hPDB-1.0: Protein Databank file format library

Safe Haskell	None

Bio.PDB

Synopsis

Documentation

parse :: FilePath -> IO (Maybe Structure)Source

Parse a .pdb file and return Structure.

write :: Structure -> FilePath -> IO ()Source

Write structure to a .pdb file.

data Structure Source

Structure holds all data parsed from a single PDB entry

Constructors

Structure
Fields models :: List Model

Instances

Eq Structure
Show Structure
NFData Structure
Iterable Structure Atom
Iterable Structure Residue
Iterable Structure Chain
Iterable Structure Model
Iterable Structure Structure

data Model Source

PDB entry may contain multiple models, with slight differences in coordinates etc.

Constructors

Model
Fields modelId :: !Int chains :: List Chain

Instances

Eq Model
Show Model
NFData Model
Iterable Model Atom
Iterable Model Residue
Iterable Model Chain
Iterable Model Model
Iterable Structure Model

data Chain Source

Single linear polymer chain of protein, or nucleic acids

Constructors

Chain
Fields chainId :: !Char residues :: List Residue

Instances

Eq Chain
Show Chain
NFData Chain
Iterable Chain Atom
Iterable Chain Residue
Iterable Chain Chain
Iterable Model Chain
Iterable Structure Chain

data Residue Source

Residue groups all atoms assigned to the same aminoacid or nucleic acid base within a polymer chain.

Constructors

Residue
Fields resName :: !String resSeq :: !Int atoms :: List Atom insCode :: !Char

Instances

Eq Residue
Show Residue
NFData Residue
Iterable Residue Atom
Iterable Residue Residue
Iterable Chain Residue
Iterable Model Residue
Iterable Structure Residue

data Atom Source

Single atom position | NOTE: disordered atoms are now reported as multiplicates

Constructors

Atom
Fields atName :: !String atSerial :: !Int coord :: !Vector3 bFactor :: !Double occupancy :: !Double element :: !String segid :: !String charge :: !String hetatm :: !Bool

Instances

Eq Atom
Show Atom
NFData Atom
Iterable Atom Atom
Iterable Residue Atom
Iterable Chain Atom
Iterable Model Atom
Iterable Structure 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

itlength :: b -> a -> Int

numAtoms :: Iterable a Atom => a -> Int Source

Number of all atoms within the structure.

numResidues :: Iterable a Residue => a -> Int Source

Number of all residues within the structure.

numChains :: Iterable a Chain => a -> Int Source

Number of all chains within the structure.

numModels :: Iterable a Model => a -> Int Source

Number of all models within the structure.

firstModel :: Iterable a Model => a -> Maybe Model Source

Takes a first model.

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.)

vnorm :: Vector3 -> Double Source

2-norm of a vector (also called a magnitude or length.)

type Element = ByteString Source

Type alias for Element names.

assignElement :: Atom -> Element Source

Given a PDB Atom extract or guess its Element name.

atomicNumber :: Element -> Int Source

Atomic number of a given element

atomicMass :: Element -> Double Source

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 -> Double Source

Van der Waals radius of the given element