This module defines functions for generating alternate conformations along normal modes.
Generate a new coordinate set for atoms along the mode. atoms must be a AtomGroup instance. New coordinate set will be appended to atoms. If rmsd is provided, mode will be scaled to generate a coordinate set with given RMSD distance to the active coordinate set.
Return an ensemble of randomly sampled conformations along given modes. If atoms are provided, sampling will be around its active coordinate set. Otherwise, sampling is around the 0 coordinate set.
Parameters: |
|
---|---|
Returns: |
For given normal modes and their eigenvalues , a new conformation is sampled using the relation:
is the active coordinate set of atoms. are normally distributed random numbers generated for conformation using numpy.random.randn().
RMSD of the new conformation from can be calculated as
Average of the generated conformations from the initial conformation is:
From this relation scaling factor obtained using the relation
Note that random numbers are generated before conformations are sampled, hence exact value of is known from this relation to ensure that the generated ensemble will have user given average rmsd value.
Note that if modes are from a PCA, variances are used instead of inverse eigenvalues, i.e. .
See also showEllipsoid().
Generates a trajectory along a given mode, which can be used to animate fluctuations in an external program.
Parameters: |
|
---|---|
Returns: |
For given normal mode , its eigenvalue , number of steps , and maximum conformations are generated.
is the active coordinate set of atoms. , where is found using , where is the number of atoms.