Class ProtProtInter

      object --+        
               |        
GeomAnalyzerBase --+    
                   |    
  _CompositeAnalyzer --+
                       |
                      ProtProtInter

Protein-protein interactions.

Return summary over the whole trajectory. For the same frame, results are unique up to residue level, e.g., even if there are multiple salt-bridges between residue A and B, only 1 is recorded.

Instance Methods

[hide private]

__init__(self, msys_model, cms_model, asl)
x.__init__(...) initializes x; see help(type(x)) for signature

dict

_get_tag2ca(self, prot_ct)

_postcalc(self, *args)

reduce(self, results, *_, **__)
Returns: counts of the various interactions over the whole trajectory

_cleanup_hbonds(self)
Remove side-chain hbond if it is salt bridge.

Inherited from _CompositeAnalyzer (private): _precalc

Inherited from GeomAnalyzerBase: __call__

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

Static Methods

[hide private]

Inherited from GeomAnalyzerBase (private): _get_sites, _sites2gids

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, msys_model, cms_model, asl)
(Constructor)

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

Parameters:

asl (str) - ASL expression to select protein atoms
msys_model (msys.System)
cms_model (schrodinger.structure.Structure)

Overrides: object.__init__

_get_tag2ca(self, prot_ct)

Parameters:

prot_ct - schrodinger.structure.Structure

Returns: dict

_postcalc(self, *args)

Overrides: GeomAnalyzerBase._postcalc: (inherited documentation)

reduce(self, results, *_, **__)

Parameters:

results (list of dicts. Its length is the number of frames.
@rtype : dict
) - interactions of all frames

Returns:

counts of the various interactions over the whole trajectory

_cleanup_hbonds(self)

Remove side-chain hbond if it is salt bridge. It is assumed that between two side-chains, there is at most 1 salt bridge and hbond interaction in total.

Class ProtProtInter

__init__(self, msys_model, cms_model, asl) (Constructor)

_get_tag2ca(self, prot_ct)

_postcalc(self, *args)

reduce(self, results, *_, **__)

_cleanup_hbonds(self)

init(self, msys_model, cms_model, asl)
(Constructor)