Safe Haskell | None |
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- 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 :: (Eq a1, Fractional a, Show a1, IsString 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.
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
class Iterable a b where
Class for iterating all nested components b
of type a
.
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
numResidues :: Iterable a Residue => a -> IntSource
Number of all residues within the structure.
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
(*|) :: Double -> Vector3 -> Vector3Source
Scalar product. (asterisk - * - indicates side on which one can put a scalar.)
(|*) :: Vector3 -> Double -> Vector3Source
Scalar product. (asterisk - * - indicates side on which one can put a scalar.)
type Element = ByteStringSource
Type alias for Element
names.
atomicNumber :: Element -> IntSource
Atomic number of a given element
atomicMass :: Element -> DoubleSource
Atomic mass of a given element in g/mol
covalentRadius :: (Eq a1, Fractional a, Show a1, IsString a1) => a1 -> aSource
Covalent radius of an element with a given name.
vanDerWaalsRadius :: Element -> DoubleSource
Van der Waals radius of the given element