message: changed assertions to CHECK_EQ
diff: @@ -309,8 +309,8 @@ std::pair<atomv, vecv> CNNScorer::get_ligand(model& m) const{
  );
  if(!cnnopts.flexopt){ // No flexible residues
  - assert(ligand_atoms.size() == m.get_movable_atoms().size());
  - assert(ligand_coords.size() == m.coordinates().size());
  + CHECK_EQ(ligand_atoms.size(), m.get_movable_atoms().size());
  + CHECK_EQ(ligand_coords.size(), m.coordinates().size());
  }
  return std::pair<atomv, vecv>(ligand_atoms, ligand_coords);
  @@ -331,11 +331,11 @@ std::pair<atomv,sz> CNNScorer::get_receptor(model& m, sz num_ligand_atoms) const
  // Check that ligand atoms and movable atoms in flexible residues sum up to the
  // total number of movable atoms
  - assert(flexible_atoms.size() + num_ligand_atoms == m.m_num_movable_atoms);
  + CHECK_EQ(flexible_atoms.size() + num_ligand_atoms, m.m_num_movable_atoms);
  if(!cnnopts.flexopt){ // No atoms from flexible residues should be present
  - assert(flexible_atoms.size() == 0);
  - assert(inflex_atoms.size() == 0);
  + CHECK_EQ(flexible_atoms.size(), 0);
  + CHECK_EQ(inflex_atoms.size(), 0);
  }
  // rmeli: Use std::move_iterator instead?
  @@ -357,7 +357,7 @@ std::pair<atomv,sz> CNNScorer::get_receptor(model& m, sz num_ligand_atoms) const
  );
  if(!cnnopts.flexopt){ // No atoms from flexible residues should be present
  - assert(receptor_atoms.size() == m.get_fixed_atoms().size());
  + CHECK_EQ(receptor_atoms.size(), m.get_fixed_atoms().size());
  }
  return std::pair<atomv,sz>(receptor_atoms, flexible_atoms.size());
  @@ -446,7 +446,7 @@ float CNNScorer::score(model& m, bool compute_gradient, float& affinity,
  // Get ligand gradient
  mgrid->getLigandGradient(0, gradient);
  - assert(gradient.size() == ligand_coords.size());
  + CHECK_EQ(gradient.size(), ligand_coords.size());
  // Get receptor gradient
  std::vector<gfloat3> gradient_rec;
  @@ -460,7 +460,7 @@ float CNNScorer::score(model& m, bool compute_gradient, float& affinity,
  );
  // rmeli: receptor coords?
  - assert(gradient_rec.size() == num_flexres_atoms);
  + CHECK_EQ(gradient_rec.size(), num_flexres_atoms);
  }
  // Merge ligand and flexible residues gradient
  @@ -486,7 +486,7 @@ float CNNScorer::score(model& m, bool compute_gradient, float& affinity,
  mgrid->getLigandChannels(0, channels);
  outputXYZ(ligname, atoms, channels, gradient);
  - mgrid->getReceptorGradient(0, gradient); // TODO: Full gradient or just flexres?
  + mgrid->getReceptorGradient(0, gradient); // rmeli: TODO Full gradient or just flexres?
  mgrid->getReceptorAtoms(0, atoms);
  mgrid->getReceptorChannels(0, channels);
  outputXYZ(recname, atoms, channels, gradient);
  