use Math::Trig; #USE THIS MODULE
#
# METHOD TO COMPUTE STRUCTURAL FACTOR FROM PDB AND PRINT IN XY FORMAT FOR XMGRACE.
# Code by - Shourjya Sanyal. Jun 2012. Dublin Ireland.

print "***************************** \n";
print "STRUCT FACTOR READER Ver 0.1 \n";
print "***************************** \n";

# *****************************
# Modify next line
$inputFile = 'mypdb.pdb';

open (FROM,$inputFile) || die("Could not open file!");
# load the file into an array
chomp(@data = );
close(FROM);

# *****************************
# FIND CENTER OF MASS OF -FROM PDB1
print "\n";
$atom=0; $atom1=1; @resid;
for ($line = 0; $line < scalar @data; $line++)
{if ($data[$line] =~ m/^ATOM/)
{
$mydata = @data[$line];
@aa= split('',$mydata);
$atom = join('',@aa[23..26]);
$tempf = join('',@aa[61..66]);
if ($atom == $atom1)
{$tot = $tot + $tempf;
}
else
{@resid[$atom1] = $tot; print "$atom1";
$tot = $tempf;
$atom1 = $atom;
}
}# end of if
}# end of for
@resid[$atom1] = $tot; print "$atom1";
# *****************************
for ($line = 0; $line < scalar @resid; $line++)
{print " $line @resid[$line]\n"
}

# *****************************
# CREATE OUTPUT FILE For XMGRACE
$prefix = $inputFile;
$prefix =~ s/\.pdb//;
$outputFile = $prefix."_rmsfProtein.xvg";
open (FH, ">$outputFile");
print FH "#File was created by Programme STRUCT FACTOR READER Ver 0.1\n";
print FH "#By Shourjya Sanyal Aug 2012\n";
print FH "#\n";
print FH "@ title \"RMS Fluctuation Per Amino Acid - Related To Temperature factor\"\n";
print FH "@ xaxis label \"Residue\"\n";
print FH "@ yaxis label \"(nm)\"\n";
print FH "\@TYPE xy\n";
if ((scalar @resid > 0) && (scalar @resid < 10))
{foreach ($line = 1; $line < scalar @resid; $line++)
{
print FH " $line @resid[$line]\n"
}
}
if ((scalar @resid > 9) && (scalar @resid < 100))
{foreach ($line = 1; $line < 10; $line++)
{
print FH " $line @resid[$line]\n"
}
foreach ($line = 10; $line < scalar @resid; $line++)
{
print FH " $line @resid[$line]\n"
}
}
if ((scalar @resid > 99) && (scalar @resid < 1000))
{
foreach ($line = 1; $line < 10; $line++)
{
print FH " $line @resid[$line]\n"
}
foreach ($line = 10; $line < 100; $line++)
{
print FH " $line @resid[$line]\n"
}
foreach ($line = 100; $line < scalar @resid; $line++)
{
print FH " $line @resid[$line]\n"
}
}
if ((scalar @resid > 999) && (scalar @resid < 10000))
{
foreach ($line = 1; $line < 10; $line++)
{
print FH " $line @resid[$line]\n"
}
foreach ($line = 10; $line < 100; $line++)
{
print FH " $line @resid[$line]\n"
}
foreach ($line = 100; $line < 1000; $line++)
{
print FH " $line @resid[$line]\n"
}
foreach ($line = 1000; $line < scalar @resid; $line++)
{
print FH " $line @resid[$line]\n"
}
}
print FH "#\n";
print FH "#\n";
print FH "# \"I want to go home now !!\"\n";
close FH;