Index

A

a_optimal_criterion() (in module rbfenetmap.core.design) a_optimal_gradient() (in module rbfenetmap.core.design) AbstractExporter (class in rbfenetmap.core.meta.exporters) AbstractIntermediateGenerator (class in rbfenetmap.core.meta.intermediates) AbstractMapper (class in rbfenetmap.core.meta.mappers) AbstractNetworkPlanner (class in rbfenetmap.core.meta.planners) AbstractScorer (class in rbfenetmap.core.meta.scorers) activate() (rbfenetmap.core.pluginregistry.PluginRegistry method) acyclic_branches() (in module rbfenetmap.core.molgraph) add_compat_argument() (in module rbfenetmap.cli._args) add_cost_units_argument() (in module rbfenetmap.cli._args) add_ligand_arguments() (in module rbfenetmap.cli._args) add_mapping_arguments() (in module rbfenetmap.cli._args) add_network_arguments() (in module rbfenetmap.cli._args) add_scorer_arguments() (in module rbfenetmap.cli._args) add_softcore_arguments() (in module rbfenetmap.cli._args) align_ligands() (in module rbfenetmap.core.align) AlignmentOptions (class in rbfenetmap.core.options) AlignmentResult (class in rbfenetmap.core.align) allocate_effort() (in module rbfenetmap.core.design)

AmberExporter (class in rbfenetmap.plugins.exporters.amber_exporter) AmberMasks (class in rbfenetmap.io.amber_masks) append_ligand() (in module rbfenetmap.core.surgery) apply_graph_consistency() (in module rbfenetmap.core.consistency) apply_transform() (in module rbfenetmap.core.kabsch) argv (rbfenetmap.gui.session.PlanRun attribute) as_dict() (rbfenetmap.gui.session.PlanRun method) (rbfenetmap.io.amber_masks.AmberMasks method) as_metadata() (rbfenetmap.core.align.LigandAlignment method) assign_clusters() (in module rbfenetmap.core.clustering) atom_names (rbfenetmap.core.models.Ligand property) AtomMapping (class in rbfenetmap.core.models) augment_with_intermediates() (in module rbfenetmap.core.pipeline) AugmentationResult (class in rbfenetmap.core.pipeline) available (rbfenetmap.core.pluginregistry.PluginSpec property) available_exporters() (in module rbfenetmap.plugins.exporters) available_intermediates() (in module rbfenetmap.plugins.intermediates) available_mappers() (in module rbfenetmap.plugins.mappers) available_planners() (in module rbfenetmap.plugins.planners) available_scorers() (in module rbfenetmap.plugins.scorers)

B

banned_pairs (rbfenetmap.core.options.NetworkOptions property) BRIDGE_CENTRALITY_WEIGHT (in module rbfenetmap.core.cbfe) bridge_rank_key() (in module rbfenetmap.core.cbfe) bridges_components (rbfenetmap.core.intermediates.IntermediateOptions property) build() (rbfenetmap.core.softcore.RepairContext class method) build_alignment_options() (in module rbfenetmap.cli._args) build_amber_masks() (in module rbfenetmap.io.amber_masks)

build_candidate() (in module rbfenetmap.core.pipeline) build_cbfe_pool() (in module rbfenetmap.core.cbfe) build_mapping_options() (in module rbfenetmap.cli._args) build_network() (in module rbfenetmap.core.pipeline) build_network_options() (in module rbfenetmap.cli._args) build_parser() (in module rbfenetmap.cli.main) build_server() (in module rbfenetmap.gui.server)

C

CachingMapper (class in rbfenetmap.gui.cache) cancel() (rbfenetmap.gui.session.PlanRun method) (rbfenetmap.gui.session.PlanSession method) cartograph_mapping() (in module rbfenetmap.plugins.mappers.cartograph_mapper) CartographMapper (class in rbfenetmap.plugins.mappers.cartograph_mapper) cbfe_bridges_components (rbfenetmap.core.options.NetworkOptions property) cbfe_closes_cycles (rbfenetmap.core.options.NetworkOptions property) cbfe_cost() (in module rbfenetmap.core.cbfe) cbfe_edges (rbfenetmap.core.models.Network property) cbfe_gpu_hours (rbfenetmap.core.cost.CostModel property) CBFE_METHOD (in module rbfenetmap.core.cbfe) CBFE_SCORER (in module rbfenetmap.core.cbfe) CHARGE_MISMATCH (rbfenetmap.core.posing.PoseRejection attribute) check_cbfe_support() (rbfenetmap.core.meta.planners.AbstractNetworkPlanner method) check_design_support() (rbfenetmap.core.meta.planners.AbstractNetworkPlanner method) check_edge_budget() (rbfenetmap.core.options.NetworkOptions method) choose_reference() (in module rbfenetmap.core.align) choose_softcore_branch() (in module rbfenetmap.core.coreprune) clear() (rbfenetmap.gui.cache.MappingCache method) cluster_by_charge() (in module rbfenetmap.core.clustering) cluster_by_fingerprint() (in module rbfenetmap.core.clustering) cluster_by_scaffold() (in module rbfenetmap.core.clustering) cluster_edge_budget() (in module rbfenetmap.core.clustering) CLUSTER_METHODS (in module rbfenetmap.core.clustering) cluster_sizes() (in module rbfenetmap.core.clustering) cmd_export() (in module rbfenetmap.cli.commands) cmd_inspect() (in module rbfenetmap.cli.commands) cmd_map() (in module rbfenetmap.cli.commands) cmd_plan() (in module rbfenetmap.cli.commands) cmd_plugins() (in module rbfenetmap.cli.commands) cmd_replan() (in module rbfenetmap.cli.commands) cmd_report() (in module rbfenetmap.cli.commands) cmd_score() (in module rbfenetmap.cli.commands)

command (rbfenetmap.gui.session.PlanRun property) COMMON_CORE_DISTANCE_THRESHOLD_ANGSTROM (in module rbfenetmap.plugins.mappers.cartograph_mapper) COMPAT_CLI_PINS (in module rbfenetmap.cli._args) COMPAT_LEVELS (in module rbfenetmap.core.options) CompletePlanner (class in rbfenetmap.plugins.planners.simple_planners) component_beyond_bond() (in module rbfenetmap.core.molgraph) component_centrality() (in module rbfenetmap.core.cbfe) compute_descriptors() (in module rbfenetmap.core.descriptors) concatenate_networks() (in module rbfenetmap.core.surgery) connected_components_of() (in module rbfenetmap.core.molgraph) consistency_groups() (in module rbfenetmap.core.consistency) CONSISTENCY_SCOPES (in module rbfenetmap.core.options) CORE_COLOR (in module rbfenetmap.viz.depict) core_rmsd() (in module rbfenetmap.core.kabsch) CorePruningPolicy (class in rbfenetmap.core.options) cost_fn() (rbfenetmap.core.softcore.RepairContext method) COST_UNITS (in module rbfenetmap.core.cost) CostModel (class in rbfenetmap.core.cost) count_cycles() (in module rbfenetmap.core.diagnostics) covariance() (in module rbfenetmap.core.design) create() (rbfenetmap.core.pluginregistry.PluginRegistry method) create_exporter() (in module rbfenetmap.plugins.exporters) create_exporter_registry() (in module rbfenetmap.plugins.exporters) create_intermediate() (in module rbfenetmap.plugins.intermediates) create_intermediate_registry() (in module rbfenetmap.plugins.intermediates) create_mapper() (in module rbfenetmap.plugins.mappers) create_mapper_registry() (in module rbfenetmap.plugins.mappers) create_planner() (in module rbfenetmap.plugins.planners) create_planner_registry() (in module rbfenetmap.plugins.planners) create_scorer() (in module rbfenetmap.plugins.scorers) create_scorer_registry() (in module rbfenetmap.plugins.scorers) criterion_value() (in module rbfenetmap.core.design) cycle_closure_errors() (in module rbfenetmap.core.replanning) cyclize_around_component() (in module rbfenetmap.core.surgery)

D

d_optimal_criterion() (in module rbfenetmap.core.design) deactivate() (rbfenetmap.core.pluginregistry.PluginRegistry method) DEFAULT_FINGERPRINT_CUTOFF (in module rbfenetmap.core.clustering) DEFAULT_LOMAP_PARAMETERS (in module rbfenetmap.plugins.scorers.lomaplike_scorer) DEFAULT_RESIDUE_NAMES (in module rbfenetmap.io.amber_masks) DEFAULT_SCORE_WEIGHTS (in module rbfenetmap.plugins.scorers.linear_scorer) default_suffix (rbfenetmap.core.meta.exporters.AbstractExporter attribute) DEFAULT_VARIANCE_WEIGHTS (in module rbfenetmap.plugins.scorers.variance_scorer) degree_summary() (in module rbfenetmap.core.diagnostics) DegreeSummary (class in rbfenetmap.core.diagnostics) delete_edge() (in module rbfenetmap.core.surgery) demote_cost() (rbfenetmap.core.softcore.RepairContext method) describe_design() (rbfenetmap.plugins.planners.optimal_planner.OptimalDesignPlanner method) describe_intermediate_attempts() (in module rbfenetmap.core.intermediates)

describe_parameters() (rbfenetmap.core.meta.intermediates.AbstractIntermediateGenerator method) (rbfenetmap.plugins.intermediates.fragment_swap.FragmentSwapGenerator method) (rbfenetmap.plugins.intermediates.pairmap_generator.PairMapGenerator method) describe_weights() (rbfenetmap.core.meta.scorers.AbstractScorer method) (rbfenetmap.plugins.scorers.linear_scorer.LinearScorer method) (rbfenetmap.plugins.scorers.lomaplike_scorer.LomapLikeScorer method) (rbfenetmap.plugins.scorers.variance_scorer.VarianceScorer method) DESCRIPTOR_NAMES (in module rbfenetmap.core.descriptors) DESIGN_CRITERIA (in module rbfenetmap.core.design) (in module rbfenetmap.core.options) detect_fragments() (in module rbfenetmap.core.softcore) diameter() (in module rbfenetmap.core.diagnostics) dispatch() (in module rbfenetmap.cli.main) dump_network() (in module rbfenetmap.io.networkio)

E

edge_budget_advice() (in module rbfenetmap.core.diagnostics) edge_gpu_hours() (rbfenetmap.core.cost.CostModel method) edge_key() (in module rbfenetmap.core.models) EDGE_SEPARATOR (in module rbfenetmap.core.models) EdgeBudgetAdvice (class in rbfenetmap.core.diagnostics) EdgeKind (class in rbfenetmap.core.models) EdgeListExporter (class in rbfenetmap.plugins.exporters.basic_exporters) EdgeScore (class in rbfenetmap.core.models) effective_resistances() (in module rbfenetmap.core.design) EMBED_FAILED (rbfenetmap.core.posing.PoseRejection attribute) enabled (rbfenetmap.core.intermediates.IntermediateOptions property) error (rbfenetmap.gui.session.PlanRun attribute) evaluate_pairs() (in module rbfenetmap.core.pipeline)

evaluate_pairs_adaptively() (in module rbfenetmap.core.pipeline) expand_ligand_paths() (in module rbfenetmap.gui.session) expand_pairs() (in module rbfenetmap.core.pairs) explicit_dests() (in module rbfenetmap.cli._args) ExplicitPlanner (class in rbfenetmap.plugins.planners.simple_planners) export() (rbfenetmap.core.meta.exporters.AbstractExporter method) (rbfenetmap.plugins.exporters.amber_exporter.AmberExporter method) (rbfenetmap.plugins.exporters.basic_exporters.EdgeListExporter method) (rbfenetmap.plugins.exporters.basic_exporters.GraphMLExporter method) (rbfenetmap.plugins.exporters.basic_exporters.JSONExporter method) (rbfenetmap.plugins.exporters.html_exporter.HTMLGalleryExporter method) EXPORT_KNOBS (in module rbfenetmap.gui.schema) ExporterError

F

failure_robustness() (in module rbfenetmap.core.diagnostics) FailureRobustness (class in rbfenetmap.core.diagnostics) failures (rbfenetmap.core.align.AlignmentResult property) feasible (rbfenetmap.core.models.Transformation property) feasible_graph() (in module rbfenetmap.core.pipeline) fills_internal_gaps (rbfenetmap.core.intermediates.IntermediateOptions property) fingerprint_pair_similarities() (in module rbfenetmap.core.pairs) fingerprint_prefilter() (in module rbfenetmap.core.pairs)

fisher_information() (in module rbfenetmap.core.design) forced_pairs (rbfenetmap.core.options.NetworkOptions property) FORCEFIELD_FAILED (rbfenetmap.core.posing.PoseRejection attribute) forward (rbfenetmap.core.models.AtomMapping property) FragmentSwapGenerator (class in rbfenetmap.plugins.intermediates.fragment_swap) from_contract() (rbfenetmap.core.models.AtomMapping class method) from_core_pairs() (rbfenetmap.core.models.AtomMapping class method) from_mol() (rbfenetmap.core.models.Ligand class method)

G

generate_candidate_pairs() (in module rbfenetmap.core.pairs) generates_intermediates (rbfenetmap.core.options.NetworkOptions property) get() (rbfenetmap.gui.cache.MappingCache method)

get_spec() (rbfenetmap.core.pluginregistry.PluginRegistry method) graph_consistent_cores() (in module rbfenetmap.core.consistency) GraphMLExporter (class in rbfenetmap.plugins.exporters.basic_exporters)

H

heavy_indices (rbfenetmap.core.models.Ligand property)

HTMLGalleryExporter (class in rbfenetmap.plugins.exporters.html_exporter) hydrogen_parents() (in module rbfenetmap.core.molgraph)

I

id (rbfenetmap.gui.session.PlanRun attribute) IdentityMapper (class in rbfenetmap.plugins.mappers.identity_mapper) inactive_dests() (in module rbfenetmap.gui.schema) intermediate_headroom() (rbfenetmap.core.options.NetworkOptions method) INTERMEDIATE_KIND (in module rbfenetmap.core.intermediates) INTERMEDIATE_MODES (in module rbfenetmap.core.intermediates) intermediate_name() (in module rbfenetmap.core.intermediates)

INTERMEDIATE_NAME_PREFIX (in module rbfenetmap.core.intermediates) IntermediateOptions (class in rbfenetmap.core.intermediates) IntermediateProposal (class in rbfenetmap.core.intermediates) IntermediateRecord (class in rbfenetmap.core.models) INVALID_MOLECULE (rbfenetmap.core.posing.PoseRejection attribute) is_active() (rbfenetmap.core.pluginregistry.PluginRegistry method) isolated (rbfenetmap.core.diagnostics.DegreeSummary property)

J

joint_closure() (in module rbfenetmap.core.softcore)

JSONExporter (class in rbfenetmap.plugins.exporters.basic_exporters)

K

kabsch_rotation() (in module rbfenetmap.core.kabsch) KartografMapper (class in rbfenetmap.plugins.mappers.kartograf_mapper)

key (rbfenetmap.core.models.Transformation property) KNOB_EXCLUSIONS (in module rbfenetmap.gui.schema) knob_parser() (in module rbfenetmap.gui.schema)

L

Ligand (class in rbfenetmap.core.models) LigandAlignment (class in rbfenetmap.core.align) LigandProvenance (class in rbfenetmap.core.models) LinearScorer (class in rbfenetmap.plugins.scorers.linear_scorer) list_active_exporters() (in module rbfenetmap.plugins.exporters) list_active_intermediates() (in module rbfenetmap.plugins.intermediates) list_active_mappers() (in module rbfenetmap.plugins.mappers) list_active_planners() (in module rbfenetmap.plugins.planners) list_active_scorers() (in module rbfenetmap.plugins.scorers)

list_plugins() (rbfenetmap.core.pluginregistry.PluginRegistry method) lmi_threshold() (in module rbfenetmap.core.replanning) load_edge_lmi() (in module rbfenetmap.core.replanning) load_fepplus_network() (in module rbfenetmap.io.loaders) load_ligands() (in module rbfenetmap.io.loaders) load_network() (in module rbfenetmap.io.networkio) load_orion_network() (in module rbfenetmap.io.loaders) load_sdf() (in module rbfenetmap.io.loaders) load_smiles() (in module rbfenetmap.io.loaders) LomapLikeScorer (class in rbfenetmap.plugins.scorers.lomaplike_scorer)

M

main() (in module rbfenetmap.cli.main) make_cbfe_transformation() (in module rbfenetmap.core.cbfe) map_pair() (rbfenetmap.core.meta.mappers.AbstractMapper method) (rbfenetmap.gui.cache.CachingMapper method) (rbfenetmap.plugins.mappers.cartograph_mapper.CartographMapper method) (rbfenetmap.plugins.mappers.identity_mapper.IdentityMapper method) (rbfenetmap.plugins.mappers.kartograf_mapper.KartografMapper method) (rbfenetmap.plugins.mappers.mcss_mapper.MCSSMapper method) MappingCache (class in rbfenetmap.gui.cache) MappingError MappingOptions (class in rbfenetmap.core.options) maybe_apply_graph_consistency() (in module rbfenetmap.core.consistency) mcs_embeddings() (in module rbfenetmap.core.mcs) mcs_query() (in module rbfenetmap.core.mcs) MCSSExtended2Mapper (class in rbfenetmap.plugins.mappers.mcss_mapper) MCSSExtendedMapper (class in rbfenetmap.plugins.mappers.mcss_mapper) MCSSMapper (class in rbfenetmap.plugins.mappers.mcss_mapper) median_rmsd (rbfenetmap.core.align.AlignmentResult property) merge_networks() (in module rbfenetmap.core.surgery) message (rbfenetmap.core.diagnostics.EdgeBudgetAdvice property) metrics (rbfenetmap.gui.session.PlanRun attribute) minimum_edge_count() (in module rbfenetmap.plugins.planners.optimal_planner) missing_requirements (rbfenetmap.core.pluginregistry.PluginSpec property) module rbfenetmap.cli._args rbfenetmap.cli.commands rbfenetmap.cli.main rbfenetmap.core.align rbfenetmap.core.cbfe rbfenetmap.core.clustering rbfenetmap.core.consistency rbfenetmap.core.coreprune rbfenetmap.core.cost rbfenetmap.core.descriptors rbfenetmap.core.design rbfenetmap.core.diagnostics rbfenetmap.core.exceptions rbfenetmap.core.intermediates rbfenetmap.core.kabsch rbfenetmap.core.mcs rbfenetmap.core.meta.exporters rbfenetmap.core.meta.intermediates rbfenetmap.core.meta.mappers rbfenetmap.core.meta.planners rbfenetmap.core.meta.scorers rbfenetmap.core.models rbfenetmap.core.molgraph rbfenetmap.core.options rbfenetmap.core.pairs rbfenetmap.core.pipeline rbfenetmap.core.pluginregistry rbfenetmap.core.posing rbfenetmap.core.replanning rbfenetmap.core.softcore rbfenetmap.core.surgery rbfenetmap.core.validate rbfenetmap.gui rbfenetmap.gui.cache rbfenetmap.gui.schema rbfenetmap.gui.server rbfenetmap.gui.session rbfenetmap.io.amber_masks rbfenetmap.io.loaders rbfenetmap.io.networkio rbfenetmap.plugins.exporters rbfenetmap.plugins.exporters.amber_exporter rbfenetmap.plugins.exporters.basic_exporters rbfenetmap.plugins.exporters.html_exporter rbfenetmap.plugins.intermediates rbfenetmap.plugins.intermediates.fragment_swap rbfenetmap.plugins.intermediates.pairmap_generator rbfenetmap.plugins.mappers rbfenetmap.plugins.mappers.cartograph_mapper rbfenetmap.plugins.mappers.identity_mapper rbfenetmap.plugins.mappers.kartograf_mapper rbfenetmap.plugins.mappers.mcss_mapper rbfenetmap.plugins.planners rbfenetmap.plugins.planners.mst_planner rbfenetmap.plugins.planners.optimal_planner rbfenetmap.plugins.planners.simple_planners rbfenetmap.plugins.scorers rbfenetmap.plugins.scorers.linear_scorer rbfenetmap.plugins.scorers.lomaplike_scorer rbfenetmap.plugins.scorers.softcore_size_scorer rbfenetmap.plugins.scorers.variance_scorer rbfenetmap.viz.depict rbfenetmap.viz.gallery rbfenetmap.viz.network_svg

mol_to_graph() (in module rbfenetmap.core.molgraph) MSTRedundancyPlanner (class in rbfenetmap.plugins.planners.mst_planner)

N

n_atoms (rbfenetmap.core.models.Ligand property) n_common_core (rbfenetmap.core.models.AtomMapping property) n_demoted (rbfenetmap.core.models.SoftcoreRepair property) n_heavy (rbfenetmap.core.models.Ligand property) n_heavy() (rbfenetmap.core.softcore.RepairContext method) n_softcore_1 (rbfenetmap.core.models.AtomMapping property) n_softcore_2 (rbfenetmap.core.models.AtomMapping property) name (rbfenetmap.core.meta.exporters.AbstractExporter attribute) (rbfenetmap.core.meta.intermediates.AbstractIntermediateGenerator attribute) (rbfenetmap.core.meta.mappers.AbstractMapper attribute) Network (class in rbfenetmap.core.models)

network (rbfenetmap.gui.session.PlanRun attribute) network_cost() (in module rbfenetmap.core.diagnostics) network_cost_summary() (in module rbfenetmap.core.cost) network_efficiency() (in module rbfenetmap.core.diagnostics) network_gpu_hours() (rbfenetmap.core.cost.CostModel method) network_price() (rbfenetmap.core.cost.CostModel method) network_to_dict() (in module rbfenetmap.io.networkio) NetworkOptions (class in rbfenetmap.core.options) NetworkPlanError NO_DONOR_ATOMS (rbfenetmap.core.posing.PoseRejection attribute) node_weighted_steiner() (in module rbfenetmap.core.molgraph) normalize_edge_specs() (in module rbfenetmap.core.options)

O

OptimalDesignPlanner (class in rbfenetmap.plugins.planners.optimal_planner)

orient_edge() (in module rbfenetmap.core.models) OUTPUT_DESTS (in module rbfenetmap.gui.schema)

P

pair_distances() (in module rbfenetmap.core.kabsch) PairMapGenerator (class in rbfenetmap.plugins.intermediates.pairmap_generator) parse_edge_key() (in module rbfenetmap.core.models) parse_key_values() (in module rbfenetmap.cli._args) pin() (rbfenetmap.gui.session.PlanSession method) PIPELINE_KNOBS (in module rbfenetmap.gui.schema) plan() (rbfenetmap.core.meta.planners.AbstractNetworkPlanner method) (rbfenetmap.plugins.planners.mst_planner.MSTRedundancyPlanner method) (rbfenetmap.plugins.planners.optimal_planner.OptimalDesignPlanner method) (rbfenetmap.plugins.planners.simple_planners.CompletePlanner method) (rbfenetmap.plugins.planners.simple_planners.ExplicitPlanner method) (rbfenetmap.plugins.planners.simple_planners.StarPlanner method) plan_schema() (in module rbfenetmap.gui.schema) PLANNER_KNOBS (in module rbfenetmap.gui.schema) PlanRun (class in rbfenetmap.gui.session) PlanSession (class in rbfenetmap.gui.session) PluginError PluginRegistry (class in rbfenetmap.core.pluginregistry) PluginSpec (class in rbfenetmap.core.pluginregistry) pose_intermediate() (in module rbfenetmap.core.posing)

POSE_RMSD_EXCEEDED (rbfenetmap.core.posing.PoseRejection attribute) POSE_RMSD_FACTOR (in module rbfenetmap.core.posing) posed (rbfenetmap.core.posing.PoseResult property) PoseDonor (class in rbfenetmap.core.posing) PoseRejection (class in rbfenetmap.core.posing) PoseResult (class in rbfenetmap.core.posing) precheck_mapping() (in module rbfenetmap.core.softcore) preset() (rbfenetmap.core.options.CorePruningPolicy class method) (rbfenetmap.core.options.NetworkOptions class method) propose() (rbfenetmap.core.meta.intermediates.AbstractIntermediateGenerator method) (rbfenetmap.plugins.intermediates.fragment_swap.FragmentSwapGenerator method) (rbfenetmap.plugins.intermediates.pairmap_generator.PairMapGenerator method) proposed (rbfenetmap.core.intermediates.IntermediateProposal property) ProposedLink (class in rbfenetmap.core.intermediates) ProposedMolecule (class in rbfenetmap.core.intermediates) prune_core() (in module rbfenetmap.core.coreprune) pruning_preset (rbfenetmap.plugins.mappers.mcss_mapper.MCSSExtended2Mapper attribute) (rbfenetmap.plugins.mappers.mcss_mapper.MCSSExtendedMapper attribute) (rbfenetmap.plugins.mappers.mcss_mapper.MCSSMapper attribute) put() (rbfenetmap.gui.cache.MappingCache method)

R

rbfe_edges (rbfenetmap.core.models.Network property) rbfenetmap.cli._args module rbfenetmap.cli.commands module rbfenetmap.cli.main module rbfenetmap.core.align module rbfenetmap.core.cbfe module rbfenetmap.core.clustering module rbfenetmap.core.consistency module rbfenetmap.core.coreprune module rbfenetmap.core.cost module rbfenetmap.core.descriptors module rbfenetmap.core.design module rbfenetmap.core.diagnostics module rbfenetmap.core.exceptions module rbfenetmap.core.intermediates module rbfenetmap.core.kabsch module rbfenetmap.core.mcs module rbfenetmap.core.meta.exporters module rbfenetmap.core.meta.intermediates module rbfenetmap.core.meta.mappers module rbfenetmap.core.meta.planners module rbfenetmap.core.meta.scorers module rbfenetmap.core.models module rbfenetmap.core.molgraph module rbfenetmap.core.options module rbfenetmap.core.pairs module rbfenetmap.core.pipeline module rbfenetmap.core.pluginregistry module rbfenetmap.core.posing module rbfenetmap.core.replanning module rbfenetmap.core.softcore module rbfenetmap.core.surgery module rbfenetmap.core.validate module rbfenetmap.gui module rbfenetmap.gui.cache module rbfenetmap.gui.schema module rbfenetmap.gui.server module rbfenetmap.gui.session module rbfenetmap.io.amber_masks module rbfenetmap.io.loaders module rbfenetmap.io.networkio module

rbfenetmap.plugins.exporters module rbfenetmap.plugins.exporters.amber_exporter module rbfenetmap.plugins.exporters.basic_exporters module rbfenetmap.plugins.exporters.html_exporter module rbfenetmap.plugins.intermediates module rbfenetmap.plugins.intermediates.fragment_swap module rbfenetmap.plugins.intermediates.pairmap_generator module rbfenetmap.plugins.mappers module rbfenetmap.plugins.mappers.cartograph_mapper module rbfenetmap.plugins.mappers.identity_mapper module rbfenetmap.plugins.mappers.kartograf_mapper module rbfenetmap.plugins.mappers.mcss_mapper module rbfenetmap.plugins.planners module rbfenetmap.plugins.planners.mst_planner module rbfenetmap.plugins.planners.optimal_planner module rbfenetmap.plugins.planners.simple_planners module rbfenetmap.plugins.scorers module rbfenetmap.plugins.scorers.linear_scorer module rbfenetmap.plugins.scorers.lomaplike_scorer module rbfenetmap.plugins.scorers.softcore_size_scorer module rbfenetmap.plugins.scorers.variance_scorer module rbfenetmap.viz.depict module rbfenetmap.viz.gallery module rbfenetmap.viz.network_svg module RBFENetworkMapError reconnect_pairs() (in module rbfenetmap.core.pairs) RedundantMSTPlanner (class in rbfenetmap.plugins.planners.mst_planner) register() (rbfenetmap.core.pluginregistry.PluginRegistry method) register_exporters() (in module rbfenetmap.plugins.exporters) register_intermediates() (in module rbfenetmap.plugins.intermediates) register_mappers() (in module rbfenetmap.plugins.mappers) register_planners() (in module rbfenetmap.plugins.planners) register_scorers() (in module rbfenetmap.plugins.scorers) rejected (rbfenetmap.core.models.Network property) rejected() (rbfenetmap.core.models.EdgeScore class method) RejectionReason (class in rbfenetmap.core.models) render_edge_svg() (in module rbfenetmap.viz.depict) render_molecule_svg() (in module rbfenetmap.viz.depict) render_network_svg() (in module rbfenetmap.viz.network_svg) render_report() (in module rbfenetmap.viz.gallery) repair_softcore_connectivity() (in module rbfenetmap.core.softcore) RepairContext (class in rbfenetmap.core.softcore) RepairError replan_after_diagnostics() (in module rbfenetmap.core.replanning) report_html() (rbfenetmap.gui.session.PlanRun method) require_exporters() (in module rbfenetmap.plugins.exporters) require_intermediates() (in module rbfenetmap.plugins.intermediates) require_mappers() (in module rbfenetmap.plugins.mappers) require_planners() (in module rbfenetmap.plugins.planners) require_scorers() (in module rbfenetmap.plugins.scorers) reserve_intermediate_names() (in module rbfenetmap.core.intermediates) resolve_compat() (in module rbfenetmap.cli._args) reverse (rbfenetmap.core.models.AtomMapping property) reversed() (rbfenetmap.core.models.Transformation method) rigid_transform() (in module rbfenetmap.core.kabsch) ring_systems() (in module rbfenetmap.core.molgraph) RunCancelled

S

sanitize_name() (in module rbfenetmap.io.loaders) save() (rbfenetmap.gui.cache.MappingCache method) SCHEMA_VERSION (in module rbfenetmap.io.networkio) score_edge() (rbfenetmap.core.meta.scorers.AbstractScorer method) (rbfenetmap.plugins.scorers.linear_scorer.LinearScorer method) (rbfenetmap.plugins.scorers.lomaplike_scorer.LomapLikeScorer method) (rbfenetmap.plugins.scorers.softcore_size_scorer.SoftcoreSizeScorer method) (rbfenetmap.plugins.scorers.variance_scorer.VarianceScorer method) select_bridges() (in module rbfenetmap.core.cbfe) select_cbfe_bridges() (in module rbfenetmap.core.cbfe) select_high_lmi_edges() (in module rbfenetmap.core.replanning) serve() (in module rbfenetmap.gui.server) set_ligands() (rbfenetmap.gui.session.PlanSession method) side() (rbfenetmap.core.softcore.RepairContext method) softcore_attachment_edges() (in module rbfenetmap.core.softcore) SOFTCORE_COLOR (in module rbfenetmap.viz.depict) SoftcorePolicy (class in rbfenetmap.core.options) SoftcoreRepair (class in rbfenetmap.core.models) SoftcoreSizeScorer (class in rbfenetmap.plugins.scorers.softcore_size_scorer) StarPlanner (class in rbfenetmap.plugins.planners.simple_planners) start() (rbfenetmap.gui.session.PlanSession method) state (rbfenetmap.gui.session.PlanRun attribute) state() (rbfenetmap.gui.session.PlanSession method)

STEREO_UNDEFINED (rbfenetmap.core.posing.PoseRejection attribute) stranded_components() (in module rbfenetmap.core.molgraph) succeeded (rbfenetmap.core.models.SoftcoreRepair property) summarize() (in module rbfenetmap.core.design) (in module rbfenetmap.core.diagnostics) summarize_json() (in module rbfenetmap.core.diagnostics) superpose() (in module rbfenetmap.core.kabsch) supports_cbfe (rbfenetmap.core.meta.planners.AbstractNetworkPlanner attribute) (rbfenetmap.plugins.planners.mst_planner.MSTRedundancyPlanner attribute) (rbfenetmap.plugins.planners.mst_planner.RedundantMSTPlanner attribute) (rbfenetmap.plugins.planners.optimal_planner.OptimalDesignPlanner attribute) supports_design (rbfenetmap.core.meta.planners.AbstractNetworkPlanner attribute) (rbfenetmap.plugins.planners.optimal_planner.OptimalDesignPlanner attribute) supports_pair() (rbfenetmap.core.meta.intermediates.AbstractIntermediateGenerator method) (rbfenetmap.core.meta.mappers.AbstractMapper method) (rbfenetmap.gui.cache.CachingMapper method) (rbfenetmap.plugins.intermediates.pairmap_generator.PairMapGenerator method) svg (rbfenetmap.gui.session.PlanRun attribute) swapped() (rbfenetmap.core.models.AtomMapping method) synthesize_ligand() (in module rbfenetmap.core.intermediates) synthesized() (rbfenetmap.core.models.Ligand class method) synthetic (rbfenetmap.core.models.Ligand property) synthetic_ligands (rbfenetmap.core.models.Network property) synthetic_names (rbfenetmap.core.pipeline.AugmentationResult property)

T

TERM_DEFINITIONS (in module rbfenetmap.plugins.scorers.linear_scorer) to_argv() (in module rbfenetmap.gui.schema)

to_contract() (rbfenetmap.core.models.AtomMapping method) to_networkx() (rbfenetmap.core.models.Network method) Transformation (class in rbfenetmap.core.models)

U

unordered_key (rbfenetmap.core.models.Transformation property)

unpin() (rbfenetmap.gui.session.PlanSession method)

V

validate() (rbfenetmap.core.meta.exporters.AbstractExporter method) (rbfenetmap.core.models.Network method) (rbfenetmap.plugins.exporters.amber_exporter.AmberExporter method)

validate_mapping() (in module rbfenetmap.core.validate) values (rbfenetmap.gui.session.PlanRun attribute) VarianceScorer (class in rbfenetmap.plugins.scorers.variance_scorer)

W

WIDGETS (in module rbfenetmap.gui.schema)