Index

B

build_index() (ppiref.comparison.IDist method)

C

chain_id (ppiref.utils.residue.Residue attribute) clean() (ppiref.surface.DR_SASA method) cluster_embeddings() (ppiref.comparison.IDist method) compare() (ppiref.comparison.FoldseekMMComparator method) (ppiref.comparison.IAlign method) (ppiref.comparison.IDist method) (ppiref.comparison.PPIComparator method) (ppiref.comparison.SequenceIdentityComparator method) (ppiref.comparison.USalign method)

compare_all_against_all() (ppiref.comparison.IDist method) (ppiref.comparison.PPIComparator method) construct() (ppiref.utils.ppipath.PPIPath class method) contains() (ppiref.utils.ppipath.PPIPath method)

D

deduplicate_embeddings() (ppiref.comparison.IDist method) display_ppi() (ppiref.visualization.PyMOL method)

download_from_zenodo() (in module ppiref.utils.misc) download_pdb() (in module ppiref.utils.pdb) DR_SASA (class in ppiref.surface)

E

embed() (ppiref.comparison.IDist method) embed_parallel() (ppiref.comparison.IDist method)

embed_without_exception() (ppiref.comparison.IDist method) extract() (ppiref.extraction.PPIExtractor method) extract_parallel() (ppiref.extraction.PPIExtractor method)

F

FoldseekMMComparator (class in ppiref.comparison)

G

get_embeddings() (ppiref.comparison.IDist method) get_first_model() (in module ppiref.utils.pdb)

get_n_models() (in module ppiref.utils.pdb) get_partition() (in module ppiref.utils.misc)

I

IAlign (class in ppiref.comparison) IDist (class in ppiref.comparison) insertion (ppiref.utils.residue.Residue attribute)

is_dummy() (ppiref.utils.ppi.PPI method) (ppiref.utils.ppipath.PPIPath method) is_equivalent_to() (ppiref.utils.ppipath.PPIPath method)

L

list_to_chunks() (in module ppiref.utils.misc)

M

MMSeqs2PPIRetriever (class in ppiref.retrieval) module ppiref ppiref.comparison ppiref.definitions ppiref.extraction ppiref.retrieval ppiref.split ppiref.surface ppiref.utils ppiref.utils.misc ppiref.utils.pdb ppiref.utils.ppi ppiref.utils.ppipath ppiref.utils.residue ppiref.visualization

N

n_residues() (ppiref.utils.ppi.PPI method)

P

parse_residue() (ppiref.surface.DR_SASA static method) partners() (ppiref.utils.ppipath.PPIPath method) path_to_partners() (in module ppiref.utils.ppipath) path_to_pdb_id() (in module ppiref.utils.ppipath) path_to_ppi_id() (in module ppiref.utils.ppipath) pdb_id() (ppiref.utils.ppipath.PPIPath method) pdb_id_to_nested_suffix() (in module ppiref.utils.ppipath) PPI (class in ppiref.utils.ppi) ppi_id() (ppiref.utils.ppipath.PPIPath method) ppi_id_to_nested_suffix() (in module ppiref.utils.ppipath) PPIComparator (class in ppiref.comparison) PPIExtractor (class in ppiref.extraction) PPIPath (class in ppiref.utils.ppipath) ppiref module ppiref.comparison module ppiref.definitions module ppiref.extraction module

ppiref.retrieval module ppiref.split module ppiref.surface module ppiref.utils module ppiref.utils.misc module ppiref.utils.pdb module ppiref.utils.ppi module ppiref.utils.ppipath module ppiref.utils.residue module ppiref.visualization module PyMOL (class in ppiref.visualization)

Q

query() (ppiref.comparison.IDist method) (ppiref.retrieval.MMSeqs2PPIRetriever method)

R

random_id() (in module ppiref.utils.misc) read_embeddings() (ppiref.comparison.IDist method) read_fold() (in module ppiref.split)

read_split() (in module ppiref.split) read_split_source() (in module ppiref.split) Residue (class in ppiref.utils.residue) residue_number (ppiref.utils.residue.Residue attribute)

S

SequenceIdentityComparator (class in ppiref.comparison)

sort_partners() (in module ppiref.utils.ppi)

U

USalign (class in ppiref.comparison)

V

visualize() (ppiref.utils.ppi.PPI method)

W

with_sorted_partners() (ppiref.utils.ppipath.PPIPath method)

write_embeddings() (ppiref.comparison.IDist method) write_split() (in module ppiref.split)