Package schrodinger :: Package trajectory :: Module analyze_trajectories :: Class _KeywordProcessor

Class _KeywordProcessor

This class processes ARK keywords coming from a .st2 input file, it turns the keywords into Analysis objects to be used by the backend. st2 files are generated by sim_event_analysis.py

Instance Methods

[hide private]

__init__(self, csim, trj_directory=None, cfgfn=None)

str(self, ark_obj)
return string value of an ark obj.

_get_atoms(self, params, count)
Returns atom lists of FIS atoms from ark_kw

process_ark(self, ark_kw)
Picks the correct function to process the keyword type

_process_energy(self, ark_kw)
Get an analysis object for energies

_process_rog(self, ark_kw)
Get analysis object for radius of gyration For these, we calculate for all solute atoms (incl hydrogens)

_process_distance(self, ark_kw)
Get analysis object for desired distance

_process_angle(self, ark_kw)
Get analysis object for desired angle

_process_torsion(self, ark_kw)
Get analysis object for desired torsion

_process_planar_angle(self, ark_kw)
Get analysis object for desired planar angle

_process_hbonds(self, ark_kw)
Generate an hbond analisys object

_process_rmsd(self, ark_kw)

_process_rmsf(self, ark_kw)

Static Methods

[hide private]

requires_energy(ark_kws)

_get_type(ark_kw)
The ark_kw passed is a sea.Map, whose single key is the kw type

Method Details

[hide private]

_process_energy(self, ark_kw)

Get an analysis object for energies

If selection is None, the solute is used as the main selection.

_process_hbonds(self, ark_kw)

Generate an hbond analisys object

This will be an HydrogenBondFinder object, which will then be processed. Note, only potential hbonding atoms are checked.