Package schrodinger :: Package application :: Package desmond :: Package packages :: Module analysis :: Class _WatLigFragDistance
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Class _WatLigFragDistance

      object --+        
               |        
GeomAnalyzerBase --+    
                   |    
  _CompositeAnalyzer --+
                       |
                      _WatLigFragDistance

For all water molecules within distance (hbond_cutoff + 0.3) to the ligand, find the mininum distance between water oxygen atom and the closest ligand fragment centroid. To further exclude water bridges, call _cleanup_water_ligand_distance. Use class WatLigFragDistance instead for automated cleaning up.

Returns a list of dict. The length of this list is the number of frames. The dict key is 'LigWatResult', and the value is a list of _WatLigFragDistance.Result, where frag_idx is the index of the ligand fragment, wat_res_num is the water residue number, distance is the distance between water oxygen atom and ligand fragment centroid.

Nested Classes [hide private]
  Result
_WatLigFragDis(frag_idx, wat_res_num, distance)
Instance Methods [hide private]
 
__init__(self, msys_model, cms_model, prot_asl, lig_asl, hbond_cutoff=2.8)
x.__init__(...) initializes x; see help(type(x)) for signature
 
_postcalc(self, calc, pbc, fr)

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, prot_asl, lig_asl, hbond_cutoff=2.8)
(Constructor)

 

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

Overrides: object.__init__
(inherited documentation)

_postcalc(self, calc, pbc, fr)

 
Overrides: GeomAnalyzerBase._postcalc
(inherited documentation)