| analog_search(const ReactionBasedAnalogSampler::Product &prod) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| apply(core::chemical::MutableResidueType &) override | protocols::drug_design::ReactionBasedAnalogSampler | virtual |
| protocols::chemistries::Chemistry::apply(core::chemical::MutableResidueType &restype, core::pose::Pose const &) | protocols::chemistries::Chemistry | inlinevirtual |
| check_reagent_validity(::RDKit::ROMOL_SPTR reag) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| Chemistry(std::string const &name) | protocols::chemistries::Chemistry | inline |
| ChemistryBase(std::string const &name) | core::chemical::modifications::ChemistryBase | inline |
| class_name() | protocols::drug_design::ReactionBasedAnalogSampler | static |
| dynamic_sampling_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| dynamic_spl_ratios_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| find_O3A_mapping(::RDKit::ROMOL_SPTR from, ::RDKit::ROMOL_SPTR to) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| geo_spl_ratio_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| geometric_sampling(numeric::random::WeightedSampler &sampler, core::Size N) | protocols::drug_design::ReactionBasedAnalogSampler | private |
| get_additional_output() | core::chemical::modifications::ChemistryBase | inlinevirtual |
| get_last_status() const | core::chemical::modifications::ChemistryBase | inline |
| get_mapping() const override | protocols::drug_design::ReactionBasedAnalogSampler | virtual |
| getMorganFingerprint(::RDKit::ROMol const &mol, bool useFeatures=false) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| has_additional_output() const | core::chemical::modifications::ChemistryBase | inlinevirtual |
| last_smiles_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| last_status_ | core::chemical::modifications::ChemistryBase | private |
| load_all_reagents() | protocols::drug_design::ReactionBasedAnalogSampler | private |
| load_all_reagents(std::string const &filename) | protocols::drug_design::ReactionBasedAnalogSampler | private |
| load_reactions(std::string const &reaction_dir, std::string const &filename) | protocols::drug_design::ReactionBasedAnalogSampler | |
| load_reactions(std::string const &filename) | protocols::drug_design::ReactionBasedAnalogSampler | |
| mapping_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| minCandidates_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| name() const | core::chemical::modifications::ChemistryBase | inline |
| name_ | core::chemical::modifications::ChemistryBase | private |
| pair(core::Size r_no, utility::vector1< utility::vector1< core::Size > > const &sets, utility::vector1< Product > &candidates, int &revisits) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| pair(core::Size curr_no, core::Size r_no, utility::vector1< core::Size > single_pair, utility::vector1< utility::vector1< core::Size > > &all_pairs, utility::vector1< utility::vector1< core::Size > > const &sets) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &datacache) override | protocols::drug_design::ReactionBasedAnalogSampler | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::drug_design::ReactionBasedAnalogSampler | static |
| ReactionBasedAnalogSampler() | protocols::drug_design::ReactionBasedAnalogSampler | |
| reagent_sampler_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| reagents_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| reset_spl_ratio() | protocols::drug_design::ReactionBasedAnalogSampler | inline |
| run_reaction(utility::vector1< core::Size > const &reagents) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| rxns_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| sample(std::list< std::pair< core::Real, core::Size > > &score_idx_set) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| sample_candidate(const utility::vector1< Product > &candidate_set, const ::RDKit::RWMOL_SPTR rdmol) | protocols::drug_design::ReactionBasedAnalogSampler | private |
| sample_fragment(utility::vector1< std::list< std::pair< core::Real, core::Size > > > &score_idx_set) const | protocols::drug_design::ReactionBasedAnalogSampler | private |
| set_last_status(ChemistryStatus setting) | core::chemical::modifications::ChemistryBase | inline |
| sortbySim(const std::pair< core::Real, core::Size > &a, const std::pair< core::Real, core::Size > &b) | protocols::drug_design::ReactionBasedAnalogSampler | privatestatic |
| visited_ | protocols::drug_design::ReactionBasedAnalogSampler | private |
| ~ReactionBasedAnalogSampler() override | protocols::drug_design::ReactionBasedAnalogSampler | |
