ConClusion.Chemistry.Topology

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).

Documentation

data Molecule

A Molecule in cartesian coordinates.

type Trajectory = Seq Molecule

xyz :: Parser Molecule

Parser for molecules in Molden XYZ format.

trajectory :: Parser Trajectory

Parser for trajectories in XYZ format as produced by CREST.

data B

Selection of a bond between two atoms.

Constructors

B Int Int

data A

Selection of an angle between three atoms.

Constructors

A Int Int Int

data D

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

Constructors

D Int Int Int Int

data Feature

Selections

Constructors

Energy

Bond B

Angle A

Dihedral D

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

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.