#include "molfile_plugin.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
/*
 * API functions start here
 */

typedef struct {
  FILE *file;
  int natoms,nbonds,coords_read;
  int *from,*to;
  char *file_name;
}vmfdata;

static void *open_vmf_read(const char *filename, const char *filetype, 
    int *natoms) {
  char input_line[80];
  int i,nbonds;
  FILE *fd;
  vmfdata *vmf;
  fd = fopen(filename, "r");
  if(!fd)
	  return NULL;
  for(i=1;;)
  {
	  fgets(input_line,sizeof(input_line),fd);
	  if(strstr(input_line,"atom"))
	  {
		  *natoms=i;
		  i++;
	  }
	  else if (strstr(input_line,"connect"))
		  break;
  }
   rewind(fd);
   for(i=1;;)
   {
	   fgets(input_line,1024,fd);
	   if(strstr(input_line,"connect"))
	   {
		   nbonds=i;
		   i++;
	   }
	   else if(strstr(input_line,"End"))
		   break;
	   else continue;
   }
  vmf=new vmfdata;
  vmf->file = fd;
  vmf->file_name=strdup(filename);
  vmf->natoms=*natoms;
  vmf->nbonds=nbonds;
  vmf->coords_read=0;
  vmf->from=NULL;
  vmf->to=NULL;
  return vmf;
}

static int read_vmf_structure(void *mydata, int *optflags, 
    molfile_atom_t *atoms)
{ 
  vmfdata *vmf = (vmfdata *)mydata;
  molfile_atom_t *atom;
  int i,j;
  char *k,filebuffer[1024];
  *optflags = MOLFILE_CHARGE;
  rewind(vmf->file);
  for(i=0;i<4;i++)
  {
	  fgets(filebuffer,1024,vmf->file);
  }
 
  for(i=0;i<vmf->natoms;i++)
  {
	  char fbuffer[1024];
      k=fgets(fbuffer,1024,vmf->file);
	  atom=atoms+i;
      j=sscanf(fbuffer,"%*s %*d %*s %*f %*f %*f %s %f",
		      atom->type,&atom->charge);
	  	  if (k==NULL)
		  {
			fprintf(stderr,"vmf structure) missing atom(s) in file'%s'\n",vmf->file_name);
		    fprintf(stderr, "vmf structure) expecting '%d' atoms, found only '%d'\n", vmf->natoms, i+1);
			return MOLFILE_ERROR;
		  }
		  else if(j<2)
		  {
			  fprintf(stderr,"vmf structure) missing type or coordinate(s) in file'%s'for atom'%d'\n",vmf->file_name,i+1);
			  return MOLFILE_ERROR;
		  }
		  strcpy(atom->chain," ");
		  strcpy(atom->segid," ");
  }
return MOLFILE_SUCCESS;		   
}

static int read_bonds(void *v, int *nbonds, int **fromptr, int **toptr)
{
   vmfdata *vmf = (vmfdata *)v;
   char line[1024],bond_type[16];
   int i,match,bond_from,bond_to,bond_index,current_nbonds;
   if(vmf->nbonds == 0)
   {
	   *nbonds=0;
	   *fromptr = NULL;
	   *toptr = NULL;
	   return MOLFILE_SUCCESS;
   }
   vmf->from = new int[vmf->nbonds]; 
   vmf->to = new int[vmf->nbonds];
   current_nbonds=vmf->nbonds;
   rewind(vmf->file);
   for(i=0;i<4;i++)
   {
	   fgets(line,1024,vmf->file);
   }
   for(i=0;i<vmf->natoms;i++)
   {
	   fgets(line,1024,vmf->file);
   }
   bond_index=0;
   for(i=0;i<vmf->nbonds;i++)
   {
	   fgets(line,1024,vmf->file);
   if (ferror(vmf->file) || feof(vmf->file))
   {
	   fprintf(stderr,"vmfplugin: error occurred reading atom record.\n");
		   return MOLFILE_ERROR;
   }
   match=sscanf(line,"%*s %d %d %s",&bond_from,&bond_to,bond_type);
   if (match<3)
   {
	   fprintf(stderr,"vmfplugin: improperly formatted bond record.\n");
	   return MOLFILE_ERROR;
   }
   if (strncmp(bond_type,"nc",2) == 0)
   {
	   current_nbonds--;
   }
   else{
	   vmf->from[bond_index]=bond_from;
	   vmf->to[bond_index]=bond_to;
	   bond_index++;
	   }
   } 
   *nbonds=current_nbonds;
   *fromptr=vmf->from;
   *toptr=vmf->to;
    return MOLFILE_SUCCESS;
}

static int read_vmf_timestep(void *mydata, int natoms, molfile_timestep_t *ts)
{
  vmfdata *vmf = (vmfdata *)mydata;
  int i,match;
  char line[1024];
  float x, y, z;
  if (vmf->coords_read)
  {
	  return MOLFILE_EOF;
  }
  rewind(vmf->file);
  for(i=0;i<4;i++)
	  fgets(line,1024,vmf->file);
  for(i=0;i<vmf->natoms;i++)
  {
  fgets(line,1024,vmf->file);
  if(ferror(vmf->file) || feof(vmf->file))
  {
	  fprintf(stderr,"vmfplugin:error occurred reading atom coordinates.\n");
		  return MOLFILE_ERROR;
  }

	  match=sscanf(line,"%*s %*d %*s %f %f %f",&x, &y, &z);
	  if (match<3)
	  {
		  fprintf(stderr,"vmfplugin: improperly formatted atom coordinates.\n");
		  return MOLFILE_ERROR;
	  }
	  if (ts)
	  {
		  ts->coords[3*i]=x;
          ts->coords[3*i+1]=y;
          ts->coords[3*i+2]=z;
	  }
  }
  
    vmf->coords_read=1;		  
    return MOLFILE_SUCCESS;
}
static void close_vmf_read(void *mydata) 
{
  vmfdata *vmf = (vmfdata *)mydata;
   if(vmf)
   {
     if(vmf->file) fclose(vmf->file);
     if(vmf->from) delete [] vmf->from;
     if(vmf->to) delete [] vmf->to;
     delete vmf;
   }
}
/* registration stuff */
static molfile_plugin_t vmfplugin = {
  vmdplugin_ABIVERSION,
  MOLFILE_PLUGIN_TYPE,                         /* type */
  "vmf",                                       /* name */
  "Mauricio Carrillo Tripp, John E. Stone, Axel Kohlmeyer",    /* author */
  0,                                           /* major version */
  6,                                           /* minor version */
  VMDPLUGIN_THREADSAFE,                        /* is reentrant */
  "vmf",
  open_vmf_read,
  read_vmf_structure,
  read_bonds,
  read_vmf_timestep,
  close_vmf_read,
  0,
  0,
  0,
  0,
  0,                            /* read_volumetric_metadata */
  0,                            /* read_volumetric_data */
  0                             /* read_rawgraphics */
};

int VMDPLUGIN_init() {
  return VMDPLUGIN_SUCCESS;
}

int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {
  (*cb)(v, (vmdplugin_t *)&vmfplugin);
  return VMDPLUGIN_SUCCESS;
}

int VMDPLUGIN_fini() {
  return VMDPLUGIN_SUCCESS;
}