Check for hydrogen bonds

[jhrmnn]

The original matlab code:

% add hydrogen bonds to bond matrix. 12/04/09

function [bond,C] = addhydrogenbonds(bond,C,R,atoms,allowed)
    H = find(atoms==1); % H atoms
    O = find(atoms==8); % O atoms
    [Oi,Hi] = find(~C(O,H) & R(O,H)<2.0);
                             % find O-H shorted than 2 angstroms
    if isempty(Hi), return, end
    H = H(Hi); % bonded H atoms
    O = O(Oi); % bonded H atoms
    for i = 1:length(H)
        if any(atoms(bond(H(i),:))==8) % if H covalently bonded to O
            bond(O(i),H(i)) = true; % make hydrogen bond
            bond(H(i),O(i)) = true;
        end
    end
    bond = onlyallowed(bond,allowed,atoms,R);
    C = conn(bond);
end