Measurement Tools

This module defines classes measuring quantities, transforming coordinates, and identifying contacts.

Identify contacts

The following class and functions are for contact identifications:

Contacts - identify intermolecular contacts

findNeighbors() - identify interacting atom pairs

iterNeighbors() - identify interacting atom pairs

Measure quantities

The following functions are for measuring simple quantities:

calcDistance() - calculate distance(s)

calcAngle() - calculate bond angle

calcDihedral() - calculate dihedral angle

calcOmega() - calculate omega (ω) angle

calcPhi() - calculate phi (φ) angle

calcPsi() - calculate psi (ψ) angle

calcGyradius() - calculate radius of gyration

calcCenter() - calculate geometric (or mass) center

calcDeformVector() - calculate deformation vector

Anisotropic factors

The following functions handle anisotropic displacement parameter (ADP) present in some X-ray structures.

buildADPMatrix() - build ADP matrix

calcADPAxes() - calculate ADP axes

calcADPs() - calculate ADPs

Transformations

The following class and functions are for handling coordinate transformations:

Transformation - store transformation matrix

alignCoordsets() - align multiple coordinate sets

applyTransformation() - apply a transformation

calcTransformation() - calculate a transformation

calcRMSD() - calculate root-mean-square distance

superpose() - superpose atoms or coordinate sets

moveAtoms() - move atoms by given offset