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/********************************************************************** |
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obutil.h - Various utility methods. |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#ifndef OB_UTIL_H |
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#define OB_UTIL_H |
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|
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#include "config.h" |
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|
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#if HAVE_IOSTREAM |
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#include <iostream> |
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#elif HAVE_IOSTREAM_H |
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#include <iostream.h> |
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#endif |
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|
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#if TIME_WITH_SYS_TIME |
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#include <sys/time.h> |
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#include <time.h> |
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#else |
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#if HAVE_SYS_TIME_H |
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#include <sys/time.h> |
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#else |
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#include <time.h> |
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#endif |
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#endif |
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|
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#include <string> |
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|
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namespace OpenBabel |
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{ |
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|
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// class introduction in obutil.cpp |
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class OBAPI OBStopwatch |
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{ |
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#if HAVE_CLOCK_T |
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clock_t start, stop; |
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#else |
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|
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timeval start; |
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timeval stop; |
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#endif |
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|
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public: |
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#if HAVE_CLOCK_T |
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|
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void Start() |
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{ |
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start= clock(); |
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} |
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double Lap() |
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{ |
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stop= clock(); |
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return((double)(stop - start) / CLOCKS_PER_SEC); |
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} |
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#else |
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void Start() |
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{ |
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gettimeofday(&start,(struct timezone *)NULL); |
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} |
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double Lap() |
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{ |
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gettimeofday(&stop,(struct timezone *)NULL); |
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return((stop.tv_sec - start.tv_sec) |
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+ (double)(stop.tv_usec - start.tv_usec)/1000000.0); |
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} |
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#endif |
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double Elapsed() |
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{ |
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return(Lap()); |
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} |
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}; |
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|
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|
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//! sqrt lookup table - given a distance squared returns distance |
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class OBAPI OBSqrtTbl |
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{ |
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double _max,_incr,*_tbl; |
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public: |
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OBSqrtTbl() |
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{ |
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_tbl=NULL; |
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_max = _incr = 0.0; |
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} |
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OBSqrtTbl(double max,double incr) |
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{ |
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Init(max,incr); |
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} |
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~OBSqrtTbl() |
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{ |
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if (_tbl) |
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{ |
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delete [] _tbl; |
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_tbl = NULL; |
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} |
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} |
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double Sqrt(double d2) const |
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{ |
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if (_tbl) |
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return((d2 < _max) ? _tbl[(int)(d2*_incr)]:sqrt(d2)); |
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else |
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return 0.0; |
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} |
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void Init(double max,double incr) |
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{ |
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int i; |
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double r; |
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_max = max*max; |
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_incr = incr; |
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//array size needs to be large enough to account for fp error |
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_tbl = new double [(unsigned int)((_max/_incr)+10)]; |
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for (r = (_incr/2.0),i=0;r <= _max;r += _incr,i++) |
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_tbl[i] = sqrt(r); |
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|
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_incr = 1/_incr; |
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} |
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}; |
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|
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|
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|
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//****************************************** |
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//*** Stuff for random number generation *** |
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//****************************************** |
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|
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//! Used for internal random number generation OBRandom (unless the system random generaor is used) |
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typedef struct |
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{ |
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unsigned int hi; |
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unsigned int lo; |
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} |
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DoubleType; |
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|
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OBAPI void DoubleMultiply( unsigned int,unsigned int,DoubleType*); |
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OBAPI void DoubleAdd( DoubleType*,unsigned int); |
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OBAPI unsigned int DoubleModulus( DoubleType*,unsigned int); |
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|
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//! Random number generator |
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class OBAPI OBRandom |
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{ |
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DoubleType d; |
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unsigned int m,a,c; |
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unsigned int p; |
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unsigned int i; |
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unsigned int x; |
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bool OBRandomUseSysRand; |
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|
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public: |
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OBRandom(bool useSys= false); |
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void Seed(int seed) |
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{ |
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x = seed; |
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} |
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void TimeSeed(); |
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int NextInt(); |
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double NextFloat(); |
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}; |
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|
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//***RMS helper methods***/ |
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#ifndef SWIG |
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OBAPI void rotate_coords(double*,double m[3][3],int); |
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#endif |
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OBAPI double calc_rms(double*,double*,unsigned int); |
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|
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//! \name String conversion utilities |
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//@{ |
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// Documentation in obutil.cpp |
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OBAPI void ToUpper(std::string&); |
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OBAPI void ToUpper(char*); |
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OBAPI void ToLower(std::string&); |
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OBAPI void ToLower(char *); |
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//! "Clean" the supplied atom type |
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OBAPI void CleanAtomType(char*); |
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//@} |
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|
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//! Comparison -- returns true if first parameter less than second |
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OBAPI bool OBCompareInt(const int &,const int &); |
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//! Comparison -- returns true if first parameter less than second |
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OBAPI bool OBCompareUnsigned(const unsigned int &,const unsigned int &); |
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//! Safe comparison for floats/doubles: true if a and b are closer than epsilon |
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OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); |
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//! Safe comparison for floats/doubles: true if a is less than epsilon |
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OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); |
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|
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//******************triple template************************* |
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//! \brief A 3-element templated, based on the design of the STL pair<> |
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template <class T1, class T2, class T3> |
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struct triple |
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{ |
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//type names for the values |
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typedef T1 first_type; |
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typedef T2 second_type; |
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typedef T3 third_type; |
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|
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//member |
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T1 first; |
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T2 second; |
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T3 third; |
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|
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/** Default constructor |
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* T1() and T2() and T3() force initialization for built in types |
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**/ |
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triple(): |
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first(T1()),second(T2()),third(T3()) |
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{} |
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|
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//! Constructor for 3 values |
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triple(const T1 &a, const T2 &b, const T3 &c): |
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first(a), second(b), third(c) |
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{} |
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|
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//! Copy constructor with implicit conversions |
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template<class U, class V, class W> |
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triple(const triple<U,V,W> &t): |
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first(t.first), second(t.second), third(t.third) |
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{} |
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|
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}; |
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|
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//**************quad template******************** |
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//! \brief A 4-element templated, based on the design of the STL pair<> |
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template <class T1, class T2, class T3, class T4> |
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struct quad |
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{ |
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//type names for the values |
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typedef T1 first_type; |
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typedef T2 second_type; |
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typedef T3 third_type; |
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typedef T4 fourth_type; |
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|
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//member |
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T1 first; |
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T2 second; |
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T3 third; |
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T4 fourth; |
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|
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/*! default constructor |
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* T1() and T2() and T3() force initialization for built in types |
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*/ |
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quad(): |
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first(T1()),second(T2()),third(T3()),fourth(T4()) |
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{} |
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|
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//! constructor for 3 values |
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quad(const T1 &a, const T2 &b, const T3 &c, const T4 &d): |
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first(a), second(b), third(c), fourth(d) |
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{} |
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|
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//! copy constructor with implicit conversions |
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template<class U, class V, class W, class X> |
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quad(const quad<U,V,W,X> &q): |
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first(q.first), second(q.second), third(q.third), fourth(q.fourth) |
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{} |
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|
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}; |
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|
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} // end namespace OpenBabel |
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|
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#endif // OBUTIL_H |
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|
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//! \file obutil.h |
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//! \brief Various utility methods. |
