Index

_

_ids_count (deeprank2.query.QueryCollection attribute)

_queries (deeprank2.query.QueryCollection attribute)

A

add() (deeprank2.query.QueryCollection method) add_atom() (deeprank2.molstruct.residue.Residue method) add_chain() (deeprank2.molstruct.structure.PDBStructure method) add_residue() (deeprank2.molstruct.structure.Chain method) add_target() (in module deeprank2.tools.target) AlignmentGNN (class in deeprank2.neuralnets.gnn.alignmentnet) amino_acid (deeprank2.molstruct.residue.Residue property)

AminoAcid (class in deeprank2.molstruct.aminoacid) Atom (class in deeprank2.molstruct.atom) atom1 (deeprank2.molstruct.pair.AtomicContact property) atom2 (deeprank2.molstruct.pair.AtomicContact property) AtomicContact (class in deeprank2.molstruct.pair) AtomicElement (class in deeprank2.molstruct.atom) atoms (deeprank2.molstruct.residue.Residue property)

B

build() (deeprank2.query.ProteinProteinInterfaceQuery method) (deeprank2.query.Query method) (deeprank2.query.SingleResidueVariantQuery method)

C

C (deeprank2.molstruct.atom.AtomicElement attribute) Chain (class in deeprank2.molstruct.structure) chain (deeprank2.molstruct.residue.Residue property) chain_ids (deeprank2.query.ProteinProteinInterfaceQuery attribute) (deeprank2.query.Query attribute) (deeprank2.query.SingleResidueVariantQuery attribute) chains (deeprank2.molstruct.structure.PDBStructure property)

change_altloc() (deeprank2.molstruct.atom.Atom method) charge (deeprank2.molstruct.aminoacid.AminoAcid property) CnnClassification (class in deeprank2.neuralnets.cnn.model3d) CnnRegression (class in deeprank2.neuralnets.cnn.model3d) compute_ppi_scores() (in module deeprank2.tools.target) configure_optimizers() (deeprank2.trainer.Trainer method) Contact (class in deeprank2.molstruct.pair)

D

deeprank2.dataset module deeprank2.molstruct.aminoacid module deeprank2.molstruct.atom module deeprank2.molstruct.pair module deeprank2.molstruct.residue module deeprank2.molstruct.structure module deeprank2.neuralnets.cnn.model3d module deeprank2.neuralnets.gnn.alignmentnet module

deeprank2.neuralnets.gnn.foutnet module deeprank2.neuralnets.gnn.ginet module deeprank2.neuralnets.gnn.ginet_nocluster module deeprank2.neuralnets.gnn.sgat module deeprank2.neuralnets.gnn.vanilla_gnn module deeprank2.query module deeprank2.tools.target module deeprank2.trainer module DeeprankDataset (class in deeprank2.dataset)

E

edge_model() (deeprank2.neuralnets.gnn.alignmentnet.GNNLayer method)

element (deeprank2.molstruct.atom.Atom property) export_dict() (deeprank2.query.QueryCollection method)

F

forward() (deeprank2.neuralnets.cnn.model3d.CnnClassification method) (deeprank2.neuralnets.cnn.model3d.CnnRegression method) (deeprank2.neuralnets.gnn.alignmentnet.AlignmentGNN method) (deeprank2.neuralnets.gnn.foutnet.FoutLayer method) (deeprank2.neuralnets.gnn.foutnet.FoutNet method) (deeprank2.neuralnets.gnn.ginet.GINet method) (deeprank2.neuralnets.gnn.ginet.GINetConvLayer method) (deeprank2.neuralnets.gnn.ginet_nocluster.GINet method) (deeprank2.neuralnets.gnn.ginet_nocluster.GINetConvLayer method) (deeprank2.neuralnets.gnn.sgat.SGAT method) (deeprank2.neuralnets.gnn.sgat.SGraphAttentionLayer method) (deeprank2.neuralnets.gnn.vanilla_gnn.VanillaConvolutionalLayer method) (deeprank2.neuralnets.gnn.vanilla_gnn.VanillaNetwork method)

FoutLayer (class in deeprank2.neuralnets.gnn.foutnet) FoutNet (class in deeprank2.neuralnets.gnn.foutnet)

G

get() (deeprank2.dataset.GraphDataset method) (deeprank2.dataset.GridDataset method) get_atoms() (deeprank2.molstruct.structure.Chain method) (deeprank2.molstruct.structure.PDBStructure method) get_center() (deeprank2.molstruct.residue.Residue method) get_chain() (deeprank2.molstruct.structure.PDBStructure method) get_pssm() (deeprank2.molstruct.residue.Residue method) get_query_id() (deeprank2.query.ProteinProteinInterfaceQuery method) (deeprank2.query.Query method) (deeprank2.query.SingleResidueVariantQuery method)

get_residue() (deeprank2.molstruct.structure.Chain method) GINet (class in deeprank2.neuralnets.gnn.ginet) (class in deeprank2.neuralnets.gnn.ginet_nocluster) GINetConvLayer (class in deeprank2.neuralnets.gnn.ginet) (class in deeprank2.neuralnets.gnn.ginet_nocluster) GNNLayer (class in deeprank2.neuralnets.gnn.alignmentnet) GraphDataset (class in deeprank2.dataset) GridDataset (class in deeprank2.dataset)

H

H (deeprank2.molstruct.atom.AtomicElement attribute) has_chain() (deeprank2.molstruct.structure.PDBStructure method) has_residue() (deeprank2.molstruct.structure.Chain method) hdf5_to_pandas() (deeprank2.dataset.DeeprankDataset method) (deeprank2.dataset.GraphDataset method) (deeprank2.dataset.GridDataset method)

hydrogen_bond_acceptors (deeprank2.molstruct.aminoacid.AminoAcid property) hydrogen_bond_donors (deeprank2.molstruct.aminoacid.AminoAcid property)

I

id (deeprank2.molstruct.structure.Chain property) (deeprank2.molstruct.structure.PDBStructure property) index (deeprank2.molstruct.aminoacid.AminoAcid property) influence_radius (deeprank2.query.ProteinProteinInterfaceQuery attribute) (deeprank2.query.Query attribute) (deeprank2.query.SingleResidueVariantQuery attribute)

insertion_code (deeprank2.molstruct.residue.Residue property) (deeprank2.query.SingleResidueVariantQuery attribute)

L

len() (deeprank2.dataset.DeeprankDataset method) (deeprank2.dataset.GraphDataset method) (deeprank2.dataset.GridDataset method)

load_one_graph() (deeprank2.dataset.GraphDataset method) load_one_grid() (deeprank2.dataset.GridDataset method)

M

mass (deeprank2.molstruct.aminoacid.AminoAcid property) max_edge_length (deeprank2.query.ProteinProteinInterfaceQuery attribute) (deeprank2.query.Query attribute) (deeprank2.query.SingleResidueVariantQuery attribute) model (deeprank2.molstruct.structure.Chain property) model_id (deeprank2.query.ProteinProteinInterfaceQuery property) (deeprank2.query.Query property) (deeprank2.query.SingleResidueVariantQuery property) module deeprank2.dataset deeprank2.molstruct.aminoacid deeprank2.molstruct.atom deeprank2.molstruct.pair deeprank2.molstruct.residue deeprank2.molstruct.structure deeprank2.neuralnets.cnn.model3d deeprank2.neuralnets.gnn.alignmentnet deeprank2.neuralnets.gnn.foutnet deeprank2.neuralnets.gnn.ginet deeprank2.neuralnets.gnn.ginet_nocluster deeprank2.neuralnets.gnn.sgat deeprank2.neuralnets.gnn.vanilla_gnn deeprank2.query deeprank2.tools.target deeprank2.trainer

N

N (deeprank2.molstruct.atom.AtomicElement attribute) name (deeprank2.molstruct.aminoacid.AminoAcid property) (deeprank2.molstruct.atom.Atom property) NEGATIVE (deeprank2.molstruct.aminoacid.Polarity attribute)

node_model() (deeprank2.neuralnets.gnn.alignmentnet.GNNLayer method) NONPOLAR (deeprank2.molstruct.aminoacid.Polarity attribute) number (deeprank2.molstruct.residue.Residue property) number_string (deeprank2.molstruct.residue.Residue property)

O

O (deeprank2.molstruct.atom.AtomicElement attribute) occupancy (deeprank2.molstruct.atom.Atom property) one_letter_code (deeprank2.molstruct.aminoacid.AminoAcid property)

onehot (deeprank2.molstruct.aminoacid.AminoAcid property) (deeprank2.molstruct.aminoacid.Polarity property) (deeprank2.molstruct.atom.AtomicElement property) output() (deeprank2.neuralnets.gnn.alignmentnet.GNNLayer method)

P

P (deeprank2.molstruct.atom.AtomicElement attribute) Pair (class in deeprank2.molstruct.pair) pdb_path (deeprank2.query.ProteinProteinInterfaceQuery attribute) (deeprank2.query.Query attribute) (deeprank2.query.SingleResidueVariantQuery attribute) PDBStructure (class in deeprank2.molstruct.structure) pI (deeprank2.molstruct.aminoacid.AminoAcid property) POLAR (deeprank2.molstruct.aminoacid.Polarity attribute) Polarity (class in deeprank2.molstruct.aminoacid) polarity (deeprank2.molstruct.aminoacid.AminoAcid property)

position (deeprank2.molstruct.atom.Atom property) (deeprank2.molstruct.residue.Residue property) POSITIVE (deeprank2.molstruct.aminoacid.Polarity attribute) preprocess() (deeprank2.neuralnets.gnn.alignmentnet.AlignmentGNN method) (deeprank2.neuralnets.gnn.alignmentnet.SuperGNN method) process() (deeprank2.query.QueryCollection method) ProteinProteinInterfaceQuery (class in deeprank2.query) pssm (deeprank2.molstruct.structure.Chain property) pssm_paths (deeprank2.query.ProteinProteinInterfaceQuery attribute) (deeprank2.query.Query attribute) (deeprank2.query.SingleResidueVariantQuery attribute)

Q

queries (deeprank2.query.QueryCollection property)

Query (class in deeprank2.query) QueryCollection (class in deeprank2.query)

R

reset_parameters() (deeprank2.neuralnets.gnn.foutnet.FoutLayer method) (deeprank2.neuralnets.gnn.ginet.GINetConvLayer method) (deeprank2.neuralnets.gnn.ginet_nocluster.GINetConvLayer method) (deeprank2.neuralnets.gnn.sgat.SGraphAttentionLayer method) Residue (class in deeprank2.molstruct.residue) residue (deeprank2.molstruct.atom.Atom property) (deeprank2.molstruct.residue.SingleResidueVariant property) residue1 (deeprank2.molstruct.pair.ResidueContact property)

residue2 (deeprank2.molstruct.pair.ResidueContact property) residue_id (deeprank2.query.SingleResidueVariantQuery property) ResidueContact (class in deeprank2.molstruct.pair) residues (deeprank2.molstruct.structure.Chain property) resolution (deeprank2.query.ProteinProteinInterfaceQuery attribute) (deeprank2.query.Query attribute) (deeprank2.query.SingleResidueVariantQuery attribute) run_through_network() (deeprank2.neuralnets.gnn.alignmentnet.AlignmentGNN method) (deeprank2.neuralnets.gnn.alignmentnet.SuperGNN method)

S

S (deeprank2.molstruct.atom.AtomicElement attribute) save_hdf5_keys() (in module deeprank2.dataset) save_hist() (deeprank2.dataset.DeeprankDataset method) (deeprank2.dataset.GraphDataset method) (deeprank2.dataset.GridDataset method) set_lossfunction() (deeprank2.trainer.Trainer method) SGAT (class in deeprank2.neuralnets.gnn.sgat) SGraphAttentionLayer (class in deeprank2.neuralnets.gnn.sgat)

SingleResidueVariant (class in deeprank2.molstruct.residue) SingleResidueVariantQuery (class in deeprank2.query) size (deeprank2.molstruct.aminoacid.AminoAcid property) sum_messages() (deeprank2.neuralnets.gnn.alignmentnet.GNNLayer method) SuperGNN (class in deeprank2.neuralnets.gnn.alignmentnet) suppress_pssm_errors (deeprank2.query.ProteinProteinInterfaceQuery attribute) (deeprank2.query.Query attribute) (deeprank2.query.SingleResidueVariantQuery attribute)

T

targets (deeprank2.query.ProteinProteinInterfaceQuery attribute) (deeprank2.query.Query attribute) (deeprank2.query.SingleResidueVariantQuery attribute)

test() (deeprank2.trainer.Trainer method) three_letter_code (deeprank2.molstruct.aminoacid.AminoAcid property) train() (deeprank2.trainer.Trainer method) Trainer (class in deeprank2.trainer)

U

update_nodes() (deeprank2.neuralnets.gnn.alignmentnet.GNNLayer method)

V

VanillaConvolutionalLayer (class in deeprank2.neuralnets.gnn.vanilla_gnn) VanillaNetwork (class in deeprank2.neuralnets.gnn.vanilla_gnn)

variant_amino_acid (deeprank2.molstruct.residue.SingleResidueVariant property) (deeprank2.query.SingleResidueVariantQuery attribute) variant_residue_number (deeprank2.query.SingleResidueVariantQuery attribute)

W

wildtype_amino_acid (deeprank2.molstruct.residue.SingleResidueVariant property) (deeprank2.query.SingleResidueVariantQuery attribute)