3.3 Largest Hydrophobic Patch

This example demonstrates how to subset a surface based on an associated molecular property. The largest hydrophobic patch will be extracted. The following simple definition of hydrophobic will be used: vertices associated with atoms in hydrophobic residues are considered hydrophobic.

This property is first mapped into the clique of one. The surface is then cropped to only be the hydrophobic parts. OEMakeConnectedSurfaceCliques is used to organize the surface into connected components. Each clique between 1 and nclqs inclusive is a different component. The area of each component is then calculated using the OESurfaceCliqueArea function. The surface is then cropped to the largest component.

 1 /*******************************************************************
 2   * Copyright 2006, 2007, OpenEye Scientific Software, Inc.
 3   *******************************************************************/
 4 #include "openeye.h"
 5
 6 #include "oeplatform.h"
 7 #include "oesystem.h"
 8 #include "oechem.h"
 9 #include "oespicoli.h"
10
11 using namespace OEChem;
12 using namespace OESystem;
13 using namespace OEPlatform;
14 using namespace OESpicoli;
15
16 bool AtomInHydrophobicResidue(OEAtomBase *atom)
17 {
18   switch(OEGetResidueIndex(atom))
19   {
20     case OEResidueIndex::ALA:
21     case OEResidueIndex::ILE:
22     case OEResidueIndex::LEU:
23     case OEResidueIndex::MET:
24     case OEResidueIndex::PHE:
25     case OEResidueIndex::PRO:
26     case OEResidueIndex::TRP:
27     case OEResidueIndex::VAL:
28       return true;
29     default:
30       return false;
31   }
32 }
33
34 int main(int argc, char *argv[])
35 {
36   if (argc!=3)
37     OEThrow.Usage("%s <protein> <surface>", argv[0]);
38
39   oemolistream ifs(argv[1]);
40   OEGraphMol mol;
41   OEReadMolecule(ifs, mol);
42   OEPerceiveResidues(mol);
43   OEAssignBondiVdWRadii(mol);
44
45   // Generate the molecular surface
46   OESurface surf;
47   OEMakeMolecularSurface(surf, mol, 0.5f);
48
49   // Mark all the vertices associated with hydrophobic atoms
50   for (unsigned int i = 0; i < surf.GetNumVertices(); ++i)
51   {
52     OEAtomBase *atom=mol.GetAtom(OEHasAtomIdx(surf.GetAtomsElement(i)));
53     if (AtomInHydrophobicResidue(atom))
54       surf.SetVertexCliqueElement(i, 1);
55   }
56
57   // Crop to only those triangles
58   OESurfaceCropToClique(surf, 1);
59
60   // nlqs is the number of different connected components
61   unsigned int nclqs = OEMakeConnectedSurfaceCliques(surf);
62
63   // Find the largest component
64   unsigned int maxclq = 0;
65   double maxarea = 0.0;
66   for (unsigned int i = 1; i <= nclqs; ++i)
67   {
68     double area = OESurfaceCliqueArea(surf, i);
69     oeout << "clique: " << i << "  area: " << area << oeendl;
70     if (area > maxarea)
71     {
72       maxclq = i;
73       maxarea = area;
74     }
75   }
76
77   // Crop to it
78   OESurfaceCropToClique(surf, maxclq);
79
80   OEWriteSurface(argv[2], surf);
81
82   return 0;
83 }

Listing:3.4 patches.cpp

Note that the same OESurface object is reused for each of the subsetted surfaces. To maintain the original surface as well as the surface subset, the OEMakeCliqueSurface function can be used.

				OESpicoli Toolkit: Generation, Manipulation, and Comparison of Surfaces