NMRdata.cc

/*  Shine - NMR NOESY simulation program
    Copyright (C) 2015  Michael Riss

    This program 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 2
    of the License, or (at your option) any later version.
    
    This program 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 this program; if not, write to the Free Software
    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA. */

#include <cmath>
#include "NMRdata.h"

#define LW_C 150.0
#define LW_N 30.0
#define LW_H 35.0
#define LW_HN 16.0

#define LEAK0 0.5
#define LEAK1 0.65
#define LEAK2 0.75


proton::proton( string Name, char aminoCode ){
  this->Name = Name;
  shift = NAN;
  spec_shift1 = NAN;
  spec_shift2 = NAN;
  hetatom = NULL;
  x = NAN;
  y = NAN;
  z = NAN;
  leak = LEAK0;

  if( Name == "HA" || 
      ( ( aminoCode == 'R' ) && 
	( Name == "HB1" || Name == "HB2" || 
	  Name == "HG1" || Name == "HG2" ||
	  Name == "HD1" || Name == "HD2" ) ) ||
      ( ( aminoCode == 'N' ) && 
	( Name == "HB1" || Name == "HB2" ) ) ||
      ( ( aminoCode == 'D' ) &&
	( Name == "HB1" || Name == "HB2" ) ) ||
      ( ( aminoCode == 'C' ) &&
	( Name == "HB1" || Name == "HB2" ) ) ||
	( ( aminoCode == 'Q' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HG1" || Name == "HG2" ) ) ||
      ( ( aminoCode == 'E' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HG1" || Name == "HG2" ) ) ||
      ( ( aminoCode == 'G' ) &&
	( Name == "HA1" || Name == "HA2" ) ) ||
      ( ( aminoCode == 'H' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HD1" || Name == "HD2" ||
	  Name == "HE1" ) ) ||
      ( ( aminoCode == 'I' ) &&
	( Name == "HB" || 
	  Name == "HG11" || Name == "HG12" ) ) ||
      ( ( aminoCode == 'L' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HG" ) ) ||
      ( ( aminoCode == 'K' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HG1" || Name == "HG2" ||
	  Name == "HD1" || Name == "HD2" ||
	  Name == "HE1" || Name == "HE2" ) ) ||
      ( ( aminoCode == 'M' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HG1" || Name == "HG2" ) ) ||
      ( ( aminoCode == 'F' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HD1" || Name == "HD2" ||
	  Name == "HE1" || Name == "HE2" ||
	  Name == "HZ" ) ) ||
      ( ( aminoCode == 'P' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HG1" || Name == "HG2" ||
	  Name == "HD1" || Name == "HD2" ) ) ||
      ( ( aminoCode == 'S' ) &&
	( Name == "HB1" || Name == "HB2" ) ) ||
      ( ( aminoCode == 'T' ) &&
	( Name == "HB" ) ) ||
      ( ( aminoCode == 'W' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HD1" || 
	  Name == "HE1" || Name == "HE3" ||
	  Name == "HZ2" || Name == "HZ3" ||
	  Name == "HH2" ) ) ||
      ( ( aminoCode == 'Y' ) &&
	( Name == "HB1" || Name == "HB2" ||
	  Name == "HD1" || Name == "HD2" ||
	  Name == "HE1" || Name == "HE2" ) ) ||
      ( ( aminoCode == 'V' ) &&
	( Name == "HB" ) ) ){
    leak = LEAK0;
  }
  else if( ( aminoCode == 'A' &&
        ( Name == "HB1" || Name == "HB2" || Name == "HB3" ) ) ||
      ( ( aminoCode == 'I' ) &&
	( Name == "HD11" || Name == "HD12" || Name == "HD13" ||
	  Name == "HG21" || Name == "HG22" || Name == "HG23" ) ) ||
      ( ( aminoCode == 'L' ) &&
	( Name == "HD11" || Name == "HD12" || Name == "HD13" ||
	  Name == "HD21" || Name == "HD22" || Name == "HD23" ) ) ||
      ( ( aminoCode == 'M' ) && 
	( Name == "HE1" || Name == "HE2" || Name == "HE3" ) ) ||
      ( ( aminoCode == 'T' ) &&
	( Name == "HG21" || Name == "HG22" || Name == "HG23" ) ) ||
      ( ( aminoCode == 'V' ) &&
	( Name == "HG11" || Name == "HG12" || Name == "HG13" ||
	  Name == "HG21" || Name == "HG22" || Name == "HG23" ) )
      ){
    leak = LEAK1;
  }
  else if( Name == "H" ||
      (aminoCode == 'R' && Name == "HE"   ) ||
      (aminoCode == 'R' && Name == "HH21" ) ||
      (aminoCode == 'R' && Name == "HH22" ) ||
      (aminoCode == 'N' && Name == "HD21" ) ||
      (aminoCode == 'N' && Name == "HD22" ) ||
      (aminoCode == 'Q' && Name == "HE21" ) ||
      (aminoCode == 'Q' && Name == "HE22" ) ||
      (aminoCode == 'K' && Name == "HZ1"  ) ||
      (aminoCode == 'K' && Name == "HZ2"  ) ||
      (aminoCode == 'K' && Name == "HZ3"  ) ){
    leak = LEAK2;
  }

  fold2 = 1.0;
  if( Name == "H" ||
      (aminoCode == 'R' && Name == "HE"   ) || 
      (aminoCode == 'R' && Name == "HH21" ) ||
      (aminoCode == 'R' && Name == "HH22" ) ||
      (aminoCode == 'N' && Name == "HD21" ) ||
      (aminoCode == 'N' && Name == "HD22" ) ||
      (aminoCode == 'Q' && Name == "HE21" ) ||
      (aminoCode == 'Q' && Name == "HE22" ) ||
      (aminoCode == 'K' && Name == "HZ1"  ) ||
      (aminoCode == 'K' && Name == "HZ2"  ) ||
      (aminoCode == 'K' && Name == "HZ3"  ) ){
    linewidth = LW_HN;
  }
  else{
    linewidth = LW_H;
  }
  lw1 = NAN;
  lw2 = NAN;
  valvef = NAN;
}

#define ALL_N 94.0

#define ALA_A 142.0
#define ALA_B 125.0

#define ARG_A 142.0
#define ARG_B 120.0
#define ARG_G 120.0
#define ARG_D 130.0

#define ASN_A 142.0
#define ASN_B 130.0

#define ASP_A 142.0
#define ASP_B 130.0

#define CYS_A 142.0
#define CYS_B 135.0

#define GLN_A 142.0
#define GLN_B 120.0
#define GLN_G 130.0

#define GLU_A 142.0
#define GLU_B 120.0
#define GLU_G 130.0
 
#define GLY_A 142.0

#define HIS_A 142.0
#define HIS_B 125.0
#define HIS_D1 100.0
#define HIS_D2 198.0
#define HIS_E1 218.0
#define HIS_E2 100.0

#define ILE_A 142.0
#define ILE_B 115.0
#define ILE_G1 120.0
#define ILE_D1 125.0
#define ILE_G2 125.0

#define LEU_A 142.0
#define LEU_B 120.0
#define LEU_G 115.0
#define LEU_D 125.0

#define LYS_A 142.0
#define LYS_B 120.0
#define LYS_G 120.0
#define LYS_D 120.0
#define LYS_E 130.0

#define MET_A 142.0
#define MET_B 120.0
#define MET_G 125.0
#define MET_E 130.0

#define PHE_A 142.0
#define PHE_B 125.0
#define PHE_D 158.0
#define PHE_E 158.0
#define PHE_Z 158.0

#define PRO_A 148.0
#define PRO_B 120.0
#define PRO_G 120.0
#define PRO_D 130.0

#define SER_A 142.0
#define SER_B 130.0

#define THR_A 142.0
#define THR_B 130.0
#define THR_G 125.0

#define TRP_A 142.0
#define TRP_B 130.0
#define TRP_D 180.0
#define TRP_E1 100.0
#define TRP_Z2 158.0
#define TRP_H 158.0
#define TRP_E3 158.0
#define TRP_Z3 158.0

#define TYR_A 142.0
#define TYR_B 125.0
#define TYR_D 158.0
#define TYR_E 158.0
#define VAL_A 142.0
#define VAL_B 115.0
#define VAL_G 125.0

hetero::hetero( string Name, char aminoCode, amino* residue ){
  this->Name = Name;
  shift = NAN;
  spec_shift2 = NAN;
  spec_shift3 = NAN;
  this->residue = residue;
  x = NAN;
  y = NAN;
  z = NAN;
  fold2 = NAN;
  fold3 = NAN;
  linewidth = NAN;
  lw2 = NAN;
  lw3 = NAN;
  valveg = NAN;

  if( Name[0] == 'N' &&
      !( aminoCode == 'H' && Name == "ND1" ) ){
    linewidth = LW_N;
  }
  // Is this exception correct? I don't know, we observe this signal so rarely.
  if( aminoCode == 'H' && Name == "ND1" ){
    linewidth = LW_C;
  }

  if( Name[0] == 'C' && 
      !( aminoCode == 'P' && Name == "CA" ) ){
    linewidth = LW_C;
  }
  // Is this exception correct? No it's not. The nitrogen linewidth was used for Pro CA (MC 2015)
  if( aminoCode == 'P' && Name == "CA" ){
    linewidth = 50;  // This looks like a reasonable value
  }

  rj = NAN;
  switch( aminoCode ){
  case 'A':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = ALA_A;
    }
    if( Name == "CB" ){
      rj = ALA_B;
    }
    break;
  case 'R':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = ARG_A;
    }
    if( Name == "CB" ){
      rj = ARG_B;
    }
    if( Name == "CG" ){
      rj = ARG_G;
    }
    if( Name == "CD" ){
      rj = ARG_D;
    }
    if( Name == "NE" ){
      rj = ALL_N;
    }
    break;
  case 'N':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = ASN_A;
    }
    if( Name == "CB" ){
      rj = ASN_B;
    }
    if( Name == "ND2" ){
      rj = ALL_N;
    }
    break;
  case 'D':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = ASP_A;
    }
    if( Name == "CB" ){
      rj = ASP_B;
    }
    break;
  case 'C':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = CYS_A;
    }
    if( Name == "CB" ){
      rj = CYS_B;
    }
    break;
  case 'Q':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = GLN_A;
    }
    if( Name == "CB" ){
      rj = GLN_B;
    }
    if( Name == "CG" ){
      rj = GLN_G;
    }
    if( Name == "NE2" ){
      rj = ALL_N;
    }
    break;
  case 'E':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = GLU_A;
    }
    if( Name == "CB" ){
      rj = GLU_B;
    }
    if( Name == "CG" ){
      rj = GLU_G;
    }
    break;
  case 'G':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = GLY_A;
    }
    break;
  case 'H':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = HIS_A;
    }
    if( Name == "CB" ){
      rj = HIS_B;
    }
    if( Name == "ND1" ){
      rj = HIS_D1;
    }
    if( Name == "CD2" ){
      rj = HIS_D2;
    }
    if( Name == "CE1" ){
      rj = HIS_E1;
    }
    break;
  case 'I':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = ILE_A;
    }
    if( Name == "CB" ){
      rj = ILE_B;
    }
    if( Name == "CG1" ){
      rj = ILE_G1;
    }
    if( Name == "CD1" ){
      rj = ILE_D1;
    }
    if( Name == "CG2" ){
      rj = ILE_G2;
    }
    break;
  case 'L':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = LEU_A;
    }
    if( Name == "CB" ){
      rj = LEU_B;
    }
    if( Name == "CG" ){
      rj = LEU_G;
    }
    if( Name == "CD1" ){
      rj = LEU_D;
    }
    if( Name == "CD2" ){
      rj = LEU_D;
    }
    break;
  case 'K':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = LYS_A;
    }
    if( Name == "CB" ){
      rj = LYS_B;
    }
    if( Name == "CG" ){
      rj = LYS_G;
    }
    if( Name == "CD" ){
      rj = LYS_D;
    }
    if( Name == "CE" ){
      rj = LYS_E;
    }
    break;
  case 'M':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = MET_A;
    }
    if( Name == "CB" ){
      rj = MET_B;
    }
    if( Name == "CG" ){
      rj = MET_G;
    }
    if( Name == "CE" ){
      rj = MET_E;
    }
    break;
  case 'F':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = PHE_A;
    }
    if( Name == "CB" ){
      rj = PHE_B;
    }
    if( Name == "CD1" ){
      rj = PHE_D;
    }
    if( Name == "CD2" ){
      rj = PHE_D;
    }
    if( Name == "CE1" ){
      rj = PHE_E;
    }
    if( Name == "CE2" ){
      rj = PHE_E;
    }
    if( Name == "CZ" ){
      rj = PHE_Z;
    }
    break;
  case 'P':
    if( Name == "CA" ){
      rj = PRO_A;
    }
    if( Name == "CB" ){
      rj = PRO_B;
    }
    if( Name == "CG" ){
      rj = PRO_G;
    }
    if( Name == "CD" ){
      rj = PRO_D;
    }
    break;
  case 'S':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = SER_A;
    }
    if( Name == "CB" ){
      rj = SER_B;
    }
    break;
  case 'T':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = THR_A;
    }
    if( Name == "CB" ){
      rj = THR_B;
    }
    if( Name == "CG2" ){
      rj = THR_G;
    }
    break;
  case 'W':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = TRP_A;
    }
    if( Name == "CB" ){
      rj = TRP_B;
    }
    if( Name == "CD1" ){
      rj = TRP_D;
    }
    if( Name == "NE1" ){
      rj = TRP_E1;
    }
    if( Name == "CZ2" ){
      rj = TRP_Z2;
    }
    if( Name == "CH2" ){
      rj = TRP_H;
    }
    if( Name == "CE3" ){
      rj = TRP_E3;
    }
    if( Name == "CZ3" ){
      rj = TRP_Z3;
    }
    break;
  case 'Y':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = TYR_A;
    }
    if( Name == "CB" ){
      rj = TYR_B;
    }
    if( Name == "CD1" ){
      rj = TYR_D;
    }
    if( Name == "CD2" ){
      rj = TYR_D;
    }
    if( Name == "CE1" ){
      rj = TYR_E;
    }
    if( Name == "CE2" ){
      rj = TYR_E;
    }
    break;
  case 'V':
    if( Name == "N" ){
      rj = ALL_N;
    }
    if( Name == "CA" ){
      rj = VAL_A;
    }
    if( Name == "CB" ){
      rj = VAL_B;
    }
    if( Name == "CG1" ){
      rj = VAL_G;
    }
    if( Name == "CG2" ){
      rj = VAL_G;
    }
    break;
  default:
    break;
  }
}

void hetero::addproton( proton* h ){
  prot.push_back( h );
  h->hetatom = this;
}

amino::amino( char residueName, int residueNumber ){
  this->residueName = residueName;
  this->residueNumber = residueNumber;
}

void amino::addC13( hetero* het ){
  C13.push_back( het );
}

void amino::addN15( hetero* het ){
  N15.push_back( het );
}

protein::protein(){
  Name = "undefined";
}