Bio.PDB

Documentation

parse :: FilePath -> IO (Maybe Structure)

Parse a .pdb file and return Structure.

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

Write structure to a .pdb file.

data Structure

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

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

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

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

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

imapM :: Monad m => (b -> m b) -> a -> m a

imap :: (b -> b) -> a -> a

ifoldM :: Monad m => (c -> b -> m c) -> c -> a -> m c

ifoldr :: (b -> c -> c) -> c -> a -> c

ifoldl :: (c -> b -> c) -> c -> a -> c

ifoldl' :: (c -> b -> c) -> c -> a -> c

ilength :: b -> a -> Int

Instances

Iterable Atom Atom

Iterable Residue Atom

Iterable Residue Residue

Iterable Chain Atom

Iterable Chain Residue

Iterable Chain Chain

Iterable Model Atom

Iterable Model Residue

Iterable Model Chain

Iterable Model Model

Iterable Structure Atom

Iterable Structure Residue

Iterable Structure Chain

Iterable Structure Model

Iterable Structure Structure

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

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

fastacode2resname :: Char -> String

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

(*|) :: Double -> Vector3 -> Vector3

Scalar product. (* indicates side on which one can put a scalar.)

(|*) :: Vector3 -> Double -> Vector3

Scalar product. (* indicates side on which one can put a scalar.)

vnorm :: Vector3 -> Double

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

type Element = ByteString

Basic elemental parameters as suggested by CSD.

TODO: May be better as a newtype, and make sure that other modules use this declaration

assignElement :: Atom -> Element

atomicNumber :: Element -> Int

Atomic number of a given element

atomicMass :: Element -> Double

Atomic mass of a given element in g/mol

covalentRadius :: (Eq a1, Fractional a, Show a1, IsString a1) => a1 -> a

vanDerWaalsRadius :: Element -> Double

Van der Waals radius of the given element