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