message: check if ROOT, ENDROOT, and TORSDOF need to be added for parsing
diff: @@ -190,7 +190,11 @@ std::string cnn_visualization::modify_pdbqt(std::vector<int> atoms_to_remove,
  std::stringstream ss;
  std::stringstream mol_stream(mol_string);
  - ss << "ROOT\n"; //add necessary lines for gnina parsing
  + //add necessary lines for gnina parsing if not present
  + if(mol_string.find("ROOT\n") == std::string::npos)
  + {
  + ss << "ROOT\n";
  + }
  bool list_ended = false;
  std::string line;
  @@ -215,8 +219,16 @@ std::string cnn_visualization::modify_pdbqt(std::vector<int> atoms_to_remove,
  }
  }
  +
  + if(mol_string.find("ENDROOT\n") == std::string::npos)
  + {
  ss << "ENDROOT\n";
  + }
  +
  + if(mol_string.find("TORSDOF") == std::string::npos)
  + {
  ss << "TORSDOF 0\n";
  + }
  if (visopts.verbose) {
  std::cout << "]\n";
  