| version 1.16 | version 1.17 |
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| /// \brief Destructor | /// \brief Destructor |
| ~atom_group(); | ~atom_group(); |
| | |
| | /// \brief Optional name to reuse properties of this in other groups |
| | std::string name; |
| | |
| /// \brief Keyword used to define the group | /// \brief Keyword used to define the group |
| // TODO Make this field part of the data structures that link a group to a CVC | // TODO Make this field part of the data structures that link a group to a CVC |
| std::string key; | std::string key; |
| |
| int parse(std::string const &conf); | int parse(std::string const &conf); |
| | |
| int add_atom_numbers(std::string const &numbers_conf); | int add_atom_numbers(std::string const &numbers_conf); |
| | int add_atoms_of_group(atom_group const * ag); |
| int add_index_group(std::string const &index_group_name); | int add_index_group(std::string const &index_group_name); |
| int add_atom_numbers_range(std::string const &range_conf); | int add_atom_numbers_range(std::string const &range_conf); |
| int add_atom_name_residue_range(std::string const &psf_segid, | int add_atom_name_residue_range(std::string const &psf_segid, |
| |
| /// cvc's (eg rmsd, eigenvector) will not override the user's choice | /// cvc's (eg rmsd, eigenvector) will not override the user's choice |
| bool b_user_defined_fit; | bool b_user_defined_fit; |
| | |
| /// \brief Whether or not the derivatives of the roto-translation | |
| /// should be included when calculating the colvar's gradients (default: yes) | |
| bool b_fit_gradients; | |
| | |
| /// \brief use reference coordinates for b_center or b_rotate | /// \brief use reference coordinates for b_center or b_rotate |
| std::vector<cvm::atom_pos> ref_pos; | std::vector<cvm::atom_pos> ref_pos; |
| | |
| |
| /// apply_colvar_force() once that is implemented for non-scalar values | /// apply_colvar_force() once that is implemented for non-scalar values |
| void apply_force(cvm::rvector const &force); | void apply_force(cvm::rvector const &force); |
| | |
| | /// Implements possible actions to be carried out |
| | /// when a given feature is enabled |
| | /// This overloads the base function in colvardeps |
| | void do_feature_side_effects(int id); |
| }; | }; |
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