| add_bonds(Hierarchy mhd) const | IMP::atom::ForceFieldParameters | |
| add_bonds(Residue rd) const (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| add_bonds(Residue rd1, Residue rd2) const (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| add_patch(CHARMMPatch *patch) (defined in IMP::atom::CHARMMParameters) | IMP::atom::CHARMMParameters | |
| add_radii(Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius")) const | IMP::atom::ForceFieldParameters | |
| add_residue_topology(CHARMMIdealResidueTopology *res) (defined in IMP::atom::CHARMMParameters) | IMP::atom::CHARMMParameters | |
| add_well_depths(Hierarchy mhd) const | IMP::atom::ForceFieldParameters | |
| atom_res_type_2_force_field_atom_type_ (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| AtomTypeMap typedef (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| ChargePair typedef (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| CHARMMParameters(base::TextInput topology_file_name, base::TextInput par_file_name=base::TextInput(), bool translate_names_to_pdb=false) | IMP::atom::CHARMMParameters | |
| clear_caches() | IMP::base::Object | virtual |
| create_angles(kernel::Particles bonds) const | IMP::atom::CHARMMParameters | |
| create_dihedrals(kernel::Particles bonds) const | IMP::atom::CHARMMParameters | |
| create_topology(Hierarchy hierarchy) const | IMP::atom::CHARMMParameters | |
| do_destroy() | IMP::base::Object | protectedvirtual |
| do_show(std::ostream &out) const (defined in IMP::atom::CHARMMParameters) | IMP::atom::CHARMMParameters | |
| force_field_2_vdW_ (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| ForceFieldParameters() (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | |
| get_angle_parameters(std::string type1, std::string type2, std::string type3) const | IMP::atom::CHARMMParameters | |
| get_bond_parameters(std::string type1, std::string type2) const | IMP::atom::CHARMMParameters | |
| get_check_level() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_dihedral_parameters(std::string type1, std::string type2, std::string type3, std::string type4) const | IMP::atom::CHARMMParameters | |
| get_epsilon(Atom atom) const | IMP::atom::ForceFieldParameters | |
| get_epsilon(const String &force_field_atom_type) const (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| get_improper_parameters(std::string type1, std::string type2, std::string type3, std::string type4) const | IMP::atom::CHARMMParameters | |
| get_log_level() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_name() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_patch(std::string name) const (defined in IMP::atom::CHARMMParameters) | IMP::atom::CHARMMParameters | |
| get_radius(Atom atom) const | IMP::atom::ForceFieldParameters | |
| get_radius(const String &force_field_atom_type) const (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| get_residue_topology(ResidueType type) const (defined in IMP::atom::CHARMMParameters) | IMP::atom::CHARMMParameters | |
| get_type_name() const (defined in IMP::atom::CHARMMParameters) | IMP::atom::CHARMMParameters | virtual |
| get_version_info() const | IMP::atom::CHARMMParameters | virtual |
| NonCopyable() (defined in IMP::base::NonCopyable) | IMP::base::NonCopyable | protected |
| Object(std::string name) | IMP::base::Object | protected |
| residue_bonds_ (defined in IMP::atom::ForceFieldParameters) | IMP::atom::ForceFieldParameters | protected |
| 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_was_used(bool tf) const | IMP::base::Object | |
| show(std::ostream &out=std::cout) const (defined in IMP::base::Object) | IMP::base::Object | |
| ~Object() (defined in IMP::base::Object) | IMP::base::Object | virtual |
