Hydrogen Bonds

The hydrogen bonds node creates bonds between Hydrogen and Oxygen / Carbon / Nitrogen atoms.

The cutoffMin and cutoff values specifies the minimum and maximum bond lengths respectively. A minimum value is required when bonds already exist between atoms of the same residue.

The graph setup is as follows.

Source code (Error checking omitted):

#include <iostream>
#include <cmath>
#include <vector>

//@in
double cutoff = 0;
//@in
double cutoffMin = 0;
//@in pcnt 3
double* positions = 0;
//@in pcnt
short* types = 0;

//@out ccnt 2
int* bonds = 0;
std::vector<int> vcons;

//@var
int pcnt = 2;
//@var
int ccnt = 0;

#define ISA(s, c) (s == *((short*)c))

//@entry
void Execute() {
    const double cut2 = cutoff*cutoff;
    const double cut2m = cutoffMin*cutoffMin;
    vcons.clear();
    for (int m = 0; m < pcnt; m++) {
        if (!ISA(types[m], "H")) continue;
        double* pm = positions + m * 3;
        for (int n = 0; n < pcnt; n++) {
            if (!ISA(types[n], "O")) continue;
            double* pn = positions + n * 3;
            double dx = pn[0]-pm[0];
            double dy = pn[1]-pm[1];
            double dz = pn[2]-pm[2];
            if (fabsf(dx) < cutoff && fabsf(dy) < cutoff && fabsf(dz) < cutoff) {
                double d = (dx*dx+dy*dy+dz*dz);
                if (d < cut2 && d > cut2m) {
                    vcons.push_back(m);
                    vcons.push_back(n);
                }
            }
        }
    }
    bonds = &vcons[0];
    ccnt = vcons.size() / 2;
}