schrodinger.application.desmond.packages.msys.pfx module

A high level interface for wrapping, centering, and alignment.

This module provides simple, yet performant methods for manipulating trajectories of systems with connected atoms and periodic boundary conditions.

schrodinger.application.desmond.packages.msys.pfx.aligned_rmsd(X, Y, weight=None) → mat, rmsd

Compute the matrix aligning Y onto X, optionally with weights. Return the matrix and the rmsd.

schrodinger.application.desmond.packages.msys.pfx.svd_3x3(A) → U, w, V

svd_3x3 computes the singular value decomposition of the 3x3 matrix A. The result is always calculated and returned in double precision.