hPDB-1.2.0.4: Protein Databank file format library

Safe HaskellNone
LanguageHaskell98

Bio.PDB.Structure

Description

Module defines all components of high-level data type description of PDB model.

Synopsis

Documentation

type String = ByteString Source

We use only strict ByteString as strings in PDB parser.

vdot :: Vector3 -> Vector3 -> Double Source

Computes a dot product of two 3D vectors.

vnorm :: Vector3 -> Double Source

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

vproj :: Vector3 -> Vector3 -> Vector3 Source

Finds a vector component of the first vector that is a projection onto direction of second vector.

vperpend :: Vector3 -> Vector3 -> Vector3 Source

Returns a component of the vector v that is perpendicular to w.

vperpends :: Foldable t => Vector3 -> t Vector3 -> Vector3 Source

Finds a component of the vector v that is perpendicular to all vectors in a list.

vdihedral :: Vector3 -> Vector3 -> Vector3 -> Double Source

Compute dihedral between three bond vectors using spherical angle formula.

(*|) :: 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.)

data Structure Source

Structure holds all data parsed from a single PDB entry

Constructors

Structure 

Fields

models :: List Model
 

data Model Source

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

Constructors

Model 

Fields

modelId :: !Int
 
chains :: List Chain
 

data Chain Source

Single linear polymer chain of protein, or nucleic acids

Constructors

Chain 

Fields

chainId :: !Char
 
residues :: List Residue
 

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
 

data Atom Source

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

Constructors

Atom