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PDB Module

Types and nested modules

Type/Module Description

ActivePatterns

Atom

atomic coordinate record containing the X,Y,Z orthogonal � coordinates for atoms in standard residues (amino acids and nucleic acids).

AtomName

Coordinate

DBREF

The DBREF record provides cross-reference links between PDB sequences (what appears in SEQRES record) and a corresponding database sequence.

HetAtom

atomic coordinate record containing the X,Y,Z orthogonal � coordinates for atoms in nonstandard residues. Nonstandard residues include inhibitors, cofactors, ions, and solvent. The only functional difference from ATOM records is that HETATM residues are by default not connected to other residues. Note that water residues should be in HETATM records.

Terminator

Functions and values

Function or value Description

parseCoordinates path

Full Usage: parseCoordinates path

Parameters:
    path : string

Returns: Coordinate seq
path : string
Returns: Coordinate seq

parseDBREFs path

Full Usage: parseDBREFs path

Parameters:
    path : string

Returns: DBREF seq
path : string
Returns: DBREF seq

tryParseCoordinateLine line

Full Usage: tryParseCoordinateLine line

Parameters:
    line : string

Returns: Coordinate option
line : string
Returns: Coordinate option

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