| add_atom_types(Hierarchy hierarchy) const | IMP::atom::CHARMMTopology | |
| add_bonds(Hierarchy hierarchy) const | IMP::atom::CHARMMTopology | |
| add_charges(Hierarchy hierarchy) const | IMP::atom::CHARMMTopology | |
| add_coordinates(Hierarchy hierarchy) const | IMP::atom::CHARMMTopology | |
| add_dihedrals(Hierarchy hierarchy) const | IMP::atom::CHARMMTopology | |
| add_impropers(Hierarchy hierarchy) const | IMP::atom::CHARMMTopology | |
| add_missing_atoms(Hierarchy hierarchy) const | IMP::atom::CHARMMTopology | |
| add_segment(CHARMMSegmentTopology *obj) (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| add_segments(const CHARMMSegmentTopologies &objs) (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| add_sequence(std::string sequence) | IMP::atom::CHARMMTopology | |
| apply_default_patches() | IMP::atom::CHARMMTopology | |
| CHARMMTopology(const CHARMMParameters *force_field, std::string name="CHARMM topology %1%") (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| clear_caches() | IMP::base::Object | virtual |
| clear_segments() (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| create_hierarchy(kernel::Model *model) const | IMP::atom::CHARMMTopology | |
| do_destroy() | IMP::base::Object | virtual |
| get_check_level() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_has_segments() (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| get_log_level() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_name() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_number_of_segments() const (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| get_parameters() (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| get_segment(unsigned int i) const (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| get_segments() const (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| get_type_name() const (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | virtual |
| get_version_info() const | IMP::atom::CHARMMTopology | virtual |
| NonCopyable() (defined in IMP::base::NonCopyable) | IMP::base::NonCopyable | protected |
| Object(std::string name) | IMP::base::Object | protected |
| Object() | IMP::base::Object | protected |
| remove_segment(CHARMMSegmentTopology *d) (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| remove_segments(const CHARMMSegmentTopologies &d) (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| reserve_segments(unsigned int sz) (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| set_check_level(CheckLevel l) | IMP::base::Object | |
| set_log_level(LogLevel l) | IMP::base::Object | |
| set_name(std::string name) (defined in IMP::base::Object) | IMP::base::Object | |
| set_segments(const CHARMMSegmentTopologies &ps) (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| set_segments_order(const CHARMMSegmentTopologies &objs) (defined in IMP::atom::CHARMMTopology) | IMP::atom::CHARMMTopology | |
| set_was_used(bool tf) const | IMP::base::Object | |
| setup_hierarchy(Hierarchy hierarchy) const | IMP::atom::CHARMMTopology | |
| show(std::ostream &out=std::cout) const (defined in IMP::base::Object) | IMP::base::Object | |
