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)
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(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 AverageSurfaceArea(mcmol):
area = 0.0
parea = 0.0
for conf in mcmol.GetConfs():
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, conf, 0.5)
MakeCliques(surf, conf)
area += oespicoli.OESurfaceArea(surf)
parea += oespicoli.OESurfaceCliqueArea(surf, 1)
area /= mcmol.NumConfs()
parea /= mcmol.NumConfs()
return area, parea
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 <molecules> <oebfile>" % args[0])
ifs = oechem.oemolistream()
if not ifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
ofs = oechem.oemolostream()
if not ofs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % args[2])
for mol in ifs.GetOEGraphMols():
oechem.OEAssignBondiVdWRadii(mol)
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol, 0.5)
ColorSurface(surf, mol)
mol.SetData("psasurf", surf)
oechem.OEWriteMolecule(ofs, mol)
return 0
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)
# @ <SNIPPET-SetData>
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol)
mol.SetData("surface", surf)
ofs = oechem.oemolostream("foo.oeb")
oechem.OEWriteMolecule(ofs, mol)
# @ </SNIPPET-SetData>
ofs.close()
# @ <SNIPPET-GetData>
ifs = oechem.oemolistream("foo.oeb")
oechem.OEReadMolecule(ifs, mol)
msrf = mol.GetData("surface")
# @ </SNIPPET-GetData>
def nmax_waters(protein, ligand, cutoff):
# Grid Spacing in A
spacing = 0.5
complex = oechem.OEMol(protein)
oechem.OEAddMols(complex, ligand)
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, complex, spacing)
# oespicoli.OEWriteSurface("test_surf.oesrf", surf)
center = oechem.OEFloatArray(3)
extents = oechem.OEFloatArray(3)
oechem.OEGetCenterAndExtents(ligand, center, extents)
extents = oechem.OEFloatArray(
[max(extents) * 2,
max(extents) * 2,
max(extents) * 2])
grid_reference = oegrid.OEScalarGrid()
oegrid.OEMakeGridFromCenterAndExtents(grid_reference, center, extents,
spacing)
grid_spicoli = oegrid.OEScalarGrid()
oespicoli.OEMakeBitGridFromSurface(grid_spicoli, surf)
for iz in range(grid_reference.GetZDim()):
for iy in range(grid_reference.GetYDim()):
for ix in range(grid_reference.GetXDim()):
x = grid_reference.GetX(ix)
y = grid_reference.GetY(iy)
z = grid_reference.GetZ(iz)
ix_spicoli = grid_spicoli.GetXIdx(x)
iy_spicoli = grid_spicoli.GetYIdx(y)
iz_spicoli = grid_spicoli.GetZIdx(z)
value = grid_spicoli.GetValue(ix_spicoli, iy_spicoli,
iz_spicoli)
grid_reference.SetValue(ix, iy, iz, value)
# Invert Grid
for iz in range(grid_reference.GetZDim()):
for iy in range(grid_reference.GetYDim()):
for ix in range(grid_reference.GetXDim()):
# print("ix = {} iy = {} iz = {} value = {}".format(ix, iy, iz , grid.GetValue(ix, iy, iz)))
if grid_reference.GetValue(ix, iy, iz) == 0.0:
grid_reference.SetValue(ix, iy, iz, 1.0)
else:
grid_reference.SetValue(ix, iy, iz, 0.0)
ligand_coords = ligand.GetCoords()
for iz in range(grid_reference.GetZDim()):
for iy in range(grid_reference.GetYDim()):
for ix in range(grid_reference.GetXDim()):
if grid_reference.GetValue(ix, iy, iz) == 1.0:
x = grid_reference.GetX(ix)
y = grid_reference.GetY(iy)
z = grid_reference.GetZ(iz)
min_sq = cutoff * cutoff
for coord in ligand_coords.values():
distsq = dist2(coord, (x, y, z))
if distsq < min_sq:
min_sq = distsq
break
if min_sq == cutoff * cutoff:
grid_reference.SetValue(ix, iy, iz, 0.0)
protein_coords = protein.GetCoords()
for iz in range(grid_reference.GetZDim()):
for iy in range(grid_reference.GetYDim()):
for ix in range(grid_reference.GetXDim()):
if grid_reference.GetValue(ix, iy, iz) == 1.0:
x = grid_reference.GetX(ix)
y = grid_reference.GetY(iy)
z = grid_reference.GetZ(iz)
min_sq = cutoff * cutoff
for coord in protein_coords.values():
distsq = dist2(coord, (x, y, z))
if distsq < min_sq:
min_sq = distsq
break
if min_sq == cutoff * cutoff:
grid_reference.SetValue(ix, iy, iz, 0.0)
# oegrid.OEWriteGrid("protein_ligand.grd", grid_reference)
count = 0
for iz in range(grid_reference.GetZDim()):
for iy in range(grid_reference.GetYDim()):
for ix in range(grid_reference.GetXDim()):
if grid_reference.GetValue(ix, iy, iz) == 1.0:
count += 1
# Calculate Volume from count in Angstrom
vcount = (spacing**3) * count
# Number of water molecule in vcount volume
nwaters = int(0.034 * vcount)
return nwaters
# def select_nmax_waters()