Class _HydrophobicInter

      object --+        
               |        
GeomAnalyzerBase --+    
                   |    
  _CompositeAnalyzer --+
                       |
                      _HydrophobicInter

Compute protein-ligand hydrophobic interaction candidates: protein atoms on hydrophobic residues and ligand aromatic/aliphatic atoms within hydrophobic distance cutoff. To further exclude hydrogen bonds and pi-pi interactions, call _cleanup_hydrophobic_inter. Use the class HydrophobicInter instead for automated cleaning up.

Returns a list of dict. The length of this list is the number of frames. The dict key is 'HydrophobicResult', and the value is a list of _HydrophobicInter.Result, where ca_aid is the AID of alpha carbon, frag_idx is the index of ligand fragment.

Nested Classes

[hide private]

Result
_Hydrophobic(ca_aid, frag_idx)

Instance Methods

[hide private]

__init__(self, msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hydrophobic_search_cutoff=3.2, hydrophobic_cutoff=3.6)
x.__init__(...) initializes x; see help(type(x)) for signature