Package Biskit :: Package Dock :: Module Analyzer :: Class Analyzer

Class Analyzer

Instance Methods

__init__(self, verbose=1, **options)

[0|1|2] __categorizeHexSurf(self, cutoff=0.1)
Compare complexes of list to native complex to see if their contact surfaces overlapp with the native complex.

setHexComplexes(self, com_lst, n=20)
add contact matrices of hex-generated (wrong) complexes for comparison

[matrix] random_contacts(self, contMat, n, maskRec=None, maskLig=None)
Create randomized surface contact matrix with same number of contacts and same shape as given contact matrix.

[any] __shuffleList(self, lst)
shuffle order of lst

[[any]] shuffledLists(self, n, lst, mask=None)
shuffle order of a list n times, leaving masked(0) elements untouched

__plotSequence(self, list, **arg)
add curve to current plot, with x1..xn = 0..n and y1..yn = |list|

report(self)
override for actual plotting

initPlot(self)
override for plot creation

plotAll(self)
Show plot

Method Details

[hide private]

init(self, verbose=1, **options)
(Constructor)

source code

Parameters:

verbose (1|0) - verbosity level (default: 1)

options (any) - needs:

                rec,lig - file name, receptor, ligand trajectories
                ref     - file name, pickled reference complex

Raises:

AnalyzeError - if atoms are not aligned

__categorizeHexSurf(self, cutoff=0.1)

source code

Compare complexes of list to native complex to see if their contact surfaces overlapp with the native complex.

Parameters:

cutoff (float) - fraction cutoff for defining a overlap (default: 0.1)

Returns: [0|1|2]: list of len(self.hexContacts) overlapping with native contact surface of lig and rec (0 - no overlap, 1 - rec OR lig overlapps, 2- rec AND lig overlapps)