| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.PDB
Description
Default interface for Bio.PDB package.
Ideally should expose all commonly used functions and classes.
- parse :: FilePath -> IO (Maybe Structure)
- write :: PDBWritable a => a -> FilePath -> IO ()
- class PDBWritable a
- data Structure = Structure {}
- data Model = Model {}
- data Chain = Chain {}
- data Residue = Residue {}
- data Atom = Atom {}
- class Iterable a b where
- numAtoms :: Iterable a Atom => a -> Int
- numResidues :: Iterable a Residue => a -> Int
- numChains :: Iterable a Chain => a -> Int
- numModels :: Iterable a Model => a -> Int
- firstModel :: Iterable a Model => a -> Maybe Model
- resname2fastacode :: ByteString -> Char
- fastacode2resname :: Char -> ByteString
- (*|) :: Double -> Vector3 -> Vector3
- (|*) :: Vector3 -> Double -> Vector3
- vnorm :: Vector3 -> Double
- type Element = ByteString
- assignElement :: Atom -> Element
- atomicNumber :: Element -> Int
- atomicMass :: Element -> Double
- covalentRadius :: Element -> Double
- vanDerWaalsRadius :: Element -> Double
Documentation
class PDBWritable a Source #
Class generating events for PDB structure fragments.
Minimal complete definition
pdbEventS
Structure holds all data parsed from a single PDB entry
PDB entry may contain multiple models, with slight differences in coordinates etc.
Single linear polymer chain of protein, or nucleic acids
Residue groups all atoms assigned to the same aminoacid or nucleic acid base within a polymer chain.
Single atom position | NOTE: disordered atoms are now reported as multiplicates
Constructors
| Atom | |
resname2fastacode :: ByteString -> Char Source #
Dictionary mapping three-letter PDB residue code to a single-letter FASTA code.
fastacode2resname :: Char -> ByteString Source #
Dictionary mapping single-letter FASTA standard aminoacid code to a PDB residue name
(*|) :: Double -> Vector3 -> Vector3 Source #
Scalar product. (asterisk - "*" - indicates side on which one can put a scalar.)
(|*) :: Vector3 -> Double -> Vector3 Source #
Scalar product. (asterisk - "*" - indicates side on which one can put a scalar.)
type Element = ByteString Source #
Type alias for Element names.
atomicNumber :: Element -> Int Source #
Atomic number of a given element
atomicMass :: Element -> Double Source #
Atomic mass of a given element in g/mol
covalentRadius :: Element -> Double Source #
Covalent radius of an element with a given name.
vanDerWaalsRadius :: Element -> Double Source #
Van der Waals radius of the given element