PPIRef
  • Welcome to PPIRef’s documentation!
  • Installation
  • PPIRef dataset
    • Downloading
    • Reconstructing from scratch
    • Using subsets and splits
  • Extracting PPIs
  • Analysing PPIs
  • Comparing PPIs
  • Deduplicating PPIs
  • Clustering PPIs
  • Retrieving PPIs
    • By similar interface structure
    • By similar sequence
  • Splitting and subsetting PPIs
  • API Reference
    • ppiref.comparison
      • FoldseekMMComparator
        • FoldseekMMComparator.compare()
      • IAlign
        • IAlign.compare()
      • IDist
        • IDist.build_index()
        • IDist.cluster_embeddings()
        • IDist.compare()
        • IDist.compare_all_against_all()
        • IDist.deduplicate_embeddings()
        • IDist.embed()
        • IDist.embed_parallel()
        • IDist.embed_without_exception()
        • IDist.get_embeddings()
        • IDist.query()
        • IDist.read_embeddings()
        • IDist.write_embeddings()
      • PPIComparator
        • PPIComparator.compare()
        • PPIComparator.compare_all_against_all()
      • SequenceIdentityComparator
        • SequenceIdentityComparator.compare()
      • USalign
        • USalign.compare()
    • ppiref.definitions
    • ppiref.extraction
      • PPIExtractor
        • PPIExtractor.extract()
        • PPIExtractor.extract_parallel()
    • ppiref.retrieval
      • MMSeqs2PPIRetriever
        • MMSeqs2PPIRetriever.query()
    • ppiref.split
      • read_fold()
      • read_split()
      • read_split_source()
      • write_split()
    • ppiref.surface
      • DR_SASA
        • DR_SASA.clean()
        • DR_SASA.parse_residue()
    • ppiref.visualization
      • PyMOL
        • PyMOL.display_ppi()
    • ppiref.utils
      • ppiref.utils.misc
        • download_from_zenodo()
        • get_partition()
        • list_to_chunks()
        • random_id()
      • ppiref.utils.pdb
        • download_pdb()
        • get_first_model()
        • get_n_models()
      • ppiref.utils.ppi
        • PPI
        • sort_partners()
      • ppiref.utils.ppipath
        • PPIPath
        • path_to_partners()
        • path_to_pdb_id()
        • path_to_ppi_id()
        • pdb_id_to_nested_suffix()
        • ppi_id_to_nested_suffix()
      • ppiref.utils.residue
        • Residue
PPIRef
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© Copyright 2024, Anton Bushuiev.

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