#include "utility.h"
#include "newgeo.h"

#define MAX_SYBYL_ATOM_TYPE 31
#define MIN_SYBYL_ATOM_TYPE 1

static char sybyl_mnemonics[MAX_SYBYL_ATOM_TYPE][6] =
   {
   "C.3",	/* 1 */
   "C.2",	/* 2 */
   "C.ar",	/* 3 */
   "C.1",	/* 4 */
   "N.3",	/* 5 */ 
   "N.2",	/* 6 */
   "N.1",	/* 7 */  
   "O.3",	/* 8 */
   "O.2",	/* 9 */
   "S.3",	/*10 */
   "N.ar",	/*11 */ 
   "P.3",	/*12 */
   "H",		/*13 */ 
   "Br",	/*14 */
   "Cl",	/*15 */ 
   "F",		/*16 */
   "I",		/*17 */ 
   "S.2",	/*18 */
   "N.pl3",	/*19 */ 
   "LP",	/*20 */
   "Na",	/*21 */ 
   "K",		/*22 */
   "Ca",	/*23 */ 
   "Li",	/*24 */
   "Al",	/*25 */
   "Du",	/*26 */
   "Si",	/*27 */
   "N.am",	/*28 */
   "S.O",	/*29 */
   "S.O2",	/*30 */
   "N.4" 	/*31 */
   };

static char sybyl_elements[MAX_SYBYL_ATOM_TYPE][3] =
   {
   "C ",	/* 1 */
   "C ",	/* 2 */
   "C ",	/* 3 */
   "C ",	/* 4 */
   "N ",	/* 5 */ 
   "N ",	/* 6 */
   "N ",	/* 7 */  
   "O ",	/* 8 */
   "O ",	/* 9 */
   "S ",	/*10 */
   "N ",	/*11 */ 
   "P ",	/*12 */
   "H ",	/*13 */ 
   "Br",	/*14 */
   "Cl",	/*15 */ 
   "F ",	/*16 */
   "I ",	/*17 */ 
   "S ",	/*18 */
   "N ",	/*19 */ 
   "LP",	/*20 */
   "Na",	/*21 */ 
   "K ",	/*22 */
   "Ca",	/*23 */ 
   "Li",	/*24 */
   "Al",	/*25 */
   "Du",	/*26 */
   "Si",	/*27 */
   "N ",	/*28 */
   "S ",	/*29 */
   "S ",	/*30 */
   "N " 	/*31 */
   };

int read_sybyl_mol(infile)
/*============================================================================*/
/* This routine reads in SYBYL MOL file from  a disk file .
/* AUTHOR:    John R. Hurst, Data Management, 051088
/* LAST MODIFICATION: 2 APRIL 1992 MVG (ADDED READ MOL2 CAPABILITY)
/*============================================================================*/
FILE *infile;
{
  int bond_cnt;
  char line[130];	/* Multipurpose character string */
  int i;		/* loop variable */
  int atom1;		/* FIRST ATOM IN BOND. */
  int atom2;		/* SECOND ATOM IN BOND. */

  /* READ IN THE HEADER. */
  if (fgets(line,sizeof line,infile) == NULL) return(FALSE);
  atom_cnt = 0;
  if (sscanf(line,"%hd",&atom_cnt)!=1) return(errmsg("Reading header",FALSE));	/* GET THE TOTAL NUMBER OF ATOMS. */
  strncpy(source_title,&line[18],20);	/* GET THE MOLECULE NAME AS TITLE. */
  source_title[20]='\0';		/* ADD NULL THAT STRNCPY LEAVES OFF. */
  notrail(source_title,' ');

  /* READ IN EACH ATOM OF THE GEOMETRY DEFINITION. */
  for (i=0; i<atom_cnt; i++)
    {
    if (fgets(line,sizeof line,infile)==NULL) return(errmsg("Reading atom record",FALSE));

    if (sscanf(line,"%*d %hd %lf %lf %lf",&intco[i].source_type,&intco[i].vector[0],&intco[i].vector[1],&intco[i].vector[2])!=4)
      return(errmsg("Reading atom record",FALSE));

    strcpy(intco[i].atom_name,sybyl_elements[intco[i].source_type-1]);
    }

  /* GET THE NUMBER OF BONDS. */
  if (fgets(line,sizeof line,infile) == NULL) return(errmsg("Reading number of bonds",FALSE));
  if (sscanf(line,"%d",&bond_cnt)!=1) return(errmsg("Reading number of bonds",FALSE));

  /* READ IN EACH BOND RECORD. */
  for (i=0; i<bond_cnt; i++)
    {
    if (fgets(line,sizeof line,infile)==NULL) return(errmsg("Reading bond record",FALSE));
    if (sscanf(line,"%*d %d %d",&atom1,&atom2)!=2) return(errmsg("Reading bond record",FALSE));

    --atom1;	/* ADJUST TO INDEX FROM ZERO. */
    --atom2;
    intco[atom1].bonds[intco[atom1].bond_cnt++]=atom2;
    intco[atom2].bonds[intco[atom2].bond_cnt++]=atom1;
    }

  return(TRUE);
}

int read_sybyl_mol2(infile)
/*============================================================================*/
/* PURPOSE: READ A SYBYL .MOL2 FILE.  NOTE WE ONLY HANDLE THREE TYPES OF
/*	RECORDS FROM THE .MOL2 FILE (MOLECULE, ATOM, AND BOND).
*/
   FILE *infile;
   {
   char line[500];		/* RAW LINE FROM INFILE. */
   int bond_cnt;		/* NUMBER OF BONDS IN MOLECULE. */
   int natom;			/* LOOP INDEX; WHICH ATOM. */
   int nbond;			/* LOOP INDEX; WHICH BOND. */
   char type_mnemonic[20];	/* SYBYL ATOM TYPE MNEMONIC. */
   int atom1;			/* FIRST ATOM IN BOND. */
   int atom2;			/* SECOND ATOM IN BOND. */

   while (fgets(line,sizeof line,infile)!=NULL)
      {
      line[strlen(line)-1]='\0';	/* TRIM TRAILING NEWLINE. */

      if (strcmp(line,"@<TRIPOS>MOLECULE")==0)
         {
         /* GRAB MOLECULE NAME, AND NUMBER OF ATOMS/BONDS. */
         if (fgets(source_title,sizeof source_title,infile)==NULL)
            return(errmsg("Reading molecule name",FALSE));
         if (fgets(line,sizeof line,infile)==NULL)
            return(errmsg("Reading number of atoms and bonds",FALSE));
         if (sscanf(line,"%hd %d",&atom_cnt,&bond_cnt)!=2)
            return(errmsg("Reading number of atoms and bonds",FALSE));

         /* SKIP MOLECULE TYPE, CHARGE TYPE, AND STATUS. */
         if (fgets(line,sizeof line,infile)==NULL)
            return(errmsg("Reading molecule type",FALSE));
         if (fgets(line,sizeof line,infile)==NULL)
            return(errmsg("Reading molecule charge type",FALSE));
         if (fgets(line,sizeof line,infile)==NULL)
            return(errmsg("Reading molecule status bits",FALSE));

         /* GET THE COMMENT LINE. */
         if (fgets(header_text[0],sizeof header_text[0],infile)==NULL)
            return(errmsg("Reading molecule comment",FALSE));
         }

      else if (strcmp(line,"@<TRIPOS>ATOM")==0)
         {
         /* GRAB THE DEFINITION OF EACH ATOM. */
         for (natom=0; natom<atom_cnt; natom++)
            {
            if (fgets(line,sizeof line,infile)==NULL)
               return(errmsg("Reading atom definition",FALSE));
            if (sscanf(line,"%*d %*s %lf %lf %lf %s",&intco[natom].vector[0],
               &intco[natom].vector[1],&intco[natom].vector[2],type_mnemonic)!=4)
               return(errmsg("Reading atom definition",FALSE));
            intco[natom].source_type=sybyl_int_type(type_mnemonic);
            strcpy(intco[natom].atom_name,sybyl_elements[intco[natom].source_type-1]);
            }
         }

      else if (strcmp(line,"@<TRIPOS>BOND")==0)
         {
         /* GRAB THE DEFINITION OF EACH BOND. */
         for (nbond=0; nbond<bond_cnt; nbond++)
            {
            if (fgets(line,sizeof line,infile)==NULL)
               return(errmsg("Reading bond definition",FALSE));
            if (sscanf(line,"%*d %d %d",&atom1,&atom2)!=2)
               return(errmsg("Reading bond definition",FALSE));

            --atom1;	/* ADJUST TO INDEX FROM ZERO. */
            --atom2;
            intco[atom1].bonds[intco[atom1].bond_cnt++]=atom2;
            intco[atom2].bonds[intco[atom2].bond_cnt++]=atom1;
            }
         }
      }

   return(TRUE);
   }

int sybyl_int_type(type_mnemonic)
/*============================================================================*/
/* PURPOSE: CONVERT A SYBYL MNEMONIC ATOM TYPE TO THE CORRESPONDING INTEGER.
*/
   char *type_mnemonic;	/* MNEMONIC STRING VERSION OF ATOM TYPE. */
   {
   int ntype;	/* LOOP INDEX; WHICH ATOM TYPE. */

   for (ntype=0; ntype<MAX_SYBYL_ATOM_TYPE; ntype++)
      {
      if (strcasecmp(type_mnemonic,sybyl_mnemonics[ntype])==0) return(ntype+1);
      }

   return(-1);
   }

char *sybyl_mnemonic_type(atom_type)
/*============================================================================*/
/* PURPOSE: CONVERT A SYBYL INTEGER ATOM TYPE TO THE CORRESPONDING MNEMONIC.
*/
   int atom_type;	/* INTEGER VERSION OF ATOM TYPE. */
   {
   if (atom_type<=MAX_SYBYL_ATOM_TYPE && atom_type>=MIN_SYBYL_ATOM_TYPE)
      return(sybyl_mnemonics[atom_type-1]);
   else return("Bad");
   }