biotite.structure.rmsd¶
- biotite.structure.rmsd(reference, subject)[source]¶
Calculate the RMSD between two structures.
The root-mean-square-deviation (RMSD) indicates the overall deviation of each model of a structure to a reference structure. It is defined as:
\[RMSD = \sqrt{ \frac{1}{n} \sum\limits_{i=1}^n (x_i - x_{ref,i})^2}\]- Parameters
- referenceAtomArray or ndarray, dtype=float, shape=(n,3)
The reference structure. Alternatively, coordinates can be provided directly as
ndarray
.- subjectAtomArray or AtomArrayStack or ndarray, dtype=float, shape=(n,3) or shape=(m,n,3)
Structure(s) to be compared with reference. Alternatively, coordinates can be provided directly as
ndarray
.
- Returns
- rmsdfloat or ndarray, dtype=float, shape=(m,)
RMSD between subject and reference. If subject is an
AtomArray
a float is returned. If subject is anAtomArrayStack
andarray
containing the RMSD for each model is returned.
See also
Notes
This function does not superimpose the subject to its reference. In most cases
superimpose()
should be called prior to this function.Examples
Calculate the RMSD of all models to the first model:
>>> superimposed, _ = superimpose(atom_array, atom_array_stack) >>> rms = rmsd(atom_array, superimposed) >>> print(np.around(rms, decimals=3)) [0.000 1.928 2.103 2.209 1.806 2.172 2.704 1.360 2.337 1.818 1.879 2.471 1.939 2.035 2.167 1.789 1.653 2.348 2.247 2.529 1.583 2.115 2.131 2.050 2.512 2.666 2.206 2.397 2.328 1.868 2.316 1.984 2.124 1.761 2.642 1.721 2.571 2.579]
Gallery¶
Docking biotin to streptavidin
Basic analysis of a MD simulation