/*============================================================================*/
/* FILENAME: READ_MM2.C (READ_MM2.O)
/* PURPOSE: TO READ IN AN MM2 INPUT FILE.
/* WRITTEN: M.V.GRIESHABER
/* LAST MODIFICATION: 13 JULY 1993 MVG (ADDED ATOM TYPES 61-110).
/*============================================================================*/

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

#define MAX_MM2_ATOM_TYPES 110

#define max(a,b) (a<b ? b : a)

int read_mm2_input(geometry_type,infile)
/*============================================================================*/
/* PURPOSE: TO READ IN AN MM2/MM3 INPUT FILE.
*/
   int geometry_type;	/* SPECIFIES MM2 OR MM3 INPUT FILE. */
   FILE *infile;
   {
   char line[130];	/* LINE READ FROM MM2 INPUT FILE. */
   char work_str[130];	/* TEMPORARY WORK STRING. */
   int method;		/* FLAG; PRESENCE OF PI SYSTEM INFORMATION. */
   int num_connected_atom_lists;
   int num_attached_atoms;
   int i;
   int pi_system_card;
   static char atomic_symbol[MAX_MM2_ATOM_TYPES][3]=
      {
      "C ","C ","C ","C ","H ","O ","O ","N ","N ","N ",
      "F ","Cl","Br","I ","S ","S ","S ","S ","Si","LP",
      "H ","C ","H ","H ","P ","B ","B ","H ","C ","C ",
      "Ge","Sn","Pb","Se","Te","H ","N ","C ","N ","N ",
      "O ","S ","N ","H ","N ","N ","O ","H ","O ","C ",
      "He","Ne","Ar","Kr","Xe","C ","C ","C ","Mg","P ",
      "Fe","Fe","Ni","Ni","Co","Co","C ","C ","O ","O ",
      "C ","N ","H ","Du","O ","O ","O ","O ","O ","O ",
      "O ","O ","O ","O ","O ","O ","O ","O ","O ","O ",
      "O ","O ","O ","O ","O ","O ","O ","O ","O ","O ",
      "O ","O ","O ","S ","S ","C ","N ","N ","N ","Du"
      };

   /* GET THE METHOD AND NUMBER OF ATOMS. */
   if (fgets(line,sizeof line,infile)==NULL) return(errmsg("Reading MM2/MM3 input file (number of atoms)",FALSE));
   strncpy(work_str,&line[60],1);
   work_str[1]=0;	/* ADD NULL THAT STRNCPY WON'T PUT ON. */
   method=atoi(work_str);
   sscanf(&line[61],"%4hd",&atom_cnt);

   /* GET THE AROMATIC FLAGS (THIS MAY CONTINUE ACROSS MULTIPLE CARDS). */
   if (method)
      {
      pi_system_card=0;	/* REMEMBER WHICH CARD WE ARE PROCESSING FOR OFFSET. */
      do
         {
         if (fgets(line,sizeof line,infile)==NULL) return(errmsg("Reading MM2/MM3 input file (aromatic flags)",FALSE));
         for (i=0; i<max(59,atom_cnt); i++)
            {
            /* COLUMNS 0-59 = AROMATIC FLAGS, COLUMN 79 = CONTINUATION FLAG. */
            if (line[i]=='T') intco[pi_system_card*60 + i].source_aromatic=TRUE;
            }
         pi_system_card++;
         } while (line[79]=='1');
      }

   /* GET NUMBER OF CONNECTED ATOM LISTS AND NUMBER OF ATTACHED ATOMS. */
   if (fgets(line,sizeof line,infile)==NULL) return(errmsg("Reading MM2/MM3 input file (number of atom lists)",FALSE));
   strncpy(work_str,&line[1],4);
   work_str[4]=0;	/* ADD NULL THAT STRNCPY WON'T PUT ON. */
   num_connected_atom_lists=atoi(work_str);
   strncpy(work_str,&line[25],5);
   work_str[5]=0;	/* ADD NULL THAT STRNCPY WON'T PUT ON. */
   num_attached_atoms=atoi(work_str);

   /* BUILD THE BONDS FROM THE INFORMATION IN THE FILE (DO NOT USE BONDGEN). */
   for (i=0; i<num_connected_atom_lists; i++)
      {
      if (fgets(line,sizeof line,infile)==NULL) return(errmsg("Reading MM2/MM3 input file (connected atom lists)",FALSE));
      if (!process_connected_atom_list(line)) return(FALSE);
      }
   for (i=0; i<num_attached_atoms; i+=8)
      {
      if (fgets(line,sizeof line,infile)==NULL) return(errmsg("Reading MM2/MM3 input file (attached atoms)",FALSE));
      if (!process_attached_atom_list(line)) return(FALSE);
      }

   /* GET THE COORDINATES AND ATOM TYPE. */
   for (i=0; i<atom_cnt; i++)
      {
      if (fgets(line,sizeof line,infile)==NULL) return(errmsg("Reading MM2/MM3 input file (atomic coordinates)",FALSE));
      sscanf(line,"%lf %lf %lf",&intco[i].vector[0],&intco[i].vector[1],&intco[i].vector[2]);
      strncpy(work_str,&line[33],2);
      work_str[2]=0;	/* ADD NULL THAT STRNCPY WON'T PUT ON. */
      intco[i].source_type=(short)atoi(work_str);
      strcpy(intco[i].atom_name,atomic_symbol[intco[i].source_type-1]);
      }

   return(TRUE);
   }

int process_connected_atom_list(line)
/*============================================================================*/
/* PURPOSE: PROCESS AN MM2 CONNECTED ATOM LIST INTO THE INDIVIDUAL BONDS.
*/
   char line[];	/* RAW CONNECTED ATOM LIST FROM MM2 INPUT FILE. */
   {
   int i;
   char atom_string[6];	/* STRING VERSION OF ATOM NUMBER. */
   int first_atom;	/* FIRST ATOM OF VALID PAIR. */
   int second_atom;	/* SECOND ATOM OF VALID PAIR. */

   /* TAKE APART A CONNECTED ATOM LIST AN ATOM PAIR AT A TIME. */
   i=0;
   while (i<15 && atoi(&line[(i+1)*5])!=0)
      {
      /* GET THE VALID ATOM PAIR. */
      strncpy(atom_string,&line[i*5],5);
      atom_string[5]=0;
      first_atom=atoi(atom_string)-1;	/* MM2 COUNTS FROM 1. */

      strncpy(atom_string,&line[++i*5],5);
      atom_string[5]=0;
      second_atom=atoi(atom_string)-1;	/* MM2 COUNTS FROM 1. */

      /* ADD THE BONDS TO EACH ATOM'S RESPECTIVE BOND LIST. */
      if (intco[first_atom].bond_cnt>=MAX_BONDS_PER_ATOM || intco[second_atom].bond_cnt>=MAX_BONDS_PER_ATOM)
         return(errmsg("Too many bonds to a single atom",FALSE));
      intco[first_atom].bonds[intco[first_atom].bond_cnt++] = second_atom;
      intco[second_atom].bonds[intco[second_atom].bond_cnt++] = first_atom;
      }

   return(TRUE);
   }

int process_attached_atom_list(line)
/*============================================================================*/
/* PURPOSE: PROCESS AN MM2 ATTACHED ATOM LIST INTO THE INDIVIDUAL BONDS.
*/
   char line[];	/* RAW ATTACHED ATOM LIST FROM MM2 INPUT FILE. */
   {
   int i;
   char atom_string[6];	/* STRING VERSION OF ATOM NUMBER. */
   int first_atom;	/* FIRST ATOM OF VALID PAIR. */
   int second_atom;	/* SECOND ATOM OF VALID PAIR. */

   /* TAKE APART AN ATTACHED ATOM LIST AN ATOM PAIR AT A TIME. */
   i=0;
   while (i<15 && atoi(&line[i*5])!=0)
      {
      /* GET THE VALID ATOM PAIR. */
      strncpy(atom_string,&line[i*5],5);
      atom_string[5]=0;
      first_atom=atoi(atom_string)-1;	/* MM2 COUNTS FROM 1. */

      strncpy(atom_string,&line[(i+1)*5],5);
      atom_string[5]=0;
      second_atom=atoi(atom_string)-1;	/* MM2 COUNTS FROM 1. */

      i+=2;	/* FINISHED THIS PAIR, SKIP AHEAD TO NEXT. */

      /* ADD THE BONDS TO EACH ATOM'S RESPECTIVE BOND LIST. */
      if (intco[first_atom].bond_cnt>=MAX_BONDS_PER_ATOM || intco[second_atom].bond_cnt>=MAX_BONDS_PER_ATOM)
         return(errmsg("Too many bonds to a single atom",FALSE));
      intco[first_atom].bonds[intco[first_atom].bond_cnt++] = second_atom;
      intco[second_atom].bonds[intco[second_atom].bond_cnt++] = first_atom;
      }

   return(TRUE);
   }