PDB Class Reference

#include <PDB.h>

Public Member Functions
	PDB (const char *pdbfilename)
	PDB (molfile_plugin_t *pIOHdl, void *pIOFileHdl, int numAtoms, const float *occupancy, const float *bfactor)
	PDB (const char *, Ambertoppar *)
	PDB (const char *filename, AmberParm7Reader::Ambertoppar *amber_data)
	PDB (const char *filename, const GromacsTopFile *topology)
	~PDB (void)
void	write (const char *outfilename, const char *commentline=NULL)
int	num_atoms (void)
PDBAtom *	atom (int place)
PDBAtomList *	atoms (void)
void	find_extremes (const Lattice &, BigReal frac=1.0)
void	get_extremes (ScaledPosition &xmin, ScaledPosition &xmax) const
void	set_all_positions (Vector *)
void	get_all_positions (Vector *)
void	get_position_for_atom (Vector *, int)

Detailed Description

Definition at line 36 of file PDB.h.

Constructor & Destructor Documentation

PDB() [1/5]

PDB::PDB

(

const char *

pdbfilename

)

Definition at line 141 of file PDB.C.

References PDBAtom::alternatelocation(), PDBData::ATOM, PDBAtom::coordinates(), PAL::data, Fclose(), Fopen(), PDBData::HETATM, NAMD_die(), NAMD_err(), new_PDBData(), PAL::next, next(), PDBAtom::occupancy(), and PDBAtom::temperaturefactor().

                                 {
  FILE *infile;
  char buf[160];

  atomCount = 0;
  atomListHead = atomListTail = NULL;
  infile = Fopen(pdbfilename, "r");
  if (! infile) {
     char s[500];
     sprintf(s, "Cannot open file '%s' for input in PDB::PDB.", pdbfilename);
     NAMD_err(s);
  }
  
    // loop through each line in the file and get a record
  while ( fgets(buf, 150, infile) ) {
   PDBData *newelement;
   char *s;
   for (s=buf; *s && *s!='\n'; s++)  // chop off the '\n'
    ;
   *s = 0;
   if ( s == (buf + 149) ) {
     char s[500];
     sprintf( s, "Line too long in pdbfile %s:\n%s\n", pdbfilename, buf);
     NAMD_die(s);
   }
   *(s+1) = 0;  // just to be on the safe side

     // I now have a string; make a PDBData element out of it
   newelement = new_PDBData(buf);
   if (!newelement) {
      NAMD_die("Could not allocate PDBData.\n");
   }
     // I only know how to deal with ATOM and HETATM types; and
     //  I want to throw away the unknown data types; so
   if (newelement -> type() != PDBData::ATOM && 
           newelement -> type() != PDBData::HETATM) {
       delete newelement;
   } else {
       add_atom_element( (PDBAtom *) newelement);
   }
  }  // input while loop
 Fclose(infile);
 
 // now I have a linked list, and I know the size.  However,
 // that's got pretty slow access time for ramdom fetches, so
 // I'll turn it into an array
 {

#ifdef MEM_OPT_VERSION
//pruning the PDBData structure into PDBCoreData by only leaving X/Y/Z, occupancy and temperaturefactor
     altlocArray = new char[atomCount];
     atomArray = new PDBCoreData[atomCount];
     if(atomArray == NULL)
         NAMD_die("memory allocation failed in PDB::PDB");

     PDBAtomList *tmp = atomListHead;
     for(int i=0; tmp!=NULL; tmp=tmp->next, i++){
         const BigReal *coor = tmp->data->coordinates();
         atomArray[i].coor[0] = coor[0];
         atomArray[i].coor[1] = coor[1];
         atomArray[i].coor[2] = coor[2];
         atomArray[i].myoccupancy = tmp->data->occupancy();
         atomArray[i].tempfactor = tmp->data->temperaturefactor();
         altlocArray[i] = tmp->data->alternatelocation()[0];
     }

     //free the PDBAtomList
     tmp = atomListHead;
     while(tmp!=NULL){
         PDBAtomList *nextTmp = tmp->next;
         delete tmp->data;
         delete tmp;
         tmp = nextTmp;
     }
     atomListHead = atomListTail = NULL;
#else
  atomAlloc = 0;
  atomArray = new PDBAtomPtr[atomCount];
  if ( atomArray == NULL )
  {
    NAMD_die("memory allocation failed in PDB::PDB");
  }
  PDBAtomList *tmp = atomListHead;
  int i=0;                              // just need to copy the pointers
  for (i=0, tmp = atomListHead; tmp != NULL; tmp = tmp -> next, i++) {
    atomArray[i] = tmp -> data;
  }
  // now delete the linked list (w/o deleting the data)
  PDBAtomList *tmp2;
  for (tmp2 = tmp = atomListHead; tmp != NULL; tmp = tmp2) {
    tmp2 = tmp->next;
    delete tmp;
  }
  atomListHead = atomListTail = NULL;
#endif 
 }  // everything converted
 
}

PDB() [2/5]

PDB::PDB	(	molfile_plugin_t *	pIOHdl,
		void *	pIOFileHdl,
		int	numAtoms,
		const float *	occupancy,
		const float *	bfactor
	)

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 83 of file PDB.C.

References PDBAtom::coordinates(), NAMD_die(), PDBAtom::occupancy(), and PDBAtom::temperaturefactor().

                                                                                                              {
#ifdef MEM_OPT_VERSION
  NAMD_die("Sorry, plugin IO is not supported in the memory optimized version.");
#else
  molfile_timestep_t ts;
  float *atomcoords;
  memset(&ts, 0, sizeof(molfile_timestep_t));

  /* set defaults for unit cell information */
  ts.A = ts.B = ts.C = 0.0f;
  ts.alpha = ts.beta = ts.gamma = 90.0f; 

  atomCount = numAtoms;

  atomcoords = (float *) malloc(3*numAtoms*sizeof(float));
  memset(atomcoords, 0, 3*numAtoms*sizeof(float));
  ts.coords = atomcoords;
  
  if (pIOHdl->read_next_timestep(pIOFileHdl, numAtoms, &ts)) {
    free(atomcoords);    
    pIOHdl->close_file_read(pIOFileHdl);
    NAMD_die("ERROR: failed reading atom coordinates");
  }

  //load coordinates to PDB object
  //Note: the PDBAtom structure is very redundant in this case
  PDBAtom *tmpAtoms = atomAlloc = new PDBAtom[numAtoms];
  atomArray = new PDBAtomPtr[numAtoms];
  BigReal tmpCoords[3];
  for(int i=0; i<numAtoms; i++) {
      PDBAtom *thisAtom = tmpAtoms+i;
      atomArray[i] = thisAtom;

      tmpCoords[0] = atomcoords[0];
      tmpCoords[1] = atomcoords[1];
      tmpCoords[2] = atomcoords[2];
      atomcoords += 3; //set to the next atom
      thisAtom->coordinates(tmpCoords);
  }
  free(ts.coords);

  if(occupancy) {
      for(int i=0; i<numAtoms; i++) {
          PDBAtom *thisAtom = tmpAtoms+i;
          thisAtom->occupancy((BigReal)occupancy[i]);          
      }
  }
  if(bfactor) {
      for(int i=0; i<numAtoms; i++) {
          PDBAtom *thisAtom = tmpAtoms+i;       
          thisAtom->temperaturefactor((BigReal)bfactor[i]);       
      }
  }
#endif
}

PDB() [3/5]

PDB::PDB	(	const char *	filename,
		Ambertoppar *	amber_data
	)

Definition at line 553 of file PDB.C.

References Ambertoppar::AtomNames, Ambertoppar::AtomRes, PDBAtom::coordinates(), PDBAtom::default_occupancy, PDBAtom::default_temperaturefactor, Fopen(), NAMD_die(), NAMD_err(), PDBAtom::name(), Ambertoppar::Natom, readtoeoln(), PDBAtom::residuename(), PDBAtom::residueseq(), Ambertoppar::ResNames, and PDBAtom::serialnumber().

{ int i,j,k;
  BigReal coor[3];
  char buf[13],resname[5],atomname[5];
  FILE *infile;
  PDBAtom *pdb;

  if ((infile=Fopen(filename, "r")) == NULL)
    NAMD_err("Can't open AMBER coordinate file!");

  readtoeoln(infile);  // Skip the first line (title)

  fscanf(infile,"%d",&atomCount);  // Read in num of atoms
  if (atomCount != amber_data->Natom)
    NAMD_die("Num of atoms in coordinate file is different from that in parm file!");
  readtoeoln(infile);

#ifdef MEM_OPT_VERSION
  altlocArray = 0;
  atomArray = new PDBCoreData[atomCount];
#else
  atomAlloc = 0;
  atomArray = new PDBAtomPtr[atomCount];
#endif

  if ( atomArray == NULL )
  {
    NAMD_die("memory allocation failed in PDB::PDB");
  }
  
  // Read in the coordinates, which are in the format of 6F12.7
  // Other fields are copied from "amber_data"
  for (i=0; i<atomCount; ++i)
  { // Read x,y,z coordinates
    for (j=0; j<3; ++j)
    { for (k=0; k<12; ++k)
      { buf[k]=getc(infile);
        if (buf[k]=='\n' || buf[k]=='\0' || buf[k]==EOF)
          NAMD_die("Error reading AMBER coordinate file!");
      }
      buf[12] = '\0';
      coor[j] = atof(buf);
    }
    if (i%2 == 1)
      readtoeoln(infile);
#ifdef MEM_OPT_VERSION
    atomArray[i].coor[0] = coor[0];
    atomArray[i].coor[1] = coor[1];
    atomArray[i].coor[2] = coor[2];
    atomArray[i].myoccupancy = PDBAtom::default_occupancy;
    atomArray[i].tempfactor = PDBAtom::default_temperaturefactor;
#else
    // Copy name, resname and resid from "amber_data"
    for (j=0; j<4; ++j)
    { resname[j] = amber_data->ResNames[amber_data->AtomRes[i]*4+j];
      atomname[j] = amber_data->AtomNames[i*4+j];
    }
    resname[4] = atomname[4] = '\0';
    // Create a new PDB record, and fill in its entries
    pdb = new PDBAtomRecord("");
    pdb->name(atomname);
    pdb->residuename(resname);
    pdb->serialnumber(i+1);
    pdb->residueseq(amber_data->AtomRes[i]+1);
    pdb->coordinates(coor);
    atomArray[i] = pdb;  // Include the new record into the array
#endif
  }
}

PDB() [4/5]

PDB::PDB	(	const char *	filename,
		AmberParm7Reader::Ambertoppar *	amber_data
	)

Definition at line 624 of file PDB.C.

References AmberParm7Reader::Ambertoppar::AtomNames, AmberParm7Reader::Ambertoppar::AtomRes, PDBAtom::default_occupancy, PDBAtom::default_temperaturefactor, Fopen(), NAMD_die(), NAMD_err(), AmberParm7Reader::Ambertoppar::Natom, readtoeoln(), and AmberParm7Reader::Ambertoppar::ResNames.

{ int i,j,k;
  BigReal coor[3];
  char buf[13],resname[5],atomname[5];
  FILE *infile;
  PDBAtom *pdb;

  if ((infile=Fopen(filename, "r")) == NULL)
    NAMD_err("Can't open AMBER coordinate file!");

  readtoeoln(infile);  // Skip the first line (title)

  fscanf(infile,"%d",&atomCount);  // Read in num of atoms
  if (atomCount != amber_data->Natom)
    NAMD_die("Num of atoms in coordinate file is different from that in parm file!");
  readtoeoln(infile);

#ifdef MEM_OPT_VERSION
  altlocArray = 0;
  atomArray = new PDBCoreData[atomCount];
#else
  atomAlloc = 0;
  atomArray = new PDBAtomPtr[atomCount];
#endif

  if ( atomArray == NULL )
  {
    NAMD_die("memory allocation failed in PDB::PDB");
  }
  
  // Read in the coordinates, which are in the format of 6F12.7
  // Other fields are copied from "amber_data"
  for (i=0; i<atomCount; ++i)
  { // Read x,y,z coordinates
    for (j=0; j<3; ++j)
    { for (k=0; k<12; ++k)
      { buf[k]=getc(infile);
        if (buf[k]=='\n' || buf[k]=='\0' || buf[k]==EOF)
          NAMD_die("Error reading AMBER coordinate file!");
      }
      buf[12] = '\0';
      coor[j] = atof(buf);
    }
    if (i%2 == 1)
      readtoeoln(infile);
#ifdef MEM_OPT_VERSION
    atomArray[i].coor[0] = coor[0];
    atomArray[i].coor[1] = coor[1];
    atomArray[i].coor[2] = coor[2];
    atomArray[i].myoccupancy = PDBAtom::default_occupancy;
    atomArray[i].tempfactor = PDBAtom::default_temperaturefactor;
#else
    // Copy name, resname and resid from "amber_data"
    strncpy(resname, amber_data->ResNames[amber_data->AtomRes[i]].c_str(), 5);
    strncpy(atomname, amber_data->AtomNames[i].c_str(), 5);
    // Create a new PDB record, and fill in its entries
    pdb = new PDBAtomRecord("");
    pdb->name(atomname);
    pdb->residuename(resname);
    pdb->serialnumber(i+1);
    pdb->residueseq(amber_data->AtomRes[i]+1);
    pdb->coordinates(coor);
    atomArray[i] = pdb;  // Include the new record into the array
#endif
  }
}

PDB() [5/5]

PDB::PDB	(	const char *	filename,
		const GromacsTopFile *	topology
	)

Definition at line 697 of file PDB.C.

References PDBAtom::coordinates(), PDBAtom::default_occupancy, PDBAtom::default_temperaturefactor, Fopen(), GromacsTopFile::getAtom(), GromacsTopFile::getNumAtoms(), LINESIZE, NAMD_die(), NAMD_err(), PDBAtom::name(), PDBAtom::residuename(), PDBAtom::residueseq(), and PDBAtom::serialnumber().

                                                             {
  int i;
  char buf[LINESIZE];
  FILE *infile;
  
  /* open up the coordinate file */
  infile=Fopen(filename, "r");
  if (infile == NULL)
    NAMD_err("Can't open GROMACS coordinate file!");

  fgets(buf,LINESIZE-1,infile); // get the title
  // if(strcmp(buf,topology->getSystemName()) != 0)
  //   NAMD_die("System names in topology and coordinate files differ.");

  fgets(buf,LINESIZE-1,infile); // get the number of atoms
  sscanf(buf,"%d",&atomCount);
  if (atomCount != topology->getNumAtoms())
    NAMD_die("Num of atoms in coordinate file is different from that in topology file!");

  /* read in the atoms */
#ifdef MEM_OPT_VERSION
  altlocArray = 0;
  atomArray = new PDBCoreData[atomCount];
#else
  atomAlloc = 0;
  atomArray = new PDBAtomPtr[atomCount];
#endif
  if ( atomArray == NULL )
    NAMD_die("memory allocation failed in PDB::PDB");

#ifdef MEM_OPT_VERSION
  for(i=0; i<atomCount; i++){
      fgets(buf,LINESIZE-1,infile); // get a line
      char *buf2 = buf+20; // skip three fields to get to the coordinates
      BigReal coor[3];
      if(3 != sscanf(buf2,"%lf%lf%lf", &coor[0],&coor[1],&coor[2]))
          NAMD_die("Couldn't get three coordinates from file.");

      coor[0] *= 10; // convert to angstroms from nanometers
      coor[1] *= 10;
      coor[2] *= 10;

      atomArray[i].coor[0] = coor[0];
      atomArray[i].coor[1] = coor[1];
      atomArray[i].coor[2] = coor[2];
      atomArray[i].myoccupancy = PDBAtom::default_occupancy;
      atomArray[i].tempfactor = PDBAtom::default_temperaturefactor;
  }
#else
  for (i=0;i<atomCount;i++) {
    char *buf2, resname[11], atomname[11], atmtype[11];
    int resnum, typenum;
    Real charge,mass;
    BigReal coor[3];
    PDBAtom *pdb = new PDBAtomRecord("");  
    
    fgets(buf,LINESIZE-1,infile); // get a line
    buf2 = buf+20; // skip three fields to get to the coordinates
    if(3 != sscanf(buf2,"%lf%lf%lf",
                   &coor[0],&coor[1],&coor[2]))
      NAMD_die("Couldn't get three coordinates from file.");
    topology->getAtom(i,&resnum,resname,
                      atomname,atmtype,&typenum,&charge,&mass);
    coor[0] *= 10; // convert to angstroms from nanometers
    coor[1] *= 10;
    coor[2] *= 10;
    
    pdb->name(atomname);
    pdb->residuename(resname);
    pdb->serialnumber(i+1);
    pdb->residueseq(resnum+1);
    pdb->coordinates(coor);
    
    atomArray[i] = pdb;  // Include the new record into the array
  }
#endif
}

~PDB()

PDB::~PDB

(

void

)

Definition at line 242 of file PDB.C.

{
#ifndef MEM_OPT_VERSION
        int i;
        if ( atomAlloc ) {
          delete [] atomAlloc;
        } else {
          for (i=atomCount-1; i>=0; i--)
            delete atomArray[i];
        }
#else
        delete [] altlocArray;
#endif
        delete [] atomArray;
        atomArray = NULL;
        atomCount = 0;
}

Member Function Documentation

atom()

PDBAtom * PDB::atom

(

int

place

)

Definition at line 393 of file PDB.C.

Referenced by Molecule::build_go_arrays(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), Molecule::build_gridforce_params(), find_extremes(), colvarproxy_namd::load_atoms_pdb(), colvarproxy_namd::load_coords_pdb(), and Molecule::prepare_qm().

{
  if (place <0 || place >= atomCount)
    return NULL;
  return atomArray[place];
}

atoms()

PDBAtomList* PDB::atoms ( void  )

inline

Definition at line 92 of file PDB.h.

{ return atomListHead; }  

find_extremes()

void PDB::find_extremes	(	const Lattice &	lattice,
		BigReal	frac = 1.0
	)

Definition at line 437 of file PDB.C.

References Lattice::a_r(), atom(), Lattice::b_r(), Lattice::c_r(), Lattice::origin(), ResizeArray< Elem >::resize(), Vector::x, PDBAtom::xcoor(), Vector::y, PDBAtom::ycoor(), Vector::z, and PDBAtom::zcoor().

Referenced by WorkDistrib::patchMapInit().

                                                            {
  if (atomCount == 0) {
    smin = smax = 0;
  }
  else if (frac < 1.0) {
    // for now use the previous "sort the array" approach
    // for solving "frac"th largest and smallest selection problems
    SortableResizeArray<BigReal> coor;
    coor.resize(atomCount);  // allocate array space once
    find_extremes_helper(coor, smin.x, smax.x, lattice.a_r(), frac);
    find_extremes_helper(coor, smin.y, smax.y, lattice.b_r(), frac);
    find_extremes_helper(coor, smin.z, smax.z, lattice.c_r(), frac);
  }
  else {
    // finding absolute min and max does not require sorting
#ifdef MEM_OPT_VERSION
    PDBCoreData *atomptr = atomArray;
    Vector p(atomptr->xcoor(),atomptr->ycoor(),atomptr->zcoor());
#else
    PDBAtomPtr *atomptr = atomArray;
    PDBAtom *atom = *atomptr;
    Vector p(atom->xcoor(),atom->ycoor(),atom->zcoor());
#endif
    Vector s(lattice.a_r()*p, lattice.b_r()*p, lattice.c_r()*p);
    smin = smax = s;
    atomptr++;
    for(int i=1; i<atomCount; i++, atomptr++){
#ifdef MEM_OPT_VERSION
      p = Vector(atomptr->xcoor(),atomptr->ycoor(),atomptr->zcoor());
#else
      atom = *atomptr;
      p = Vector (atom->xcoor(),atom->ycoor(),atom->zcoor());
#endif
      s = Vector(lattice.a_r()*p, lattice.b_r()*p, lattice.c_r()*p);
      if      (smin.x > s.x) smin.x = s.x;
      else if (smax.x < s.x) smax.x = s.x;
      if      (smin.y > s.y) smin.y = s.y;
      else if (smax.y < s.y) smax.y = s.y;
      if      (smin.z > s.z) smin.z = s.z;
      else if (smax.z < s.z) smax.z = s.z;
    }
  }
  // shift using the origin
  BigReal origin_shift;
  origin_shift = lattice.a_r() * lattice.origin();
  smin.x -= origin_shift;
  smax.x -= origin_shift;
  origin_shift = lattice.b_r() * lattice.origin();
  smin.y -= origin_shift;
  smax.y -= origin_shift;
  origin_shift = lattice.c_r() * lattice.origin();
  smin.z -= origin_shift;
  smax.z -= origin_shift;
}

get_all_positions()

void PDB::get_all_positions

(

Vector *

pos

)

Definition at line 365 of file PDB.C.

References Vector::x, Vector::y, and Vector::z.

Referenced by WorkDistrib::createAtomLists().

{
#ifdef MEM_OPT_VERSION
    for(int i=0; i<atomCount; i++){
        pos[i].x = atomArray[i].coor[0];
        pos[i].y = atomArray[i].coor[1];
        pos[i].z = atomArray[i].coor[2];        
    }
#else
        int i;
        PDBAtomPtr *atomptr;

        for (i=0, atomptr=atomArray; i<atomCount; atomptr++, i++)
        {
                pos[i].x = (*atomptr)->xcoor();
                pos[i].y = (*atomptr)->ycoor();
                pos[i].z = (*atomptr)->zcoor();
        }
#endif
}

get_extremes()

void PDB::get_extremes ( ScaledPosition &  xmin, ScaledPosition &  xmax  ) const

inline

Definition at line 104 of file PDB.h.

Referenced by WorkDistrib::patchMapInit(), and Node::startup().

                                                                        {
      xmin = smin;  xmax = smax;
    }

get_position_for_atom()

void PDB::get_position_for_atom	(	Vector *	pos,
		int	aid
	)

Definition at line 351 of file PDB.C.

References Vector::x, Vector::y, and Vector::z.

                                                   {
#ifdef MEM_OPT_VERSION
    pos->x = atomArray[aid].coor[0];
    pos->y = atomArray[aid].coor[1];
    pos->z = atomArray[aid].coor[2];
#else
    PDBAtomPtr *atomptr = &atomArray[aid];
    pos->x = (*atomptr)->xcoor();
    pos->y = (*atomptr)->ycoor();
    pos->z = (*atomptr)->zcoor();
#endif
}

num_atoms()

int PDB::num_atoms

(

void

)

Definition at line 323 of file PDB.C.

Referenced by Molecule::build_go_arrays(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), Molecule::build_gridforce_params(), WorkDistrib::createAtomLists(), colvarproxy_namd::load_atoms_pdb(), colvarproxy_namd::load_coords_pdb(), NamdState::loadStructure(), WorkDistrib::patchMapInit(), Molecule::prepare_qm(), and read_binary_coors().

{
  return atomCount;
}

set_all_positions()

void PDB::set_all_positions

(

Vector *

pos

)

Definition at line 331 of file PDB.C.

References Vector::x, PDBAtom::xcoor(), Vector::y, and Vector::z.

Referenced by read_binary_coors().

{
#ifdef MEM_OPT_VERSION
    for(int i=0; i<atomCount; i++){
        atomArray[i].coor[0] = pos[i].x;
        atomArray[i].coor[1] = pos[i].y;
        atomArray[i].coor[2] = pos[i].z;
    }
#else
        int i;
        PDBAtomPtr *atomptr;
        for (i=0, atomptr=atomArray; i<atomCount; atomptr++, i++)
        {
                (*atomptr)->xcoor(pos[i].x);
                (*atomptr)->ycoor(pos[i].y);
                (*atomptr)->zcoor(pos[i].z);
        }
#endif
}

write()

void PDB::write	(	const char *	outfilename,
		const char *	commentline = NULL
	)

Definition at line 261 of file PDB.C.

References PDBData::COLUMNS, NAMD_err(), and PDBAtom::sprint().

{
        int i;
        char s[200];
        FILE *outfile;
        if ((outfile = fopen(outfilename, "w")) == NULL) {
           sprintf(s, "Cannot open file '%s' in PDB::write.", outfilename);
           NAMD_err(s);
        }

        if (commentline != NULL)
        {
                sprintf(s, "REMARK  %s\n", commentline);
                if (fputs(s, outfile) == EOF)
                {
                        NAMD_err("EOF in PDB::write writing the comment line - file system full?");
                }
        }

        for (i=0; i<atomCount; i++){ // I only contain ATOM/HETATM records
#ifdef MEM_OPT_VERSION    
      atomArray[i].sprint(s, PDBData::COLUMNS);  
#else
          atomArray[i]->sprint(s, PDBData::COLUMNS);
#endif
          if ( (fputs(s, outfile)    == EOF) || 
               (fputs("\n", outfile) == EOF)    ) {
            sprintf(s, "EOF in PDB::write line %d - file system full?", i);
            NAMD_err(s);
          }
        }
        if (fputs("END\n", outfile) == EOF) {
           NAMD_err("EOF in PDB::write while printing 'END' -- file system full?");
        }
        if (fclose(outfile) == EOF) {
           NAMD_err("EOF in PDB::write while closing -- file system full?");
        }
          
}

---

The documentation for this class was generated from the following files:

• PDB.h
• PDB.C