Logo Search packages:      
Sourcecode: pymol version File versions  Download package


A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program
C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice.
F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information. 
H* -------------------------------------------------------------------
I* Additional authors of this source file include:
Z* -------------------------------------------------------------------
#ifndef _H_Vector
#define _H_Vector



/* NOTE: Matrices are assumed to be row-major (C-like not
 * OpenGL-like) unless explictly labeled as per the following
 * conventions:
 * row-major:    33f, 33d, 44f, 44d, R33f, R33d, R44f, R44d
 * column-major: C33f, C33d, C44f, C44d

#define cPI            3.14159265358979323846   /* pi */

typedef float Vector3f[3];      /* for local vars only - use float* for parameters */
typedef int Vector3i[3];

typedef float Matrix33f[3][3];
typedef double Matrix33d[3][3];
typedef float Matrix53f[5][3];
typedef double Matrix53d[5][3];

unsigned int optimizer_workaround1u(unsigned int value);

float get_random0to1f(void);

float deg_to_rad(float angle);
float rad_to_deg(float angle);

double slow_sqrt1f(float f);
double slow_sqrt1d(double d);

void slow_normalize3f(float *v1);
void normalize23f(float *v1, float *v2);
void normalize3d(double *v1);

void clamp3f(float *v1);
void get_divergent3f(float *src, float *dst);
void get_random3f(float *x);
void scatter3f(float *v, float weight);
void wiggle3f(float *v, float *p, float *s);
void extrapolate3f(float *v1, float *unit, float *result);

void mix3f(float *v1, float *v2, float fxn, float *v3);
void mix3d(double *v1, double *v2, double fxn, double *v3);

void get_system3f(float *x, float *y, float *z);        /* make random system */
void get_system1f3f(float *x, float *y, float *z);      /* make system in direction of x */
void get_system2f3f(float *x, float *y, float *z);      /* make system in direction of x, perp to x,y */

double dot_product3d(double *v1, double *v2);
float slow_project3f(float *v1, float *v2, float *proj);
void slow_remove_component3f(float *v1, float *unit, float *result);
void remove_component3d(double *v1, double *unit, double *result);
void cross_product3d(double *v1, double *v2, double *cross);
void scale3d(double *v1, double v0, double *v2);
void add3d(double *v1, double *v0, double *v2);

double distance_line2point3f(float *base, float *normal, float *point,
                             float *alongNormalSq);
double distance_halfline2point3f(float *base, float *normal, float *point,
                                 float *alongNormalSq);

float slow_diffsq3f(float *v1, float *v2);
double slow_diff3f(float *v1, float *v2);
int slow_within3f(float *v1, float *v2, float dist);
int slow_within3fsq(float *v1, float *v2, float dist, float dist2);
int slow_within3fret(float *v1, float *v2, float cutoff, float cutoff2, float *diff,
                     float *dist);

int equal3f(float *v1, float *v2);

int pymol_roundf(float f);

float get_angle3f(float *v1, float *v2);
float get_dihedral3f(float *v0, float *v1, float *v2, float *v3);
double length3d(double *v1);

void min3f(float *v1, float *v2, float *v3);
void max3f(float *v1, float *v2, float *v3);

void dump3i(int *v, char *prefix);
void dump3f(float *v, char *prefix);
void dump3d(double *v, char *prefix);
void dump4f(float *v, char *prefix);
void dump33f(float *m, char *prefix);
void dump33d(double *m, char *prefix);
void dump44f(float *m, char *prefix);
void dump44d(double *m, char *prefix);

void copy44f(float *src, float *dst);
void copy44d(double *src, double *dst);

void identity33f(float *m1);
void identity33d(double *m);
void identity44f(float *m1);
void identity44d(double *m1);

void copy44f44f(float *src, float *dst);
void copy44d44f(double *src, float *dst);
void copy44f44d(float *src, double *dst);

void copy44d33f(double *src, float *dst);
void copy44f33f(float *src, float *dst);
void copy33f44d(float *src, double *dst);
void copy33f44f(float *src, float *dst);
void copy3d3f(double *v1, float *v2);
void copy3f3d(float *v1, double *v2);

/* in the following matrix multiplies and transformations:
   the last two matrices can be the same matrix! */

void transpose33f33f(float *m1, float *m2);
void transpose33d33d(double *m1, double *m2);
void transpose44f44f(float *m1, float *m2);
void transpose44d44d(double *m1, double *m2);

void transform33f3f(float *m1, float *m2, float *m3);
void transform33Tf3f(float *m1, float *m2, float *m3);  /* uses transpose */

void transform44f3f(float *m1, float *m2, float *m3);
void transform44f4f(float *m1, float *m2, float *m3);

void transform44d3f(double *m1, float *m2, float *m3);
void transform44d3d(double *m1, double *m2, double *m3);
void inverse_transformC44f3f(float *m1, float *m2, float *m3);
void inverse_transform44f3f(float *m1, float *m2, float *m3);
void inverse_transform44d3f(double *m1, float *m2, float *m3);
void inverse_transform44d3d(double *m1, double *m2, double *m3);
void transform44f3fas33f3f(float *m1, float *m2, float *m3);
void transform44d3fas33d3f(double *m1, float *m2, float *m3);

void multiply33f33f(float *m1, float *m2, float *m3);
void multiply33d33d(double *m1, double *m2, double *m3);

/* as matrix types */

void matrix_transform33f3f(Matrix33f m1, float *v1, float *v2);
void matrix_inverse_transform33f3f(Matrix33f m1, float *v1, float *v2);

void rotation_to_matrix33f(float *axis, float angle, Matrix33f mat);
void matrix_multiply33f33f(Matrix33f m1, Matrix33f m2, Matrix33f m3);
void matrix_multiply33d33d(Matrix33d m1, Matrix33d m2, Matrix33d m3);

/* A 4x4 TTT matrix is really a 3x3 rotation matrix with two translation vectors:
   (1) a pre-translation stored in forth row, first three columns.
   (2) and a post-translation stored in forth column, first three rows.
   There are certain cases where this representation is more convenient.
void combineTTT44f44f(float *m1, float *m2, float *m3);
void transformTTT44f3f(float *m1, float *m2, float *m3);
void transform_normalTTT44f3f(float *m1, float *m2, float *m3);
void initializeTTT44f(float *m);

void multiply44d44d44d(double *left, double *right, double *product);
void left_multiply44d44d(double *left, double *right);
void right_multiply44d44d(double *left, double *right);

void multiply44f44f44f(float *left, float *right, float *product);
void left_multiply44f44f(float *left, float *right);
void right_multiply44f44f(float *left, float *right);

void reorient44d(double *matrix);

void recondition33d(double *matrix);
void recondition44d(double *matrix);

/* invert a 4x4 homogenous that contains just rotation & tranlation
  (e.g. no scaling & fourth row is 0,0,0,1) */
void invert_special44d44d(double *original, double *inv);
void invert_special44f44f(float *original, float *inv);

void invert_rotation_only44d44d(double *original, double *inv);

void convertTTTfR44d(float *ttt, double *homo);
void convertTTTfR44f(float *ttt, float *homo);
void convertR44dTTTf(double *homo, float *ttt);
void convert44d44f(double *dbl, float *flt);
void convert44f44d(float *flt, double *dbl);

void get_rotation_about3f3fTTTf(float angle, float *dir, float *origin, float *ttt);

/* end revised matrix routines */



void rotation_matrix3f(float angle, float x, float y, float z, float *m);

typedef float *oMatrix5f[5];    /* PHASE THESE OUT! - THEY CAUSE PROBLEMS! */

typedef float *oMatrix3f[3];

typedef float *oMatrix3d[3];

double matdiffsq(float *v1, oMatrix5f m, float *v2);

/*void matcopy ( oMatrix5f to, oMatrix5f from );
  void mattran ( oMatrix5f nm, oMatrix5f om, int axis, float dist );
  void matrot ( oMatrix5f nm, oMatrix5f om, int axis, float angle );*/

void matrix_to_rotation(Matrix53f rot, float *axis, float *angle);
void rotation_to_matrix(Matrix53f rot, float *axis, float angle);

void transform3d3f(oMatrix3d m1, float *v1, float *v2);
void transform33d3f(Matrix33d m1, float *v1, float *v2);
void transform5f3f(oMatrix5f m, float *v1, float *v2);

/* macros */



float dot_product3f(float *v1, float *v2);
void invert3f(float *v);
void invert3f3f(float *v1, float *v2);
void scale3f(float *v1, float v0, float *v2);
void copy3f(float *src, float *dst);
void copy3d(double *src, double *dst);
void copy4f(float *src, float *dst);
void add3f(float *v1, float *v2, float *sum);
void subtract3f(float *v1, float *v2, float *v3);
double lengthsq3f(float *v1);
double length3f(float *v1);
void cross_product3f(float *v1, float *v2, float *cross);
void average3f(float *v1, float *v2, float *avg);
void zero3f(float *v1)
     void ones3f(float *v1);
     void set3f(float *v1, float x, float y, float z);
     void swap1f(float *f, float *g);


#define set3f(v1,x,y,z) { (v1)[0]=(x);(v1)[1]=(y);(v1)[2]=(z); }
#define zero3f(v1) { (v1)[0]=0.0;(v1)[1]=0.0;(v1)[2]=0.0; }
#define ones3f(v1) { (v1)[0]=1.0F;(v1)[1]=1.0F;(v1)[2]=1.0F; }
#define dot_product3f(v1,v2) ((v1)[0]*(v2)[0] + (v1)[1]*(v2)[1] + (v1)[2]*(v2)[2])
#define invert3f(v) {(v)[0]=-(v)[0]; (v)[1]=-(v)[1]; (v)[2]=-(v)[2];}
#define invert3f3f(v1,v2) {(v2)[0]=-(v1)[0]; (v2)[1]=-(v1)[1]; (v2)[2]=-(v1)[2];}
#define scale3f(v1,v0,v2) {(v2)[0]=(v1)[0]*(v0); (v2)[1]=(v1)[1]*(v0); (v2)[2]=(v1)[2]*(v0);}
#define copy3f(v1,v2) {(v2)[0]=(v1)[0]; (v2)[1]=(v1)[1]; (v2)[2]=(v1)[2];}
#define copy3d(v1,v2) {(v2)[0]=(v1)[0]; (v2)[1]=(v1)[1]; (v2)[2]=(v1)[2];}
#define copy4f(v1,v2) {(v2)[0]=(v1)[0]; (v2)[1]=(v1)[1]; (v2)[2]=(v1)[2]; (v2)[3]=(v1)[3];}
#define add3f(v1,v2,v3) {(v3)[0]=(v1)[0]+(v2)[0]; (v3)[1]=(v1)[1]+(v2)[1]; (v3)[2]=(v1)[2]+(v2)[2];}
#define subtract3f(v1,v2,v3) {(v3)[0]=(v1)[0]-(v2)[0]; (v3)[1]=(v1)[1]-(v2)[1]; (v3)[2]=(v1)[2]-(v2)[2];}
#define lengthsq3f(v1) (((v1)[0]*(v1)[0]) + ((v1)[1]*(v1)[1]) + ((v1)[2]*(v1)[2]))
#define length3f(v1) (sqrt1f(((v1)[0]*(v1)[0]) + ((v1)[1]*(v1)[1]) + ((v1)[2]*(v1)[2])))
#define average3f(v1,v2,avg) { \
  (avg)[0] = ((v1)[0]+(v2)[0])/2; \
  (avg)[1] = ((v1)[1]+(v2)[1])/2; \
  (avg)[2] = ((v1)[2]+(v2)[2])/2; \
#define cross_product3f(v1,v2,cross) { \
  (cross)[0] = ((v1)[1]*(v2)[2]) - ((v1)[2]*(v2)[1]); \
  (cross)[1] = ((v1)[2]*(v2)[0]) - ((v1)[0]*(v2)[2]); \
  (cross)[2] = ((v1)[0]*(v2)[1]) - ((v1)[1]*(v2)[0]); \
#define swap1f(f,g) { float h;h=*(f);*(f)=*(g);*(g)=h; }


static const float _0f_inline = 0.0F;
static const double _0d_inline = 0.0;
static const float _1f_inline = 1.0F;
static const double _1d_inline = 1.0;
static const float R_SMALL_inline = 0.000000001F;
static const double R_SMALLd_inline = 0.000000001;

#define normalize3f inline_normalize3f
#define sqrt1f inline_sqrt1f
#define sqrt1d inline_sqrt1d
#define diff3f inline_diff3f
#define diffsq3f inline_diffsq3f
#define within3f inline_within3f
#define within3fsq inline_within3fsq
#define within3fret inline_within3fret
#define remove_component3f inline_remove_component3f
#define project3f inline_project3f

__inline__ static double inline_sqrt1f(float f)
{                               /* no good as a macro because f is used twice */
  if(f > _0f_inline)
    return (sqrt(f));
    return (_0d_inline);

__inline__ static double inline_sqrt1d(double f)
{                               /* no good as a macro because f is used twice */
  if(f > _0d_inline)
    return (sqrt(f));
    return (_0d_inline);

__inline__ static void inline_normalize3f(float *v1)
  register double vlen = length3f(v1);
  if(vlen > R_SMALLd_inline) {
    register float inV = (float) (_1d_inline / vlen);
    v1[0] *= inV;
    v1[1] *= inV;
    v1[2] *= inV;
  } else {
    v1[0] = v1[1] = v1[2] = _0f_inline;

__inline__ static double inline_diff3f(float *v1, float *v2)
  register float dx, dy, dz;
  dx = (v1[0] - v2[0]);
  dy = (v1[1] - v2[1]);
  dz = (v1[2] - v2[2]);
  return (sqrt1d(dx * dx + dy * dy + dz * dz));

__inline__ static float inline_diffsq3f(float *v1, float *v2)
  register float dx, dy, dz;
  dx = (v1[0] - v2[0]);
  dy = (v1[1] - v2[1]);
  dx = dx * dx;
  dz = (v1[2] - v2[2]);
  dy = dy * dy;
  return (dz * dz + (dx + dy));

__inline__ static int inline_within3f(float *v1, float *v2, float dist)
  register float dx, dy, dz, dist2;
  dx = (float) fabs(v1[0] - v2[0]);
  dy = (float) fabs(v1[1] - v2[1]);
  if(dx > dist)
    return (0);
  dz = (float) fabs(v1[2] - v2[2]);
  dx = dx * dx;
  if(dy > dist)
    return (0);
  dy = dy * dy;
  dist2 = dist * dist;
  if(dz > dist)
    return (0);
  return (((dx + dy) + dz * dz) <= dist2);

__inline__ static int inline_within3fsq(float *v1, float *v2, float dist, float dist2)
  /* manually optimized to take advantage of parallel execution units */
  register float dx, dy, dz;
  dx = v1[0] - v2[0];
  dy = v1[1] - v2[1];
  dx = (float) fabs(dx);
  dy = (float) fabs(dy);
  if(dx > dist)
    return (0);
  dz = v1[2] - v2[2];
  dx = dx * dx;
  if(dy > dist)
    return (0);
  dz = (float) fabs(dz);
  dy = dy * dy;
  if(dz > dist)
    return (0);
  dx = dx + dy;
  dz = dz * dz;
  if(dx > dist2)
    return (0);
  return ((dx + dz) <= (dist2));

__inline__ static int inline_within3fret(float *v1, float *v2, float cutoff,
                                         float cutoff2, float *diff, float *dist)
  register float dx, dy, dz, dist2;
  dx = (float) fabs((diff[0] = v1[0] - v2[0]));
  dy = (float) fabs((diff[1] = v1[1] - v2[1]));
  if(dx > cutoff)
    return 0;
  dz = (float) fabs((diff[2] = v1[2] - v2[2]));
  dx = dx * dx;
  if(dy > cutoff)
    return 0;
  dy = dy * dy;
  if(dz > cutoff)
    return 0;
  if((dist2 = ((dx + dy) + dz * dz)) > cutoff2)
    return 0;
  *dist = (float) sqrt1f(dist2);
  return 1;

__inline__ static void inline_remove_component3f(float *v1, float *unit, float *result)
  register float dot;

  dot = v1[0] * unit[0] + v1[1] * unit[1] + v1[2] * unit[2];
  result[0] = v1[0] - unit[0] * dot;
  result[1] = v1[1] - unit[1] * dot;
  result[2] = v1[2] - unit[2] * dot;

__inline__ static float inline_project3f(float *v1, float *v2, float *proj)
  register float dot;

  dot = v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2];
  proj[0] = v2[0] * dot;
  proj[1] = v2[1] * dot;
  proj[2] = v2[2] * dot;

  return (dot);


#define normalize3f slow_normalize3f
#define sqrt1f slow_sqrt1f
#define sqrt1d slow_sqrt1d
#define diff3f slow_diff3f
#define diffsq3f slow_diffsq3f
#define within3f slow_within3f
#define within3fsq slow_within3fsq
#define within3fret slow_within3fret
#define project3f slow_project3f
#define remove_component3f slow_remove_component3f



Generated by  Doxygen 1.6.0   Back to index