hPDB-1.2.0: Protein Databank file format library

Safe HaskellNone

Bio.PDB.Fasta

Description

Conversion of PDB residue codes to FASTA single-letter sequence codes.

Synopsis

Documentation

resname2fastacode :: String -> CharSource

Dictionary mapping three-letter PDB residue code to a single-letter FASTA code.

fastacode2resname :: Char -> StringSource

Dictionary mapping single-letter FASTA standard aminoacid code to a PDB residue name

defaultResname :: StringSource

Three-letter PDB code for an unknown type of residue.

defaultFastaCode :: CharSource

One-letter aminoacid code for an unknown type of residue.

fastaSequence :: Iterable a Residue => a -> [Char]Source

Converts an Iterable yielding Residues into a list of aminoacid one-character codes.

fastaGappedSequence :: Iterable a Residue => a -> [Char]Source

Converts an Iterable yielding Residues into a list of aminoacid one-character codes.

fastaRecord :: [Char] -> Chain -> [Char]Source

Returns String with ungapped sequence of a given PDB Chain.

fastaGappedRecord :: [Char] -> Chain -> [Char]Source

Returns String with gapped sequence of a given PDB Chain. Gaps are placed to assure consistent numbering of residues and indices in the output String.