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vtfplugin.c

/* MACHINE GENERATED FILE, DO NOT EDIT! */

#define VMDPLUGIN molfile_vtfplugin
#define STATIC_PLUGIN 1

/* VTF plugin by Olaf Lenz <olenz@fias.uni-frankfurt.de> */
/* $Id: vtfplugin.c,v 1.13 2009/05/18 05:01:56 johns Exp $ */

/*
VMD file reader plugin for:
- VTF structure format (VSF)
- VTF coordinate format (VCF)
- VTF trajectory format (VTF)
*/
#include <molfile_plugin.h>
#include <stdlib.h>
#include <stdio.h>
#include <errno.h>
#include <ctype.h>
#include <string.h>

#ifdef _USE_ZLIB
#include <zlib.h>
#define VTFFILE gzFile
#define fopen gzopen
#define feof gzeof
#define fgets(buf,size,file) gzgets(file,buf,size)
#define fclose gzclose
#else
#define VTFFILE FILE*
#endif

#define VERSION_MAJOR 1
#define VERSION_MINOR 3

/* TODO:
- volumetric/graphics format
- file write support
*/

/***************************************************
 * Data structures
 ***************************************************/
/* Default atom. 
   Used by vtf_parse_atom to initialise new atoms. */
static molfile_atom_t default_atom;

/* Plugin data structure to communciate data between the functions. */
typedef struct {
  /* opened file */
  VTFFILE file;
  /* return code */
  int return_code;

  /* STRUCTURE DATA (used by read_structure) */
  /* atom info */
  int natoms;
  molfile_atom_t *atoms;
  int optflags;

  /* bond info */
  int nbonds;
  int *from;
  int *to;

  /* TIMESTEP DATA (used by get_next_timestep) */
  /* reading mode for the next timestep */
  int timestep_mode;
  /* last timestep */
  float A, B, C, alpha, beta, gamma;
  float *coords;
} vtf_data;

/* constants for timestep_mode */
#define TIMESTEP_INDEXED 0
#define TIMESTEP_ORDERED 1
#define TIMESTEP_VCFSTART 2

/* global variable: contains the line number of the file */
static int vtf_lineno = 0;

/***************************************************
 * Print an error message.
 ***************************************************/
static void vtf_error(const char *msg, const char *line) {
  char message[200];
  sprintf(message, "vtfplugin:%d: error: %s: %-20s\n",        
        vtf_lineno, msg, line);

/* #if vmdplugin_ABIVERSION > 13 */
/*   if (cons_fputs) */
/*     cons_fputs(VMDCON_ERROR, message); */
/*   else */
/* #else */
    printf(message);
/* #endif */
}

/***************************************************
 * Read a line
 ***************************************************/

/* Read a whole line from the file. 
   The line may have arbitrary length and continuation lines ending
   with '\' are heeded.
   The function will return a pointer to a buffer or NULL if an
   error occured or eof occurs while no characters have been read.
   The function will set the global variable lineno.
*/
static char *vtf_getline(VTFFILE file) {
  static char *buffer = NULL;
  static int buffer_size = 0;
  char *s;   /* pointer to the place where the line will be read to */
  int bytes_left;        /* the number of bytes that are left */
  int l;

  if (buffer == NULL) {
    buffer_size = 255;
    buffer = malloc(buffer_size);
    /* TODO: error handling */
  }

  /* Point s to the beginning of buffer. */
  s = buffer;
  bytes_left = buffer_size;

  if (feof(file)) {
    free(buffer);
    buffer = NULL;
    return NULL;
  }
  do {
    /* read a line */
    if (fgets(s, bytes_left, file) == NULL) {
      free(buffer);
      buffer = NULL;
      return NULL;
    }

    vtf_lineno++;

    /* if we reached eof, finish */
    if (feof(file)) break;

    /* pos of the last char */
    l = strlen(s) - 1;
    if (l >= 0 && ( s[l] == '\n' || s[l] == '\r')) {
      l--;
      /* remove all line endings */
      while (l >= 0 && (s[l] == '\n' || s[l] == '\r')) l--;
      /* overwrite the first line ending char */
      s[l+1] = '\0';
      /* check the previous char, whether it is '\' */
      if (l >= 0 && s[l] == '\\') {
      /* last char before is continuation char */
      /* position s to the continuation char */
      bytes_left -= l+1;
      s += l+1;
      } else 
      /* otherwise, the line is complete */
      break;
    } else {
      /* last char is not a newline */
      /* enlarge the buffer */
      buffer_size += 255;
      buffer = realloc(buffer, buffer_size);
      /* TODO: error handling */
      /* reposition s */
      l = strlen(buffer);
      s = buffer + l;
      bytes_left += buffer_size - l;
      vtf_lineno--;
    }
  } while (1);

  /* now check the whole string */
  s = buffer;
  
  /* skip all leading whitespace */
  while (isspace(s[0])) s++;

  /* ignore comment lines */
  if (s[0] == '#') return vtf_getline(file);

  l = strlen(s);

  /* handle empty lines */
  if (l == 0) {
    if (feof(file)) {
      free(buffer);
      buffer = NULL;
      return NULL;
    }
    else return vtf_getline(file);
  }

  return s;
}

/***************************************************
 * Parse ATOM
 ***************************************************/
/* Parse atom data from line. 
   Return MOLFILE_SUCCESS, if data was sucessfully parsed, 
   MOLFILE_ERROR if an error occured. */
static int vtf_parse_atom(char *line, vtf_data *d) {
  static molfile_atom_t atom;
  static char aid_specifier[255];
  static char keyword[255];
  static char msg[255];
  char *s;
  int n;
  int ignorerest;
  unsigned int from, to, aid;

  atom = default_atom;
  s = line;

  /* save the aid specifier */
  if (sscanf(s, "%255s %n", aid_specifier, &n) < 1) {
    vtf_error("atom specifier is missing", line);
    return MOLFILE_ERROR;
  }
  s += n;
  ignorerest = 0;
  
  /* handle the keywords */
  while (sscanf(s, "%255s %n", keyword, &n) == 1) {
    if (ignorerest) break;
    s += n;
    switch (tolower(keyword[0])) {
    case 'n': {
      /* name */
      if (sscanf(s, "%16s %n", &atom.name, &n) < 1) {
      vtf_error("could not get name in atom record", line);
      return MOLFILE_ERROR;
      }
      s += n;
      break;
    }
    case 't': {
      /* type */
      if (sscanf(s, "%16s %n", &atom.type, &n) < 1) {
      vtf_error("could not get type in atom record", line);
      return MOLFILE_ERROR;
      }
      s += n;
      break;
    }
    case 'r': {
      /* resname, resid, radius */
      if (strlen(keyword) == 1 || 
        strncmp(keyword, "rad", 3) == 0) { 
      /* radius */
      if (sscanf(s, "%f %n", &atom.radius, &n) < 1) {
        vtf_error("could not get radius in atom record", line);
        return MOLFILE_ERROR;
      }
      d->optflags |= MOLFILE_RADIUS;
      } else if (strcmp(keyword, "resid") == 0) {
      /* resid */
      if (sscanf(s, "%d %n", &atom.resid, &n) < 1) {
        vtf_error("could not get resid in atom record", line);
        return MOLFILE_ERROR;
      }
      } else if (strcmp(keyword, "res") == 0 || 
             strcmp(keyword, "resname") == 0) {
      /* resname */
      if (sscanf(s, "%8s %n", &atom.resname, &n) < 1) {
        vtf_error("could not get resname in atom record", line);
        return MOLFILE_ERROR;
      }
      } else {
      strcpy(msg, "unrecognized keyword in atom record: ");
      strncat(msg, keyword, 200);
      vtf_error(msg, line);
      return MOLFILE_ERROR;
      }
      s += n;
      break;
    }
    case 's': {
      /* segid */
      if (sscanf(s, "%8s %n", &atom.segid, &n) < 1) {
      vtf_error("could not get segid in atom record", line);
      return MOLFILE_ERROR;
      }
      s += n;
      break;
    }
    case 'i': {
      /* insertion */
      if (sscanf(s, "%2s %n", &atom.insertion, &n) < 1) {
      vtf_error("could not get insertion in atom record", line);
      return MOLFILE_ERROR;
      }
      d->optflags |= MOLFILE_INSERTION;
      s += n;
      break;
    }
    case 'c': {
      /* chain, charge */
      if (strlen(keyword) == 1 || 
        strcmp(keyword, "chain") == 0) {
      if (sscanf(s, "%2s %n", &atom.chain, &n) < 1) {
        vtf_error("could not get chain in atom record", line);
        return MOLFILE_ERROR;
      }
      }
    } /* if "chain" is not recognized, continue with next case */
    case 'q': {
      /* q and charge */
      if (strlen(keyword) == 1 ||
        strcmp(keyword, "charge") == 0) {
      if (sscanf(s, "%f %n", &atom.charge, &n) < 1) {
        vtf_error("could not get charge in atom record", line);
        return MOLFILE_ERROR;
      }
      d->optflags |= MOLFILE_CHARGE;
      } else {
      strcpy(msg, "unrecognized keyword in atom record: ");
      strncat(msg, keyword, 200);
      vtf_error(msg, line);
      return MOLFILE_ERROR;
      }
      s += n;
      break;
    }
    case 'a': {
      /* altloc, atomicnumber */
      if (strlen(keyword)== 1 || 
        strcmp(keyword, "atomicnumber") == 0) {
      if (sscanf(s, "%d %n", &atom.atomicnumber, &n) < 1) {
        vtf_error("could not get atomicnumber in atom record", line);
        return MOLFILE_ERROR;
      }
      d->optflags |= MOLFILE_ATOMICNUMBER;
      } else if (strcmp(keyword, "altloc")) {
      if (sscanf(s, "%2s %n", &atom.altloc, &n) < 1) {
        vtf_error("could not get altloc in atom record", line);
        return MOLFILE_ERROR;
      }
      d->optflags |= MOLFILE_ALTLOC;
      } else { 
      strcpy(msg, "unrecognized keyword in atom record: ");
      strncat(msg, keyword, 200);
      vtf_error(msg, line);
      return MOLFILE_ERROR;
      }
      s += n;
      break;
    }
    case 'o': {
      /* occupancy */
      if (sscanf(s, "%f %n", &atom.occupancy, &n) < 1) {
      vtf_error("could not get occupancy in atom record", line);
      return MOLFILE_ERROR;
      }
      d->optflags |= MOLFILE_OCCUPANCY;
      s += n;
      break;
    }
    case 'b': {
      /* bfactor */
      if (sscanf(s, "%f %n", &atom.bfactor, &n) < 1) {
      vtf_error("could not get bfactor in atom record", line);
      return MOLFILE_ERROR;
      }
      d->optflags |= MOLFILE_BFACTOR;
      s += n;
      break;
    }
    case 'm': {
      /* mass */
      if (sscanf(s, "%f %n", &atom.mass, &n) < 1) {
      vtf_error("could not get mass in atom record", line);
      return MOLFILE_ERROR;
      }
      d->optflags |= MOLFILE_MASS;
      s += n;
      break;
    }
    case 'u': {
      /* user data: ignore rest of the line */
      ignorerest = 1;
      break;
    }
    default: { 
      /* unrecognized */
      strcpy(msg, "unrecognized keyword in atom record: ");
      strncat(msg, keyword, 200);
      vtf_error(msg, line);
      return MOLFILE_ERROR;
    }
    }
  }

  /* handle the aid specifier */

  /* if the specifier is "default", set the default_atom */
  if (aid_specifier[0] == 'd') {
    default_atom = atom;
  } else {
    /* otherwise parse the aid specifier */
    s = aid_specifier;
    while (1) {
      from = d->natoms;
      if (sscanf(s, "%u:%u%n", &from, &to, &n) == 2) {
      /* range given */
      if (from > to) { 
        vtf_error("bad range specifier (from > to):", s); 
        return MOLFILE_ERROR;
      }
      d->atoms = realloc(d->atoms, (to+1)*sizeof(molfile_atom_t));
      /* TODO: error handling */
      /* fill up with default atoms */
      for (aid = d->natoms; aid < to; aid++)
        d->atoms[aid] = default_atom;
      /* create new atoms */
      if (to+1 > d->natoms) d->natoms = to+1;
      /* TODO: error handling */
      for (aid = from; aid <= to; aid++)
        d->atoms[aid] = atom;
      } else if (sscanf(s, "%u%n", &to, &n) == 1) {
      /* single aid given */
      d->atoms = realloc(d->atoms, (to+1)*sizeof(molfile_atom_t));
      /* TODO: error handling */
      /* fill up with default atoms */
      for (aid = d->natoms; aid < to; aid++)
        d->atoms[aid] = default_atom;
      /* create the new atom */
      if (to+1 > d->natoms) d->natoms = to+1;
      d->atoms[to] = atom;
      } else {
      vtf_error("bad atom specifier", s);
      return MOLFILE_ERROR;
      }

      /* advance s */
      s += n;

      /* if there is no more to parse, break */
      if (strlen(s) == 0) break;

      /* otherwise the next char should be a ',' */
      if (s[0] != ',') {
      vtf_error("bad atom specifier in line", line);
      return MOLFILE_ERROR;
      }
      /* skip the ',' */
      s++;
    };
  }

  return MOLFILE_SUCCESS;
}

/***************************************************
 * Parse BOND
 ***************************************************/
/* Parse bond data from line. 
   Return MOLFILE_SUCCESS, if data was sucessfully parsed, 
   MOLFILE_ERROR if an error occured. */
static int vtf_parse_bond(char *line, vtf_data *d) {
  char *s;
  int n;
  int from, to, aid, bid;

  s = line;

  while (1) {
    if (sscanf(s, "%u::%u%n", &from, &to, &n) == 2) {
      /* chain specifier */
      if (from > to) {
      vtf_error("bad chain specifier (from > to):", s); 
      return MOLFILE_ERROR;
      }
      bid = d->nbonds;
      d->nbonds += to-from;
      d->from = realloc(d->from, d->nbonds*sizeof(int));
      d->to = realloc(d->to, d->nbonds*sizeof(int));
      /* TODO: error handling */
      for (aid = from; aid < to; aid++) {
      /*printf("creating bond from %d to %d\n", aid, aid+1);*/
      d->from[bid] = aid+1;
      d->to[bid] = aid+2;
      bid++;
      }
    } else if (sscanf(s, "%u:%u%n", &from, &to, &n) == 2) {
      /* single bond specifier */
      d->nbonds += 1;
      d->from = realloc(d->from, d->nbonds*sizeof(int));
      d->to = realloc(d->to, d->nbonds*sizeof(int));
      /* TODO: error handling */
      d->from[d->nbonds-1] = from+1;
      d->to[d->nbonds-1] = to+1;
    } else {
      vtf_error("bad bond specifier", s);
      return MOLFILE_ERROR;
    }

    s += n;
    
    /* if there is no more to parse, break */
    if (strlen(s) == 0) break;
    
    /* otherwise the next char should be a ',' */
    if (s[0] != ',') {
      vtf_error("bad bond specifier in line", line);
      return MOLFILE_ERROR;
    }
    /* skip the ',' */
    s++;
  }

  return MOLFILE_SUCCESS;
}


/***************************************************
 * Parse PBC
 ***************************************************/
/* Parse periodic boundary condition data from line. 
   Return MOLFILE_SUCCESS, if data was sucessfully parsed, 
   MOLFILE_ERROR if an error occured. */
static int vtf_parse_pbc(char *line, vtf_data *d) {
  char *s;
  int n;

  if (sscanf(line, "%f %f %f %n", 
    &d->A, &d->B, &d->C, &n) < 3) {
    s = line;
    vtf_error("Couldn't parse unit cell dimensions", s);
    return MOLFILE_ERROR;
  }
  s = line+n;

  n = sscanf(s, "%f %f %f", &d->alpha, &d->beta, &d->gamma);
  if (n > 0 && n < 3) {
    vtf_error("Couldn't parse unit cell angles", line);
    return MOLFILE_ERROR;
  }
  return MOLFILE_SUCCESS;
} 

/* Parse timestep command from line. 
   Return MOLFILE_SUCCESS, if it was sucessfully parsed, 
   MOLFILE_ERROR if an error occured. */
static int vtf_parse_timestep(char *line, vtf_data *d) {
  if (strlen(line) == 0) {
    d->timestep_mode = TIMESTEP_ORDERED;
  } else {
    switch (tolower(line[0])) {
    case 'o': { d->timestep_mode = TIMESTEP_ORDERED; break; }
    case 'i': { d->timestep_mode = TIMESTEP_INDEXED; break; }
    default: {
      vtf_error("bad timestep line", line);
      return MOLFILE_ERROR;
    }
    }
  }
  return MOLFILE_SUCCESS;
}

static void vtf_parse_structure(vtf_data *d) {
  char *line;                 /* next line in the file */
  char s[255];
  int n;
  
  /* initialize the default atom */
  strcpy(default_atom.name, "X");
  strcpy(default_atom.type, "X");
  strcpy(default_atom.resname, "X");
  default_atom.resid = 0;
  strcpy(default_atom.segid, "");
  strcpy(default_atom.chain, "");

  strcpy(default_atom.altloc, "");
  strcpy(default_atom.insertion, "");
  default_atom.occupancy = 1.0;
  default_atom.bfactor = 1.0;
  default_atom.mass = 1.0;
  default_atom.charge = 0.0;
  default_atom.radius = 1.0;

  do {
    line = vtf_getline(d->file);
    if (line == NULL) break;
    switch (tolower(line[0])) {
      /* ATOM RECORD */
    case 'a': {
      /* Remove the "atom" keyword" */
      sscanf(line, "%255s %n", s, &n);
      line += n;
    }
    case '0':
    case '1':
    case '2':
    case '3':
    case '4':
    case '5':
    case '6':
    case '7':
    case '8':
    case '9':     
    case 'd': { 
      /* parse atom */
      d->return_code = vtf_parse_atom(line, d);
      break; 
    }

      /* BOND RECORD */
    case 'b': {
      /* Remove the "bond" keyword" */
      sscanf(line, "%255s %n", s, &n);
      line += n;
      d->return_code = vtf_parse_bond(line, d);
      break;
    }

      /* PBC/UNITCELL RECORD */
    case 'u':
    case 'p': {
      /* Remove the "pbc" or "unitcell" keyword */
      sscanf(line, "%255s %n", s, &n);
      line += n;
      d->return_code = vtf_parse_pbc(line, d);
      break;
    }

      /* TIMESTEP RECORD*/
    case 'c': 
    case 't': {
      /* Remove the "timestep" or "coordinates" keyword */
      sscanf(line, "%255s %n", s, &n);
      line += n;
      
    }
    case 'i': 
    case 'o': { 
      d->return_code = vtf_parse_timestep(line, d);
      line = NULL; /* indicate the end of the structure block */
      break; 
    }

      /* UNKNOWN RECORD */
    default: {
      vtf_error("unknown line type", line);
      d->return_code = MOLFILE_ERROR;
      break;
    }
    }
  } while (line != NULL && 
         d->return_code == MOLFILE_SUCCESS);

  /* test if structure data was parsed */
  if (d->atoms == NULL && 
      d->return_code == MOLFILE_SUCCESS) {
    d->return_code = MOLFILE_NOSTRUCTUREDATA;
  }

  /* test whether another error has occured */
  if (errno != 0) {
    perror("vtfplugin");
    d->return_code = MOLFILE_ERROR;
  }
}

/***************************************************
 * Open file and parse structure info
 ***************************************************/
/* Opens the file for reading. 
   To determine the number of atoms in the file, it is necessary to
   parse the structure information, anyway. Therefore, this function
   will do the parsing and save the information in the handle.
*/
static void *vtf_open_file_read(const char *filepath, 
                        const char *filetype, 
                        int *natoms) {
  vtf_data *d;

  /* printf("Loading file %s\n  of type %s using vtfplugin v%i.%i.\n", 
     filepath, filetype, VERSION_MAJOR, VERSION_MINOR); */

  /* initialize the data structure */
  d = malloc(sizeof(vtf_data));

  errno = 0;

  /* Open the file */
  d->file = fopen(filepath, "r");
  if (d->file == NULL) {
    /* Could not open file */
    perror("vtfplugin");
    free(d);
    return NULL;
  }
  d->return_code = MOLFILE_SUCCESS;

  /* initialize structure data */
  d->optflags = MOLFILE_NOOPTIONS;
  d->natoms = 0;
  d->atoms = NULL;
  d->nbonds = 0;
  d->from = NULL;
  d->to = NULL;

  /* initialize timestep data */
  d->timestep_mode = TIMESTEP_ORDERED;
  d->coords = NULL;
  d->A = 0.0;
  d->B = 0.0;
  d->C = 0.0;
  d->alpha = 90.0;
  d->beta = 90.0;
  d->gamma = 90.0;

  if (strcmp(filetype, "vcf") == 0) {
    d->timestep_mode = TIMESTEP_VCFSTART;
    d->natoms = MOLFILE_NUMATOMS_UNKNOWN;
    *natoms = MOLFILE_NUMATOMS_UNKNOWN;
    d->return_code = MOLFILE_NOSTRUCTUREDATA;
  } else {
    vtf_parse_structure(d);
    
    if (d->return_code != MOLFILE_SUCCESS) {
      free(d);
      return NULL;
    }
   
    *natoms = d->natoms;
  }

  return d;
}

static int vtf_read_next_timestep(void *data, 
                          int natoms, 
                          molfile_timestep_t *ts) {
  vtf_data *d;
  char *line;
  static char s[255];
  float x,y,z;
  unsigned int aid;
  int n;

  if (data == NULL) {
    vtf_error("Internal error: data==NULL in vtf_read_next_timestep", 0);
    return MOLFILE_ERROR;
  }

  if (natoms <= 0) {
    vtf_error("Internal error: natoms <= 0 in vtf_read_next_timestep", 0);
    return MOLFILE_ERROR;
  }

  errno = 0;

  d = (vtf_data*)data;

  aid = 0;

  if (feof(d->file)) return MOLFILE_EOF;

  if (d->coords == NULL) {
    /* initialize coords */
    d->coords = malloc(natoms*3*sizeof(float));
    /* TODO: error handling */
    for (n = 0; n < natoms*3; n++)
      d->coords[n] = 0.0;
  } 
  
  /* read in the data, until the next timestep or EOF is reached */
  do {
    line = vtf_getline(d->file);

    if (line == NULL) {
      if (errno != 0) {
      perror("vtfplugin");
      return MOLFILE_ERROR;
      }
      break;
    } 

    /* At the beginning of a vcf file, skip a timestep line */
    if (d->timestep_mode == TIMESTEP_VCFSTART) {
      switch (tolower(line[0])) {
      case 'c': 
      case 't':
      /* Remove the "timestep" or "coordinates" keyword */
      sscanf(line, "%255s %n", s, &n);
      line += n;
      case 'i': 
      case 'o': 
      if (vtf_parse_timestep(line, d) != MOLFILE_SUCCESS)
        return MOLFILE_ERROR;
      line = vtf_getline(d->file);
      break;
      default:
      /* if this is already a coordinate line, expect an ordered block */
      d->timestep_mode = TIMESTEP_ORDERED;
      }
    }

    /* parse timestep data */
    if (d->timestep_mode == TIMESTEP_ORDERED 
      && sscanf(line, " %f %f %f", &x, &y, &z) == 3) {
      if (aid < natoms) {
      d->coords[aid*3] = x;
      d->coords[aid*3+1] = y;
      d->coords[aid*3+2] = z;
      aid++;
      } else {
      vtf_error("too many atom coordinates in ordered timestep block", line);
      return MOLFILE_ERROR;
      }
    } else if (d->timestep_mode == TIMESTEP_INDEXED 
             && sscanf(line, " %u %f %f %f", 
                   &aid, &x, &y, &z) == 4) {
      if (aid < natoms) {
      d->coords[aid*3] = x;
      d->coords[aid*3+1] = y;
      d->coords[aid*3+2] = z;
      } else {
      vtf_error("atom id too large in indexed timestep block", line);
      return MOLFILE_ERROR;
      }
    } else switch (tolower(line[0])) {
      /* PBC/UNITCELL RECORD */
    case 'u':
    case 'p': {
      /* Remove the "pbc" or "unitcell" keyword */
      sscanf(line, "%255s %n", s, &n);
      line += n;
      if (vtf_parse_pbc(line, d) != MOLFILE_SUCCESS) 
      return MOLFILE_ERROR;
      break;
    }
      
      /* TIMESTEP RECORD*/
    case 'c': 
    case 't': {
      /* Remove the "timestep" or "coordinates" keyword */
      sscanf(line, "%255s %n", s, &n);
      line += n;
    }
    case 'i': 
    case 'o': { 
      if (vtf_parse_timestep(line, d) != MOLFILE_SUCCESS)
      return MOLFILE_ERROR;
      line = NULL; /* indicate end of this timestep */
      break;
    }

    default: { 
      if (d->timestep_mode == TIMESTEP_INDEXED)
      vtf_error("unknown line in indexed timestep block", line);
      else
      vtf_error("unknown line in ordered timestep block", line);
      return MOLFILE_ERROR;
    }
    }

    if (line == NULL) break;
  } while (1);

  if (ts != NULL) {
    /* copy the ts data */
    ts->A = d->A;
    ts->B = d->B;
    ts->C = d->C;
    ts->alpha = d->alpha;
    ts->beta = d->beta;
    ts->gamma = d->gamma;
    memcpy(ts->coords, d->coords, natoms*3*sizeof(float));
    ts->velocities = NULL;
    ts->physical_time = 0.0;
  }
  
  return MOLFILE_SUCCESS;
}

/***************************************************
 * Copy the info collected in vtf_open_file_read
 ***************************************************/
static int vtf_read_structure(void *data, 
                        int *optflags, 
                        molfile_atom_t *atoms) {
  vtf_data *d;
  d = (vtf_data*)data;

  if (d->return_code != MOLFILE_SUCCESS) 
    return d->return_code;

  if (d->natoms > 0) {
    /* copy the data parsed in vtf_open_file_read() */
    memcpy(atoms, d->atoms, d->natoms*sizeof(molfile_atom_t));
    /* free the data parsed in vtf_open_file_read() */
    free(d->atoms);
    d->atoms = NULL;
  }

  *optflags = d->optflags;

  return MOLFILE_SUCCESS;
}

static int vtf_read_bonds(void *data, 
                    int *nbonds, 
                    int **from, 
                    int **to,
                    float **bondorder, 
                    int **bondtype, 
                    int *nbondtypes, 
                    char ***bondtypename) {
  vtf_data *d;
  if (!data) {
    vtf_error("Internal error: data==NULL in vtf_read_bonds", 0);
    return MOLFILE_ERROR;
  }

  d = (vtf_data*)data;

  *nbonds = d->nbonds;
  *from = d->from;
  *to = d->to;
  *bondorder = NULL;
  *bondtype = NULL;
  *nbondtypes = 0;
  *bondtypename = NULL;

  return MOLFILE_SUCCESS;
}

static void vtf_close_file_read(void *data) {
  vtf_data *d;

  if (data == NULL) return;
  d = (vtf_data*)data;

  /* printf("Finished reading file.\n"); */

  /* close the file */
  fclose(d->file);

  /* free the data */
  free(d->coords);
  free(d->from);
  free(d->to);
  free(d);
}

static molfile_plugin_t vsfplugin;
static molfile_plugin_t vtfplugin;
static molfile_plugin_t vcfplugin;

VMDPLUGIN_API int VMDPLUGIN_init() {
  memset(&vsfplugin, 0, sizeof(molfile_plugin_t));
  vsfplugin.abiversion = vmdplugin_ABIVERSION;
  vsfplugin.type = MOLFILE_PLUGIN_TYPE;
  vsfplugin.name = "vsf";
  vsfplugin.author = "Olaf Lenz";
  vsfplugin.majorv = VERSION_MAJOR;
  vsfplugin.minorv = VERSION_MINOR;
  vsfplugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;
  vsfplugin.filename_extension = "vsf";
  vsfplugin.open_file_read = vtf_open_file_read;
  vsfplugin.read_structure = vtf_read_structure;
  vsfplugin.read_bonds = vtf_read_bonds;
  /* plugin.read_next_timestep = vtf_read_next_timestep; */
  vsfplugin.close_file_read = vtf_close_file_read;
#if vmdplugin_ABIVERSION >= 9
  vsfplugin.prettyname = "VTF structure format";
#endif

  memset(&vcfplugin, 0, sizeof(molfile_plugin_t));
  vcfplugin.abiversion = vmdplugin_ABIVERSION;
  vcfplugin.type = MOLFILE_PLUGIN_TYPE;
  vcfplugin.name = "vcf";
  vcfplugin.author = "Olaf Lenz";
  vcfplugin.majorv = VERSION_MAJOR;
  vcfplugin.minorv = VERSION_MINOR;
  vcfplugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;
  vcfplugin.filename_extension = "vcf";
  vcfplugin.open_file_read = vtf_open_file_read;
  vcfplugin.read_next_timestep = vtf_read_next_timestep;
  vcfplugin.close_file_read = vtf_close_file_read;
#if vmdplugin_ABIVERSION >= 9
  vcfplugin.prettyname = "VTF coordinate format";
#endif

  memset(&vtfplugin, 0, sizeof(molfile_plugin_t));
  vtfplugin.abiversion = vmdplugin_ABIVERSION;
  vtfplugin.type = MOLFILE_PLUGIN_TYPE;
  vtfplugin.name = "vtf";
  vtfplugin.author = "Olaf Lenz";
  vtfplugin.majorv = VERSION_MAJOR;
  vtfplugin.minorv = VERSION_MINOR;
  vtfplugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;
  vtfplugin.filename_extension = "vtf";
  vtfplugin.open_file_read = vtf_open_file_read;
  vtfplugin.read_structure = vtf_read_structure;
  vtfplugin.read_bonds = vtf_read_bonds;
  vtfplugin.read_next_timestep = vtf_read_next_timestep;
  vtfplugin.close_file_read = vtf_close_file_read;
#if vmdplugin_ABIVERSION >= 9
  vtfplugin.prettyname = "VTF trajectory format";
#endif

  /*printf("Loaded VTF/VSF/VCF plugins v%i.%i.\n", VERSION_MAJOR, VERSION_MINOR); */

  return VMDPLUGIN_SUCCESS;
}

VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {
  (*cb)(v, (vmdplugin_t *)&vsfplugin);
  (*cb)(v, (vmdplugin_t *)&vcfplugin);
  (*cb)(v, (vmdplugin_t *)&vtfplugin);
  return VMDPLUGIN_SUCCESS;
}

VMDPLUGIN_API int VMDPLUGIN_fini() {
  return VMDPLUGIN_SUCCESS;
}

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