# ** Program:   iXLINK.pl 

# ** File:      params.pl 

# ** Author:    Parag Mallick, pmallick@systemsbiology.net 

# ** Date:      9.29.2005 

# ** 

# ** Copyright (c) 2005 Institute for Systems Biology 

# **               Parag Mallick, Ruedi Aebersold 

# ** 

# ** This library is free software; you can redistribute it and/or  modify it 

# ** under the terms of the GNU Lesser General Public License as  published 

# ** by the Free Software Foundation; either version 2.1 of the  License, or 

# ** any later version. 

# ** 

# ** This library is distributed in the hope that it will be useful, but 

# ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF 

# ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The  software and 

# ** documentation provided hereunder is on an "as is" basis, and the 

# ** Institute for Systems Biology 

# ** have no obligations to provide maintenance, support, 

# ** updates, enhancements or modifications.  In no event shall the 

# ** Institute for Systems Biology 

# ** be liable to any party for direct, indirect, special, 

# ** incidental or consequential damages, including lost profits,  arising 

# ** out of the use of this software and its documentation, even if the 

# ** Institute for Systems Biology 

# ** have been advised of the possibility of such damage.  See 

# ** the GNU Lesser General Public License for more details. 

# ** 

# ** You should have received a copy of the GNU Lesser General Public  License 

# ** along with this library; if not, write to the Free Software  Foundation, 

# ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. 

# ** 





sub LoadParams{

  my $params=$_[0];



  $params->{aa_lib} = "aa_mass.txt";

  $params->{time_lib} = "timeConversion.txt";



  $params->{lonelyPeaksThreshold} = 1000; 		#/* Intensity Threshold for Protein ID, no Isotope Pairs */ 

  $params->{lonelyPeaksSNRThreshold} = 150; 		#/* Signal-to-Noise Threshold for Protein ID, no Isotope Pairs */ 



  $params->{signalThreshold} = 500; 			#/* Intesity Threshold for Isotope Pairs */

  $params->{snrRatioThreshold} = 25; 			#/* Signal-to-Noise Threshold for Isotope Pairs */ 

  $params->{relativeIntensityRatio} = 3; 		#/* Mass Pair Intesity Ratio: Int1/Int2= 1/x - x*/



  $params->{pairDistance} = 12.0727; 			#/* delta m [Da] for DSS-d0/d12 Isotope Pairs*/

  $params->{pairDistanceError} = 0.05; 



#  $params->{pairDistance} = 6.0364; 			#/* delta m [Da] for DSG-d0/d6 Isotope Pairs*/

#  $params->{pairDistanceError} = 0.05; 



#  $params->{pairDistance} = 4.02471; 			#/* delta m [Da] for BS3-d0/d4 Isotope Pairs*/

#  $params->{pairDistanceError} = 0.05; 



#  $params->{pairDistance} = 4.02471; 			#/* delta m [Da] for BS2-d0/d4 Isotope Pairs*/

#  $params->{pairDistanceError} = 0.05; 





  $params->{heavyLightDistance} = 2.0; 			#/* delta m [Da] for mono-links */

  $params->{heavyLightDistanceError} = 0.1;



  $params->{massCalibrationError} = 0.0; 		#/* systematic m_obs-m_calc [Da] */



  $params->{heavyLightRTShift} = 0; 			#/* number of MALDI spots */

  $params->{heavyLightRTError} = 10; 			#/* number of MALDI spots */



  $params->{IdentificationMassError} = 1.2; 		#/* [Da] */



  $params->{numberOfSpots} = 192;



  $params->{SN_or_Inten} = "SN";



  $params->{numberOfEnzymes} = 4; 



  $params->{enzymeName0} = "trypsin";

  $params->{enzymeSpecificity0} = "KR";

  $params->{enzymeSide0} = "c";

  

  $params->{enzymeName1} = "aspn";

  $params->{enzymeSpecificity1} = "D";

  $params->{enzymeSide1} = "n";



  $params->{enzymeName2} = "front";

  $params->{enzymeSpecificity2} = "n";

  $params->{enzymeSide2} = "n";



  $params->{enzymeName3} = "back";

  $params->{enzymeSpecificity3} = "t";

  $params->{enzymeSide3} = "c";



  $params->{numberOfReagents} = 1;



  $params->{reagentName0} = "dss"; 			#/* DSS crosslinker (or BS3)*/

  $params->{reagentModifiesResidues0} = ("Kn");

  $params->{reagentMass0} = "156.0786";  		



#  $params->{reagentName0} = "dsg";			#/* DSG crosslinker (or BS2)*/

#  $params->{reagentModifiesResidues0} = ("Kn");

#  $params->{reagentMass0} = "114.03169"; 



  $params->{minimumDigestMass} = "50";

  $params->{maximumDigestMass} = "4000";

  $params->{minimumXlinkMass} = "500";

  $params->{maximumXlinkMass} = "4000";



  $params->{allowCysMods} = "1"; 

  $params->{allowMethMods} = "1";



  $params->{numAllowedMisCleavages} = 5; 		#/* max # of allowed missed cleav. */



  if($params->{SN_or_Inten} eq "SN"){

    $params->{SN_or_Inten} = 2;

  }

  else{

    $params->{SN_or_Inten} = 1;

  }

}



sub LoadMasses{

  my $massAtm = $_[0];

  ##avg

  #$massAtm->{'h'}=  1.00794;  #/* hydrogen */

  #$massAtm->{'o'}= 15.9994;   #/* oxygen */

  #$massAtm->{'c'}= 12.0107;   #/* carbon */

  #$massAtm->{'n'}= 14.00674;  #/* nitrogen */

  #$massAtm->{'p'}= 30.973761; #/* phosporus */

  #$massAtm->{'s'}= 32.066;    #/* sulphur */



  ##mono

  $massAtm->{'mass_h'}=  1.0078250;

  $massAtm->{'mass_o'}= 15.9949146;

  $massAtm->{'mass_c'}= 12.0000000;

  $massAtm->{'mass_n'}= 14.0030740;

  $massAtm->{'mass_p'}= 30.9737633;

  $massAtm->{'mass_s'}= 31.9720718;



  $massAtm->{'mass_nh3'} = $massAtm->{'mass_n'} + $massAtm->{'mass_h'} + $massAtm->{'mass_h'} + $massAtm->{'mass_h'};

  $massAtm->{'mass_co'} = $massAtm->{'mass_c'} + $massAtm->{'mass_o'};

  $massAtm->{'mass_co_2h'} = $massAtm->{'mass_co'} - $massAtm->{'mass_h'} - $massAtm->{'mass_h'};

  $massAtm->{'mass_Nterm'} = $massAtm->{'mass_h'};

  $massAtm->{'mass_Cterm'} = $massAtm->{'mass_o'} + $massAtm->{'mass_h'};



  $massAtm->{'mass_HOH'} = $massAtm->{'mass_o'} + $massAtm->{'mass_h'} + $massAtm->{'mass_h'};

  $massAtm->{'mass_HOOH'} = $massAtm->{'mass_o'} + $massAtm->{'mass_h'} + $massAtm->{'mass_h'} +  $massAtm->{'mass_o'};

  $massAtm->{'mass_HH'} = $massAtm->{'mass_h'} + $massAtm->{'mass_h'}; #//check this!!!



  $massAtm->{'mass_termini'} = $massAtm->{'mass_Nterm'} + $massAtm->{'mass_Cterm'} + $massAtm->{'mass_h'};  #/* peptide calc masses are MH+ */

  #$massAtm->{'TerminiMass'} = $dNterm + $dCterm ;  	#/* peptide calc masses are M */



  $massAtm->{'cysMod'} = 57.0215;			#/* carbamidomethylation */

  $massAtm->{'metMod'} = $massAtm->{'mass_o'};

}



1;