schrodinger.application.glide.newxp_reorg

Class FitNewxpReorgEnergy

Helper class to fit the newXP reorganization energy

Instance Methods

__init__(self, basename, host=['localhost', 1], run_mode='ALL', default_zroff=0.0, default_offset=2.0)
Options for run_mode: GENSTD = generate stanard Glide inputs and stop ...

import_newxp_qsar_file(self, newxp_qsar_file)
Method causes newxp qsar input file to be read; alternative is to use add_complex() method to add information directly to class

fit_data(self)
Method fits the available data in self.complexes and returns a fitting file with python code representing the fitted paramters

_print_validation_results(self, best_fits)
Method reports data comparing predicted versus actual GlideScores

_rmsd(self, x, y)
Compute RMSD

import_validation_results(self, best_fits)
Method imports GlideScores from validation calculations Takes best GlideScore/reorg energy from pose with s_glide_XP_pose_type = "finalpose"

validate(self, best_fits)
Method takes newXP parameters in best_fits and ensures Glide calcs reproduce results from fit.

add_complex(self, complex, params)
Method to add data into a Complex() object.

_read_newxp_qsar_file(self, newxp_qsar_file)
Method imports data from a newxp_qsar_file and returns a list of Complex objects

_write_pyfit_code(self, results, complex, reorg=None)
Method to generate the python fitting file used by Glide to compute the reorganization energy.

_get_best_fit(self, results, rmsd_prop='rmsd', r2_prop='r2')
Method to deduce 'best' fitting result using RMSD and r2

init(self, basename, host=`['localhost',` 1`]`, run_mode=`'ALL'`, default_zroff=0.0, default_offset=2.0)
(Constructor)

Options for run_mode: GENSTD = generate stanard Glide inputs and stop 
RUNSTD = generate and run standard Glide inputs and stop
ONLYFIT = only run fitting step; assumes inputs and outputs
          have already been generated 
ALL     = generate and run standard Glide inputs and
          perform fitting to generate a fitting file

validate(self, best_fits)

Method takes newXP parameters in best_fits and ensures Glide calcs reproduce results from fit. Necessary due to structure dependence on the parameters

add_complex(self, complex, params)

Method to add data into a Complex() object. Can be used in place of import_newxp_qsar_file(). Following keys are expected in dict params: watref, wmap, hr

_write_pyfit_code(self, results, complex, reorg=None)

Method to generate the python fitting file used by Glide to
compute the reorganization energy.  
With reorg = None  the native ligand Reorg energy isn't
                   subtracted from each ligand's reorg energy
           = float  the native ligand Reorg energy is subtracted
                    from each ligands' reorg energy

Class FitNewxpReorgEnergy

__init__(self, basename, host=['localhost', 1], run_mode='ALL', default_zroff=0.0, default_offset=2.0) (Constructor)

validate(self, best_fits)

add_complex(self, complex, params)

_write_pyfit_code(self, results, complex, reorg=None)

init(self, basename, host=`['localhost',` 1`]`, run_mode=`'ALL'`, default_zroff=0.0, default_offset=2.0)
(Constructor)