| add_chain_restraints(FGChain *chain) | IMP::npctransport::Scoring | |
| add_custom_restraint(IMP::Restraint *r) (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| add_custom_restraints(IMP::Restraints R) (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| add_interaction(const ::npctransport_proto::Assignment_InteractionAssignment &idata) | IMP::npctransport::Scoring | |
| add_restrained_anchor_bead(IMP::Particle *p) | IMP::npctransport::Scoring | |
| add_z_bias_restraint(SingletonContainerAdaptor ps, double k) | IMP::npctransport::Scoring | |
| add_z_bias_restraint(Particle *p, double k) | IMP::npctransport::Scoring | |
| clear_caches() | IMP::Object | virtual |
| clear_custom_restraints() (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| create_backbone_restraint(double rest_length_factor, double backbone_k, ParticlesTemp beads, std::string name) const | IMP::npctransport::Scoring | |
| create_bounding_box_restraint(SingletonContainerAdaptor beads) const | IMP::npctransport::Scoring | |
| create_close_beads_container(SingletonContainerAdaptor non_optimiziable_beads, SingletonContainerAdaptor optimizable_beads) const | IMP::npctransport::Scoring | |
| create_close_beads_container(ParticleIndexes non_optimizable_beads, SingletonContainerAdaptor optimizable_beads) const | IMP::npctransport::Scoring | |
| create_predicates_pair_restraint(PairContainer *bead_pairs, bool is_attr_interactions_on=true) const | IMP::npctransport::Scoring | |
| create_slab_restraint(SingletonContainerAdaptor beads) const | IMP::npctransport::Scoring | |
| create_z_bias_restraint(SingletonContainerAdaptor ps, double k) const | IMP::npctransport::Scoring | |
| do_destroy() | IMP::Object | protectedvirtual |
| get_all_chain_restraints() const | IMP::npctransport::Scoring | |
| get_bounding_box_restraint(bool update=false) | IMP::npctransport::Scoring | |
| get_chain_restraints_on(SingletonContainerAdaptor beads) const | IMP::npctransport::Scoring | |
| get_check_level() const (defined in IMP::Object) | IMP::Object | |
| get_close_beads_container(bool update=false) | IMP::npctransport::Scoring | |
| get_custom_restraints() const (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| get_custom_scoring_function(const RestraintsTemp &extra_restraints, SingletonContainerAdaptor non_optimizable_beads, SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=true) const | IMP::npctransport::Scoring | |
| get_custom_scoring_function(const RestraintsTemp &extra_restraints, ParticleIndexes non_optimizable_beads, SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=true) const | IMP::npctransport::Scoring | |
| get_default_backbone_k() const | IMP::npctransport::Scoring | |
| get_excluded_volume_k() const | IMP::npctransport::Scoring | |
| get_fg_chains() | IMP::npctransport::Scoring | |
| get_has_bounding_box() const (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| get_interaction_k() const | IMP::npctransport::Scoring | |
| get_interaction_range_for(core::ParticleType t1, core::ParticleType t2, bool site_specific=true, bool non_specific=false) const | IMP::npctransport::Scoring | |
| get_is_backbone_harmonic() const (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| get_log_level() const (defined in IMP::Object) | IMP::Object | |
| get_model() | IMP::npctransport::Scoring | |
| get_model() const | IMP::npctransport::Scoring | |
| get_name() const (defined in IMP::Object) | IMP::Object | |
| get_ordered_type_pair_predicate() (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| get_ordered_type_pair_predicate() const (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| get_pore_radius_restraint() const (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| get_predicate_pair_score(core::ParticleType t1, core::ParticleType t2) const | IMP::npctransport::Scoring | |
| get_predicate_pair_score(core::ParticleType t1, core::ParticleType t2) | IMP::npctransport::Scoring | |
| get_predicates_pair_restraint(bool update=false) | IMP::npctransport::Scoring | |
| get_range() const (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | |
| get_scoring_function(bool force_update=false) | IMP::npctransport::Scoring | |
| get_scoring_function_restraints(bool force_update=false) | IMP::npctransport::Scoring | |
| get_sd() | IMP::npctransport::Scoring | |
| get_sd() const | IMP::npctransport::Scoring | |
| get_site_interactions_statistics(ParticleIndex pi1, ParticleIndex pi2) const | IMP::npctransport::Scoring | |
| get_site_interactions_statistics(Particle const *p1, Particle const *p2) const | IMP::npctransport::Scoring | |
| get_slab_restraint(bool update=false) | IMP::npctransport::Scoring | |
| get_type_name() const (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | virtual |
| get_version_info() const | IMP::npctransport::Scoring | virtual |
| get_z_bias_restraints() | IMP::npctransport::Scoring | |
| NonCopyable() (defined in IMP::NonCopyable) | IMP::NonCopyable | protected |
| Object(std::string name) | IMP::Object | protected |
| Scoring(SimulationData *owner_sd, const ::npctransport_proto::Assignment &data) | IMP::npctransport::Scoring | |
| set_check_level(CheckLevel l) | IMP::Object | |
| set_interaction_k_factor(IMP::core::ParticleType type, double value) | IMP::npctransport::Scoring | |
| set_interaction_range_factor(IMP::core::ParticleType type, double value) | IMP::npctransport::Scoring | |
| set_log_level(LogLevel l) | IMP::Object | |
| set_name(std::string name) (defined in IMP::Object) | IMP::Object | |
| set_was_used(bool tf) const | IMP::Object | |
| show(std::ostream &out=std::cout) const (defined in IMP::Object) | IMP::Object | |
| ~Object() (defined in IMP::Object) | IMP::Object | virtual |
| ~Scoring() (defined in IMP::npctransport::Scoring) | IMP::npctransport::Scoring | protectedvirtual |
