Index A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U | V | W | X A add_vina_hbond_potential() (prolif.interactions.interactions.ImplicitHBAcceptor method) all() (prolif.interactions.base.Interaction method) Anionic (class in prolif.interactions.interactions) any() (prolif.interactions.base.Interaction method) assign_bond_orders_from_smiles() (in module prolif.io.protein_helper) assign_intra_props() (in module prolif.io.protein_helper) B Barcode (class in prolif.plotting.barcode) BasePiStacking (class in prolif.interactions.base) BaseRDKitMol (class in prolif.rdkitmol) best() (prolif.interactions.base.Interaction method) bitvector() (prolif.fingerprint.Fingerprint method) BRIDGED_INTERACTIONS (prolif.plotting.complex3d.Complex3D attribute) BridgedInteraction (class in prolif.interactions.base) C Cationic (class in prolif.interactions.interactions) CationPi (class in prolif.interactions.interactions) centroid (prolif.rdkitmol.BaseRDKitMol attribute) check_geometry() (prolif.interactions.interactions.ImplicitHBAcceptor method) check_resnames() (prolif.io.protein_helper.ProteinHelper static method) check_water_residue() (prolif.interactions.interactions.ImplicitHBAcceptor method) cif_parser_lite() (in module prolif.io.cif) cif_template_reader() (in module prolif.io.cif) close() (prolif.parallel.Progress method), [1] COLORS (prolif.plotting.barcode.Barcode attribute) (prolif.plotting.complex3d.Complex3D attribute) compare() (prolif.plotting.complex3d.Complex3D method) Complex3D (class in prolif.plotting.complex3d) convert_to_standard_resname() (prolif.io.protein_helper.ProteinHelper static method) count (prolif.fingerprint.Fingerprint attribute) D delay (prolif.parallel.Progress attribute), [1] detect() (prolif.interactions.interactions.ImplicitHBAcceptor method) (prolif.interactions.interactions.ImplicitHBDonor method) DISABLE_HOVER_CALLBACK (prolif.plotting.complex3d.Complex3D attribute) display() (prolif.plotting.barcode.Barcode method) (prolif.plotting.complex3d.Complex3D method) display_residues() (in module prolif.plotting.residues) Distance (class in prolif.interactions.base) DoubleAngle (class in prolif.interactions.base) E EdgeToFace (class in prolif.interactions.interactions) event_loop() (prolif.parallel.Progress method), [1] executor() (prolif.parallel.MolIterablePool class method), [1] (prolif.parallel.TrajectoryPool class method), [1] (prolif.parallel.TrajectoryPoolQueue class method), [1] F FaceToFace (class in prolif.interactions.interactions) Fingerprint (class in prolif.fingerprint) fix_molecule_bond_orders() (prolif.io.protein_helper.ProteinHelper static method) forcefield_guesser() (prolif.io.protein_helper.ProteinHelper static method) from_atom() (prolif.residue.ResidueId class method) from_fingerprint() (prolif.plotting.barcode.Barcode class method) (prolif.plotting.complex3d.Complex3D class method) from_mda() (prolif.molecule.Molecule class method) from_pickle() (prolif.fingerprint.Fingerprint class method) from_rdkit() (prolif.molecule.Molecule class method) from_string() (prolif.residue.ResidueId class method) G generate() (prolif.fingerprint.Fingerprint method) get_mda_parallel_strategy() (in module prolif.parallel), [1] get_n_jobs() (in module prolif.parallel), [1] get_residues_near_ligand() (in module prolif.utils) get_ring_centroid() (prolif.plotting.complex3d.Complex3D static method) H HBAcceptor (class in prolif.interactions.interactions) HBDonor (class in prolif.interactions.interactions) Hydrophobic (class in prolif.interactions.interactions) I IFP (class in prolif.ifp) ifp (prolif.fingerprint.Fingerprint attribute) IFPResults (in module prolif.typeshed) ImplicitHBAcceptor (class in prolif.interactions.interactions) ImplicitHBDonor (class in prolif.interactions.interactions) initializer() (prolif.parallel.MolIterablePool class method), [1] (prolif.parallel.TrajectoryPool class method), [1] (prolif.parallel.TrajectoryPoolQueue class method), [1] Interaction (class in prolif.interactions.base) interaction (prolif.ifp.InteractionData attribute) INTERACTION_HOVER_CALLBACK (prolif.plotting.complex3d.Complex3D attribute) InteractionData (class in prolif.ifp) interactions (prolif.fingerprint.Fingerprint attribute) interactions() (prolif.ifp.IFP method) invert_role() (prolif.interactions.base.Interaction class method) L ligand (prolif.ifp.InteractionData attribute) LIGAND_DISPLAYED_ATOM (prolif.plotting.complex3d.Complex3D attribute) LIGAND_RING_INTERACTIONS (prolif.plotting.complex3d.Complex3D attribute) LIGAND_STYLE (prolif.plotting.complex3d.Complex3D attribute) list_available() (prolif.fingerprint.Fingerprint static method) M MAX_JOBS (in module prolif.parallel), [1] MDA_PARALLEL_STRATEGY_THRESHOLD (in module prolif.parallel), [1] MDAObject (in module prolif.typeshed) metadata (prolif.ifp.InteractionData attribute) metadata() (prolif.fingerprint.Fingerprint method) (prolif.interactions.base.Interaction method) MetalAcceptor (class in prolif.interactions.interactions) MetalDonor (class in prolif.interactions.interactions) module prolif.fingerprint prolif.ifp prolif.interactions.base prolif.interactions.interactions prolif.interactions.water_bridge prolif.io.cif prolif.io.protein_helper prolif.molecule prolif.parallel, [1] prolif.plotting.barcode prolif.plotting.complex3d prolif.plotting.network prolif.plotting.residues prolif.rdkitmol prolif.residue prolif.typeshed prolif.utils mol2_supplier (class in prolif.molecule) Molecule (class in prolif.molecule) MolIterablePool (class in prolif.parallel), [1] N n_interactions (prolif.fingerprint.Fingerprint attribute) (prolif.fingerprint.Fingerprint property) n_residue_heavy_atoms() (prolif.io.protein_helper.ProteinHelper static method) n_residues (prolif.molecule.Molecule attribute) (prolif.residue.ResidueGroup attribute) n_template_residue_heavy_atoms() (prolif.io.protein_helper.ProteinHelper static method) P pdbqt_supplier (class in prolif.molecule) PEPTIDE_STYLE (prolif.plotting.complex3d.Complex3D attribute) PEPTIDE_THRESHOLD (prolif.plotting.complex3d.Complex3D attribute) PiCation (class in prolif.interactions.interactions) PiStacking (class in prolif.interactions.interactions) plot_3d() (prolif.fingerprint.Fingerprint method) plot_barcode() (prolif.fingerprint.Fingerprint method) plot_lignetwork() (prolif.fingerprint.Fingerprint method) pool (prolif.parallel.MolIterablePool attribute), [1] (prolif.parallel.TrajectoryPool attribute), [1] process() (prolif.parallel.MolIterablePool method), [1] (prolif.parallel.TrajectoryPool method), [1] (prolif.parallel.TrajectoryPoolQueue method), [1] Progress (class in prolif.parallel), [1] prolif.fingerprint module prolif.ifp module prolif.interactions.base module prolif.interactions.interactions module prolif.interactions.water_bridge module prolif.io.cif module prolif.io.protein_helper module prolif.molecule module prolif.parallel module, [1] prolif.plotting.barcode module prolif.plotting.complex3d module prolif.plotting.network module prolif.plotting.residues module prolif.rdkitmol module prolif.residue module prolif.typeshed module prolif.utils module protein (prolif.ifp.InteractionData attribute) PROTEIN_DISPLAYED_ATOM (prolif.plotting.complex3d.Complex3D attribute) PROTEIN_RING_INTERACTIONS (prolif.plotting.complex3d.Complex3D attribute) PROTEIN_STYLE (prolif.plotting.complex3d.Complex3D attribute) ProteinHelper (class in prolif.io.protein_helper) R resid (prolif.residue.Residue attribute) Residue (class in prolif.residue) RESIDUE_HOVER_CALLBACK (prolif.plotting.complex3d.Complex3D attribute) ResidueGroup (class in prolif.residue) ResidueId (class in prolif.residue) residues (prolif.molecule.Molecule attribute) RESIDUES_STYLE (prolif.plotting.complex3d.Complex3D attribute) run() (prolif.fingerprint.Fingerprint method) (prolif.interactions.water_bridge.WaterBridge method) run_from_iterable() (prolif.fingerprint.Fingerprint method) (prolif.interactions.water_bridge.WaterBridge method) S save_png() (prolif.plotting.complex3d.Complex3D method) sdf_supplier (class in prolif.molecule) select() (prolif.residue.ResidueGroup method) select_over_trajectory() (in module prolif.utils) setup() (prolif.interactions.base.BridgedInteraction method) (prolif.interactions.water_bridge.WaterBridge method) SingleAngle (class in prolif.interactions.base) split_molecule() (in module prolif.molecule) standardize_protein() (prolif.io.protein_helper.ProteinHelper method) strip_bonds() (in module prolif.io.protein_helper) T templates (prolif.io.protein_helper.ProteinHelper attribute) to_bitvectors() (in module prolif.utils) (prolif.fingerprint.Fingerprint method) to_countvectors() (prolif.fingerprint.Fingerprint method) to_dataframe() (in module prolif.utils) (prolif.fingerprint.Fingerprint method) to_pickle() (prolif.fingerprint.Fingerprint method) tqdm_pbar (prolif.parallel.Progress attribute), [1] tracker (prolif.parallel.TrajectoryPool attribute), [1] Trajectory (in module prolif.typeshed) TrajectoryPool (class in prolif.parallel), [1] TrajectoryPoolQueue (class in prolif.parallel), [1] U update() (prolif.parallel.Progress method), [1] use_segid (prolif.fingerprint.Fingerprint attribute) V VdWContact (class in prolif.interactions.interactions) vicinity_cutoff (prolif.fingerprint.Fingerprint attribute) W WaterBridge (class in prolif.interactions.water_bridge) X XBAcceptor (class in prolif.interactions.interactions) XBDonor (class in prolif.interactions.interactions) xyz (prolif.rdkitmol.BaseRDKitMol attribute)