message: named comments instead of TODOs
diff: @@ -314,9 +314,13 @@ float CNNScorer::score(model& m, bool compute_gradient, float& affinity,
  mgrid->setGridCenter(current_center);
  }
  - // TODO: Here ligand and receptor are initialized
  - // TODO: Ligand is initialized from movable atoms, receptor from fixed atoms
  + // rmeli: Here ligand and receptor are initialized
  + // rmeli: Ligand is initialized from movable atoms, receptor from fixed atoms
  mgrid->setLigand(m.get_movable_atoms(), m.coordinates(), cnnopts.move_minimize_frame);
  +
  + // rmeli: Concatenate fixed and movable part of the receptor
  +
  +
  if (!cnnopts.move_minimize_frame) { //if fixed_receptor, rec_conf will be identify
  mgrid->setReceptor(m.get_fixed_atoms(), m.rec_conf.position, m.rec_conf.orientation);
  } else { //don't move receptor
  @@ -332,7 +336,7 @@ float CNNScorer::score(model& m, bool compute_gradient, float& affinity,
  if(compute_gradient || cnnopts.outputxyz) {
  mgrid->enableLigandGradients();
  if(cnnopts.moving_receptor() || cnnopts.outputxyz || cnnopts.flexopt)
  - mgrid->enableReceptorGradients(); // Enable computation of full receptor gradient
  + mgrid->enableReceptorGradients(); // rmeli: Enable computation of full receptor gradient
  }
  m.clear_minus_forces();
  @@ -368,7 +372,7 @@ float CNNScorer::score(model& m, bool compute_gradient, float& affinity,
  std::vector<gfloat3> gradient_rec;
  if (cnnopts.flexopt) { // Optimization of flexible residues
  mgrid->getReceptorGradient(0, gradient_rec);
  - // TODO: Select components of flexible residues!
  + // rmeli: Select components of flexible residues!
  }
  // Merge ligand and flexible residues gradient
  