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parm7plugin.C

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/***************************************************************************
 *cr
 *cr            (C) Copyright 1995-2016 The Board of Trustees of the
 *cr                        University of Illinois
 *cr                         All Rights Reserved
 *cr
 ***************************************************************************/

/***************************************************************************
 * RCS INFORMATION:
 *
 *      $RCSfile: parm7plugin.C,v $
 *      $Author: johns $       $Locker:  $             $State: Exp $
 *      $Revision: 1.35 $       $Date: 2017/08/30 17:42:33 $
 *
 ***************************************************************************/

#include <string.h>
#include "molfile_plugin.h"
#include "ReadPARM7.h"

typedef struct {
  parmstruct *prm;
  int popn;
  FILE *fd;
  int nbonds;
  int *from, *to;
} parmdata;

static void *open_parm7_read(const char *filename, const char *,int *natoms) {
  FILE *fd;
  int popn = 0;
  if(!(fd = open_parm7_file(filename, &popn))) {
    fprintf(stderr, "parm7plugin) Cannot open parm file '%s'\n", filename);
    return NULL;
  }
  parmstruct *prm = read_parm7_header(fd);
  if (!prm) {
    close_parm7_file(fd, popn);
    return NULL; 
  }

  *natoms = prm->Natom;
  parmdata *p = new parmdata;
  memset(p, 0, sizeof(parmdata));
  p->prm = prm;
  p->popn = popn;
  p->fd = fd;
  p->from = new int[prm->Nbonh + prm->Nbona];
  p->to   = new int[prm->Nbonh + prm->Nbona];
  return p;
}

static int read_parm7_structure(void *mydata, int *optflags, molfile_atom_t *atoms) {
  parmdata *p = (parmdata *)mydata;
  const parmstruct *prm = p->prm;
  FILE *file = p->fd;
  char buf[85];
  char field[85];
  char *resnames = NULL;

  *optflags = MOLFILE_NOOPTIONS; /* no optional data to start with */

  while (fgets(buf, 85, file)) {
    // find the next line starting with %FLAG, indicating a new section
    if (strncmp(buf, "%FLAG ", 6)) 
      continue;
    sscanf(buf+6, "%s\n", field); // type of record

    // skip any number of lines until we get to "FORMAT". This handles
    // the %COMMENT lines that may or may not be present
    while (strncmp(buf, "%FORMAT", 7)) {
        fgets(buf, 85, file);
    }

    if (!strcmp(field, "ATOM_NAME")) {
      if (!parse_parm7_atoms(buf, prm->Natom, atoms, file)) break;
    } else if (!strcmp(field, "CHARGE")) {
      *optflags |= MOLFILE_CHARGE;
      if (!parse_parm7_charge(buf, prm->Natom, atoms, file)) break;
    } else if (!strcmp(field, "MASS")) {
      *optflags |= MOLFILE_MASS;
      if (!parse_parm7_mass(buf, prm->Natom, atoms, file)) break;
    } else if (!strcmp(field, "AMBER_ATOM_TYPE")) {
      if (!parse_parm7_atype(buf, prm->Natom, atoms, file)) break;
    } else if (!strcmp(field, "ATOMIC_NUMBER")) {
      *optflags |= MOLFILE_ATOMICNUMBER;
      if (!parse_parm7_atomicnumber(buf, prm->Natom, atoms, file)) break;
    } else if (!strcmp(field, "RESIDUE_LABEL")) {
      resnames = new char[4*prm->Nres];
      if (!parse_parm7_resnames(buf, prm->Nres, resnames, file)) break;
    } else if (!strcmp(field, "RESIDUE_POINTER")) {
      if (!resnames) {
        fprintf(stderr, 
            "parm7plugin) Cannot parse RESIDUE_POINTER before RESIDUE_LABEL\n");
        continue;
      }
      if (!parse_parm7_respointers(buf, prm->Natom, atoms, 
                                   prm->Nres, resnames, file)) 
        break;
      // XXX: we could count the bonded parameters and assign bond types.
    } else if (!strcmp(field, "BONDS_WITHOUT_HYDROGEN")) {
      if (!parse_parm7_bonds(buf, prm->Nbona, p->from+p->nbonds,
            p->to+p->nbonds, file)) break;
      p->nbonds += prm->Nbona;
    } else if (!strcmp(field, "BONDS_INC_HYDROGEN")) {
      if (!parse_parm7_bonds(buf, prm->Nbonh, p->from+p->nbonds,
            p->to+p->nbonds, file)) break;
      p->nbonds += prm->Nbonh;
    }
  }

  // unused items
  for (int i=0; i<prm->Natom; i++) {
    atoms[i].chain[0] = '\0';
    atoms[i].segid[0] = '\0';
  }

  delete [] resnames;
  return MOLFILE_SUCCESS;
}

static int read_parm7_bonds(void *v, int *nbonds, int **fromptr, int **toptr, 
                            float **bondorderptr, int **bondtype, 
                            int *nbondtypes, char ***bondtypename){
  parmdata *p = (parmdata *)v;
  *nbonds = p->nbonds;
  *fromptr = p->from;
  *toptr = p->to;
  *bondorderptr = NULL; // parm files don't contain bond order information
  *bondtype = NULL;
  *nbondtypes = 0;
  *bondtypename = NULL;
  return MOLFILE_SUCCESS;
}

static void close_parm7_read(void *mydata) {
  parmdata *p = (parmdata *)mydata;
  close_parm7_file(p->fd, p->popn);
  delete p->prm;
  delete [] p->from;
  delete [] p->to;
  delete p;
}
 
/*
 * Initialization stuff down here
 */

static molfile_plugin_t plugin;

VMDPLUGIN_API int VMDPLUGIN_init(){
  memset(&plugin, 0, sizeof(molfile_plugin_t));
  plugin.abiversion = vmdplugin_ABIVERSION;
  plugin.type = MOLFILE_PLUGIN_TYPE;
  plugin.name = "parm7";
  plugin.prettyname = "AMBER7 Parm";
  plugin.author = "Brian Bennion, Justin Gullingsrud, John Stone";
  plugin.majorv = 0;
  plugin.minorv = 16;
  plugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;
  plugin.filename_extension = "prmtop,parm7";
  plugin.open_file_read = open_parm7_read;
  plugin.read_structure = read_parm7_structure;
  plugin.read_bonds = read_parm7_bonds;
  plugin.close_file_read = close_parm7_read;
  return VMDPLUGIN_SUCCESS;
}

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

VMDPLUGIN_API int VMDPLUGIN_fini(){
  return VMDPLUGIN_SUCCESS;
}

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