This module defines classes measuring quantities, transforming coordinates, and identifying contacts.
Following class and functions are for contact identifications:
- Contacts - identify intermolecular contacts
- findNeighbors() - identify interacting atom pairs
- iterNeighbors() - identify interacting atom pairs
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
Following functions handle anisotropic displacement parameter (ADP) present in some X-ray structures.
- buildADPMatrix() - build ADP matrix
- calcADPAxes() - calculate ADP axes
- calcADPs() - calculate ADPs
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