ResidenceTime

Classes

class ResidenceTime.ResidenceTime(data, sel, tMax=25, step=1, nbrTimeOri=20)

This class defines methods to compute retention time of atoms in a certain region. This determines how fast atoms in sel2 can leave the vicinity of sel1.

Some plotting methods are also available to quicly check the results.

Parameters:

• data – a Dataset class instance containing trajectories data
• sel – selection corresponding to analysis region (with ‘within’ keyword’)
• tMax – maximum number of frames to be used
• step – time interval between each computed frame
• nbrTimeOri – number of time origins to be averaged over (optional, default 20)

compResidenceTime()

For each frame in the range of tMax with given step, the number of atoms in selected region is computed and divided by the number of atoms at time origin. The result is averaged over multiple time origins.

The result is stored in resTime attribute.

compResidueWiseResidenceTime(dt=25)

Computes, for a given time dt, the residence time for selected atoms around each residue in the protein.

By default all atoms pertaining to protein are selected. If different proteins are present, the segName argument can be used in selection text.

Parameters:dt – time step to compute residence time. Basically, the number of selected molecules wihtin the given region at initial time divides the number that stayed within the region after a time dt (in number of frames).

The result is stored in residueWise attribute

plotResidenceTime()

Used to quickly plot residence time.

plotResidueWiseResidenceTime()

Used to quickly plot residue wise residence time.