pyviblib.calc.qtrfit

Superimpose molecules using a quaternion fit

This is a Python port of the QTRFIT algorithm written by David J. Heisterberg. Copyright: Ohio Supercomputer Center, David J. Heisterberg, 1990. See http://www.ccl.net/cca/software/SOURCES/C/quaternion-mol-fit/quatfit.c.

There is, however, a subtle difference between this implementation and the original one. It consists in a way how the center of a molecule is calculated. We use the plain weighting coefficients rather than square roots from them. This corresponds to physically meaningful results.

Functions

fit()

perform a quaternion fit

Author:Maxim Fedorovsky

pyviblib.calc.qtrfit.fit(pairs, coords_ref, coords_fit, weight)

Perform a quaternion fit.

Parameters:

• pairs – atom pairs to be superimposed (null-based ndarray), shape : (npairs, 2) with npairs being the number of atom pairs, atom numbers are one-based, example : array([ [1, 1], [5, 5], [7, 7] ])
• coords_ref – coordinates of the reference frame (one-based ndarray), shape : (Natoms_ref, 4) with Natoms_ref being the number of atoms in the reference frame
• coords_fit – coordinates of the fitted frame (one-based ndarray), shape : (Natoms_fit, 4) with Natoms_fit being the number of atoms in the fitted frame
• weight – weights for the atoms to be superimposed (one-based ndarray)

Return value is a dictionary with the following keys:

pairs

passed pairs positional argument

weight

passed weight positional argument

rms

root mean square (RMS) deviation

q

quaternion (null-based ndarray of the length 4)

U

left rotation matrix (one-based two-dimensional ndarray)

ref_center

center of the reference molecule (one-based ndarray)

fit_center

center of the fitted molecule (one-based ndarray)

xyz_f

rotated and translated fitted fragment