def main(argv=[__name__]):
itf = oechem.OEInterface()
if not SetupInterface(argv, itf):
return 1
zap = oezap.OEZap()
zap.SetInnerDielectric(itf.GetFloat("-epsin"))
zap.SetOuterDielectric(itf.GetFloat("-epsout"))
zap.SetGridSpacing(itf.GetFloat("-grid_spacing"))
zap.SetBoundarySpacing(itf.GetFloat("-buffer"))
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(itf.GetString("-in")):
oechem.OEThrow.Fatal("Unable to open %s for reading" %
itf.GetString("-in"))
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
zap.SetMolecule(mol)
grid = oegrid.OEScalarGrid()
if zap.CalcPotentialGrid(grid):
if itf.GetBool("-mask"):
oegrid.OEMaskGridByMolecule(grid, mol)
oegrid.OEWriteGrid(itf.GetString("-out"), grid)
return 0
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
zap = oezap.OEZap()
zap.SetInnerDielectric(1.0)
zap.SetGridSpacing(0.5)
zap.SetMolecule(mol)
# calculate standard 2-dielectric grid
grid1 = oegrid.OEScalarGrid()
zap.CalcPotentialGrid(grid1)
# calculate grid with single dielectric
grid2 = oegrid.OEScalarGrid()
zap.SetOuterDielectric(zap.GetInnerDielectric())
zap.CalcPotentialGrid(grid2)
# take the difference
oegrid.OESubtractScalarGrid(grid1, grid2)
# mask out everything outside the molecule
oegrid.OEMaskGridByMolecule(grid1, mol,
oegrid.OEGridMaskType_GaussianMinus)
oegrid.OEWriteGrid("zap_diff.grd", grid1)
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
epsin = 1.0
zap = oezap.OEZap()
zap.SetInnerDielectric(epsin)
zap.SetMolecule(mol)
grid = oegrid.OEScalarGrid()
if zap.CalcPotentialGrid(grid):
oegrid.OEWriteGrid("zap.grd", grid)
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <ref> <fit>" % args[0])
refifs = oechem.oemolistream()
if not refifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
refmol = oechem.OEGraphMol()
oechem.OEReadMolecule(refifs, refmol)
oechem.OEAssignBondiVdWRadii(refmol)
fitifs = oechem.oemolistream()
if not fitifs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[2])
fitmol = oechem.OEGraphMol()
oechem.OEReadMolecule(fitifs, fitmol)
oechem.OEAssignBondiVdWRadii(fitmol)
# Map the reference molecule onto a grid
grd = oegrid.OEScalarGrid()
oegrid.OEMakeMolecularGaussianGrid(grd, refmol, 0.5)
# Get the total volume of the reference molecule
refsrf = oespicoli.OESurface()
oespicoli.OEMakeSurfaceFromGrid(refsrf, grd, 1.0)
totalv = oespicoli.OESurfaceVolume(refsrf)
# Mask out the fit molecule
oegrid.OEMaskGridByMolecule(grd, fitmol)
# Find how much of the reference volume is remaining
fitsrf = oespicoli.OESurface()
oespicoli.OEMakeSurfaceFromGrid(fitsrf, grd, 1.0)
remaining = oespicoli.OESurfaceVolume(fitsrf)
print("Percent overlap: %f" % ((1 - remaining / totalv) * 100))
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
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()
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
import sys
from openeye import oechem
from openeye import oegrid
ifs = oechem.oemolistream(sys.argv[1])
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
grid = oegrid.OEScalarGrid()
oegrid.OEMakeMolecularGaussianGrid(grid, mol, 0.5)
# @ <SNIPPET-SquarePoints>
for i in range(grid.GetSize()):
val = grid.GetValue(i)
grid.SetValue(i, val * val)
# @ </SNIPPET-SquarePoints>
# @ </SNIPPET>
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oegrid
grid = oegrid.OEScalarGrid(2, 2, 2, 0.0, 0.0, 0.0, 0.5)
grid.SetTitle("Simple Grid")
print("Title:", grid.GetTitle())
print("Mid: %12.6f %12.6f %12.6f" % grid.GetMid())
print("Dim: %6d %6d %6d" % grid.GetDim())
print("Spacing: %12.6f" % grid.GetSpacing())
print("Values:")
for iz in range(grid.GetZDim()):
for iy in range(grid.GetYDim()):
for ix in range(grid.GetXDim()):
print("%-12.6e" % grid.GetValue(ix, iy, iz))
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData, argv)
NPolyMax = itf.GetInt("-NPolyMax")
gridspacing = itf.GetFloat("-gridspacing")
ifname = itf.GetString("-inputfile")
ofname = itf.GetString("-outputgrid")\
ifs = oechem.oemolistream()
if (not ifs.open(ifname)):
oechem.OEThrow.Fatal("Unable to open %s for reading" % ifname)
if (not ofname.endswith(".grd")):
oechem.OEThrow.Fatal("Output grid file extension hast to be '.grd' ")
mol = oechem.OEMol()
if (not oechem.OEReadMolecule(ifs, mol)):
oechem.OEThrow.Fatal("Unable to read molecule in %s" % ifname)
prep = oeshape.OEOverlapPrep()
prep.SetAssignColor(False)
prep.Prep(mol)
transfm = oechem.OETrans()
oeshape.OEOrientByMomentsOfInertia(mol, transfm)
hermiteoptions = oeshape.OEHermiteOptions()
hermiteoptions.SetNPolyMax(NPolyMax)
hermiteoptions.SetUseOptimalLambdas(True)
hermite = oeshape.OEHermite(hermiteoptions)
if (not hermite.Setup(mol)):
oechem.OEThrow.Fatal(
"Was not able to Setup the molecule for the OEHermite class.")
hopts = hermite.GetOptions()
print("Best lambdas found X=" + str(hopts.GetLambdaX()) + " Y=" +
str(hopts.GetLambdaY()) + " Z=" + str(hopts.GetLambdaZ()))
print("Hermite self-overlap=", hermite.GetSelfOverlap())
basis_size = int((NPolyMax + 1) * (NPolyMax + 2) * (NPolyMax + 3) / 6)
coeffs = oechem.OEDoubleVector(basis_size)
hermite.GetCoefficients(coeffs)
NPolyMaxstring = str(NPolyMax)
print("Hermite coefficients f_{l,m,n} in the following order l = 0..." +
NPolyMaxstring + ", m = 0..." + NPolyMaxstring + "-l, n = " +
NPolyMaxstring + "-l-m :")
for x in coeffs:
print(str(x) + " "),
grid = oegrid.OEScalarGrid()
hermite.CreateGrid(grid, gridspacing)
if (not oegrid.OEWriteGrid(ofname, grid)):
oechem.OEThrow.Fatal("Unable to write grid file")
return 0
#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from openeye import oegrid
grid = oegrid.OEScalarGrid(64, 64, 64, 0.0, 0.0, 0.0, 0.5)
# @ </SNIPPET>