https://github.com/michal-brylinski/efindsite
Revision 72f012435573ecfab2dc5c5478bf16ec459f5937 authored by Michal Brylinski on 25 October 2018, 17:56:05 UTC, committed by GitHub on 25 October 2018, 17:56:05 UTC
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Tip revision: 72f012435573ecfab2dc5c5478bf16ec459f5937 authored by Michal Brylinski on 25 October 2018, 17:56:05 UTC
Update 13gsA.profile
Update 13gsA.profile
Tip revision: 72f0124
data.C
/*
===============================================================================
___________.__ .____________.__ __
____\_ _____/|__| ____ __| _/ _____/|__|/ |_ ____
_/ __ \| __) | |/ \ / __ |\_____ \ | \ __\/ __ \
\ ___/| \ | | | \/ /_/ |/ \| || | \ ___/
\___ >___ / |__|___| /\____ /_______ /|__||__| \___ >
\/ \/ \/ \/ \/ \/
eFindSite - ligand-binding site prediction from meta-threading
Computational Systems Biology Group
Department of Biological Sciences
Center for Computation & Technology
Louisiana State University
407 Choppin Hall, Baton Rouge, LA 70803, USA
http://www.brylinski.org
Report bugs to michal@brylinski.org
Copyright 2013 Michal Brylinski
This file is part of eFindSite.
eFindSite is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
eFindSite is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with eFindSite. If not, see <http://www.gnu.org/licenses/>.
===============================================================================
*/
#include "data.h"
using namespace std;
double getBkgFreq( string resnam1 )
{
// Release notes for UniProtKB/Swiss-Prot release 2011_09 - September 2011
if ( resnam1 == "ALA" || resnam1 == "A" ) { return 0.0826; }
else if ( resnam1 == "CYS" || resnam1 == "C" ) { return 0.0136; }
else if ( resnam1 == "ASP" || resnam1 == "D" ) { return 0.0546; }
else if ( resnam1 == "GLU" || resnam1 == "E" ) { return 0.0675; }
else if ( resnam1 == "PHE" || resnam1 == "F" ) { return 0.0386; }
else if ( resnam1 == "GLY" || resnam1 == "G" ) { return 0.0708; }
else if ( resnam1 == "HIS" || resnam1 == "H" ) { return 0.0227; }
else if ( resnam1 == "ILE" || resnam1 == "I" ) { return 0.0597; }
else if ( resnam1 == "LYS" || resnam1 == "K" ) { return 0.0585; }
else if ( resnam1 == "LEU" || resnam1 == "L" ) { return 0.0966; }
else if ( resnam1 == "MET" || resnam1 == "M" ) { return 0.0242; }
else if ( resnam1 == "ASN" || resnam1 == "N" ) { return 0.0406; }
else if ( resnam1 == "PRO" || resnam1 == "P" ) { return 0.0469; }
else if ( resnam1 == "GLN" || resnam1 == "Q" ) { return 0.0393; }
else if ( resnam1 == "ARG" || resnam1 == "R" ) { return 0.0553; }
else if ( resnam1 == "SER" || resnam1 == "S" ) { return 0.0655; }
else if ( resnam1 == "THR" || resnam1 == "T" ) { return 0.0534; }
else if ( resnam1 == "VAL" || resnam1 == "V" ) { return 0.0687; }
else if ( resnam1 == "TRP" || resnam1 == "W" ) { return 0.0108; }
else if ( resnam1 == "TYR" || resnam1 == "Y" ) { return 0.0292; }
else
{
cout << "Unknown residue passed to getBackFreq: " << resnam1 << endl << endl;
exit(EXIT_FAILURE);
}
exit(EXIT_FAILURE);
}
std::string three2oneS( std::string resnam1 )
{
if ( resnam1 == "ALA" ) { return "A"; }
else if ( resnam1 == "CYS" ) { return "C"; }
else if ( resnam1 == "ASP" ) { return "D"; }
else if ( resnam1 == "GLU" ) { return "E"; }
else if ( resnam1 == "PHE" ) { return "F"; }
else if ( resnam1 == "GLY" ) { return "G"; }
else if ( resnam1 == "HIS" ) { return "H"; }
else if ( resnam1 == "ILE" ) { return "I"; }
else if ( resnam1 == "LYS" ) { return "K"; }
else if ( resnam1 == "LEU" ) { return "L"; }
else if ( resnam1 == "MET" ) { return "M"; }
else if ( resnam1 == "ASN" ) { return "N"; }
else if ( resnam1 == "PRO" ) { return "P"; }
else if ( resnam1 == "GLN" ) { return "Q"; }
else if ( resnam1 == "ARG" ) { return "R"; }
else if ( resnam1 == "SER" ) { return "S"; }
else if ( resnam1 == "THR" ) { return "T"; }
else if ( resnam1 == "VAL" ) { return "V"; }
else if ( resnam1 == "TRP" ) { return "W"; }
else if ( resnam1 == "TYR" ) { return "Y"; }
else
{
cout << "Unknown residue passed to three2oneS: " << resnam1 << endl << endl;
exit(EXIT_FAILURE);
}
exit(EXIT_FAILURE);
}
char three2oneC( std::string resnam1 )
{
if ( resnam1 == "ALA" ) { return 'A'; }
else if ( resnam1 == "CYS" ) { return 'C'; }
else if ( resnam1 == "ASP" ) { return 'D'; }
else if ( resnam1 == "GLU" ) { return 'E'; }
else if ( resnam1 == "PHE" ) { return 'F'; }
else if ( resnam1 == "GLY" ) { return 'G'; }
else if ( resnam1 == "HIS" ) { return 'H'; }
else if ( resnam1 == "ILE" ) { return 'I'; }
else if ( resnam1 == "LYS" ) { return 'K'; }
else if ( resnam1 == "LEU" ) { return 'L'; }
else if ( resnam1 == "MET" ) { return 'M'; }
else if ( resnam1 == "ASN" ) { return 'N'; }
else if ( resnam1 == "PRO" ) { return 'P'; }
else if ( resnam1 == "GLN" ) { return 'Q'; }
else if ( resnam1 == "ARG" ) { return 'R'; }
else if ( resnam1 == "SER" ) { return 'S'; }
else if ( resnam1 == "THR" ) { return 'T'; }
else if ( resnam1 == "VAL" ) { return 'V'; }
else if ( resnam1 == "TRP" ) { return 'W'; }
else if ( resnam1 == "TYR" ) { return 'Y'; }
else
{
cout << "Unknown residue passed to three2oneC: " << resnam1 << endl << endl;
exit(EXIT_FAILURE);
}
exit(EXIT_FAILURE);
}
std::string one2three( std::string resnam1 )
{
if ( resnam1 == "A" ) { return "ALA"; }
else if ( resnam1 == "C" ) { return "CYS"; }
else if ( resnam1 == "D" ) { return "ASP"; }
else if ( resnam1 == "E" ) { return "GLU"; }
else if ( resnam1 == "F" ) { return "PHE"; }
else if ( resnam1 == "G" ) { return "GLY"; }
else if ( resnam1 == "H" ) { return "HIS"; }
else if ( resnam1 == "I" ) { return "ILE"; }
else if ( resnam1 == "K" ) { return "LYS"; }
else if ( resnam1 == "L" ) { return "LEU"; }
else if ( resnam1 == "M" ) { return "MET"; }
else if ( resnam1 == "N" ) { return "ASN"; }
else if ( resnam1 == "P" ) { return "PRO"; }
else if ( resnam1 == "Q" ) { return "GLN"; }
else if ( resnam1 == "R" ) { return "ARG"; }
else if ( resnam1 == "S" ) { return "SER"; }
else if ( resnam1 == "T" ) { return "THR"; }
else if ( resnam1 == "V" ) { return "VAL"; }
else if ( resnam1 == "W" ) { return "TRP"; }
else if ( resnam1 == "Y" ) { return "TYR"; }
else
{
cout << "Unknown residue passed to one2three: " << resnam1 << endl << endl;
exit(EXIT_FAILURE);
}
exit(EXIT_FAILURE);
}
int one2num( char resnam1 )
{
if ( resnam1 == 'A' ) { return 0; }
else if ( resnam1 == 'C' ) { return 4; }
else if ( resnam1 == 'D' ) { return 3; }
else if ( resnam1 == 'E' ) { return 6; }
else if ( resnam1 == 'F' ) { return 13; }
else if ( resnam1 == 'G' ) { return 7; }
else if ( resnam1 == 'H' ) { return 8; }
else if ( resnam1 == 'I' ) { return 9; }
else if ( resnam1 == 'K' ) { return 11; }
else if ( resnam1 == 'L' ) { return 10; }
else if ( resnam1 == 'M' ) { return 12; }
else if ( resnam1 == 'N' ) { return 2; }
else if ( resnam1 == 'P' ) { return 14; }
else if ( resnam1 == 'Q' ) { return 5; }
else if ( resnam1 == 'R' ) { return 1; }
else if ( resnam1 == 'S' ) { return 15; }
else if ( resnam1 == 'T' ) { return 16; }
else if ( resnam1 == 'V' ) { return 19; }
else if ( resnam1 == 'W' ) { return 17; }
else if ( resnam1 == 'Y' ) { return 18; }
else
{
cout << "Unknown residue passed to one2num: " << resnam1 << endl << endl;
exit(EXIT_FAILURE);
}
exit(EXIT_FAILURE);
}
std::string num2one( int resnum1 )
{
if ( resnum1 == 0 ) { return "A"; }
else if ( resnum1 == 4 ) { return "C"; }
else if ( resnum1 == 3 ) { return "D"; }
else if ( resnum1 == 6 ) { return "E"; }
else if ( resnum1 == 13 ) { return "F"; }
else if ( resnum1 == 7 ) { return "G"; }
else if ( resnum1 == 8 ) { return "H"; }
else if ( resnum1 == 9 ) { return "I"; }
else if ( resnum1 == 11 ) { return "K"; }
else if ( resnum1 == 10 ) { return "L"; }
else if ( resnum1 == 12 ) { return "M"; }
else if ( resnum1 == 2 ) { return "N"; }
else if ( resnum1 == 14 ) { return "P"; }
else if ( resnum1 == 5 ) { return "Q"; }
else if ( resnum1 == 1 ) { return "R"; }
else if ( resnum1 == 15 ) { return "S"; }
else if ( resnum1 == 16 ) { return "T"; }
else if ( resnum1 == 19 ) { return "V"; }
else if ( resnum1 == 17 ) { return "W"; }
else if ( resnum1 == 18 ) { return "Y"; }
else
{
cout << "Unknown residue passed to num2one: " << resnum1 << endl << endl;
exit(EXIT_FAILURE);
}
exit(EXIT_FAILURE);
}
double one2plb( std::string resnam1 )
{
if ( resnam1 == "A" ) { return 0.701; }
else if ( resnam1 == "C" ) { return 1.650; }
else if ( resnam1 == "D" ) { return 1.015; }
else if ( resnam1 == "E" ) { return 0.956; }
else if ( resnam1 == "F" ) { return 1.952; }
else if ( resnam1 == "G" ) { return 0.788; }
else if ( resnam1 == "H" ) { return 2.286; }
else if ( resnam1 == "I" ) { return 1.006; }
else if ( resnam1 == "K" ) { return 0.468; }
else if ( resnam1 == "L" ) { return 1.045; }
else if ( resnam1 == "M" ) { return 1.894; }
else if ( resnam1 == "N" ) { return 0.811; }
else if ( resnam1 == "P" ) { return 0.212; }
else if ( resnam1 == "Q" ) { return 0.669; }
else if ( resnam1 == "R" ) { return 0.916; }
else if ( resnam1 == "S" ) { return 0.883; }
else if ( resnam1 == "T" ) { return 0.730; }
else if ( resnam1 == "V" ) { return 0.884; }
else if ( resnam1 == "W" ) { return 3.084; }
else if ( resnam1 == "Y" ) { return 1.672; }
else
{
cout << "Unknown residue passed to one2plb: " << resnam1 << endl << endl;
exit(EXIT_FAILURE);
}
exit(EXIT_FAILURE);
}
double num2plb( int resnum1 )
{
if ( resnum1 == 0 ) { return 0.701; }
else if ( resnum1 == 4 ) { return 1.650; }
else if ( resnum1 == 3 ) { return 1.015; }
else if ( resnum1 == 6 ) { return 0.956; }
else if ( resnum1 == 13 ) { return 1.952; }
else if ( resnum1 == 7 ) { return 0.788; }
else if ( resnum1 == 8 ) { return 2.286; }
else if ( resnum1 == 9 ) { return 1.006; }
else if ( resnum1 == 11 ) { return 0.468; }
else if ( resnum1 == 10 ) { return 1.045; }
else if ( resnum1 == 12 ) { return 1.894; }
else if ( resnum1 == 2 ) { return 0.811; }
else if ( resnum1 == 14 ) { return 0.212; }
else if ( resnum1 == 5 ) { return 0.669; }
else if ( resnum1 == 1 ) { return 0.916; }
else if ( resnum1 == 15 ) { return 0.883; }
else if ( resnum1 == 16 ) { return 0.730; }
else if ( resnum1 == 19 ) { return 0.884; }
else if ( resnum1 == 17 ) { return 3.084; }
else if ( resnum1 == 18 ) { return 1.672; }
else
{
cout << "Unknown residue passed to one2plb: " << resnum1 << endl << endl;
exit(EXIT_FAILURE);
}
exit(EXIT_FAILURE);
}
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