riding_h.hpp

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// Copyright 2018-2022 Global Phasing Ltd.
//
// Place hydrogens according to bond lengths and angles from monomer library.
 
#ifndef GEMMI_RIDING_H_HPP_
#define GEMMI_RIDING_H_HPP_
 
#include <cmath>         // for isnan
#include "topo.hpp"      // for Topo
 
namespace gemmi {
 
GEMMI_DLL void place_hydrogens_on_all_atoms(Topo& topo);
 
inline void adjust_hydrogen_distances(Topo& topo, Restraints::DistanceOf of,
                                      double default_scale=1.) {
  for (const Topo::Bond& t : topo.bonds) {
    assert(t.atoms[0] != nullptr && t.atoms[1] != nullptr);
    if (t.atoms[0]->is_hydrogen() || t.atoms[1]->is_hydrogen()) {
      Position u = t.atoms[1]->pos - t.atoms[0]->pos;
      double scale = t.restr->distance(of) / u.length();
      if (std::isnan(scale))
        scale = default_scale;
      if (t.atoms[1]->is_hydrogen())
        t.atoms[1]->pos = t.atoms[0]->pos + u * scale;
      else
        t.atoms[0]->pos = t.atoms[1]->pos - u * scale;
    }
  }
}
 
} // namespace gemmi
#endif