void sphereVolSample(vector<float>& cen, float rad, vector<float>& sample) {
float dx, dy, dz;
while(1) {
dx = (ran01() * 2 - 1) * rad;
dy = (ran01() * 2 - 1) * rad;
dz = rad*rad - dx*dx - dy*dy;
if(dz < 0) continue;
dz = sqrt(dz);
if(ran01() > 0.5) dz *= -1;
sample[0] = cen[0] + dx;
sample[1] = cen[1] + dy;
sample[2] = cen[2] + dz;
return;
}
}
// generates a random normalized vector
// is uniformly distributed over sphere surface
// taken from sphere point picking in mathworld
void randomNormalVector(vector<float> & v) {
// while(1) {
// v[0] = -1. + 2.* ran01();
// v[1] = -1. + 2.* ran01();
// v[2] = 1 - v[0]*v[0] + v[1]*v[1];
// if(v[2] < 0) continue;
// v[2] = sqrt(v[2]);
// return;
// }
float theta = 2. * M_PI * ran01();
float phi = acos(2. * ran01() - 1);
v[0] = sin(phi) * cos(theta);
v[1] = sin(phi) * sin(theta);
v[2] = cos(phi);
}
long int roulette(double* elments, long element_size)
{
int i=0;
double sum=0.0;
double rnd=0.0;
double* prob=malloc( element_size*sizeof(double) );
rnd = ran01( &seed );
for(i=0;i<element_size; i++)
{
sum += elments[i];
}
for(i=0;i<element_size; i++)
{
prob[i]=elments[i]/sum;
}
i=0;
sum=prob[i];
while(sum<=rnd)
{
i++;
sum+=prob[i];
}
free(prob);
return i;
}
// given a vector X, find normal vectors Y,Z such that X,Y,Z are mutually perpendicular
void findYZgivenX( vector<float> & givenX, vector<float> & Y, vector<float> & Z ) {
vector<float> X(3);
normalize_point(X, givenX);
int a=0, b=1, c=2;
if( fabs(X[a]) < 1e-2 ) { a=1; b=2; c=0; }
if( fabs(X[a]) < 1e-2 ) { a=2; b=0; c=1; }
assert ( fabs(X[a]) > 1e-2 );
Y[b] = -1. + (2.*ran01()); Y[c] = -1. + (2.*ran01());
//cout << "rands " << Y[b] << "\nrands " << Y[c] << endl;
Y[a] = -1 * (X[b]*Y[b] + X[c]*Y[c]) / X[a];
normalize_point(Y, Y);
cross_product(Z, X, Y);
normalize_point(Z, Z);
}
int rnd(int low,int high)
/* Pick a random integer between low and high */
{
int i;
if(low >= high)
i = low;
else
{
i = (int)((ran01(&seed) * (high - low + 1)) + low);
if(i > high) i = high;
}
return(i);
}
int find_var_valueno(int vno)
{
double q , sum ,ranno;
int valueno, nmax;
find_prob(vno);
q=ran01(&seed);
ranno=ran01(&seed);
valueno = find_no_of_max( vno, &nmax );
/*printf(" for %d vno, q= %f ,ranno= %f , nmax =%d valueno= %d \n",vno,q,ranno,nmax,valueno);*/
if((q<q0) && (nmax==1))
{
#if (localupdate==1)
(var[vno]).trail[valueno] *= (1-gamma);
#endif
return valueno;
}
else
{
sum=0.0;
for(valueno=0; valueno -1 < var[vno].nvalues && sum < ranno ; valueno++)
{
sum += (var[vno]).prob[valueno] ;
}//endfo valueno loop
#if (localupdate==1)
if(valueno > 0 && valueno -1 < var[vno].nvalues)
{
(var[vno]).trail[valueno-1] *= (1-rho);
}
#endif
return (valueno-1);
}//end of else
}//end of find valueno
int sample_from_probs(double *probs, int num_elements){
double sum=0;
int i;
for(i=0; i<num_elements; i++) sum+= probs[i];
double randnum = ran01(&seed) * sum;
sum = 0.0;
for(i=0; i<num_elements; i++){
sum+= probs[i];
if( randnum <= sum ) break;
}
if( i>= num_elements ){
printf("Error in sampling, didn't sample any of the values, sum=%lf\n, randnum=%lf", sum, randnum);
exit(-1);
}
return i;
}
// if fwd, C,N,CA are C,N,CA, else assumed to be N,C,CA
void InformedPhipsiSampler::sample(
vector<float>& curC, vector<float>& curN, vector<float>& curCA,
float & phi, float & psi, float & omega, float & r, float & a, float & t) {
float d0 = calcDist(target, curCA);
float cisdist = 2.8, transdist = 3.81;
bool cis = false, trans = false;
if(cisdist > d0 - targetTol && cisdist < d0 + targetTol) cis = true;
if(transdist > d0 - targetTol && transdist < d0 + targetTol) trans = true;
if(cis && trans) { // if both cis and trans are possible, choose one
if(ran01() > 0.95) trans = false;
} else if(!cis && !trans) {
cout << "target unreachable "
<<curCA[0]<<" "<<curCA[1]<<" "<<curCA[2] << " : " << d0 <<" : "<< targetTol <<" : "<< target[0]<<" "<<target[1]<<" "<<target[2]
<< endl;
exit(0);
}
// now either cis or trans is true
float interCA;
if(cis) { omega = 0; interCA = cisdist; }
if(trans) { omega = -180; interCA = transdist; }
phi = -999; psi = -999;
// find a,t which take u into restraint sphere with this interCA
vector<float> tar(3,0), noi(3,0);
while(1) {
// add some noise to target, proportional to noise
randomNormalVector(noi);
linear_combination(tar, 1, target, targetTol*ran01(), noi);
// for this interCA, find a,t that takes you closest to target
r = calcDist(curCA, tar);
a = calcAngle(curN, curCA, tar);
t = calcDihed(curC, curN, curCA, tar);
find4thPoint(tar, curC, curN, curCA, interCA, a, t);
if( calcDist(target, tar) <= targetTol ) break;
}
// return a phi-psi value for this a,t if available
if(fwd) {
RATdata & ratdata = RATdata::fwdinstance(RATdataPath.c_str());
vector<PSO>::iterator bi, ei;
ratdata.range(resn, interCA, a, t, bi, ei);
int rs = ei - bi;
assert(rs >= 0);
if(rs == 0) { return; }
int incr = (int) floor ( (0.+rs) * ran01() );
bi += incr;
phi = bi->r; psi = bi->a; omega = bi->t;
} else {
RATdata & ratdata = RATdata::bwdinstance(RATdataPath.c_str());
vector<PSO>::iterator bi, ei;
ratdata.range(resn, interCA, a, t, bi, ei);
int rs = ei - bi;
assert(rs >= 0);
if(rs == 0) { return; }
int incr = (int) floor ( (0.+rs) * ran01() );
bi += incr;
psi = bi->r; phi = bi->a; omega = bi->t;
}
//cout << phi <<" "<< psi <<" "<< omega << " shd take u from ("<< curCA[0]<<" "<< curCA[1]<<" "<< curCA[2] <<" ";
//vector<float> exppt(3,0);
//find4thPoint(exppt, curC, curN, curCA, interCA, a, t);
//cout << ") to ("<< exppt[0]<<" "<< exppt[1]<<" "<< exppt[2] <<") " << endl;;
}
int FragSampler::sample(vector<vector<float> > & pts) {
int myrand = (int) floor ( pts.size() * ran01() );
pts = samples[myrand];
}
double rndreal(double lo ,double hi)
/* real random number between specified limits */
{
return((ran01(&seed) * (hi - lo)) + lo);
}