Class GeomAnalyzerBase

object --+
         |
        GeomAnalyzerBase

Known Subclasses:

Base class of all geometry analyzer classes

All subclasses are expected to define two private methods:

_precalc
- This private method will be called by a GeomCalc object to register wanted geometry calculations.
_postcalc
- This private method will be called by a GeomCalc object to finish the particular analysis calculation. And the results should are saved in the self._result
In between the _precalc and _postcalc calls, the GeomCalc object will be called (outside the analyzer class) for the current frame to calculate all requested geometry calculation. Also see the docstring of the analyze function below.

Instance Methods

_precalc(self, calc)

_postcalc(self, calc, pbc, fr)

__call__(self)

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods

list of combinations of GIDs or Positer

_get_sites(cms_model, xids)
This function takes a list of XIDs (AIDs or CenterOf objects) and turns them into a list of sites (GIDs or Positer).

list of GIDs

_sites2gids(calc, sites, gid_offset)
This function returns GIDs for the provided sites.

Properties

Inherited from object: __class__

Method Details

Parameters:

Parameters:

This function takes a list of XIDs (AIDs or CenterOf objects) and turns them into a list of sites (GIDs or Positer).

Parameters:

Returns: list of combinations of GIDs or Positer

This function returns GIDs for the provided sites. If Positer type is detected, a new GIDs is registered.

Parameters:

gid_offset (int) - number of sites/GIDs in the msys_model, the GIDs generated for all the particles are being offset by this value, which is equal to the total number of GIDs.
particles (a list that contains either int and/or Positer)
calc (GeomCalc)

Returns: list of GIDs