#include "pdb.h"
#include "ProgramParameters.h"

/* incorporates modifications by Vossman on 11.17.2000
   to accomodate nucleic acids
*/


int A_type ;
int G_type ;
int U_type ;
int C_type ;
int GLY_type ;
int ALA_type ;
int VAL_type ;
int LEU_type ;
int ILE_type ;
int PRO_type ;
int MET_type ;
int PHE_type ;
int TYR_type ;
int TRP_type ;
int SER_type ;
int THR_type ;
int ASN_type ;
int GLN_type ;
int CYS_type ;
int HIS_type ;
int GLU_type ;
int ASP_type ;
int ARG_type ;
int LYS_type ;

int residue_character_types[128] ;

extern atom_definition  *default_C_atom  ;
extern atom_definition  *default_O_atom  ;
extern atom_definition  *default_N_atom  ;

/* initial things to the defaults. */

void initial_residues (char *types_file,char *res_file,int chc)
{
  if (types_file != NULL) {
    FILE * ff = fopen(types_file, "r") ;
    if(ff ==NULL) {
      serious_error(1,"Failed to open types file", types_file);
    } else {
      fprintf(stderr,"Reading types file %s\n",types_file);
      read_atom_types (ff) ;
      fclose(ff) ;
    }
  } else {
    /* This is moved from before the "if" as compared to init.c */
		fprintf(stderr,"Reading default atom type defs\n");
    read_atom_types (stream_from_string(NUCPROT_RADII)) ;
  }

  if (res_file != NULL) {
    FILE * ff = fopen(res_file, "r") ;
    if(ff ==NULL) {
      serious_error(1,"Failed to open residue definitions file", res_file);
    } else {
      fprintf(stderr,"Reading residue definitions file %s\n",res_file);
      read_residue_definitions(ff) ;
      fclose(ff) ;
    }
  } else {
    /* This is moved from before the "if" as compared to init.c */
		fprintf(stderr,"Reading default residue defs\n");
    read_residue_definitions (stream_from_string(DEFAULT_RESIDUES)) ;
  }

  dumm_residue = find_residue_type ("DUM") ;
  default_atom = find_atom_definition(dumm_residue, "DUM");
  default_C_atom  = find_atom_definition(dumm_residue, "CDUM");
  default_O_atom  =find_atom_definition(dumm_residue, "ODUM");
  default_N_atom  = find_atom_definition(dumm_residue, "NDUM");
  
  { residue_description * res  = find_residue_type("WAT") ;
    first_water_type = res->index ; }
  { residue_description * res  = find_residue_type("HOH") ;
    second_water_type = res->index ; }
  { residue_description * res = find_residue_type("GLY") ;
    GLY_type = res->index ;}
  { residue_description * res = find_residue_type("ALA") ;
    ALA_type = res->index ; }
  { residue_description * res = find_residue_type("VAL") ;
    VAL_type = res->index ;}
  { residue_description * res = find_residue_type("LEU") ;
    LEU_type = res->index ;}
  { residue_description * res = find_residue_type("ILE") ;
    ILE_type = res->index ;}
  { residue_description * res = find_residue_type("PRO") ;
    PRO_type = res->index ;}
  { residue_description * res = find_residue_type("MET") ;
    MET_type = res->index ;}
  { residue_description * res = find_residue_type("PHE") ;
    PHE_type = res->index ;}
  { residue_description * res = find_residue_type("TYR") ;
    TYR_type = res->index ;}
  { residue_description * res = find_residue_type("TRP") ;
    TRP_type = res->index ;}
  { residue_description * res = find_residue_type("SER") ;
    SER_type = res->index ;}
  { residue_description * res = find_residue_type("THR") ;
    THR_type = res->index ;}
  { residue_description * res = find_residue_type("ASN") ;
    ASN_type = res->index ;}
  { residue_description * res = find_residue_type("GLN") ;
    GLN_type = res->index ;}
  { residue_description * res = find_residue_type("CYS") ;
    CYS_type = res->index ;}
  { residue_description * res = find_residue_type("HIS") ;
    HIS_type = res->index ;}
  { residue_description * res = find_residue_type("GLU") ;
    GLU_type = res->index ;}
  { residue_description * res = find_residue_type("ASP") ;
    ASP_type = res->index ;}
  { residue_description * res = find_residue_type("ARG") ;
    ARG_type = res->index ;}
  { residue_description * res = find_residue_type("LYS") ;
    LYS_type = res->index ;}


  {
    int ii ;
    for(ii =0 ; ii< 128; ii++)
      residue_character_types[ii] = -1 ;

    residue_character_types['G']= residue_character_types['g'] = GLY_type;
    residue_character_types['A']= residue_character_types['a'] = ALA_type;
    residue_character_types['V']= residue_character_types['v'] = VAL_type;
    residue_character_types['L']= residue_character_types['l'] = LEU_type;
    residue_character_types['I']= residue_character_types['i'] = ILE_type;
    residue_character_types['M']= residue_character_types['m'] = MET_type;
    residue_character_types['P']= residue_character_types['p'] = PRO_type;
    residue_character_types['F']= residue_character_types['f'] = PHE_type;
    residue_character_types['Y']= residue_character_types['y'] = TYR_type;
    residue_character_types['W']= residue_character_types['w'] = TRP_type;
    residue_character_types['S']= residue_character_types['s'] = SER_type;
    residue_character_types['T']= residue_character_types['t'] = THR_type;
    residue_character_types['C']= residue_character_types['c'] = CYS_type;
    residue_character_types['K']= residue_character_types['k'] = LYS_type;
    residue_character_types['R']= residue_character_types['r'] = ARG_type;
    residue_character_types['D']= residue_character_types['d'] = ASP_type;
    residue_character_types['E']= residue_character_types['e'] = GLU_type;
    residue_character_types['N']= residue_character_types['n'] = ASN_type;
    residue_character_types['Q']= residue_character_types['q'] = GLN_type;
    residue_character_types['H']= residue_character_types['h'] = HIS_type;
  }
}

void default_initialization (void)
{
  initial_residues_nt(NULL,NULL,1);
}

void initial_residues_nt (char *types_file, char *res_file, int chc)
{
  if (types_file != NULL) {
    FILE * ff = fopen(types_file, "r") ;
    if(ff ==NULL) {
      serious_error(1,"Failed to open types file", types_file);
    } else {
      fprintf(stderr,"Reading types file %s\n",types_file);
      read_atom_types (ff) ;
      fclose(ff) ;
    }
  } else {
    /* This is moved from before the "if" as compared to init.c */
		fprintf(stderr,"Reading default atom type defs\n");
    read_atom_types (stream_from_string(NUCPROT_RADII)) ;
  }

  if (res_file != NULL) {
    FILE * ff = fopen(res_file, "r") ;
    if(ff == NULL) {
      serious_error(1,"Failed to open residue definitions file", res_file);
    } else {
      fprintf(stderr,"Reading residue definitions file %s\n",res_file);
      read_residue_definitions(ff) ;
      fclose(ff) ;
    }
  } else {
    /* This is moved from before the "if" as compared to init.c */
		fprintf(stderr,"Reading default residue defs\n");
    read_residue_definitions (stream_from_string(DEFAULT_RESIDUES)) ;
  }

  dumm_residue = find_residue_type ("DUM") ;
  default_atom = find_atom_definition(dumm_residue, "DUM");
  default_C_atom  = find_atom_definition(dumm_residue, "CDUM");
  default_O_atom  =find_atom_definition(dumm_residue, "ODUM");
  default_N_atom  = find_atom_definition(dumm_residue, "NDUM");
  
  { residue_description * res  = find_residue_type("WAT") ;
    first_water_type = res->index ; }
  { residue_description * res  = find_residue_type("HOH") ;
    second_water_type = res->index ; }
  { residue_description * res = find_residue_type("  A") ;
    A_type = res->index ;}
  { residue_description * res = find_residue_type("  G") ;
    G_type = res->index ;}
  { residue_description * res = find_residue_type("  U") ;
    U_type = res->index ;}
  { residue_description * res = find_residue_type("  C") ;
    C_type = res->index ;}
  { residue_description * res = find_residue_type("GLY") ;
    GLY_type = res->index ;}
  { residue_description * res = find_residue_type("ALA") ;
    ALA_type = res->index ; }
  { residue_description * res = find_residue_type("VAL") ;
    VAL_type = res->index ;}
  { residue_description * res = find_residue_type("LEU") ;
    LEU_type = res->index ;}
  { residue_description * res = find_residue_type("ILE") ;
    ILE_type = res->index ;}
  { residue_description * res = find_residue_type("PRO") ;
    PRO_type = res->index ;}
  { residue_description * res = find_residue_type("MET") ;
    MET_type = res->index ;}
  { residue_description * res = find_residue_type("PHE") ;
    PHE_type = res->index ;}
  { residue_description * res = find_residue_type("TYR") ;
    TYR_type = res->index ;}
  { residue_description * res = find_residue_type("TRP") ;
    TRP_type = res->index ;}
  { residue_description * res = find_residue_type("SER") ;
    SER_type = res->index ;}
  { residue_description * res = find_residue_type("THR") ;
    THR_type = res->index ;}
  { residue_description * res = find_residue_type("ASN") ;
    ASN_type = res->index ;}
  { residue_description * res = find_residue_type("GLN") ;
    GLN_type = res->index ;}
  { residue_description * res = find_residue_type("CYS") ;
    CYS_type = res->index ;}
  { residue_description * res = find_residue_type("HIS") ;
    HIS_type = res->index ;}
  { residue_description * res = find_residue_type("GLU") ;
    GLU_type = res->index ;}
  { residue_description * res = find_residue_type("ASP") ;
    ASP_type = res->index ;}
  { residue_description * res = find_residue_type("ARG") ;
    ARG_type = res->index ;}
  { residue_description * res = find_residue_type("LYS") ;
    LYS_type = res->index ;}


  {
    int ii ;
    for(ii =0 ; ii< 128; ii++)
      residue_character_types[ii] = -1 ;

    residue_character_types['1']= G_type;
    residue_character_types['2']= A_type;
    residue_character_types['3']= U_type;
    residue_character_types['4']= C_type;
    residue_character_types['G']= residue_character_types['g'] = GLY_type;
    residue_character_types['A']= residue_character_types['a'] = ALA_type;
    residue_character_types['V']= residue_character_types['v'] = VAL_type;
    residue_character_types['L']= residue_character_types['l'] = LEU_type;
    residue_character_types['I']= residue_character_types['i'] = ILE_type;
    residue_character_types['M']= residue_character_types['m'] = MET_type;
    residue_character_types['P']= residue_character_types['p'] = PRO_type;
    residue_character_types['F']= residue_character_types['f'] = PHE_type;
    residue_character_types['Y']= residue_character_types['y'] = TYR_type;
    residue_character_types['W']= residue_character_types['w'] = TRP_type;
    residue_character_types['S']= residue_character_types['s'] = SER_type;
    residue_character_types['T']= residue_character_types['t'] = THR_type;
    residue_character_types['C']= residue_character_types['c'] = CYS_type;
    residue_character_types['K']= residue_character_types['k'] = LYS_type;
    residue_character_types['R']= residue_character_types['r'] = ARG_type;
    residue_character_types['D']= residue_character_types['d'] = ASP_type;
    residue_character_types['E']= residue_character_types['e'] = GLU_type;
    residue_character_types['N']= residue_character_types['n'] = ASN_type;
    residue_character_types['Q']= residue_character_types['q'] = GLN_type;
    residue_character_types['H']= residue_character_types['h'] = HIS_type;
  }
}