Appendix: Additional Examples in Python

These are full listings of programming examples that are excerpted or offered for download, elsewhere in this chapter.

Listing 1: CalculateTriangleAreas.py full listing.

#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence) 
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of Cadence products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oespicoli

if len(sys.argv) != 2:
    oechem.OEThrow.Usage("%s <input>" % sys.argv[0])

ims = oechem.oemolistream()
if not ims.open(sys.argv[1]):
    oechem.OEThrow.Fatal("Unable to open %s" % sys.argv[1])

mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
    oechem.OEThrow.Fatal("Unable to read a molecule")
oechem.OEAssignBondiVdWRadii(mol)

surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol)

areas = oechem.OEFloatArray(surf.GetNumTriangles())
oespicoli.OECalculateTriangleAreas(surf, areas)

atomareas = [0.0] * mol.GetMaxAtomIdx()

for i in range(surf.GetNumTriangles()):
    tri = surf.GetTriangle(i)

    a1 = surf.GetAtomsElement(tri[0])
    a2 = surf.GetAtomsElement(tri[1])
    a3 = surf.GetAtomsElement(tri[2])

    atomareas[a1] += areas[i]/3.0
    atomareas[a2] += areas[i]/3.0
    atomareas[a3] += areas[i]/3.0

for atom in mol.GetAtoms():
    print("atom %d area = %2.4f" % (atom.GetIdx(), atomareas[atom.GetIdx()]))

Listing 2: MakeConnectedSurfaceCliques.py full listing.

#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence) 
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of Cadence products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oespicoli

if len(sys.argv) != 2:
    oechem.OEThrow.Usage("%s <input>" % sys.argv[0])

ims = oechem.oemolistream()
if not ims.open(sys.argv[1]):
    oechem.OEThrow.Fatal("Unable to open %s" % sys.argv[1])

mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
    oechem.OEThrow.Fatal("Unable to read a molecule")
oechem.OEAssignBondiVdWRadii(mol)

surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol)

nclqs = oespicoli.OEMakeConnectedSurfaceCliques(surf)

areas = []
for i in range(1, nclqs+1):
    areas.append((oespicoli.OESurfaceCliqueArea(surf, i), i))

maxarea, maxclq = max(areas)
oespicoli.OESurfaceCropToClique(surf, maxclq)

print(maxarea)
print(oespicoli.OESurfaceArea(surf))

Listing 3: AttachSurface.py full listing.

#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence) 
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of Cadence products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oespicoli

if len(sys.argv) != 2:
    oechem.OEThrow.Usage("%s <input>" % sys.argv[0])

ims = oechem.oemolistream()
if not ims.open(sys.argv[1]):
    oechem.OEThrow.Fatal("Unable to open %s" % sys.argv[1])

mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
    oechem.OEThrow.Fatal("Unable to read a molecule")
oechem.OEAssignBondiVdWRadii(mol)

surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol)
mol.SetData("surface", surf)

ofs = oechem.oemolostream("foo.oeb")
oechem.OEWriteMolecule(ofs, mol)
ofs.close()

ifs = oechem.oemolistream("foo.oeb")
oechem.OEReadMolecule(ifs, mol)

msrf = mol.GetData("surface")

Listing 4: SurfaceDataAccess.py full listing.

#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence) 
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of Cadence products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

from openeye import oechem
from openeye import oespicoli

surf = oespicoli.OESurface()

coords = oechem.OEFloatArray(surf.GetNumVertices() * 3)
surf.GetVertices(coords)


for i in range(surf.GetNumVertices()):
    vert = surf.GetVertex(i)


coords = oechem.OEUIntArray(surf.GetNumTriangles() * 3)
surf.GetTriangles(coords)


for i in range(surf.GetNumTriangles()):
    tri = surf.GetTriangle(i)