constants.h

c++编写的并行拉马克遗传算法的程序。实现分析对接程序

/* constants.h */

#ifndef _AUTOCOMM
#include "autocomm.h" /* PI, TWOPI. */
#endif
#include "dpftoken.h"

/******************************************************************************
 *      Name: constants.h                                                     *
 *  Function: Automated Docking of Small Molecule to Macromolecule            *
 *              Header file for Autodock modules.                             *
 * Copyright: (C) 1994, TSRI                                                  *
 *----------------------------------------------------------------------------*
 *    Author: Garrett Matthew Morris*                                         *
 *                                                                            *
 *              The Scripps Research Institute                                *
 *              Department of Molecular Biology, MB5                          *
 *              10666 North Torrey Pines Road                                 *
 *              La Jolla, CA 92037.                                           *
 *              e-mail: [e-mail]                                   *
 *                                                                            *
 *      Date: 10/04/94                                                        *
 *----------------------------------------------------------------------------*
 * Modification Record                                                        *
 * Date     Inits   Comments                                                  *
 *          DSG     Quaternion rotations                                      *
 *          DSG     Generates torsions from annotated pdb list                *
 *          DSG     Generates internal energies                               *
 *          DSG     Performs a limited cluster analysis of conformations      *
 * 07/05/92 GMM     C translation                                             *
 * 14/05/92 GMM     Time-dependent seed in random-number generation           *
 * 29/10/92 GMM     Application Visualization System (AVS) readable grid      *
 *                    display file input.                                     *
 *                    [AVS is a trademark of Stardent Computer Inc.]          *
 * 06/11/92 GMM     Command line parsing, using Bruce S. Duncan's "setflags". *
 * 06/11/92 GMM     New command mode, allowing communication between Autodock *
 *                    and other, invoking programs.                           *
 ******************************************************************************/

#ifndef CONSTANTS
#define CONSTANTS

#define REJECT                0
#define ACCEPT                1

#define U                0 /* x-coordinate in trilinear interpolation. */
#define V                1 /* y-coordinate in trilinear interpolation. */
#define W                2 /* z-coordinate in trilinear interpolation. */
#define QX                3 /* quaternion x-coordinate */
#define QY                4 /* quaternion y-coordinate */
#define QZ                5 /* quaternion z-coordinate */
#define QW                6 /* quaternion w-rotation */
#define QUAT                7 /* No. of translation & rotations in quaternion */

#define NTRN                3 /* Number of translation axes                 */
#define NQTN                4 /* Number of quaternion components         */

#define LOWER 0 /* Lower limit of torsion constraint. */
#define UPPER 1 /* Upper limit of torsion constraint. */

#define NLIG                4 /* Max. num. of ligands to be docked         */
#define NLIGTOR                64 /* Max. num. of torsions in each ligand         */

#define NRES                32 /* Max. num. of flexible residue */
#define NRESTOR                5 /* Max. num. of torsions in a residue */

#define NMOL                36 /* NMOL = NLIG + NRES, always!!! */

#define WORDLEN                9 /* Length of coordinates in characters. */

#define MAX_RUNS        128 /* Maximum number of runs. */
#define MAX_ATOMS        512 /* Maximum number of atoms in Small Molecule. */
#define MAX_RECORDS       512/* Maximum number of PDBQ records =~1.5*MAX_ATOMS */
#define MAX_NONBONDS        524288 /* Maximum number of non-bonds in Small Molecule.*/

#define MAX_TREES        8 /* Maximum number of torsion trees */
#define MAX_TORS        64/* Maximum number of torsions in Small Molecule. */
#define MAX_TORS_IN_ROTAMER        8 /* Maximum number of torsions in rotamer. */
#define MAX_TOR_CON         8 /* Maximum number of constraints per torsion. */

/* Note, torsion constraints will allocate (MAX_TORS *MAX_TOR_CON *2) floats */

#define NTORDIVS        256 /* Integer # angular divisions in torsion profiles*/
#define NTORDIVS_2        128 /* Integer half of NTORDIVS */
#define ONE_RAD_IN_DIVS 40.74366543  /* 1 radian = NTORDIVS_2 / PI divisions */

/* #define ONE_RAD_IN_DIVS 81.48733086 512,256,1 radian = NTORDIVS / (2*PI) divisions */

/* Convert angle to index */
#define Rad2Div(radians) ((int)((radians)*ONE_RAD_IN_DIVS) + NTORDIVS_2)

/* Convert index to angle */
#define Div2Rad(divs) (((float)((divs) - NTORDIVS_2))/ONE_RAD_IN_DIVS)

#define TORBARMAX        65535 /* Torsion barrier-energy maximum value */
#define DEFHWDTH        10. /* Default half-width (deg)for torsion-constraints*/

/*
 * Number of &tor0 entries in TOR_ARG_LIST must equal MAX_TORS...
 * It's a kludge, I know, but you only need to get this line right once.
 */
#define TOR_ARG_LIST        &sInit.tor[0], &sInit.tor[1], &sInit.tor[2], &sInit.tor[3], &sInit.tor[4], &sInit.tor[5], &sInit.tor[6], &sInit.tor[7], &sInit.tor[8], &sInit.tor[9], &sInit.tor[10], &sInit.tor[11], &sInit.tor[12], &sInit.tor[13], &sInit.tor[14], &sInit.tor[15], &sInit.tor[16], &sInit.tor[17], &sInit.tor[18], &sInit.tor[19], &sInit.tor[20], &sInit.tor[21], &sInit.tor[22], &sInit.tor[23], &sInit.tor[24], &sInit.tor[25], &sInit.tor[26], &sInit.tor[27], &sInit.tor[28], &sInit.tor[29], &sInit.tor[30], &sInit.tor[31]


#define ENERGY_CUTOFF                500. /* Arbitrary intermolecular cutoff, above 
                               which intramolecular energy is not calculated. */
#define HI_NRG_JUMP_FACTOR        2. /* Scale up the range of random jumps by this when the last energy was higher than ENERGY_CUTOFF. */

#define NEINT  131072       /* Number of values in internal energy table */
#define NEINT_1 (NEINT - 1) /* index of last entry in internal energy table */
#define A_DIV     100.00    /* Used in distance look-up table. */
#define INV_A_DIV   0.01    /* Used in distance look-up table. */
#define SQA_DIV    32.00    /* Used in square-distance look-up table. */
#define INV_SQA_DIV 0.03125 /* INV_SQA_DIV = NBC2 / NEINT = 1 / SQA_DIV */
#define NBC        64.00    /* Non-bonded cutoff for internal energy calc./Ang*/
#define NBC2     4096.00    /* NBC^2, units: Angstrom^2 */

/*
 * Alternate Scheme:-
 *                        (Uses less memory; for smaller ligands, < 8.0 Ang.)
 *
 * #define NEINT       8192        Number of values in internal energy table
 * #define A_DIV    128.00        Used in look-up table.
 * #define INV_A_DIV  0.0078125        INV_A_DIV = NBC2 / NEINT
 * #define NBC        8.00        Non-bonded cutoff for internal energy calc./Ang
 * #define NBC2      64.00        NBC^2, units: Angstrom^2
 */

#define ATM1                0 /* Index for the first atom in torsion A-B */
#define ATM2                1 /* Index for the second atom in torsion A-B */
#define NUM_ATM_MOVED   2 /* Index for the number of atoms moved by tor. */

#define TINYDELTA 0.001         /* To nudge ligand into grid... */

/* Prevent internal electrostatic energy calculation from blowing up! */

#define RMIN_ELEC 0.1          /* if atoms closer than this in Angstroms, clamp distance in internal elec. calc.*/
#define RMIN_ELEC2  (RMIN_ELEC * RMIN_ELEC) /* if atoms closer than this, clamp square of distance in internal elec. calc.*/

/* Number of cluster-energies per line of output. */

#define OUTNUMCLUST     5  /* Number of cluster-energies per line of output. */

/*
 * Number of columns for torsion profile output.
 * Keep NCOLS less than 72, to ensure whole line
 * fits into 80 columns.
 */

#define NCOLS 64

/* Number of rows for torsion profile output. */

#define NROWS 16

#endif  /* CONSTANTS */


/*----------------------------------------------------------------------------* 
 * Macros,                                                                    * 
 *----------------------------------------------------------------------------*/

#ifndef MACROS
#define MACROS

#define equal(a,b,n)    ( strncmp(a,b,(size_t)(n)) == (int)0 )

#define max(x,y)        ( ((x) > (y)) ? (x) : (y) )
#define min(x,y)        ( ((x) < (y)) ? (x) : (y) )
#define clamp(x,lowerbound)        ( ((x) < (lowerbound)) ? (lowerbound) : (x) )

#define Rad(deg)        ( (deg) * 0.01745329252 )
#define Deg(rad)        ( (rad) * 57.29577951 )

#define ModDeg(a)        fmod((double)(a),(double)360.)
#define ModRad(a)        fmod((double)(a),(double)TWOPI)

#define Wrp(a)            (((a)>180.)? ((a)-360.) :(((a)<-180.)? ((a)+360.) :(a)))
#define WrpDeg(a)   (((a)>180.)? ((a)-360.) :(((a)<-180.)? ((a)+360.) :(a)))
#define WrpRad(a)   (((a)> PI)? ((a)-TWOPI) :(((a)< -PI)?  ((a)+TWOPI) :(a)))
#define WrpModRad(a)   (((a)> PI)? (ModRad(a)-TWOPI) :(((a)< -PI)?  (ModRad(a)+TWOPI) :(a)))

/*
 * #define        RedFac(s0,sN,N)                expf( logf((sN)/(s0)) / ((N)-1))
 * N.B. You must compile with ANSI (-Aa on HPPA) in order to use expf 
 * and logf, otherwise floats are automatically promoted to doubles.
 */
#define        RedFac(s0,sN,N)                exp( log((sN)/(s0)) / ((N)-1))

#define Reqm12( r1, r2 )        ((r1) + (r2))
#define Epsilon12( e1, e2 )        sqrt((double)(e1) * (double)(e2))

#define sq(a)                        ( (a) * (a) )
#define SQ(a)                        ( (a) * (a) )
#define sqhypotenuse(x,y,z)        ( sq(x) + sq(y) + sq(z) )
#define hypotenuse(x,y,z)        (sqrt((double)(sq(x) + sq(y) + sq(z)) )  )
#define hypotenuse_F(x,y,z)        (sqrtf( sq(x) + sq(y) + sq(z) )  )
#define hypotenuse4(x,y,z,w)        (sqrt((double)(sq(x) + sq(y) + sq(z) + sq(w))))
#define hypotenuse4_F(x,y,z,w)        (sqrtf( sq(x) + sq(y) + sq(z) + sq(w) )  )


/* index_to_Ang converts from an array index to a distance */
#define index_to_Ang(i)                ( ( (float) (i) ) * INV_A_DIV )

/* Ang_to_index converts from a distance to an array index */
#define Ang_to_index(r)                ( (int) ( (r) * A_DIV ) )

/* BoundedAng_to_index converts from a distance to an array index, but never returns an index out of bounds. */
#define BoundedAng_to_index(r)                ((((int)((r)*A_DIV)) > NEINT_1) ? NEINT_1 : ((int)((r)*A_DIV))

/* index_to_SqAng converts from an array index to the square of a distance */
#define index_to_SqAng(i)        ( ( (float) (i) ) * INV_SQA_DIV )

/* SqAng_to_index converts from the square of a distance to an array index */
#define SqAng_to_index(r)        ( (int) ( (r) * SQA_DIV ) )

/* BoundedSqAng_to_index converts from the square of a distance to an array index, but never returns an index out of bounds. */
#define BoundedSqAng_to_index(r)        ( (((int)((r)*SQA_DIV)) > NEINT_1) ? NEINT_1 : ((int)((r)*SQA_DIV)) )

/* BoundedNeint never returns an index out of bounds. */
#define BoundedNeint(i)                (((i) > NEINT_1) ? NEINT_1 : (i))

#define sqminlookup(r)           ( (int) ( ( min( r, NBC2 ) ) * SQA_DIV ) )

#define is_out_grid(x,y,z) (((x)<(xlo)) || ((x)>(xhi)) || ((y)<(ylo)) || ((y)>(yhi)) || ((z)<(zlo)) || ((z)>(zhi))) 


/*----------------------------------------------------------------------------* 
 * Random numbers,                                                            * 
 *----------------------------------------------------------------------------*/

#ifndef MAXIRAND
#ifdef  HPPA
#define MAXIRAND        32768
#else
#define MAXIRAND        65536
#endif  /* HPPA */
#endif  /* MAXIRAND */

#define rannum()        (float)(random() % MAXIRAND) / ((float)(MAXIRAND-1))

/* 
 *  local_random is >= 0.0 and <1.0
 */
#ifdef        __convexc__
#define seed_random(t)      srand( (t) )
#define local_random()      ( rand() / 2147483647.0 )
#else
#include <stdlib.h>
#define seed_random(t)      srand48( (FourByteLong)(t) )
#define local_random()      drand48()
#endif  /* !__convexc__ */

#ifdef sgi
    #include <ieeefp.h>
    #define        ISNAN(n)        isnand(n)
#else
    #define        ISNAN(n)        isnan(n)
#endif /* !sgi */

#define random_sign        ( (local_random() < 0.5) ?  (-1.0) : (+1.0) )
#define random_pm1()    ( 2.*local_random() - 1. ) /* ..."pm"="Plus or Minus" */
#define Randpm1                random_pm1()
#define RandpmPI        PI * Randpm1
#define random_pm(x)    ( (x) * Randpm1 )    /* ...random num. between +/- x; */
/* Return a random number in the range a to b...  */
#define random_range(a,b)    ( (a) + (((b)-(a))*local_random()) )

#endif  /* MACROS */


/*----------------------------------------------------------------------------* 
 * Debugging,                                                                 * 
.*----------------------------------------------------------------------------*/

#ifndef DEBUG_STUFF
#define DEBUG_STUFF

/*
 * Uncomment next line, and re-make executable, for general debugging...
 */
/* #define DEBUG        1         / * Switch on debugging output */

#ifdef DEBUG

/*  For debugging torsions... */

#define    PrintDebugTors    (void)fprintf(logFile, "%-2d %-2d %-4s %c %-8d %-9d %-2d %-4d      [%-2d] [ ", i, atomnumber[i],rec4,C,atomlast,nbranches,j, ntor, ntor )
#define    PrintDebugTors2   for(oo=0; oo<3+tlist[ntor][2]; oo++)  (void)fprintf(logFile, "%-2d ", tlist[ ntor ][ oo ] )

#endif /* DEBUG */

#define DPrint(expr)        (void)printf(#expr " = %.4g\n", expr)

#endif /* DEBUG_STUFF */


/*----------------------------------------------------------------------------* 
 * For system timings,                                                        * 
 *----------------------------------------------------------------------------*/

#ifndef sgi
#ifndef CLOCKS_PER_SEC
#define CLOCKS_PER_SEC 60
#endif /* CLOCKS_PER_SEC */
#endif /* sgi */

/*
 * const int and const float are allowed by the SGI "CC" compiler
 */

#ifdef sgi
#define CONST_INT const int
#define CONST_FLOAT const float
#else /* Not on an SGI */
#define CONST_INT int
#define CONST_FLOAT float
#endif /*sgi*/


/*----------------------------------------------------------------------------* 
 * End of file                                                                * 
 *----------------------------------------------------------------------------*/