ExperimentalFeaturesReporters

PdbDataFeatures

The PdbDataFeatures records information that is stored in the protein databank structure format.

    <feature name=PdbDataFeatures/>

• residue_pdb_identification : Identify residues using the PDB nomenclature. Note, this numbering has biological relevance and therefore may be negative, skip numbers, etc. When using the DatabaseInputer or DatabaseOutputter with the Rosetta job distributor, this table is mapped to the PDBInfo object.
  • struct_id , residue_number : References the primary key in the residues table
  • chain_id : ATOM record columns 21
  • insertion_code : ATOM record column 26
  • pdb_residue_number : PDB identification 22-25

    CREATE TABLE IF NOT EXISTS residue_pdb_identification (
        struct_id INTEGER AUTOINCREMENT,
        residue_number INTEGER,
        chain_id TEXT,
        insertion_code TEXT,
        pdb_residue_number INTEGER,
        FOREIGN KEY (struct_id, residue_number)
            REFERENCES residues (struct_id, resNum)
            DEFERRABLE INITIALLY DEFERRED,
        PRIMARY KEY (struct_id, residue_number));

• residue_pdb_confidence : Summarize atom level confidence measures (B-factors and occupancy) to the residue level with the intention that they will be used to filter out residues.
  • max_\_temperature* : The maximum temperature (ATOM record columns 60-65) over different atom subsets: all, backbone, sidechain.
  • min_\_occupancy* : The minimum occupancy (ATOM record columns 54-59) over different atom subsets: all, backbone, sidechain.

    CREATE TABLE IF NOT EXISTS residue_pdb_confidence (
        struct_id INTEGER,
        residue_number INTEGER,
        max_temperature REAL,
        max_bb_temperature REAL,
        max_sc_temperature REAL,
        min_occupancy REAL,
        min_bb_occupancy REAL,
        min_sc_occupancy REAL,
        FOREIGN KEY (struct_id, residue_number)
            REFERENCES residues (struct_id, resNum)
            DEFERRABLE INITIALLY DEFERRED,
        PRIMARY KEY (struct_id, residue_number));