3.2 Polar Surface Area

This example demonstrates how to correlate portions of a surface with atoms. OEMakeMolecularSurface automatically initializes the atoms array with the atom index responsible for that particular vertex. The atom indices can be used to map molecular properties onto the surface using cliques. Most surface property calculations in OESpicoli can use cliques.

Only one clique is used in this example. The cliques array is initially all NULL (zero). Vertices considered ``polar'' are marked with the clique of one. OESurfaceCliqueArea is then used to calculate the polar surface area. The area is then averaged over all the conformers of the molecule.

 1 /*******************************************************************
 2   * Copyright 2006, 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 OESpicoli;
12 using namespace OEChem;
13 using namespace OESystem;
14 using namespace OEPlatform;
15
16 bool MakeCliques(OESurface &surf, const OEMolBase &mol)
17 {
18   OEAtomBase *atom;
19   for (unsigned int i=0;i<surf.GetNumVertices();++i)
20   {
21     atom=mol.GetAtom(OEHasAtomIdx(surf.GetAtomsElement(i)));
22     if (atom->IsOxygen() || atom->IsNitrogen() || atom->IsPolarHydrogen())
23       surf.SetVertexCliqueElement(i, 1);
24   }
25   return true;
26 }
27
28 bool AverageSurfaceArea(const OEMCMolBase &mcmol, float *area, float *parea)
29 {
30   float a=0.0f;
31   float pa=0.0f;
32   for (OEIter<OEConfBase> conf=mcmol.GetConfs();conf;++conf)
33   {
34     OESurface surf;
35     OEMakeMolecularSurface(surf, conf, 0.5f);
36     //MakeCliques(surf, conf);
37
38     a += OESurfaceArea(surf);
39     pa += OESurfaceCliqueArea(surf, 1);
40   }
41   a /= mcmol.NumConfs();
42   pa /= mcmol.NumConfs();
43
44   *area = a;
45   *parea = pa;
46
47   return true;
48 }
49
50 int main(int argc, char *argv[])
51 {
52   if (argc!=2)
53     OEThrow.Usage("%s <molecules>", argv[0]);
54
55   float area, polararea;
56   oemolistream ifs(argv[1]);
57   OEMol mol;
58   while (OEReadMolecule(ifs, mol))
59   {
60     OEAssignBondiVdWRadii(mol);
61     AverageSurfaceArea(mol, &area, &polararea);
62     oeerr << mol.GetTitle() << oeendl;
63     oeerr << "molecule has " << mol.NumConfs() << " conformers" << oeendl;
64     oeerr << "Average total surface area: " << area << oeendl;
65     oeerr << "Average polar area        : " << polararea << oeendl;
66     oeerr << "Average % polar           : " << polararea/area
67           << oeendl << oeendl;
68   }
69   return 0;
70 }

Listing:3.2 psa.cpp

Polar surface area information can also be mapped onto the surface as the surface color. This surface can then be stored on its associated molecule to be written out and viewed.

 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 OESpicoli;
12 using namespace OEChem;
13 using namespace OESystem;
14 using namespace OEPlatform;
15
16 bool ColorSurface(OESurface &surf, const OEMolBase &mol)
17 {
18   OEAtomBase *atom;
19   for (unsigned int i=0;i<surf.GetNumVertices();++i)
20   {
21     atom=mol.GetAtom(OEHasAtomIdx(surf.GetAtomsElement(i)));
22     if (atom->IsOxygen() || atom->IsNitrogen() || atom->IsPolarHydrogen())
23       surf.SetColorElement(i, 0.0f, 0.0f, 1.0f);
24     else
25       surf.SetColorElement(i, 1.0f, 0.0f, 0.0f);
26   }
27   return true;
28 }
29
30 int main(int argc, char *argv[])
31 {
32   if (argc!=3)
33     OEThrow.Usage("%s <molecules> <oebfile>", argv[0]);
34
35   oemolistream ifs(argv[1]);
36   oemolostream ofs(argv[2]);
37   OEInitSurfaceHandlers(ofs);
38
39   OEGraphMol mol;
40   while (OEReadMolecule(ifs, mol))
41   {
42     OEAssignBondiVdWRadii(mol);
43
44     OESurface surf;
45     OEMakeMolecularSurface(surf, mol, 0.5f);
46     ColorSurface(surf, mol);
47     mol.SetData<OESurface>("psasurf", surf);
48
49     OEWriteMolecule(ofs, mol);
50   }
51   return 0;
52 }

Listing:3.3 psa-surf.cpp

Note that OEInitSurfaceHandlers has to be called on the oemolostream in order for the surface to be attached to the molecule.

				OESpicoli Toolkit: Generation, Manipulation, and Comparison of Surfaces