void test_orientation(long i, long j, long **seidx, char **AtomName,
double **xyz, long *nn1, long *nn2)
{
long k, k1, n1=0, n2=0;
double dx[4];
for(k=seidx[i][1]; k<=seidx[i][2]; k++){
if(!strcmp(AtomName[k], " O2'")){
for(k1=seidx[j][1]; k1<=seidx[j][2]; k1++){
if(AtomName[k1][1] !='N' && AtomName[k1][1] !='O') continue;
dx[1] = xyz[k][1]-xyz[k1][1];
dx[2] = xyz[k][2]-xyz[k1][2];
dx[3] = xyz[k][3]-xyz[k1][3];
if(!strcmp(AtomName[k1], " O2'")){
if(veclen(dx)<3.8){
n1++;
}
}
if((AtomName[k1][1] =='N' || AtomName[k1][1] =='O')&&
AtomName[k1][3] !='\'' ) {
if(veclen(dx)<3.8){
n2++;
}
}
}
/* printf("atom1-2 = %s-%s %d %d %d %d\n", AtomName[k],AtomName[k1],n1,n2, i, j);*/
break;
}
}
*nn1=n1;
*nn2=n2;
}
void BumpMapper::input( const Data &d )
{
int w = d.width(), h = d.height();
int lz = 260;
int a, b;
double nx, ny, nz, nl;
double dx, dy, dz, dl, dot;
Data out( w, h );
if( smooth == 0 )
smooth = 1;
for( int y=1; y<h-1; y++ ) {
for( int x=1; x<w-1; x++ ) {
// Calculate the the normal vector..
a = d.value( x, y+1 ) - d.value( x, y-1 );
b = d.value( x+1, y ) - d.value( x-1, y );
nx = -2*b;
ny = -2*a;
nz = smooth;
nl = veclen( nx, ny, nz );
nx /= nl;
ny /= nl;
nz /= nl;
dx = lp.x()-x;
dy = lp.y()-y;
dz = lz-d.value( x, y );
dl = veclen( dx, dy, dz );
if( dl>rad ) {
out.setValue( x, y, 0 );
continue;
}
dx /= dl;
dy /= dl;
dz /= dl;
dot = dx*nx + dy*ny + dz*nz;
dl = (rad-dl)/(float)rad;
if( dot<0 || dl<0 ) {
out.setValue( x, y, 0 );
continue;
}
out.setValue( x, y, (int)(dl*dot*255) );
}
}
qApp->processEvents();
emit output( out );
}
/*--
Cat lbxgl;Entity;Query
Form
double LBXGL_Entity_GetRadius(LBXGL_Entity *ent);
Description
Get the radius associated with an entity.
The radius is computed via the bounding boxes, and will fully \
enclose the box.
--*/
double LBXGL_Entity_GetRadius(LBXGL_Entity *ent)
{
double *cmins, *cmaxs;
double crad;
crad=0;
cmins=LBXGL_Entity_GetProperty(ent, "mins");
cmaxs=LBXGL_Entity_GetProperty(ent, "maxs");
if(cmins)if(veclen(cmins)>crad)crad=veclen(cmins);
if(cmaxs)if(veclen(cmaxs)>crad)crad=veclen(cmaxs);
return(crad);
}
double torsion(double **d)
/* get torsion angle a-b-c-d in degrees */
{
double ang_deg, dij;
double **vec3;
long i, j;
vec3 = dmatrix(1, 3, 1, 3);
for (i = 1; i <= 3; i++) {
for (j = 1; j <= 3; j++)
if (i == 1)
vec3[i][j] = d[i][j] - d[i + 1][j]; /* b-->a */
else
vec3[i][j] = d[i + 1][j] - d[i][j];
dij = veclen(vec3[i]);
if (dij > BOND_UPPER_LIMIT) {
free_dmatrix(vec3, 1, 3, 1, 3);
return EMPTY_NUMBER;
}
}
ang_deg = vec_ang(vec3[1], vec3[3], vec3[2]);
free_dmatrix(vec3, 1, 3, 1, 3);
return ang_deg;
}
static inline double vecdist(double *avec, double *bvec)
{
double cvec[3];
cvec[0]=bvec[0]-avec[0];
cvec[1]=bvec[1]-avec[1];
cvec[2]=bvec[2]-avec[2];
return(veclen(cvec));
}
// calculate a normalized vector pointint from one vector to another
void pointat(const GLfloat *from, const GLfloat *to, float *result){
int i=0;
float dist;
assert(NULL != from);
assert(NULL != to);
assert(NULL != result);
vecdiff(from,to,result);
dist = veclen(result);
assert(dist > 0);
for(;i<3;i++){
result[i] /= dist;
}
}
/*============================================================================
* Test routines.
*==========================================================================*/
int main(int argc, char **argv)
{
/*=======================================================================
* Vector operation tests
*=====================================================================*/
{ /* vecdot */
float X[3] = {1.0, 2.0, 3.0};
float Y[3] = {3.0, 2.0, 1.0};
assert(vecdot(X, Y, 3) == 10.0);
}
{ /* vecdot */
float X[3] = {10.0};
float Y[3] = {13.0};
assert(vecdot(X, Y, 1) == 130.0);
}
{ /* veclen */
float X[3] = {3.0, 4.0};
assert(veclen(X, 2) == 5.0);
}
{ /* vecmul */
float X[5] = {1.0, 2.0, 3.0, 4.0, 5.0};
float Y[5] = {2.0, 4.0, 6.0, 8.0, 10.0};
vecmul(X, 2, 5, X);
assert(vecveceq(X, Y, 5));
}
{ /* vecdiv */
float X[5] = {2.0, 4.0, 6.0, 8.0, 10.0};
float Y[5] = {1.0, 2.0, 3.0, 4.0, 5.0};
vecdiv(X, 2, 5, X);
assert(vecveceq(X, Y, 5));
}
{ /* vecvecsub */
float X[5] = {1.0, 2.0, 3.0, 4.0, 5.0};
float Y[5] = {2.0, 4.0, 6.0, 8.0, 10.0};
float Z[5] = {-1.0, -2.0, -3.0, -4.0, -5.0};
vecvecsub(X, Y, 5, X);
assert(vecveceq(X, Z, 5));
}
{ /* vecvecadd */
float X[5] = {1.0, 2.0, 3.0, 4.0, 5.0};
float Y[5] = {2.0, 4.0, 6.0, 8.0, 10.0};
float Z[5] = {3.0, 6.0, 9.0, 12.0, 15.0};
vecvecadd(X, Y, 5, X);
assert(vecveceq(X, Z, 5));
}
return 0;
}
void do_eigen_projections(int nev, float *M,
float **models, float *mean, int num_models,
eigen_t *eigen, int dim)
{
int i, m;
struct
{
float *proj;
float best_dot;
float best_dot_index;
char symbol;
} proj_model[2];
assert(models != NULL);
assert(mean != NULL);
assert(eigen != NULL);
assert(dim > 0);
assert(num_models > 0);
assert(0 < nev && nev <= dim);
proj_model[0].proj = (float *)malloc(dim * sizeof(float));
proj_model[1].proj = (float *)malloc(dim * sizeof(float));
proj_model[0].symbol = '+';
proj_model[1].symbol = '-';
if (!opt_multi_out) fprintf(out, "#BEGIN ENSEM\n");
for (i=0; i < nev; i++)
{
/*================================================================
* Find the models that have the largest and smallest projections
* onto the current eigenvector.
*==============================================================*/
proj_model[0].best_dot = 0;
proj_model[0].best_dot_index = -1;
proj_model[1].best_dot = 0;
proj_model[1].best_dot_index = -1;
for (m=0; m < num_models; m++)
{
float dot = vecdot(models[m], eigen[i].rvec, dim);
if (dot >= 0 && dot >= proj_model[0].best_dot)
{
proj_model[0].best_dot = dot;
proj_model[0].best_dot_index = m;
vecmul(eigen[i].rvec, dot, dim, proj_model[0].proj);
}
if (dot <= 0 && dot <= proj_model[1].best_dot)
{
proj_model[1].best_dot = dot;
proj_model[1].best_dot_index = m;
vecmul(eigen[i].rvec, dot, dim, proj_model[1].proj);
}
}
if (opt_interp_proj)
{
if (proj_model[0].best_dot_index != -1
&& proj_model[1].best_dot_index != -1)
{
int j;
float *newp = (float *)malloc(dim * sizeof(float));
float *step = (float *)malloc(dim * sizeof(float));
#define NSTEPS 20
#define OVERSHOOT 20
vecvecsub(proj_model[1].proj, proj_model[0].proj, dim, step);
vecdiv(step, NSTEPS, dim, step);
for (j=0; j < NSTEPS+OVERSHOOT; j++)
{
vecmul(step, j, dim, newp);
vecvecadd(proj_model[0].proj, newp, dim, newp);
undo_scale(newp, dim, M);
vecvecadd(newp, mean, dim, newp);
multi_out_write_ev_model((i+1)*100 + j, 'p', 0, 0,
newp, dim);
}
free(newp);
free(step);
#undef NSTEPS
#undef OVERSHOOT
}
}
else
{
/*================================================================
* Write out the new models
*==============================================================*/
for (m=0; m < 2; m++)
{
if (proj_model[m].best_dot_index != -1)
{
float proj_len_before_scale
= veclen(proj_model[m].proj, dim);
undo_scale(proj_model[m].proj, dim, M);
/* add back mean */
vecvecadd(proj_model[m].proj,mean, dim, proj_model[m].proj);
multi_out_write_ev_model(i,
proj_model[m].symbol,
proj_len_before_scale,
proj_model[m].best_dot,
proj_model[m].proj, dim);
}
}
}
}
if (!opt_multi_out)
fprintf(out, "#END ENSEM\n");
free(proj_model[0].proj);
free(proj_model[1].proj);
}