| add_atom_slot(int atom_id) | colvarproxy_atoms | [protected] |
| apply_atom_force(int index, cvm::rvector const &new_force) | colvarproxy_atoms | [inline] |
| atoms_charges | colvarproxy_atoms | [protected] |
| atoms_ids | colvarproxy_atoms | [protected] |
| atoms_masses | colvarproxy_atoms | [protected] |
| atoms_max_applied_force_ | colvarproxy_atoms | [protected] |
| atoms_max_applied_force_id_ | colvarproxy_atoms | [protected] |
| atoms_new_colvar_forces | colvarproxy_atoms | [protected] |
| atoms_positions | colvarproxy_atoms | [protected] |
| atoms_refcount | colvarproxy_atoms | [protected] |
| atoms_rms_applied_force_ | colvarproxy_atoms | [protected] |
| atoms_total_forces | colvarproxy_atoms | [protected] |
| check_atom_id(int atom_number) | colvarproxy_atoms | [virtual] |
| check_atom_id(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) | colvarproxy_atoms | [virtual] |
| clear_atom(int index) | colvarproxy_atoms | [virtual] |
| colvarproxy_atoms() | colvarproxy_atoms | |
| compute_max_atoms_applied_force() | colvarproxy_atoms | |
| compute_rms_atoms_applied_force() | colvarproxy_atoms | |
| get_atom_applied_forces() const | colvarproxy_atoms | [inline] |
| get_atom_charge(int index) const | colvarproxy_atoms | [inline] |
| get_atom_charges() | colvarproxy_atoms | [inline] |
| get_atom_id(int index) const | colvarproxy_atoms | [inline] |
| get_atom_ids() const | colvarproxy_atoms | [inline] |
| get_atom_mass(int index) const | colvarproxy_atoms | [inline] |
| get_atom_masses() const | colvarproxy_atoms | [inline] |
| get_atom_position(int index) const | colvarproxy_atoms | [inline] |
| get_atom_positions() const | colvarproxy_atoms | [inline] |
| get_atom_total_force(int index) const | colvarproxy_atoms | [inline] |
| get_atom_total_forces() const | colvarproxy_atoms | [inline] |
| get_atom_velocity(int) | colvarproxy_atoms | [inline] |
| get_num_active_atoms() const | colvarproxy_atoms | |
| increase_refcount(int index) | colvarproxy_atoms | [inline] |
| init_atom(int atom_number) | colvarproxy_atoms | [virtual] |
| init_atom(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) | colvarproxy_atoms | [virtual] |
| load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double pdb_field_value=0.0) | colvarproxy_atoms | [virtual] |
| load_coords(char const *filename, std::vector< cvm::atom_pos > &pos, std::vector< int > const &sorted_ids, std::string const &pdb_field, double pdb_field_value=0.0) | colvarproxy_atoms | [virtual] |
| max_atoms_applied_force() const | colvarproxy_atoms | [inline] |
| max_atoms_applied_force_id() const | colvarproxy_atoms | [inline] |
| modify_atom_applied_forces() | colvarproxy_atoms | [inline] |
| modify_atom_charges() | colvarproxy_atoms | [inline] |
| modify_atom_masses() | colvarproxy_atoms | [inline] |
| modify_atom_positions() | colvarproxy_atoms | [inline] |
| modify_atom_total_forces() | colvarproxy_atoms | [inline] |
| reset() | colvarproxy_atoms | |
| rms_atoms_applied_force() const | colvarproxy_atoms | [inline] |
| updated_charges() const | colvarproxy_atoms | [inline] |
| updated_charges_ | colvarproxy_atoms | [protected] |
| updated_masses() const | colvarproxy_atoms | [inline] |
| updated_masses_ | colvarproxy_atoms | [protected] |
| ~colvarproxy_atoms() | colvarproxy_atoms | [virtual] |
