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) 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) 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) executor() (prolif.parallel.MolIterablePool class method) (prolif.parallel.TrajectoryPool class method) 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_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) (prolif.parallel.TrajectoryPool class method) 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 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 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) 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) (prolif.parallel.TrajectoryPool attribute) process() (prolif.parallel.MolIterablePool method) (prolif.parallel.TrajectoryPool method) Progress (class in prolif.parallel) 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 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) 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) tracker (prolif.parallel.TrajectoryPool attribute) Trajectory (in module prolif.typeshed) TrajectoryPool (class in prolif.parallel) U update() (prolif.parallel.Progress method) 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)