| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.PDB
- 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 :: String -> Char
- fastacode2resname :: Char -> String
- (*|) :: Double -> Vector3 -> Vector3
- (|*) :: Vector3 -> Double -> Vector3
- vnorm :: Vector3 -> Double
- type Element = ByteString
- assignElement :: Atom -> Element
- atomicNumber :: Element -> Int
- atomicMass :: Element -> Double
- covalentRadius :: (IsString a1, Show a1, Fractional a, Eq a1) => a1 -> a
- vanDerWaalsRadius :: Element -> Double
Documentation
write :: PDBWritable a => a -> FilePath -> IO () Source
Write structure to a .pdb file.
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 | |
class Iterable a b where
Class for iterating all nested components b of type a.
Methods
itmapM :: Monad m => (b -> m b) -> a -> m a
itmap :: (b -> b) -> a -> a
itfoldM :: Monad m => (c -> b -> m c) -> c -> a -> m c
itfoldr :: (b -> c -> c) -> c -> a -> c
itfoldl :: (c -> b -> c) -> c -> a -> c
itfoldl' :: (c -> b -> c) -> c -> a -> c
Instances
numResidues :: Iterable a Residue => a -> Int Source
Number of all residues within the structure.
resname2fastacode :: String -> Char Source
Dictionary mapping three-letter PDB residue code to a single-letter FASTA code.
fastacode2resname :: Char -> String 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 :: (IsString a1, Show a1, Fractional a, Eq a1) => a1 -> a Source
Covalent radius of an element with a given name.
vanDerWaalsRadius :: Element -> Double Source
Van der Waals radius of the given element