def GetSzmapEnergies(lig, prot):
"""
run szmap at ligand coordinates in the protein context
@rtype : None
@param lig: mol defining coordinates for szmap calcs
@param prot: context mol for szmap calcs (must have charges and radii)
"""
print("num\tatom\t%s\t%s\t%s\t%s\t%s" %
(oeszmap.OEGetEnsembleName(oeszmap.OEEnsemble_NeutralDiffDeltaG),
oeszmap.OEGetEnsembleName(oeszmap.OEEnsemble_PSolv),
oeszmap.OEGetEnsembleName(oeszmap.OEEnsemble_WSolv),
oeszmap.OEGetEnsembleName(oeszmap.OEEnsemble_VDW),
oeszmap.OEGetEnsembleName(oeszmap.OEEnsemble_OrderParam)))
coord = oechem.OEFloatArray(3)
sz = oeszmap.OESzmapEngine(prot)
rslt = oeszmap.OESzmapResults()
for i, atom in enumerate(lig.GetAtoms()):
lig.GetCoords(atom, coord)
if not oeszmap.OEIsClashing(sz, coord):
oeszmap.OECalcSzmapResults(rslt, sz, coord)
print("%2d\t%s\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f" %
(i, atom.GetName(),
rslt.GetEnsembleValue(oeszmap.OEEnsemble_NeutralDiffDeltaG),
rslt.GetEnsembleValue(oeszmap.OEEnsemble_PSolv),
rslt.GetEnsembleValue(oeszmap.OEEnsemble_WSolv),
rslt.GetEnsembleValue(oeszmap.OEEnsemble_VDW),
rslt.GetEnsembleValue(oeszmap.OEEnsemble_OrderParam)))
else:
print("%2d\t%s CLASH" % (i, atom.GetName()))
def GenerateSzmapProbes(oms, cumulativeProb, lig, prot):
"""
generate multiconf probes and data-rich points at ligand coords
@rtype : None
@param oms: output mol stream for points and probes
@param cumulativeProb: cumulative probability for cutoff of point set
@param lig: mol defining coordinates for szmap calcs
@param prot: context mol for szmap calcs (must have charges and radii)
"""
coord = oechem.OEFloatArray(3)
sz = oeszmap.OESzmapEngine(prot)
rslt = oeszmap.OESzmapResults()
points = oechem.OEGraphMol()
points.SetTitle("points %s" % lig.GetTitle())
probes = oechem.OEMol()
for i, atom in enumerate(lig.GetAtoms()):
lig.GetCoords(atom, coord)
if not oeszmap.OEIsClashing(sz, coord):
oeszmap.OECalcSzmapResults(rslt, sz, coord)
rslt.PlaceNewAtom(points)
clear = False
rslt.PlaceProbeSet(probes, cumulativeProb, clear)
oechem.OEWriteMolecule(oms, points)
oechem.OEWriteMolecule(oms, probes)
def GenerateSzmapProbes(oms, cumulativeProb, lig, prot):
"""
generate multiconf probes and data-rich points at ligand coords
@rtype : None
@param oms: output mol stream for points and probes
@param cumulativeProb: cumulative probability for cutoff of point set
@param lig: mol defining coordinates for szmap calcs
@param prot: context mol for szmap calcs (must have charges and radii)
"""
sz = oeszmap.OESzmapEngine(prot)
rslt = oeszmap.OESzmapResults()
points = oechem.OEGraphMol()
points.SetTitle("points %s" % lig.GetTitle())
probes = oechem.OEMol()
coord = oechem.OEFloatArray(3)
for i, atom in enumerate(lig.GetAtoms()):
lig.GetCoords(atom, coord)
if not oeszmap.OEIsClashing(sz, coord):
oeszmap.OECalcSzmapResults(rslt, sz, coord)
rslt.PlaceNewAtom(points)
clear = False
rslt.PlaceProbeSet(probes, cumulativeProb, clear)
name = oeszmap.OEGetEnsembleName(oeszmap.OEEnsemble_NeutralDiffDeltaG)
nddG = rslt.GetEnsembleValue(oeszmap.OEEnsemble_NeutralDiffDeltaG)
print("%2d (%7.3f, %7.3f, %7.3f): %s = %.3f"
% (i, coord[0], coord[1], coord[2], name, nddG))
else:
print("%2d (%7.3f, %7.3f, %7.3f): CLASH"
% (i, coord[0], coord[1], coord[2]))
oechem.OEWriteMolecule(oms, points)
oechem.OEWriteMolecule(oms, probes)
def RunSzmap(lig, prot):
"""
run szmap at ligand coordinates in the protein context
@rtype : None
@param lig: mol defining coordinates for szmap calcs
@param prot: context mol for szmap calcs (must have charges and radii)
"""
# @ <SNIPPET-CREATE-SZMAPENGINEOPTIONS-OBJECT>
opt = oeszmap.OESzmapEngineOptions()
# @ </SNIPPET-CREATE-SZMAPENGINEOPTIONS-OBJECT>
# @ <SNIPPET-GETPROBEMOL>
mol = oechem.OEGraphMol()
opt.GetProbeMol(mol)
# @ </SNIPPET-GETPROBEMOL>
print("probe mol smiles: %s" % oechem.OEMolToSmiles(mol))
# @ <SNIPPET-SETPROBE>
opt.SetProbe(360)
# @ </SNIPPET-SETPROBE>
print("norient = %d" % opt.NumOrientations())
# @ <SNIPPET-COMBINE-OPTIONS>
opt.SetProbe(24).SetMaskCutoff(999.99)
# @ </SNIPPET-COMBINE-OPTIONS>
print("norient = %d" % opt.NumOrientations())
print("cutoff = %.3f" % opt.GetMaskCutoff())
opt.SetMaskCutoff(0.0) # reset cutoff
print("cutoff = %.3f" % opt.GetMaskCutoff())
# @ <SNIPPET-GET-PROBE>
p = opt.GetProbe()
print("probe nconf = %d" % p.NumConfs())
# @ </SNIPPET-GET-PROBE>
# @ <SNIPPET-CREATE-SZMAPENGINE-OBJECT>
sz = oeszmap.OESzmapEngine(prot, opt)
# @ </SNIPPET-CREATE-SZMAPENGINE-OBJECT>
# @ <SNIPPET-GET-OPTIONS>
opt = sz.GetOptions()
print("norient= %d" % opt.NumOrientations())
print("name = %s" % opt.GetProbeName())
print("cutoff = %.3f" % opt.GetMaskCutoff())
# @ </SNIPPET-GET-OPTIONS>
# @ <SNIPPET-GET-CONTEXT>
mol = sz.GetContext()
print("context mol: %s" % mol.GetTitle())
# @ </SNIPPET-GET-CONTEXT>
print("probe smiles: %s" % oechem.OEMolToSmiles(opt.GetProbe()))
# @ <SNIPPET-CREATE-COORDSARRAY-OBJECT>
coord = oechem.OEFloatArray(3)
# @ </SNIPPET-CREATE-COORDSARRAY-OBJECT>
# @ <SNIPPET-CREATE-SZMAPRESULTS-OBJECT>
rslt = oeszmap.OESzmapResults()
# @ </SNIPPET-CREATE-SZMAPRESULTS-OBJECT>
for atom in lig.GetAtoms():
lig.GetCoords(atom, coord)
# @ <SNIPPET-GET-ENSEMBLE-NAME>
name = oeszmap.OEGetEnsembleName(oeszmap.OEEnsemble_NeutralDiffDeltaG)
# @ </SNIPPET-GET-ENSEMBLE-NAME>
print("ensemble name: %s" % name)
# @ <SNIPPET-GET-LONG-ENSEMBLE-NAME>
longName = True
name = oeszmap.OEGetEnsembleName(oeszmap.OEEnsemble_NeutralDiffDeltaG,
longName)
# @ </SNIPPET-GET-LONG-ENSEMBLE-NAME>
# @ <SNIPPET-CALC-SZMAP-VALUE>
nddg = oeszmap.OECalcSzmapValue(sz, coord)
# @ </SNIPPET-CALC-SZMAP-VALUE>
print("ensemble name: %s, value: %.3f" % (name, nddg))
# @ <SNIPPET-GET-COMPONENT-NAME>
name = oeszmap.OEGetComponentName(oeszmap.OEComponent_Interaction)
# @ </SNIPPET-GET-COMPONENT-NAME>
print("component name: %s" % name)
# @ <SNIPPET-CLASH-RSLTS-EVAL>
if not oeszmap.OEIsClashing(sz, coord):
oeszmap.OECalcSzmapResults(rslt, sz, coord)
nddg = rslt.GetEnsembleValue(oeszmap.OEEnsemble_NeutralDiffDeltaG)
# @ </SNIPPET-CLASH-RSLTS-EVAL>
# @ <SNIPPET-CALC-SZMAP-RESULTS>
if not oeszmap.OEIsClashing(sz, coord):
oeszmap.OECalcSzmapResults(rslt, sz, coord)
# ...
# @ </SNIPPET-CALC-SZMAP-RESULTS>
print("result norient = %d" % rslt.NumOrientations())
# @ <SNIPPET-GET-ENSEMBLE-VALUE>
nddg = rslt.GetEnsembleValue(oeszmap.OEEnsemble_NeutralDiffDeltaG)
# @ </SNIPPET-GET-ENSEMBLE-VALUE>
print("nddG = %.3f" % nddg)
print("vdw = %.3f" %
rslt.GetEnsembleValue(oeszmap.OEEnsemble_VDW))
# @ <SNIPPET-GET-COMPONENT>
coulomb = rslt.GetComponent(oeszmap.OEComponent_Interaction)
print("interaction:")
print(" ".join("%.3f" % c for c in coulomb))
# @ </SNIPPET-GET-COMPONENT>
# @ <SNIPPET-GET-ORDER>
order = rslt.GetProbabilityOrder()
print("conf with greatest prob = %d" % order[0])
# @ </SNIPPET-GET-ORDER>
# @ <SNIPPET-GET-PROBABILITIES>
prob = rslt.GetProbabilities()
print("greatest prob = %.3f" % prob[order[0]])
# @ </SNIPPET-GET-PROBABILITIES>
# @ <SNIPPET-GET-ORIENTATION-COMPONENT>
vdw = oechem.OEDoubleArray(rslt.NumOrientations())
rslt.GetComponent(vdw, oeszmap.OEComponent_VDW)
print("vdw greatest prob = %.3f" % vdw[order[0]])
# @ </SNIPPET-GET-ORIENTATION-COMPONENT>
# @ <SNIPPET-GET-COORDS>
point = oechem.OEFloatArray(3)
rslt.GetCoords(point)
# @ </SNIPPET-GET-COORDS>
print("calc point: (%.3f, %.3f, %.3f)" %
(point[0], point[1], point[2]))
# @ <SNIPPET-PLACE-PROBE-SET-ALL>
mcmol = oechem.OEMol()
rslt.PlaceProbeSet(mcmol)
# @ </SNIPPET-PLACE-PROBE-SET-ALL>
# @ <SNIPPET-PLACE-PROBE-SET-PROB>
probCutoff = 0.5
rslt.PlaceProbeSet(mcmol, probCutoff)
print("nconf to yield 50pct = %d" % mcmol.NumConfs())
# @ </SNIPPET-PLACE-PROBE-SET-PROB>
# @ <SNIPPET-PLACE-PROBE-SET-COUNT>
clear = False
cumulativeProb = rslt.PlaceProbeSet(mcmol, 10, clear)
print("best 10 cumulative prob = %.3f" % cumulativeProb)
# @ </SNIPPET-PLACE-PROBE-SET-COUNT>
# @ <SNIPPET-PLACE-NEW-ATOM>
amol = oechem.OEGraphMol()
atom = rslt.PlaceNewAtom(amol)
print("vdw = %s" % atom.GetData("vdw"))
# @ </SNIPPET-PLACE-NEW-ATOM>
# @ <SNIPPET-PLACE-PROBE-MOL>
pmol = oechem.OEGraphMol()
rslt.PlaceProbeMol(pmol, order[0])