0.025 -beta=0.025 -useca -usecb -useco -useha -priorType="malliavin" -minConnectivityCount=5 > & AssFound/4.out &
#!/bin/csh
foreach x ( 0 )
nohup ./doIt -dataset=4027 -maxMissings=0 -maxWindowSize=300000 -alpha=0.00001 -beta=0.00001 -useca -usecb -useha -useco -adjacency=$x priorType="malliavin" > & SimAssFound/4027_$x.out &
end
#!/bin/csh
foreach x ( 4144 )
nohup ./doIt -dataset=$x -maxMissings=5 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=-1 > & SimAssFound/$x:t_0.out
end
#!/bin/csh
foreach x ( 4144 )
nohup ./doIt -dataset=$x -maxMissings=5 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=-1 > & SimAssFound/$x:t_0.out
end
#!/bin/csh
foreach x ( 4144 )
nohup ./doIt -dataset=$x -maxMissings=5 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=-1 > & SimAssFound/$x:t_0.out
end
#!/bin/csh
foreach x ( 4309 )
nohup ./doIt -dataset=$x -maxMissings=11 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=4 -adjacency=.6 > & SimAssFound/$x:t_6.out
end
#!/bin/csh
foreach x ( 4144 )
nohup ./doIt -dataset=$x -maxMissings=5 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=-1 > & SimAssFound/$x:t_0.out
end
#!/bin/csh
foreach x ( 4318 )
nohup ./doIt -dataset=$x -maxMissings=0 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=.6 > & SimAssFound/$x:t_6.out
end
#!/bin/csh
foreach x ( 4353 )
nohup ./doIt -dataset=$x -maxMissings=12 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=.6 > & SimAssFound/$x:t_6.out
end
#!/bin/csh
foreach x ( 4391 )
nohup ./doIt -dataset=$x -maxMissings=3 -maxWindowSize=300000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=4 -adjacency=-1 > & SimAssFound/$x:t_0.out
end
#!/bin/csh
foreach x ( 4393 )
nohup ./doIt -dataset=$x -maxMissings=0 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=4 -adjacency=.6 > & SimAssFound/$x:t_6.out
end
#!/bin/csh
foreach x ( 4144 )
nohup ./doIt -dataset=$x -maxMissings=5 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=-1 > & SimAssFound/$x:t_0.out
end
#!/bin/csh
foreach x ( 4670 )
nohup ./doIt -dataset=$x -maxMissings=0 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=.3 > & SimAssFound/$x:t_3.out
end
#!/bin/csh
foreach x ( 4144 )
nohup ./doIt -dataset=$x -maxMissings=5 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=-1 > & SimAssFound/$x:t_0.out
end
#!/bin/csh
foreach x ( 4144 )
nohup ./doIt -dataset=$x -maxMissings=5 -maxWindowSize=100000 -alpha=0.0001 -beta=0 -useca -usecb -useha -usen -useco -minConnectivityCount=5 -adjacency=-1 > & SimAssFound/$x:t_0.out
end
#!/bin/csh
nohup ./doIt -dataset=5 -maxMissings=3 -maxWindowSize=300000 -alpha=0.025 -beta=0.025 -useca -usecb -useco -useha -priorType="malliavin" -minConnectivityCount=4 > & AssFound/5_3miss.out &
#!/bin/csh
nohup ./doIt -dataset=6 -maxMissings=0 -maxWindowSize=300000 -alpha=0.025 -beta=0.025 -useca -usecb -useco -useha -priorType="malliavin" -minConnectivityCount=5 > & AssFound/6.out &
#!/bin/csh
nohup ./doIt -dataset=7 -maxMissings=14 -maxWindowSize=300000 -alpha=.0001 -beta=0.000001 -useca -usecb -usen -useha -useco -minConnectivityCount=0 > & 7.out &
#!/bin/csh
nohup ./doIt -dataset=8 -maxMissings=2 -maxWindowSize=300000 -alpha=0.025 -beta=0.025 -useca -usecb -useco -useha -priorType="malliavin" > & AssFound/8.out &
MBA2/bin/run 0100755 0000765 0000024 00000000175 10066206172 012543 0 ustar janvitek staff #! /bin/sh
time java -Xmx1079m -verbose:gc -XX:+PrintGCDetails -classpath lib/concurrent.jar:lib/Jama-1.0.1.jar:. Main "$@"
MBA2/bin/spin-shift-counts 0100755 0000765 0000024 00000001337 10066551161 015336 0 ustar janvitek staff #! /usr/bin/perl -w
# For an input protein, counts the number of chemical shifts listed in each
# spin system.
use strict;
my @totals = (0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
# Discard the header.
for (1..3)
{
my $dummy = <>;
}
# Per-spin-system information.
while (<>)
{
chomp;
my @data = split ',';
my $id = $data[0];
my $missing = scalar grep /NaN/, @data;
my $count = 10 - $missing;
$totals[$count]++;
printf "%4d => %2d chemical shifts\n", $id, $count;
}
# Summary information.
print "*********************\n";
for (0..10)
{
my $accum = 0;
map { $accum += $_ } @totals[$_..10];
printf "Number of spin systems with exactly %2d chemical shifts: %3d (at least %2d: %3d)\n",
$_, $totals[$_], $_, $accum;
}
exit 0;
MBA2/bin/utilization 0100755 0000765 0000024 00000004054 10066206172 014312 0 ustar janvitek staff #! /usr/bin/perl -w
# Script that looks at the DEBUG lines from the client and uses them to
# figure out the utilization of each server; i.e., how much time it spent
# busy and how much time it spent waiting for something to do.
#
# This script assumes that less than 24 hours will pass between output
# lines mentioning a particular server's status. Probably a safe
# assumption, unless there's a really pathological data set....
use strict;
my %last_timestamp = ();
my %busy = ();
my %time_busy = ();
my %time_idle = ();
while (<>)
{
chomp;
next unless /^DEBUG \[(\d+):(\d+):(\d+) ([AP])M\] (.*)$/;
my $timestamp = reassemble_timestamp($1, $2, $3, $4);
my $info = $5;
if ($info =~ /Telling (.*) to start/)
{
$last_timestamp{$1} = $timestamp;
$busy{$1} = 1;
$time_busy{$1} = 0;
$time_idle{$1} = 0;
}
elsif ($info =~ /(.*) is asking for more work/)
{
change_state($1, $timestamp, 0);
}
elsif ($info =~ /No work is available for (.*)/)
{
change_state($1, $timestamp, 0);
}
elsif ($info =~ /\*\*\*\*\* Sending (.*) another task/)
{
change_state($1, $timestamp, 1);
}
elsif ($info =~ /Closed connection to (.*)/)
{
change_state($1, $timestamp, 0);
}
}
foreach my $server (sort keys %last_timestamp)
{
my $total_time = $time_busy{$server} + $time_idle{$server};
my $percent_busy = $time_busy{$server} * 100 / $total_time;
my $percent_idle = $time_idle{$server} * 100 / $total_time;
print "${server}: $time_busy{$server} s ($percent_busy\%) busy, $time_idle{$server} s ($percent_idle\%) idle\n";
}
exit 0;
sub reassemble_timestamp
{
my ($hour, $minute, $second, $flag) = @_;
$hour += 12 if ($flag eq 'P' && $hour != 12);
return $second + 60 * ($minute + 60 * $hour);
}
sub change_state
{
my ($server, $timestamp, $is_now_busy) = @_;
$timestamp += 24 * 60 * 60 if $timestamp < $last_timestamp{$server};
if ($busy{$server})
{
$time_busy{$server} += $timestamp - $last_timestamp{$server};
}
else
{
$time_idle{$server} += $timestamp - $last_timestamp{$server};
}
$busy{$server} = $is_now_busy;
$last_timestamp{$server} = $timestamp;
}
MBA2/COPYING 0100640 0000765 0000024 00000003015 10066404545 012270 0 ustar janvitek staff Copyright (c) 2004, Purdue University
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
Neither the name of the Purdue University nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
MBA2/CVS/ 0040755 0000765 0000024 00000000000 10067072100 011665 5 ustar janvitek staff MBA2/CVS/Entries 0100644 0000765 0000024 00000000746 10066413731 013235 0 ustar janvitek staff /.DS_Store/1.1.1.1/Fri Jun 18 14:24:16 2004//
/.project/1.1.1.1/Fri Jun 18 14:24:16 2004//
D/assign////
D/input////
D/output////
D/parallel////
D/util////
/.classpath/1.2/Wed Jun 23 22:45:17 2004//
/Main.java/1.2/Wed Jun 23 22:45:18 2004//
/registry/1.2/Wed Jun 23 22:45:18 2004//
/run/1.5/Wed Jun 23 22:45:18 2004//
D/bin////
D/lib////
D/data////
D/examples////
/COPYING/1.1/Wed Jun 23 22:51:17 2004//
/README/1.3/Wed Jun 23 23:23:53 2004/-kb/
/Makefile/1.2/Wed Jun 23 23:52:25 2004//
MBA2/CVS/Entries.Log 0100644 0000765 0000024 00000000414 10067072106 013743 0 ustar janvitek staff A D/AssFound////
A D/observedData////
A D/origDataREFDBformat////
A D/simSpinSystemsMBAformat////
A D/trueChemicalShiftsTXTformat////
R D/trueChemicalShiftsTXTformat////
R D/simSpinSystemsMBAformat////
R D/origDataREFDBformat////
R D/observedData////
R D/AssFound////
MBA2/CVS/Entries~ 0100644 0000765 0000024 00000001044 10066413313 013417 0 ustar janvitek staff /.DS_Store/1.1.1.1/Fri Jun 18 14:24:16 2004//
/.project/1.1.1.1/Fri Jun 18 14:24:16 2004//
D/assign////
D/input////
D/output////
D/parallel////
D/util////
/.classpath/1.2/Wed Jun 23 22:45:17 2004//
/Main.java/1.2/Wed Jun 23 22:45:18 2004//
/registry/1.2/Wed Jun 23 22:45:18 2004//
/run/1.5/Wed Jun 23 22:45:18 2004//
D/bin////
D/lib////
D/data////
D/examples////
/COPYING/1.1/Wed Jun 23 22:51:17 2004//
/README/1.3/Wed Jun 23 23:23:53 2004/-kb/
/changes/-1.1.1.1/dummy timestamp//
/r/-1.2/dummy timestamp//
/Makefile/1.1/Wed Jun 23 23:35:29 2004//
MBA2/CVS/Repository 0100644 0000765 0000024 00000000020 10065431355 013765 0 ustar janvitek staff /p/sss/cvs/MBA2
MBA2/CVS/Root 0100644 0000765 0000024 00000000050 10065431355 012534 0 ustar janvitek staff :ext:jv@arthur.cs.purdue.edu:/p/sss/cvs
MBA2/CVS/Template 0100644 0000765 0000024 00000000000 10065431355 013357 0 ustar janvitek staff MBA2/data/ 0040755 0000765 0000024 00000000000 10066406044 012152 5 ustar janvitek staff MBA2/data/bpti.mba 0100644 0000765 0000024 00000006517 10066405655 013606 0 ustar janvitek staff Real Bpti, 58 residues, Prolines at 1,7,8,12. Missing spin systems at 2,9,10,11,27,37,38,57. Extras: 5. Max 7 connective resonances.
RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA
2,9,10,11,27,37,38,57
3, 7.81,116.5,176.6,57.6,40.0,4.45,NaN,NaN,59.4,37.6,4.78,NaN,
4, 7.43,121.1,179.2,59.5,37.6,4.76,NaN,NaN,58.1,39.9,4.56,NaN,
5, 7.54,113.7,183.4,58.1,39.8,4.55,NaN,NaN,55.0,41.8,4.67,NaN,
6, 7.49,120.4,178.2,54.9,41.9,4.71,NaN,NaN,55.1,30.9,4.73,NaN,
13, 8.67,119.9,177.9,64.6,33.1,4.74,NaN,NaN,60.8,46.0,4.75,NaN,
14, 7.95,115.4,NaN,60.8,46.0,4.75,NaN,NaN,56.5,32.9,4.63,NaN,
15, 8.17,123.4,179.1,56.6,32.8,4.60,NaN,NaN,52.1,19.8,4.50,NaN,
16, 8.18,118.4,181.6,51.9,19.6,4.50,NaN,NaN,55.2,30.6,4.49,NaN,
17, 8.09,125.7,182.0,55.1,30.5,4.42,NaN,NaN,60.5,40.3,4.42,NaN,
18, 8.68,128.4,181.0,60.5,40.3,4.39,NaN,NaN,61.2,35.7,4.44,NaN,
19, 8.36,130.0,180.1,61.4,35.7,4.52,NaN,NaN,52.0,35.3,4.87,NaN,
20, 9.15,115.2,183.2,51.9,35.1,4.88,NaN,NaN,57.7,42.5,5.90,NaN,
21, 9.74,119.8,181.0,57.8,42.4,5.92,NaN,NaN,55.5,42.7,5.50,NaN,
22,10.53,124.8,183.7,55.4,42.8,5.51,NaN,NaN,60.0,39.6,4.48,NaN,
23, 7.72,125.3,182.9,60.0,39.4,4.51,NaN,NaN,51.0,38.8,NaN,NaN,
24, 8.77,126.3,181.3,51.0,38.3,4.76,NaN,NaN,55.1,19.2,3.92,NaN,
25, 7.89,116.9,177.2,55.1,19.1,3.92,NaN,NaN,58.9,32.3,4.23,NaN,
26, 6.77,118.4,178.9,58.9,32.4,4.27,NaN,NaN,52.2,20.4,4.41,NaN,
28, 6.78,114.5,183.0,46.1,NaN,4.07,NaN,NaN,54.0,45.5,4.95,NaN,
29, 8.37,118.4,181.0,54.1,45.2,5.01,NaN,NaN,58.2,49.3,5.81,NaN,
30, 8.73,122.8,182.8,58.2,49.3,5.81,NaN,NaN,54.2,33.3,5.03,NaN,
31, 8.01,108.1,182.4,54.2,33.4,5.02,NaN,NaN,60.9,72.5,5.51,NaN,
32, 9.34,119.0,181.2,61.0,72.3,5.52,NaN,NaN,55.8,41.4,5.05,NaN,
33, 8.34,118.6,185.1,56.0,41.5,5.03,NaN,NaN,62.6,31.9,4.09,NaN,
34, 9.37,129.7,183.2,62.8,32.2,4.10,NaN,NaN,55.1,40.7,5.09,NaN,
35, 8.59,114.0,182.0,55.1,40.7,5.07,NaN,NaN,45.9,NaN,4.49,3.39,
36, 4.28, 97.8,181.6,45.7,NaN,4.54,NaN,NaN,46.1,NaN,4.41,3.09,
39, 7.37,117.9,182.2,56.9,27.0,4.12,NaN,NaN,54.2,19.8,4.24,NaN,
40, 8.28,121.0,176.3,54.2,19.7,4.29,NaN,NaN,55.8,34.4,4.55,NaN,
41, 8.34,115.6,179.9,56.0,34.1,4.61,NaN,NaN,59.1,29.9,3.81,NaN,
42, 7.18,116.0,178.7,59.2,29.6,3.80,NaN,NaN,51.3,35.7,5.26,NaN,
43, 6.73,120.7,182.0,51.2,35.6,5.32,NaN,NaN,54.2,39.1,5.15,NaN,
44, 9.90,122.5,182.4,54.2,39.1,5.09,NaN,NaN,56.4,44.5,5.30,NaN,
45, 9.91,120.5,NaN,56.5,44.4,5.40,NaN,NaN,58.8,NaN,4.54,NaN,
46, 7.42,108.5,180.6,58.7,33.3,4.57,NaN,NaN,56.4,67.4,4.69,NaN,
47, 8.12,125.4,183.1,56.5,67.3,4.68,NaN,NaN,55.5,17.6,3.30,NaN,
48, 8.59,117.5,177.1,55.5,17.8,3.33,NaN,NaN,60.8,29.3,4.02,NaN,
49, 7.83,120.2,177.3,60.8,29.0,4.05,NaN,NaN,57.6,41.4,4.47,NaN,
50, 6.95,119.6,178.8,57.6,41.5,4.45,NaN,NaN,58.8,44.1,1.77,NaN,
51, 8.56,120.7,181.2,59.2,44.1,1.83,NaN,NaN,56.8,31.2,4.36,NaN,
52, 8.24,121.2,176.3,56.8,31.3,4.38,NaN,NaN,59.8,30.7,4.21,NaN,
53, 7.36,113.0,178.2,59.8,30.4,4.21,NaN,NaN,66.4,69.6,4.22,NaN,
54, 8.21,114.7,180.3,66.6,69.7,4.27,NaN,NaN,54.6,42.6,4.80,NaN,
55, 7.93,107.4,182.8,54.8,42.5,4.83,NaN,NaN,46.9,NaN,4.02,NaN,
56, 8.17,108.8,181.4,46.7,NaN,4.02,NaN,NaN,45.3,NaN,4.05,NaN,
1000, 7.13,106.9,179.8,67.6,70.7,4.72,NaN,NaN,46.5,NaN,4.07,3.41,
1001, 7.71,114.8,183.1,45.9,NaN,4.43,2.99,NaN,55.9,NaN,5.13,NaN,
1002, 7.78,123.3,180.7,63.0,30.3,3.87,NaN,NaN,56.6,41.2,5.11,NaN,
1003, 7.92,129.4,183.5,45.3,NaN,4.08,NaN,NaN,54.5,19.9,4.11,NaN,
1004, 8.09,106.7,178.5,52.2,20.2,4.50,NaN,NaN,46.3,NaN,3.93,NaN,
MBA2/data/csp.mba 0100644 0000765 0000024 00000010436 10066405655 013430 0 ustar janvitek staff Csp, 70 residues. Missings at 1,2, Prolines at 22,61, Extras: 4. Max 7 connective resonances.
MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL
1,2
3,8.18,117.4,173.4,44.8,NaN,4.01,NaN,NaN,56.6,33.5,4.29,NaN,
4,8.6,120.1,176,56.5,33.4,4.29,NaN,NaN,53.6,NaN,4.58,NaN,
5,7.66,104.8,174.1,53.5,34,4.57,NaN,NaN,59.3,NaN,5.51,NaN,
6,8.93,106,175.7,59.9,71.4,5.52,NaN,NaN,46.2,NaN,4.59,3.98,
7,8.18,116.5,171.1,46.1,NaN,4.57,NaN,NaN,58.3,NaN,5.14,NaN,
8,8.81,123.6,175.6,58.3,41.9,5.14,NaN,NaN,64.4,NaN,3.62,NaN,
9,9.09,133.2,175,64.6,NaN,3.62,NaN,NaN,58.6,NaN,4.23,NaN,
10,7.42,108.5,176.3,58.5,NaN,4.22,NaN,NaN,56.2,NaN,4.68,NaN,
11,9.22,118.8,173.7,56.2,NaN,4.66,NaN,NaN,59.4,NaN,4.29,NaN,
12,8.1,123.9,NaN,59.3,42.2,4.29,NaN,NaN,51.4,NaN,4.84,NaN,
13,9.04,125.9,174.1,51.2,39.3,4.85,NaN,NaN,54.5,18.6,4.1,NaN,
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17,6.63,109.6,172.4,46.2,NaN,4.13,3.82,NaN,54.6,42.2,5.13,NaN,
18,8.01,102.6,171.9,54.8,42.3,5.12,NaN,NaN,NaN,NaN,3.95,NaN,
19,7.93,112.2,170.5,45.3,NaN,3.93,NaN,NaN,56.3,NaN,NaN,NaN,
20,9.4,119,174.6,56.6,45.2,5.26,NaN,NaN,59.3,NaN,4.26,NaN,
21,9.35,123.9,174.7,59.5,42,4.24,NaN,NaN,59.3,NaN,5.19,NaN,
23,9.19,120.4,177.5,62.9,33.6,4.74,NaN,NaN,56.6,40.4,4.68,NaN,
24,7.95,114.1,176.5,56.5,40.5,4.67,NaN,NaN,53.6,40.7,4.57,NaN,
25,7.67,104.5,177.6,53.6,40,4.57,NaN,NaN,45.8,NaN,4.2,3.91,
26,7.97,113.1,174.7,45.8,NaN,4.19,3.9,NaN,58.6,63.1,4.39,NaN,
27,7.69,114.2,172.5,58.5,63.2,4.38,NaN,NaN,56.9,33.2,4.11,NaN,
28,7.89,115.3,175.1,56.9,33.1,4.11,NaN,NaN,55.3,41.3,4.92,NaN,
29,9.27,117.7,176.3,55.5,41.5,4.92,NaN,NaN,60.6,NaN,4.35,NaN,
30,8.52,127,174.7,60.6,NaN,4.34,NaN,NaN,58.1,NaN,3.73,NaN,
31,7.74,121.6,172.6,58.2,40.2,3.72,NaN,NaN,57.9,NaN,4.5,NaN,
32,8.69,124.4,170.4,57.8,NaN,4.5,NaN,NaN,55.4,NaN,4.8,NaN,
33,8.29,120.4,177.2,55.5,34.1,4.81,NaN,NaN,59.9,37.3,4.16,NaN,
34,7.56,114.3,176,59.9,37.4,4.15,NaN,NaN,59.9,62.4,3.88,NaN,
35,8.03,121.4,175,59.9,62.6,3.89,NaN,NaN,52.3,20.8,4.47,NaN,
36,7.47,116.5,177.5,52.2,20.9,4.46,NaN,NaN,62.6,NaN,3.91,NaN,
37,8.99,124.4,176.1,62.6,NaN,3.91,NaN,NaN,55.2,NaN,4.37,NaN,
38,7.5,116,175.6,55.2,28.7,4.4,NaN,NaN,53.3,39.1,4.64,NaN,
39,8.56,118.8,174.6,53.2,39.3,4.64,NaN,NaN,54.9,40.9,4.53,NaN,
40,8.26,106.2,176.5,54.9,40.9,4.53,NaN,NaN,45.2,NaN,3.99,3.79,
41,8.05,118.5,173.7,45.1,NaN,3.96,3.79,NaN,58.2,38.5,4.42,NaN,
42,8.24,122.4,176,58.2,38.4,4.42,NaN,NaN,54.9,NaN,4.21,NaN,
43,7.38,111.1,174,54.9,31.8,4.22,NaN,NaN,56.2,64,3.99,NaN,
44,5.82,116.3,171.7,56.3,64.2,3.99,NaN,NaN,52.6,NaN,NaN,NaN,
45,8.19,116.3,174.1,52.6,NaN,4.41,NaN,NaN,52.5,42.9,4.9,NaN,
46,8.63,118.2,175.5,52.5,43,4.9,NaN,NaN,58,NaN,3.6,NaN,
47,9.09,110.9,177.3,58.2,29.4,3.6,NaN,NaN,45.2,NaN,4.36,NaN,
48,7.74,117.9,173.6,45.1,NaN,4.35,3.55,NaN,56.3,NaN,4.2,NaN,
49,8.76,123.3,175.6,56.2,30.3,4.19,NaN,NaN,56.3,33.1,5.06,NaN,
50,8.6,112.8,177.1,56.5,33.1,5.07,NaN,NaN,58.5,NaN,5.37,NaN,
51,9.11,112,174.3,58.6,36.8,5.37,NaN,NaN,55.3,65.8,5.72,NaN,
52,8.67,114.6,173.9,55.8,66,5.7,NaN,NaN,56.2,40.4,5.29,NaN,
53,8.95,107.7,172.8,56.5,40.5,5.29,NaN,NaN,59.9,NaN,4.73,NaN,
54,8.65,118.4,174.5,59.9,70.4,4.73,NaN,NaN,61,NaN,4.7,NaN,
55,9.15,125.2,175.6,61,38.8,4.7,NaN,NaN,54.2,NaN,4.68,NaN,
56,8.74,115.7,176,54.2,31.5,4.67,NaN,NaN,58,63.1,4.51,NaN,
57,7.79,109.2,174.4,57.9,63.3,4.51,NaN,NaN,44.5,NaN,4.32,3.95,
58,8.56,120.8,174.6,44.5,NaN,3.95,NaN,NaN,54.3,18.9,4.14,NaN,
59,8.34,112.5,179.1,54.5,18.8,4.13,NaN,NaN,55.2,31.9,4.39,NaN,
60,7.49,105.5,175.9,55.2,32.1,4.36,NaN,NaN,44.2,NaN,4.37,3.84,
62,8.72,122.4,176.7,62.9,32.7,4.86,NaN,NaN,50.6,22.6,5.15,NaN,
63,8.87,119.4,175.2,50.8,22.5,5.15,NaN,NaN,50.8,20.2,5.11,NaN,
64,9.26,106,177.4,51.1,20.1,5.09,NaN,NaN,43.5,NaN,NaN,NaN,
65,9.19,113.7,172.9,43.4,NaN,4.64,3.56,NaN,54.2,38.1,4.19,NaN,
66,8.17,115.4,174.1,54.2,38.1,4.18,NaN,NaN,63.3,NaN,4.7,NaN,
67,9.02,117.9,176.1,63.3,NaN,4.7,NaN,NaN,59.6,NaN,4.77,NaN,
68,8.78,116.8,173.9,59.6,71.7,4.79,NaN,NaN,59.3,63.4,4.67,NaN,
69,7.97,128.4,173.8,59.3,63.6,4.65,NaN,NaN,56.3,43.4,4.27,NaN,
1000,8.17,118,176.2,NaN,NaN,NaN,NaN,NaN,54.3,41,4.58,NaN,
1001,7.83,116.1,176,54.3,41.1,NaN,NaN,NaN,62,NaN,4.04,NaN,
1002,8.44,106.3,177.2,NaN,40.9,NaN,NaN,NaN,45.5,NaN,4.57,3.94,
1003,8.19,112.8,174.8,45.5,NaN,3.98,NaN,NaN,58.9,NaN,4.39,NaN
MBA2/data/CVS/ 0040755 0000765 0000024 00000000000 10066413465 012612 5 ustar janvitek staff MBA2/data/CVS/Entries 0100644 0000765 0000024 00000000654 10066413465 014150 0 ustar janvitek staff /bpti.mba/1.1/Wed Jun 23 23:01:01 2004//
/csp.mba/1.1/Wed Jun 23 23:01:01 2004//
/fgf.mba/1.1/Wed Jun 23 23:01:01 2004//
/lixin.mba/1.1/Wed Jun 23 23:01:01 2004//
/ns1.mba/1.1/Wed Jun 23 23:01:01 2004//
/rnaseC6572S.mba/1.1/Wed Jun 23 23:01:01 2004//
/rnaseWt.mba/1.1/Wed Jun 23 23:01:00 2004//
/teri.mba/1.1/Wed Jun 23 23:01:00 2004//
/ubiquitin.mba/1.1/Wed Jun 23 23:01:00 2004//
/zdomain.mba/1.1/Wed Jun 23 23:01:01 2004//
D
MBA2/data/CVS/Repository 0100644 0000765 0000024 00000000025 10066406044 014701 0 ustar janvitek staff /p/sss/cvs/MBA2/data
MBA2/data/CVS/Root 0100644 0000765 0000024 00000000050 10066406044 013443 0 ustar janvitek staff :ext:jv@arthur.cs.purdue.edu:/p/sss/cvs
MBA2/data/CVS/Template 0100644 0000765 0000024 00000000000 10066406044 014266 0 ustar janvitek staff MBA2/data/fgf.mba 0100644 0000765 0000024 00000024675 10066405655 013417 0 ustar janvitek staff Real Fgf, 154 residues, Prolines at 8,11,20,21,27,43,56,139,148. Missings at 22, 89. Extras: 24. Max 8 connective resonances.
AEGEITTLPALPEDGGSGAFPPGHFKDPKRLYBKNGGFFLRIHPDGRVDGVREKSDPHIKLQLQAEERGVVSIKGVSANRYLAMKEDGRLLASKSVTDEBFFFERLESNNYNTYRSRKYTSWYVALKRTGQYKLGSKTGPGQKAILFLPMSAKS
22,89
1,8.73,118.5,173.4,51.4,18.9,4.05,NaN,176.4,56.5,29.7,4.24,NaN,
2,8.56,108.5,176.4,56.5,29.7,4.24,NaN,NaN,44.8,NaN,3.89,NaN,
3,8.07,118.1,173.6,44.9,NaN,3.87,NaN,176.1,55.9,30,4.26,NaN,
4,8.34,120.5,176.1,55.8,30.1,4.26,NaN,NaN,60.7,38.2,4.18,NaN,
5,8.29,116.9,176.1,60.6,38.2,4.19,NaN,174,61.3,69.3,4.36,NaN,
6,8.11,115.2,174,61.3,69.3,4.36,NaN,173.6,61.2,69.3,4.27,NaN,
7,8.26,124.2,173.6,61.2,69.4,NaN,NaN,174.7,52.6,41.3,4.55,NaN,
9,8.25,122.1,175.8,62.4,31.7,4.32,NaN,176.9,51.6,18.8,4.24,NaN,
10,8.25,120.8,177,51.7,18.9,4.24,NaN,175.1,52.4,41.2,4.55,NaN,
12,8.6,118.7,176.9,62.7,31.6,4.32,NaN,176,56.4,29.5,4.16,NaN,
13,8.26,118.7,176,56.4,29.6,4.17,NaN,176.5,53.8,40.8,4.54,NaN,
14,8.34,107.3,176.5,53.8,40.9,4.54,NaN,NaN,45.3,NaN,3.87,NaN,
15,8.35,106.6,174.6,45.3,NaN,3.88,NaN,NaN,45,NaN,3.95,3.65,
16,8.26,113.3,174.1,45,NaN,3.95,NaN,174.8,58.4,63.3,4.36,NaN,
17,8.43,108.5,174.8,58.4,63.4,4.36,NaN,NaN,44.9,NaN,3.85,NaN,
18,7.88,120.9,173.1,45,NaN,3.85,3.66,176.5,51.8,19.2,4.18,NaN,
19,8.09,117,176.5,51.8,18.9,4.19,NaN,172.9,55.2,38.9,NaN,NaN,
23,8.09,117.2,174.4,NaN,NaN,NaN,NaN,174.1,57,29.3,4.25,NaN,
24,8.08,114.8,174.1,57,29.3,4.25,NaN,175.6,57.2,39,4.54,NaN,
25,7.96,118.2,175.6,57.2,39.1,4.54,NaN,175.8,57,NaN,4.14,NaN,
26,7.94,117.3,175.8,57,32.8,4.14,NaN,173.6,52.1,40.4,4.95,NaN,
28,9.31,117.1,175,62.5,32,4.72,NaN,175.1,53.3,37.3,5.14,NaN,
29,8.79,115.1,175.1,53.3,37.4,5.13,NaN,174.8,54.1,33.3,4.85,NaN,
30,10.34,123,174.8,54.1,33.4,4.86,NaN,173.9,53.8,43.4,4.86,NaN,
31,8.61,124.6,173.9,53.8,43,4.89,NaN,173.2,56.6,39.6,4.27,NaN,
32,9.32,128.1,173.2,56.6,39.9,4.28,NaN,174.3,57.3,29.5,4.36,NaN,
33,8.36,126.4,174.3,57.4,29.2,4.35,NaN,176.3,57.4,33.8,3.68,NaN,
34,7.69,116.2,176.3,57.4,33.7,3.7,NaN,172.2,50.8,37,4.48,NaN,
35,7.65,106.1,172.2,50.8,36.9,4.49,NaN,NaN,44.5,NaN,4.21,3.45,
36,7.01,106.1,174.4,44.5,NaN,4.21,3.45,NaN,46.2,NaN,3.31,2.78,
37,5.82,110.8,172.4,46.3,NaN,3.31,2.79,174.2,56.6,42.2,3.88,NaN,
38,9.33,118.4,174.2,56.6,42.1,3.89,NaN,176.2,56.6,39.8,5.53,NaN,
39,8.34,121.2,176.1,56.4,40,5.53,NaN,NaN,56.3,43.3,NaN,NaN,
40,9.59,126.4,173.7,56.3,43,4.32,NaN,173,55.3,NaN,4.47,NaN,
41,7.43,120.9,173,55.2,33.1,4.49,NaN,174.2,59.8,NaN,4.33,NaN,
42,8.75,122.8,174.2,59.8,39.3,4.31,NaN,175.6,54.8,31.4,4.13,NaN,
44,7.89,112.2,175.5,64.5,31.5,4.12,NaN,177.1,52.8,39.8,4.47,NaN,
45,7.93,105.3,177.1,52.8,39.9,4.48,NaN,NaN,45,NaN,4.55,3.58,
46,7.7,117.6,173.2,45.1,NaN,4.55,3.6,174.8,57,31.1,4.36,NaN,
47,8.25,118.9,174.8,57,NaN,4.37,NaN,174.3,60.5,34.5,4.99,NaN,
48,9.05,126.5,174.3,60.5,34.5,4.99,NaN,171.8,53,40.3,4.29,NaN,
49,8.09,128.5,171.8,53.1,40.3,4.29,NaN,NaN,44.1,NaN,5.56,NaN,
50,8.84,113.5,171.8,44.1,NaN,5.57,NaN,174.3,59.8,35.9,4.95,NaN,
51,9.28,123,174.4,59.8,36,4.95,NaN,175.9,57.6,29.6,4.47,NaN,
52,7.05,117.1,175.9,57.6,29.9,4.48,NaN,175,56.3,29.6,4.31,NaN,
53,8.43,122.6,175,56.3,29.6,4.31,NaN,175.7,57.6,32,3.47,NaN,
54,8.11,109.9,175.7,57.7,32.1,3.49,NaN,173.7,57.5,63.1,4.24,NaN,
55,7.01,123.4,173.8,57.5,63.1,4.23,NaN,175.4,52.6,42.8,4.49,NaN,
57,9.45,116,178.7,64,31.7,4.19,NaN,173.4,58.4,28.1,4.66,NaN,
58,6.75,105.5,173.4,58.5,28.1,4.65,NaN,174.8,59.7,37.5,5.09,NaN,
59,6.55,117.9,174.8,59.7,37.2,5.09,NaN,174.7,56.9,31.9,4.17,NaN,
60,9.68,127.6,174.7,56.8,32,4.18,NaN,175,53,44.1,5.38,NaN,
61,9.37,118,175,53,44.1,5.38,NaN,174.5,53.8,31.1,4.56,NaN,
62,9.12,129.7,174.5,53.8,31.2,4.57,NaN,175.7,54.6,42,5.24,NaN,
63,8.3,119.3,175.7,54.6,41.9,5.23,NaN,174.1,54.3,31.4,4.53,NaN,
64,8.45,126.3,174.2,54.3,31.3,4.52,NaN,177.1,51.8,18.4,4.69,NaN,
65,8.4,124.6,177.1,51.8,18.5,4.7,NaN,175.8,56,NaN,4.43,NaN,
66,8.53,117.3,175.8,56,29.4,4.42,NaN,174.6,55,30.7,4.26,NaN,
67,8.59,118.1,174.6,54.9,30.9,4.25,NaN,NaN,58.3,NaN,4.04,NaN,
68,8.74,112.1,177.7,58.3,29,4.08,NaN,173.4,45.8,NaN,4.34,NaN,
69,8.31,119.6,173.2,45.8,NaN,4.36,NaN,175.6,60.6,33.5,5.1,NaN,
70,9.71,117.6,175.6,60.6,33.7,5.09,NaN,175.4,58.2,35.5,5.83,NaN,
71,8.73,112.4,175.3,58.3,35.6,5.83,NaN,173.4,56.7,66.1,5.15,NaN,
72,10.46,120.4,173.4,56.7,66.1,5.14,NaN,172.3,61.4,40.3,4.27,NaN,
73,8.76,125.2,172.2,61.4,40.2,4.3,NaN,177,53.4,35.8,4.57,NaN,
74,9.17,111.7,177,53.4,35.8,4.58,NaN,NaN,46.5,NaN,4.19,3.29,
75,7.88,125.9,174,46.5,NaN,4.2,3.32,NaN,66.9,31.3,3.29,NaN,
76,9.31,113.4,177.8,66.9,31.4,3.31,NaN,176.4,61,61.9,4.16,NaN,
77,8.59,117.7,176.4,61,61.8,4.18,NaN,176.4,52.9,19.3,3.86,NaN,
78,8.11,113.2,176.3,52.9,19,3.85,NaN,173.8,52.8,NaN,3.97,NaN,
79,6.63,110,173.8,52.9,36.9,3.98,NaN,173,53.3,37.4,4.65,NaN,
80,9.49,118.3,173,53.3,37.6,4.66,NaN,175.4,56.9,40.1,4.85,NaN,
81,9.08,122.1,175.3,56.9,40.2,4.87,NaN,173.8,56,42.7,4.04,NaN,
82,9,125.1,173.8,55.9,42.7,4.04,NaN,174.8,50.1,22.2,5.12,NaN,
83,7.63,116.9,174.7,50,22.3,5.11,NaN,174.7,53.3,NaN,5.35,NaN,
84,8.4,119.7,174.6,53.3,35.4,5.35,NaN,178.1,52.8,31.5,4.82,NaN,
85,8.67,115.8,NaN,52.8,31.5,4.82,NaN,NaN,58.1,NaN,NaN,NaN,
86,7.81,114.1,175,58,NaN,NaN,NaN,176.7,51.8,39.9,4.56,NaN,
87,8.53,106.9,176.7,51.8,39.9,4.57,NaN,NaN,44.2,NaN,3.63,NaN,
88,7.42,116.5,173.6,44.2,NaN,3.62,3.38,173.8,56.7,30.4,3.98,NaN,
90,8.64,118.7,175,52.3,43,NaN,NaN,173.5,54.1,44.5,4.48,NaN,
91,8.76,120.6,173.5,54.1,44.5,4.49,NaN,176.4,49.8,21.8,5.32,NaN,
92,9.74,119.3,176.4,49.7,21.9,5.31,NaN,175.2,56,65.3,4.66,NaN,
93,9.37,124.1,175.2,56,65.3,4.67,NaN,175.8,59.4,32.6,4.24,NaN,
94,7.68,108.5,175.9,59.5,32.6,4.24,NaN,172.6,55.9,64.7,4.73,NaN,
95,8.35,120.9,172.6,55.9,64.8,4.72,NaN,NaN,62.9,30,3.6,NaN,
96,7.24,117.4,175.4,62.8,30.6,3.6,NaN,174,58.7,71.8,4.64,NaN,
97,8.77,115.4,174.1,58.8,71.9,4.65,NaN,177.2,55.7,38.8,4.25,NaN,
98,7.69,117.2,177.2,55.7,39,4.25,NaN,NaN,57,29.6,4.08,NaN,
99,7.66,113.5,176.7,57.1,29.9,4.09,NaN,172.7,57.6,NaN,5.23,NaN,
100,6.39,113.1,172.7,57.7,27.4,5.22,NaN,174.7,56.1,41,5.09,NaN,
101,9.38,119.1,174.6,56.1,41,5.09,NaN,174.7,56.2,42.4,4.98,NaN,
102,10.23,120.1,174.6,56.2,42.8,4.98,NaN,175.7,57.3,NaN,5.25,NaN,
103,8.65,126.9,175.7,57.3,39.2,5.27,NaN,174.9,54.3,32.1,4.97,NaN,
104,8.5,127.5,174.9,54.2,32.1,4.97,NaN,173.4,54,33.5,4.74,NaN,
105,8.31,124.9,173.4,54,33.6,4.73,NaN,176.3,54.9,42.1,4.76,NaN,
106,9.36,126.2,176.4,54.9,42.1,4.76,NaN,176.3,55,29.8,4.64,NaN,
107,8.31,111.3,176.3,55,29.9,4.64,NaN,NaN,58.9,63,3.86,NaN,
108,8.7,116.7,174.3,59,63.2,3.87,NaN,173.6,53.8,NaN,NaN,NaN,
109,8.38,106.3,173.7,53.7,37.2,4.43,NaN,NaN,55.2,NaN,4.21,NaN,
110,7.77,116,173.3,55.1,37.1,4.21,NaN,173.7,58.7,40.2,4.5,NaN,
111,9.72,117,173.7,58.8,40.2,4.5,NaN,174.9,51,42.1,5.96,NaN,
112,8.69,104.9,174.8,51.1,42.2,5.97,NaN,173.1,59.1,72.7,5.14,NaN,
113,10.62,117.8,173.1,59.1,72.6,5.12,NaN,173,57.6,NaN,5.19,NaN,
114,8.72,124.4,173,57.7,39.5,5.19,NaN,176,53.8,NaN,4.85,NaN,
115,8.79,118.7,176,53.7,34.7,4.85,NaN,NaN,59.1,NaN,NaN,NaN,
116,7.43,121.6,173,59.1,62.2,4.6,NaN,174.9,56.6,30.8,3.93,NaN,
117,7.5,116.6,174.9,56.7,30.8,3.93,NaN,175.7,56.7,34.1,3.84,NaN,
118,7.97,121,175.7,56.7,34.1,3.84,NaN,176.2,54.9,NaN,4.39,NaN,
119,6.7,129.2,176.2,54.9,36.5,NaN,NaN,176.1,64.2,69.3,4.56,NaN,
120,8.1,114.3,176.1,64.2,69.4,4.59,NaN,172.7,57.8,63.3,4.67,NaN,
121,8.27,120,172.7,57.9,63.4,4.68,NaN,174,54,NaN,5.17,NaN,
122,8.28,117.6,173.9,54.1,NaN,5.18,NaN,176.4,56.7,NaN,5.34,NaN,
123,8.66,120,176.3,56.6,41.4,5.36,NaN,NaN,63.7,32,3.67,NaN,
124,8.77,127.1,176.3,63.7,32.2,3.69,NaN,175.4,51.6,25.7,5.34,NaN,
125,7.81,114.8,175.4,51.7,25.7,5.34,NaN,175.9,53.1,44.7,4.81,NaN,
126,8.52,115.1,175.9,53.1,44.7,4.82,NaN,177.6,55.6,34.9,4.2,NaN,
127,9.16,117,177.7,55.6,NaN,4.2,NaN,175.5,57.6,NaN,NaN,NaN,
128,6.71,129.3,175.6,57.7,28.9,4.07,NaN,176.1,60.6,69.3,4.17,NaN,
129,7.7,110.8,175.9,60.6,69.6,NaN,NaN,NaN,43.8,NaN,3.08,NaN,
130,6.49,113.1,171.5,43.8,NaN,3.11,1.72,175.5,53,29.7,4.58,NaN,
131,8.51,115.7,175.5,53.1,29.7,4.6,NaN,172.6,57.9,38.1,4.84,NaN,
132,8.11,121.2,172.6,57.9,38.1,4.85,NaN,173.9,53.7,34.9,4.19,NaN,
133,8.56,125.2,173.9,53.6,35,4.2,NaN,179.9,55.3,42.7,3.95,NaN,
134,9.71,108.1,179.9,55.3,42.6,3.98,NaN,NaN,46.4,NaN,3.57,NaN,
135,6.3,108.3,174.8,46.5,NaN,3.86,3.54,NaN,58,NaN,3.18,NaN,
136,7.74,118.1,174.6,58,61.8,3.14,NaN,176.5,54.3,32,4.56,NaN,
137,7.4,108.2,176.6,54.3,31.9,4.57,NaN,173.5,60.9,72.7,4.88,NaN,
138,6.57,128.7,173.5,60.9,72.7,4.88,NaN,NaN,44.9,NaN,4.34,4.25,
140,8.57,107.9,177.4,62.7,31.8,4.02,NaN,NaN,45,NaN,3.96,3.59,
141,6.68,115.5,173.9,45,NaN,3.97,3.59,176.6,54.8,28.6,4.22,NaN,
142,8.89,122.2,176.7,54.8,NaN,4.22,NaN,177.3,59.1,32,NaN,NaN,
143,7.74,112.2,177.4,59.1,32,3.7,NaN,175.1,54.1,20.9,NaN,NaN,
144,6.12,126,175.1,54,20.9,3.96,NaN,175.1,59.3,38.4,5.06,NaN,
145,6.97,119.8,175.1,59.3,38.1,5.07,NaN,175.5,53.7,42.1,4.73,NaN,
146,9.77,118.8,175.5,53.7,42.3,4.73,NaN,174.1,56.2,43.9,5.55,NaN,
147,10.24,126.5,174.1,56.2,43.8,5.56,NaN,175,51,44.3,4.96,NaN,
149,9.44,123.2,176.1,61.3,30.4,5.19,NaN,174.9,54.2,36.2,4.67,NaN,
150,8.73,113.5,174.9,54.2,36.2,4.67,NaN,NaN,58.9,63.1,4.34,NaN,
151,8.46,125.1,174.8,58.9,63.2,4.33,NaN,175.6,51,18.5,4.36,NaN,
152,8,117.7,175.7,51,18.6,4.36,NaN,175.5,56.5,32.8,4.16,NaN,
153,7.82,119.8,175.5,56.4,32.8,4.17,NaN,178.2,59.7,64.2,4.11,NaN,
1000,8.7,106.5,178,63.6,31.6,4.44,NaN,NaN,45.4,NaN,3.95,NaN,
1001,7.94,121.1,173.2,NaN,NaN,3.87,NaN,NaN,NaN,NaN,4.19,NaN,
1002,8.56,122.5,175.2,62,34.1,4.43,NaN,176.9,51.9,19.2,4.27,NaN,
1003,8.29,117.2,NaN,60.7,38.2,NaN,NaN,NaN,NaN,NaN,4.36,NaN,
1004,8.08,117.9,175.7,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1005,8.02,122.1,172.6,61.4,69.5,4.24,NaN,175.1,52.1,42.7,4.39,NaN,
1006,7,107.4,NaN,NaN,NaN,NaN,NaN,NaN,43.6,NaN,2.76,2.29,
1007,8.11,115.6,NaN,NaN,NaN,3.79,NaN,176.4,55.7,28.6,4.25,NaN,
1008,8.49,108.6,174.8,NaN,NaN,NaN,NaN,NaN,44.9,NaN,3.91,NaN,
1009,8.33,119.9,NaN,NaN,NaN,NaN,NaN,176.2,56.8,NaN,4.18,NaN,
1010,8.29,122.7,NaN,62.4,31.7,NaN,NaN,NaN,51.7,NaN,4.23,NaN,
1011,8.87,119.7,176,62,34.1,4.48,NaN,176,56.9,29.6,4.22,NaN,
1012,8.43,118.9,176,56.8,29.7,4.23,NaN,NaN,53.7,40.8,4.54,NaN,
1013,7.83,118.3,175.8,51.8,18.9,4.22,NaN,NaN,51.9,NaN,4.35,NaN,
1014,8.5,116.9,175.8,56,29.4,NaN,NaN,NaN,NaN,NaN,4.31,NaN,
1015,8.46,106.7,NaN,62.9,31.5,4.35,NaN,NaN,45.1,NaN,3.78,NaN,
1016,8.17,118.9,175.5,57.6,NaN,4.57,NaN,175.5,56.4,NaN,4.17,NaN,
1017,8.32,120,NaN,NaN,NaN,NaN,NaN,NaN,54.4,NaN,4.54,NaN,
1018,8.01,118.5,NaN,56.5,32.6,4.2,NaN,NaN,52.3,NaN,4.86,NaN,
1019,8.36,107.5,NaN,NaN,NaN,4.21,NaN,NaN,NaN,NaN,NaN,NaN,
1020,8.62,126.6,174.2,NaN,NaN,4.57,NaN,NaN,51.8,18.6,4.84,NaN,
1021,8.17,118.1,NaN,55.6,28.9,4.49,NaN,NaN,57.7,38.9,NaN,NaN,
1022,8.81,112.1,NaN,58.4,28.9,NaN,NaN,NaN,45.7,NaN,4.34,NaN,
1023,8.64,118.8,173.5,NaN,NaN,NaN,NaN,173.5,NaN,NaN,NaN,NaN,
MBA2/data/lixin.mba 0100644 0000765 0000024 00000015070 10066405655 013765 0 ustar janvitek staff Lixin data with fixed variances, 100 residues, Prolines at 11,42,59,60. Missing at 1,24,25,29,33,34,35,36,39,40,48,49,53,54. No extras. Max 4 connective resonances.
MNDQRKKARNTPFNMLKRERNRVSTVQQLTKRFSLGMLQGRGPLKLFMALVAFLRFLTIPPTAGILKRWGTIKKSKAINVLRGFRKEIGRMLNILNRRRR
1,24,25,29,33,34,35,36,39,40,48,49,53,54
2,8.522333,121.3998,NaN,53.81800,39.07233,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
3,8.533750,121.1738,NaN,54.96867,41.58633,NaN,NaN,NaN,56.75200,29.47100,NaN,NaN,
4,8.347429,121.3443,NaN,56.75550,29.50933,NaN,NaN,NaN,56.99600,30.86600,NaN,NaN,
5,8.261857,121.9690,NaN,57.04100,30.98033,NaN,NaN,NaN,56.97500,33.38100,NaN,NaN,
6,8.281714,122.6814,NaN,56.92200,33.38150,NaN,NaN,NaN,56.76700,33.49600,NaN,NaN,
7,8.340222,125.6912,NaN,56.73600,33.53967,NaN,NaN,NaN,52.90400,19.75000,NaN,NaN,
8,8.379000,120.4753,NaN,52.88100,19.74867,NaN,NaN,NaN,56.53600,31.37100,NaN,NaN,
9,8.560250,120.1767,NaN,56.54683,31.36033,NaN,NaN,NaN,53.65000,39.48700,NaN,NaN,
10,8.006567,114.9332,NaN,53.61955,39.49809,NaN,NaN,NaN,59.72800,70.25900,NaN,NaN,
12,7.903333,123.4922,NaN,63.84956,33.05189,NaN,NaN,NaN,59.12467,40.20100,NaN,NaN,
13,8.308000,119.7967,NaN,58.76200,39.82200,NaN,NaN,NaN,53.80900,39.16900,NaN,NaN,
14,8.232750,120.6746,NaN,53.83833,39.12367,NaN,NaN,NaN,56.39600,33.18200,NaN,NaN,
15,8.242778,123.0583,NaN,56.32140,32.98929,NaN,NaN,NaN,56.03533,42.59533,NaN,NaN,
16,8.258313,122.3078,NaN,55.92417,42.61817,NaN,NaN,NaN,56.97600,33.28350,NaN,NaN,
17,8.386214,122.1716,NaN,56.95475,33.35533,NaN,NaN,NaN,56.80500,31.20850,NaN,NaN,
18,8.525000,122.5008,NaN,56.63750,31.28850,NaN,NaN,NaN,56.83900,30.85300,NaN,NaN,
19,8.457000,122.0866,NaN,56.92833,30.86650,NaN,NaN,NaN,56.93550,31.02150,NaN,NaN,
20,8.514769,119.5975,NaN,56.73275,31.25260,NaN,NaN,NaN,53.73600,39.41400,NaN,NaN,
21,8.270333,121.9204,NaN,53.72720,39.40580,NaN,NaN,NaN,56.71200,31.35800,NaN,NaN,
22,7.923125,116.0170,NaN,56.96733,31.43600,NaN,NaN,NaN,60.31500,35.79900,NaN,NaN,
23,8.062200,119.7432,NaN,60.48400,35.60100,NaN,NaN,NaN,58.38100,65.68100,NaN,NaN,
26,8.645000,120.6240,NaN,67.48100,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
27,7.889333,118.6243,NaN,60.05400,28.24250,NaN,NaN,NaN,59.33200,29.03100,NaN,NaN,
28,7.982000,118.9037,NaN,59.18950,29.12700,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
30,7.348200,119.1592,NaN,66.96700,69.26600,NaN,NaN,NaN,58.36700,32.50500,NaN,NaN,
31,7.530000,116.8934,NaN,58.47600,32.88600,NaN,NaN,NaN,57.14600,NaN,NaN,NaN,
32,8.693667,120.6587,NaN,56.81300,31.23700,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
37,8.422250,120.3912,NaN,58.43200,39.58400,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
38,7.605833,115.0545,NaN,57.27550,41.58250,NaN,NaN,NaN,55.74800,30.17700,NaN,NaN,
41,8.719750,109.3102,NaN,56.06750,28.18600,NaN,NaN,NaN,44.38100,NaN,NaN,NaN,
43,8.776600,123.8948,NaN,63.28333,32.99000,NaN,NaN,NaN,59.44000,NaN,NaN,NaN,
44,9.157800,117.7014,NaN,59.28800,41.89400,NaN,NaN,NaN,61.81200,32.56600,NaN,NaN,
45,6.639000,118.0450,NaN,62.02400,32.86800,NaN,NaN,NaN,58.49800,NaN,NaN,NaN,
46,8.207000,118.6050,NaN,NaN,NaN,NaN,NaN,NaN,61.50400,NaN,NaN,NaN,
47,9.160000,114.7830,NaN,61.50300,39.68550,NaN,NaN,NaN,56.42700,30.87400,NaN,NaN,
50,8.496000,118.9073,NaN,58.20500,41.72600,NaN,NaN,NaN,67.94200,NaN,NaN,NaN,
51,8.244333,120.5587,NaN,67.93550,31.18200,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
52,8.138000,117.2150,NaN,NaN,17.68100,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
55,9.249000,120.8165,NaN,59.70850,26.82700,NaN,NaN,NaN,NaN,37.55300,NaN,NaN,
56,6.947000,115.7887,NaN,56.40300,37.28200,NaN,NaN,NaN,54.13900,43.21300,NaN,NaN,
57,7.865857,116.2447,NaN,54.20350,43.13133,NaN,NaN,NaN,62.78100,68.49000,NaN,NaN,
58,8.285750,123.3849,NaN,62.90100,68.61333,NaN,NaN,NaN,58.63400,40.19000,NaN,NaN,
61,6.103400,104.8768,NaN,62.21750,32.47800,NaN,NaN,NaN,59.97200,72.12900,NaN,NaN,
62,9.407750,123.6669,NaN,60.03567,71.96100,NaN,NaN,NaN,56.00200,18.69700,NaN,NaN,
63,9.150800,106.8476,NaN,56.03250,18.46350,NaN,NaN,NaN,47.48200,NaN,NaN,NaN,
64,7.409600,122.2454,NaN,47.46300,NaN,NaN,NaN,NaN,66.04000,38.61900,NaN,NaN,
65,8.327833,120.5517,NaN,66.25250,38.96100,NaN,NaN,NaN,NaN,42.30400,NaN,NaN,
66,8.395000,119.7600,NaN,58.64700,42.53350,NaN,NaN,NaN,59.48600,32.78500,NaN,NaN,
67,7.631500,120.1478,NaN,59.74850,32.88000,NaN,NaN,NaN,58.81500,29.50700,NaN,NaN,
68,9.134000,120.8760,NaN,58.81400,29.52800,NaN,NaN,NaN,60.16900,30.10700,NaN,NaN,
69,7.724200,102.1582,NaN,60.27050,30.37000,NaN,NaN,NaN,46.56600,NaN,NaN,NaN,
70,7.881200,109.0760,NaN,46.54900,NaN,NaN,NaN,NaN,62.15500,70.76800,NaN,NaN,
71,7.078429,118.6254,NaN,62.12500,70.83367,NaN,NaN,NaN,62.07300,39.48600,NaN,NaN,
72,8.571857,124.6134,NaN,62.09233,39.23150,NaN,NaN,NaN,56.73100,32.64400,NaN,NaN,
73,8.915375,127.7034,NaN,56.57967,32.65100,NaN,NaN,NaN,61.11400,32.68500,NaN,NaN,
74,8.706500,113.5105,NaN,61.48967,32.73300,NaN,NaN,NaN,61.89700,NaN,NaN,NaN,
75,6.950600,120.5646,NaN,62.07167,NaN,NaN,NaN,NaN,58.66500,33.20200,NaN,NaN,
76,8.185500,122.0583,NaN,58.61750,33.07750,NaN,NaN,NaN,55.97300,20.58200,NaN,NaN,
77,8.658500,118.4725,NaN,55.81800,20.39600,NaN,NaN,NaN,66.37700,38.48400,NaN,NaN,
78,7.482000,117.9160,NaN,66.36067,38.27550,NaN,NaN,NaN,57.22400,38.44200,NaN,NaN,
79,7.743000,120.1013,NaN,57.34600,38.47400,NaN,NaN,NaN,66.15700,31.96000,NaN,NaN,
80,7.964800,119.6166,NaN,66.25250,31.93700,NaN,NaN,NaN,58.15500,41.98700,NaN,NaN,
81,8.701000,119.8827,NaN,58.35000,42.26000,NaN,NaN,NaN,61.06200,NaN,NaN,NaN,
82,7.632500,108.4010,NaN,61.17650,29.53400,NaN,NaN,NaN,47.85000,NaN,NaN,NaN,
83,7.962000,123.3585,NaN,47.65800,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
84,8.750000,120.8450,NaN,NaN,36.14600,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
85,8.000500,121.1080,NaN,61.32150,30.85200,NaN,NaN,NaN,59.84400,32.73100,NaN,NaN,
86,8.207500,121.8923,NaN,59.97333,32.84900,NaN,NaN,NaN,59.06400,NaN,NaN,NaN,
87,8.632400,120.1870,NaN,59.39200,32.09500,NaN,NaN,NaN,64.31300,36.90100,NaN,NaN,
88,8.159600,107.1668,NaN,64.62867,36.97400,NaN,NaN,NaN,48.28400,NaN,NaN,NaN,
89,8.274250,123.5350,NaN,48.20833,NaN,NaN,NaN,NaN,60.34600,NaN,NaN,NaN,
90,8.418500,119.3595,NaN,60.40300,30.21900,NaN,NaN,NaN,60.50200,NaN,NaN,NaN,
91,8.657500,119.6450,NaN,60.82050,35.27300,NaN,NaN,NaN,59.13600,NaN,NaN,NaN,
92,8.171667,118.6673,NaN,58.92500,42.34400,NaN,NaN,NaN,56.98300,38.79200,NaN,NaN,
93,8.121833,120.0252,NaN,56.83050,38.82700,NaN,NaN,NaN,65.67400,38.78500,NaN,NaN,
94,7.991000,119.3818,NaN,65.91150,39.11300,NaN,NaN,NaN,58.15500,42.58800,NaN,NaN,
95,8.601833,116.0707,NaN,58.06400,42.38800,NaN,NaN,NaN,56.12000,39.51700,NaN,NaN,
96,7.398125,116.1207,NaN,56.16667,39.51833,NaN,NaN,NaN,57.32600,31.27300,NaN,NaN,
97,7.571333,119.9703,NaN,57.30800,31.39400,NaN,NaN,NaN,57.18100,32.09700,NaN,NaN,
98,8.881500,121.6352,NaN,57.07850,32.03150,NaN,NaN,NaN,57.15600,31.44100,NaN,NaN,
99,7.783429,122.9557,NaN,57.40850,31.59000,NaN,NaN,NaN,57.47600,32.07700,NaN,NaN,
MBA2/data/ns1.mba 0100644 0000765 0000024 00000010571 10066405655 013344 0 ustar janvitek staff Real Ns1, 73 residues, Proline at 30, Missing at 9,19,26,36, Extras: 2. Max 7 connective resonances.
MDSNTVSSFQVDBFLWHVRKQVVDQELGDAPFLDRLRRDQKSLRGRGSTLGLNIEAATHVGKQIVEKILKEES
9,19,26,36
1,8.92,122.6,174.5,54.6,32.4,4.25,NaN,NaN,54.3,41.3,4.93,NaN,
2,8.89,116.0,177.9,54.0,41.4,4.92,NaN,NaN,60.2,62.9,4.38,NaN,
3,8.86,117.3,177.4,60.2,63.0,4.41,NaN,NaN,54.1,35.4,4.88,NaN,
4,8.08,120.1,178.9,53.9,35.7,4.87,NaN,NaN,65.8,NaN,4.49,NaN,
5,7.62,121.2,178.3,66.0,NaN,4.48,NaN,NaN,67.5,NaN,3.64,NaN,
6,8.45,111.9,178.5,67.7,NaN,3.64,NaN,NaN,61.2,61.8,4.81,NaN,
7,8.00,114.4,178.4,61.3,61.9,4.80,NaN,NaN,63.4,62.8,NaN,NaN,
8,7.38,118.5,176.3,63.5,63.6,3.67,NaN,NaN,61.3,38.9,4.59,NaN,
10,8.63,116.3,179.5,59.3,NaN,3.65,NaN,NaN,68.1,NaN,3.54,NaN,
11,8.57,117.2,177.0,68.3,NaN,3.54,NaN,NaN,58.1,40.3,4.71,NaN,
12,8.65,116.9,180.8,58.1,39.6,4.69,NaN,NaN,64.8,26.1,4.20,NaN,
13,8.36,118.3,178.9,65.0,NaN,4.21,NaN,NaN,62.2,NaN,NaN,NaN,
14,9.33,115.2,178.1,62.2,38.4,4.75,NaN,NaN,57.9,38.9,3.88,NaN,
15,8.31,117.9,179.5,57.9,NaN,3.87,NaN,NaN,63.7,29.1,3.81,NaN,
16,7.76,114.7,177.9,63.8,NaN,3.77,NaN,NaN,59.8,27.3,4.31,NaN,
17,7.88,115.9,178.0,59.8,NaN,4.31,NaN,NaN,66.9,NaN,3.20,NaN,
18,7.79,115.7,178.4,66.9,NaN,3.21,NaN,NaN,59.0,NaN,3.77,NaN,
20,7.51,115.3,178.9,58.6,30.5,3.54,NaN,NaN,58.4,28.5,4.10,NaN,
21,7.75,117.3,179.2,58.4,28.8,4.13,NaN,NaN,66.9,NaN,3.32,NaN,
22,7.76,117.1,178.9,67.1,NaN,3.32,NaN,NaN,65.8,30.8,3.87,NaN,
23,8.74,121.7,181.0,66.0,NaN,3.88,NaN,NaN,57.0,39.2,4.54,NaN,
24,7.58,114.5,178.6,56.9,39.3,4.54,NaN,NaN,55.5,27.3,4.43,NaN,
25,8.10,109.6,176.1,55.3,27.5,4.42,NaN,NaN,57.2,25.1,4.26,NaN,
27,7.93,101.9,177.6,53.8,44.1,4.48,NaN,NaN,43.4,NaN,2.74,NaN,
28,7.85,121.3,175.7,43.4,NaN,NaN,NaN,NaN,51.5,40.9,4.83,NaN,
29,8.55,117.1,178.5,51.3,40.9,4.82,NaN,NaN,51.5,15.1,NaN,NaN,
31,8.03,117.4,178.9,65.9,NaN,4.53,NaN,NaN,62.0,NaN,4.04,NaN,
32,8.38,120.1,180.0,62.1,NaN,4.09,NaN,NaN,58.1,41.1,NaN,NaN,
33,8.42,117.9,179.1,58.1,41.1,4.20,NaN,NaN,57.9,40.9,4.54,NaN,
34,8.40,115.3,179.6,57.7,41.2,4.53,NaN,NaN,60.0,30.3,3.98,NaN,
35,7.67,118.4,179.3,60.0,NaN,3.99,NaN,NaN,58.8,42.0,3.98,NaN,
37,8.48,118.2,180.2,59.8,29.7,4.38,NaN,NaN,59.6,29.7,4.20,NaN,
38,8.72,117.1,180.3,59.6,29.8,4.19,NaN,NaN,56.3,39.8,4.76,NaN,
39,8.22,119.1,178.5,56.2,39.7,4.76,NaN,NaN,59.3,27.9,3.25,NaN,
40,7.07,114.3,178.7,59.3,27.7,3.25,NaN,NaN,59.3,31.8,4.10,NaN,
41,7.84,112.7,180.2,59.3,31.9,4.10,NaN,NaN,60.8,NaN,4.48,NaN,
42,8.84,120.5,178.9,60.8,61.9,4.47,NaN,NaN,58.3,41.2,4.27,NaN,
43,7.79,115.9,179.7,58.2,41.1,4.30,NaN,NaN,59.6,29.3,4.21,NaN,
44,7.81,104.1,180.3,59.5,29.2,4.20,NaN,NaN,47.0,NaN,3.92,NaN,
45,8.43,120.6,177.9,47.0,NaN,NaN,NaN,NaN,59.0,31.5,4.10,NaN,
46,8.90,104.2,179.2,59.0,NaN,4.09,NaN,NaN,47.9,NaN,2.94,NaN,
47,7.81,113.2,177.4,48.0,NaN,2.93,3.25,NaN,61.2,62.3,4.43,NaN,
48,7.91,115.4,178.5,61.2,62.4,4.41,NaN,NaN,66.0,68.5,4.04,NaN,
49,7.85,115.5,177.5,66.2,NaN,4.05,NaN,NaN,55.2,42.5,4.25,NaN,
50,7.74,106.0,178.0,55.0,42.5,4.25,NaN,NaN,46.0,NaN,4.21,3.91,
51,7.73,115.6,176.4,46.0,NaN,4.15,NaN,NaN,52.9,45.2,4.82,NaN,
52,8.35,118.4,176.7,52.8,45.0,4.81,NaN,NaN,52.9,40.3,4.87,NaN,
53,9.06,124.9,177.6,52.9,40.4,4.88,NaN,NaN,65.3,38.0,3.93,NaN,
54,8.72,123.0,179.4,65.3,37.7,3.94,NaN,NaN,60.7,27.9,4.10,NaN,
55,8.39,119.7,179.7,60.7,28.1,4.09,NaN,NaN,54.8,17.7,4.32,NaN,
56,8.31,118.1,181.0,54.9,17.7,4.31,NaN,NaN,55.0,19.3,4.43,NaN,
57,8.42,112.4,180.0,55.0,19.6,4.47,NaN,NaN,67.6,68.3,3.81,NaN,
58,7.33,115.3,176.9,67.8,NaN,3.80,NaN,NaN,58.6,27.9,4.49,NaN,
59,7.44,116.6,178.2,58.6,27.9,4.48,NaN,NaN,66.0,31.5,3.82,NaN,
60,8.69,104.9,179.3,66.0,NaN,3.82,NaN,NaN,46.8,NaN,NaN,NaN,
61,7.73,118.7,176.1,46.8,NaN,NaN,NaN,NaN,59.3,32.1,1.80,NaN,
62,6.80,113.5,178.3,58.9,32.3,1.80,NaN,NaN,58.4,27.7,4.03,NaN,
63,7.94,117.0,NaN,58.3,27.8,4.03,NaN,NaN,65.1,NaN,3.60,NaN,
64,8.31,115.4,179.2,65.3,NaN,3.63,NaN,NaN,66.9,NaN,3.53,NaN,
65,8.86,115.9,178.4,67.0,NaN,3.53,NaN,NaN,58.8,28.2,3.98,NaN,
66,7.35,116.4,179.5,59.4,28.3,3.98,NaN,NaN,59.8,31.8,4.14,NaN,
67,7.35,117.0,179.3,59.8,31.9,4.13,NaN,NaN,64.4,37.7,3.87,NaN,
68,8.42,115.9,179.5,64.6,NaN,3.87,NaN,NaN,57.2,40.6,4.32,NaN,
69,7.88,116.4,180.0,57.2,40.7,4.31,NaN,NaN,58.2,32.2,4.27,NaN,
70,7.68,114.5,179.0,58.1,32.2,4.26,NaN,NaN,56.7,28.8,4.37,NaN,
71,7.67,116.1,177.9,56.7,29.2,4.37,NaN,NaN,56.0,29.7,4.64,NaN,
72,7.87,119.5,177.1,56.0,29.8,4.64,NaN,NaN,60.1,64.4,4.43,NaN,
1000,7.35,113.0,177.5,NaN,25.1,NaN,NaN,NaN,NaN,27.3,NaN,NaN,
1001,7.86,117.4,177.1,NaN,23.8,4.60,NaN,NaN,NaN,NaN,NaN,NaN,
MBA2/data/rnaseC6572S.mba 0100644 0000765 0000024 00000023444 10066405655 014530 0 ustar janvitek staff Real RnaseC6572S, 124 residues, Prolines at 41,92,113,116, No missing spin systems. 37 extras. Max 8 connective resonances.
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVASKNGQTNSYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV
-1
1,8.79,123.5,172.1,55.4,32.9,4.02,NaN,176.7,55.8,31.5,4.53,NaN,
2,8.55,116.3,176.7,55.9,31.4,4.53,NaN,174.7,61.2,70.7,4.41,NaN,
3,9.03,121.8,174.7,61.2,70.9,4.41,NaN,181.4,55.3,17.8,4.2,NaN,
4,8.88,119.2,181.4,55.4,17.7,4.2,NaN,180.3,55.1,18.5,4.3,NaN,
5,8.01,120.4,180.3,55,18.6,4.32,NaN,181,54.8,18.3,4.21,NaN,
6,8.78,120.2,181,54.8,18.5,4.22,NaN,178.1,60,31.7,4.09,NaN,
7,8,117.5,178.1,60,32,4.08,NaN,177.6,61.6,38.7,4.49,NaN,
8,7.91,117.1,177.6,61.6,38.4,4.49,NaN,179.1,60.1,29,3.74,NaN,
9,8.35,118.5,179.1,60.1,28.9,3.74,NaN,178.3,59,29.9,4.25,NaN,
10,8.63,109.4,178.3,59,30.3,4.25,NaN,175.6,58.6,29.4,3.82,NaN,
11,7.91,102.6,175.6,58.5,28.9,3.82,NaN,174.7,54.6,29.9,4.97,NaN,
12,8.11,114.6,174.7,54.6,30.1,4.96,NaN,176.8,52.8,29.7,5.48,NaN,
13,8.86,118.7,176.8,52.8,29.5,5.47,NaN,175,53.2,39.8,5.01,NaN,
14,9.01,116.9,175,53.4,39.8,5.01,NaN,174.6,59.8,62.9,4.36,NaN,
15,8.06,112.7,174.7,59.8,62.6,4.36,NaN,173.5,59.5,63.8,4.4,NaN,
16,7.52,109.9,173.7,59.5,NaN,4.38,NaN,174.6,59.7,NaN,4.57,NaN,
17,8.64,115.9,174.7,59.7,NaN,4.56,NaN,174.2,59.3,63.3,4.32,NaN,
18,7.55,120,174.2,59.3,63.2,4.32,NaN,175.8,51,20,3.35,NaN,
19,7.69,119.2,175.7,51,20.1,3.35,NaN,177.7,52.3,18.2,3.51,NaN,
20,8.04,112.9,177.7,52.3,18.3,3.51,NaN,173.9,58.2,63.8,4.3,NaN,
21,7.71,112.3,173.9,58.2,63.7,4.32,NaN,175.5,57.2,65.2,4.76,NaN,
22,9.14,115.9,175.6,57.2,65.2,4.76,NaN,176,60.4,62.8,4.45,NaN,
23,8.45,118.1,175.8,60.4,62.4,4.45,NaN,174.5,52.9,39.4,5.01,NaN,
24,7.7,118.3,174.5,52.9,39.5,5.03,NaN,176.7,61.8,39.3,4.09,NaN,
25,7.91,112.3,176.7,61.8,39.5,4.08,NaN,175.5,61.2,39.5,3.88,NaN,
26,8.05,117.5,175.5,61.1,39.4,3.86,NaN,178.2,56.4,37,4.45,NaN,
27,7.63,114.8,178.2,56.4,36.9,4.45,NaN,178.8,58.3,28.1,4.02,NaN,
28,8.52,117.5,178.8,58.4,28.3,4.02,NaN,178.7,55.5,30.9,4.21,NaN,
29,8.77,113.6,178.6,55.4,31.1,4.22,NaN,178.2,56.4,28.8,4.29,NaN,
30,6.6,113.4,178.2,56.4,28.7,4.3,NaN,180.9,58.3,32.6,4.33,NaN,
31,8.62,114.8,181,58.3,32.5,4.36,NaN,176.4,61.6,62.2,4.22,NaN,
32,7.88,114.4,176.4,61.7,62.2,4.22,NaN,174.5,53.2,27.7,4.49,NaN,
33,7.99,110.9,174.5,53.2,27.9,4.49,NaN,175.8,54,36.3,4.88,NaN,
34,8.16,112.7,175.7,54,36.3,4.87,NaN,176.7,54.8,40.3,4.68,NaN,
35,7.68,104.7,176.7,54.8,40.4,4.68,NaN,174.1,59.7,68.5,5.47,NaN,
36,7.06,119.4,174.2,59.7,68.4,5.44,NaN,178.2,58.3,32.7,4.25,NaN,
37,8.84,117.3,178.2,58.3,32.6,4.26,NaN,174,56.3,40.8,4.4,NaN,
38,7.76,113.4,174,56.2,40.9,4.4,NaN,173.9,54.1,30.6,3.57,NaN,
39,9.08,115.2,173.9,54.2,30.5,3.58,NaN,174.3,52.6,36,4.78,NaN,
40,7.42,127.2,174.3,52.5,36,4.77,NaN,177.5,55.7,33.5,4.49,NaN,
42,6.89,111.5,176.7,66.6,NaN,4.64,NaN,174.7,59.4,35.9,5.11,NaN,
43,8.92,118.7,174.7,59.6,35.9,5.11,NaN,173.4,54,43.8,5.2,NaN,
44,7.53,119.6,173.4,53.9,43.7,5.2,NaN,173.7,62,68.9,5.04,NaN,
45,9.19,122.1,173.7,62,NaN,5.03,NaN,174.2,56.8,43.2,4.99,NaN,
46,9.34,119.2,174.2,56.8,43,4.97,NaN,175.4,61.9,32.5,4.3,NaN,
47,9.18,126.2,175.4,61.9,32.8,4.3,NaN,173.5,52.4,26,5.35,NaN,
48,6.85,113.2,173.5,52.3,26.1,5.35,NaN,174.6,52.5,33,4.88,NaN,
49,9.62,114.4,174.6,52.4,32.9,4.88,NaN,174.5,57.7,64.1,4.29,NaN,
50,8.86,120.8,174.5,57.7,63.8,4.3,NaN,179.1,58,40.7,4.13,NaN,
51,8.57,117.3,179.1,58.1,40.7,4.13,NaN,180.7,55.2,17.9,4.17,NaN,
52,7.88,116.5,180.7,55.1,17.8,4.17,NaN,178.4,56.7,39,4.38,NaN,
53,7.77,118.1,178.4,56.7,39.1,4.4,NaN,178,66.6,31.5,3.71,NaN,
54,9.18,115.9,178,66.7,NaN,3.71,NaN,179.4,59,26.9,3.62,NaN,
55,7.7,116.9,179.4,59.1,27,3.62,NaN,178.9,53.7,17.7,4.09,NaN,
56,7.58,117.5,178.8,53.6,17.6,4.09,NaN,175.9,65.7,30.7,2.98,NaN,
57,6.79,110.1,175.9,65.8,NaN,2.98,NaN,172.5,54.4,40.1,3.54,NaN,
58,7.46,108.4,172.4,54.3,40,3.54,NaN,174.6,57,63.9,4.53,NaN,
59,7.59,121,174.7,57,63.7,4.53,NaN,174.1,55.2,23.8,4.38,NaN,
60,7.43,119.6,174.2,55.2,23.7,4.38,NaN,175.2,56.6,32.9,4.37,NaN,
61,9.05,125.6,175.2,56.6,32.9,4.38,NaN,174.7,54.1,39.4,4.14,NaN,
62,8.05,121.4,174.8,54.2,39.3,4.14,NaN,174.4,60.8,32.8,4.14,NaN,
63,8.2,124.7,174.6,60.8,32.7,4.14,NaN,177.4,52.1,19,4.32,NaN,
64,8.44,113.4,177.4,52,18.9,4.33,NaN,175.4,57,64.7,4.57,NaN,
65,8.65,121.2,175.3,57,64.8,4.57,NaN,176.7,57.1,32.1,4.25,NaN,
66,8.3,114,176.7,57.3,32.1,4.25,NaN,175.6,52.9,38.3,4.72,NaN,
67,8.09,105.9,175.6,52.8,38.3,4.72,NaN,173.9,45.2,NaN,4.16,3.81,
68,8.12,117.3,173.9,45,NaN,4.13,3.86,176.9,55.9,29.3,4.45,NaN,
69,8.42,110.9,177,55.9,29.2,4.45,NaN,174.5,61.4,69.8,4.71,NaN,
70,8.56,117.7,174.5,61.5,69.8,4.69,NaN,173.7,53,38.9,4.96,NaN,
71,8.15,113.8,173.7,53.1,38.7,4.96,NaN,172.9,58.3,64.1,5.5,NaN,
72,9.2,120.6,172.8,58.2,64.3,5.49,NaN,172.7,56.8,44.4,5.04,NaN,
73,9.6,119.4,172.6,56.8,44.2,5.04,NaN,175.4,52,33.2,5.55,NaN,
74,9.18,118.7,175.4,51.9,33.3,5.54,NaN,176.8,57.4,64.4,4.68,NaN,
75,8.73,121.8,176.8,57.4,NaN,4.68,NaN,178.7,59.4,37.8,4.69,NaN,
76,9.05,110.9,178.7,59.4,37.7,4.69,NaN,175.2,56.7,64.3,4.92,NaN,
77,8.35,111.3,175.2,56.7,64.4,4.92,NaN,173.2,61.8,69.5,3.38,NaN,
78,8.67,118.9,173.2,61.9,69.5,3.38,NaN,173.8,54.9,36.5,4.61,NaN,
79,8.77,112.7,173.9,55,36.4,4.61,NaN,174.6,57,62.7,4.85,NaN,
80,9.19,120,174.6,57,62.9,4.84,NaN,174.9,58.5,43.1,5.54,NaN,
81,9.45,113.6,174.8,58.5,42.7,5.54,NaN,172.2,61.6,72.2,5.07,NaN,
82,9.32,126.2,172.2,61.6,72,5.07,NaN,174.4,53.6,43.4,4.88,NaN,
83,8.44,120,174.4,53.6,43.5,4.87,NaN,173.7,51.4,38.5,5.99,NaN,
84,8.15,117.9,173.7,51.5,38.6,6,NaN,175.4,54.4,33.3,5.51,NaN,
85,8.45,123.3,175.4,54.4,33.2,5.51,NaN,177.6,57.5,31.2,4.32,NaN,
86,8.02,111.5,177.7,57.5,31.1,4.32,NaN,176.3,60.2,70,4.52,NaN,
87,8.88,104.5,176.3,60.2,70.1,4.53,NaN,174.7,46.3,NaN,3.94,NaN,
88,7.64,109.7,174.7,46.2,NaN,3.94,NaN,173.9,57.4,63.4,4.53,NaN,
89,7.02,115,174,57.4,63.3,4.53,NaN,175.1,58.9,62.7,3.97,NaN,
90,7.53,127,175.1,58.8,62.8,3.94,NaN,174.2,56,33.6,4.44,NaN,
91,9.44,129.1,174.3,55.9,33.7,4.44,NaN,174.2,58.2,38.4,3.78,NaN,
93,8.85,128.3,175.1,63.6,33.4,3.27,NaN,174.4,52,37.3,4.96,NaN,
94,7.63,119,174.4,51.9,37.2,4.96,NaN,174,53.7,38.8,4.88,NaN,
95,8.64,125.8,174.2,53.7,38.5,4.88,NaN,175.3,51.5,21.8,4.76,NaN,
96,9.38,114.8,175.3,51.6,21.8,4.76,NaN,176.1,58.3,43.7,4.89,NaN,
97,9.52,122.9,176.1,58.3,43.6,4.89,NaN,176.4,54.7,34,4.81,NaN,
98,9.27,123.9,176.3,54.7,34.1,4.8,NaN,174.9,62.5,71.9,5.29,NaN,
99,8.94,121.2,174.9,62.5,71.4,5.31,NaN,172.5,62.1,70.1,4.66,NaN,
100,9.12,127.4,172.5,62,70.3,4.65,NaN,174.6,54.4,29.3,4.99,NaN,
101,9.11,125.8,174.7,54.4,29,4.99,NaN,174,51.7,22.9,4.69,NaN,
102,8.47,116.3,174,51.7,22.8,4.69,NaN,174.7,52.5,39.5,5.83,NaN,
103,8.58,118.1,174.7,52.5,39.6,5.84,NaN,177.2,54.3,NaN,4.89,NaN,
104,9.23,116.1,177.2,54.2,38.9,4.89,NaN,174.7,56.6,27.4,4.48,NaN,
105,8.48,111.5,174.7,56.6,27.5,4.48,NaN,173.3,59.8,40.5,5,NaN,
106,8.16,118.9,173.3,59.9,NaN,5,NaN,176,60,38.9,5.39,NaN,
107,8.95,115.2,176,60,38.7,5.38,NaN,172.6,57.4,34.8,4.8,NaN,
108,8.2,120.4,172.5,57.4,34.8,4.8,NaN,177.8,49.8,21,5.39,NaN,
109,8.59,118,177.8,49.7,21,5.39,NaN,172.3,55.8,49.5,5.28,NaN,
110,8.63,117.7,172.3,55.8,48.9,5.29,NaN,175.8,56.3,35.2,4.61,NaN,
111,8.81,107.4,175.8,56.4,35,4.6,NaN,173.2,44.1,NaN,3.77,NaN,
112,7.81,111.5,173.2,43.9,NaN,3.78,NaN,173.2,50.3,40.1,4.77,NaN,
114,8.55,123.1,173.9,63,33.9,4.68,NaN,174.4,58.2,37.7,4.28,NaN,
115,7.48,116.5,174.4,58.1,37.7,4.28,NaN,173,58.3,33.1,4.88,NaN,
117,9.05,107.6,176.4,62.3,29.7,4.4,NaN,176.5,60.8,34.2,4.52,NaN,
118,7.68,115,176.5,60.8,33.9,4.52,NaN,172.5,54.9,32.1,5.43,NaN,
119,8.77,124.7,172.5,54.9,32.3,5.43,NaN,173,57.5,38.2,4.44,NaN,
120,8.64,126,173,57.4,38.5,4.45,NaN,175.8,56,40.7,4.76,NaN,
121,7.35,115.9,175.7,56,40.6,4.73,NaN,173.9,52,21.7,4.64,NaN,
122,8.25,109.9,173.9,52,21.5,4.64,NaN,173.5,56.7,66.1,5.4,NaN,
123,8.78,121.2,173.5,56.7,66.2,5.4,NaN,179.5,63.2,35.2,4.36,NaN,
1000,7.2,131.2,175.2,NaN,NaN,NaN,NaN,NaN,43,NaN,3.03,NaN,
1001,7.6,109.8,NaN,NaN,52.9,NaN,NaN,NaN,NaN,NaN,2.84,NaN,
1002,6.93,109.8,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1003,7.43,108.6,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1004,7.71,111.7,NaN,NaN,53,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1005,7.82,112.5,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1006,7.58,109.2,177.3,NaN,NaN,2.83,NaN,NaN,NaN,NaN,NaN,NaN,
1007,7.15,111.7,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1008,7.05,112.5,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1009,7.5,110.2,NaN,NaN,48.6,4.38,NaN,NaN,NaN,70.7,4.37,NaN,
1010,8.27,132.2,175.5,NaN,NaN,NaN,NaN,NaN,42.9,NaN,3.3,NaN,
1011,9.75,130.1,176.2,NaN,NaN,NaN,NaN,NaN,42.9,NaN,NaN,NaN,
1012,7.52,109.4,180.5,NaN,NaN,NaN,NaN,NaN,NaN,29.4,2.33,NaN,
1013,8.19,117.9,178.1,NaN,52.4,4.21,NaN,176.5,NaN,NaN,4.21,NaN,
1014,7.16,111.2,177.1,NaN,53,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1015,6.94,109.2,177.3,NaN,52.9,2.83,NaN,NaN,NaN,52.6,2.83,NaN,
1016,7.82,112.1,177.6,NaN,51.9,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1017,7.72,111.3,177.1,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1018,8.36,117.9,NaN,NaN,56.5,4.25,NaN,NaN,56.2,NaN,NaN,NaN,
1019,8.21,121,177.9,NaN,NaN,4.28,NaN,178.1,52.6,18.5,4.24,NaN,
1020,8.4,119.8,NaN,55.3,28.2,4.64,NaN,NaN,55.3,NaN,4.49,NaN,
1021,7.58,108.6,177.6,NaN,50.4,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1022,8.27,120.2,176,58,39.1,NaN,NaN,NaN,57.7,NaN,NaN,NaN,
1023,7.43,108.1,177.5,54.4,39.9,3.54,NaN,NaN,NaN,54.2,4.53,NaN,
1024,7.06,112.1,177.5,NaN,51.9,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1025,8.32,120.8,177.8,52.7,18.6,4.29,NaN,177.9,52.6,18.5,4.26,NaN,
1026,8.3,119.4,176.4,56.2,29.6,4.25,NaN,176.4,56.4,NaN,4.26,NaN,
1027,8.19,118.3,176.5,56.7,NaN,NaN,NaN,NaN,57.9,NaN,4.59,NaN,
1028,8.29,115.6,176.9,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1029,8.36,123.7,174.6,58.4,NaN,4.46,NaN,NaN,52.7,18.7,NaN,NaN,
1030,8.51,115.8,174.9,58.4,52,NaN,NaN,NaN,58.9,63.9,NaN,NaN,
1031,8.51,119.6,175.7,55.3,32.7,4.49,NaN,176.3,53.9,NaN,4.68,NaN,
1032,8.48,114.8,176.3,56,NaN,4.49,NaN,NaN,61.6,NaN,4.32,NaN,
1033,8.54,124.3,174.2,61.7,NaN,4.33,NaN,NaN,52.7,NaN,4.29,NaN,
1034,8.21,112.1,178.2,52.6,18.6,4.29,NaN,NaN,NaN,52.6,4.45,NaN,
1035,8.31,115.2,174.9,58.5,NaN,4.47,NaN,174.4,58.6,63.9,4.47,NaN,
1036,8.26,115.6,174.9,62,NaN,4.41,NaN,NaN,58.4,NaN,4.45,NaN,
MBA2/data/rnaseWt.mba 0100644 0000765 0000024 00000023535 10066405654 014271 0 ustar janvitek staff Real RnaseWT, 124 residues, Prolines at 41,92,113,116. No missing.37 extras. Max 8 connective resonances.
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV
-1
1,8.78,123.4,172.1,55.3,32.6,4.04,NaN,176.6,55.5,32.5,4.56,NaN,
2,8.53,116.3,176.6,55.7,31.2,4.55,NaN,174.6,61.1,70.9,4.43,NaN,
3,9.02,121.7,174.7,61,70.9,4.43,NaN,181.4,55.1,17.7,4.2,NaN,
4,8.85,119.1,181.4,55.2,17.5,4.2,NaN,180.2,54.9,18.2,4.28,NaN,
5,8.02,120.4,180.2,54.7,18.5,4.3,NaN,181,54.6,18.2,4.22,NaN,
6,8.76,120.2,181,54.6,18.2,4.22,NaN,178,59.9,31.9,4.13,NaN,
7,7.96,117.5,178,59.8,31.6,4.09,NaN,177.5,61.5,38.7,4.55,NaN,
8,7.9,117.3,177.5,61.4,38.5,4.53,NaN,179.2,59.9,28.6,3.77,NaN,
9,8.32,118.5,179,59.9,28.8,3.75,NaN,178.3,58.8,29.9,4.27,NaN,
10,8.63,109.5,178.3,58.8,30,4.26,NaN,175.6,58.4,29,3.85,NaN,
11,7.94,102.7,175.6,58.3,28.9,3.86,NaN,174.6,54.5,30,4.99,NaN,
12,8.1,114.8,174.7,54.5,30,5,NaN,176.7,52.7,29.6,5.49,NaN,
13,8.85,118.7,176.8,52.6,29.2,5.49,NaN,174.9,53.4,39.7,4.28,NaN,
14,9.01,117,174.9,53.3,39.8,4.35,NaN,174.5,59.6,63.2,4.35,NaN,
15,8.06,112.6,174.6,59.7,62.6,4.36,NaN,173.7,59.3,63.2,4.35,NaN,
16,7.5,110.2,173.6,59.3,63.7,4.4,NaN,174.5,59.5,71.2,4.56,NaN,
17,8.64,116,174.6,59.5,70.6,4.58,NaN,174.2,59.2,63.1,4.34,NaN,
18,7.55,120.1,174.2,59,63.2,4.33,NaN,175.7,50.8,20.2,3.35,NaN,
19,7.68,119.3,175.7,50.9,19.9,3.35,NaN,177.6,51.9,17.8,3.49,NaN,
20,8.02,112.9,177.6,52.1,18.1,3.51,NaN,173.7,58.1,63.2,4.35,NaN,
21,7.7,112.4,173.8,58,63.6,4.35,NaN,175.5,57,65.2,4.77,NaN,
22,9.13,116,175.5,57.1,65,4.77,NaN,175.7,60.3,61.9,4.48,NaN,
23,8.44,118,175.8,60.2,62.6,4.47,NaN,174.5,52.8,39.3,5.05,NaN,
24,7.7,118.4,174.5,52.8,39.3,5.05,NaN,176.6,61.6,39.2,4.07,NaN,
25,7.92,112.2,176.6,61.7,38.9,4.09,NaN,175.5,61.1,39.4,3.92,NaN,
26,8.05,117.5,175.5,60.9,39.3,3.89,NaN,178.1,56.2,37.1,4.48,NaN,
27,7.63,114.8,178.1,56.2,36.8,4.49,NaN,178.7,58.2,28.1,4.05,NaN,
28,8.52,117.5,178.7,58.2,28.1,4.05,NaN,178.6,58.1,NaN,NaN,NaN,
29,8.77,113.7,178.6,55.2,30.8,4.22,NaN,178.1,56.2,28.5,4.28,NaN,
30,6.6,113.5,178.1,56.2,28.7,4.3,NaN,180.9,58.1,32.5,4.35,NaN,
31,8.63,114.9,180.9,58.2,32.4,4.36,NaN,176.4,61.5,62.4,4.28,NaN,
32,7.88,114.5,176.3,61.5,62.5,4.23,NaN,174.5,53.1,27.7,4.49,NaN,
33,8,111.2,174.5,53.1,27.7,4.42,NaN,175.8,53.8,36.3,4.91,NaN,
34,8.17,112.7,175.7,53.8,36.2,4.9,NaN,176.6,54.6,40.1,4.7,NaN,
35,7.68,104.8,176.6,54.7,40.1,4.7,NaN,174.1,59.5,68.3,5.48,NaN,
36,7.06,119.6,174.1,59.5,68.4,5.47,NaN,178.1,58.1,32.6,4.27,NaN,
37,8.84,117.4,178.1,58.1,32.4,4.27,NaN,174,56.1,40.8,4.35,NaN,
38,7.76,113.6,174,56.1,40.7,4.41,NaN,173.9,54,30.7,3.57,NaN,
39,9.08,115.1,173.9,54.1,30.5,3.56,NaN,174.2,52.4,36.1,4.78,NaN,
40,7.41,127.2,174.3,52.4,35.8,4.79,NaN,177.5,55.5,32.9,4.49,NaN,
42,6.86,111.7,176.7,66.3,NaN,4.64,NaN,174.7,59.3,35.9,5.12,NaN,
43,8.98,119,174.7,59.4,35.8,5.11,NaN,174.7,59.1,35.8,4.63,NaN,
44,8.17,112.8,175.1,58.7,36.2,4.7,NaN,173.7,61.8,69.2,NaN,NaN,
45,9.19,122.2,173.8,61.9,68.6,5.05,NaN,174.2,56.6,43.4,5.05,NaN,
46,9.35,119.2,174.2,56.6,43,5.03,NaN,175.4,61.8,32.6,4.34,NaN,
47,9.17,126.4,175.3,61.8,32.5,4.32,NaN,173.4,52.1,25.9,5.35,NaN,
48,6.85,113.4,173.4,52.1,26,5.38,NaN,174.5,52.3,32.9,4.91,NaN,
49,9.62,114.5,174.6,52.3,32.8,4.91,NaN,174.5,57.6,64,4.29,NaN,
50,8.86,120.9,174.5,57.5,64,4.32,NaN,179,57.7,40.8,4.2,NaN,
51,8.57,117.3,179,57.9,NaN,4.14,NaN,180.6,55,17.7,4.19,NaN,
52,7.87,116.5,180.7,54.9,17.6,4.19,NaN,178.4,56.5,38.9,4.41,NaN,
53,7.78,118.2,178.4,56.5,38.8,4.41,NaN,178,66.5,31.5,3.71,NaN,
54,9.21,116.2,178,66.6,31,3.72,NaN,179.5,58.9,26.9,3.64,NaN,
55,7.71,117.2,179.5,59,26.8,3.62,NaN,178.8,53.5,17.5,4.08,NaN,
56,7.59,117.3,178.8,53.5,17.4,4.12,NaN,176,65.6,30.8,3,NaN,
57,6.82,110.3,176,65.5,30.5,2.97,NaN,172.4,54.6,39.7,3.56,NaN,
58,7.45,108.8,172.4,54.5,39.8,3.56,NaN,174.6,56.9,63.3,4.57,NaN,
59,7.74,121.3,174.6,56.9,63.7,4.59,NaN,174.1,55.1,23.1,4.43,NaN,
60,7.21,119.5,174.1,55.1,23.2,4.43,NaN,175.2,56.6,33.3,4.41,NaN,
61,9.06,126.5,175.2,56.7,33.1,4.39,NaN,173.9,53.5,39.6,4.36,NaN,
62,8.25,119.7,174,53.5,39.4,4.36,NaN,173.1,58.8,36.1,4.41,NaN,
63,7.89,117.9,173.1,58.7,36.1,4.43,NaN,179.2,51.7,17.9,4.35,NaN,
64,8.7,117.1,179.2,51.8,18,4.32,NaN,178.1,51.9,40.4,4.56,NaN,
65,10.97,126.3,178,51.9,40.4,4.57,NaN,NaN,59.5,31.3,3.98,NaN,
66,8.21,111.7,178,59.6,31.2,3.96,NaN,176.8,52,37.1,4.55,NaN,
67,8.06,105.9,176.8,51.9,36.9,4.55,NaN,175.5,44.6,NaN,3.5,NaN,
68,7.9,116.6,175.5,45,NaN,3.62,NaN,176,56.5,28.6,4.41,NaN,
69,8.52,104.2,176,56.4,28.5,4.4,NaN,174.4,61.5,68.2,4.56,NaN,
70,8.9,117.9,174.4,61.4,68.2,4.61,NaN,173.3,52.7,36.3,4.99,NaN,
71,6.62,111.7,173.3,52.7,36.3,4.93,NaN,173,58.8,45.2,5.84,NaN,
72,8.9,118,173,58.8,45,5.89,NaN,173.3,56.8,NaN,5.85,NaN,
73,8.17,118.3,173.6,56.4,32.4,4.78,NaN,NaN,57.7,NaN,5.55,NaN,
74,9.18,119,175.4,57.2,33.2,5.48,NaN,176.8,57.2,64.7,4.69,NaN,
75,8.69,122.5,176.9,57.2,64.5,4.68,NaN,178.6,59.2,37.5,4.7,NaN,
76,9.03,111.1,178.6,59.1,37.4,4.72,NaN,175.2,56.6,64.5,4.92,NaN,
77,8.4,111.8,175.2,56.7,64.3,4.93,NaN,173.2,61.8,68.6,3.36,NaN,
78,8.68,119.2,173.2,61.8,69.1,3.37,NaN,173.8,54.7,36.6,4.64,NaN,
79,8.72,112.6,173.8,54.8,36.4,4.63,NaN,174.5,62.7,62.7,4.85,NaN,
80,9.19,119.9,174.6,62.7,62.7,4.88,NaN,174.7,58.4,42.9,5.61,NaN,
81,9.44,113.7,174.7,58.4,42.8,5.6,NaN,172.2,61.5,72.7,5.06,NaN,
82,9.32,126,172.2,61.4,NaN,5.1,NaN,174.3,53.5,43.5,4.85,NaN,
83,8.42,120,174.3,53.5,43.5,4.85,NaN,173.6,51.2,38.5,5.99,NaN,
84,8.15,117.8,173.6,51.3,38.5,5.99,NaN,175.3,54.3,33,5.55,NaN,
85,8.4,123,175.3,54.2,33.1,5.54,NaN,177.6,57.3,31.3,4.34,NaN,
86,8.01,111.3,177.6,57.3,31.1,4.42,NaN,176.3,60,69.7,4.49,NaN,
87,8.87,104.7,176.3,60.1,70.1,4.53,NaN,174.6,46.1,NaN,3.93,NaN,
88,7.62,109.7,174.6,46.2,NaN,3.92,NaN,173.9,57.3,63.1,4.55,NaN,
89,7.02,115,173.9,57.2,63.1,4.54,NaN,175.1,58.7,62.4,3.98,NaN,
90,7.51,127,175.1,58.7,62.4,3.97,NaN,174.2,55.8,33,4.43,NaN,
91,9.44,129.2,174.2,55.8,33.6,4.45,NaN,174.1,58,38.3,3.79,NaN,
93,8.85,128.3,175.1,63.3,33.1,3.27,NaN,174.4,51.7,37.4,4.98,NaN,
94,7.63,119.2,174.4,51.7,37.2,4.99,NaN,174.2,53.5,38.6,4.92,NaN,
95,8.65,125.8,174.1,53.5,38.7,4.91,NaN,175.3,51.5,21.7,4.78,NaN,
96,9.38,114.9,175.3,51.5,21.7,4.77,NaN,176.1,58.1,43.8,4.85,NaN,
97,9.52,123,176,58.2,43.5,4.92,NaN,176.2,54.6,33.8,4.85,NaN,
98,9.28,124,176.3,54.5,33.9,4.84,NaN,174.9,62.3,71.7,5.28,NaN,
99,8.94,121.3,174.9,62.4,71.3,5.33,NaN,172.5,61.8,71.3,4.69,NaN,
100,9.12,127.5,172.5,61.8,70.5,4.68,NaN,174.6,54.3,29.1,4.99,NaN,
101,9.1,125.9,174.6,54.3,28.9,5,NaN,NaN,51.5,22.8,4.7,NaN,
102,8.46,116.4,173.9,51.5,22.6,4.7,NaN,174.7,52.3,39.5,5.85,NaN,
103,8.57,117.9,174.7,52.4,39.5,5.85,NaN,177,53.9,38.9,4.91,NaN,
104,9.32,116.5,177,53.9,38.7,4.92,NaN,174.9,56.4,27.1,4.49,NaN,
105,8.48,112.4,174.9,56.4,27,4.49,NaN,173.4,59.8,40.1,4.91,NaN,
106,8.08,118.3,173.4,59.8,40.2,4.89,NaN,176.1,59.9,38.8,5.41,NaN,
107,8.75,114.6,176.1,59.8,38.4,5.41,NaN,173.4,57.2,34.1,4.83,NaN,
108,8.32,120.7,173.4,57.2,34.2,4.82,NaN,177.8,50.1,20.9,5.42,NaN,
109,8.34,117.3,177.7,50.2,21,5.42,NaN,172.2,55.7,49.3,5.4,NaN,
110,8.57,117.8,172.2,55.7,48.7,5.36,NaN,175.9,55.8,35.5,4.7,NaN,
111,8.78,106.7,175.9,56,35.4,4.68,NaN,173.2,43.9,NaN,4.64,3.78,
112,7.8,111.7,173.2,43.9,NaN,4.64,3.86,173.2,50.1,39.9,4.77,NaN,
114,8.55,123,173.9,62.8,33.6,4.7,NaN,174.5,58,37.8,4.28,NaN,
115,7.54,116.7,174.5,57.9,37.6,4.29,NaN,172.9,58.2,33.1,4.91,NaN,
117,8.94,107.7,176.6,61.9,29.6,4.48,NaN,176.5,60.5,33.8,4.49,NaN,
118,7.61,114.4,176.4,60.5,34,4.49,NaN,172.8,54.6,32.6,5.55,NaN,
119,8.84,125.2,172.8,54.7,32.5,5.54,NaN,172.6,57.6,NaN,4.41,NaN,
120,8.98,128.4,172.5,57.6,38,4.41,NaN,175.8,56.6,46.2,4.85,NaN,
121,7.49,113.5,175.8,56.6,46.2,4.85,NaN,173.4,51.6,21.4,4.63,NaN,
122,8.19,109.2,173.5,51.6,21.2,4.62,NaN,173.4,56.8,66.3,5.34,NaN,
123,8.77,121.2,173.3,56.8,66.2,5.36,NaN,179.2,63.1,34.9,4.35,NaN,
1000,7.36,108.7,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1001,7.18,131.2,172,NaN,NaN,NaN,NaN,NaN,42.8,NaN,3.07,NaN,
1002,7.42,108.8,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1003,8.3,119.5,176.3,56.1,29.8,NaN,NaN,175.3,56.2,29.8,4.63,NaN,
1004,7.54,119.8,173.4,53.7,43.6,5.24,NaN,173.7,61.9,43.7,5.05,NaN,
1005,8.18,117.8,178.1,52.5,NaN,NaN,NaN,NaN,56.2,NaN,NaN,NaN,
1006,9.72,121.3,172.4,56.8,43.8,5.12,NaN,175.4,51.9,33.3,5.48,NaN,
1007,8.5,119.8,175.7,NaN,32.5,NaN,NaN,176.2,NaN,NaN,4.71,NaN,
1008,8.21,121,NaN,55.1,41.5,4.29,NaN,178.1,52.4,18.8,NaN,NaN,
1009,8.3,132.2,172.3,NaN,NaN,NaN,NaN,NaN,42.7,NaN,3.29,NaN,
1010,8.36,118,176.4,NaN,NaN,NaN,NaN,NaN,53.2,38.8,4.76,NaN,
1011,8.23,120.3,177.8,52.6,18.5,NaN,NaN,NaN,52.4,NaN,NaN,NaN,
1012,8.26,117.5,176.4,NaN,NaN,NaN,NaN,NaN,NaN,NaN,4.56,NaN,
1013,7.6,110.3,NaN,NaN,38.3,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1014,8.27,120.2,175.9,57.7,NaN,4.62,NaN,NaN,NaN,29.7,NaN,NaN,
1015,8.35,123.7,174.5,58.2,63.6,4.47,NaN,NaN,52.4,18.7,NaN,NaN,
1016,8.31,115.2,174.8,58.3,63.6,4.49,NaN,174.8,58.4,63.2,4.49,NaN,
1017,8.26,115.7,174.8,61.8,69.1,4.42,NaN,174.5,NaN,63.2,NaN,NaN,
1018,8.32,120.8,177.8,52.6,18.5,4.3,NaN,NaN,57.2,19,4.27,NaN,
1019,8.21,112.1,NaN,52.4,18.5,4.29,NaN,NaN,58.4,63.3,NaN,NaN,
1020,8.6,120.2,NaN,61.9,32.4,4.03,NaN,174.1,NaN,28.4,4.69,NaN,
1021,8.52,115.7,174.9,58.3,63.4,NaN,NaN,NaN,58.7,63,NaN,NaN,
1022,8.53,124.4,174.2,61.5,69.8,4.34,NaN,177.7,52.4,18.5,4.29,NaN,
1023,8.15,117.4,NaN,56,32,4.41,NaN,176.7,NaN,56.3,4.41,NaN,
1024,7.47,109.8,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,
1025,8.48,114.7,176.2,56,29.8,4.49,NaN,174.1,61.5,62.6,NaN,NaN,
1026,8.56,120.6,174.1,54.9,28.6,4.7,NaN,176,56.1,29.2,4.35,NaN,
1027,8.26,119.4,174.9,61.8,63.6,NaN,NaN,NaN,NaN,32.5,NaN,NaN,
1028,7.36,108.2,179.8,NaN,NaN,2.36,NaN,NaN,NaN,NaN,NaN,NaN,
1029,8.06,111.9,175.1,52.7,38.5,4.79,NaN,NaN,61.6,69.4,NaN,NaN,
1030,7.93,127.4,176.1,54.8,41.9,4.4,NaN,182.1,NaN,NaN,NaN,NaN,
1031,8.25,117.7,176.8,62.7,NaN,NaN,NaN,175.9,62.3,NaN,4.14,NaN,
1032,8.44,114.5,NaN,53.9,40.7,4.7,NaN,NaN,58.3,40.8,NaN,NaN,
1033,8.33,121.9,NaN,54.8,40.6,4.71,NaN,174,53.9,32.4,4.68,NaN,
1034,8.34,115.9,175.8,56,30.1,4.34,NaN,173.9,53.1,38.4,4.7,NaN,
1035,7.99,119.5,NaN,57.3,39,4.67,NaN,175.4,61.9,NaN,NaN,NaN,
1036,8.92,121.9,NaN,55.3,32.6,4.05,NaN,NaN,NaN,29.9,NaN,NaN,
MBA2/data/teri.mba 0100644 0000765 0000024 00000014553 10066405654 013611 0 ustar janvitek staff Teri's data, 106 residues, Prolines at locations 3,29,42,88,98. Missing (11) at 1,19,25,50,58,59,72,90,91,93,103. Extras: 2. Max 4 connective resonances.
MGSPGIHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDLISYYEKHPLYRKMKLRYPINEENSS
1,19,25,50,58,59,72,90,91,93,103
2,8.316,116.865,NaN,44.918,NaN,NaN,NaN,NaN,56.348,63.528,NaN,NaN,
4,8.612,109.057,NaN,63.519,32.215,NaN,NaN,NaN,45.349,NaN,NaN,NaN,
5,8.24,120.628,NaN,45.363,NaN,NaN,NaN,NaN,62.236,38.194,NaN,NaN,
6,8.208,118.893,NaN,62.311,38.26,NaN,NaN,NaN,56.8,30.379,NaN,NaN,
7,7.584,119.265,NaN,56.799,30.424,NaN,NaN,NaN,57.795,29.885,NaN,NaN,
8,7.603,112.839,NaN,57.941,29.586,NaN,NaN,NaN,57.935,63.554,NaN,NaN,
9,7.639,121.746,NaN,58.009,63.58,NaN,NaN,NaN,54.839,31.318,NaN,NaN,
10,8.914,120.534,NaN,54.94,31.392,NaN,NaN,NaN,58.548,29.774,NaN,NaN,
11,6.309,109.059,NaN,58.675,29.634,NaN,NaN,NaN,53.783,31.213,NaN,NaN,
12,7.739,123.207,NaN,53.872,31.319,NaN,NaN,NaN,59.024,38.81,NaN,NaN,
13,8.683,128.083,NaN,59.091,38.825,NaN,NaN,NaN,54.185,31.717,NaN,NaN,
14,8.311,124.822,NaN,54.198,31.807,NaN,NaN,NaN,54.367,19.525,NaN,NaN,
15,8.35,111.264,NaN,54.709,19.559,NaN,NaN,NaN,56.715,63.118,NaN,NaN,
16,8.104,126.464,NaN,56.81,63.26,NaN,NaN,NaN,54.824,45.618,NaN,NaN,
17,8.807,116.825,NaN,54.864,45.62,NaN,NaN,NaN,60.524,71.285,NaN,NaN,
18,9.114,122.586,NaN,60.92,71.652,NaN,NaN,NaN,60.656,30.203,NaN,NaN,
20,7.878,118.126,NaN,55.273,18.354,NaN,NaN,NaN,58.627,28.839,NaN,NaN,
21,8.722,122.688,NaN,58.67,28.9,NaN,NaN,NaN,55.037,18.57,NaN,NaN,
22,8.492,116.242,NaN,55.112,18.544,NaN,NaN,NaN,60.911,28.077,NaN,NaN,
23,8.049,116.737,NaN,61.008,28.104,NaN,NaN,NaN,59.25,28.63,NaN,NaN,
24,8.001,117.781,NaN,59.311,28.814,NaN,NaN,NaN,59.284,33.685,NaN,NaN,
26,8.137,118.809,NaN,57.181,42.369,NaN,NaN,NaN,57.265,31.838,NaN,NaN,
27,7.141,116.003,NaN,57.182,32.31,NaN,NaN,NaN,57.291,30.7,NaN,NaN,
28,7.141,118.878,NaN,57.249,30.726,NaN,NaN,NaN,59.144,32.469,NaN,NaN,
30,7.972,121.612,NaN,62.76,29.241,NaN,NaN,NaN,NaN,33.66,NaN,NaN,
31,8.806,124.398,NaN,54.804,33.711,NaN,NaN,NaN,55.317,40.542,NaN,NaN,
32,9.627,109.561,NaN,55.556,40.585,NaN,NaN,NaN,45.369,NaN,NaN,NaN,
33,7.964,126.119,NaN,45.393,NaN,NaN,NaN,NaN,52.096,19.409,NaN,NaN,
34,8.691,117.278,NaN,52.107,19.441,NaN,NaN,NaN,56.508,44.819,NaN,NaN,
35,9.358,114.305,NaN,56.591,44.76,NaN,NaN,NaN,54.583,44.919,NaN,NaN,
36,9.62,120.611,NaN,54.61,45.065,NaN,NaN,NaN,61.01,34.869,NaN,NaN,
37,9.599,122.603,NaN,61.079,34.908,NaN,NaN,NaN,52,33.694,NaN,NaN,
38,8.124,124.334,NaN,52.106,33.659,NaN,NaN,NaN,57.539,33.343,NaN,NaN,
39,8.098,126.594,NaN,NaN,33.274,NaN,NaN,NaN,NaN,31.102,NaN,NaN,
40,8.63,118.182,NaN,56.616,30.995,NaN,NaN,NaN,54.43,38.035,NaN,NaN,
41,7.468,119.801,NaN,54.169,38.042,NaN,NaN,NaN,54.545,30.546,NaN,NaN,
43,8.912,116.018,NaN,63.577,32.468,NaN,NaN,NaN,54.387,37.399,NaN,NaN,
44,7.711,108.743,NaN,54.377,37.443,NaN,NaN,NaN,57.705,65.198,NaN,NaN,
45,9.209,123.931,NaN,57.747,65.281,NaN,NaN,NaN,56.4,42.838,NaN,NaN,
46,9.656,121.023,NaN,56.473,42.81,NaN,NaN,NaN,50.558,21.656,NaN,NaN,
47,9.117,120.57,NaN,50.612,NaN,NaN,NaN,NaN,60.481,NaN,NaN,NaN,
48,9.246,126.417,NaN,60.555,39.87,NaN,NaN,NaN,58.313,65.078,NaN,NaN,
49,8.89,121.085,NaN,58.399,65.183,NaN,NaN,NaN,55.408,41.75,NaN,NaN,
51,9.033,126.63,NaN,54.221,33.254,NaN,NaN,NaN,51.911,23.139,NaN,NaN,
52,9.38,121.692,NaN,51.862,23.16,NaN,NaN,NaN,56.749,NaN,NaN,NaN,
53,9.548,105.781,NaN,56.734,27.815,NaN,NaN,NaN,45.638,NaN,NaN,NaN,
54,7.948,120.502,NaN,45.625,NaN,NaN,NaN,NaN,54.207,35.84,NaN,NaN,
55,8.37,119.71,NaN,55.025,35.929,NaN,NaN,NaN,60.018,36.535,NaN,NaN,
56,8.51,128.191,NaN,59.961,NaN,NaN,NaN,NaN,52.705,36.825,NaN,NaN,
57,8.058,114.489,NaN,53,NaN,NaN,NaN,NaN,54.215,35.459,NaN,NaN,
60,8.932,123.82,NaN,56.593,31.788,NaN,NaN,NaN,60.955,35.556,NaN,NaN,
61,8.623,125.974,NaN,61.007,35.534,NaN,NaN,NaN,54.318,32.396,NaN,NaN,
62,8.718,125.01,NaN,54.421,32.401,NaN,NaN,NaN,54.728,30.748,NaN,NaN,
63,8.789,129.379,NaN,54.956,30.816,NaN,NaN,NaN,55.006,30.889,NaN,NaN,
64,9.008,116.075,NaN,55.225,30.902,NaN,NaN,NaN,47.166,NaN,NaN,NaN,
65,9.125,126.271,NaN,47.178,NaN,NaN,NaN,NaN,55.993,29.751,NaN,NaN,
66,7.825,113.397,NaN,56.028,29.737,NaN,NaN,NaN,61.716,71.072,NaN,NaN,
67,8.79,117.222,NaN,61.83,71.167,NaN,NaN,NaN,59.989,33.877,NaN,NaN,
68,9.097,121.343,NaN,59.943,33.991,NaN,NaN,NaN,54.471,36.266,NaN,NaN,
69,8.462,124.868,NaN,54.58,36.379,NaN,NaN,NaN,54.376,44.578,NaN,NaN,
70,9.421,118.318,NaN,54.406,44.587,NaN,NaN,NaN,47.327,NaN,NaN,NaN,
71,8.973,124.681,NaN,47.336,NaN,NaN,NaN,NaN,53.108,38.721,NaN,NaN,
73,7.996,123.533,NaN,58.654,64.848,NaN,NaN,NaN,54.847,32.835,NaN,NaN,
74,9.153,119.905,NaN,54.907,32.797,NaN,NaN,NaN,56.545,43.885,NaN,NaN,
75,9.481,119.466,NaN,56.515,43.903,NaN,NaN,NaN,56.554,41.24,NaN,NaN,
76,7.446,104.759,NaN,56.233,41.123,NaN,NaN,NaN,56.86,65.556,NaN,NaN,
77,9.331,122.511,NaN,57.123,65.813,NaN,NaN,NaN,57.429,42.341,NaN,NaN,
78,7.952,116.329,NaN,57.927,42.378,NaN,NaN,NaN,66.719,31.759,NaN,NaN,
79,7.8,121.49,NaN,66.741,31.806,NaN,NaN,NaN,57.399,41.214,NaN,NaN,
80,7.386,123.179,NaN,57.435,41.295,NaN,NaN,NaN,58.801,41.713,NaN,NaN,
81,7.873,119.327,NaN,58.923,41.891,NaN,NaN,NaN,61.495,34.768,NaN,NaN,
82,8.073,112.372,NaN,61.582,34.821,NaN,NaN,NaN,61.345,62.966,NaN,NaN,
83,7.92,121.762,NaN,61.471,63.087,NaN,NaN,NaN,NaN,38.676,NaN,NaN,
84,7.744,118.687,NaN,62.957,38.684,NaN,NaN,NaN,61.215,37.266,NaN,NaN,
85,7.524,117.156,NaN,61.263,37.313,NaN,NaN,NaN,57.252,30.363,NaN,NaN,
86,7.165,116.184,NaN,NaN,30.34,NaN,NaN,NaN,55.654,34.718,NaN,NaN,
87,7.777,119.837,NaN,56.03,34.727,NaN,NaN,NaN,52.452,29.522,NaN,NaN,
89,8.489,123.24,NaN,63.523,32.053,NaN,NaN,NaN,55.491,43.596,NaN,NaN,
92,8.443,119.316,NaN,60.731,30.25,NaN,NaN,NaN,55.129,NaN,NaN,NaN,
94,8.021,127.164,NaN,56.772,32.592,NaN,NaN,NaN,NaN,34.342,NaN,NaN,
95,8.377,119.582,NaN,54.319,34.424,NaN,NaN,NaN,54.955,38.807,NaN,NaN,
96,8.534,121.612,NaN,NaN,38.848,NaN,NaN,NaN,NaN,34.903,NaN,NaN,
97,7.839,117.831,NaN,57.414,34.883,NaN,NaN,NaN,53.99,39.713,NaN,NaN,
99,8.393,124.071,NaN,61.97,33.038,NaN,NaN,NaN,59.076,37.249,NaN,NaN,
100,8.572,124.663,NaN,59.167,37.282,NaN,NaN,NaN,52.379,40.008,NaN,NaN,
101,8.682,119.976,NaN,52.43,40.036,NaN,NaN,NaN,NaN,30.338,NaN,NaN,
102,8.516,121,NaN,57.586,30.311,NaN,NaN,NaN,57.64,30.219,NaN,NaN,
104,8.159,115.548,NaN,53.269,38.888,NaN,NaN,NaN,58.201,64.111,NaN,NaN,
105,7.926,123.094,NaN,58.24,64.211,NaN,NaN,NaN,60.144,64.773,NaN,NaN,
1000,8.818,110.587,NaN,63.001,34.606,NaN,NaN,NaN,45.423,NaN,NaN,NaN,
1001,8.099,117.581,NaN,59.506,32.755,NaN,NaN,NaN,NaN,42.332,NaN,NaN,
MBA2/data/ubiquitin.mba 0100644 0000765 0000024 00000012560 10066405654 014653 0 ustar janvitek staff Ubiquitin Ansig with fixed variances. 76 residues. Prolines at 18,36,37. Missing at 23,52. No extras. Max 6 connective resonances.
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
23,52
1,8.949,123.177,171.072,54.415,32.805,NaN,NaN,176.589,NaN,30.398,NaN,NaN,
2,8.313,115.36,176.586,54.69,30.35,NaN,NaN,172.906,59.209,41.885,NaN,NaN,
3,8.608,118.749,172.918,59.197,41.819,NaN,NaN,175.749,54.687,NaN,NaN,NaN,
4,9.305,121.457,175.559,54.683,40.944,NaN,NaN,NaN,60.026,33.988,NaN,NaN,
5,8.917,128.049,175.38,60.027,33.977,NaN,NaN,177.674,54.165,NaN,NaN,NaN,
6,8.752,115.689,177.596,54.156,34.181,NaN,NaN,NaN,60.097,NaN,NaN,NaN,
7,9.121,121.506,177.477,60.094,70.16,NaN,NaN,179.412,57.088,41.406,NaN,NaN,
8,7.643,106.092,179.39,57.085,41.629,NaN,NaN,176.068,60.986,68.687,NaN,NaN,
9,7.826,109.404,176.068,60.986,68.605,NaN,NaN,174.534,44.968,NaN,NaN,NaN,
10,7.271,122.157,174.544,44.944,NaN,NaN,NaN,176.326,55.887,33.03,NaN,NaN,
11,8.646,120.842,176.332,55.85,33.091,NaN,NaN,174.907,61.935,69.405,NaN,NaN,
12,9.538,127.9,174.907,61.934,69.431,NaN,NaN,175.737,59.59,NaN,NaN,NaN,
13,8.742,121.921,175.743,59.591,40.48,NaN,NaN,174.315,61.626,69.166,NaN,NaN,
14,8.736,125.36,174.314,61.61,69.33,NaN,NaN,175.11,52.375,NaN,NaN,NaN,
15,8.129,122.72,175.109,52.351,46.647,NaN,NaN,176.385,54.526,29.441,NaN,NaN,
16,8.939,117.757,176.382,54.478,29.458,NaN,NaN,174.611,58.005,36.141,NaN,NaN,
17,8.657,119.547,174.618,58.021,36.123,NaN,NaN,176.824,52.349,30.637,NaN,NaN,
19,7.033,103.624,175.492,64.858,31.581,NaN,NaN,NaN,56.934,62.944,NaN,NaN,
20,8.054,124.091,175.169,56.939,63.042,NaN,NaN,176.867,55.434,40.688,NaN,NaN,
21,7.889,109.187,176.863,55.431,40.648,NaN,NaN,177.303,59.252,70.841,NaN,NaN,
22,8.527,121.456,177.308,59.232,70.841,NaN,NaN,179.483,61.936,34.227,NaN,NaN,
24,7.931,121.613,179.195,60.277,28.308,NaN,NaN,NaN,55.59,38.056,NaN,NaN,
25,8.108,122.401,178.666,55.597,38.093,NaN,NaN,NaN,67.198,30.398,NaN,NaN,
26,8.563,119.156,178.474,67.203,30.398,NaN,NaN,181.061,58.796,33.509,NaN,NaN,
27,7.988,123.723,180.921,58.778,33.42,NaN,NaN,NaN,54.954,17.475,NaN,NaN,
28,7.865,120.415,180.773,54.941,17.452,NaN,NaN,180.848,59.353,33.03,NaN,NaN,
29,8.287,121.523,180.853,59.343,33.038,NaN,NaN,178.759,65.647,36.62,NaN,NaN,
30,8.56,123.798,178.738,65.666,36.443,NaN,NaN,179.417,59.621,27.526,NaN,NaN,
31,8.021,119.929,179.411,59.616,27.484,NaN,NaN,177.874,56.993,40.688,NaN,NaN,
32,7.43,115.657,177.858,56.969,40.721,NaN,NaN,178.391,57.69,33.748,NaN,NaN,
33,8.729,114.547,178.423,57.718,33.725,NaN,NaN,NaN,54.864,NaN,NaN,NaN,
34,8.508,109.098,178.488,54.88,33.005,NaN,NaN,174.489,45.645,NaN,NaN,NaN,
35,6.154,120.491,174.237,45.632,NaN,NaN,NaN,NaN,57.345,40.21,NaN,NaN,
38,8.535,113.832,178.829,65.688,32.535,NaN,NaN,177.616,55.341,39.492,NaN,NaN,
39,7.821,117.084,177.614,55.239,39.477,NaN,NaN,175.969,55.202,29.68,NaN,NaN,
40,7.485,118.269,175.963,55.139,29.741,NaN,NaN,176.726,56.227,31.355,NaN,NaN,
41,8.511,123.273,176.727,56.224,31.298,NaN,NaN,174.438,54.7,NaN,NaN,NaN,
42,8.838,124.62,174.442,54.699,31.416,NaN,NaN,175.842,52.614,45.474,NaN,NaN,
43,9.092,122.463,175.842,52.592,45.46,NaN,NaN,176.408,58.516,40.928,NaN,NaN,
44,8.852,125.399,176.411,58.512,40.898,NaN,NaN,175.134,56.188,43.321,NaN,NaN,
45,8.958,133.052,175.133,56.178,43.343,NaN,NaN,177.894,52.14,16.279,NaN,NaN,
46,8.131,102.708,177.891,52.106,16.246,NaN,NaN,174.298,44.959,NaN,NaN,NaN,
47,7.986,122.212,174.312,44.935,NaN,NaN,NaN,175.186,54.164,NaN,NaN,NaN,
48,8.644,123.223,175.187,54.155,34.072,NaN,NaN,176.139,55.456,28.723,NaN,NaN,
49,8.562,125.918,176.144,55.431,28.76,NaN,NaN,177.192,53.797,41.167,NaN,NaN,
50,8.395,123.348,177.194,53.775,41.008,NaN,NaN,176.047,55.481,31.595,NaN,NaN,
51,8.165,120.603,176.052,55.877,31.599,NaN,NaN,177.975,NaN,40.449,NaN,NaN,
53,7.464,119.537,175.337,44.796,NaN,NaN,NaN,175.893,53.852,NaN,NaN,NaN,
54,8.829,109.051,175.894,53.836,32.449,NaN,NaN,177.072,59.288,71.798,NaN,NaN,
55,8.153,118.272,177.074,59.255,71.93,NaN,NaN,181.344,58.272,39.97,NaN,NaN,
56,8.485,113.755,181.332,58.232,39.972,NaN,NaN,178.87,60.646,61.987,NaN,NaN,
57,7.94,124.753,178.413,60.654,62.125,NaN,NaN,NaN,56.974,39.97,NaN,NaN,
58,7.259,115.981,177.99,56.945,40.045,NaN,NaN,175.221,57.79,39.731,NaN,NaN,
59,8.158,116.207,175.034,57.812,39.712,NaN,NaN,NaN,53.728,37.099,NaN,NaN,
60,7.248,119.093,174.841,53.712,37.091,NaN,NaN,175.083,62.008,36.62,NaN,NaN,
61,7.625,125.163,175.1,62.004,36.4,NaN,NaN,176.336,53.192,31.355,NaN,NaN,
62,8.497,120.829,176.32,53.172,31.342,NaN,NaN,NaN,57.423,32.313,NaN,NaN,
63,9.319,114.808,176.031,57.605,32.312,NaN,NaN,NaN,NaN,25.612,NaN,NaN,
64,7.67,115.155,175.774,57.913,25.768,NaN,NaN,172.591,60.478,64.619,NaN,NaN,
65,8.737,117.631,172.601,60.488,64.664,NaN,NaN,174.331,62.029,NaN,NaN,NaN,
66,9.42,127.922,174.331,62.027,69.645,NaN,NaN,175.939,53.385,44.039,NaN,NaN,
67,9.238,119.368,175.944,53.383,44.112,NaN,NaN,174.18,55.428,31.595,NaN,NaN,
68,8.301,124.288,174.191,55.412,31.565,NaN,NaN,175.933,53.41,44.039,NaN,NaN,
69,9.191,126.958,175.937,53.395,43.877,NaN,NaN,174.595,60.187,34.466,NaN,NaN,
70,8.114,123.308,174.6,60.166,34.504,NaN,NaN,178.407,53.57,42.603,NaN,NaN,
71,8.603,124.021,178.399,53.564,42.565,NaN,NaN,175.88,55.273,31.116,NaN,NaN,
72,8.355,124.783,175.885,55.234,30.96,NaN,NaN,177.986,54.422,42.124,NaN,NaN,
73,8.443,122.202,177.707,54.369,42.154,NaN,NaN,NaN,56.163,30.398,NaN,NaN,
74,8.493,111.294,177.442,56.14,30.366,NaN,NaN,174.201,44.847,NaN,NaN,NaN,
75,7.947,115.289,174.209,45.236,NaN,NaN,NaN,179.708,46.671,NaN,NaN,NaN,
MBA2/data/zdomain.mba 0100644 0000765 0000024 00000010266 10066405655 014305 0 ustar janvitek staff Zdomain, 70 residues, prolines at 32,50,69. Missing at 9, 70. Extra: 2. Max 7 connective resonances.
KAIFVLNAQHDEAVDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPK
9,70
1,8.35,123.4,172.4,56.2,33.2,4.34,NaN,NaN,52.2,19.5,4.31,NaN,
2,7.97,116.9,173.9,52.2,19.3,4.3,NaN,NaN,60.9,NaN,4.11,NaN,
3,8.17,121.2,172.4,60.9,NaN,4.11,NaN,NaN,57.3,39.7,4.68,NaN,
4,7.95,120,171.8,57.3,39.8,4.68,NaN,NaN,61.8,NaN,4.05,NaN,
5,8.19,123.1,172.1,61.9,32.8,4.05,NaN,NaN,55.3,42.5,4.25,NaN,
6,8.38,116.7,173.6,55.3,42.3,4.26,NaN,NaN,53.1,38.9,4.66,NaN,
7,8.16,121.2,171.5,53.1,38.8,4.66,NaN,NaN,52.7,19.4,4.27,NaN,
8,8.24,115.9,174.2,52.6,19.2,4.28,NaN,NaN,55.9,29.5,4.28,NaN,
10,8.27,119.3,171.2,55.9,30.2,4.65,NaN,NaN,54.2,41.5,4.61,NaN,
11,8.45,119.2,172.9,54.2,41.4,4.61,NaN,NaN,57,30.2,4.21,NaN,
12,8.22,121.1,173.1,57,30.1,4.21,NaN,NaN,52.8,19.2,4.25,NaN,
13,7.79,115.3,174.8,52.7,18.9,4.26,NaN,NaN,62.6,NaN,3.79,NaN,
14,7.97,119.1,172.7,62.6,NaN,3.8,NaN,NaN,54.6,41.4,4.43,NaN,
15,8.07,116,173.1,54.6,41.2,4.43,NaN,NaN,53.8,38.9,4.58,NaN,
16,8.17,116.6,172.1,53.8,38.8,4.57,NaN,NaN,56.7,32.4,4.21,NaN,
17,7.84,116.1,173.4,56.7,32.4,4.21,NaN,NaN,55.1,39.9,5.08,NaN,
18,8.42,117.8,173.5,55.1,39.9,5.08,NaN,NaN,51.7,38.1,4.75,NaN,
19,8.3,115.9,172.5,51.8,38,4.76,NaN,NaN,59.8,NaN,4,NaN,
20,8.2,116.8,175.2,59.8,32.1,4,NaN,NaN,59.7,29.1,4.12,NaN,
21,8.48,118.7,176.8,59.6,28.9,4.12,NaN,NaN,58.6,NaN,3.9,NaN,
22,8.73,116.3,174.5,58.6,NaN,3.9,NaN,NaN,59,NaN,3.96,NaN,
23,8.29,114.8,174.9,59.1,28.5,3.96,NaN,NaN,56.2,38.3,4.63,NaN,
24,7.86,119.5,174.2,56.2,38.2,4.62,NaN,NaN,55.4,18.4,4.1,NaN,
25,8.1,115.2,174.8,55.3,18.2,4.1,NaN,NaN,61,39.1,3.81,NaN,
26,8.13,113.9,172.8,61,39,3.81,NaN,NaN,62.1,38.3,3.96,NaN,
27,8.46,116.3,175.4,62.1,38.1,3.96,NaN,NaN,60.3,NaN,4.02,NaN,
28,8.35,116.7,177.1,60.3,29.7,4.02,NaN,NaN,65.5,NaN,3.4,NaN,
29,7.86,115,174.7,65.6,NaN,3.39,NaN,NaN,57.3,41.9,3.67,NaN,
30,7.17,109,173.7,57.3,41.9,3.68,NaN,NaN,55.8,29.9,4.51,NaN,
31,7.2,121.6,171.7,55.8,29.7,4.51,NaN,NaN,53.4,40.5,4.5,NaN,
33,8.86,111,174.8,65,32.5,4.43,NaN,NaN,52.7,38.8,5.03,NaN,
34,6.48,114.6,173,52.6,38.7,5.03,NaN,NaN,54.3,38.6,4.43,NaN,
35,8.51,116.5,173.3,54.2,38.8,4.43,NaN,NaN,51.3,38.8,4.93,NaN,
36,8.59,115.6,172.5,51.2,38.6,4.94,NaN,NaN,59.8,29.6,3.97,NaN,
37,8.23,116.9,174.9,59.8,29.4,3.98,NaN,NaN,59.7,29.2,4.06,NaN,
38,8.46,116.9,176.9,59.8,28.9,4.06,NaN,NaN,57.9,29.1,3.98,NaN,
39,8.53,116.1,175.2,57.9,29,3.98,NaN,NaN,60.6,38.8,3.78,NaN,
40,8.43,112.3,174.6,60.6,38.1,3.78,NaN,NaN,55.9,38.1,4.4,NaN,
41,7.82,120.4,174.4,55.9,37.9,4.4,NaN,NaN,55.2,17.9,4.18,NaN,
42,7.95,114.2,177.7,55.1,17.7,4.18,NaN,NaN,62.3,39.9,4.37,NaN,
43,8.24,115.6,174.8,62.3,39.6,4.38,NaN,NaN,64.2,NaN,3.75,NaN,
44,8.4,116.6,174.4,64.2,NaN,3.75,NaN,NaN,58.6,NaN,3.94,NaN,
45,8.02,112.3,175,58.6,28.1,3.94,NaN,NaN,62.4,NaN,4.28,NaN,
46,8.08,121.4,172.8,62.4,62.3,4.28,NaN,NaN,57.7,42.5,3.78,NaN,
47,7.97,112.7,174.1,57.7,42.3,3.79,NaN,NaN,59.6,NaN,4.01,NaN,
48,8.11,115.3,175.8,59.6,NaN,4.01,NaN,NaN,56.6,41.1,4.43,NaN,
49,7.55,111.1,174.2,56.6,41,4.43,NaN,NaN,51.7,40.5,4.93,NaN,
51,7.99,110.2,175.2,64.5,31.7,4.5,NaN,NaN,61,62.9,4.33,NaN,
52,7.83,117.6,173,61,62.7,4.34,NaN,NaN,55,NaN,4.63,NaN,
53,7.75,112.7,173.1,55,28,4.63,NaN,NaN,63.5,NaN,3.72,NaN,
54,8.44,120.3,171,63.5,62.7,3.73,NaN,NaN,55.5,18,4.15,NaN,
55,7.86,115.7,177.7,55.5,17.9,4.16,NaN,NaN,55.8,38.3,4.55,NaN,
56,8.55,118.7,174.6,55.8,38.1,4.54,NaN,NaN,57.7,42.5,4.18,NaN,
57,8.38,116,175.1,57.7,42.4,4.18,NaN,NaN,57.8,41.9,3.83,NaN,
58,7.56,116.7,174.7,57.8,41.9,3.83,NaN,NaN,55.3,18,4.05,NaN,
59,8.02,116.5,178,55.3,17.8,4.05,NaN,NaN,59,29.6,4.05,NaN,
60,8.43,121.2,175.7,59,29.6,4.05,NaN,NaN,55.3,17.3,3.49,NaN,
61,8.45,115.2,176.4,55.3,17.3,3.48,NaN,NaN,60.2,NaN,3.77,NaN,
62,7.66,117.4,175.5,60.3,32.1,3.78,NaN,NaN,59.6,32.5,4.13,NaN,
63,7.9,119.3,176.5,59.6,32.4,4.13,NaN,NaN,57.5,NaN,4.18,NaN,
64,8.53,114.2,174.8,57.4,42,4.19,NaN,NaN,57.7,41.9,3.98,NaN,
65,8.21,116,174.3,57.7,41.8,3.98,NaN,NaN,56.9,40.1,4.48,NaN,
66,7.99,120.1,175.7,56.9,40,4.48,NaN,NaN,54.3,18.6,4.26,NaN,
67,7.51,112.2,176.1,54.2,18.5,4.26,NaN,NaN,54.9,28.5,4.4,NaN,
68,7.08,121.6,170.9,54.9,28.2,4.41,NaN,NaN,51,17.9,4.37,NaN,
1000,7.76,124.2,171.2,61.9,NaN,4.07,NaN,NaN,54.9,41.4,4.4,NaN,
1001,8.01,124.6,172.9,63.3,31.8,4.45,NaN,NaN,57.3,33.9,4.21,NaN
MBA2/examples/ 0040755 0000765 0000024 00000000000 10066412746 013065 5 ustar janvitek staff MBA2/examples/csp.mba 0100644 0000765 0000024 00000010436 10066405623 014330 0 ustar janvitek staff Csp, 70 residues. Missings at 1,2, Prolines at 22,61, Extras: 4. Max 7 connective resonances.
MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL
1,2
3,8.18,117.4,173.4,44.8,NaN,4.01,NaN,NaN,56.6,33.5,4.29,NaN,
4,8.6,120.1,176,56.5,33.4,4.29,NaN,NaN,53.6,NaN,4.58,NaN,
5,7.66,104.8,174.1,53.5,34,4.57,NaN,NaN,59.3,NaN,5.51,NaN,
6,8.93,106,175.7,59.9,71.4,5.52,NaN,NaN,46.2,NaN,4.59,3.98,
7,8.18,116.5,171.1,46.1,NaN,4.57,NaN,NaN,58.3,NaN,5.14,NaN,
8,8.81,123.6,175.6,58.3,41.9,5.14,NaN,NaN,64.4,NaN,3.62,NaN,
9,9.09,133.2,175,64.6,NaN,3.62,NaN,NaN,58.6,NaN,4.23,NaN,
10,7.42,108.5,176.3,58.5,NaN,4.22,NaN,NaN,56.2,NaN,4.68,NaN,
11,9.22,118.8,173.7,56.2,NaN,4.66,NaN,NaN,59.4,NaN,4.29,NaN,
12,8.1,123.9,NaN,59.3,42.2,4.29,NaN,NaN,51.4,NaN,4.84,NaN,
13,9.04,125.9,174.1,51.2,39.3,4.85,NaN,NaN,54.5,18.6,4.1,NaN,
14,7.95,114.3,178.6,54.5,18.5,4.12,NaN,NaN,56.6,40.7,4.36,NaN,
15,7.42,113.1,177.7,56.6,40.8,4.37,NaN,NaN,56.2,33.5,4.22,NaN,
16,8.13,104.8,177.4,55.9,33.7,4.22,NaN,NaN,46.2,NaN,4.12,3.8,
17,6.63,109.6,172.4,46.2,NaN,4.13,3.82,NaN,54.6,42.2,5.13,NaN,
18,8.01,102.6,171.9,54.8,42.3,5.12,NaN,NaN,NaN,NaN,3.95,NaN,
19,7.93,112.2,170.5,45.3,NaN,3.93,NaN,NaN,56.3,NaN,NaN,NaN,
20,9.4,119,174.6,56.6,45.2,5.26,NaN,NaN,59.3,NaN,4.26,NaN,
21,9.35,123.9,174.7,59.5,42,4.24,NaN,NaN,59.3,NaN,5.19,NaN,
23,9.19,120.4,177.5,62.9,33.6,4.74,NaN,NaN,56.6,40.4,4.68,NaN,
24,7.95,114.1,176.5,56.5,40.5,4.67,NaN,NaN,53.6,40.7,4.57,NaN,
25,7.67,104.5,177.6,53.6,40,4.57,NaN,NaN,45.8,NaN,4.2,3.91,
26,7.97,113.1,174.7,45.8,NaN,4.19,3.9,NaN,58.6,63.1,4.39,NaN,
27,7.69,114.2,172.5,58.5,63.2,4.38,NaN,NaN,56.9,33.2,4.11,NaN,
28,7.89,115.3,175.1,56.9,33.1,4.11,NaN,NaN,55.3,41.3,4.92,NaN,
29,9.27,117.7,176.3,55.5,41.5,4.92,NaN,NaN,60.6,NaN,4.35,NaN,
30,8.52,127,174.7,60.6,NaN,4.34,NaN,NaN,58.1,NaN,3.73,NaN,
31,7.74,121.6,172.6,58.2,40.2,3.72,NaN,NaN,57.9,NaN,4.5,NaN,
32,8.69,124.4,170.4,57.8,NaN,4.5,NaN,NaN,55.4,NaN,4.8,NaN,
33,8.29,120.4,177.2,55.5,34.1,4.81,NaN,NaN,59.9,37.3,4.16,NaN,
34,7.56,114.3,176,59.9,37.4,4.15,NaN,NaN,59.9,62.4,3.88,NaN,
35,8.03,121.4,175,59.9,62.6,3.89,NaN,NaN,52.3,20.8,4.47,NaN,
36,7.47,116.5,177.5,52.2,20.9,4.46,NaN,NaN,62.6,NaN,3.91,NaN,
37,8.99,124.4,176.1,62.6,NaN,3.91,NaN,NaN,55.2,NaN,4.37,NaN,
38,7.5,116,175.6,55.2,28.7,4.4,NaN,NaN,53.3,39.1,4.64,NaN,
39,8.56,118.8,174.6,53.2,39.3,4.64,NaN,NaN,54.9,40.9,4.53,NaN,
40,8.26,106.2,176.5,54.9,40.9,4.53,NaN,NaN,45.2,NaN,3.99,3.79,
41,8.05,118.5,173.7,45.1,NaN,3.96,3.79,NaN,58.2,38.5,4.42,NaN,
42,8.24,122.4,176,58.2,38.4,4.42,NaN,NaN,54.9,NaN,4.21,NaN,
43,7.38,111.1,174,54.9,31.8,4.22,NaN,NaN,56.2,64,3.99,NaN,
44,5.82,116.3,171.7,56.3,64.2,3.99,NaN,NaN,52.6,NaN,NaN,NaN,
45,8.19,116.3,174.1,52.6,NaN,4.41,NaN,NaN,52.5,42.9,4.9,NaN,
46,8.63,118.2,175.5,52.5,43,4.9,NaN,NaN,58,NaN,3.6,NaN,
47,9.09,110.9,177.3,58.2,29.4,3.6,NaN,NaN,45.2,NaN,4.36,NaN,
48,7.74,117.9,173.6,45.1,NaN,4.35,3.55,NaN,56.3,NaN,4.2,NaN,
49,8.76,123.3,175.6,56.2,30.3,4.19,NaN,NaN,56.3,33.1,5.06,NaN,
50,8.6,112.8,177.1,56.5,33.1,5.07,NaN,NaN,58.5,NaN,5.37,NaN,
51,9.11,112,174.3,58.6,36.8,5.37,NaN,NaN,55.3,65.8,5.72,NaN,
52,8.67,114.6,173.9,55.8,66,5.7,NaN,NaN,56.2,40.4,5.29,NaN,
53,8.95,107.7,172.8,56.5,40.5,5.29,NaN,NaN,59.9,NaN,4.73,NaN,
54,8.65,118.4,174.5,59.9,70.4,4.73,NaN,NaN,61,NaN,4.7,NaN,
55,9.15,125.2,175.6,61,38.8,4.7,NaN,NaN,54.2,NaN,4.68,NaN,
56,8.74,115.7,176,54.2,31.5,4.67,NaN,NaN,58,63.1,4.51,NaN,
57,7.79,109.2,174.4,57.9,63.3,4.51,NaN,NaN,44.5,NaN,4.32,3.95,
58,8.56,120.8,174.6,44.5,NaN,3.95,NaN,NaN,54.3,18.9,4.14,NaN,
59,8.34,112.5,179.1,54.5,18.8,4.13,NaN,NaN,55.2,31.9,4.39,NaN,
60,7.49,105.5,175.9,55.2,32.1,4.36,NaN,NaN,44.2,NaN,4.37,3.84,
62,8.72,122.4,176.7,62.9,32.7,4.86,NaN,NaN,50.6,22.6,5.15,NaN,
63,8.87,119.4,175.2,50.8,22.5,5.15,NaN,NaN,50.8,20.2,5.11,NaN,
64,9.26,106,177.4,51.1,20.1,5.09,NaN,NaN,43.5,NaN,NaN,NaN,
65,9.19,113.7,172.9,43.4,NaN,4.64,3.56,NaN,54.2,38.1,4.19,NaN,
66,8.17,115.4,174.1,54.2,38.1,4.18,NaN,NaN,63.3,NaN,4.7,NaN,
67,9.02,117.9,176.1,63.3,NaN,4.7,NaN,NaN,59.6,NaN,4.77,NaN,
68,8.78,116.8,173.9,59.6,71.7,4.79,NaN,NaN,59.3,63.4,4.67,NaN,
69,7.97,128.4,173.8,59.3,63.6,4.65,NaN,NaN,56.3,43.4,4.27,NaN,
1000,8.17,118,176.2,NaN,NaN,NaN,NaN,NaN,54.3,41,4.58,NaN,
1001,7.83,116.1,176,54.3,41.1,NaN,NaN,NaN,62,NaN,4.04,NaN,
1002,8.44,106.3,177.2,NaN,40.9,NaN,NaN,NaN,45.5,NaN,4.57,3.94,
1003,8.19,112.8,174.8,45.5,NaN,3.98,NaN,NaN,58.9,NaN,4.39,NaN
MBA2/examples/CVS/ 0040755 0000765 0000024 00000000000 10066413466 013520 5 ustar janvitek staff MBA2/examples/CVS/Entries 0100644 0000765 0000024 00000000175 10066413466 015054 0 ustar janvitek staff /README/1.1/Wed Jun 23 23:44:38 2004//
/csp.mba/1.1/Wed Jun 23 23:00:35 2004//
/results.out/1.1/Wed Jun 23 23:46:55 2004//
D
MBA2/examples/CVS/Repository 0100644 0000765 0000024 00000000031 10066406044 015603 0 ustar janvitek staff /p/sss/cvs/MBA2/examples
MBA2/examples/CVS/Root 0100644 0000765 0000024 00000000050 10066406044 014350 0 ustar janvitek staff :ext:jv@arthur.cs.purdue.edu:/p/sss/cvs
MBA2/examples/CVS/Template 0100644 0000765 0000024 00000000000 10066406044 015173 0 ustar janvitek staff MBA2/examples/README 0100644 0000765 0000024 00000001716 10066412746 013747 0 ustar janvitek staff This directory contains one example data set and the expected output.
If you do not get the same result on your machine there may be something
wrong with your version of Java.
The time given at the end of the *.out file indicates the duration
of the run on Mac 1GHz G4 processor with 1GB of memory. In general
more memory is better!
The result file was created by the following commands:
cd ..
bin/doIt -dataset=examples/csp.mba -maxWindowSize=200000 -maxMissings=2 \
-alpha=.025 -beta=.025 >& examples/results.out
The max missing argument is used to bound the number of missing spin systems
in the protein. The complexity rises very quickly with high missing counts.
The max window size is used to bound the size of our internal data structures.
Typically larger values are better, but they also require more memory.
Alpha and beta are cut offs used to reject inconsistent observations. Higher
values lead to more agressive pruning of the search space.
MBA2/examples/results.out 0100644 0000765 0000024 00000125545 10066413157 015325 0 ustar janvitek staff Model-Based Assignment v0.1 (c) 2003, O&J Vitek, Purdue University.
ARGUMENTS:
-dataset=examples/csp.mba
-maxWindowSize=200000
-maxMissings=2
-alpha=.025
-beta=.025
COMMENT:
Csp, 70 residues. Missings at 1,2, Prolines at 22,61, Extras: 4. Max 7 connective resonances.
DESCRIPTION OF THE ORIGINAL DATA SET:
Missing spin systems in reference solution: 2
Extra spin systems in reference solution: 4
Min chemical shifts per spin system in the original data set: 4
Max chemical shifts per spin system in the original data set: 7
Prop missing resonances in all observed spin systems: 23.0%
DESCRIPTION OF THE SPIN SYSTEMS USED
Missing spin systems used: 2
Extra spin systems used: 4
Min chemical shifts per spin system used: 4
Max chemical shifts per spin system used: 7
Prop missing resonances in all spin systems used: 23.0%
DESCRIPTION OF THE SCORES:
Number of valid pairs = 9815
Mean number of following spin systems: 3.65;
Number of uniquely followed spin systems: 0 (Prop out of number of non-missing SS: 0%).
REFERENCE MAPPING:
Score joint = 235.693 df = 408
Score match = 61.7399 df = 151
Score align = 173.953 df = 257
Inconsistent pairs:
None
INITIALIZATION:
M [ 0] * 1
S [ 1] * 35
G [ 2] * 39
K [ 3] * 20
M [ 4] * 58
T [ 5] * 58
G [ 6] * 39
I [ 7] * 20
V [ 8] * 58
K [ 9] * 58
W [ 10] * 58
F [ 11] * 58
N [ 12] * 58
A [ 13] * 58
D [ 14] * 58
K [ 15] * 58
G [ 16] * 39
F [ 17] * 20
G [ 18] * 39
F [ 19] * 20
I [ 20] * 58
T [ 21] * 34
P [ 22] * 1
D [ 23] * 21
D [ 24] * 58
G [ 25] * 39
S [ 26] * 20
K [ 27] * 58
D [ 28] * 58
V [ 29] * 58
F [ 30] * 58
V [ 31] * 58
H [ 32] * 58
F [ 33] * 58
S [ 34] * 58
A [ 35] * 58
I [ 36] * 58
Q [ 37] * 58
N [ 38] * 58
D [ 39] * 58
G [ 40] * 39
Y [ 41] * 20
K [ 42] * 58
S [ 43] * 58
L [ 44] * 58
D [ 45] * 58
E [ 46] * 58
G [ 47] * 39
Q [ 48] * 20
K [ 49] * 58
V [ 50] * 58
S [ 51] * 58
F [ 52] * 58
T [ 53] * 58
I [ 54] * 58
E [ 55] * 58
S [ 56] * 58
G [ 57] * 39
A [ 58] * 20
K [ 59] * 58
G [ 60] * 11
P [ 61] * 1
A [ 62] * 21
A [ 63] * 58
G [ 64] * 39
N [ 65] * 20
V [ 66] * 58
T [ 67] * 58
S [ 68] * 58
L [ 69] * 35
EXTEND WINDOWS:
Merged[ 0, 0] * 1 with [ 1, 1] * 35 --> 35 Min missings 0
Merged[ 0, 1] * 35 with [ 2, 2] * 39 --> 47 Min missings 0
Merged[ 0, 2] * 47 with [ 3, 3] * 20 --> 297 Min missings 0
Merged[ 0, 3] * 297 with [ 4, 4] * 58 --> 1162 Min missings 0
Merged[ 0, 4] * 1162 with [ 5, 5] * 58 --> 6381 Min missings 0
Merged[ 0, 5] * 6381 with [ 6, 6] * 39 --> 6513 Min missings 0
Merged[ 0, 6] * 6513 with [ 7, 7] * 20 --> 8390 Min missings 0
Merged[ 0, 7] * 8390 with [ 8, 8] * 58 --> 15988 Min missings 0
Merged[ 0, 8] * 15988 with [ 9, 9] * 58 --> 18469 Min missings 0
Merged[ 0, 9] * 18469 with [ 10, 10] * 58 --> 21350 Min missings 0
Merged[ 0, 10] * 21350 with [ 11, 11] * 58 --> 17287 Min missings 0
Merged[ 0, 11] * 17287 with [ 12, 12] * 58 --> 30702 Min missings 0
Merged[ 0, 12] * 30702 with [ 13, 13] * 58 --> 36064 Min missings 0
Merged[ 0, 13] * 36064 with [ 14, 14] * 58 --> 16165 Min missings 0
Merged[ 0, 14] * 16165 with [ 15, 15] * 58 --> 22551 Min missings 0
Merged[ 0, 15] * 22551 with [ 16, 16] * 39 --> 12637 Min missings 0
Merged[ 0, 16] * 12637 with [ 17, 17] * 20 --> 13417 Min missings 0
Merged[ 0, 17] * 13417 with [ 18, 18] * 39 --> 28355 Min missings 0
Merged[ 0, 18] * 28355 with [ 19, 19] * 20 --> 68878 Min missings 0
Merged[ 0, 19] * 68878 with [ 20, 20] * 58 --> 138684 Min missings 0
Merged[ 0, 20] * 138684 with [ 21, 21] * 34 --> 125454 Min missings 0
Merged[ 0, 21] * 125454 with [ 22, 22] * 1 --> 125413 Min missings 0
MaxSizeExceeded
Merged[ 23, 23] * 21 with [ 24, 24] * 58 --> 82 Min missings 0
Merged[ 23, 24] * 82 with [ 25, 25] * 39 --> 546 Min missings 0
Merged[ 23, 25] * 546 with [ 26, 26] * 20 --> 1615 Min missings 0
Merged[ 23, 26] * 1615 with [ 27, 27] * 58 --> 4796 Min missings 0
Merged[ 23, 27] * 4796 with [ 28, 28] * 58 --> 17897 Min missings 0
Merged[ 23, 28] * 17897 with [ 29, 29] * 58 --> 56974 Min missings 0
Merged[ 23, 29] * 56974 with [ 30, 30] * 58 --> 100891 Min missings 0
MaxSizeExceeded
Merged[ 31, 31] * 58 with [ 32, 32] * 58 --> 118 Min missings 0
Merged[ 31, 32] * 118 with [ 33, 33] * 58 --> 1067 Min missings 0
Merged[ 31, 33] * 1067 with [ 34, 34] * 58 --> 4786 Min missings 0
Merged[ 31, 34] * 4786 with [ 35, 35] * 58 --> 16343 Min missings 0
Merged[ 31, 35] * 16343 with [ 36, 36] * 58 --> 21854 Min missings 0
Merged[ 31, 36] * 21854 with [ 37, 37] * 58 --> 38976 Min missings 0
Merged[ 31, 37] * 38976 with [ 38, 38] * 58 --> 38156 Min missings 0
Merged[ 31, 38] * 38156 with [ 39, 39] * 58 --> 55012 Min missings 0
Merged[ 31, 39] * 55012 with [ 40, 40] * 39 --> 99432 Min missings 0
MaxSizeExceeded
Merged[ 41, 41] * 20 with [ 42, 42] * 58 --> 103 Min missings 0
Merged[ 41, 42] * 103 with [ 43, 43] * 58 --> 588 Min missings 0
Merged[ 41, 43] * 588 with [ 44, 44] * 58 --> 1683 Min missings 0
Merged[ 41, 44] * 1683 with [ 45, 45] * 58 --> 7925 Min missings 0
Merged[ 41, 45] * 7925 with [ 46, 46] * 58 --> 27227 Min missings 0
Merged[ 41, 46] * 27227 with [ 47, 47] * 39 --> 15990 Min missings 0
Merged[ 41, 47] * 15990 with [ 48, 48] * 20 --> 14621 Min missings 0
Merged[ 41, 48] * 14621 with [ 49, 49] * 58 --> 14362 Min missings 0
Merged[ 41, 49] * 14362 with [ 50, 50] * 58 --> 16373 Min missings 0
Merged[ 41, 50] * 16373 with [ 51, 51] * 58 --> 13697 Min missings 0
Merged[ 41, 51] * 13697 with [ 52, 52] * 58 --> 14017 Min missings 0
Merged[ 41, 52] * 14017 with [ 53, 53] * 58 --> 22845 Min missings 0
Merged[ 41, 53] * 22845 with [ 54, 54] * 58 --> 25159 Min missings 0
Merged[ 41, 54] * 25159 with [ 55, 55] * 58 --> 32556 Min missings 0
Merged[ 41, 55] * 32556 with [ 56, 56] * 58 --> 21699 Min missings 0
Merged[ 41, 56] * 21699 with [ 57, 57] * 39 --> 15152 Min missings 0
Merged[ 41, 57] * 15152 with [ 58, 58] * 20 --> 21662 Min missings 0
Merged[ 41, 58] * 21662 with [ 59, 59] * 58 --> 21950 Min missings 0
Merged[ 41, 59] * 21950 with [ 60, 60] * 11 --> 6584 Min missings 0
Merged[ 41, 60] * 6584 with [ 61, 61] * 1 --> 6584 Min missings 0
Merged[ 41, 61] * 6584 with [ 62, 62] * 21 --> 90637 Min missings 0
Merged[ 41, 62] * 90637 with [ 63, 63] * 58 --> 45393 Min missings 0
Merged[ 41, 63] * 45393 with [ 64, 64] * 39 --> 17156 Min missings 0
Merged[ 41, 64] * 17156 with [ 65, 65] * 20 --> 16106 Min missings 0
Merged[ 41, 65] * 16106 with [ 66, 66] * 58 --> 27303 Min missings 0
Merged[ 41, 66] * 27303 with [ 67, 67] * 58 --> 33542 Min missings 0
Merged[ 41, 67] * 33542 with [ 68, 68] * 58 --> 24739 Min missings 0
Merged[ 41, 68] * 24739 with [ 69, 69] * 35 --> 19812 Min missings 0
AFTER PRECOMPUTATION:
M [ 0] * 1
S [ 1] * 23
G [ 2] * 3
K [ 3] * 8
M [ 4] * 17
T [ 5] * 20
G [ 6] * 3
I [ 7] * 10
V [ 8] * 21
K [ 9] * 15
W [ 10] * 12
F [ 11] * 16
N [ 12] * 23
A [ 13] * 9
D [ 14] * 6
K [ 15] * 16
G [ 16] * 4
F [ 17] * 10
G [ 18] * 7
F [ 19] * 10
I [ 20] * 31
T [ 21] * 24
P [ 22] * 1
D [ 23] * 16
D [ 24] * 23
G [ 25] * 7
S [ 26] * 6
K [ 27] * 12
D [ 28] * 18
V [ 29] * 22
F [ 30] * 25
V [ 31] * 36
H [ 32] * 16
F [ 33] * 23
S [ 34] * 28
A [ 35] * 9
I [ 36] * 8
Q [ 37] * 24
N [ 38] * 15
D [ 39] * 20
G [ 40] * 25
Y [ 41] * 18
K [ 42] * 22
S [ 43] * 12
L [ 44] * 11
D [ 45] * 18
E [ 46] * 16
G [ 47] * 3
Q [ 48] * 6
K [ 49] * 12
V [ 50] * 11
S [ 51] * 13
F [ 52] * 12
T [ 53] * 21
I [ 54] * 12
E [ 55] * 19
S [ 56] * 9
G [ 57] * 3
A [ 58] * 4
K [ 59] * 6
G [ 60] * 4
P [ 61] * 1
A [ 62] * 10
A [ 63] * 4
G [ 64] * 2
N [ 65] * 9
V [ 66] * 16
T [ 67] * 13
S [ 68] * 11
L [ 69] * 13
Fix 1 positions.
Fix 64-64 0/2;
[ 0, 22] * 125413 Min missings 0
[ 23, 30] * 100891 Min missings 0
[ 31, 40] * 99432 Min missings 0
[ 41, 69] * 17676 Min missings 0
No merge.
Fix 2 positions.
Fix 64-64 0/2; 63-63 0/2;
[ 0, 22] * 125413 Min missings 0
[ 23, 30] * 100891 Min missings 0
[ 31, 40] * 99432 Min missings 0
[ 41, 69] * 15249 Min missings 0
No merge.
Fix 3 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2;
[ 0, 22] * 125413 Min missings 0
[ 23, 30] * 97625 Min missings 0
[ 31, 40] * 99432 Min missings 0
[ 41, 69] * 14924 Min missings 0
No merge.
Fix 4 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; 6-2 0/3;
[ 0, 22] * 467 Min missings 1 Reference strand excluded
[ 23, 30] * 8036 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 325 Min missings 0
Trying to merge window 2 (1467) with 3 (325)
Merged[ 31, 40] * 1467 with [ 41, 69] * 325 --> 1610 Min missings 0
Trying to merge window 0 (467) with 1 (8036)
Merged[ 0, 22] * 467 with [ 23, 30] * 8036 --> 2353 Min missings 1
Trying to merge window 1 (2353) with 3 (1610)
Merged[ 0, 30] * 2353 with [ 31, 69] * 1610 --> 91 Min missings 1
Merged windows:
[ 0, 69] * 91 Min missings 1 Reference strand excluded
*************** Now have 30 completed mappings ***************
Fix 4 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; 57-2 1/3;
[ 0, 22] * 2930 Min missings 0 Reference strand excluded
[ 23, 30] * 8036 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 535 Min missings 1 Reference strand excluded
No merge.
Fix 5 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; 57-2 1/3; 6-6 0/2;
[ 0, 22] * 2780 Min missings 0 Reference strand excluded
[ 23, 30] * 8036 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 487 Min missings 1 Reference strand excluded
Trying to merge window 2 (1467) with 3 (487)
Merged[ 31, 40] * 1467 with [ 41, 69] * 487 --> 1826 Min missings 1
Trying to merge window 1 (8036) with 3 (1826)
Merged[ 23, 30] * 8036 with [ 31, 69] * 1826 --> 6585 Min missings 1
Trying to merge window 0 (2780) with 3 (6585)
Merged[ 0, 22] * 2780 with [ 23, 69] * 6585 --> 129 Min missings 2
Merged windows:
[ 0, 69] * 129 Min missings 2 Reference strand excluded
*************** Now have 12 completed mappings ***************
Fix 5 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; 57-2 1/3; -1-6 1/2;
[ 0, 22] * 150 Min missings 1 Reference strand excluded
[ 23, 30] * 120 Min missings 0
[ 31, 40] * 7 Min missings 0
[ 41, 69] * 4 Min missings 1 Reference strand excluded
Trying to merge window 2 (7) with 3 (4)
Merged[ 31, 40] * 7 with [ 41, 69] * 4 --> 10 Min missings 1
Trying to merge window 1 (120) with 3 (10)
Merged[ 23, 30] * 120 with [ 31, 69] * 10 --> 60 Min missings 1
Trying to merge window 0 (150) with 3 (60)
Dead End
Fix 4 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3;
[ 0, 22] * 40310 Min missings 1
[ 23, 30] * 8036 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 325 Min missings 0
Trying to merge window 2 (1467) with 3 (325)
Merged[ 31, 40] * 1467 with [ 41, 69] * 325 --> 1610 Min missings 0
Trying to merge window 1 (8036) with 3 (1610)
Merged[ 23, 30] * 8036 with [ 31, 69] * 1610 --> 5817 Min missings 0
Merged windows:
[ 0, 22] * 40310 Min missings 1
[ 23, 69] * 5817 Min missings 0
Fix 5 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2;
[ 0, 22] * 36203 Min missings 1
[ 23, 69] * 5817 Min missings 0
No merge.
Fix 6 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2;
[ 0, 22] * 32897 Min missings 1
[ 23, 69] * 5574 Min missings 0
No merge.
Fix 7 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2;
[ 0, 22] * 31102 Min missings 1
[ 23, 69] * 4566 Min missings 0
No merge.
Fix 8 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2;
[ 0, 22] * 29821 Min missings 1
[ 23, 69] * 3816 Min missings 0
No merge.
Fix 9 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2;
[ 0, 22] * 28048 Min missings 1
[ 23, 69] * 3795 Min missings 0
No merge.
Fix 10 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2;
[ 0, 22] * 27228 Min missings 1
[ 23, 69] * 3732 Min missings 0
No merge.
Fix 11 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2; 10-10 0/2;
[ 0, 22] * 25993 Min missings 1
[ 23, 69] * 2091 Min missings 0
No merge.
Fix 12 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2; 10-10 0/2; 32-32 0/2;
[ 0, 22] * 23665 Min missings 1
[ 23, 69] * 2053 Min missings 0
No merge.
Fix 13 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2; 10-10 0/2; 32-32 0/2; 31-31 0/2;
[ 0, 22] * 21206 Min missings 1
[ 23, 69] * 2016 Min missings 0
No merge.
Fix 14 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2; 10-10 0/2; 32-32 0/2; 31-31 0/2; 30-30 0/2;
[ 0, 22] * 17836 Min missings 1
[ 23, 69] * 1971 Min missings 0
Trying to merge window 0 (17836) with 1 (1971)
Merged[ 0, 22] * 17836 with [ 23, 69] * 1971 --> 3408 Min missings 1
Merged windows:
[ 0, 69] * 3408 Min missings 1
*************** Now have 33 completed mappings ***************
Fix 14 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2; 10-10 0/2; 32-32 0/2; 31-31 0/2; -1-30 1/2;
[ 0, 22] * 597 Min missings 1 Reference strand excluded
[ 23, 69] * 45 Min missings 1 Reference strand excluded
Trying to merge window 0 (597) with 1 (45)
Merged[ 0, 22] * 597 with [ 23, 69] * 45 --> 97 Min missings 2
Merged windows:
[ 0, 69] * 97 Min missings 2 Reference strand excluded
*************** Now have 33 completed mappings ***************
Fix 13 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2; 10-10 0/2; 32-32 0/2; -1-31 1/2;
[ 0, 22] * 633 Min missings 1 Reference strand excluded
[ 23, 69] * 37 Min missings 1 Reference strand excluded
Trying to merge window 0 (633) with 1 (37)
Merged[ 0, 22] * 633 with [ 23, 69] * 37 --> 89 Min missings 2
Merged windows:
[ 0, 69] * 89 Min missings 2 Reference strand excluded
*************** Now have 33 completed mappings ***************
Fix 12 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2; 10-10 0/2; -1-32 1/2;
[ 0, 22] * 743 Min missings 1 Reference strand excluded
[ 23, 69] * 38 Min missings 1 Reference strand excluded
Trying to merge window 0 (743) with 1 (38)
Merged[ 0, 22] * 743 with [ 23, 69] * 38 --> 92 Min missings 2
Merged windows:
[ 0, 69] * 92 Min missings 2 Reference strand excluded
*************** Now have 33 completed mappings ***************
Fix 11 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; 7-7 0/2; -1-10 1/2;
[ 0, 22] * 1065 Min missings 2 Reference strand excluded
[ 23, 69] * 48 Min missings 0
Trying to merge window 0 (1065) with 1 (48)
Merged[ 0, 22] * 1065 with [ 23, 69] * 48 --> 134 Min missings 2
Merged windows:
[ 0, 69] * 134 Min missings 2 Reference strand excluded
*************** Now have 38 completed mappings ***************
Fix 10 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; 8-8 0/2; -1-7 1/2;
[ 0, 22] * 789 Min missings 2 Reference strand excluded
[ 23, 69] * 48 Min missings 0
Trying to merge window 0 (789) with 1 (48)
Merged[ 0, 22] * 789 with [ 23, 69] * 48 --> 37 Min missings 2
Merged windows:
[ 0, 69] * 37 Min missings 2 Reference strand excluded
*************** Now have 38 completed mappings ***************
Fix 9 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; 9-9 0/2; -1-8 1/2;
[ 0, 22] * 1682 Min missings 2 Reference strand excluded
[ 23, 69] * 48 Min missings 0
Trying to merge window 0 (1682) with 1 (48)
Merged[ 0, 22] * 1682 with [ 23, 69] * 48 --> 92 Min missings 2
Merged windows:
[ 0, 69] * 92 Min missings 2 Reference strand excluded
*************** Now have 38 completed mappings ***************
Fix 8 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; 4-4 0/2; -1-9 1/2;
[ 0, 22] * 1164 Min missings 2 Reference strand excluded
[ 23, 69] * 55 Min missings 0
Trying to merge window 0 (1164) with 1 (55)
Merged[ 0, 22] * 1164 with [ 23, 69] * 55 --> 41 Min missings 2
Merged windows:
[ 0, 69] * 41 Min missings 2 Reference strand excluded
*************** Now have 38 completed mappings ***************
Fix 7 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; 5-5 0/2; -1-4 1/2;
[ 0, 22] * 1632 Min missings 2 Reference strand excluded
[ 23, 69] * 60 Min missings 0
Trying to merge window 0 (1632) with 1 (60)
Merged[ 0, 22] * 1632 with [ 23, 69] * 60 --> 105 Min missings 2
Merged windows:
[ 0, 69] * 105 Min missings 2 Reference strand excluded
*************** Now have 40 completed mappings ***************
Fix 6 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; 6-6 0/2; -1-5 1/2;
[ 0, 22] * 3200 Min missings 2 Reference strand excluded
[ 23, 69] * 60 Min missings 0
Trying to merge window 0 (3200) with 1 (60)
Merged[ 0, 22] * 3200 with [ 23, 69] * 60 --> 102 Min missings 2
Merged windows:
[ 0, 69] * 102 Min missings 2 Reference strand excluded
*************** Now have 44 completed mappings ***************
Fix 5 positions.
Fix 64-64 0/2; 63-63 0/2; 62-62 0/2; -1-2 2/3; -1-6 1/2;
[ 0, 22] * 2782 Min missings 2 Reference strand excluded
[ 23, 69] * 60 Min missings 0
Trying to merge window 0 (2782) with 1 (60)
Merged[ 0, 22] * 2782 with [ 23, 69] * 60 --> 57 Min missings 2
Merged windows:
[ 0, 69] * 57 Min missings 2 Reference strand excluded
*************** Now have 44 completed mappings ***************
Fix 3 positions.
Fix 64-64 0/2; 63-63 0/2; -1-62 1/2;
[ 0, 22] * 3763 Min missings 0 Reference strand excluded
[ 23, 30] * 8211 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 325 Min missings 1 Reference strand excluded
Trying to merge window 2 (1467) with 3 (325)
Merged[ 31, 40] * 1467 with [ 41, 69] * 325 --> 1610 Min missings 1
Trying to merge window 1 (8211) with 3 (1610)
Merged[ 23, 30] * 8211 with [ 31, 69] * 1610 --> 5804 Min missings 1
Trying to merge window 0 (3763) with 3 (5804)
Merged[ 0, 22] * 3763 with [ 23, 69] * 5804 --> 38 Min missings 2
Merged windows:
[ 0, 69] * 38 Min missings 2 Reference strand excluded
*************** Now have 44 completed mappings ***************
Fix 2 positions.
Fix 64-64 0/2; -1-63 1/2;
[ 0, 22] * 3763 Min missings 0 Reference strand excluded
[ 23, 30] * 8211 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 2427 Min missings 1 Reference strand excluded
No merge.
Fix 3 positions.
Fix 64-64 0/2; -1-63 1/2; 6-6 0/2;
[ 0, 22] * 3607 Min missings 0 Reference strand excluded
[ 23, 30] * 8211 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 2427 Min missings 1 Reference strand excluded
Trying to merge window 2 (1467) with 3 (2427)
Merged[ 31, 40] * 1467 with [ 41, 69] * 2427 --> 9031 Min missings 1
Trying to merge window 0 (3607) with 1 (8211)
Merged[ 0, 22] * 3607 with [ 23, 30] * 8211 --> 37325 Min missings 0
Merged windows:
[ 0, 30] * 37325 Min missings 0 Reference strand excluded
[ 31, 69] * 9031 Min missings 1 Reference strand excluded
Fix 4 positions.
Fix 64-64 0/2; -1-63 1/2; 6-6 0/2; 57-2 0/2;
[ 0, 30] * 268 Min missings 0 Reference strand excluded
[ 31, 69] * 60 Min missings 2 Reference strand excluded
Trying to merge window 0 (268) with 1 (60)
Dead End
Fix 4 positions.
Fix 64-64 0/2; -1-63 1/2; 6-6 0/2; -1-2 1/2;
[ 0, 30] * 3922 Min missings 1 Reference strand excluded
[ 31, 69] * 59 Min missings 1 Reference strand excluded
Trying to merge window 0 (3922) with 1 (59)
Merged[ 0, 30] * 3922 with [ 31, 69] * 59 --> 37 Min missings 2
Merged windows:
[ 0, 69] * 37 Min missings 2 Reference strand excluded
*************** Now have 44 completed mappings ***************
Fix 3 positions.
Fix 64-64 0/2; -1-63 1/2; -1-6 1/2;
[ 0, 22] * 156 Min missings 1 Reference strand excluded
[ 23, 30] * 120 Min missings 0
[ 31, 40] * 7 Min missings 0
[ 41, 69] * 32 Min missings 1 Reference strand excluded
Trying to merge window 2 (7) with 3 (32)
Merged[ 31, 40] * 7 with [ 41, 69] * 32 --> 60 Min missings 1
Trying to merge window 1 (120) with 3 (60)
Merged[ 23, 30] * 120 with [ 31, 69] * 60 --> 248 Min missings 1
Trying to merge window 0 (156) with 3 (248)
Merged[ 0, 22] * 156 with [ 23, 69] * 248 --> 1 Min missings 2
Merged windows:
[ 0, 69] * 1 Min missings 2 Reference strand excluded
*************** Now have 44 completed mappings ***************
Fix 1 positions.
Fix -1-64 1/2;
[ 0, 22] * 3763 Min missings 0 Reference strand excluded
[ 23, 30] * 8211 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 2135 Min missings 1 Reference strand excluded
No merge.
Fix 2 positions.
Fix -1-64 1/2; 6-6 0/2;
[ 0, 22] * 3607 Min missings 0 Reference strand excluded
[ 23, 30] * 8211 Min missings 0
[ 31, 40] * 1467 Min missings 0
[ 41, 69] * 2104 Min missings 1 Reference strand excluded
Trying to merge window 2 (1467) with 3 (2104)
Merged[ 31, 40] * 1467 with [ 41, 69] * 2104 --> 6446 Min missings 1
Trying to merge window 0 (3607) with 1 (8211)
Merged[ 0, 22] * 3607 with [ 23, 30] * 8211 --> 36606 Min missings 0
Merged windows:
[ 0, 30] * 36606 Min missings 0 Reference strand excluded
[ 31, 69] * 6446 Min missings 1 Reference strand excluded
Fix 3 positions.
Fix -1-64 1/2; 6-6 0/2; 57-2 0/2;
[ 0, 30] * 261 Min missings 0 Reference strand excluded
[ 31, 69] * 43 Min missings 2 Reference strand excluded
Trying to merge window 0 (261) with 1 (43)
Dead End
Fix 3 positions.
Fix -1-64 1/2; 6-6 0/2; -1-2 1/2;
[ 0, 30] * 3834 Min missings 1 Reference strand excluded
[ 31, 69] * 41 Min missings 1 Reference strand excluded
Trying to merge window 0 (3834) with 1 (41)
Merged[ 0, 30] * 3834 with [ 31, 69] * 41 --> 37 Min missings 2
Merged windows:
[ 0, 69] * 37 Min missings 2 Reference strand excluded
*************** Now have 44 completed mappings ***************
Fix 2 positions.
Fix -1-64 1/2; -1-6 1/2;
[ 0, 22] * 156 Min missings 1 Reference strand excluded
[ 23, 30] * 120 Min missings 0
[ 31, 40] * 7 Min missings 0
[ 41, 69] * 18 Min missings 1 Reference strand excluded
Trying to merge window 2 (7) with 3 (18)
Merged[ 31, 40] * 7 with [ 41, 69] * 18 --> 43 Min missings 1
Trying to merge window 1 (120) with 3 (43)
Merged[ 23, 30] * 120 with [ 31, 69] * 43 --> 146 Min missings 1
Trying to merge window 0 (156) with 3 (146)
Merged[ 0, 22] * 156 with [ 23, 69] * 146 --> 1 Min missings 2
Merged windows:
[ 0, 69] * 1 Min missings 2 Reference strand excluded
*************** Now have 44 completed mappings ***************
Thread Q Cap Scans New Runs
T0* 4096 1 1 76
Total 1 1 76
Execute: 1 Time: 231.432 Rate: 0
Remote scans: 0
Remote steals: 0
MAPPINGS FOUND: SUMMARY
There are 44 solution(s).
M0 * [-1 ]
S1 * [4 5 10 11 21 34 43 50 56 1001 -1 ]
G2 * [57 -1 ]
K3 * [3 ]
M4 * [4 -1 ]
T5 * [5 -1 ]
G6 * [6 ]
I7 * [7 ]
V8 * [8 ]
K9 * [9 ]
W10 * [10 -1 ]
F11 * [11 1000 -1 ]
N12 * [12 -1 ]
A13 * [13 ]
D14 * [14 ]
K15 * [15 ]
G16 * [16 ]
F17 * [17 1000 ]
G18 * [18 1002 ]
F19 * [19 1000 1003 -1 ]
I20 * [20 1000 1001 -1 ]
T21 * [21 1001 -1 ]
P22 * [-1 ]
D23 * [23 ]
D24 * [24 1000 ]
G25 * [25 1002 ]
S26 * [26 1003 ]
K27 * [27 ]
D28 * [28 ]
V29 * [29 ]
F30 * [30 ]
V31 * [31 ]
H32 * [32 ]
F33 * [33 1000 ]
S34 * [34 -1 ]
A35 * [35 ]
I36 * [36 ]
Q37 * [37 ]
N38 * [38 ]
D39 * [39 ]
G40 * [40 ]
Y41 * [41 ]
K42 * [42 ]
S43 * [43 -1 ]
L44 * [44 ]
D45 * [45 ]
E46 * [46 ]
G47 * [47 ]
Q48 * [48 ]
K49 * [49 ]
V50 * [50 -1 ]
S51 * [51 ]
F52 * [52 ]
T53 * [53 ]
I54 * [54 ]
E55 * [55 ]
S56 * [56 -1 ]
G57 * [57 -1 ]
A58 * [58 ]
K59 * [59 ]
G60 * [60 ]
P61 * [-1 ]
A62 * [62 ]
A63 * [63 ]
G64 * [64 ]
N65 * [65 ]
V66 * [66 ]
T67 * [67 ]
S68 * [68 ]
L69 * [69 1000 ]
MAPPINGS FOUND: DETAILS
########## EXPECTED ############
Assignment: -1, -1, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 235.6930392289345
PenalizedScore: 272.6085726288935
Df: 408
Assignment: -1, 11, -1, 3, 4, 5, 6, 7, 8, 9, 10, -1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 236.40759040641652
PenalizedScore: 273.3231238063755
Df: 408
Assignment: -1, 56, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, -1, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 235.82374597969599
PenalizedScore: 272.739279379655
Df: 408
Assignment: -1, 11, -1, 3, 4, 5, 6, 7, 8, 9, 10, 1000, -1, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 235.83408923239963
PenalizedScore: 274.5085723287472
Df: 407
Assignment: -1, 10, -1, 3, 4, 5, 6, 7, 8, 9, -1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 237.1925756030026
PenalizedScore: 274.1081090029616
Df: 408
Assignment: -1, 5, -1, 3, 4, -1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 238.98530899651306
PenalizedScore: 275.90084239647206
Df: 408
Assignment: -1, -1, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1003, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 234.6833668104694
PenalizedScore: 275.0859382228676
Df: 406
Assignment: -1, 1001, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1003, -1, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 240.26443767341894
PenalizedScore: 277.17997107337794
Df: 408
Assignment: -1, 10, -1, 3, 4, 5, 6, 7, 8, 9, -1, 11, 12, 13, 14, 15, 16, 17, 18, 1003, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 236.1829031845375
PenalizedScore: 276.5854745969357
Df: 406
Assignment: -1, 11, -1, 3, 4, 5, 6, 7, 8, 9, 10, -1, 12, 13, 14, 15, 16, 17, 18, 1003, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 235.39791798795144
PenalizedScore: 275.8004894003496
Df: 406
Assignment: -1, 56, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1003, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, -1, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 234.81407356123088
PenalizedScore: 275.21664497362906
Df: 406
Assignment: -1, -1, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 1002, 1003, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 234.43781735360236
PenalizedScore: 278.2174264517027
Df: 404
Assignment: -1, 56, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, -1, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 1000
Score: 235.78149485536525
PenalizedScore: 277.88481065327784
Df: 405
Assignment: -1, -1, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 1000
Score: 235.65078810460372
PenalizedScore: 277.7541039025163
Df: 405
Assignment: -1, 43, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, -1, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 241.67093091019868
PenalizedScore: 278.5864643101577
Df: 408
Assignment: -1, 5, -1, 3, 4, -1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1003, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 237.97563657804795
PenalizedScore: 278.3782079904461
Df: 406
Assignment: -1, 10, -1, 3, 4, 5, 6, 7, 8, 9, -1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 1002, 1003, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 235.93735372767046
PenalizedScore: 279.7169628257708
Df: 404
Assignment: -1, 11, -1, 3, 4, 5, 6, 7, 8, 9, 10, -1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 1002, 1003, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 235.15236853108436
PenalizedScore: 278.9319776291847
Df: 404
Assignment: -1, 56, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 1002, 1003, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, -1, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 234.56852410436383
PenalizedScore: 278.34813320246417
Df: 404
Assignment: -1, 1001, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 252.56763633771217
PenalizedScore: 280.02118547545103
Df: 413
Assignment: -1, 11, -1, 3, 4, 5, 6, 7, 8, 9, 10, 1000, -1, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 1002, 1003, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 234.57886735706748
PenalizedScore: 280.01273238099856
Df: 403
Assignment: -1, 10, -1, 3, 4, 5, 6, 7, 8, 9, -1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 1000
Score: 237.15032447867182
PenalizedScore: 279.2536402765844
Df: 405
Assignment: -1, 11, -1, 3, 4, 5, 6, 7, 8, 9, 10, -1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 1000
Score: 236.36533928208578
PenalizedScore: 278.46865507999837
Df: 405
Assignment: -1, 4, -1, 3, -1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 241.99550344321537
PenalizedScore: 278.9110368431744
Df: 408
Assignment: -1, -1, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 238.29117813364954
PenalizedScore: 280.3944939315621
Df: 405
Assignment: -1, 5, -1, 3, 4, -1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 1002, 1003, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 237.7300871211809
PenalizedScore: 281.50969621928124
Df: 404
Assignment: -1, 34, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 1000, -1, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 239.7022845601581
PenalizedScore: 281.8056003580707
Df: 405
Assignment: -1, 1001, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, -1, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 246.25157855715852
PenalizedScore: 281.37295051412855
Df: 409
Assignment: -1, 5, -1, 3, 4, -1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 1000
Score: 238.94305787218227
PenalizedScore: 281.04637367009485
Df: 405
Assignment: -1, -1, 57, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, -1, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 243.2121001547796
PenalizedScore: 280.1276335547386
Df: 408
Assignment: -1, 56, 57, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, -1, -1, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 244.69188520676394
PenalizedScore: 281.60741860672294
Df: 408
Assignment: -1, 11, -1, 3, 4, 5, 6, 7, 8, 9, 10, -1, 12, 13, 14, 15, 16, 17, 18, 19, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 239.0057293111316
PenalizedScore: 281.1090451090442
Df: 405
Assignment: -1, 34, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, -1, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 244.01479243475856
PenalizedScore: 280.93032583471756
Df: 408
Assignment: -1, 50, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, -1, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 243.9349746771692
PenalizedScore: 280.8505080771282
Df: 408
Assignment: -1, 56, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, -1, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 238.421884884411
PenalizedScore: 280.5252006823236
Df: 405
Assignment: -1, -1, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1000, 1002, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 237.90352171235654
PenalizedScore: 280.0068375102691
Df: 405
Assignment: -1, 56, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1000, 1002, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, -1, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 238.034228463118
PenalizedScore: 280.1375442610306
Df: 405
Assignment: -1, 10, -1, 3, 4, 5, 6, 7, 8, 9, -1, 11, 12, 13, 14, 15, 16, 1000, 1002, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 239.40305808642464
PenalizedScore: 281.5063738843372
Df: 405
Assignment: -1, 11, -1, 3, 4, 5, 6, 7, 8, 9, 10, -1, 12, 13, 14, 15, 16, 1000, 1002, 19, 20, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 238.61807288983857
PenalizedScore: 280.7213886877512
Df: 405
Assignment: -1, -1, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, -1, 23, 1000, 1002, 1003, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 233.09080654498624
PenalizedScore: 281.77493027185005
Df: 401
Assignment: -1, 21, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1000, 1001, -1, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 242.15646779354378
PenalizedScore: 280.83095088989137
Df: 407
Assignment: -1, 1001, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1000, -1, 21, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 241.53765836842373
PenalizedScore: 280.2121414647713
Df: 407
Assignment: -1, 4, -1, 3, -1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1003, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 240.98583102475027
PenalizedScore: 281.38840243714844
Df: 406
Assignment: -1, 43, -1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1003, 1000, 1001, -1, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, -1, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, -1, 62, 63, 64, 65, 66, 67, 68, 69
Score: 240.66125849173358
PenalizedScore: 281.06382990413175
Df: 406
Done.
344.200u 5.340s 6:46.10 86.0% 0+0k 0+17io 0pf+0w
MBA2/input/ 0040755 0000765 0000024 00000000000 10066413704 012401 5 ustar janvitek staff MBA2/input/Bmrb.java 0100644 0000765 0000024 00000261547 10065572564 014153 0 ustar janvitek staff /*
* Means and covariance matrices from the restricted bmrb
* Ref: Malliavin
* */
package input;
import util.BitSet;
import util.Util;
import Jama.Matrix;
public class Bmrb {
//------------------------------------------------------------------------------------------
//--------------------------------AMINO ACID TYPES------------------------------------------
//------------------------------------------------------------------------------------------
//----------------------------------amino acid types----------------------------------------
static public String[] aaNames1 = new String[] { "A", "R", "D", "N", "C", "E", "Q", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B" };
static public String[] aaNames3 = new String[] { "Ala", "Arg", "Asp", "Asn", "Cys", "Glu", "Gln", "Gly", "His", "Ile", "Leu", "Lys", "Met", "Phe", "Pro", "Ser", "Thr", "Trp", "Tyr", "Val", "Unk" };
//--------------------------------------dimensions------------------------------------------
static private String[] dimAla = new String[] { "H", "HA", "HB", "C", "CA", "CB", "N" };
static private String[] dimArg = new String[] { "H", "HA", "HB2", "HB3", "HG2", "HG3", "HD2", "HD3", "HE", "HH11", "HH12", "HH21", "HH22", "C", "CA", "CB", "CG", "CD", "CZ", "N", "NE", "NH1", "NH2" };
static private String[] dimAsp = new String[] { "H", "HA", "HB2", "HB3", "C", "CA", "CB", "CG", "N" };
static private String[] dimAsn = new String[] { "H", "HA", "HB2", "HB3", "HD21", "HD22", "C", "CA", "CB", "CG", "N", "ND2" };
static private String[] dimCys = new String[] { "H", "HA", "HB2", "HB3", "HG", "C", "CA", "CB", "N" };
static private String[] dimGlu = new String[] { "H", "HA", "HB2", "HB3", "HG2", "HG3", "C", "CA", "CB", "CG", "CD", "N" };
static private String[] dimGln = new String[] { "H", "HA", "HB2", "HB3", "HG2", "HG3", "HE21", "HE22", "C", "CA", "CB", "CG", "CD", "N", "NE2" };
static private String[] dimGly = new String[] { "H", "HA", "HA2", "C", "CA", "N" };
static private String[] dimHis = new String[] { "H", "HA", "HB2", "HB3", "HD1", "HD2", "HE1", "HE2", "C", "CA", "CB", "CG", "CD2", "CE1", "N", "ND1", "NE2" };
static private String[] dimIle = new String[] { "H", "HA", "HB", "HG12", "HG13", "HG2", "HD1", "C", "CA", "CB", "CG1", "CG2", "CD1", "N" };
static private String[] dimLeu = new String[] { "H", "HA", "HB2", "HB3", "HG", "HD1", "HD2", "C", "CA", "CB", "CG", "CD1", "CD2", "N" };
static private String[] dimLys = new String[] { "H", "HA", "HB2", "HB3", "HG2", "HG3", "HD2", "HD3", "HE2", "HE3", "HZ", "C", "CA", "CB", "CG", "CD", "CE", "N", "NZ" };
static private String[] dimMet = new String[] { "H", "HA", "HB2", "HB3", "HG2", "HG3", "HE", "C", "CA", "CB", "CG", "CE", "N" };
static private String[] dimPhe = new String[] { "H", "HA", "HB2", "HB3", "HD1", "HD2", "HE1", "HE2", "HZ", "C", "CA", "CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "N" };
static private String[] dimPro = new String[] { "HA", "HB2", "HB3", "HG2", "HG3", "HD2", "HD3", "C", "CA", "CB", "CG", "CD", "N" };
static private String[] dimSer = new String[] { "H", "HA", "HB2", "HB3", "HG", "C", "CA", "CB", "N" };
static private String[] dimThr = new String[] { "H", "HA", "HB", "HG1", "HG2", "C", "CA", "CB", "CG2", "N" };
static private String[] dimTrp = new String[] { "H", "HA", "HB2", "HB3", "HD1", "HE1", "HE3", "HZ2", "HZ3", "HH2", "C", "CA", "CB", "CG", "CD1", "CD2", "CE2", "CE3", "CZ2", "CZ3", "CH2", "N", "NE1" };
static private String[] dimTyr = new String[] { "H", "HA", "HB2", "HB3", "HD1", "HD2", "HE1", "HE2", "HH", "C", "CA", "CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "N" };
static private String[] dimVal = new String[] { "H", "HA", "HB", "HG1", "HG2", "C", "CA", "CB", "CG1", "CG2", "N" };
static private String[] dimUnk = new String[] { "H", "HA", "C", "CA", "CB", "N" };
public static String[][] dim = new String[][] { dimAla, dimArg, dimAsp, dimAsn, dimCys, dimGlu, dimGln, dimGly, dimHis, dimIle, dimLeu, dimLys, dimMet, dimPhe, dimPro, dimSer, dimThr, dimTrp, dimTyr, dimVal, dimUnk };
//------------------------------------------------------------------------------------------------
//-----------------------------------------MEANS--------------------------------------------------
//------------------------------------------------------------------------------------------------
//------------------------------------malliavin means---------------------------------------------
static private Matrix malMeanAla = new Matrix(new double[] { 8.194, 4.2694, 1.3582, 177.7117, 53.1099, 19.0253, 123.2269 }, dimAla.length);
static private Matrix malMeanArg = new Matrix(new double[] { 8.246, 4.2914, 1.8033, 1.7668, 1.5879, 1.5549, 3.1216, 3.109, 7.3358, 6.7996, 6.7771, 6.7286, 6.7666, 176.5078, 56.8464, 30.6366, 27.3036, 43.1232, 159.1613, 120.714, 90.7652, 72.9152, 75.2665 }, dimArg.length);
static private Matrix malMeanAsp = new Matrix(new double[] { 8.3192, 4.5997, 2.7407, 2.6693, 176.427, 54.6836, 40.8949, 179.0951, 120.7556 }, dimAsp.length);
static private Matrix malMeanAsn = new Matrix(new double[] { 8.3745, 4.675, 2.8236, 2.7584, 7.3529, 7.1707, 175.319, 53.4842, 38.6704, 176.4267, 119.1223, 112.6939 }, dimAsn.length);
static private Matrix malMeanCys = new Matrix(new double[] { 8.4047, 4.6922, 2.9717, 2.9351, 1.9777, 174.9524, 57.7606, 33.8233, 120.1659 }, dimCys.length);
static private Matrix malMeanGlu = new Matrix(new double[] { 8.3681, 4.26, 2.0325, 2.0079, 2.2944, 2.2687, 176.8991, 57.3652, 29.9897, 35.9824, 182.0436, 120.6137 }, dimGlu.length);
static private Matrix malMeanGln = new Matrix(new double[] { 8.2306, 4.291, 2.057, 2.0166, 2.324, 2.3115, 7.1979, 7.0618, 176.4376, 56.5968, 29.1875, 33.8189, 179.5307, 119.907, 111.7725 }, dimGln.length);
static private Matrix malMeanGly = new Matrix(new double[] { 8.3144, 3.9781, 3.8907, 174.0644, 45.3565, 109.6352 }, dimGly.length);
static private Matrix malMeanHis = new Matrix(new double[] { 8.2582, 4.5987, 3.1314, 3.0623, 8.7188, 6.9379, 7.8215, 9.9298, 175.2926, 56.5356, 30.2568, 132.5345, 119.7836, 136.742, 119.4047, 178.1194, 173.5946 }, dimHis.length);
static private Matrix malMeanIle = new Matrix(new double[] { 8.2741, 4.194, 1.7913, 1.3073, 1.2136, 0.7894, 0.7018, 175.8349, 61.5753, 38.6809, 27.7243, 17.5928, 13.714, 121.5939 }, dimIle.length);
static private Matrix malMeanLeu = new Matrix(new double[] { 8.214, 4.3255, 1.6508, 1.5469, 1.5236, 0.7668, 0.7465, 176.9595, 55.599, 42.2581, 26.7022, 24.6443, 24.0965, 121.9072 }, dimLeu.length);
static private Matrix malMeanLys = new Matrix(new double[] { 8.1902, 4.2699, 1.7852, 1.7506, 1.3762, 1.3497, 1.6574, 1.6038, 2.9295, 2.9217, 7.5173, 176.5782, 56.881, 32.7689, 24.9267, 28.8329, 41.805, 120.9421, 43.1993 }, dimLys.length);
static private Matrix malMeanMet = new Matrix(new double[] { 8.2328, 4.3983, 2.0351, 2.0107, 2.4339, 2.4004, 1.873, 176.1329, 56.0923, 33.1121, 31.8934, 17.3504, 120.0479 }, dimMet.length);
static private Matrix malMeanPhe = new Matrix(new double[] { 8.3321, 4.6486, 2.9994, 2.9485, 7.0464, 7.0537, 7.0591, 7.0656, 7.0132, 175.4665, 57.9954, 39.9316, 138.5379, 131.4885, 131.4676, 130.4128, 130.3269, 129.0796, 120.5105 }, dimPhe.length);
static private Matrix malMeanPro = new Matrix(new double[] { 4.4, 2.07, 2.03, 1.94, 1.92, 3.64, 3.62, 176.78, 63.25, 31.74, 27.2, 50.3, 130.78 }, dimPro.length);
static private Matrix malMeanSer = new Matrix(new double[] { 8.29, 4.5, 3.88, 3.86, 5.36, 174.62, 58.6, 63.79, 116.25 }, dimSer.length);
static private Matrix malMeanThr = new Matrix(new double[] { 8.26, 4.47, 4.17, 4.77, 1.15, 174.55, 62.12, 69.59, 21.45, 115.59 }, dimThr.length);
static private Matrix malMeanTrp = new Matrix(new double[] { 8.31, 4.7, 3.21, 3.17, 7.16, 10.11, 7.24, 7.2, 6.76, 6.9, 176.18, 57.67, 30, 110.21, 126.37, 127.46, 137.67, 120.45, 114.14, 121.37, 123.57, 121.63, 129.5 }, dimTrp.length);
static private Matrix malMeanTyr = new Matrix(new double[] { 8.35, 4.63, 2.91, 2.88, 6.9, 6.9, 6.68, 6.67, 9.04, 175.41, 58.08, 39.26, 128.67, 132.59, 132.46, 117.79, 117.86, 156.44, 120.8 }, dimTyr.length);
static private Matrix malMeanVal = new Matrix(new double[] { 8.29, 4.17, 1.99, 0.84, 0.82, 175.74, 62.49, 32.6, 21.43, 21.31, 121.1 }, dimVal.length);
static private Matrix malMeanUnk = new Matrix(new double[] { 5, 5, 100, 100, 100, 100 }, dimUnk.length);
public static Matrix[] malMean = new Matrix[] { malMeanAla, malMeanArg, malMeanAsp, malMeanAsn, malMeanCys, malMeanGlu, malMeanGln, malMeanGly, malMeanHis, malMeanIle, malMeanLeu, malMeanLys, malMeanMet, malMeanPhe, malMeanPro, malMeanSer, malMeanThr, malMeanTrp, malMeanTyr, malMeanVal, malMeanUnk };
//-------------------------------------bmrb means---------------------------------------------
static private Matrix bmrbMeanAla = new Matrix(new double[] { 8.19, 4.26, 1.37, 177.84, 53.17, 18.89, 123.18 }, dimAla.length);
static private Matrix bmrbMeanArg = new Matrix(new double[] { 8.24, 4.29, 1.8, 1.78, 1.58, 1.57, 3.13, 3.12, 7.34, 6.79, 6.76, 6.78, 6.76, 176.51, 56.84, 30.57, 27.27, 43.13, 159.16, 120.7, 92.62, 73.44, 73.98 }, dimArg.length);
static private Matrix bmrbMeanAsp = new Matrix(new double[] { 8.33, 4.61, 2.74, 2.69, 176.45, 54.6, 40.79, 179.22, 120.77 }, dimAsp.length);
static private Matrix bmrbMeanAsn = new Matrix(new double[] { 8.36, 4.68, 2.81, 2.78, 7.32, 7.17, 175.34, 53.49, 38.61, 176.8, 119.08, 112.87 }, dimAsn.length);
static private Matrix bmrbMeanCys = new Matrix(new double[] { 8.42, 4.71, 2.96, 2.94, 3.32, 174.75, 57.55, 34.13, 119.89 }, dimCys.length);
static private Matrix bmrbMeanGlu = new Matrix(new double[] { 8.34, 4.25, 2.04, 2.03, 2.3, 2.29, 177.02, 57.44, 29.99, 36.04, 182.38, 120.71 }, dimGlu.length);
static private Matrix bmrbMeanGln = new Matrix(new double[] { 8.22, 4.28, 2.04, 2.03, 2.32, 2.31, 7.19, 7.05, 176.39, 56.56, 29.14, 33.71, 179.75, 119.87, 111.86 }, dimGln.length);
static private Matrix bmrbMeanGly = new Matrix(new double[] { 8.33, 3.95, 3.92, 173.97, 45.34, 109.7 }, dimGly.length);
static private Matrix bmrbMeanHis = new Matrix(new double[] { 8.25, 4.63, 3.1, 3.08, 9.15, 7.07, 8.04, 10.12, 175.24, 56.47, 30.18, 130.85, 119.57, 136.75, 119.41, 193.4, 175.14 }, dimHis.length);
static private Matrix bmrbMeanIle = new Matrix(new double[] { 8.28, 4.19, 1.8, 1.29, 1.23, 0.8, 0.7, 175.91, 61.58, 38.53, 27.63, 17.49, 13.43, 121.57 }, dimIle.length);
static private Matrix bmrbMeanLeu = new Matrix(new double[] { 8.22, 4.32, 1.63, 1.56, 1.52, 0.77, 0.75, 176.98, 55.62, 42.23, 26.69, 24.59, 24.11, 121.8 }, dimLeu.length);
static private Matrix bmrbMeanLys = new Matrix(new double[] { 8.21, 4.27, 1.78, 1.76, 1.38, 1.36, 1.61, 1.6, 2.92, 2.92, 7.51, 176.68, 56.9, 32.72, 24.88, 28.86, 41.82, 121.05, 73.82 }, dimLys.length);
static private Matrix bmrbMeanMet = new Matrix(new double[] { 8.25, 4.38, 2.04, 2.01, 2.44, 2.41, 1.88, 176.36, 56.22, 32.96, 32.08, 17.24, 120.01 }, dimMet.length);
static private Matrix bmrbMeanPhe = new Matrix(new double[] { 8.39, 4.61, 3, 2.97, 6.99, 6.98, 7.02, 7.01, 6.96, 175.56, 58.23, 39.88, 137.04, 131.39, 131.4, 130.49, 130.63, 129.09, 120.67 }, dimPhe.length);
static private Matrix bmrbMeanPro = new Matrix(new double[] { 4.3968, 2.093, 2.0034, 1.9548, 1.9211, 3.6541, 3.6011, 176.7048, 63.2741, 31.8309, 27.164, 50.257, 131.1711 }, dimPro.length);
static private Matrix bmrbMeanSer = new Matrix(new double[] { 8.2679, 4.5013, 3.8746, 3.8466, 5.5337, 174.6235, 58.6299, 63.8086, 116.1614 }, dimSer.length);
static private Matrix bmrbMeanThr = new Matrix(new double[] { 8.2432, 4.4761, 4.1629, 4.8792, 1.1484, 174.5491, 62.1207, 69.5832, 21.5071, 115.5305 }, dimThr.length);
static private Matrix bmrbMeanTrp = new Matrix(new double[] { 8.2999, 4.733, 3.2244, 3.1473, 7.1502, 10.0729, 7.366, 7.297, 6.9006, 6.9868, 176.2158, 57.7335, 29.911, 110.7864, 126.4757, 126.4587, 136.1602, 120.4665, 114.1167, 120.8216, 123.4696, 121.727, 128.9081 }, dimTrp.length);
static private Matrix bmrbMeanTyr = new Matrix(new double[] { 8.3149, 4.6323, 2.915, 2.855, 6.9393, 6.9363, 6.7188, 6.7165, 9.2689, 175.4491, 58.0655, 39.2919, 128.6176, 132.2411, 132.1788, 117.9382, 118.0229, 154.3759, 120.7748 }, dimTyr.length);
static private Matrix bmrbMeanVal = new Matrix(new double[] { 8.2762, 4.1864, 1.9955, 0.8508, 0.8222, 175.6898, 62.3866, 32.682, 21.5301, 21.2539, 121.1766 }, dimVal.length);
//static private Matrix bmrbMeanUnk = new Matrix(new double[] { 5, 5, 100, 100, 100, 100 }, dimUnk.length);
public static Matrix[] bmrbMean = new Matrix[] { bmrbMeanAla, bmrbMeanArg, bmrbMeanAsp, bmrbMeanAsn, bmrbMeanCys, bmrbMeanGlu, bmrbMeanGln, bmrbMeanGly, bmrbMeanHis, bmrbMeanIle, bmrbMeanLeu, bmrbMeanLys, bmrbMeanMet, bmrbMeanPhe, bmrbMeanPro, bmrbMeanSer, bmrbMeanThr, bmrbMeanTrp, bmrbMeanTyr, bmrbMeanVal, malMeanUnk };
//-------------------------------------refdb means---------------------------------------------
static private Matrix refdbMeanAla = new Matrix(new double[] { 8.2, 4.29, Double.NaN, 178.16, 53.44, 19.22, 122.83 }, dimAla.length);
static private Matrix refdbMeanArg = new Matrix(new double[] { 8.26, 4.29, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 176.79, 57.11, 30.83, Double.NaN, Double.NaN, Double.NaN, 120.35, Double.NaN, Double.NaN, Double.NaN }, dimArg.length);
static private Matrix refdbMeanAsp = new Matrix(new double[] { 8.33, 4.62, Double.NaN, Double.NaN, 176.69, 54.9, 41.03, Double.NaN, 120.22 }, dimAsp.length);
static private Matrix refdbMeanAsn = new Matrix(new double[] { 8.4, 4.71, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 175.47, 53.69, 38.93, Double.NaN, 118.83, Double.NaN }, dimAsn.length);
static private Matrix refdbMeanCys = new Matrix(new double[] { 8.49, 4.79, Double.NaN, Double.NaN, Double.NaN, 174.76, 57.7, 34.65, 119.16 }, dimCys.length);
static private Matrix refdbMeanGlu = new Matrix(new double[] { 8.34, 4.28, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 177.25, 57.66, 30.19, Double.NaN, Double.NaN, 120.23 }, dimGlu.length);
static private Matrix refdbMeanGln = new Matrix(new double[] { 8.22, 4.3, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 176.58, 56.77, 29.39, Double.NaN, Double.NaN, 119.54, Double.NaN }, dimGln.length);
static private Matrix refdbMeanGly = new Matrix(new double[] { 8.33, 3.98, 3.98, 173.97, 45.63, Double.NaN }, dimGly.length);
static private Matrix refdbMeanHis = new Matrix(new double[] { 8.3, 4.64, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 175.34, 56.65, 30.29, Double.NaN, Double.NaN, Double.NaN, 119.09, Double.NaN, Double.NaN }, dimHis.length);
static private Matrix refdbMeanIle = new Matrix(new double[] { 8.3, 4.23, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 176.05, 61.89, 38.81, Double.NaN, Double.NaN, Double.NaN, 121.37 }, dimIle.length);
static private Matrix refdbMeanLeu = new Matrix(new double[] { 8.24, 4.37, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 177.26, 55.78, 42.52, Double.NaN, Double.NaN, Double.NaN, 121.55 }, dimLeu.length);
static private Matrix refdbMeanLys = new Matrix(new double[] { 8.21, 4.29, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 176.85, 57.12, 33.09, Double.NaN, Double.NaN, Double.NaN, 120.52, Double.NaN }, dimLys.length);
static private Matrix refdbMeanMet = new Matrix(new double[] { 8.27, 4.4, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 176.67, 56.58, 33.25, Double.NaN, Double.NaN, 119.48 }, dimMet.length);
static private Matrix refdbMeanPhe = new Matrix(new double[] { 8.42, 4.67, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 175.65, 58.43, 40.08, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 120.12 }, dimPhe.length);
static private Matrix refdbMeanPro = new Matrix(new double[] { 4.4, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 177.01, 63.61, 31.94, Double.NaN, Double.NaN, Double.NaN }, dimPro.length);
static private Matrix refdbMeanSer = new Matrix(new double[] { 8.29, 4.56, Double.NaN, Double.NaN, Double.NaN, 174.65, 58.74, 64.15, 115.89 }, dimSer.length);
static private Matrix refdbMeanThr = new Matrix(new double[] { 8.28, 4.53, Double.NaN, Double.NaN, Double.NaN, 174.62, 62.31, 70.07, Double.NaN, 114.94 }, dimThr.length);
static private Matrix refdbMeanTrp = new Matrix(new double[] { 8.28, 4.79, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 176.6, 58.05, 30.23, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 120.9, Double.NaN }, dimTrp.length);
static private Matrix refdbMeanTyr = new Matrix(new double[] { 8.37, 4.7, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 175.54, 58.21, 39.71, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 120.36 }, dimTyr.length);
static private Matrix refdbMeanVal = new Matrix(new double[] { 8.31, 4.2, Double.NaN, Double.NaN, Double.NaN, 175.91, 62.82, 32.87, Double.NaN, Double.NaN, 120.62 }, dimVal.length);
//static private Matrix refdbMeanUnk = new Matrix(new double[] { 5, 5, 100, 100, 100, 100 }, dimUnk.length);
public static Matrix[] refdbMean = new Matrix[] { refdbMeanAla, refdbMeanArg, refdbMeanAsp, refdbMeanAsn, refdbMeanCys, refdbMeanGlu, refdbMeanGln, refdbMeanGly, refdbMeanHis, refdbMeanIle, refdbMeanLeu, refdbMeanLys, refdbMeanMet, refdbMeanPhe, refdbMeanPro, refdbMeanSer, refdbMeanThr, refdbMeanTrp, refdbMeanTyr, refdbMeanVal, malMeanUnk };
//------------------------------------------------------------------------------------------------
//---------------------------------------VARIANCES------------------------------------------------
//------------------------------------------------------------------------------------------------
//-----------------------------------malliavin variances------------------------------------------
static private Matrix malVarAla = new Matrix(new double[][] {
//H,HA,HB,C,CA,CB,N
{ 0.388893157,0.066753641,0.010302246,-0.138129771,-0.103758693,0.201784223,0.910506964 },
{ 0.066753641,0.201181904,0.015240384,-0.410387933,-0.545394898,0.518817782,0.354123414 },
{ 0.010302246,0.015240384,0.076845922,0.148634031,0.159432262,-0.03066792,-0.071097814 },
{ -0.138129771,-0.410387933,0.148634031,10.41564941,2.355870247,-1.571960092,-1.539009452 },
{ -0.103758693,-0.545394898,0.159432262,2.355870247,4.022233009,-1.555367827,-1.771723867 },
{ 0.201784223,0.518817782,-0.03066792,-1.571960092,-1.555367827,4.426242352,0.985119462 },
{ 0.910506964,0.354123414,-0.071097814,-1.539009452,-1.771723867,0.985119462,17.54739189 }
});
static private Matrix malVarArg = new Matrix(new double[][] {
//H,HA,HB2,HB3,HG2,HG3,HD2,HD3,HE,HH11,HH12,HH21,HH22,C,CA,CB,CG,CD,CZ,N,NE,NH1,NH2
{ 0.379979909,0.051817566,0.000958621,0.012327435,0.003826897,0.009430617,0.009558307,0.009310055,0.014222514,0.020849505,0.021879235,0.01754947,0.019110261,-0.126444355,-0.05765,0.175971821,0.118065149,-0.01375687,-0.244349822,1.066172004,0.50870347,-0.051735725,0.458440602 },
{ 0.051817566,0.214918256,0.001440523,-0.001226812,0.012165285,0.0084738,0.009135448,0.005618382,0.016726105,0.000140013,-0.000668956,-0.014071219,-0.005295761,-0.389707029,-0.712622643,0.451718301,-0.068087183,-0.001262049,-0.05263776,0.319080055,0.529541194,0.117559843,-0.7924878 },
{ 0.000958621,0.001440523,0.081140414,0.057067953,0.041980177,0.038436018,0.033406444,0.028489599,0.020000504,-0.00534679,-0.003740857,-0.001686329,-0.004859534,0.150960445,0.165514246,-0.069765255,0.037114497,0.023786008,0.059674684,-0.185843945,-0.284457088,-0.133802325,0.270157009 },
{ 0.012327435,-0.001226812,0.057067953,0.089523427,0.038244858,0.045193575,0.030828707,0.039626773,0.019319404,-0.014516214,-0.016633472,-0.00222552,-0.009524342,0.185488984,0.221467808,-0.089470007,0.068574578,0.020054258,0.094535239,-0.153717741,-0.113850504,-0.355702728,0.471149772 },
{ 0.003826897,0.012165285,0.041980177,0.038244858,0.072888032,0.056042854,0.039835174,0.035786264,0.019818299,0.016875813,0.013280939,0.022495661,0.021750487,0.122781508,0.124689207,-0.025540886,0.064726226,0.032310519,0.015641492,-0.091805711,-0.125375003,0.240932435,-1.642984986 },
{ 0.009430617,0.0084738,0.038436018,0.045193575,0.056042854,0.082825147,0.03865562,0.044331558,0.022940394,0.018059189,0.016410871,0.008481729,0.01107843,0.11799103,0.14340727,-0.04882161,0.073529765,0.027995093,0.06491866,-0.081127666,-0.156307235,0.167049721,0.66926837 },
{ 0.009558307,0.009135448,0.033406444,0.030828707,0.039835174,0.03865562,0.080115885,0.065564327,0.053123847,-0.005537785,-0.011958919,0.008952266,-0.001166542,0.061086562,0.059675604,-0.036777243,0.022850126,0.037708476,0.036099996,-0.014247335,0.216743559,-0.296014637,-0.006254569 },
{ 0.009310055,0.005618382,0.028489599,0.039626773,0.035786264,0.044331558,0.065564327,0.082091272,0.04330226,0.015703678,0.011613175,0.020304499,0.020536665,0.072025225,0.087418191,-0.057420138,0.026637178,0.052082118,0.046918664,-0.023806825,0.110268287,0.064397387,-1.132968307 },
{ 0.014222514,0.016726105,0.020000504,0.019319404,0.019818299,0.022940394,0.053123847,0.04330226,0.521420538,-0.025009245,-0.030597115,0.02166334,-0.012888725,-0.105928764,-0.08433573,0.151291505,0.030580152,0.082117692,0.216478109,0.052466869,-0.143638507,-0.697642207,-0.274001658 },
{ 0.020849505,0.000140013,-0.00534679,-0.014516214,0.016875813,0.018059189,-0.005537785,0.015703678,-0.025009245,0.240078732,0.242857829,0.153420851,0.226436287,0.042238608,-0.504824817,0.32984966,-0.355910003,-0.105241314,0,0.125768706,-1.971115232,2.919858694,-0.676888764 },
{ 0.021879235,-0.000668956,-0.003740857,-0.016633472,0.013280939,0.016410871,-0.011958919,0.011613175,-0.030597115,0.242857829,0.244806096,0.150188327,0.224744588,-0.080114104,-0.745274425,1.144865632,-0.410706788,0.184495956,0,0.143786475,-3.575856686,3.028257132,-0.682150304 },
{ 0.01754947,-0.014071219,-0.001686329,-0.00222552,0.022495661,0.008481729,0.008952266,0.020304499,0.02166334,0.153420851,0.150188327,0.160554126,0.178316996,-0.078606196,0.188984141,0.03674103,-0.284289748,0.092434675,0,-0.246194348,-1.367176771,1.047047734,-0.080515936 },
{ 0.019110261,-0.005295761,-0.004859534,-0.009524342,0.021750487,0.01107843,-0.001166542,0.020536665,-0.012888725,0.226436287,0.224744588,0.178316996,0.234199897,-0.090350583,-0.18473354,0.539184451,-0.269837111,0.14623706,0,-0.003499071,-2.773162127,2.620878935,-0.418439329 },
{ -0.126444355,-0.389707029,0.150960445,0.185488984,0.122781508,0.11799103,0.061086562,0.072025225,-0.105928764,0.042238608,-0.080114104,-0.078606196,-0.090350583,4.177666187,3.248889446,-1.152763248,0.36692366,0.084675223,0.697700143,-1.656728745,-1.450802088,0.230884522,6.362699509 },
{ -0.05765,-0.712622643,0.165514246,0.221467808,0.124689207,0.14340727,0.059675604,0.087418191,-0.08433573,-0.504824817,-0.745274425,0.188984141,-0.18473354,3.248889446,6.237079144,-1.459036231,1.070277691,0.525550842,0.506015897,-1.816591024,-0.621117353,-2.492296696,9.299624443 },
{ 0.175971821,0.451718301,-0.069765255,-0.089470007,-0.025540886,-0.04882161,-0.036777243,-0.057420138,0.151291505,0.32984966,1.144865632,0.03674103,0.539184451,-1.152763248,-1.459036231,3.521093845,0.212346211,0.416589141,-0.042601351,0.938016355,0.676394403,2.852878332,-1.122067809 },
{ 0.118065149,-0.068087183,0.037114497,0.068574578,0.064726226,0.073529765,0.022850126,0.026637178,0.030580152,-0.355910003,-0.410706788,-0.284289748,-0.269837111,0.36692366,1.070277691,0.212346211,3.723428011,0.489250869,0.311872095,-0.350748599,2.03805089,-1.131906629,-0.553189993 },
{ -0.01375687,-0.001262049,0.023786008,0.020054258,0.032310519,0.027995093,0.037708476,0.052082118,0.082117692,-0.105241314,0.184495956,0.092434675,0.14623706,0.084675223,0.525550842,0.416589141,0.489250869,1.264561892,0.163033471,-0.280709267,1.592207193,0.323189199,-0.002051254 },
{ -0.244349822,-0.05263776,0.059674684,0.094535239,0.015641492,0.06491866,0.036099996,0.046918664,0.216478109,0,0,0,0,0.697700143,0.506015897,-0.042601351,0.311872095,0.163033471,0.793557227,-1.356283903,0.160462171,-0.003500313,-0.04239982 },
{ 1.066172004,0.319080055,-0.185843945,-0.153717741,-0.091805711,-0.081127666,-0.014247335,-0.023806825,0.052466869,0.125768706,0.143786475,-0.246194348,-0.003499071,-1.656728745,-1.816591024,0.938016355,-0.350748599,-0.280709267,-1.356283903,17.18375206,3.762029886,-0.513838828,-0.559501708 },
{ 0.50870347,0.529541194,-0.284457088,-0.113850504,-0.125375003,-0.156307235,0.216743559,0.110268287,-0.143638507,-1.971115232,-3.575856686,-1.367176771,-2.773162127,-1.450802088,-0.621117353,0.676394403,2.03805089,1.592207193,0.160462171,3.762029886,191.2032318,-9.767277718,2.35022974 },
{ -0.051735725,0.117559843,-0.133802325,-0.355702728,0.240932435,0.167049721,-0.296014637,0.064397387,-0.697642207,2.919858694,3.028257132,1.047047734,2.620878935,0.230884522,-2.492296696,2.852878332,-1.131906629,0.323189199,-0.003500313,-0.513838828,-9.767277718,7.900000095,-1.475518107 },
{ 0.458440602,-0.7924878,0.270157009,0.471149772,-1.642984986,0.66926837,-0.006254569,-1.132968307,-0.274001658,-0.676888764,-0.682150304,-0.080515936,-0.418439329,6.362699509,9.299624443,-1.122067809,-0.553189993,-0.002051254,-0.04239982,-0.559501708,2.35022974,-1.475518107,116.4577179 }
});
static private Matrix malVarAsp = new Matrix(new double[][] {
//H,HA,HB2,HB3,C,CA,CB,CG,N
{ 0.347514451,0.009918958,0.011685844,0.00977586,0.019775732,0.077173002,-0.06688007,0.025454829,0.862218857 },
{ 0.009918958,0.103872769,0.018663958,0.009422291,-0.135963962,-0.284284771,0.208441883,-0.001664506,0.177029923 },
{ 0.011685844,0.018663958,0.078198828,0.023993485,0.011786553,0.002407215,-0.009253411,0.107153624,-0.050359514 },
{ 0.00977586,0.009422291,0.023993485,0.07743758,0.038460225,0.046944935,-0.044882055,-0.051478948,-0.032066908 },
{ 0.019775732,-0.135963962,0.011786553,0.038460225,3.102408648,1.743408203,-0.372338533,-0.152701736,-0.805108011 },
{ 0.077173002,-0.284284771,0.002407215,0.046944935,1.743408203,4.082903862,-0.541946173,0.246954501,-0.737179697 },
{ -0.06688007,0.208441883,-0.009253411,-0.044882055,-0.372338533,-0.541946173,5.876079559,0.708511949,0.887095153 },
{ 0.025454829,-0.001664506,0.107153624,-0.051478948,-0.152701736,0.246954501,0.708511949,2.270706415,0.39374435 },
{ 0.862218857,0.177029923,-0.050359514,-0.032066908,-0.805108011,-0.737179697,0.887095153,0.39374435,18.30779648 }
});
static private Matrix malVarAsn = new Matrix(new double[][] {
//H,HA,HB2,HB3,HD21,HD22,C,CA,CB,CG,N,ND2
{ 0.450923204,0.015392673,0.020287829,0.01774529,0.005217238,0.003334899,0.035737548,0.081147604,-0.077372,0.042460188,1.193587899,-0.156893075 },
{ 0.015392673,0.143643573,0.009927389,0.005660936,0.006789073,0.006418524,-0.165111452,-0.346845806,0.309844106,-0.048919752,0.252007335,0.012389151 },
{ 0.020287829,0.009927389,0.112062357,0.036604416,0.050484002,0.007363749,0.062938124,0.059189841,-0.075909011,0.032276213,-0.079282031,-0.070749261 },
{ 0.01774529,0.005660936,0.036604416,0.109299339,0.011408614,0.043230522,0.074792422,0.111169584,-0.072707571,0.015920484,-0.084229626,-0.017699372 },
{ 0.005217238,0.006789073,0.050484002,0.011408614,0.257179767,-0.054853052,0.00115192,0.037128016,-0.041304998,0.198502407,-0.08484035,0.357497633 },
{ 0.003334899,0.006418524,0.007363749,0.043230522,-0.054853052,0.253361166,0.031232841,0.049651392,0.00972622,-0.026022615,-0.048862524,0.364813387 },
{ 0.035737548,-0.165111452,0.062938124,0.074792422,0.00115192,0.031232841,3.335206032,1.661010027,-0.493608058,-0.660892546,-0.173590928,-0.514589429 },
{ 0.081147604,-0.346845806,0.059189841,0.111169584,0.037128016,0.049651392,1.661010027,3.566640377,-0.285396427,-0.124333404,-1.096744418,0.679273069 },
{ -0.077372,0.309844106,-0.075909011,-0.072707571,-0.041304998,0.00972622,-0.493608058,-0.285396427,2.772483587,-0.32532683,0.702663243,0.485689312 },
{ 0.042460188,-0.048919752,0.032276213,0.015920484,0.198502407,-0.026022615,-0.660892546,-0.124333404,-0.32532683,17.17627525,-1.309406877,0.661716104 },
{ 1.193587899,0.252007335,-0.079282031,-0.084229626,-0.08484035,-0.048862524,-0.173590928,-1.096744418,0.702663243,-1.309406877,17.92962646,0.61985445 },
{ -0.156893075,0.012389151,-0.070749261,-0.017699372,0.357497633,0.364813387,-0.514589429,0.679273069,0.485689312,0.661716104,0.61985445,19.49282265 }
});
static private Matrix malVarCys = new Matrix(new double[][] {
//H,HA,HB2,HB3,HG,C,CA,CB,N
{ 0.485996723,0.080462121,0.004246237,-0.016780363,-0.014921153,-0.144330621,-0.213110566,0.434573323,1.211585283 },
{ 0.080462121,0.333546102,0.126979798,0.113348849,-0.009434484,-0.576139212,-1.163940072,1.590186,-0.053903706 },
{ 0.004246237,0.126979798,0.610078633,0.369536281,-0.00305167,0.040264025,0.006539376,0.672870696,-0.151115254 },
{ -0.016780363,0.113348849,0.369536281,0.682826817,0.016822012,0.148233414,0.009076054,0.474792212,-0.291136473 },
{ -0.014921153,-0.009434484,-0.00305167,0.016822012,0.006654344,0,0.07565856,0.015222012,-0.300354809 },
{ -0.144330621,-0.576139212,0.040264025,0.148233414,0,4.439799309,3.520421028,-3.187528133,0.071404062 },
{ -0.213110566,-1.163940072,0.006539376,0.009076054,0.07565856,3.520421028,12.10360527,-12.6082077,0.066212125 },
{ 0.434573323,1.590186,0.672870696,0.474792212,0.015222012,-3.187528133,-12.6082077,45.60238266,-1.981469274 },
{ 1.211585283,-0.053903706,-0.151115254,-0.291136473,-0.300354809,0.071404062,0.066212125,-1.981469274,20.41576767 }
});
static private Matrix malVarGlu = new Matrix(new double[][] {
//H,HA,HB2,HB3,HG2,HG3,C,CA,CB,CG,CD,N
{ 1.065708041,0.028409584,0.002206761,0.008373436,0.006230299,0.007387238,-0.112140514,0.076923966,0.006586985,0.005443899,-0.248474166,0.840083718 },
{ 0.028409584,0.184435129,0.001588819,0.000158923,-0.003926818,-0.004524304,-0.358527064,-0.62476927,0.471290678,-0.016700104,-0.550286233,0.305847883 },
{ 0.002206761,0.001588819,0.053614773,0.035170961,0.02647928,0.022427199,0.101565577,0.109461591,-0.02618487,0.027129212,0.050470106,-0.099745125 },
{ 0.008373436,0.000158923,0.035170961,0.057030134,0.023785438,0.028986948,0.101480976,0.13136515,-0.034423258,0.032988116,0.225959614,-0.074220605 },
{ 0.006230299,-0.003926818,0.02647928,0.023785438,0.049791902,0.038037453,0.108549252,0.119066514,-0.054522321,0.025667623,0.072222568,-0.124507822 },
{ 0.007387238,-0.004524304,0.022427199,0.028986948,0.038037453,0.054786138,0.109169655,0.126473948,-0.054097701,0.021346334,0.087695144,-0.08707916 },
{ -0.112140514,-0.358527064,0.101565577,0.101480976,0.108549252,0.109169655,3.776587725,2.533161163,-1.332312226,0.351864696,1.480964422,-1.506004453 },
{ 0.076923966,-0.62476927,0.109461591,0.13136515,0.119066514,0.126473948,2.533161163,4.447103024,-1.644090891,0.657714665,2.215839863,-1.45833981 },
{ 0.006586985,0.471290678,-0.02618487,-0.034423258,-0.054522321,-0.054097701,-1.332312226,-1.644090891,3.236092091,0.375369012,-1.014446616,0.908443809 },
{ 0.005443899,-0.016700104,0.027129212,0.032988116,0.025667623,0.021346334,0.351864696,0.657714665,0.375369012,2.206023455,2.189632416,-0.202201992 },
{ -0.248474166,-0.550286233,0.050470106,0.225959614,0.072222568,0.087695144,1.480964422,2.215839863,-1.014446616,2.189632416,4.528904438,0.050848518 },
{ 0.840083718,0.305847883,-0.099745125,-0.074220605,-0.124507822,-0.08707916,-1.506004453,-1.45833981,0.908443809,-0.202201992,0.050848518,23.61843109 }
});
static private Matrix malVarGln = new Matrix(new double[][] {
//H,HA,HB2,HB3,HG2,HG3,HE21,HE22,C,CA,CB,CG,CD,N,NE2
{ 0.368584126,0.055863302,-0.001812782,0.000770839,0.001105834,-0.001074365,0.025132069,0.001920117,-0.129195258,-0.066168971,0.093533218,0.040379763,0.063028522,0.993085027,0.017260131 },
{ 0.055863302,0.19768773,-0.000149899,0.000313699,0.006173618,0.005079888,0.024931675,0.000848616,-0.364306837,-0.562370718,0.468110621,-0.017777367,0.025463624,0.343462646,0.023098327 },
{ -0.001812782,-0.000149899,0.086818561,0.056104787,0.043496929,0.036574181,0.027571511,0.006559907,0.107242234,0.161624655,-0.023033479,0.044952232,-0.025828024,-0.19031845,0.027203318 },
{ 0.000770839,0.000313699,0.056104787,0.092359245,0.039452348,0.04730482,0.006320799,0.033439431,0.108070672,0.170721039,-0.050566431,0.045227174,-0.018491957,-0.160538256,0.013587028 },
{ 0.001105834,0.006173618,0.043496929,0.039452348,0.08339645,0.066120125,0.039669942,0.018093286,0.116872788,0.14886561,-0.046881836,0.068726927,-0.036759123,-0.139596269,0.030257519 },
{ -0.001074365,0.005079888,0.036574181,0.04730482,0.066120125,0.092431828,0.024415772,0.03541296,0.139095157,0.164560542,-0.037570395,0.06994658,-0.000327453,-0.159037307,0.022331867 },
{ 0.025132069,0.024931675,0.027571511,0.006320799,0.039669942,0.024415772,0.21509634,-0.057956159,-0.06498456,-0.039540682,0.035743546,0.031334907,0.154282674,0.082966216,0.319128931 },
{ 0.001920117,0.000848616,0.006559907,0.033439431,0.018093286,0.03541296,-0.057956159,0.224030569,-0.023538815,0.044894002,0.004211839,0.050235365,-0.090171084,-0.039824188,0.309993506 },
{ -0.129195258,-0.364306837,0.107242234,0.108070672,0.116872788,0.139095157,-0.06498456,-0.023538815,3.704949617,2.760192156,-1.360268235,0.122351341,0.527840078,-1.290239453,-0.571699858 },
{ -0.066168971,-0.562370718,0.161624655,0.170721039,0.14886561,0.164560542,-0.039540682,0.044894002,2.760192156,5.821583271,-1.694233298,0.517704666,-0.602347493,-1.57735455,-0.629381061 },
{ 0.093533218,0.468110621,-0.023033479,-0.050566431,-0.046881836,-0.037570395,0.035743546,0.004211839,-1.360268235,-1.694233298,3.739701033,0.264872015,0.111244105,0.95373112,0.165592164 },
{ 0.040379763,-0.017777367,0.044952232,0.045227174,0.068726927,0.06994658,0.031334907,0.050235365,0.122351341,0.517704666,0.264872015,7.391874313,0.116118826,-0.412349343,0.232089549 },
{ 0.063028522,0.025463624,-0.025828024,-0.018491957,-0.036759123,-0.000327453,0.154282674,-0.090171084,0.527840078,-0.602347493,0.111244105,0.116118826,2.700308085,0.593761683,0.582103312 },
{ 0.993085027,0.343462646,-0.19031845,-0.160538256,-0.139596269,-0.159037307,0.082966216,-0.039824188,-1.290239453,-1.57735455,0.95373112,-0.412349343,0.593761683,14.2077055,0.129646301 },
{ 0.017260131,0.023098327,0.027203318,0.013587028,0.030257519,0.022331867,0.319128931,0.309993506,-0.571699858,-0.629381061,0.165592164,0.232089549,0.582103312,0.129646301,10.8489399 }
});
static private Matrix malVarGly = new Matrix(new double[][] {
//H,HA,HA2,C,CA,N
{ 0.476614893,0.031159639,0.040471006,0.089514405,0.063403405,1.046840668 },
{ 0.031159639,0.166928515,0.000991856,-0.056205414,-0.05082513,0.068168528 },
{ 0.040471006,0.000991856,0.179835036,0.030719781,0.031373944,0.130095691 },
{ 0.089514405,-0.056205414,0.030719781,3.643553257,0.931718171,-0.455880135 },
{ 0.063403405,-0.05082513,0.031373944,0.931718171,1.731123567,0.005346781 },
{ 1.046840668,0.068168528,0.130095691,-0.455880135,0.005346781,17.74514389 }
});
static private Matrix malVarHis = new Matrix(new double[][] {
//H,HA,HB2,HB3,HD1,HD2,HE1,HE2,C,CA,CB,CG,CD2,CE1,N,ND1,NE2
{ 0.560518622,0.183814809,0.228441402,0.171102226,1.021531344,0.293755025,0.348634094,-0.183493435,-0.110542052,-0.058894478,0.061059579,1.071029782,-0.204658896,0.244749188,1.235189915,3.099734783,3.011609078 },
{ 0.183814809,0.38754645,0.301816404,0.216300234,1.255033851,0.26925993,0.330682457,-0.150097549,-0.2557652,-0.538579464,0.399473369,-1.549946189,-0.393185347,0.219108984,0.223175168,5.704565525,3.510776997 },
{ 0.228441402,0.301816404,0.719412923,0.461874396,3.026674271,0.3380211,0.369158655,-0.277232856,0.136567712,0.473954409,-0.210543439,-0.164266944,-0.068276458,0.134873375,0.003221622,-2.493439913,5.621762753 },
{ 0.171102226,0.216300234,0.461874396,0.419169724,2.223877668,0.341952294,0.382903069,-0.143724993,0.157058999,0.471633047,-0.226402089,-1.300931215,-0.17344664,0.1433236,-0.070541114,-0.752676606,2.118610144 },
{ 1.021531344,1.255033851,3.026674271,2.223877668,7.380751133,0.950828552,0.20852387,4.075683594,-1.241470337,4.725707531,-1.99736774,0,8.407128334,2.81966424,-1.715700507,0.293700695,17.25972366 },
{ 0.293755025,0.26925993,0.3380211,0.341952294,0.950828552,1.169705033,1.122253656,0.096209772,0.152888402,0.113683991,-0.039161034,0.348412544,-0.38318038,0.476072609,0.235061646,20.60833359,-3.650742292 },
{ 0.348634094,0.330682457,0.369158655,0.382903069,0.20852387,1.122253656,1.459575415,0.291646123,-0.024624916,-0.021811064,-0.197268173,-3.028702498,-0.736699522,0.344595939,0.046519838,34.47285843,-0.764078915 },
{ -0.183493435,-0.150097549,-0.277232856,-0.143724993,4.075683594,0.096209772,0.291646123,6.446722031,-1.853567004,-1.56320262,1.58668375,0,-0.14166151,-0.247185916,-5.698187828,85.97528076,-31.47099876 },
{ -0.110542052,-0.2557652,0.136567712,0.157058999,-1.241470337,0.152888402,-0.024624916,-1.853567004,4.330826283,3.07640481,-0.215609223,3.463238955,0.183384985,0.814362228,0.380845487,2.967477083,7.6914711 },
{ -0.058894478,-0.538579464,0.473954409,0.471633047,4.725707531,0.113683991,-0.021811064,-1.56320262,3.07640481,6.517858982,-0.58682102,8.312403679,0.67960012,0.782496035,-0.75383234,-50.17486191,6.706722736 },
{ 0.061059579,0.399473369,-0.210543439,-0.226402089,-1.99736774,-0.039161034,-0.197268173,1.58668375,-0.215609223,-0.58682102,4.777988911,6.017297268,-1.885950208,1.6885463,2.014951944,15.08877087,-8.211297035 },
{ 1.071029782,-1.549946189,-0.164266944,-1.300931215,0,0.348412544,-3.028702498,0,3.463238955,8.312403679,6.017297268,9.820725441,-0.913077891,3.485716581,10.72814178,24.10454178,-6.588027 },
{ -0.204658896,-0.393185347,-0.068276458,-0.17344664,8.407128334,-0.38318038,-0.736699522,-0.14166151,0.183384985,0.67960012,-1.885950208,-0.913077891,11.51477242,-1.225262642,-1.83494091,-66.7223587,48.81427383 },
{ 0.244749188,0.219108984,0.134873375,0.1433236,2.81966424,0.476072609,0.344595939,-0.247185916,0.814362228,0.782496035,1.6885463,3.485716581,-1.225262642,6.151823998,1.146819949,8.312621117,1.881917715 },
{ 1.235189915,0.223175168,0.003221622,-0.070541114,-1.715700507,0.235061646,0.046519838,-5.698187828,0.380845487,-0.75383234,2.014951944,10.72814178,-1.83494091,1.146819949,17.87412643,5.397219181,7.462571621 },
{ 3.099734783,5.704565525,-2.493439913,-0.752676606,0.293700695,20.60833359,34.47285843,85.97528076,2.967477083,-50.17486191,15.08877087,24.10454178,-66.7223587,8.312621117,5.397219181,1288.212891,71.61542511 },
{ 3.011609078,3.510776997,5.621762753,2.118610144,17.25972366,-3.650742292,-0.764078915,-31.47099876,7.6914711,6.706722736,-8.211297035,-6.588027,48.81427383,1.881917715,7.462571621,71.61542511,925.5718994 }
});
static private Matrix malVarIle = new Matrix(new double[][] {
//H,HA,HB,HG12,HG13,HG2,HD1,C,CA,CB,CG1,CG2,CD1,N
{ 0.484548509,0.127270296,0.005570898,0.017388731,0.001924306,0.007919082,0.007094514,-0.220632389,-0.331657857,0.363998234,0.099463232,-0.002571468,0.111518599,1.548962116 },
{ 0.127270296,0.327042133,-0.008132693,0.00073034,0.00599015,0.013268435,0.009878452,-0.589402795,-1.154142857,0.637375414,-0.286921293,0.042633802,0.03245496,0.254771411 },
{ 0.005570898,-0.008132693,0.093615174,0.05237738,0.047427479,0.045170773,0.04412885,0.128242433,0.144444302,-0.15630807,0.037618343,0.043982197,-0.092296638,-0.154917836 },
{ 0.017388731,0.00073034,0.05237738,0.179707617,0.027600518,0.041362137,0.05371077,0.098250136,0.138551906,-0.051598966,0.154917494,0.0030659,-0.002406804,-0.009465648 },
{ 0.001924306,0.00599015,0.047427479,0.027600518,0.16397652,0.04671073,0.053208165,0.061237413,0.078637436,-0.043060966,0.080541104,0.052237142,-0.028105453,0.02001127 },
{ 0.007919082,0.013268435,0.045170773,0.041362137,0.04671073,0.079187736,0.047898028,0.070435248,0.065912776,0.011957497,0.066349015,0.040473923,-0.033101942,-0.046897564 },
{ 0.007094514,0.009878452,0.04412885,0.05371077,0.053208165,0.047898028,0.130686417,0.046235025,0.077127151,0.029233135,0.101971552,0.033564031,0.055895608,-0.004172215 },
{ -0.220632389,-0.589402795,0.128242433,0.098250136,0.061237413,0.070435248,0.046235025,3.710621357,3.244227409,-1.472673178,1.186219811,0.461382359,0.392790824,-1.339672923 },
{ -0.331657857,-1.154142857,0.144444302,0.138551906,0.078637436,0.065912776,0.077127151,3.244227409,7.502469063,-1.826658011,2.392494917,0.335178286,1.294619083,-1.802263022 },
{ 0.363998234,0.637375414,-0.15630807,-0.051598966,-0.043060966,0.011957497,0.029233135,-1.472673178,-1.826658011,4.308437347,0.028018797,0.44331196,1.699410081,0.16695562 },
{ 0.099463232,-0.286921293,0.037618343,0.154917494,0.080541104,0.066349015,0.101971552,1.186219811,2.392494917,0.028018797,16.46050262,0.301725,0.661206663,0.427210987 },
{ -0.002571468,0.042633802,0.043982197,0.0030659,0.052237142,0.040473923,0.033564031,0.461382359,0.335178286,0.44331196,0.301725,4.408631802,3.078730583,-0.73594439 },
{ 0.111518599,0.03245496,-0.092296638,-0.002406804,-0.028105453,-0.033101942,0.055895608,0.392790824,1.294619083,1.699410081,0.661206663,3.078730583,10.88808823,-0.374605894 },
{ 1.548962116,0.254771411,-0.154917836,-0.009465648,0.02001127,-0.046897564,-0.004172215,-1.339672923,-1.802263022,0.16695562,0.427210987,-0.73594439,-0.374605894,20.16040993 }
});
static private Matrix malVarLeu = new Matrix(new double[][] {
//H,HA,HB2,HB3,HG,HD1,HD2,C,CA,CB,CG,CD1,CD2,N
{ 0.45207876,0.100313984,0.017883798,0.012751126,0.011032813,0.011017458,0.009247968,-0.187006608,-0.17667307,0.269041568,0.101834238,0.058505852,0.157362923,1.375810146 },
{ 0.100313984,0.228157952,0.003678693,0.001059857,0.005755223,0.015079363,0.015744939,-0.454466075,-0.715846479,0.550790012,0.087588303,0.062419761,0.15511997,0.723896861 },
{ 0.017883798,0.003678693,0.130525515,0.048293229,0.047780279,0.044392262,0.043201398,0.125484362,0.156280622,-0.051658023,0.046725027,0.051981378,0.00533441,-0.060698327 },
{ 0.012751126,0.001059857,0.048293229,0.139994428,0.046007354,0.044291291,0.054013912,0.116722301,0.180219084,-0.034467172,0.057423726,0.003471095,0.060668495,-0.051154964 },
{ 0.011032813,0.005755223,0.047780279,0.046007354,0.122200862,0.051284455,0.051044419,0.161390901,0.141473591,-0.024310228,0.086708702,0.095941372,0.012989668,-0.154039994 },
{ 0.011017458,0.015079363,0.044392262,0.044291291,0.051284455,0.084196977,0.058156882,0.046133097,0.076913163,0.029939178,0.078088753,0.068972983,0.056352742,0.028014612 },
{ 0.009247968,0.015744939,0.043201398,0.054013912,0.051044419,0.058156882,0.092079796,0.058133345,0.091737367,0.045366004,0.064232461,0.041875444,0.0918869,-0.010726376 },
{ -0.187006608,-0.454466075,0.125484362,0.116722301,0.161390901,0.046133097,0.058133345,4.16681385,2.65796566,-1.134650469,0.084009416,0.390790463,-0.261619508,-2.527002573 },
{ -0.17667307,-0.715846479,0.156280622,0.180219084,0.141473591,0.076913163,0.091737367,2.65796566,4.682406426,-1.449820042,0.402556419,0.372201026,0.218418837,-2.316148996 },
{ 0.269041568,0.550790012,-0.051658023,-0.034467172,-0.024310228,0.029939178,0.045366004,-1.134650469,-1.449820042,3.636039496,0.466767967,0.661672771,0.915551245,1.899347663 },
{ 0.101834238,0.087588303,0.046725027,0.057423726,0.086708702,0.078088753,0.064232461,0.084009416,0.402556419,0.466767967,3.171270371,1.340020299,1.341677427,0.642024696 },
{ 0.058505852,0.062419761,0.051981378,0.003471095,0.095941372,0.068972983,0.041875444,0.390790463,0.372201026,0.661672771,1.340020299,3.610803843,0.442387879,0.359935045 },
{ 0.157362923,0.15511997,0.00533441,0.060668495,0.012989668,0.056352742,0.0918869,-0.261619508,0.218418837,0.915551245,1.341677427,0.442387879,3.751878262,1.120585442 },
{ 1.375810146,0.723896861,-0.060698327,-0.051154964,-0.154039994,0.028014612,-0.010726376,-2.527002573,-2.316148996,1.899347663,0.642024696,0.359935045,1.120585442,17.00507736 }
});
static private Matrix malVarLys = new Matrix(new double[][] {
//H,HA,HB2,HB3,HG2,HG3,HD2,HD3,HE2,HE3,HZ,C,CA,CB,CG,CD,CE,N,NZ
{ 0.367121309,0.062532507,0.004121268,0.004690644,0.001090434,0.003444264,0.018341096,0.005802787,0.001296729,0.006390645,0.006332773,-0.148652032,-0.102331311,0.160853237,0.039667156,0.028898148,-0.012304786,1.069184065,-3.763871193 },
{ 0.062532507,0.195193738,0.011272421,0.006012486,0.019330254,0.020705788,0.004628004,0.007838311,0.004423411,0.005538389,0.005369531,-0.35887599,-0.619154155,0.464206696,-0.027883945,0.009580785,0.017151382,0.333582789,-4.101567745 },
{ 0.004121268,0.011272421,0.072749667,0.054673281,0.043525871,0.041609429,0.033242334,0.032213487,0.021478085,0.021482335,0.00687643,0.095966972,0.124693699,-0.06379962,0.041089356,0.013491998,0.017240513,-0.145710722,-0.549108684 },
{ 0.004690644,0.006012486,0.054673281,0.082605578,0.044222374,0.051965524,0.036628868,0.037560396,0.022796812,0.02632728,0.011047157,0.110487357,0.165404692,-0.082456134,0.052594669,0.010079783,0.026572414,-0.149214178,-0.376936585 },
{ 0.001090434,0.019330254,0.043525871,0.044222374,0.080975384,0.072466724,0.037850905,0.039911859,0.03151267,0.034436744,0.004698867,0.107882917,0.094429888,-0.01860695,0.080833383,0.004217204,0.030914901,-0.087109044,-3.4998703 },
{ 0.003444264,0.020705788,0.041609429,0.051965524,0.072466724,0.0965259,0.044206545,0.046387196,0.035857819,0.041065529,0.009124496,0.10425745,0.095117204,-0.017644435,0.08228042,0.011213314,0.032897778,-0.059915114,-0.266055673 },
{ 0.018341096,0.004628004,0.033242334,0.036628868,0.037850905,0.044206545,4.992360115,0.069541052,0.025761874,0.033027522,0.007052155,0.058029681,0.196594447,-0.024179649,0.004254587,0.107598223,0.031414464,-0.123908699,-1.565703034 },
{ 0.005802787,0.007838311,0.032213487,0.037560396,0.039911859,0.046387196,0.069541052,0.071575359,0.032259073,0.033035599,0.013237556,0.08468847,0.078394227,-0.021910701,0.01021717,0.071214669,0.025902484,-0.050493799,-1.314378619 },
{ 0.001296729,0.004423411,0.021478085,0.022796812,0.03151267,0.035857819,0.025761874,0.032259073,0.046358373,0.044494193,0.007083127,0.045381606,0.031664498,-0.019317076,0.022328079,0.017843096,0.034023933,-0.026317181,15.11536789 },
{ 0.006390645,0.005538389,0.021482335,0.02632728,0.034436744,0.041065529,0.033027522,0.033035599,0.044494193,0.056605689,0.007875184,0.039613333,0.027892381,-0.019866154,-0.001169609,0.015554182,0.046563782,-0.00349308,18.80609512 },
{ 0.006332773,0.005369531,0.00687643,0.011047157,0.004698867,0.009124496,0.007052155,0.013237556,0.007083127,0.007875184,0.095262967,-1.470523,-0.109725297,0.354304344,0.245889738,0.15706414,-0.152978033,-0.302469313,16.30794144 },
{ -0.148652032,-0.35887599,0.095966972,0.110487357,0.107882917,0.10425745,0.058029681,0.08468847,0.045381606,0.039613333,-1.470523,5.085006714,2.805569172,-1.115717292,0.430886179,0.355721265,0.174190611,-1.142899394,35.8031311 },
{ -0.102331311,-0.619154155,0.124693699,0.165404692,0.094429888,0.095117204,0.196594447,0.078394227,0.031664498,0.027892381,-0.109725297,2.805569172,4.865513325,-1.322877288,0.813579381,0.665118635,0.258071929,-1.300399542,-9.931623459 },
{ 0.160853237,0.464206696,-0.06379962,-0.082456134,-0.01860695,-0.017644435,-0.024179649,-0.021910701,-0.019317076,-0.019866154,0.354304344,-1.115717292,-1.322877288,3.175163984,0.339087486,0.56142205,0.394934952,1.009116888,-4.496578693 },
{ 0.039667156,-0.027883945,0.041089356,0.052594669,0.080833383,0.08228042,0.004254587,0.01021717,0.022328079,-0.001169609,0.245889738,0.430886179,0.813579381,0.339087486,2.655885935,0.071716681,0.248851925,-0.073662549,-1.903862 },
{ 0.028898148,0.009580785,0.013491998,0.010079783,0.004217204,0.011213314,0.107598223,0.071214669,0.017843096,0.015554182,0.15706414,0.355721265,0.665118635,0.56142205,0.071716681,1.876264691,0.356755585,-0.045868911,-5.952273846 },
{ -0.012304786,0.017151382,0.017240513,0.026572414,0.030914901,0.032897778,0.031414464,0.025902484,0.034023933,0.046563782,-0.152978033,0.174190611,0.258071929,0.394934952,0.248851925,0.356755585,1.193255901,-0.188530088,7.958240509 },
{ 1.069184065,0.333582789,-0.145710722,-0.149214178,-0.087109044,-0.059915114,-0.123908699,-0.050493799,-0.026317181,-0.00349308,-0.302469313,-1.142899394,-1.300399542,1.009116888,-0.073662549,-0.045868911,-0.188530088,15.94315529,-35.75146103 },
{ -3.763871193,-4.101567745,-0.549108684,-0.376936585,-3.4998703,-0.266055673,-1.565703034,-1.314378619,15.11536789,18.80609512,16.30794144,35.8031311,-9.931623459,-4.496578693,-1.903862,-5.952273846,7.958240509,-35.75146103,1375.68103 }
});
static private Matrix malVarMet = new Matrix(new double[][] {
//H,HA,HB2,HB3,HG2,HG3,HE,C,CA,CB,CG,CE,N
{ 0.379910737,0.073540278,0.033204105,0.020433428,0.006451493,0.018314024,0.007794171,-0.075774916,-0.10517633,0.194674715,-0.000527668,0.01284879,1.036224484 },
{ 0.073540278,0.236991897,0.035211787,0.038094997,0.039034139,0.052051544,0.045107599,-0.272179902,-0.695379257,0.348967612,0.12472634,0.18072775,0.331306279 },
{ 0.033204105,0.035211787,0.167457789,0.109973155,0.118740946,0.121467002,0.154245541,0.161310509,0.125277892,0.050280865,0.16222766,0.081022255,-0.11221502 },
{ 0.020433428,0.038094997,0.109973155,0.147581056,0.088801868,0.106410846,0.109937541,0.098233409,0.096929945,0.02276622,0.195842505,0.006073722,-0.044454228 },
{ 0.006451493,0.039034139,0.118740946,0.088801868,0.205239192,0.169335976,0.196313754,0.15497677,0.065145746,0.080463611,0.207901016,0.126820907,-0.23334302 },
{ 0.018314024,0.052051544,0.121467002,0.106410846,0.169335976,0.242941648,0.212639391,0.136581704,0.06556461,0.106728241,0.278554857,0.282053202,-0.112973683 },
{ 0.007794171,0.045107599,0.154245541,0.109937541,0.196313754,0.212639391,0.27474153,0.106673032,0.034212198,0.159190983,0.165893227,0.109454334,-0.048359267 },
{ -0.075774916,-0.272179902,0.161310509,0.098233409,0.15497677,0.136581704,0.106673032,4.178848267,2.243742466,-1.604590297,0.312306047,-0.198460132,-1.816891432 },
{ -0.10517633,-0.695379257,0.125277892,0.096929945,0.065145746,0.06556461,0.034212198,2.243742466,4.969119549,-0.704387784,0.444886476,-0.372276515,-1.372543097 },
{ 0.194674715,0.348967612,0.050280865,0.02276622,0.080463611,0.106728241,0.159190983,-1.604590297,-0.704387784,5.353907108,0.317944616,0.352276415,1.069101572 },
{ -0.000527668,0.12472634,0.16222766,0.195842505,0.207901016,0.278554857,0.165893227,0.312306047,0.444886476,0.317944616,3.985911846,0.456732452,-0.338241875 },
{ 0.01284879,0.18072775,0.081022255,0.006073722,0.126820907,0.282053202,0.109454334,-0.198460132,-0.372276515,0.352276415,0.456732452,11.18597889,0.2225793 },
{ 1.036224484,0.331306279,-0.11221502,-0.044454228,-0.23334302,-0.112973683,-0.048359267,-1.816891432,-1.372543097,1.069101572,-0.338241875,0.2225793,20.99051857 }
});
static private Matrix malVarPhe = new Matrix(new double[][] {
//H,HA,HB2,HB3,HD1,HD2,HE1,HE2,HZ,C,CA,CB,CG,CD1,CD2,CE1,CE2,CZ,N
{ 0.543549538,0.153633237,0.006905453,0.014116059,0.016036941,0.015260615,-0.010345147,-0.012876884,-0.033586852,-0.180800453,-0.186233267,0.349561602,0.166688994,0.001640222,0.014371216,-0.085852519,-0.087689489,-0.155288622,1.614772797 },
{ 0.153633237,6.998471737,-0.000138866,0.004275927,0.028231494,0.030358732,0.034367185,0.041801319,0.008654501,-0.465769947,-1.136533141,0.648683906,0.228754938,0.069748826,0.091341101,-0.293262899,-0.419885099,-0.236114994,0.110386431 },
{ 0.006905453,-0.000138866,0.156688362,0.06814336,0.058801223,0.057398733,0.023001006,0.025360024,0.018439043,0.151408419,0.158458233,-0.124513038,0.093792491,0.027861331,0.062565915,0.103985615,0.162798911,0.00486455,-0.03623924 },
{ 0.014116059,0.004275927,0.06814336,0.212764829,0.060103133,0.061259147,0.026036479,0.022871444,0.021206178,0.186362222,0.195705712,-0.144533813,-0.147607297,0.033495911,0.02305541,0.114519127,0.127706736,0.028226338,-0.112925693 },
{ 0.016036941,0.028231494,0.058801223,0.060103133,0.144898683,0.137386218,0.066180773,0.058730401,0.055637024,0.148493916,0.067915909,-0.002022276,-0.011685636,0.085737653,0.068103291,0.137021914,0.145711064,0.081009239,0.019108253 },
{ 0.015260615,0.030358732,0.057398733,0.061259147,0.137386218,0.140606955,0.072371997,0.06683521,0.06124248,0.114432253,0.045469925,-0.014423213,-0.011685636,0.071193628,0.070719548,0.126550496,0.137203828,0.060659707,0.004745624 },
{ -0.010345147,0.034367185,0.023001006,0.026036479,0.066180773,0.072371997,0.163978621,0.15066883,0.147632137,0.091954559,0.055586267,-0.030307509,-0.040184412,0.066204712,0.046088323,0.156555012,0.146133557,0.336455792,-0.047151856 },
{ -0.012876884,0.041801319,0.025360024,0.022871444,0.058730401,0.06683521,0.15066883,0.143551081,0.151753187,0.067149781,0.048767034,-0.036008757,-0.040184412,0.043506514,0.04687196,0.151191771,0.146071717,0.361023396,-0.051001336 },
{ -0.033586852,0.008654501,0.018439043,0.021206178,0.055637024,0.06124248,0.147632137,0.151753187,1.584564209,0.12000142,0.247112811,-0.032287572,-0.081123859,0.058456611,0.045260321,0.121702477,0.112187043,0.424770922,-0.220938608 },
{ -0.180800453,-0.465769947,0.151408419,0.186362222,0.148493916,0.114432253,0.091954559,0.067149781,0.12000142,5.993542671,2.9839468,-1.307312846,-0.273788244,0.28660968,0.05117362,0.251683921,-0.250434548,0.266022503,-0.692630947 },
{ -0.186233267,-1.136533141,0.158458233,0.195705712,0.067915909,0.045469925,0.055586267,0.048767034,0.247112811,2.9839468,7.354676247,-1.737214565,-0.674133658,0.48930797,0.321583331,1.396826983,1.590946317,0.866353035,-0.376057118 },
{ 0.349561602,0.648683906,-0.124513038,-0.144533813,-0.002022276,-0.014423213,-0.030307509,-0.036008757,-0.032287572,-1.307312846,-1.737214565,4.394043446,0.294051409,0.515188158,0.336122453,-0.495895922,-0.983998537,-0.403524578,0.700869799 },
{ 0.166688994,0.228754938,0.093792491,-0.147607297,-0.011685636,-0.011685636,-0.040184412,-0.040184412,-0.081123859,-0.273788244,-0.674133658,0.294051409,1.03084743,0.66493398,0.66493398,0.193338588,0.193338588,-0.101259418,-0.489985287 },
{ 0.001640222,0.069748826,0.027861331,0.033495911,0.085737653,0.071193628,0.066204712,0.043506514,0.058456611,0.28660968,0.48930797,0.515188158,0.66493398,1.738998413,1.695225835,0.73507297,0.70740211,0.53402859,-0.471299887 },
{ 0.014371216,0.091341101,0.062565915,0.02305541,0.068103291,0.070719548,0.046088323,0.04687196,0.045260321,0.05117362,0.321583331,0.336122453,0.66493398,1.695225835,1.695531964,0.709843755,0.708992958,0.568887413,-0.476287842 },
{ -0.085852519,-0.293262899,0.103985615,0.114519127,0.137021914,0.126550496,0.156555012,0.151191771,0.121702477,0.251683921,1.396826983,-0.495895922,0.193338588,0.73507297,0.709843755,29.72649384,43.78829575,1.112157345,0.85968858 },
{ -0.087689489,-0.419885099,0.162798911,0.127706736,0.145711064,0.137203828,0.146133557,0.146071717,0.112187043,-0.250434548,1.590946317,-0.983998537,0.193338588,0.70740211,0.708992958,43.78829575,43.3463707,1.167173147,1.461098075 },
{ -0.155288622,-0.236114994,0.00486455,0.028226338,0.081009239,0.060659707,0.336455792,0.361023396,0.424770922,0.266022503,0.866353035,-0.403524578,-0.101259418,0.53402859,0.568887413,1.112157345,1.167173147,14.25286484,-0.208609492 },
{ 1.614772797,0.110386431,-0.03623924,-0.112925693,0.019108253,0.004745624,-0.047151856,-0.051001336,-0.220938608,-0.692630947,-0.376057118,0.700869799,-0.489985287,-0.471299887,-0.476287842,0.85968858,1.461098075,-0.208609492,19.08541489 }
});
static private Matrix malVarPro = new Matrix(new double[][] {
//HA,HB2,HB3,HG2,HG3,HD2,HD3,C,CA,CB,CG,CD,N
{ 0.127948582,0.047235888,0.056189362,0.03332131,0.037042987,0.032584723,0.036460623,-0.04755611,-0.109820783,0.073510021,-0.022358265,0.03069205,0.387137532 },
{ 0.047235888,0.125374019,0.052163582,0.055185419,0.044674143,0.051821236,0.023038918,0.074782223,0.05664571,0.048317723,0.014355249,0.064463228,0.128864378 },
{ 0.056189362,0.052163582,0.158007279,0.053368233,0.07311637,0.033230692,0.069313638,0.069562271,0.076943889,0.074731596,0.027263019,0.057429213,-0.178820118 },
{ 0.03332131,0.055185419,0.053368233,0.111212038,0.097072661,0.065490454,0.06369663,0.05691528,0.081356481,0.03318787,0.0773146,0.070018172,-0.196720749 },
{ 0.037042987,0.044674143,0.07311637,0.097072661,0.133993655,0.057497066,0.085908271,0.070056014,0.043164812,0.082001917,0.099156082,0.094146259,-0.224820033 },
{ 0.032584723,0.051821236,0.033230692,0.065490454,0.057497066,0.149486661,0.094618753,0.061851088,0.086105719,0.050814983,0.058313724,0.164076403,0.302142292 },
{ 0.036460623,0.023038918,0.069313638,0.06369663,0.085908271,0.094618753,0.17821686,0.029822048,0.101648718,0.065006174,0.051942363,0.161657929,-0.291708231 },
{ -0.04755611,0.074782223,0.069562271,0.05691528,0.070056014,0.061851088,0.029822048,2.570146322,0.99639988,-0.185524568,0.492183268,0.024638675,1.168789625 },
{ -0.109820783,0.05664571,0.076943889,0.081356481,0.043164812,0.086105719,0.101648718,0.99639988,3.507337093,-0.476301968,0.62570852,0.449263603,0.324586749 },
{ 0.073510021,0.048317723,0.074731596,0.03318787,0.082001917,0.050814983,0.065006174,-0.185524568,-0.476301968,2.411034823,-0.050461303,0.312410653,0.0303312 },
{ -0.022358265,0.014355249,0.027263019,0.0773146,0.099156082,0.058313724,0.051942363,0.492183268,0.62570852,-0.050461303,1.319811702,0.401096851,2.05501771 },
{ 0.03069205,0.064463228,0.057429213,0.070018172,0.094146259,0.164076403,0.161657929,0.024638675,0.449263603,0.312410653,0.401096851,3.156873703,1.674100757 },
{ 0.387137532,0.128864378,-0.178820118,-0.196720749,-0.224820033,0.302142292,-0.291708231,1.168789625,0.324586749,0.0303312,2.05501771,1.674100757,88.07623291 }
});
static private Matrix malVarSer = new Matrix(new double[][] {
//H,HA,HB2,HB3,HG,C,CA,CB,N
{ 0.398513109,0.04623181,0.016665854,0.022241443,0.046292558,0.056789555,0.032011122,-0.022381591,1.104091644 },
{ 0.04623181,0.183807597,0.001240865,0.001217798,-0.071638539,-0.230514571,-0.468509942,0.377238542,0.232677847 },
{ 0.016665854,0.001240865,0.080144256,0.052704539,0.032950364,0.092147455,0.0897751,-0.030368004,0.0114533 },
{ 0.022241443,0.001217798,0.052704539,0.094000556,0.000357445,0.108926728,0.116596431,-0.039312188,-0.051076565 },
{ 0.046292558,-0.071638539,0.032950364,0.000357445,1.62681365,0.625875235,0.449889183,0.51812619,-0.554987013 },
{ 0.056789555,-0.230514571,0.092147455,0.108926728,0.625875235,3.300351858,1.80311513,-0.833756506,-0.199274048 },
{ 0.032011122,-0.468509942,0.0897751,0.116596431,0.449889183,1.80311513,4.545715809,-1.266839624,-0.29854995 },
{ -0.022381591,0.377238542,-0.030368004,-0.039312188,0.51812619,-0.833756506,-1.266839624,5.087539196,0.381844163 },
{ 1.104091644,0.232677847,0.0114533,-0.051076565,-0.554987013,-0.199274048,-0.29854995,0.381844163,14.38586426 }
});
static private Matrix malVarThr = new Matrix(new double[][] {
//H,HA,HB,HG1,HG2,C,CA,CB,CG2,N
{ 0.399677485,0.079332367,5.31825E-05,-0.055077191,0.00865848,-0.092531294,-0.054172218,0.066410445,-0.002123201,1.294419646 },
{ 0.079332367,0.237935677,0.002027369,-0.010361892,0.00212599,-0.314469934,-0.786431372,0.433335424,-0.046037499,0.171396822 },
{ 5.31825E-05,0.002027369,0.126356199,0.072322309,0.039713461,0.130247355,-0.079461716,0.036667526,0.052739848,-0.510240972 },
{ -0.055077191,-0.010361892,0.072322309,2.649239779,0.03939411,0.111775741,0.900414348,-0.265966266,0.642437577,0.054507546 },
{ 0.00865848,0.00212599,0.039713461,0.03939411,0.061567552,0.076484963,0.061861191,0.011568365,0.08149793,-0.079259321 },
{ -0.092531294,-0.314469934,0.130247355,0.111775741,0.076484963,3.074912071,1.993779779,-0.467184514,0.635851085,-1.260207892 },
{ -0.054172218,-0.786431372,-0.079461716,0.900414348,0.061861191,1.993779779,6.733168602,-1.653884053,0.847847939,2.164549828 },
{ 0.066410445,0.433335424,0.036667526,-0.265966266,0.011568365,-0.467184514,-1.653884053,7.415740013,0.192319259,-0.84431541 },
{ -0.002123201,-0.046037499,0.052739848,0.642437577,0.08149793,0.635851085,0.847847939,0.192319259,3.047462463,0.026707284 },
{ 1.294419646,0.171396822,-0.510240972,0.054507546,-0.079259321,-1.260207892,2.164549828,-0.84431541,0.026707284,25.3979454 }
});
static private Matrix malVarTrp = new Matrix(new double[][] {
//H,HA,HB2,HB3,HD1,HE1,HE3,HZ2,HZ3,HH2,C,CA,CB,CG,CD1,CD2,CE2,CE3,CZ2,CZ3,CH2,N,NE1
{ 0.661329746,0.132090196,0.020765161,0.015894927,0.007389797,0.006906026,-0.010167865,-0.015487382,-0.037558824,-0.015786661,0.009516691,0.00665119,0.441847771,0.104767002,-0.190362752,-2.114088535,-0.017072132,0.129406199,-0.272973567,-0.071197748,0.535183191,2.106140375,-0.287125439 },
{ 0.132090196,0.315868825,0.014522251,0.017121641,0.004743131,0.000315615,0.008252796,0.0011519,-0.016208008,0.009290006,-0.263874203,-0.887101293,0.612602413,-0.078827515,-0.193338186,-0.514159858,1.980393648,-0.041501593,0.270474821,0.351163,0.115935512,0.318475395,0.126986861 },
{ 0.020765161,0.014522251,0.126530409,0.064015567,0.035533153,0.028172933,0.032624327,0.013270613,0.013702227,0.013742022,0.133945242,0.172670007,-0.157479942,0.030200236,-0.036088325,-0.001207251,-0.246646836,0.000094689,-0.085696429,-0.07762678,0.130246118,0.019535713,-0.027619368 },
{ 0.015894927,0.017121641,0.064015567,0.148985609,0.053458635,0.01812847,0.060853973,0.029651206,0.027186869,0.023641719,0.11944776,0.228025615,-0.039295558,-0.251549989,0.116067663,-0.167012751,-0.385442525,0.011529104,-0.333288223,-0.341743052,0.331099331,0.038808439,-0.330518425 },
{ 0.007389797,0.004743131,0.035533153,0.053458635,0.113754526,0.049717538,0.027461793,0.027316304,0.020764226,0.026383638,0.052310664,0.116902784,-0.046868015,-0.003455273,0.23430413,0.439785689,-0.358501822,0.051015008,-0.061566491,-0.076822713,0.051828314,-0.03581531,0.053032141 },
{ 0.006906026,0.000315615,0.028172933,0.01812847,0.049717538,0.409550905,0.011688895,0.057730421,0.023747465,0.036362756,0.00091709,0.085936502,-0.134609759,-0.144362241,0.11515411,-0.057400324,-1.2027601,0.028360447,0.138085321,-0.17038846,0.039613932,0.037227172,0.793321014 },
{ -0.010167865,0.008252796,0.032624327,0.060853973,0.027461793,0.011688895,0.208750501,0.048835624,0.079881579,0.061424799,0.096131295,0.198998958,-0.095802173,-0.288267165,0.171279773,0.027484631,0.026160657,0.1143867,-0.028764701,-0.039241124,0.088730782,-0.164604455,-0.107454732 },
{ -0.015487382,0.0011519,0.013270613,0.029651206,0.027316304,0.057730421,0.048835624,0.130023524,0.044330705,0.072504178,-0.011085736,-0.006370402,-0.009878446,0.111533552,0.090558007,0.461490721,-0.117983706,0.067999832,0.329961509,0.289491892,0.069931589,-0.124593109,0.07156311 },
{ -0.037558824,-0.016208008,0.013702227,0.027186869,0.020764226,0.023747465,0.079881579,0.044330705,0.163874626,0.095901363,-0.022358105,0.106238894,-0.110912964,-0.057450336,0.146114633,0.029011229,0.31572932,0.039704789,0.085357972,0.137192562,0.037278,-0.129124865,0.186238989 },
{ -0.015786661,0.009290006,0.013742022,0.023641719,0.026383638,0.036362756,0.061424799,0.072504178,0.095901363,0.192525551,-0.07654839,-0.052928962,-0.01324157,-0.066366673,0.169071585,-0.010524049,-0.957291126,0.154791027,0.334657878,0.25467059,-0.018785745,-0.103453443,0.082332879 },
{ 0.009516691,-0.263874203,0.133945242,0.11944776,0.052310664,0.00091709,0.096131295,-0.011085736,-0.022358105,-0.07654839,3.631575346,2.33945322,-0.870782912,0.714103282,-0.362164468,-0.909205318,0.300866813,-0.338301599,-0.155202195,0.197302043,0.452268452,-1.119035602,-0.405825079 },
{ 0.00665119,-0.887101293,0.172670007,0.228025615,0.116902784,0.085936502,0.198998958,-0.006370402,0.106238894,-0.052928962,2.33945322,6.004242897,-1.66727674,0.006123972,0.786833108,-1.441877246,-4.484669209,0.337298572,-1.732644081,-2.255311251,0.719937444,-0.596547902,-1.332642913 },
{ 0.441847771,0.612602413,-0.157479942,-0.039295558,-0.046868015,-0.134609759,-0.095802173,-0.009878446,-0.110912964,-0.01324157,-0.870782912,-1.66727674,4.448700905,2.439207792,0.308979452,-1.835621119,-0.137719721,0.224739924,1.535282612,1.313479066,0.70079422,1.353014827,-0.322219372 },
{ 0.104767002,-0.078827515,0.030200236,-0.251549989,-0.003455273,-0.144362241,-0.288267165,0.111533552,-0.057450336,-0.066366673,0.714103282,0.006123972,2.439207792,1.620525003,-0.148247734,1.613602638,0.909652352,0.676803649,2.493831396,3.073373795,0.18686451,0.523722351,-1.175410509 },
{ -0.190362752,-0.193338186,-0.036088325,0.116067663,0.23430413,0.11515411,0.171279773,0.090558007,0.146114633,0.169071585,-0.362164468,0.786833108,0.308979452,-0.148247734,2.928669691,-1.145414114,-0.637731433,0.909006298,-0.447238296,-0.801229835,-0.317866266,-1.37936008,0.427921981 },
{ -2.114088535,-0.514159858,-0.001207251,-0.167012751,0.439785689,-0.057400324,0.027484631,0.461490721,0.029011229,-0.010524049,-0.909205318,-1.441877246,-1.835621119,1.613602638,-1.145414114,8.452910423,7.463749886,-1.571911931,1.667182207,0.614959359,-1.883159995,-12.39416313,-0.67500037 },
{ -0.017072132,1.980393648,-0.246646836,-0.385442525,-0.358501822,-1.2027601,0.026160657,-0.117983706,0.31572932,-0.957291126,0.300866813,-4.484669209,-0.137719721,0.909652352,-0.637731433,7.463749886,39.61133194,0.107531481,-4.3554883,-0.460731298,-6.877117634,4.477484226,-0.725069404 },
{ 0.129406199,-0.041501593,0.000094689,0.011529104,0.051015008,0.028360447,0.1143867,0.067999832,0.039704789,0.154791027,-0.338301599,0.337298572,0.224739924,0.676803649,0.909006298,-1.571911931,0.107531481,4.328186035,3.124161243,5.577692986,0.807518184,-0.044028614,-1.879525542 },
{ -0.272973567,0.270474821,-0.085696429,-0.333288223,-0.061566491,0.138085321,-0.028764701,0.329961509,0.085357972,0.334657878,-0.155202195,-1.732644081,1.535282612,2.493831396,-0.447238296,1.667182207,-4.3554883,3.124161243,57.56800079,66.62944031,-1.153520823,-1.387021303,-0.360761434 },
{ -0.071197748,0.351163,-0.07762678,-0.341743052,-0.076822713,-0.17038846,-0.039241124,0.289491892,0.137192562,0.25467059,0.197302043,-2.255311251,1.313479066,3.073373795,-0.801229835,0.614959359,-0.460731298,5.577692986,66.62944031,72.58539581,0.638285101,-1.010909796,2.547362328 },
{ 0.535183191,0.115935512,0.130246118,0.331099331,0.051828314,0.039613932,0.088730782,0.069931589,0.037278,-0.018785745,0.452268452,0.719937444,0.70079422,0.18686451,-0.317866266,-1.883159995,-6.877117634,0.807518184,-1.153520823,0.638285101,13.86545849,3.965545416,-2.949623108 },
{ 2.106140375,0.318475395,0.019535713,0.038808439,-0.03581531,0.037227172,-0.164604455,-0.124593109,-0.129124865,-0.103453443,-1.119035602,-0.596547902,1.353014827,0.523722351,-1.37936008,-12.39416313,4.477484226,-0.044028614,-1.387021303,-1.010909796,3.965545416,19.75927353,0.37001276 },
{ -0.287125439,0.126986861,-0.027619368,-0.330518425,0.053032141,0.793321014,-0.107454732,0.07156311,0.186238989,0.082332879,-0.405825079,-1.332642913,-0.322219372,-1.175410509,0.427921981,-0.67500037,-0.725069404,-1.879525542,-0.360761434,2.547362328,-2.949623108,0.37001276,57.28811646 }
});
static private Matrix malVarTyr = new Matrix(new double[][] {
//H,HA,HB2,HB3,HD1,HD2,HE1,HE2,HH,C,CA,CB,CG,CD1,CD2,CE1,CE2,CZ,N
{ 0.593182266,0.108372688,-0.013951996,-0.009172456,-0.002041235,-0.003607854,-0.009192387,-0.017190138,0.245930985,-0.151328787,-0.083633415,0.421942502,-0.090605065,0.151859522,0.140021354,-0.059875958,-0.139920935,-1.316010356,1.680685997 },
{ 0.108372688,0.322918624,0.001834079,-0.00616676,0.018064331,0.0209044,0.00050226,0.001345329,0.060590621,-0.350153714,-0.988772869,0.648959935,-0.048856244,0.101504132,0.320888847,0.059629548,0.099672422,-2.212325811,0.185940728 },
{ -0.013951996,0.001834079,0.153599635,0.072728738,0.05062601,0.051618215,0.018540761,0.018409425,-0.119642891,0.100123026,0.136481628,-0.116533265,-0.010560672,-0.060096137,-0.142275274,0.07844501,0.052260451,-0.611113429,-0.219174713 },
{ -0.009172456,-0.00616676,0.072728738,0.165575817,0.048222464,0.052226346,0.017602183,0.018124726,0.16217871,0.134526715,0.19755052,-0.129450366,0.005388705,-0.033480365,-0.061781149,0.050454345,0.055690955,0.466223657,-0.187072247 },
{ -0.002041235,0.018064331,0.05062601,0.048222464,0.094594829,0.091209106,0.038927071,0.03812483,0.15082325,0.059667252,0.05599599,-0.015689598,-0.022359747,0.051453389,0.022639947,0.037207507,0.046747167,0.102732278,-0.079012409 },
{ -0.003607854,0.0209044,0.051618215,0.052226346,0.091209106,0.094311781,0.037860513,0.038628887,0.131953299,0.059250742,0.051216427,-0.009852424,-0.021204097,0.025891474,0.02825664,0.01173131,0.033259351,0.102732278,-0.08195705 },
{ -0.009192387,0.00050226,0.018540761,0.017602183,0.038927071,0.037860513,0.066373296,0.063802227,0.216514826,0.033907067,0.057463553,-0.012825001,0.025955677,0.033018608,-0.029791443,0.124814935,0.080434352,0.520955443,-0.01878001 },
{ -0.017190138,0.001345329,0.018409425,0.018124726,0.03812483,0.038628887,0.063802227,0.064408228,0.298426837,0.041355856,0.062579192,-0.018979991,0.02665052,-0.01729692,-0.023091208,0.063785479,0.080633827,0.520955443,-0.042288218 },
{ 0.245930985,0.060590621,-0.119642891,0.16217871,0.15082325,0.131953299,0.216514826,0.298426837,3.650907278,0.58292824,0.041142989,-0.523603141,0,1.71144414,-0.2799384,1.974590302,0.513059557,0,1.305423975 },
{ -0.151328787,-0.350153714,0.100123026,0.134526715,0.059667252,0.059250742,0.033907067,0.041355856,0.58292824,3.89579773,2.77870822,-1.214239478,0.453299373,0.018813076,-1.071421146,1.494295001,0.82475394,-0.01217334,-0.694135666 },
{ -0.083633415,-0.988772869,0.136481628,0.19755052,0.05599599,0.051216427,0.057463553,0.062579192,0.041142989,2.77870822,6.368896961,-1.413163185,0.402646303,0.50013119,-1.261783361,1.00295496,0.277997166,-1.803325057,-0.854195356 },
{ 0.421942502,0.648959935,-0.116533265,-0.129450366,-0.015689598,-0.009852424,-0.012825001,-0.018979991,-0.523603141,-1.214239478,-1.413163185,4.830979824,-0.014666396,1.054337621,0.596610606,0.812415302,0.471265346,-6.128417015,0.839488387 },
{ -0.090605065,-0.048856244,-0.010560672,0.005388705,-0.022359747,-0.021204097,0.025955677,0.02665052,0,0.453299373,0.402646303,-0.014666396,1.438317895,0.087459005,0.142365769,0.313322663,0.309906155,0.032700528,-1.02494061 },
{ 0.151859522,0.101504132,-0.060096137,-0.033480365,0.051453389,0.025891474,0.033018608,-0.01729692,1.71144414,0.018813076,0.50013119,1.054337621,0.087459005,30.16939735,33.36718369,6.159466267,-0.055209424,-2.146585226,-0.428141683 },
{ 0.140021354,0.320888847,-0.142275274,-0.061781149,0.022639947,0.02825664,-0.029791443,-0.023091208,-0.2799384,-1.071421146,-1.261783361,0.596610606,0.142365769,33.36718369,34.10924912,-0.159435526,-0.084375605,-2.42848444,-0.21037142 },
{ -0.059875958,0.059629548,0.07844501,0.050454345,0.037207507,0.01173131,0.124814935,0.063785479,1.974590302,1.494295001,1.00295496,0.812415302,0.313322663,6.159466267,-0.159435526,11.67894077,6.174175263,-2.897614718,-0.747496188 },
{ -0.139920935,0.099672422,0.052260451,0.055690955,0.046747167,0.033259351,0.080434352,0.080633827,0.513059557,0.82475394,0.277997166,0.471265346,0.309906155,-0.055209424,-0.084375605,6.174175263,6.190960407,-3.171273947,-0.795468032 },
{ -1.316010356,-2.212325811,-0.611113429,0.466223657,0.102732278,0.102732278,0.520955443,0.520955443,0,-0.01217334,-1.803325057,-6.128417015,0.032700528,-2.146585226,-2.42848444,-2.897614718,-3.171273947,40.32577133,-6.926008225 },
{ 1.680685997,0.185940728,-0.219174713,-0.187072247,-0.079012409,-0.08195705,-0.01878001,-0.042288218,1.305423975,-0.694135666,-0.854195356,0.839488387,-1.02494061,-0.428141683,-0.21037142,-0.747496188,-0.795468032,-6.926008225,20.13540649 }
});
static private Matrix malVarVal = new Matrix(new double[][] {
//H,HA,HB,HG1,HG2,C,CA,CB,CG1,CG2,N
{ 0.474454433,0.124050438,-0.011127413,0.010563846,0.002759714,-0.231536984,-0.385617137,0.297521889,-0.040059399,0.007962246,1.448510766 },
{ 0.124050438,0.354129314,0.002574488,0.013190175,0.005394742,-0.557517707,-1.336580992,0.675501943,-0.141067296,-0.30491674,0.029538153 },
{ -0.011127413,0.002574488,0.102354877,0.046423148,0.056876943,0.138835639,0.195689172,-0.089964628,0.071880579,0.04024864,-0.309310794 },
{ 0.010563846,0.013190175,0.046423148,0.082328841,0.061420683,0.06349805,0.116302341,-0.008479784,0.106810585,0.046158329,-0.034708511 },
{ 0.002759714,0.005394742,0.056876943,0.061420683,0.104502946,0.117281072,0.174566284,-0.03354777,0.048513815,0.135745823,-0.075891838 },
{ -0.231536984,-0.557517707,0.138835639,0.06349805,0.117281072,3.640900135,3.51388526,-1.325410605,0.640890002,1.176813245,-0.750159442 },
{ -0.385617137,-1.336580992,0.195689172,0.116302341,0.174566284,3.51388526,8.229063988,-2.851556301,1.332353354,2.424005747,0.063049749 },
{ 0.297521889,0.675501943,-0.089964628,-0.008479784,-0.03354777,-1.325410605,-2.851556301,3.418505669,0.104608432,-0.384231836,-0.127606899 },
{ -0.040059399,-0.141067296,0.071880579,0.106810585,0.048513815,0.640890002,1.332353354,0.104608432,6.466031551,0.824112415,0.081443407 },
{ 0.007962246,-0.30491674,0.04024864,0.046158329,0.135745823,1.176813245,2.424005747,-0.384231836,0.824112415,3.187404156,1.213735223 },
{ 1.448510766,0.029538153,-0.309310794,-0.034708511,-0.075891838,-0.750159442,0.063049749,-0.127606899,0.081443407,1.213735223,22.49996376 }
});
static private Matrix malVarUnk = new Matrix(new double[][] {
//H,HA,C,CA,CB,N
{ 506.25, 0, 0, 0, 0, 0 }, {
0, 506.25, 0, 0, 0, 0 }, {
0, 0, 40000, 0, 0, 0 }, {
0, 0, 0, 40000, 0, 0 }, {
0, 0, 0, 0, 40000, 0 }, {
0, 0, 0, 0, 0, 10000 }, });
public static Matrix[] malVar = new Matrix[] { malVarAla, malVarArg, malVarAsp, malVarAsn, malVarCys, malVarGlu, malVarGln, malVarGly, malVarHis, malVarIle, malVarLeu, malVarLys, malVarMet, malVarPhe, malVarPro, malVarSer, malVarThr, malVarTrp, malVarTyr, malVarVal, malVarUnk };
//--------------------------------------bmrb standard deviations-------------------------------------
static private Matrix bmrbSdAla = new Matrix(new double[] { 0.61, 0.43, 0.25, 2.13, 2.04, 1.88, 3.69 }, dimAla.length);
static private Matrix bmrbSdArg = new Matrix(new double[] { 0.6, 0.45, 0.27, 0.28, 0.27, 0.28, 0.23, 0.24, 0.57, 0.39, 0.35, 0.42, 0.4, 2.04, 2.39, 1.83, 1.39, 1.04, 0.98, 3.88, 14.8, 6.39, 6.9 }, dimArg.length);
static private Matrix bmrbSdAsp = new Matrix(new double[] { 0.58, 0.32, 0.27, 0.29, 1.77, 2.09, 1.66, 1.57, 4.09 }, dimAsp.length);
static private Matrix bmrbSdAsn = new Matrix(new double[] { 0.63, 0.37, 0.33, 0.34, 0.52, 0.52, 1.82, 1.97, 1.8, 1.34, 4.26, 2.51 }, dimAsn.length);
static private Matrix bmrbSdCys = new Matrix(new double[] { 0.67, 0.57, 0.45, 0.48, 2.54, 2.04, 3.41, 6.67, 4.61 }, dimCys.length);
static private Matrix bmrbSdGlu = new Matrix(new double[] { 0.61, 0.42, 0.22, 0.22, 0.22, 0.22, 2.01, 2.14, 1.79, 1.37, 1.91, 3.7 }, dimGlu.length);
static private Matrix bmrbSdGln = new Matrix(new double[] { 0.6, 0.44, 0.27, 0.29, 0.29, 0.29, 0.49, 0.49, 1.96, 2.2, 1.91, 1.23, 1.08, 3.84, 2.11 }, dimGln.length);
static private Matrix bmrbSdGly = new Matrix(new double[] { 0.7, 0.39, 0.38, 1.86, 1.36, 4.19 }, dimGly.length);
static private Matrix bmrbSdHis = new Matrix(new double[] { 0.69, 0.48, 0.39, 0.4, 3.01, 0.49, 0.55, 2.73, 2.05, 2.47, 2.19, 3.35, 2.92, 2.47, 4.32, 34.07, 20.55 }, dimHis.length);
static private Matrix bmrbSdIle = new Matrix(new double[] { 0.7, 0.56, 0.3, 0.39, 0.41, 0.27, 0.3, 1.95, 2.78, 2.09, 2.17, 1.55, 1.78, 4.46 }, dimIle.length);
static private Matrix bmrbSdLeu = new Matrix(new double[] { 0.65, 0.47, 0.35, 0.36, 0.33, 0.28, 0.28, 2.04, 2.2, 1.92, 1.27, 1.77, 1.8, 4 }, dimLeu.length);
static private Matrix bmrbSdLys = new Matrix(new double[] { 0.63, 0.45, 0.26, 0.27, 0.27, 0.29, 0.26, 0.25, 0.21, 0.22, 0.37, 2.18, 2.26, 1.86, 1.24, 1.26, 0.91, 3.97, 50.29 }, dimLys.length);
static private Matrix bmrbSdMet = new Matrix(new double[] { 0.59, 0.47, 0.35, 0.37, 0.35, 0.39, 0.41, 2.09, 2.28, 2.28, 1.32, 2.89, 3.71 }, dimMet.length);
static private Matrix bmrbSdPhe = new Matrix(new double[] { 0.72, 0.58, 0.37, 0.38, 0.62, 0.67, 0.62, 0.66, 0.66, 2.02, 2.7, 2.09, 3.04, 1.4, 1.33, 1.61, 1.03, 1.76, 4.3 }, dimPhe.length);
static private Matrix bmrbSdPro = new Matrix(new double[] { 0.34, 0.36, 0.37, 0.34, 0.35, 0.36, 0.39, 1.57, 1.64, 1.26, 1.14, 1.17, 10.03 }, dimPro.length);
static private Matrix bmrbSdSer = new Matrix(new double[] { 0.61, 0.42, 0.28, 0.29, 1.14, 1.76, 2.18, 1.63, 3.82 }, dimSer.length);
static private Matrix bmrbSdThr = new Matrix(new double[] { 0.62, 0.48, 0.35, 1.76, 0.25, 1.78, 2.72, 2.04, 1.29, 4.99 }, dimThr.length);
static private Matrix bmrbSdTrp = new Matrix(new double[] { 0.81, 0.55, 0.36, 0.36, 0.34, 0.56, 0.81, 0.69, 0.81, 0.75, 1.95, 2.61, 2.17, 1.84, 2.07, 1.37, 6.64, 1.96, 1.55, 1.95, 1.62, 4.55, 2.4 }, dimTrp.length);
static private Matrix bmrbSdTyr = new Matrix(new double[] { 0.76, 0.57, 0.38, 0.38, 0.51, 0.54, 0.44, 0.47, 1.59, 2.01, 2.61, 2.21, 2.32, 1.35, 1.62, 1.6, 1.85, 2.28, 4.54 }, dimTyr.length);
static private Matrix bmrbSdVal = new Matrix(new double[] { 0.7, 0.58, 0.32, 0.26, 0.29, 1.95, 2.98, 1.84, 1.49, 1.66, 4.85 }, dimVal.length);
static private Matrix bmrbSdUnk = new Matrix(new double[] { 22.5, 22.5, 200, 200, 200, 100 }, dimUnk.length);
public static Matrix[] bmrbSd = new Matrix[] { bmrbSdAla, bmrbSdArg, bmrbSdAsp, bmrbSdAsn, bmrbSdCys, bmrbSdGlu, bmrbSdGln, bmrbSdGly, bmrbSdHis, bmrbSdIle, bmrbSdLeu, bmrbSdLys, bmrbSdMet, bmrbSdPhe, bmrbSdPro, bmrbSdSer, bmrbSdThr, bmrbSdTrp, bmrbSdTyr, bmrbSdVal, bmrbSdUnk };
//--------------------------------------refdb standard deviations-------------------------------------
static private Matrix refdbSdAla = new Matrix(new double[] { 0.66, 0.49, Double.NaN, 1.99, 1.91, 1.78, 4.04 }, dimAla.length);
static private Matrix refdbSdArg = new Matrix(new double[] { 0.64, 0.5, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.98, 2.29, 1.68, Double.NaN, Double.NaN, Double.NaN, 3.96, Double.NaN, Double.NaN, Double.NaN }, dimArg.length);
static private Matrix refdbSdAsp = new Matrix(new double[] { 0.6, 0.34, Double.NaN, Double.NaN, 1.66, 2.01, 1.5, Double.NaN, 4.07 }, dimAsp.length);
static private Matrix refdbSdAsn = new Matrix(new double[] { 0.71, 0.42, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.78, 1.82, 1.66, Double.NaN, 4.46, Double.NaN }, dimAsn.length);
static private Matrix refdbSdCys = new Matrix(new double[] { 0.73, 0.64, Double.NaN, Double.NaN, Double.NaN, 2.01, 3.35, 6.86, 4.33 }, dimCys.length);
static private Matrix refdbSdGlu = new Matrix(new double[] { 0.64, 0.45, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.87, 2.09, 1.74, Double.NaN, Double.NaN, 3.67 }, dimGlu.length);
static private Matrix refdbSdGln = new Matrix(new double[] { 0.62, 0.48, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.87, 2.05, 1.8, Double.NaN, Double.NaN, 3.73, Double.NaN }, dimGln.length);
static private Matrix refdbSdGly = new Matrix(new double[] { 0.76, 0.41, 0.41, 1.63, 1.18, Double.NaN }, dimGly.length);
static private Matrix refdbSdHis = new Matrix(new double[] { 0.73, 0.52, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.94, 2.44, 2.23, Double.NaN, Double.NaN, Double.NaN, 4.09, Double.NaN, Double.NaN }, dimHis.length);
static private Matrix refdbSdIle = new Matrix(new double[] { 0.75, 0.6, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.9, 2.65, 1.93, Double.NaN, Double.NaN, Double.NaN, 4.46 }, dimIle.length);
static private Matrix refdbSdLeu = new Matrix(new double[] { 0.7, 0.52, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.91, 2.06, 1.8, Double.NaN, Double.NaN, Double.NaN, 4.13 }, dimLeu.length);
static private Matrix refdbSdLys = new Matrix(new double[] { 0.68, 0.49, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.89, 2.11, 1.72, Double.NaN, Double.NaN, Double.NaN, 3.85, Double.NaN }, dimLys.length);
static private Matrix refdbSdMet = new Matrix(new double[] { 0.65, 0.53, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 2, 2.2, 2.28, Double.NaN, Double.NaN, 3.66 }, dimMet.length);
static private Matrix refdbSdPhe = new Matrix(new double[] { 0.77, 0.61, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.99, 2.57, 2.09, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 4.23 }, dimPhe.length);
static private Matrix refdbSdPro = new Matrix(new double[] { 0.39, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.53, 1.46, 1.02, Double.NaN, Double.NaN, Double.NaN }, dimPro.length);
static private Matrix refdbSdSer = new Matrix(new double[] { 0.65, 0.45, Double.NaN, Double.NaN, Double.NaN, 1.66, 2.01, 1.5, 3.81 }, dimSer.length);
static private Matrix refdbSdThr = new Matrix(new double[] { 0.65, 0.51, Double.NaN, Double.NaN, Double.NaN, 1.65, 2.65, 1.54, Double.NaN, 4.94 }, dimThr.length);
static private Matrix refdbSdTrp = new Matrix(new double[] { 0.86, 0.58, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.87, 2.34, 1.88, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 4.65, Double.NaN }, dimTrp.length);
static private Matrix refdbSdTyr = new Matrix(new double[] { 0.79, 0.63, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 1.89, 2.52, 2.02, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 4.55 }, dimTyr.length);
static private Matrix refdbSdVal = new Matrix(new double[] { 0.72, 0.61, Double.NaN, Double.NaN, Double.NaN, 1.87, 2.9, 1.68, Double.NaN, Double.NaN, 4.85 }, dimVal.length);
static private Matrix refdbSdUnk = new Matrix(new double[] { 22.5, 22.5, 200, 200, 200, 100 }, dimUnk.length);
public static Matrix[] refdbSd = new Matrix[] { refdbSdAla, refdbSdArg, refdbSdAsp, refdbSdAsn, refdbSdCys, refdbSdGlu, refdbSdGln, refdbSdGly, refdbSdHis, refdbSdIle, refdbSdLeu, refdbSdLys, refdbSdMet, refdbSdPhe, refdbSdPro, refdbSdSer, refdbSdThr, refdbSdTrp, refdbSdTyr, refdbSdVal, refdbSdUnk };
//-----------------------------------------------------------------------------------------------
//-------------------------------------------METHODS---------------------------------------------
//-----------------------------------------------------------------------------------------------
public static String getShortName(String aa) {
int aaIndex = computeAaIndex(aa);
return aaNames1[aaIndex];
}
public static String getLongName(String aa) {
int aaIndex = computeAaIndex(aa);
return aaNames3[aaIndex];
}
public static String[] getDimensions(String aa) {
int aaIndex = computeAaIndex(aa);
return dim[aaIndex];
}
public static Matrix[] getMeanAndVar(String aaToSelect, String[] dimNamesToSelect, String priorType) {
int aaIndex = computeAaIndex(aaToSelect);
BitSet isToSelect = dimToSelect(dim[aaIndex], dimNamesToSelect);
// mean
Matrix meanToReturn = null;
if (priorType.equalsIgnoreCase("malliavin"))
meanToReturn = malMean[aaIndex].copy();
if (priorType.equalsIgnoreCase("bmrb"))
meanToReturn = bmrbMean[aaIndex].copy();
if (priorType.equalsIgnoreCase("refdb"))
meanToReturn = refdbMean[aaIndex].copy();
meanToReturn = Util.subset(meanToReturn, isToSelect, null);
// var
Matrix varToReturn = null;
if (priorType.equalsIgnoreCase("malliavin"))
varToReturn = malVar[aaIndex].copy();
else {
Matrix sdToReturn = null;
if (priorType.equalsIgnoreCase("bmrb"))
sdToReturn = bmrbSd[aaIndex].copy();
if (priorType.equalsIgnoreCase("refdb"))
sdToReturn = refdbSd[aaIndex].copy();
varToReturn = new Matrix(sdToReturn.getRowDimension(), sdToReturn.getRowDimension());
for (int i = 0; i < sdToReturn.getRowDimension(); i++)
varToReturn.set(i, i, sdToReturn.get(i, 0) * sdToReturn.get(i, 0));
}
varToReturn = Util.subset(varToReturn, isToSelect, isToSelect);
return new Matrix[] { meanToReturn, varToReturn };
}
private static int computeAaIndex(String aa) {
int index = -1;
if (aa.length() == 1) {
for (index = 0; index < aaNames1.length; index++)
if (aaNames1[index].equals(aa))
break;
} else if (aa.length() == 3) {
for (index = 0; index < aaNames1.length; index++)
if (aaNames3[index].equals(aa))
break;
}
return index;
}
public static boolean hasDimension(String aa, String myDim) {
int aaIndex = computeAaIndex(aa);
for (int i = 0; i < dim[aaIndex].length; i++)
if (dim[aaIndex][i].equals(myDim))
return true;
return false;
}
private static BitSet dimToSelect(String[] origDim, String[] dimToSelect) {
BitSet isToSelect = new BitSet(0, origDim.length);
for (int i = 0; i < dimToSelect.length; i++) {
for (int j = 0; j < origDim.length; j++) {
if (dimToSelect[i].equalsIgnoreCase(origDim[j])) {
isToSelect.set(j);
break;
}
}
}
return isToSelect;
}
//-------
public static void main(String[] args) {
// means
String s;
s = "CA:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "CA")) {
double dif = Util.subset(refdbMean[i], dimToSelect(dim[i], new String[] { "CA"}), null).get(0, 0) -
Util.subset(bmrbMean[i], dimToSelect(dim[i], new String[] { "CA"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
s = "CB:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "CB")) {
double dif = Util.subset(refdbMean[i], dimToSelect(dim[i], new String[] { "CB"}), null).get(0, 0) -
Util.subset(bmrbMean[i], dimToSelect(dim[i], new String[] { "CB"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
s = "C:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "C")) {
double dif = Util.subset(refdbMean[i], dimToSelect(dim[i], new String[] { "C"}), null).get(0, 0) -
Util.subset(bmrbMean[i], dimToSelect(dim[i], new String[] { "C"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
s = "HA:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "HA")) {
double dif = Util.subset(refdbMean[i], dimToSelect(dim[i], new String[] { "HA"}), null).get(0, 0) -
Util.subset(bmrbMean[i], dimToSelect(dim[i], new String[] { "HA"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
s = "HA2:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "HA2")) {
double dif = Util.subset(refdbMean[i], dimToSelect(dim[i], new String[] { "HA2"}), null).get(0, 0) -
Util.subset(bmrbMean[i], dimToSelect(dim[i], new String[] { "HA2"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
// variances
s = "sdCA:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "CA")) {
double dif = Util.subset(refdbSd[i], dimToSelect(dim[i], new String[] { "CA"}), null).get(0, 0) -
Util.subset(bmrbSd[i], dimToSelect(dim[i], new String[] { "CA"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
s = "sdCB:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "CB")) {
double dif = Util.subset(refdbSd[i], dimToSelect(dim[i], new String[] { "CB"}), null).get(0, 0) -
Util.subset(bmrbSd[i], dimToSelect(dim[i], new String[] { "CB"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
s = "sdC:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "C")) {
double dif = Util.subset(refdbSd[i], dimToSelect(dim[i], new String[] { "C"}), null).get(0, 0) -
Util.subset(bmrbSd[i], dimToSelect(dim[i], new String[] { "C"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
s = "sdHA:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "HA")) {
double dif = Util.subset(refdbSd[i], dimToSelect(dim[i], new String[] { "HA"}), null).get(0, 0) -
Util.subset(bmrbSd[i], dimToSelect(dim[i], new String[] { "HA"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
s = "sdHA2:\n";
for (int i = 0; i < dim.length; i++) {
if (hasDimension(aaNames1[i], "HA2")) {
double dif = Util.subset(refdbSd[i], dimToSelect(dim[i], new String[] { "HA2"}), null).get(0, 0) -
Util.subset(bmrbSd[i], dimToSelect(dim[i], new String[] { "HA2"}), null).get(0, 0);
s += aaNames3[i] + ": " + dif;
}
s += "\n";
}
Util.pln(s);
}
}
MBA2/input/CVS/ 0040755 0000765 0000024 00000000000 10066413731 013034 5 ustar janvitek staff MBA2/input/CVS/Entries 0100644 0000765 0000024 00000000443 10066413731 014366 0 ustar janvitek staff /DataGenerator.java/1.1.1.1/Fri Jun 18 14:24:20 2004//
/Residue.java/1.1.1.1/Fri Jun 18 14:24:20 2004//
/ScoreHandler.java/1.2/Mon Jun 21 02:43:10 2004//
/Protein.java/1.5/Wed Jun 23 22:45:19 2004//
/SpinSystem.java/1.3/Wed Jun 23 22:45:19 2004//
/Bmrb.java/1.2/Mon Jun 21 14:49:24 2004//
D
MBA2/input/CVS/Repository 0100644 0000765 0000024 00000000026 10065433506 015132 0 ustar janvitek staff /p/sss/cvs/MBA2/input
MBA2/input/CVS/Root 0100644 0000765 0000024 00000000050 10065433506 013673 0 ustar janvitek staff :ext:jv@arthur.cs.purdue.edu:/p/sss/cvs
MBA2/input/CVS/Template 0100644 0000765 0000024 00000000000 10065433506 014516 0 ustar janvitek staff MBA2/input/DataGenerator.java 0100644 0000765 0000024 00000046244 10064575424 016001 0 ustar janvitek staff package input;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Random;
import java.util.StringTokenizer;
import util.Util;
import assign.Worker;
public class DataGenerator {
// original data
String comment = "";
String sequence = "";
double[][] trueChemicalShifts;
// simulated data
Random random = new Random();
//-----------------------------------------------------------------------------------------
//------------------------------------CONSTRUCTORS-----------------------------------------
//-----------------------------------------------------------------------------------------
//---------- takes data in the bmrb format and writes into the mba and txt formats---------
public DataGenerator(String inFileREFDB, String outFileTxt, String outFileMBA_full, String outFileMBA, double hnv, double nv, double cov, double cav, double cbv, double hav) {
// read the BMRB file and memorise
readTrueDataREFDBformat(inFileREFDB);
Util.pln("The original data has " + sequence.length() + " positions.");
// generate simulated chemical shifts
if (!outFileMBA.equals(""))
simulateMissingChemicalShifts();
// write the simulated data in the readable format
writeTrueChemicalShiftsTxtFormat(outFileTxt);
//write the simulated spin systems into the outFile in the MBA format
if (outFileMBA.equals(""))
return;
writeSimSpinSystemsMBAformat(outFileMBA_full, outFileMBA, hnv, nv, cov, cav, cbv, hav);
}
//----------------------- takes data in the txt format and memorizes-------------------------------------
public DataGenerator(String inFileTXT) {
trueChemicalShifts = new double[Worker.protein.getLength()][8];
try {
BufferedReader inputStream = new BufferedReader(new FileReader(inFileTXT));
String line = inputStream.readLine();
int pos = 0;
while (line != null) {
StringTokenizer tokenizer = new StringTokenizer(line, ",");
tokenizer.nextToken();
for (int j = 0; j < 8; j++)
trueChemicalShifts[pos][j] = Double.parseDouble(tokenizer.nextToken().trim());
pos++;
line = inputStream.readLine();
}
inputStream.close();
} catch (FileNotFoundException e) {
Util.pln("File " + inFileTXT + " not found. The program will now stop");
System.exit(0);
} catch (IOException e) {
Util.pln("Error reading from file " + inFileTXT + ". The program will now stop");
System.exit(0);
}
}
//-----------------------------------------------------------------------------------------
//----------------------------------------METHODS------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------read the original data in REFDB format----------------------------------
private void readTrueDataREFDBformat(String inFileBMRB) {
try {
BufferedReader inputStream = new BufferedReader(new FileReader(inFileBMRB));
// comment and sequence
comment = "Protein " + inputStream.readLine();
sequence = inputStream.readLine();
comment += "; " + sequence.length() + " residues.";
// original spin systems: array with columns id, HN, N15, CO, CA, CB, HA, HA2
trueChemicalShifts = new double[sequence.length()][8];
for (int i = 0; i < sequence.length(); i++) {
for (int j = 0; j < 8; j++)
trueChemicalShifts[i][j] = Double.NaN;
}
String line = inputStream.readLine();
while (line != null) {
StringTokenizer tokenizer = new StringTokenizer(line, " ");
int pos = -1;
int dim = -1;
double chemicalShift = -1;
for (int i = 0; i < 6; i++) {
if (i == 1)
pos = (int) Integer.parseInt(tokenizer.nextToken()) - 1;
if (i == 3) {
String dimName = tokenizer.nextToken();
if (dimName.equals("H"))
dim = 1;
if (dimName.equals("N"))
dim = 2;
if (dimName.equals("C"))
dim = 3;
if (dimName.equals("CA"))
dim = 4;
if (dimName.equals("CB"))
dim = 5;
if (dimName.equals("HA") || dimName.equals("HA2"))
dim = 6;
if (dimName.equals("HA3"))
dim = 7;
}
if (i == 5)
chemicalShift = (double) Double.parseDouble(tokenizer.nextToken());
if (i == 0 || i == 2 || i == 4)
tokenizer.nextToken();
}
if (pos != -1 && dim != -1) {
trueChemicalShifts[pos][0] = pos;
trueChemicalShifts[pos][dim] = chemicalShift;
}
line = inputStream.readLine();
}
inputStream.close();
} catch (FileNotFoundException e) {
Util.pln("File " + inFileBMRB + " not found. The program will now stop");
System.exit(0);
} catch (IOException e) {
Util.pln("Error reading from file " + inFileBMRB + ". The program will now stop");
System.exit(0);
}
// generate missing position ids
for (int pos = 0; pos < sequence.length(); pos++)
if (Double.isNaN(trueChemicalShifts[pos][0]))
trueChemicalShifts[pos][0] = pos;
}
//---------------------------------generate simulated chemical shifts -------------------------------------------------------
private void simulateMissingChemicalShifts() {
String[] resTypes = { "H", "N", "C", "CA", "CB", "HA", "HA2" };
for (int pos = 0; pos < sequence.length(); pos++) {
// simulated residue
Residue r = new Residue(sequence.substring(pos, pos + 1));
r.simulate();
for (int i = 1; i < 8; i++)
if (Double.isNaN(trueChemicalShifts[pos][i]))
trueChemicalShifts[pos][i] = r.getSimChemicalShift(resTypes[i - 1]);
}
}
//-------------------write the simulated chemical shifts in the readable format----------------------------------
private void writeTrueChemicalShiftsTxtFormat(String outFileTxt) {
PrintWriter outputStream = null;
try {
outputStream = new PrintWriter(new FileOutputStream(outFileTxt));
} catch (FileNotFoundException e) {
Util.pln("The output file for TXT format could not be created. The program will now stop");
System.exit(0);
}
String s = "";
for (int pos = 0; pos < sequence.length(); pos++) {
s += sequence.substring(pos, pos + 1) + "," + Util.pad("" + ((int) trueChemicalShifts[pos][0]), 8);
for (int j = 1; j < 8; j++)
s += "," + Util.pad("" + Util.round(trueChemicalShifts[pos][j], 2), 8);
s += "\n";
}
outputStream.print(s);
outputStream.close();
}
//-------------------write the simulated spin systems into the outFile in the MBA format----------------------------------
private void writeSimSpinSystemsMBAformat(String outFileMBA_full, String outFileMBA, double hv, double nv, double cov, double cav, double cbv, double hav) {
String s_full = "";
String s = "";
int countMissingSS = 0;
String simMissingSSat = "";
int countExtraSS = 0;
for (int pos = 1; pos < sequence.length(); pos++) {
if (sequence.substring(pos, pos + 1).equals("P"))
continue;
// correct spin system
String t =
pos
+ ","
+ Util.round(trueChemicalShifts[pos][1] + random.nextGaussian() * Math.sqrt(hv), 2)
+ ","
+ Util.round(trueChemicalShifts[pos][2] + random.nextGaussian() * Math.sqrt(nv), 2)
+ ",";
// C-1
if (random.nextDouble() > 0.006225374)
t += Util.round(trueChemicalShifts[pos - 1][3] + random.nextGaussian() * Math.sqrt(cov), 2) + ",";
else
t += Double.NaN + ",";
// CA-1
if (random.nextDouble() > 0.001173709)
t += Util.round(trueChemicalShifts[pos - 1][4] + random.nextGaussian() * Math.sqrt(cav), 2) + ",";
else
t += Double.NaN + ",";
// CB -1
if (random.nextDouble() > 0.1709347)
t += Util.round(trueChemicalShifts[pos - 1][5] + random.nextGaussian() * Math.sqrt(cbv), 2) + ",";
else
t += Double.NaN + ",";
// HA-1
if (random.nextDouble() > 0.01450494)
t += Util.round(trueChemicalShifts[pos - 1][6] + random.nextGaussian() * Math.sqrt(hav), 2) + ",";
else
t += Double.NaN + ",";
//HA2-1
if (random.nextDouble() > 0.01450494)
t += Util.round(trueChemicalShifts[pos - 1][7] + random.nextGaussian() * Math.sqrt(hav), 2) + ",";
else
t += Double.NaN + ",";
// C
if (random.nextDouble() > 0.07178364)
t += Util.round(trueChemicalShifts[pos][3] + random.nextGaussian() * Math.sqrt(cov), 2) + ",";
else
t += Double.NaN + ",";
// CA
if (random.nextDouble() > 0.002564103)
t += Util.round(trueChemicalShifts[pos][4] + random.nextGaussian() * Math.sqrt(cav), 2) + ",";
else
t += Double.NaN + ",";
// CB
if (random.nextDouble() > 0.2310209)
t += Util.round(trueChemicalShifts[pos][5] + random.nextGaussian() * Math.sqrt(cbv), 2) + ",";
else
t += Double.NaN + ",";
// HA
if (random.nextDouble() > 0.03232091)
t += Util.round(trueChemicalShifts[pos][6] + random.nextGaussian() * Math.sqrt(hav), 2) + ",";
else
t += Double.NaN + ",";
// HA2
if (random.nextDouble() > 0.03232091)
t += Util.round(trueChemicalShifts[pos][7] + random.nextGaussian() * Math.sqrt(hav), 2) + ",";
else
t += Double.NaN + ",";
// HNv
t += hv + ","
// N15v
+nv + ","
// COv
+cov + ","
// CAv
+cav + ","
// CBv
+cbv + ","
// HAv
+hav + ","
// HA2v
+hav + ","
//COv
+cov + ","
// CAv
+cav + ","
// CBv
+cbv + ","
// HAv
+hav + ","
// HA2v
+hav + ",\n";
s_full += t;
if (random.nextDouble() < 0.02) {
simMissingSSat += pos + ",";
countMissingSS++;
} else
s += t;
// no extra spin system
if (random.nextDouble() > 0.15)
continue;
// extra spin system: different from the existing spin systems
boolean isSimilar = random.nextDouble() < 0.06906907;
if (isSimilar == false) {
Residue r1 = new Residue(sequence.substring(pos - 1, pos));
r1.simulate();
Residue r2 = new Residue(sequence.substring(pos, pos + 1));
r2.simulate();
t = (pos + 1000) + "," + Util.round(r2.getSimChemicalShift("H"), 2) + "," + Util.round(r2.getSimChemicalShift("N"), 2) + ",";
// C-1
if (random.nextDouble() > 0.175488)
t += Util.round(r1.getSimChemicalShift("C"), 2) + ",";
else
t += Double.NaN + ",";
// CA-1
if (random.nextDouble() > 0.3617117)
t += Util.round(r1.getSimChemicalShift("CA"), 2) + ",";
else
t += Double.NaN + ",";
// CB-1
if (random.nextDouble() > 0.3781907)
t += Util.round(r1.getSimChemicalShift("CB"), 2) + ",";
else
t += Double.NaN + ",";
// HA-1
if (random.nextDouble() > 0.4354354)
t += Util.round(r1.getSimChemicalShift("HA"), 2) + ",";
else
t += Double.NaN + ",";
// HA2-1
if (random.nextDouble() > 0.4354354)
t += Util.round(r1.getSimChemicalShift("HA2"), 2) + ",";
else
t += Double.NaN + ",";
// C
if (random.nextDouble() > 0.6955706)
t += Util.round(r2.getSimChemicalShift("C"), 2) + ",";
else
t += Double.NaN + ",";
// CA
if (random.nextDouble() > 0.2337838)
t += Util.round(r2.getSimChemicalShift("CA"), 2) + ",";
else
t += Double.NaN + ",";
// CB
if (random.nextDouble() > 0.5110736)
t += Util.round(r2.getSimChemicalShift("CB"), 2) + ",";
else
t += Double.NaN + ",";
// HA
if (random.nextDouble() > 0.4354354)
t += Util.round(r2.getSimChemicalShift("HA"), 2) + ",";
else
t += Double.NaN + ",";
// HA2
if (random.nextDouble() > 0.4354354)
t += Util.round(r2.getSimChemicalShift("HA2"), 2) + ",";
else
t += Double.NaN + ",";
}
// extra spin system: similar to the existing spin systems
if (isSimilar == true) {
t = (pos + 1000)
+ ","
+ Util.round(trueChemicalShifts[pos][1] + random.nextGaussian() * Math.sqrt(hv), 2)
+ ","
+ Util.round(trueChemicalShifts[pos][2] + random.nextGaussian() * Math.sqrt(nv), 2)
+ ",";
// C-1
if (random.nextDouble() > 0.175488)
t += Util.round(trueChemicalShifts[pos - 1][3] + random.nextGaussian() * Math.sqrt(cov), 2) + ",";
else
t += Double.NaN + ",";
// CA-1
if (random.nextDouble() > 0.3617117)
t += Util.round(trueChemicalShifts[pos - 1][4] + random.nextGaussian() * Math.sqrt(cav), 2) + ",";
else
t += Double.NaN + ",";
// CB -1
if (random.nextDouble() > 0.3781907)
t += Util.round(trueChemicalShifts[pos - 1][5] + random.nextGaussian() * Math.sqrt(cbv), 2) + ",";
else
t += Double.NaN + ",";
// HA-1
if (random.nextDouble() > 0.4354354)
t += Util.round(trueChemicalShifts[pos - 1][6] + random.nextGaussian() * Math.sqrt(hav), 2) + ",";
else
t += Double.NaN + ",";
//HA2-1
if (random.nextDouble() > 0.4354354)
t += Util.round(trueChemicalShifts[pos - 1][7] + random.nextGaussian() * Math.sqrt(hav), 2) + ",";
else
t += Double.NaN + ",";
// C
if (random.nextDouble() > 0.6955706)
t += Util.round(trueChemicalShifts[pos][3] + random.nextGaussian() * Math.sqrt(cov), 2) + ",";
else
t += Double.NaN + ",";
// CA
if (random.nextDouble() > 0.2337838)
t += Util.round(trueChemicalShifts[pos][4] + random.nextGaussian() * Math.sqrt(cav), 2) + ",";
else
t += Double.NaN + ",";
// CB
if (random.nextDouble() > 0.5110736)
t += Util.round(trueChemicalShifts[pos][5] + random.nextGaussian() * Math.sqrt(cbv), 2) + ",";
else
t += Double.NaN + ",";
// HA
if (random.nextDouble() > 0.03232091)
t += Util.round(trueChemicalShifts[pos][6] + random.nextGaussian() * Math.sqrt(hav), 2) + ",";
else
t += Double.NaN + ",";
// HA2
if (random.nextDouble() > 0.2387387)
t += Util.round(trueChemicalShifts[pos][7] + random.nextGaussian() * Math.sqrt(hav), 2) + ",";
else
t += Double.NaN + ",";
}
t += hv + "," + nv + "," + cov + "," + cav + "," + cbv + "," + hav + "," + hav + "," + cov + "," + cav + "," + cbv + "," + hav + "," + hav + ",\n";
s_full += t;
s += t;
countExtraSS++;
}
// no missing spin systems
PrintWriter outputStream = null;
try {
outputStream = new PrintWriter(new FileOutputStream(outFileMBA_full));
} catch (FileNotFoundException e) {
Util.pln("The output file " + outFileMBA_full + " could not be created. The program will now stop");
System.exit(0);
}
// comment and sequence
outputStream.println(comment);
outputStream.println(sequence);
outputStream.println(Integer.MIN_VALUE);
outputStream.print(s_full);
outputStream.close();
// missing spin systems
try {
outputStream = new PrintWriter(new FileOutputStream(outFileMBA));
} catch (FileNotFoundException e) {
Util.pln("The output file " + outFileMBA + " could not be created. The program will now stop");
System.exit(0);
}
// comment and sequence
outputStream.println(comment);
outputStream.println(sequence);
outputStream.println(simMissingSSat);
outputStream.print(s);
outputStream.close();
Util.pln("There are " + countMissingSS + " missing and " + countExtraSS + " extra spin systems");
}
//-----------------------------------------------------------------------------------------
//---------------------------------------ACCESSORS-----------------------------------------
//-----------------------------------------------------------------------------------------
public double getTrueCA(int pos) {
return trueChemicalShifts[pos][4];
}
}
MBA2/input/Protein.java 0100644 0000765 0000024 00000024536 10066403777 014704 0 ustar janvitek staff /*
* Created on Dec 22, 2003
*
* To change the template for this generated file go to
* Window>Preferences>Java>Code Generation>Code and Comments
*/
package input;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.Arrays;
import java.util.Comparator;
import java.util.StringTokenizer;
import util.BitSet;
import util.Util;
import assign.Worker;
import assign.Worker.Argument;
public class Protein {
// protein
private String comment;
private int length;
private Residue[] sequence;
private BitSet isAssignablePos;
private BitSet isAssignedInReference;
private int lastPos;
private SpinSystem[] spinSystems;
private SpinSystem[] rejectedSpinSystems;
//-----------------------------------------------------------------------
//-----------------------------CONSTRUCTOR-------------------------------
//-----------------------------------------------------------------------
//---------------constructor from both real and simulated data-----------
// takes data in MBA format brom a file and constructs a protein
public Protein(String file, Argument arg) {
BufferedReader inputStream = null;
int j = 0;
int k = 0;
try {
inputStream = new BufferedReader(new FileReader(file));
// comment
comment = inputStream.readLine();
// length
String string = inputStream.readLine();
length = string.length();
lastPos = length - 1;
// sequence
sequence = new Residue[length];
for (int i = 0; i < length; i++)
sequence[i] = new Residue(string.substring(i, i + 1));
// set to true if assignable
isAssignablePos = new BitSet(0, length);
for (int i = 1; i < length; i++) {
if (!this.sequence[i].isProline()) {
isAssignablePos.set(i);
}
}
// is assigned in reference solution
isAssignedInReference = isAssignablePos.copy();
StringTokenizer stringTokenizer = new StringTokenizer(inputStream.readLine(), ",");
while (stringTokenizer.hasMoreTokens()) {
int pos = Integer.parseInt(stringTokenizer.nextToken());
if (pos == -1)
break;
isAssignedInReference.unset(pos);
}
// spin systems
spinSystems = new SpinSystem[length * 2];
rejectedSpinSystems = new SpinSystem[length];
String line = inputStream.readLine();
while (line != null) {
stringTokenizer = new StringTokenizer(line, ",");
spinSystems[j] =
new SpinSystem(
j,
Integer.parseInt(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
Double.parseDouble(stringTokenizer.nextToken()),
arg.tauH,
arg.tauN,
arg.tauC,
arg.tauCA,
arg.tauCB,
arg.tauHA,
arg.tauHA,
arg.tauC,
arg.tauCA,
arg.tauCB,
arg.tauHA,
arg.tauHA);
if (spinSystems[j].getChemicalShiftCount() >= arg.minChemicalShiftCount)
j++;
else {
rejectedSpinSystems[k] = spinSystems[j];
k++;
}
line = inputStream.readLine();
}
} catch (FileNotFoundException e) {
Util.pln("File " + file + " with input data not found. The program will now stop");
System.exit(0);
} catch (IOException e) {
Util.pln("Error reading from file " + file + ". The program will now stop");
System.exit(0);
}
spinSystems[j] = new SpinSystem(j);
spinSystems = (SpinSystem[]) Util.truncate(spinSystems, j + 1);
rejectedSpinSystems = (SpinSystem[]) Util.truncate(rejectedSpinSystems, k);
}
//-----------------------------------------------------------------------
//------------------------------METHODS----------------------------------
//-----------------------------------------------------------------------
public int computeMaxDf() {
SpinSystem[] copyOfSpinSystems = (SpinSystem[]) Util.copy(spinSystems);
// sort spin systems
Arrays.sort(copyOfSpinSystems, new Comparator() {
public int compare(Object a, Object b) {
return - ((SpinSystem) a).getDf() + ((SpinSystem) b).getDf();
}
});
// count number of assignable positions
int assignablePositions = 0;
for (int i = 1; i < length; i++)
if (!sequence[i].isProline())
assignablePositions++;
// compute maxDf
int maxDF = 0;
for (int i = 0; i < assignablePositions && i < spinSystems.length; i++)
maxDF += copyOfSpinSystems[i].getDf();
return maxDF;
}
public String toStringStats() {
// used data set stats
int countExtraSSused = Math.max(spinSystems.length - 1 + Worker.maxMissings - isAssignablePos.cardinality(), 0);
int countMissSSused = Worker.maxMissings;
int countMinCSused = Integer.MAX_VALUE;
int countMaxCSused = Integer.MIN_VALUE;
int countPresentResInSSused = 0;
for (int i = 0; i < spinSystems.length - 1; i++) {
countMinCSused = Math.min(countMinCSused, spinSystems[i].getChemicalShiftCount());
countMaxCSused = Math.max(countMaxCSused, spinSystems[i].getChemicalShiftCount());
countPresentResInSSused += spinSystems[i].getChemicalShiftCount();
}
double propMissResInSSused = (spinSystems.length * 8 - countPresentResInSSused) * 100 / (spinSystems.length * 8);
// original data set stats
int countMissSS = isAssignablePos.cardinality() - isAssignedInReference.cardinality();
int countExtraSS = spinSystems.length - 1 + rejectedSpinSystems.length - isAssignedInReference.cardinality();
int countMinCS = countMinCSused;
int countMaxCS = countMaxCSused;
int countPresentResInSS = countPresentResInSSused;
for (int i = 0; i < rejectedSpinSystems.length; i++) {
countMinCS = Math.min(countMinCS, rejectedSpinSystems[i].getChemicalShiftCount());
countMaxCS = Math.max(countMaxCS, rejectedSpinSystems[i].getChemicalShiftCount());
countPresentResInSS += rejectedSpinSystems[i].getChemicalShiftCount();
}
double propMissResInSS =
(spinSystems.length * 8 + rejectedSpinSystems.length * 8 - countPresentResInSS)
* 100
/ (spinSystems.length * 8 + rejectedSpinSystems.length * 8);
String s =
"\n\n\nCOMMENT:\n"
+ comment
+ "\n\n\nDESCRIPTION OF THE ORIGINAL DATA SET:"
+ "\nMissing spin systems in reference solution: "
+ countMissSS
+ "\nExtra spin systems in reference solution: "
+ countExtraSS
+ "\nMin chemical shifts per spin system in the original data set: "
+ countMinCS
+ "\nMax chemical shifts per spin system in the original data set: "
+ countMaxCS
+ "\nProp missing resonances in all observed spin systems: "
+ Util.round(propMissResInSS, 2)
+ "%";
s += "\n\n\nDESCRIPTION OF THE SPIN SYSTEMS USED"
+ "\nMissing spin systems used: "
+ countMissSSused
+ "\nExtra spin systems used: "
+ countExtraSSused
+ "\nMin chemical shifts per spin system used: "
+ countMinCSused
+ "\nMax chemical shifts per spin system used: "
+ countMaxCSused
+ "\nProp missing resonances in all spin systems used: "
+ Util.round(propMissResInSSused, 2)
+ "%";
return s;
}
//-----------------------------------------------------------------------
//------------------------------ACCESSORS----------------------------------
//-----------------------------------------------------------------------
public String getComment() {
return comment;
}
public int getLength() {
return length;
}
public int getLastPos() {
return lastPos;
}
public SpinSystem[] getSpinSystems() {
return spinSystems;
}
public BitSet getAssignablePositions() {
return isAssignablePos;
}
public BitSet getAssignedInReference() {
return isAssignedInReference;
}
public Residue getResidueAt(int i) {
return sequence[i];
}
public SpinSystem getEmptySpinSystem() {
return spinSystems[spinSystems.length - 1];
}
public SpinSystem getSpinSystemByReferenceId(int id) {
for (int i = 0; i < spinSystems.length; i++)
if (spinSystems[i].getReferenceId() == id)
return spinSystems[i];
return getEmptySpinSystem();
}
public int[] getReferenceSequenceById() {
int[] id = new int[length];
for (int pos = 0; pos < length; pos++) {
if (isAssignedInReference.test(pos) == true)
id[pos] = pos;
else
id[pos] = -1;
}
return id;
}
}
MBA2/input/Residue.java 0100644 0000765 0000024 00000005427 10064575424 014657 0 ustar janvitek staff /*
* Created on Dec 22, 2003
*
* To change the template for this generated file go to
* Window>Preferences>Java>Code Generation>Code and Comments
*/
package input;
import java.util.Random;
import util.Util;
import Jama.Matrix;
import Jama.SingularValueDecomposition;
import assign.Worker;
public class Residue {
// --------FIELDS----------------
String longName;
String shortName;
String[] dimNames = { "H", "HA", "HA2", "C", "CA", "CB", "N" };
Matrix mean;
Matrix var;
double[] simChemicalShifts = null;
// --------CONSTRUCTOR----------------
public Residue(String aa) {
if (aa.length() == 1) {
shortName = aa;
longName = Bmrb.getLongName(aa);
}
if (aa.length() == 3) {
longName = aa;
shortName = Bmrb.getShortName(aa);
}
for (int i = 0; i < dimNames.length; i++) {
if (!Bmrb.hasDimension(aa, dimNames[i]))
dimNames[i] = null;
}
dimNames = (String[]) Util.stripEmpties(dimNames);
Matrix[] meanAndVar = Bmrb.getMeanAndVar(aa, dimNames, Worker.priorType);
mean = meanAndVar[0];
var = meanAndVar[1];
}
// --------METHODS----------------
public boolean isProline() {
return shortName.equals("P");
}
public boolean isGlycine() {
return shortName.equals("G");
}
public void simulate() {
Random random = new Random();
SingularValueDecomposition svd = var.svd();
Matrix S = svd.getS();
for (int i = 0; i < S.getColumnDimension(); i++) {
if (S.get(0, 0) == 0) {
Util.pln("Singular prior variance for residue type " + shortName + ". Can not simulate missing resonances. The program will now stop.");
System.exit(0);
}
S.set(i, i, Math.sqrt(S.get(i, i)));
}
Matrix simVar = svd.getU().times(S).times(svd.getV().transpose());
Matrix x = new Matrix(var.getRowDimension(), 1);
for (int i = 0; i < var.getRowDimension(); i++)
x.set(i, 0, random.nextGaussian());
simChemicalShifts = mean.plus(simVar.times(x)).getColumnPackedCopy();
}
// --------ACCESSORS----------------
public String getShortName() {
return shortName;
}
public String getLongName() {
return longName;
}
public String[] getDimNames() {
return dimNames;
}
public Matrix getMean() {
return mean;
}
public Matrix getVar() {
return var;
}
public double getSimChemicalShift(String resType) {
for (int i = 0; i < dimNames.length; i++)
if (dimNames[i].equals(resType))
return simChemicalShifts[i];
return Double.NaN;
}
}
MBA2/input/ScoreHandler.java 0100644 0000765 0000024 00000046164 10065445476 015637 0 ustar janvitek staff package input;
import util.BitSet;
import util.ChiSquareDistribution;
import util.Util;
import Jama.Matrix;
import assign.Worker;
public class ScoreHandler {
private Protein protein = Worker.protein;
private double alpha;
private double[][] scoreMatch;
private double[][][] scoreAlign;
private double[][][] scoreJoint;
private int[][] dfAlign;
private int[][] dfMatch;
private int[][] dfJoint;
private boolean[][] isValidMatch;
private boolean[][][] isValidAlign;
private boolean[][][] isValidJoint;
private int numberValidPairs;
private double maxScoreJoint;
//-----------------------------------------------------------------------
//---------------------------CONSTRUCTOR---------------------------------
//-----------------------------------------------------------------------
public ScoreHandler(boolean insure) {
alpha = Worker.alpha;
maxScoreJoint = ChiSquareDistribution.quantile(1 - alpha, protein.computeMaxDf()); //900 for fgf
int l = protein.getSpinSystems().length;
int p = protein.getLength();
scoreMatch = new double[l][l];
scoreAlign = new double[p][l][l];
scoreJoint = new double[p][l][l];
dfAlign = new int[l][l];
dfMatch = new int[l][l];
dfJoint = new int[l][l];
isValidMatch = new boolean[l][l];
isValidAlign = new boolean[p][l][l];
isValidJoint = new boolean[p][l][l];
numberValidPairs = 0;
for (int i = 0; i < l; i++) {
for (int j = 0; j < l; j++) {
SpinSystem within = protein.getSpinSystems()[i];
SpinSystem seq = protein.getSpinSystems()[j];
boolean order = orderHA(within.getHAw(), within.getHA2w(), seq.getHAs(), seq.getHA2s(), within.getHAwv(), within.getHA2wv(), seq.getHAsv(), seq.getHA2sv());
scoreMatch[i][j] = computeScoreMatch(within, seq, order);
dfMatch[i][j] = computeDfMatch(within, seq, order);
isValidMatch[i][j] = isValid(scoreMatch[i][j], dfMatch[i][j]);
dfAlign[i][j] = computeDfAlign(within, seq, order);
dfJoint[i][j] = dfAlign[i][j] + dfMatch[i][j];
for (int pos = 0; pos < p; pos++) {
if (!isValidMatch[i][j]) {
scoreAlign[pos][i][j] = -1;
isValidAlign[pos][i][j] = false;
scoreJoint[pos][i][j] = -1;
isValidJoint[pos][i][j] = false;
continue;
} else {
scoreAlign[pos][i][j] = computeScoreAlign(within, seq, order, pos);
isValidAlign[pos][i][j] = isValid(scoreAlign[pos][i][j], dfAlign[i][j]);
scoreJoint[pos][i][j] = scoreAlign[pos][i][j] + scoreMatch[i][j];
isValidJoint[pos][i][j] = isValid(scoreJoint[pos][i][j], dfJoint[i][j]);
}
if (isValidMatch[i][j] && isValidAlign[pos][i][j] && isValidJoint[pos][i][j])
numberValidPairs++;
}
}
}
if (insure)
insureUniqueMatch();
}
//-----------------------------------------------------------------------
//------------------------------METHODS----------------------------------
//-----------------------------------------------------------------------
// -------------is the score valid-------------------------------------------
public boolean isValid(double score, int df) {
if (df < 0 || score < 0)
return false;
if (df == 0 && score == 0)
return true;
if (df == 0 && score > 0)
return false;
return score < ChiSquareDistribution.quantile(1 - alpha, df);
}
// -------------df of alignment-------------------------------------------
public int computeDfAlign(SpinSystem within, SpinSystem seq, boolean order) {
int df = 0;
if (!Double.isNaN(within.getHw()))
df += 1;
if (!Double.isNaN(within.getNw()))
df += 1;
if (!Double.isNaN(within.getCw()) || !Double.isNaN(seq.getCs()))
df += 1;
if (!Double.isNaN(within.getCAw()) || !Double.isNaN(seq.getCAs()))
df += 1;
if (!Double.isNaN(within.getCBw()) || !Double.isNaN(seq.getCBs()))
df += 1;
if (!Double.isNaN(within.getHAw()) || !Double.isNaN(seq.getHAs())) {
if (order) {
df += 1;
if (!Double.isNaN(within.getHA2w()) || !Double.isNaN(seq.getHA2s()))
df += 1;
} else {
if (!Double.isNaN(within.getHAw()) || !Double.isNaN(seq.getHA2s()))
df += 1;
if (!Double.isNaN(within.getHA2w()) || !Double.isNaN(seq.getHAs()))
df += 1;
}
}
return df;
}
// -------------df of match-------------------------------------------
private int computeDfMatch(SpinSystem within, SpinSystem seq, boolean order) {
int df = 0;
if (!Double.isNaN(within.getCw()) && !Double.isNaN(seq.getCs()))
df += 1;
if (!Double.isNaN(within.getCAw()) && !Double.isNaN(seq.getCAs()))
df += 1;
if (!Double.isNaN(within.getCBw()) && !Double.isNaN(seq.getCBs()))
df += 1;
if (!Double.isNaN(within.getHAw()) && !Double.isNaN(seq.getHAs())) {
if (order) {
df += 1;
if (!Double.isNaN(within.getHA2w()) && !Double.isNaN(seq.getHA2s()))
df += 1;
} else {
if (!Double.isNaN(within.getHAw()) && !Double.isNaN(seq.getHA2s()))
df += 1;
if (!Double.isNaN(within.getHA2w()) && !Double.isNaN(seq.getHAs()))
df += 1;
}
}
return df;
}
// --------------score of alignment------------------------------------------
public double computeScoreAlign(SpinSystem within, SpinSystem seq, boolean order, int pos) throws Error {
// alignment before an unassignable position
if (protein.getAssignablePositions().test(pos + 1) == false && !seq.isEmpty())
return -1;
// alignment to an unassignable position
if (protein.getAssignablePositions().test(pos) == false && !within.isEmpty())
return -1;
// alignment to the last position
if (pos == protein.getLastPos() && !seq.isEmpty())
return -1;
// restrictions for Gly
Residue residue = protein.getResidueAt(pos);
if (residue.isGlycine() && !within.canBeGly())
return -1;
if (!residue.isGlycine() && !within.canBeNonGly())
return -1;
if (residue.isGlycine() && !seq.canFollowGly())
return -1;
if (!residue.isGlycine() && !seq.canFollowNonGly())
return -1;
// compute the score
//H, HA, HA2, HA3, C, CA, CB, N
Matrix mean = residue.getMean().copy();
Matrix var = residue.getVar().copy();
String[] dimNames = residue.getDimNames();
BitSet dimUsed = new BitSet(0, var.getColumnDimension());
for (int i = 0; i < dimNames.length; i++) {
if (dimNames[i] == "H" && !Double.isNaN(within.getHw())) {
mean.set(i, 0, updateMean(within.getHw(), Double.NaN, mean.get(i, 0)));
var.set(i, i, updateVar(within.getHw(), Double.NaN, within.getHwv(), Double.NaN, var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "N" && !Double.isNaN(within.getNw())) {
mean.set(i, 0, updateMean(within.getNw(), Double.NaN, mean.get(i, 0)));
var.set(i, i, updateVar(within.getNw(), Double.NaN, within.getNwv(), Double.NaN, var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "C" && (!Double.isNaN(within.getCw()) || !Double.isNaN(seq.getCs()))) {
mean.set(i, 0, updateMean(within.getCw(), seq.getCs(), mean.get(i, 0)));
var.set(i, i, updateVar(within.getCw(), seq.getCs(), within.getCwv(), seq.getCsv(), var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "CA" && (!Double.isNaN(within.getCAw()) || !Double.isNaN(seq.getCAs()))) {
mean.set(i, 0, updateMean(within.getCAw(), seq.getCAs(), mean.get(i, 0)));
var.set(i, i, updateVar(within.getCAw(), seq.getCAs(), within.getCAwv(), seq.getCAsv(), var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "CB" && (!Double.isNaN(within.getCBw()) || !Double.isNaN(seq.getCBs()))) {
mean.set(i, 0, updateMean(within.getCBw(), seq.getCBs(), mean.get(i, 0)));
var.set(i, i, updateVar(within.getCBw(), seq.getCBs(), within.getCBwv(), seq.getCBsv(), var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "HA" && (!Double.isNaN(within.getHAw()) || !Double.isNaN(seq.getHAs()))) {
mean.set(i, 0, updateMean(within.getHAw(), seq.getHAs(), mean.get(i, 0)));
var.set(i, i, updateVar(within.getHAw(), seq.getHAs(), within.getHAwv(), seq.getHAsv(), var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "HA2" && order && (!Double.isNaN(within.getHAw()) || !Double.isNaN(seq.getHAs()))) {
mean.set(i, 0, updateMean(within.getHAw(), seq.getHAs(), mean.get(i, 0)));
var.set(i, i, updateVar(within.getHAw(), seq.getHAs(), within.getHAwv(), seq.getHAsv(), var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "HA2" && !order && (!Double.isNaN(within.getHAw()) || !Double.isNaN(seq.getHA2s()))) {
mean.set(i, 0, updateMean(within.getHAw(), seq.getHA2s(), mean.get(i, 0)));
var.set(i, i, updateVar(within.getHAw(), seq.getHA2s(), within.getHAwv(), seq.getHA2sv(), var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "HA3" && order && (!Double.isNaN(within.getHA2w()) || !Double.isNaN(seq.getHA2s()))) {
mean.set(i, 0, updateMean(within.getHA2w(), seq.getHA2s(), mean.get(i, 0)));
var.set(i, i, updateVar(within.getHA2w(), seq.getHA2s(), within.getHA2wv(), seq.getHA2sv(), var.get(i, i)));
dimUsed.set(i);
}
if (dimNames[i] == "HA3" && !order && (!Double.isNaN(within.getHA2w()) || !Double.isNaN(seq.getHAs()))) {
mean.set(i, 0, updateMean(within.getHA2w(), seq.getHAs(), mean.get(i, 0)));
var.set(i, i, updateVar(within.getHA2w(), seq.getHAs(), within.getHA2wv(), seq.getHAsv(), var.get(i, i)));
dimUsed.set(i);
}
}
if (dimUsed.cardinality() == 0)
return 0;
mean = Util.subset(mean, dimUsed, null);
var = Util.subset(var, dimUsed, dimUsed);
if (var.rank() < var.getColumnDimension())
throw new Error("Singular variance matrix");
return mean.transpose().times(var.inverse()).times(mean).get(0, 0);
//-----
}
// --------------score of match----------------------------------------------
private double computeScoreMatch(SpinSystem within, SpinSystem seq, boolean order) {
// match of a spin system with itself is impossible
if (!seq.isEmpty() && within.getReferenceId() == seq.getReferenceId())
return -1000;
double score = 0;
if (!Double.isNaN(within.getCw()) && !Double.isNaN(seq.getCs()))
score += computeScore(within.getCw(), seq.getCs(), within.getCwv(), seq.getCsv());
if (!Double.isNaN(within.getCAw()) && !Double.isNaN(seq.getCAs()))
score += computeScore(within.getCAw(), seq.getCAs(), within.getCAwv(), seq.getCAsv());
if (!Double.isNaN(within.getCBw()) && !Double.isNaN(seq.getCBs()))
score += computeScore(within.getCBw(), seq.getCBs(), within.getCBwv(), seq.getCBsv());
if (!Double.isNaN(within.getHAw()) && !Double.isNaN(seq.getHAs())) {
if (order) {
score += computeScore(within.getHAw(), seq.getHAs(), within.getHAwv(), seq.getHAsv());
score += computeScore(within.getHA2w(), seq.getHA2s(), within.getHA2wv(), seq.getHA2sv());
} else {
score += computeScore(within.getHAw(), seq.getHA2s(), within.getHAwv(), seq.getHA2sv());
score += computeScore(within.getHA2w(), seq.getHAs(), within.getHA2wv(), seq.getHAsv());
}
}
return score;
}
// -------------------score of match in one dimension-------------------------------
private double computeScore(double x1, double x2, double x1v, double x2v) {
if (!Double.isNaN(x1) && !Double.isNaN(x2)) {
double x_sub = x1 - x2;
return (x_sub * x_sub) / (x1v + x2v);
} else
return 0;
}
// ----compute mean chemical shift in one dimension for alignment with covariance----
private double updateMean(double x1, double x2, double theta) {
if (Double.isNaN(x1) && !Double.isNaN(x2)) {
return x2 - theta;
} else if (!Double.isNaN(x1) && Double.isNaN(x2)) {
return x1 - theta;
} else if (!Double.isNaN(x1) && !Double.isNaN(x2)) {
return (x1 + x2) / 2 - theta;
} else
return Double.MAX_VALUE;
}
// ---update the posterior variance in one dimension for alignment with covariance---
private double updateVar(double x1, double x2, double x1v, double x2v, double sigma) {
if (Double.isNaN(x1) && !Double.isNaN(x2)) {
return sigma + x2v;
} else if (!Double.isNaN(x1) && Double.isNaN(x2)) {
return sigma + x1v;
} else if (!Double.isNaN(x1) && !Double.isNaN(x2)) {
return sigma + x1v + x1v / 4 + x2v / 4;
}
return -1;
}
// -----------determine the order of HA and HA2--------------------
private boolean orderHA(double x11, double x12, double x21, double x22, double x11v, double x12v, double x21v, double x22v) {
if (!Double.isNaN(x12) || !Double.isNaN(x22)) {
double score11 = computeScore(x11, x21, x11v, x21v);
double score22 = computeScore(x12, x22, x12v, x22v);
double score12 = computeScore(x11, x22, x11v, x22v);
double score21 = computeScore(x12, x21, x12v, x21v);
if (score11 + score22 <= score12 + score21)
return true;
else
return false;
} else
return true;
}
private void insureUniqueMatch() {
BitSet uniqueMatch = new BitSet(0, protein.getSpinSystems().length);
for (int i = 0; i < protein.getSpinSystems().length; i++) {
if (isUniquelyFollowed(i))
uniqueMatch.set(i);
}
//set unique
for (int i = 0; i < protein.getSpinSystems().length; i++)
if (uniqueMatch.test(i))
for (int j = 0; j < protein.getSpinSystems().length; j++) {
isValidMatch[i][j] = false;
isValidMatch[j][i + 1] = false;
isValidMatch[i][i + 1] = true;
}
}
//-----------------------------------------------------------------------
//-----------------------COMPUTATION OF STATISTICS-----------------------
//-----------------------------------------------------------------------
public String toStringStats() {
double meanNumberFollowingSpinSystems = 0;
for (int i = 0; i < protein.getSpinSystems().length - 1; i++) {
meanNumberFollowingSpinSystems += computeNumberFollowingSpinSystems(i);
}
meanNumberFollowingSpinSystems = meanNumberFollowingSpinSystems / (protein.getSpinSystems().length - 1);
int numberUniquelyFollowedSpinSystems = 0;
for (int i = 0; i < protein.getSpinSystems().length - 1; i++) {
if (isUniquelyFollowed(i))
numberUniquelyFollowedSpinSystems++;
}
String s =
"\n\nDESCRIPTION OF THE SCORES:\nNumber of valid pairs = "
+ numberValidPairs
+ "\nMean number of following spin systems: "
+ Util.round(meanNumberFollowingSpinSystems, 2)
+ ";\nNumber of uniquely followed spin systems: "
+ numberUniquelyFollowedSpinSystems
+ " (Prop out of number of non-missing SS: "
+ Util.round(((double) numberUniquelyFollowedSpinSystems * 100) / (protein.getSpinSystems().length - 1), 2)
+ "%).\n";
return s;
}
private int computeNumberFollowingSpinSystems(int spinSystemId) {
int result = 0;
for (int i = 0; i < protein.getSpinSystems().length - 1; i++)
if (isValidMatch[spinSystemId][i])
result++;
return result;
}
private int computeNumberPreceedingSpinSystems(int spinSystemId) {
int result = 0;
for (int i = 0; i < protein.getSpinSystems().length - 1; i++)
if (isValidMatch[i][spinSystemId])
result++;
return result;
}
private boolean isUniquelyFollowed(int spinSystemId) {
if (computeNumberFollowingSpinSystems(spinSystemId) != 1)
return false;
int i;
for (i = 0; i < protein.getSpinSystems().length - 1; i++)
if (isValidMatch[spinSystemId][i] && i != spinSystemId)
break;
if (computeNumberPreceedingSpinSystems(i) == 1)
return true;
else
return false;
}
//-----------------------------------------------------------------------
//-----------------------------ACCESSORS---------------------------------
//-----------------------------------------------------------------------
public double getScoreAlign(int pos, SpinSystem within, SpinSystem seq) {
return scoreAlign[pos][within.getId()][seq.getId()];
}
public double getScoreMatch(SpinSystem within, SpinSystem seq) {
return scoreMatch[within.getId()][seq.getId()];
}
public double getScoreJoint(int pos, SpinSystem within, SpinSystem seq) {
return scoreJoint[pos][within.getId()][seq.getId()];
}
public int getDfAlign(SpinSystem within, SpinSystem seq) {
return dfAlign[within.getId()][seq.getId()];
}
public int getDfMatch(SpinSystem within, SpinSystem seq) {
return dfMatch[within.getId()][seq.getId()];
}
public int getDfJoint(SpinSystem within, SpinSystem seq) {
return dfJoint[within.getId()][seq.getId()];
}
public boolean isValidAlign(int pos, SpinSystem within, SpinSystem seq) {
return isValidAlign[pos][within.getId()][seq.getId()];
}
public boolean isValidMatch(SpinSystem within, SpinSystem seq) {
return isValidMatch[within.getId()][seq.getId()];
}
public boolean isValidJoint(int pos, SpinSystem within, SpinSystem seq) {
return isValidJoint[pos][within.getId()][seq.getId()];
}
public double getMaxScoreJoint() {
return maxScoreJoint;
}
}
MBA2/input/SpinSystem.java 0100644 0000765 0000024 00000014445 10066403777 015400 0 ustar janvitek staff package input;
import assign.Worker.Argument;
import java.io.Serializable;
public class SpinSystem implements Serializable {
// --------FIELDS----------------
private final int id, referenceId;
private final double hw, nw, cs, cas, cbs, has, ha2s, cw, caw, cbw, haw, ha2w;
private final double hwv, nwv, csv, casv, cbsv, hasv, ha2sv, cwv, cawv, cbwv, hawv, ha2wv;
private static boolean useH;
private static boolean useN;
private static boolean useC;
private static boolean useCA;
private static boolean useCB;
private static boolean useHA;
// --------CONSTRUCTORS----------------
// empty spin system
public SpinSystem(int id) {
//id, HNw, N15w, COs, CAs, CBs, HAs, HA2s, COw, CAw, CBw, HAw, HA2w
this.id = id;
referenceId = -1;
hw = Double.NaN;
nw = Double.NaN;
cs = Double.NaN;
cas = Double.NaN;
cbs = Double.NaN;
has = Double.NaN;
ha2s = Double.NaN;
cw = Double.NaN;
caw = Double.NaN;
cbw = Double.NaN;
haw = Double.NaN;
ha2w = Double.NaN;
hwv = Double.NaN;
nwv = Double.NaN;
csv = Double.NaN;
casv = Double.NaN;
cbsv = Double.NaN;
hasv = Double.NaN;
ha2sv = Double.NaN;
cwv = Double.NaN;
cawv = Double.NaN;
cbwv = Double.NaN;
hawv = Double.NaN;
ha2wv = Double.NaN;
}
// observed spin system
public SpinSystem(
int id,
int referenceId,
double hw,
double nw,
double cs,
double cas,
double cbs,
double has,
double ha2s,
double cw,
double caw,
double cbw,
double haw,
double ha2w,
double hwv,
double nwv,
double csv,
double casv,
double cbsv,
double hasv,
double ha2sv,
double cwv,
double cawv,
double cbwv,
double hawv,
double ha2wv) {
//id, HNw, N15w, COs, CAs, CBs, HAs, HA2s, COw, CAw, CBw, HAw, HA2w
this.id = id;
this.referenceId = referenceId;
this.hw = useH ? hw : Double.NaN;
this.nw = useN ? nw : Double.NaN;
this.cs = useC ? cs : Double.NaN;
this.cas = useCA ? cas : Double.NaN;
this.cbs = useCB ? cbs : Double.NaN;
this.has = useHA ? has : Double.NaN;
this.ha2s = useHA ? ha2s : Double.NaN;
this.cw = useC ? cw : Double.NaN;
this.caw = useCA ? caw : Double.NaN;
this.cbw = useCB ? cbw : Double.NaN;
this.haw = useHA ? haw : Double.NaN;
this.ha2w = useHA ? ha2w : Double.NaN;
this.hwv = useH ? hwv : Double.NaN;
this.nwv = useN ? nwv : Double.NaN;
this.csv = useC ? csv : Double.NaN;
this.casv = useCA ? casv : Double.NaN;
this.cbsv = useCB ? cbsv : Double.NaN;
this.hasv = useHA ? hasv : Double.NaN;
this.ha2sv = useHA ? ha2sv : Double.NaN;
this.cwv = useC ? cwv : Double.NaN;
this.cawv = useCA ? cawv : Double.NaN;
this.cbwv = useCB ? cbwv : Double.NaN;
this.hawv = useHA ? hawv : Double.NaN;
this.ha2wv = useHA ? ha2wv : Double.NaN;
}
// set the flags that specify what information about new spin systems to use
public static void setFlags(Argument arg) {
useH = arg.useh;
useN = arg.usen;
useC = arg.usec;
useCA = arg.useca;
useCB = arg.usecb;
useHA = arg.useha;
}
// --------METHODS----------------
public int getDf() {
int result = 0;
result += (Double.isNaN(hw)) ? 0 : 1;
result += (Double.isNaN(nw)) ? 0 : 1;
result += (Double.isNaN(cs)) ? 0 : 1;
result += (Double.isNaN(cw)) ? 0 : 1;
result += (Double.isNaN(cas)) ? 0 : 1;
result += (Double.isNaN(caw)) ? 0 : 1;
result += (Double.isNaN(cbs)) ? 0 : 1;
result += (Double.isNaN(cbw)) ? 0 : 1;
result += (Double.isNaN(has)) ? 0 : 1;
result += (Double.isNaN(haw)) ? 0 : 1;
result += (Double.isNaN(ha2s)) ? 0 : 1;
result += (Double.isNaN(ha2w)) ? 0 : 1;
return result;
}
public int getChemicalShiftCount() {
int result = 0;
result += (Double.isNaN(cs)) ? 0 : 1;
result += (Double.isNaN(cw)) ? 0 : 1;
result += (Double.isNaN(cas)) ? 0 : 1;
result += (Double.isNaN(caw)) ? 0 : 1;
result += (Double.isNaN(cbs)) ? 0 : 1;
result += (Double.isNaN(cbw)) ? 0 : 1;
result += (Double.isNaN(has)) ? 0 : 1;
result += (Double.isNaN(haw)) ? 0 : 1;
result += (Double.isNaN(ha2s)) ? 0 : 1;
result += (Double.isNaN(ha2w)) ? 0 : 1;
return result;
}
public boolean isEmpty() {
return referenceId == -1;
}
public boolean canFollowGly() {
return Double.isNaN(cbs);
}
public boolean canBeGly() {
return Double.isNaN(cbw);
}
public boolean canFollowNonGly() {
return Double.isNaN(ha2s);
}
public boolean canBeNonGly() {
return Double.isNaN(ha2w);
}
public SpinSystem copy() {
return new SpinSystem(
id,
referenceId,
hw,
nw,
cs,
cas,
cbs,
has,
ha2s,
cw,
caw,
cbw,
haw,
ha2w,
hwv,
nwv,
csv,
casv,
cbsv,
hasv,
ha2sv,
cwv,
cawv,
cbwv,
hawv,
ha2wv);
}
public String toString() {
if (isEmpty())
return "-1";
return "" + referenceId;
}
//-----------------------------------------------------------------------------------
//---------------------------------OBJECT IDENTITY-----------------------------------
//-----------------------------------------------------------------------------------
// The id field completely determines the object's identity.
public boolean equals(Object o) {
SpinSystem s = (SpinSystem) o;
return (id == s.id);
}
public int hashCode() {
return id;
}
// --------ACCESSORS----------------
public int getId() {
return id;
}
public int getReferenceId() {
return referenceId;
}
public double getHw() {
return hw;
}
public double getNw() {
return nw;
}
public double getCs() {
return cs;
}
public double getCAs() {
return cas;
}
public double getCBs() {
return cbs;
}
public double getHAs() {
return has;
}
public double getHA2s() {
return ha2s;
}
public double getCw() {
return cw;
}
public double getCAw() {
return caw;
}
public double getCBw() {
return cbw;
}
public double getHAw() {
return haw;
}
public double getHA2w() {
return ha2w;
}
public double getHwv() {
return hwv;
}
public double getNwv() {
return nwv;
}
public double getCsv() {
return csv;
}
public double getCAsv() {
return casv;
}
public double getCBsv() {
return cbsv;
}
public double getHAsv() {
return hasv;
}
public double getHA2sv() {
return ha2sv;
}
public double getCwv() {
return cwv;
}
public double getCAwv() {
return cawv;
}
public double getCBwv() {
return cbwv;
}
public double getHAwv() {
return hawv;
}
public double getHA2wv() {
return ha2wv;
}
}
MBA2/lib/ 0040755 0000765 0000024 00000000000 10066404000 011775 5 ustar janvitek staff MBA2/lib/concurrent.jar 0100644 0000765 0000024 00000571705 10066206447 014710 0 ustar janvitek staff PK
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