biotite.structure.average¶
- biotite.structure.average(atoms)[source]¶
Calculate an average structure.
The average structure has the average coordinates of the input models.
- Parameters
- atomsAtomArrayStack or ndarray, dtype=float, shape=(m,n,3)
The structure models to be averaged. Alternatively, coordinates can be provided directly as
ndarray
.
- Returns
- averageAtomArray or ndarray, dtype=float, shape=(n,3)
Structure with averaged atom coordinates. If atoms is a
ndarray
andndarray
is also returned.
Notes
The calculated average structure is not suitable for visualization or geometric calculations, since bond lengths and angles will deviate from meaningful values. This method is rather useful to provide a reference structure for calculation of e.g. the RMSD or RMSF.
Gallery¶
Basic analysis of a MD simulation
Basic analysis of a MD simulation