Copyright	Phillip Seeber 2021
License	AGPL-3
Maintainer	phillip.seeber@googlemail.com
Stability	experimental
Portability	POSIX, Windows
Safe Haskell	None
Language	Haskell2010

ConClusion.Chemistry.Topology

Description

This module implements routines to work with simple molden style XYZ trajectories. This includes parsers as well as functions to obtain structural features in internal coordinates.

For an introduction into PCA see https://www.cs.cmu.edu/~elaw/papers/pca.pdf.

Diherdrals require a special metric, see https://onlinelibrary.wiley.com/doi/full/10.1002/prot.20310).

Synopsis

data Molecule
type Trajectory = Seq Molecule
xyz :: Parser Molecule
trajectory :: Parser Trajectory
data B = B Int Int
data A = A Int Int Int
data D = D Int Int Int Int
data Feature
- = Energy
- | Bond B
- | Angle A
- | Dihedral D
getFeatures :: (MonadThrow m, Traversable f) => f Feature -> Trajectory -> m (Matrix DL Double)

Documentation

data Molecule Source #

A Molecule in cartesian coordinates.

type Trajectory = Seq Molecule Source #

xyz :: Parser Molecule Source #

Parser for molecules in Molden XYZ format.

trajectory :: Parser Trajectory Source #

Parser for trajectories in XYZ format as produced by CREST.

data B Source #

Selection of a bond between two atoms.

Constructors

B Int Int

data A Source #

Selection of an angle between three atoms.

Constructors

A Int Int Int

data D Source #

Selection of a dihedral angle between four atoms. Rotation around the central two.

Constructors

D Int Int Int Int

data Feature Source #

Selections

Constructors

Energy
Bond B
Angle A
Dihedral D

getFeatures :: (MonadThrow m, Traversable f) => f Feature -> Trajectory -> m (Matrix DL Double) Source #

Obtains the feature matrix \(\mathbf{X}\) for a principal component analysis. Given \(m\) features to analyse in \(n\) measurements, \(\mathbf{X}\) will be a \(m \times n\) matrix.