def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <protein> <ligand>" % args[0])
pifs = oechem.oemolistream()
if not pifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading protein." %
args[1])
prot = oechem.OEGraphMol()
if not oechem.OEReadMolecule(pifs, prot):
oechem.OEThrow.Fatal("Unable to read protein")
oechem.OEAddExplicitHydrogens(prot)
oechem.OEAssignBondiVdWRadii(prot)
lifs = oechem.oemolistream()
if not lifs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading ligand." % args[2])
lig = oechem.OEGraphMol()
if not oechem.OEReadMolecule(lifs, lig):
oechem.OEThrow.Fatal("Unable to read ligand")
oechem.OEAddExplicitHydrogens(lig)
oechem.OEAssignBondiVdWRadii(lig)
comp = oechem.OEGraphMol(prot)
oechem.OEAddMols(comp, lig)
compSurf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(compSurf, comp)
protSurf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(protSurf, prot)
ligSurf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(ligSurf, lig)
compVol = oespicoli.OESurfaceVolume(compSurf)
protVol = oespicoli.OESurfaceVolume(protSurf)
ligVol = oespicoli.OESurfaceVolume(ligSurf)
oespicoli.OEWriteSurface("comp.oesrf", compSurf)
oespicoli.OEWriteSurface("prot.oesrf", protSurf)
oespicoli.OEWriteSurface("lig.oesrf", ligSurf)
oechem.OEThrow.Info(
"%s-%s: dV(C-P) = %.1f V(L) = %.1f V(C) = %.1f V(P) = %.1f" %
(prot.GetTitle(), lig.GetTitle(), compVol - protVol, ligVol, compVol,
protVol))
return 0
def main(args):
if len(args) != 4:
oechem.OEThrow.Usage("%s <protein> <ligand> <surface>" % args[0])
pfs = oechem.oemolistream(args[1])
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(pfs, prot)
oechem.OEAssignBondiVdWRadii(prot)
lfs = oechem.oemolistream(args[2])
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(lfs, lig)
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, prot)
# Iterate through all the protein surface vertices
for i in range(surf.GetNumVertices()):
vert = surf.GetVertex(i)
# Check the distance to each atom
for atom in lig.GetAtoms():
dist2 = GetDist2(lig.GetCoords(atom), vert)
if dist2 < MAX_DIST * MAX_DIST:
surf.SetVertexCliqueElement(i, 1)
# Crop to the binding site and output
oespicoli.OESurfaceCropToClique(surf, 1)
oespicoli.OEWriteSurface(args[3], surf)
return 0
def main(args):
if len(args) != 4:
oechem.OEThrow.Usage("%s <protein> <ligand> <surface>" % args[0])
pfs = oechem.oemolistream(args[1])
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(pfs, prot)
oechem.OEAssignBondiVdWRadii(prot)
lfs = oechem.oemolistream(args[2])
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(lfs, lig)
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, prot)
oespicoli.OESurfaceToMoleculeDistance(surf, lig)
# Mark the vertices to keep
for i in range(surf.GetNumVertices()):
if surf.GetDistanceElement(i) < MAX_DIST:
surf.SetVertexCliqueElement(i, 1)
# Crop to the binding site and output
oespicoli.OESurfaceCropToClique(surf, 1)
oespicoli.OEWriteSurface(args[3], surf)
return 0
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <molfile.pdb> <out.srf>" % argv[0])
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream(argv[1])
oechem.OEReadMolecule(ifs, mol)
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
serials = {}
for atom in mol.GetAtoms():
res = oechem.OEAtomGetResidue(atom)
serials[res.GetSerialNumber()] = atom
outsurf = oespicoli.OESurface()
center = oechem.OEFloatArray(3)
for line in open(argv[1]):
if line.startswith("ANISOU"):
serno, factors = ParseFactors(line)
if serno in serials:
mol.GetCoords(serials[serno], center)
surf = GetEllipsoidalSurface(center, factors)
oespicoli.OEAddSurfaces(outsurf, surf)
oespicoli.OEWriteSurface(argv[2], outsurf)
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <protein> <surface>" % args[0])
ifs = oechem.oemolistream()
if not ifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oechem.OEPerceiveResidues(mol)
oechem.OEAssignBondiVdWRadii(mol)
# Generate the molecular surface
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol, 0.5)
# Mark all the vertices associated with hydrophobic atoms
for i in range(surf.GetNumVertices()):
atom = mol.GetAtom(oechem.OEHasAtomIdx(surf.GetAtomsElement(i)))
if (AtomInHydrophobicResidue(atom)):
surf.SetVertexCliqueElement(i, 1)
# Crop to only those triangles
oespicoli.OESurfaceCropToClique(surf, 1)
# nlqs is the number of different connected components
nclqs = oespicoli.OEMakeConnectedSurfaceCliques(surf)
# Find the largest component
maxclq = 0
maxarea = 0.0
for i in range(nclqs):
area = oespicoli.OESurfaceCliqueArea(surf, i+1)
print("clique: %d area: %f" % (i+1, area))
if (area > maxarea):
maxclq = i+1
maxarea = area
# Crop to it
oespicoli.OESurfaceCropToClique(surf, maxclq)
oespicoli.OEWriteSurface(args[2], surf)
return 0
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <protein> <surface>" % args[0])
prtfs = oechem.oemolistream()
if not prtfs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
prt = oechem.OEGraphMol()
oechem.OEReadMolecule(prtfs, prt)
oechem.OEAssignBondiVdWRadii(prt)
surf = oespicoli.OESurface()
oespicoli.OEMakeCavitySurfaces(prt, surf)
oespicoli.OEInvertSurface(surf)
oespicoli.OEWriteSurface(args[2], surf)
return 0
def main(args):
if len(args) != 4:
oechem.OEThrow.Usage("%s <protein> <ligand> <surface>" % args[0])
prtfs = oechem.oemolistream(args[1])
prt = oechem.OEGraphMol()
oechem.OEReadMolecule(prtfs, prt)
oechem.OESuppressHydrogens(prt)
oechem.OEAssignBondiVdWRadii(prt)
ligfs = oechem.oemolistream(args[2])
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(ligfs, lig)
oechem.OESuppressHydrogens(lig)
oechem.OEAssignBondiVdWRadii(lig)
grid = oegrid.OEScalarGrid()
oespicoli.OEMakeVoidVolume(prt, lig, grid, 0.5)
surf = oespicoli.OESurface()
oespicoli.OEMakeSurfaceFromGrid(surf, grid, 0.5)
oespicoli.OEWriteSurface(args[3], surf)
return 0