Package schrodinger :: Package application :: Package desmond :: Module replica_sid_generator :: Class FEPReport

Class FEPReport

object --+
         |
        FEPReport

Instance Methods

[hide private]

__init__(self, basename=None, fep_type='lambda_hopping', sid_file=None)
x.__init__(...) initializes x; see help(type(x)) for signature

load_all(self)

get_ark_results(self)
Function organizes and returns ARK abject

export(self, filename=None)
Writes a file with SID results in them, so they can be read into SID gui

ark_str(self, str_in)
sanitize ARK string, by removing the doubleqotes

launch_SID(self, traj_fn, st2_fn, eaf_fn)
This method launches analyze_trajectories, a backend for SID analysis

get_pl_analysis(self, lig_rep, fep_lambda)
This method generates an analysis input file, submits the analysis, and returns an ARK object with results.

find_ligands(self)

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, basename=None, fep_type=`'lambda_hopping'`, sid_file=None)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

get_pl_analysis(self, lig_rep, fep_lambda)

This method generates an analysis input file, submits the analysis, and returns an ARK object with results.

Parameters:

lig_rep (LigandReport) - list of two LigandReport objects
fep_lambda (int @rtype ARK object) - use ligand from lambda0 or lambda 1, to generate report for

Class FEPReport

__init__(self, basename=None, fep_type='lambda_hopping', sid_file=None) (Constructor)

get_pl_analysis(self, lig_rep, fep_lambda)

init(self, basename=None, fep_type=`'lambda_hopping'`, sid_file=None)
(Constructor)