/**********************************************************************
  XTCFormat - portable compressed trajectory format (gromacs)

  Copyright (C) 2008 by Tim Vandermeersch

  Parts of the code are from libxdrf:
  frans van hoesel hoesel@chem.rug.nl
  http://hpcv100.rc.rug.nl/xdrf.html

  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation version 2 of the License.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
 ***********************************************************************/

#include <openbabel/babelconfig.h>
#include <openbabel/obmolecformat.h>

#include <rpc/types.h>
#include <rpc/xdr.h>
#include <vector>

#define MAXID 20
#define MAXABS INT_MAX-2

#ifndef MIN
#define MIN(x,y) ((x) < (y) ? (x):(y))
#endif
#ifndef MAX
#define MAX(x,y) ((x) > (y) ? (x):(y))
#endif
#ifndef SQR
#define SQR(x) ((x)*(x))
#endif

#define FIRSTIDX 9
/* note that magicints[FIRSTIDX-1] == 0 */
#define LASTIDX (sizeof(magicints) / sizeof(*magicints))

namespace OpenBabel
{

  class XTCFormat : public OBMoleculeFormat
  {
  private:
    XDR 	xd;
    FILE*	xdrfiles[MAXID];
    XDR*	xdridptr[MAXID];
    char 	xdrmodes[MAXID];
    unsigned int cnt;

    static int magicints[]; // defined below
    int	xdropen(XDR *xdrs, const char *filename, const char *type);
    int	xdrclose(XDR *xdrs);
    void	sendbits(int buf[], int num_of_bits, int num);
    int	sizeofint(const int size);
    int	sizeofints( const int num_of_ints, unsigned int sizes[]);
    void	sendints(int buf[], const int num_of_ints, const int num_of_bits,
                   unsigned int sizes[], unsigned int nums[]);
    int	receivebits(int buf[], int num_of_bits);
    void	receiveints(int buf[], const int num_of_ints, int num_of_bits,
                      unsigned int sizes[], int nums[]);
    int	xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision);

  public:
    //Register this format type ID
    XTCFormat()
    {
      OBConversion::RegisterFormat("xtc",this);
    }

    virtual const char* Description() //required
    {
      return
        "XTC format\n"
        "A portable format for trajectories (gromacs)\n";
    };

    virtual const char* SpecificationURL()
    { return "http://www.gromacs.org/documentation/reference/online/xtc.html"; }; //optional

    //Flags() can return be any the following combined by | or be omitted if none apply
    // NOTREADABLE  READONEONLY  NOTWRITABLE  WRITEONEONLY
    virtual unsigned int Flags()
    {
      return NOTWRITABLE;
    };

    //*** This section identical for most OBMol conversions ***
    ////////////////////////////////////////////////////
    /// The "API" interface functions
    virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);
    //virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);
  };
  //***

  // define the static magicints
  int XTCFormat::magicints[] = {
    0, 0, 0, 0, 0, 0, 0, 0, 0,
    8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
    80, 101, 128, 161, 203, 256, 322, 406, 512, 645,
    812, 1024, 1290, 1625, 2048, 2580, 3250, 4096, 5060, 6501,
    8192, 10321, 13003, 16384, 20642, 26007, 32768, 41285, 52015, 65536,
    82570, 104031, 131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561,
    832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021, 4194304, 5284491, 6658042,
    8388607, 10568983, 13316085, 16777216 };

  //Make an instance of the format class
  XTCFormat theXTCFormat;

  /////////////////////////////////////////////////////////////////
  bool XTCFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
  {
    //OBMol* pmol = pOb->CastAndClear<OBMol>();
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
      return false;

    OBMol &mol = *pmol;
    std::string filename = pConv->GetInFilename();

    if (xdropen(&xd, filename.c_str(),"r") == 0) {
      std::stringstream errorMsg;
      errorMsg << "Error while opening " << filename << " for reading.";
      obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning);
      return false;
    }

    int magic, natoms, step;
    float prec = 1000.0;
    float time, box[3][3];
    std::vector<float> floatCoord;
    std::vector<double*> vconf;


    while (true) {
      // Check the magic int starting each frame
      xdr_int(&xd, &magic);
      if (magic != 1995) {
        std::stringstream errorMsg;
        errorMsg << "Error: magic int is " << magic << ", should be 1995.";
        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning);
        return false;
      }

      // Get the number of atoms
      xdr_int(&xd, &natoms);
      if (natoms != mol.NumAtoms()) {
        std::stringstream errorMsg;
        errorMsg << "Error: number of atoms in the trajectory (" << natoms
                 << ") doesn't match the number of atoms in the supplied "
                 << "molecule (" << mol.NumAtoms() << ").";
        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning);
        return false;
      }

      // Get the frame step number
      xdr_int(&xd, &step);
      // Get the frame time
      xdr_float(&xd, &time);
      // Get the frame box
      xdr_float(&xd, &box[0][0]);
      xdr_float(&xd, &box[0][1]);
      xdr_float(&xd, &box[0][2]);
      xdr_float(&xd, &box[1][0]);
      xdr_float(&xd, &box[1][1]);
      xdr_float(&xd, &box[1][2]);
      xdr_float(&xd, &box[2][0]);
      xdr_float(&xd, &box[2][1]);
      xdr_float(&xd, &box[2][2]);

      if (!floatCoord.size())
        floatCoord.resize(natoms * 3);

      // Read the positions
      if (xdr3dfcoord(&xd, &floatCoord[0], &natoms, &prec) == 0) {
        // printf("end reached...\n");
        break;
      }

      // Convert positions from single to double precision and convert from
      // nm to A
      std::vector<double> confs;
      confs.resize(natoms * 3);
      for (int i=0; i < natoms * 3; ++i) // unroll??
        confs[i] = static_cast<double>(10.0 * floatCoord.at(i));

      vconf.push_back(&confs[0]);
    }

    // Close the XDR file
    xdrclose(&xd);

    // Set the conformers in the mol object
    mol.SetConformers(vconf);

    return(true);
  }

  /*____________________________________________________________________________
    |
    | libxdrf - portable fortran interface to xdr. some xdr routines
    |	     are C routines for compressed coordinates
    |
    | version 1.1
    |
    | This collection of routines is intended to write and read
    | data in a portable way to a file, so data written on one type
    | of machine can be read back on a different type.
    | ________________________________________________________________________
    |
    | Below are the routines to be used by C programmers. Use the 'normal'
    | xdr routines to write integers, floats, etc (see man xdr)
    |
    | int xdropen(XDR *xdrs, const char *filename, const char *type)
    |	This will open the file with the given filename and the
    |	given mode. You should pass it an allocated XDR struct
    |	in xdrs, to be used in all other calls to xdr routines.
    |	Mode is 'w' to create, or update an file, and for all
    |	other values of mode the file is opened for reading.
    |	You need to call xdrclose to flush the output and close
    |	the file.
    |
    |	Note that you should not use xdrstdio_create, which
    |	comes with the standard xdr library.
    |
    | int xdrclose(XDR *xdrs)
    |	Flush the data to the file, and close the file;
    |	You should not use xdr_destroy (which comes standard
    |	with the xdr libraries).
    |
    | int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
    |	This is \fInot\fR a standard xdr routine. I named it this
    |	way, because it invites people to use the other xdr
    |	routines.
    |
    |	frans van hoesel hoesel@chem.rug.nl
  */


  /*___________________________________________________________________________
    |
    | what follows are the C routines for opening, closing xdr streams
    | and the routine to read/write compressed coordinates together
    | with some routines to assist in this task (those are marked
    | static and cannot be called from user programs)
  */

  /*__________________________________________________________________________
    |
    | xdropen - open xdr file
    |
    | This versions differs from xdrstdio_create, because I need to know
    | the state of the file (read or write) so I can use xdr3dfcoord
    | in eigther read or write mode, and the file descriptor
    | so I can close the file (something xdr_destroy doesn't do).
    |
  */

  int XTCFormat::xdropen(XDR *xdrs, const char *filename, const char *type) {
    int init_done = 0;
    enum xdr_op lmode;
    int xdrid;

    if (init_done == 0) {
      for (xdrid = 1; xdrid < MAXID; xdrid++) {
        xdridptr[xdrid] = NULL;
      }
      init_done = 1;
    }
    xdrid = 1;
    while (xdrid < MAXID && xdridptr[xdrid] != NULL) {
      xdrid++;
    }
    if (xdrid == MAXID) {
      return 0;
    }
    if (*type == 'w' || *type == 'W') {
	    type = "w+";
	    lmode = XDR_ENCODE;
    } else {
	    type = "r";
	    lmode = XDR_DECODE;
    }
    xdrfiles[xdrid] = fopen(filename, type);
    if (xdrfiles[xdrid] == NULL) {
      xdrs = NULL;
      return 0;
    }
    xdrmodes[xdrid] = *type;
    /* next test isn't useful in the case of C language
     * but is used for the Fortran interface
     * (C users are expected to pass the address of an already allocated
     * XDR staructure)
     */
    if (xdrs == NULL) {
      xdridptr[xdrid] = (XDR *) malloc(sizeof(XDR));
      xdrstdio_create(xdridptr[xdrid], xdrfiles[xdrid], lmode);
    } else {
      xdridptr[xdrid] = xdrs;
      xdrstdio_create(xdrs, xdrfiles[xdrid], lmode);
    }
    return xdrid;
  }

  /*_________________________________________________________________________
    |
    | xdrclose - close a xdr file
    |
    | This will flush the xdr buffers, and destroy the xdr stream.
    | It also closes the associated file descriptor (this is *not*
    | done by xdr_destroy).
    |
  */

  int XTCFormat::xdrclose(XDR *xdrs) {
    int xdrid;

    if (xdrs == NULL) {
      fprintf(stderr, "xdrclose: passed a NULL pointer\n");
      return 0;
    }
    for (xdrid = 1; xdrid < MAXID; xdrid++) {
      if (xdridptr[xdrid] == xdrs) {

        xdr_destroy(xdrs);
        fclose(xdrfiles[xdrid]);
        xdridptr[xdrid] = NULL;
        return 1;
      }
    }
    fprintf(stderr, "xdrclose: no such open xdr file\n");
    return 0;

  }

  /*____________________________________________________________________________
    |
    | sendbits - encode num into buf using the specified number of bits
    |
    | This routines appends the value of num to the bits already present in
    | the array buf. You need to give it the number of bits to use and you
    | better make sure that this number of bits is enough to hold the value
    | Also num must be positive.
    |
  */

  void XTCFormat::sendbits(int buf[], int num_of_bits, int num) {

    unsigned int cnt, lastbyte;
    int lastbits;
    unsigned char * cbuf;

    cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
    cnt = (unsigned int) buf[0];
    lastbits = buf[1];
    lastbyte =(unsigned int) buf[2];
    while (num_of_bits >= 8) {
      lastbyte = (lastbyte << 8) | ((num >> (num_of_bits -8)) /* & 0xff*/);
      cbuf[cnt++] = lastbyte >> lastbits;
      num_of_bits -= 8;
    }
    if (num_of_bits > 0) {
      lastbyte = (lastbyte << num_of_bits) | num;
      lastbits += num_of_bits;
      if (lastbits >= 8) {
        lastbits -= 8;
        cbuf[cnt++] = lastbyte >> lastbits;
      }
    }
    buf[0] = cnt;
    buf[1] = lastbits;
    buf[2] = lastbyte;
    if (lastbits>0) {
      cbuf[cnt] = lastbyte << (8 - lastbits);
    }
  }

  /*_________________________________________________________________________
    |
    | sizeofint - calculate bitsize of an integer
    |
    | return the number of bits needed to store an integer with given max size
    |
  */

  int XTCFormat::sizeofint(const int size) {
    unsigned int num = 1;
    int num_of_bits = 0;

    while (size >= num && num_of_bits < 32) {
      num_of_bits++;
      num <<= 1;
    }
    return num_of_bits;
  }

  /*___________________________________________________________________________
    |
    | sizeofints - calculate 'bitsize' of compressed ints
    |
    | given the number of small unsigned integers and the maximum value
    | return the number of bits needed to read or write them with the
    | routines receiveints and sendints. You need this parameter when
    | calling these routines. Note that for many calls I can use
    | the variable 'smallidx' which is exactly the number of bits, and
    | So I don't need to call 'sizeofints for those calls.
  */

  int XTCFormat::sizeofints( const int num_of_ints, unsigned int sizes[]) {
    int i, num;
    unsigned int num_of_bytes, num_of_bits, bytes[32], bytecnt, tmp;
    num_of_bytes = 1;
    bytes[0] = 1;
    num_of_bits = 0;
    for (i=0; i < num_of_ints; i++) {
      tmp = 0;
      for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
        tmp = bytes[bytecnt] * sizes[i] + tmp;
        bytes[bytecnt] = tmp & 0xff;
        tmp >>= 8;
      }
      while (tmp != 0) {
        bytes[bytecnt++] = tmp & 0xff;
        tmp >>= 8;
      }
      num_of_bytes = bytecnt;
    }
    num = 1;
    num_of_bytes--;
    while (bytes[num_of_bytes] >= num) {
      num_of_bits++;
      num *= 2;
    }
    return num_of_bits + num_of_bytes * 8;

  }

  /*____________________________________________________________________________
    |
    | sendints - send a small set of small integers in compressed format
    |
    | this routine is used internally by xdr3dfcoord, to send a set of
    | small integers to the buffer.
    | Multiplication with fixed (specified maximum ) sizes is used to get
    | to one big, multibyte integer. Allthough the routine could be
    | modified to handle sizes bigger than 16777216, or more than just
    | a few integers, this is not done, because the gain in compression
    | isn't worth the effort. Note that overflowing the multiplication
    | or the byte buffer (32 bytes) is unchecked and causes bad results.
    |
  */

  void XTCFormat::sendints(int buf[], const int num_of_ints, const int num_of_bits,
                           unsigned int sizes[], unsigned int nums[]) {

    int i;
    unsigned int bytes[32], num_of_bytes, bytecnt, tmp;

    tmp = nums[0];
    num_of_bytes = 0;
    do {
      bytes[num_of_bytes++] = tmp & 0xff;
      tmp >>= 8;
    } while (tmp != 0);

    for (i = 1; i < num_of_ints; i++) {
      if (nums[i] >= sizes[i]) {
        fprintf(stderr,"major breakdown in sendints num %d doesn't "
                "match size %d\n", nums[i], sizes[i]);
        return;
      }
      /* use one step multiply */
      tmp = nums[i];
      for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
        tmp = bytes[bytecnt] * sizes[i] + tmp;
        bytes[bytecnt] = tmp & 0xff;
        tmp >>= 8;
      }
      while (tmp != 0) {
        bytes[bytecnt++] = tmp & 0xff;
        tmp >>= 8;
      }
      num_of_bytes = bytecnt;
    }
    if (num_of_bits >= num_of_bytes * 8) {
      for (i = 0; i < num_of_bytes; i++) {
        sendbits(buf, 8, bytes[i]);
      }
      sendbits(buf, num_of_bits - num_of_bytes * 8, 0);
    } else {
      for (i = 0; i < num_of_bytes-1; i++) {
        sendbits(buf, 8, bytes[i]);
      }
      sendbits(buf, num_of_bits- (num_of_bytes -1) * 8, bytes[i]);
    }
  }


  /*___________________________________________________________________________
    |
    | receivebits - decode number from buf using specified number of bits
    |
    | extract the number of bits from the array buf and construct an integer
    | from it. Return that value.
    |
  */

  int XTCFormat::receivebits(int buf[], int num_of_bits) {
    int cnt, num;
    unsigned int lastbits, lastbyte;
    unsigned char * cbuf;
    int mask = (1 << num_of_bits) -1;

    cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
    cnt = buf[0];
    lastbits = (unsigned int) buf[1];
    lastbyte = (unsigned int) buf[2];

    num = 0;
    while (num_of_bits >= 8) {
      lastbyte = ( lastbyte << 8 ) | cbuf[cnt++];
      num |=  (lastbyte >> lastbits) << (num_of_bits - 8);
      num_of_bits -=8;
    }
    if (num_of_bits > 0) {
      if (lastbits < num_of_bits) {
        lastbits += 8;
        lastbyte = (lastbyte << 8) | cbuf[cnt++];
      }
      lastbits -= num_of_bits;
      num |= (lastbyte >> lastbits) & ((1 << num_of_bits) -1);
    }
    num &= mask;
    buf[0] = cnt;
    buf[1] = lastbits;
    buf[2] = lastbyte;
    return num;
  }

  /*____________________________________________________________________________
    |
    | receiveints - decode 'small' integers from the buf array
    |
    | this routine is the inverse from sendints() and decodes the small integers
    | written to buf by calculating the remainder and doing divisions with
    | the given sizes[]. You need to specify the total number of bits to be
    | used from buf in num_of_bits.
    |
  */

  void XTCFormat::receiveints(int buf[], const int num_of_ints, int num_of_bits,
                              unsigned int sizes[], int nums[]) {
    int bytes[32];
    int i, j, num_of_bytes, p, num;

    bytes[1] = bytes[2] = bytes[3] = 0;
    num_of_bytes = 0;
    while (num_of_bits > 8) {
      bytes[num_of_bytes++] = receivebits(buf, 8);
      num_of_bits -= 8;
    }
    if (num_of_bits > 0) {
      bytes[num_of_bytes++] = receivebits(buf, num_of_bits);
    }
    for (i = num_of_ints-1; i > 0; i--) {
      num = 0;
      for (j = num_of_bytes-1; j >=0; j--) {
        num = (num << 8) | bytes[j];
        p = num / sizes[i];
        bytes[j] = p;
        num = num - p * sizes[i];
      }
      nums[i] = num;
    }
    nums[0] = bytes[0] | (bytes[1] << 8) | (bytes[2] << 16) | (bytes[3] << 24);
  }

  /*____________________________________________________________________________
    |
    | xdr3dfcoord - read or write compressed 3d coordinates to xdr file.
    |
    | this routine reads or writes (depending on how you opened the file with
    | xdropen() ) a large number of 3d coordinates (stored in *fp).
    | The number of coordinates triplets to write is given by *size. On
    | read this number may be zero, in which case it reads as many as were written
    | or it may specify the number if triplets to read (which should match the
    | number written).
    | Compression is achieved by first converting all floating numbers to integer
    | using multiplication by *precision and rounding to the nearest integer.
    | Then the minimum and maximum value are calculated to determine the range.
    | The limited range of integers so found, is used to compress the coordinates.
    | In addition the differences between successive coordinates is calculated.
    | If the difference happens to be 'small' then only the difference is saved,
    | compressing the data even more. The notion of 'small' is changed dynamically
    | and is enlarged or reduced whenever needed or possible.
    | Extra compression is achieved in the case of GROMOS and coordinates of
    | water molecules. GROMOS first writes out the Oxygen position, followed by
    | the two hydrogens. In order to make the differences smaller (and thereby
    | compression the data better) the order is changed into first one hydrogen
    | then the oxygen, followed by the other hydrogen. This is rather special, but
    | it shouldn't harm in the general case.
    |
  */

  int XTCFormat::xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) {
    int *ip = NULL;
    int oldsize;
    int *buf;

    int minint[3], maxint[3], mindiff, *lip, diff;
    int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;
    int minidx, maxidx;
    unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;
    int flag, k;
    int small_, smaller, larger, i;
    int is_small, is_smaller, run, prevrun;
    float *lfp, lf;
    int tmp, *thiscoord,  prevcoord[3];
    unsigned int tmpcoord[30];

    int bufsize, xdrid, lsize;
    unsigned int bitsize;
    float inv_precision;
    int errval = 1;

    /* find out if xdrs is opened for reading or for writing */
    xdrid = 0;
    while (xdridptr[xdrid] != xdrs) {
      xdrid++;
      if (xdrid >= MAXID) {
        fprintf(stderr, "xdr error. no open xdr stream\n");
        return 0;
      }
    }
    if (xdrmodes[xdrid] == 'w') {

      /* xdrs is open for writing */

      if (xdr_int(xdrs, size) == 0)
        return 0;
      size3 = *size * 3;
      /* when the number of coordinates is small, don't try to compress; just
       * write them as floats using xdr_vector
       */
      if (*size <= 9 ) {
        return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
                           (xdrproc_t)xdr_float));
      }

      xdr_float(xdrs, precision);
      if (ip == NULL) {
        ip = (int *)malloc(size3 * sizeof(*ip));
        if (ip == NULL) {
          fprintf(stderr,"malloc failed\n");
          return 0;
        }
        bufsize = static_cast<int> (size3 * 1.2);
        buf = (int *)malloc(bufsize * sizeof(*buf));
        if (buf == NULL) {
          fprintf(stderr,"malloc failed\n");
          return 0;
        }
        oldsize = *size;
      } else if (*size > oldsize) {
        ip = (int *)realloc(ip, size3 * sizeof(*ip));
        if (ip == NULL) {
          fprintf(stderr,"malloc failed\n");
          return 0;
        }
        bufsize = static_cast<int> (size3 * 1.2);
        buf = (int *)realloc(buf, bufsize * sizeof(*buf));
        if (buf == NULL) {
          fprintf(stderr,"malloc failed\n");
          return 0;
        }
        oldsize = *size;
      }
      /* buf[0-2] are special and do not contain actual data */
      buf[0] = buf[1] = buf[2] = 0;
      minint[0] = minint[1] = minint[2] = INT_MAX;
      maxint[0] = maxint[1] = maxint[2] = INT_MIN;
      prevrun = -1;
      lfp = fp;
      lip = ip;
      mindiff = INT_MAX;
      oldlint1 = oldlint2 = oldlint3 = 0;
      while(lfp < fp + size3 ) {
        /* find nearest integer */
        if (*lfp >= 0.0)
          lf = *lfp * *precision + 0.5f;
        else
          lf = *lfp * *precision - 0.5f;
        if (fabs(lf) > MAXABS) {
          /* scaling would cause overflow */
          errval = 0;
        }
        lint1 = static_cast<int> (lf);
        if (lint1 < minint[0]) minint[0] = lint1;
        if (lint1 > maxint[0]) maxint[0] = lint1;
        *lip++ = lint1;
        lfp++;
        if (*lfp >= 0.0)
          lf = *lfp * *precision + 0.5f;
        else
          lf = *lfp * *precision - 0.5f;
        if (fabs(lf) > MAXABS) {
          /* scaling would cause overflow */
          errval = 0;
        }
        lint2 = static_cast<int> (lf);
        if (lint2 < minint[1]) minint[1] = lint2;
        if (lint2 > maxint[1]) maxint[1] = lint2;
        *lip++ = lint2;
        lfp++;
        if (*lfp >= 0.0)
          lf = *lfp * *precision + 0.5f;
        else
          lf = *lfp * *precision - 0.5f;
        if (fabs(lf) > MAXABS) {
          /* scaling would cause overflow */
          errval = 0;
        }
        lint3 = static_cast<int> (lf);
        if (lint3 < minint[2]) minint[2] = lint3;
        if (lint3 > maxint[2]) maxint[2] = lint3;
        *lip++ = lint3;
        lfp++;
        diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
        if (diff < mindiff && lfp > fp + 3)
          mindiff = diff;
        oldlint1 = lint1;
        oldlint2 = lint2;
        oldlint3 = lint3;
      }
      xdr_int(xdrs, &(minint[0]));
      xdr_int(xdrs, &(minint[1]));
      xdr_int(xdrs, &(minint[2]));

      xdr_int(xdrs, &(maxint[0]));
      xdr_int(xdrs, &(maxint[1]));
      xdr_int(xdrs, &(maxint[2]));

      if ((float)maxint[0] - (float)minint[0] >= MAXABS ||
          (float)maxint[1] - (float)minint[1] >= MAXABS ||
          (float)maxint[2] - (float)minint[2] >= MAXABS) {
        /* turning value in unsigned by subtracting minint
         * would cause overflow
         */
        errval = 0;
      }
      sizeint[0] = maxint[0] - minint[0]+1;
      sizeint[1] = maxint[1] - minint[1]+1;
      sizeint[2] = maxint[2] - minint[2]+1;

      /* check if one of the sizes is to big to be multiplied */
      if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
        bitsizeint[0] = sizeofint(sizeint[0]);
        bitsizeint[1] = sizeofint(sizeint[1]);
        bitsizeint[2] = sizeofint(sizeint[2]);
        bitsize = 0; /* flag the use of large sizes */
      } else {
        bitsize = sizeofints(3, sizeint);
      }
      lip = ip;
      luip = (unsigned int *) ip;
      smallidx = FIRSTIDX;
      while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
        smallidx++;
      }
      xdr_int(xdrs, &smallidx);
      maxidx = MIN(LASTIDX, smallidx + 8) ;
      minidx = maxidx - 8; /* often this equal smallidx */
      smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
      small_ = magicints[smallidx] / 2;
      sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
      larger = magicints[maxidx] / 2;
      i = 0;
      while (i < *size) {
        is_small = 0;
        thiscoord = (int *)(luip) + i * 3;
        if (smallidx < maxidx && i >= 1 &&
            abs(thiscoord[0] - prevcoord[0]) < larger &&
            abs(thiscoord[1] - prevcoord[1]) < larger &&
            abs(thiscoord[2] - prevcoord[2]) < larger) {
          is_smaller = 1;
        } else if (smallidx > minidx) {
          is_smaller = -1;
        } else {
          is_smaller = 0;
        }
        if (i + 1 < *size) {
          if (abs(thiscoord[0] - thiscoord[3]) < small_ &&
              abs(thiscoord[1] - thiscoord[4]) < small_ &&
              abs(thiscoord[2] - thiscoord[5]) < small_) {
            /* interchange first with second atom for better
             * compression of water molecules
             */
            tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
            thiscoord[3] = tmp;
            tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
            thiscoord[4] = tmp;
            tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
            thiscoord[5] = tmp;
            is_small = 1;
          }

        }
        tmpcoord[0] = thiscoord[0] - minint[0];
        tmpcoord[1] = thiscoord[1] - minint[1];
        tmpcoord[2] = thiscoord[2] - minint[2];
        if (bitsize == 0) {
          sendbits(buf, bitsizeint[0], tmpcoord[0]);
          sendbits(buf, bitsizeint[1], tmpcoord[1]);
          sendbits(buf, bitsizeint[2], tmpcoord[2]);
        } else {
          sendints(buf, 3, bitsize, sizeint, tmpcoord);
        }
        prevcoord[0] = thiscoord[0];
        prevcoord[1] = thiscoord[1];
        prevcoord[2] = thiscoord[2];
        thiscoord = thiscoord + 3;
        i++;

        run = 0;
        if (is_small == 0 && is_smaller == -1)
          is_smaller = 0;
        while (is_small && run < 8*3) {
          if (is_smaller == -1 && (
                                   SQR(thiscoord[0] - prevcoord[0]) +
                                   SQR(thiscoord[1] - prevcoord[1]) +
                                   SQR(thiscoord[2] - prevcoord[2]) >= smaller * smaller)) {
            is_smaller = 0;
          }

          tmpcoord[run++] = thiscoord[0] - prevcoord[0] + small_;
          tmpcoord[run++] = thiscoord[1] - prevcoord[1] + small_;
          tmpcoord[run++] = thiscoord[2] - prevcoord[2] + small_;

          prevcoord[0] = thiscoord[0];
          prevcoord[1] = thiscoord[1];
          prevcoord[2] = thiscoord[2];

          i++;
          thiscoord = thiscoord + 3;
          is_small = 0;
          if (i < *size &&
              abs(thiscoord[0] - prevcoord[0]) < small_ &&
              abs(thiscoord[1] - prevcoord[1]) < small_ &&
              abs(thiscoord[2] - prevcoord[2]) < small_) {
            is_small = 1;
          }
        }
        if (run != prevrun || is_smaller != 0) {
          prevrun = run;
          sendbits(buf, 1, 1); /* flag the change in run-length */
          sendbits(buf, 5, run+is_smaller+1);
        } else {
          sendbits(buf, 1, 0); /* flag the fact that runlength did not change */
        }
        for (k=0; k < run; k+=3) {
          sendints(buf, 3, smallidx, sizesmall, &tmpcoord[k]);
        }
        if (is_smaller != 0) {
          smallidx += is_smaller;
          if (is_smaller < 0) {
            small_ = smaller;
            smaller = magicints[smallidx-1] / 2;
          } else {
            smaller = small_;
            small_ = magicints[smallidx] / 2;
          }
          sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
        }
      }
      if (buf[1] != 0) buf[0]++;;
      xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */
      return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]));
    } else {

      /* xdrs is open for reading */

      if (xdr_int(xdrs, &lsize) == 0)
        return 0;
      if (*size != 0 && lsize != *size) {
        fprintf(stderr, "wrong number of coordinates in xdr3dfcoor; "
                "%d arg vs %d in file", *size, lsize);
      }
      *size = lsize;
      size3 = *size * 3;
      if (*size <= 9) {
        return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
                           (xdrproc_t)xdr_float));
      }
      xdr_float(xdrs, precision);
      if (ip == NULL) {
        ip = (int *)malloc(size3 * sizeof(*ip));
        if (ip == NULL) {
          fprintf(stderr,"malloc failed\n");
          return 0;
        }
        bufsize = static_cast<int> (size3 * 1.2);
        buf = (int *)malloc(bufsize * sizeof(*buf));
        if (buf == NULL) {
          fprintf(stderr,"malloc failed\n");
          return 0;
        }
        oldsize = *size;
      } else if (*size > oldsize) {
        ip = (int *)realloc(ip, size3 * sizeof(*ip));
        if (ip == NULL) {
          fprintf(stderr,"malloc failed\n");
          return 0;
        }
        bufsize = static_cast<int> (size3 * 1.2);
        buf = (int *)realloc(buf, bufsize * sizeof(*buf));
        if (buf == NULL) {
          fprintf(stderr,"malloc failed\n");
          return 0;
        }
        oldsize = *size;
      }
      buf[0] = buf[1] = buf[2] = 0;

      xdr_int(xdrs, &(minint[0]));
      xdr_int(xdrs, &(minint[1]));
      xdr_int(xdrs, &(minint[2]));

      xdr_int(xdrs, &(maxint[0]));
      xdr_int(xdrs, &(maxint[1]));
      xdr_int(xdrs, &(maxint[2]));

      sizeint[0] = maxint[0] - minint[0]+1;
      sizeint[1] = maxint[1] - minint[1]+1;
      sizeint[2] = maxint[2] - minint[2]+1;

      /* check if one of the sizes is to big to be multiplied */
      if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
        bitsizeint[0] = sizeofint(sizeint[0]);
        bitsizeint[1] = sizeofint(sizeint[1]);
        bitsizeint[2] = sizeofint(sizeint[2]);
        bitsize = 0; /* flag the use of large sizes */
      } else {
        bitsize = sizeofints(3, sizeint);
      }

      xdr_int(xdrs, &smallidx);
      maxidx = MIN(LASTIDX, smallidx + 8) ;
      minidx = maxidx - 8; /* often this equal smallidx */
      smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
      small_ = magicints[smallidx] / 2;
      sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
      larger = magicints[maxidx];

    	/* buf[0] holds the length in bytes */

      if (xdr_int(xdrs, &(buf[0])) == 0)
        return 0;
      if (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]) == 0)
        return 0;
      buf[0] = buf[1] = buf[2] = 0;

      lfp = fp;
      inv_precision = 1.0f / * precision;
      run = 0;
      i = 0;
      lip = ip;
      while ( i < lsize ) {
        thiscoord = (int *)(lip) + i * 3;

        if (bitsize == 0) {
          thiscoord[0] = receivebits(buf, bitsizeint[0]);
          thiscoord[1] = receivebits(buf, bitsizeint[1]);
          thiscoord[2] = receivebits(buf, bitsizeint[2]);
        } else {
          receiveints(buf, 3, bitsize, sizeint, thiscoord);
        }

        i++;
        thiscoord[0] += minint[0];
        thiscoord[1] += minint[1];
        thiscoord[2] += minint[2];

        prevcoord[0] = thiscoord[0];
        prevcoord[1] = thiscoord[1];
        prevcoord[2] = thiscoord[2];


        flag = receivebits(buf, 1);
        is_smaller = 0;
        if (flag == 1) {
          run = receivebits(buf, 5);
          is_smaller = run % 3;
          run -= is_smaller;
          is_smaller--;
        }
        if (run > 0) {
          thiscoord += 3;
          for (k = 0; k < run; k+=3) {
            receiveints(buf, 3, smallidx, sizesmall, thiscoord);
            i++;
            thiscoord[0] += prevcoord[0] - small_;
            thiscoord[1] += prevcoord[1] - small_;
            thiscoord[2] += prevcoord[2] - small_;
            if (k == 0) {
              /* interchange first with second atom for better
               * compression of water molecules
               */
              tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
              prevcoord[0] = tmp;
              tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
              prevcoord[1] = tmp;
              tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
              prevcoord[2] = tmp;
              *lfp++ = prevcoord[0] * inv_precision;
              *lfp++ = prevcoord[1] * inv_precision;
              *lfp++ = prevcoord[2] * inv_precision;
            } else {
              prevcoord[0] = thiscoord[0];
              prevcoord[1] = thiscoord[1];
              prevcoord[2] = thiscoord[2];
            }
            *lfp++ = thiscoord[0] * inv_precision;
            *lfp++ = thiscoord[1] * inv_precision;
            *lfp++ = thiscoord[2] * inv_precision;
          }
        } else {
          *lfp++ = thiscoord[0] * inv_precision;
          *lfp++ = thiscoord[1] * inv_precision;
          *lfp++ = thiscoord[2] * inv_precision;
        }
        smallidx += is_smaller;
        if (is_smaller < 0) {
          small_ = smaller;
          if (smallidx > FIRSTIDX) {
            smaller = magicints[smallidx - 1] /2;
          } else {
            smaller = 0;
          }
        } else if (is_smaller > 0) {
          smaller = small_;
          small_ = magicints[smallidx] / 2;
        }
        sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
      }
    }
    return 1;
  }

} //namespace OpenBabel

