obutil.h

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/**********************************************************************
obutil.h - Various utility methods.
 
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
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.
***********************************************************************/

#ifndef OB_UTIL_H
#define OB_UTIL_H

#include "babelconfig.h"

#if HAVE_IOSTREAM
#include <iostream>
#elif HAVE_IOSTREAM_H
#include <iostream.h>
#endif

#if TIME_WITH_SYS_TIME
#include <sys/time.h>
#include <time.h>
#else
#if HAVE_SYS_TIME_H
#include <sys/time.h>
#else
#include <time.h>
#endif
#endif

#include <string>

namespace OpenBabel
{

// class introduction in obutil.cpp
class OBAPI OBStopwatch
{
#if HAVE_CLOCK_T
    clock_t start, stop;
#else

    timeval start;
    timeval stop;
#endif

public:
#if HAVE_CLOCK_T

    void  Start()
    {
        start= clock();
    }
    double Lap()
    {
        stop= clock();
        return((double)(stop - start) / CLOCKS_PER_SEC);
    }
#else
    void Start()
    {
        gettimeofday(&start,(struct timezone *)NULL);
    }
    double Lap()
    {
        gettimeofday(&stop,(struct timezone *)NULL);
        return((stop.tv_sec - start.tv_sec)
               + (double)(stop.tv_usec - start.tv_usec)/1000000.0);
    }
#endif
    double Elapsed()
    {
        return(Lap());
    }
};


class OBAPI OBSqrtTbl
{
    double _max,_incr,*_tbl;
public:
    OBSqrtTbl()
    {
        _tbl=NULL;
        _max = _incr = 0.0;
    }
    OBSqrtTbl(double max,double incr)
    {
        Init(max,incr);
    }
    ~OBSqrtTbl()
    {
        if (_tbl)
        {
            delete [] _tbl;
            _tbl = NULL;
        }
    }
    double Sqrt(double d2) const
    {
        if (_tbl)
            return((d2 < _max) ? _tbl[(int)(d2*_incr)]:sqrt(d2));
        else
            return 0.0;
    }
    void Init(double max,double incr)
    {
        int i;
        double r;
        _max = max*max;
        _incr = incr;
        //array size needs to be large enough to account for fp error
        _tbl = new double [(unsigned int)((_max/_incr)+10)];
        for (r = (_incr/2.0),i=0;r <= _max;r += _incr,i++)
            _tbl[i] = sqrt(r);

        _incr = 1/_incr;
    }
};



//******************************************
//*** Stuff for random number generation ***
//******************************************

typedef struct
{
    unsigned int hi;
    unsigned int lo;
}
DoubleType;

OBAPI void DoubleMultiply( unsigned int,unsigned int,DoubleType*);
OBAPI void DoubleAdd( DoubleType*,unsigned int);
OBAPI unsigned int DoubleModulus( DoubleType*,unsigned int);

class OBAPI OBRandom
{
    DoubleType d;
    unsigned int m,a,c;
    unsigned int p;
    unsigned int i;
    unsigned int x;
    bool OBRandomUseSysRand;

public:
    OBRandom(bool useSys= false);
    void Seed(int seed)
    {
        x = seed;
    }
    void TimeSeed();
    int NextInt();
    double NextFloat();
};

//***RMS helper methods***/
#ifndef SWIG
OBAPI void  rotate_coords(double*,double m[3][3],int);
#endif
OBAPI double calc_rms(double*,double*,unsigned int);


// Documentation in obutil.cpp
OBAPI void ToUpper(std::string&);
OBAPI void ToUpper(char*);
OBAPI void ToLower(std::string&);
OBAPI void ToLower(char *);
OBAPI void CleanAtomType(char*);

OBAPI bool OBCompareInt(const int &,const int &);
OBAPI bool OBCompareUnsigned(const unsigned int &,const unsigned int &);
OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6);
OBAPI bool IsNearZero(const double &, const double epsilon=2e-6);

//******************triple template*************************
template <class T1, class T2, class T3>
struct triple
{
    //type names for the values
    typedef T1 first_type;
    typedef T2 second_type;
    typedef T3 third_type;

    //member
    T1 first;
    T2 second;
    T3 third;
  
  triple():
    first(T1()),second(T2()),third(T3())
  {}

  triple(const T1 &a, const T2 &b, const T3 &c):
    first(a), second(b), third(c)
  {}

  template<class U, class V, class W>
    triple(const triple<U,V,W> &t):
      first(t.first), second(t.second), third(t.third)
  {}

};

//**************quad template********************
template <class T1, class T2, class T3, class T4>
struct quad
{
    //type names for the values
    typedef T1 first_type;
    typedef T2 second_type;
    typedef T3 third_type;
    typedef T4 fourth_type;

    //member
    T1 first;
    T2 second;
    T3 third;
    T4 fourth;

  quad():
    first(T1()),second(T2()),third(T3()),fourth(T4())
  {}

  quad(const T1 &a, const T2 &b, const T3 &c, const T4 &d):
    first(a), second(b), third(c), fourth(d)
  {}

  template<class U, class V, class W, class X>
    quad(const quad<U,V,W,X> &q):
      first(q.first), second(q.second), third(q.third), fourth(q.fourth)
  {}

};

} // end namespace OpenBabel

#endif // OBUTIL_H

---

This file is part of the documentation for Open Babel, version 2.0.2.

Documentation copyright © 1998-2005, the Open Babel Developers.
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