def main(argv=[__name__]):
if len(argv) != 4:
oechem.OEThrow.Usage("%s <prot-infile> <lig-infile> <max-distance>" %
argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open protein %s for reading" % argv[1])
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, prot)
if not oechem.OEHasResidues(prot):
oechem.OEPerceiveResidues(prot, oechem.OEPreserveResInfo_All)
ifs = oechem.oemolistream()
if not ifs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open ligand %s for reading" % argv[2])
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, lig)
if not oechem.OEHasResidues(lig):
oechem.OEPerceiveResidues(lig, oechem.OEPreserveResInfo_All)
maxgap = float(argv[3])
PrintCloseContacts(prot, lig, maxgap)
def ResHist(ifs):
nrmol = 0
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
nrmol += 1
print("==============================")
print("Molecule: %d Title: %s" % (nrmol, mol.GetTitle()))
nrres = 0
resmap = {}
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
hv = oechem.OEHierView(mol)
for res in hv.GetResidues():
nrres += 1
name = res.GetOEResidue().GetName()
if name in resmap:
resmap[name] += 1
else:
resmap[name] = 1
sortedres = sorted(resmap.keys())
for name in sortedres:
percent = 100.0*float(resmap[name])/float(nrres)
print("%3s %3d %4.1f %%" % (name, resmap[name], percent))
def CisCheck(ifs):
nrmol = 0
nrcis = 0
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
nrmol += 1
print("===========================================================")
print("Molecule: %s Title: %s" % (nrmol, mol.GetTitle()))
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
hv = oechem.OEHierView(mol)
resiter = oechem.ConstOEHierResidueIter()
resiter = hv.GetResidues()
while (resiter.IsValid()):
res = resiter.Target()
resiter.Next()
if not oechem.OEIsStandardProteinResidue(res):
continue
torsion = oechem.OEGetTorsion(res, oechem.OEProtTorType_Omega)
if torsion != -100.0:
if torsion < math.pi / 2.0 and torsion > -math.pi / 2.0:
if resiter.IsValid():
nextres = resiter.Target()
oenextres = nextres.GetOEResidue()
if oechem.OEGetResidueIndex(
oenextres) == oechem.OEResidueIndex_PRO:
continue
nrcis += 1
oeres = res.GetOEResidue()
print("%s %s %2d omega torsion = %.2f degree" %
(oeres.GetName(), oeres.GetChainID(),
oeres.GetResidueNumber(),
torsion * oechem.cvar.Rad2Deg))
print(" %d cis amide bond(s) identified\n" % nrcis)
def ResCount(ifs):
nrmol = 0
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
nrmol += 1
nratom = 0
nrwat = 0
nrres = 0
nrfrag = 0
nrchain = 0
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
hv = oechem.OEHierView(mol)
for chain in hv.GetChains():
nrchain += 1
for frag in chain.GetFragments():
nrfrag += 1
for res in frag.GetResidues():
nrres += 1
if oechem.OEGetResidueIndex(res.GetOEResidue()) == oechem.OEResidueIndex_HOH:
nrwat += 1
else:
for atom in res.GetAtoms():
nratom += 1
print("===============================================")
print("Molecule : %d Title: %s" % (nrmol, mol.GetTitle()))
print("Chains : %d" % nrchain)
print("Fragments: %d" % nrfrag)
print("Residues : %d (%d waters)" % (nrres, nrwat))
print("Atoms : %d" % nratom)
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 set_serial(molecule, chainid, first_serial):
import oechem
if not oechem.OEHasResidues(molecule):
oechem.OEPerceiveResidues(molecule, oechem.OEPreserveResInfo_All)
for atom in molecule.GetAtoms():
residue = oechem.OEAtomGetResidue(atom)
residue.SetExtChainID(chainid)
serial_number = residue.GetSerialNumber()
residue.SetSerialNumber(serial_number + first_serial)
def MakeAlpha(ifs, ofs):
phival = math.pi / -3.0
psival = math.pi / -3.0
chival = math.pi
nrphis = 0
nrpsis = 0
nrchis = 0
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
# remove cross-links
for bond in mol.GetBonds():
if bond.GetBgn().GetAtomicNum() == oechem.OEElemNo_S and \
bond.GetEnd().GetAtomicNum() == oechem.OEElemNo_S:
mol.DeleteBond(bond)
oechem.OEFindRingAtomsAndBonds(mol)
hv = oechem.OEHierView(mol)
for res in hv.GetResidues():
if not oechem.OEIsStandardProteinResidue(res):
continue
# set psi and phi angles
if not oechem.OESetTorsion(res, oechem.OEProtTorType_Phi, phival):
oeres = res.GetOEResidue()
print("Unable to set phi for %s %d" %
(oeres.GetName(), oeres.GetResidueNumber()))
else:
nrphis += 1
if not oechem.OESetTorsion(res, oechem.OEProtTorType_Psi, psival):
oeres = res.GetOEResidue()
print("Unable to set psi for %s %d" %
(oeres.GetName(), oeres.GetResidueNumber()))
else:
nrpsis += 1
# set chis
if oechem.OEGetResidueIndex(
res.GetOEResidue().GetName()) == oechem.OEResidueIndex_PRO:
continue # It does not make sense to set Proline chi angles to 180
for chi in oechem.OEGetChis(res):
if not oechem.OESetTorsion(res, chi, chival):
oeres = res.GetOEResidue()
print("Unable to set chi %s for %s %d" %
(oechem.OEGetProteinTorsionName(chi),
oeres.GetName(), oeres.GetResidueNumber()))
else:
nrchis += 1
oechem.OEWriteMolecule(ofs, mol)
print(nrphis, " phi torsion angle set to ", phival * oechem.cvar.Rad2Deg)
print(nrpsis, " psi torsion angle set to ", psival * oechem.cvar.Rad2Deg)
print(nrchis, " chis torsion angle set to ", chival * oechem.cvar.Rad2Deg)
def PrintAltGroupInfo(mol):
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol) # create factory for mol
print("%s\t(%s groups)" % (mol.GetTitle(), alf.GetGroupCount()))
for grp in alf.GetGroups():
print("\t%s locs:%s" %
(grp.GetLocationCount(), alf.GetLocationCodes(grp)))
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <mol-infile>" % argv[0])
ims = oechem.oemolistream()
if not ims.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
for mol in ims.GetOEGraphMols():
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
CalcResCounts(mol)
def PrintGroups(mol):
"""summarize alternate location group info"""
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
print("%s\t(%s groups)" % (mol.GetTitle(), alf.GetGroupCount()))
for grp in alf.GetGroups():
print("\t%s locs:%s" %
(grp.GetLocationCount(), alf.GetLocationCodes(grp)))
def PrintResidues(mol):
"""list alternate location code and occupancy by group and residue"""
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
print("%s - %d alternate location groups:" %
(mol.GetTitle(), alf.GetGroupCount()))
for grp in alf.GetGroups():
print("%d) %d alternate locations" %
(grp.GetGroupID() + 1, grp.GetLocationCount()),
end=" ")
prev = oechem.OEResidue()
prevCodes = ""
sumOcc = []
atNum = []
for atom in alf.GetAltAtoms(grp):
res = oechem.OEAtomGetResidue(atom)
if not oechem.OESameResidue(res, prev):
for i, code in enumerate(prevCodes):
print("%c(%.0f%c) " %
(code, (sumOcc[i] * 100.0) / atNum[i], "%"),
end=" ")
print()
prevCodes = ""
sumOcc = []
atNum = []
print("\t%s%d%c chain '%c': " %
(res.GetName(), res.GetResidueNumber(),
res.GetInsertCode(), res.GetChainID()),
end=" ")
prev = res
code = res.GetAlternateLocation()
whichCode = prevCodes.find(code)
if whichCode < 0:
prevCodes += code
sumOcc.append(res.GetOccupancy())
atNum.append(1)
else:
sumOcc[whichCode] += res.GetOccupancy()
atNum[whichCode] += 1
for i, code in enumerate(prevCodes):
print("%c(%.0f%c) " % (code, (sumOcc[i] * 100.0) / atNum[i], "%"),
end=" ")
print()
def LoopOverResAtoms(ims):
for mol in ims.GetOEGraphMols():
# @ <SNIPPET-PERCEIVE-RES>
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
# @ </SNIPPET-PERCEIVE-RES>
# @ <SNIPPET-RES-ATOMS-CORE>
hv = oechem.OEHierView(mol)
hres = hv.GetResidue("A", "LEU", 27)
for atom in hres.GetAtoms(): # only this residue's atoms
res = oechem.OEAtomGetResidue(atom)
print(res.GetSerialNumber(), atom.GetName())
def BackBone(ifs, ofs):
adjustHCount = True
mol = oechem.OEGraphMol()
backboneMol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
aiter = mol.GetAtoms(oechem.OEIsBackboneAtom())
member = oechem.OEIsAtomMember(aiter)
oechem.OESubsetMol(backboneMol, mol, member, adjustHCount)
oechem.OEWriteMolecule(ofs, backboneMol)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
# @ <SNIPPET-ALTLOCFACT-FLAVOR>
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_ALTLOC)
# @ </SNIPPET-ALTLOCFACT-FLAVOR>
inputFile = itf.GetString("-in")
if not ims.open(inputFile):
oechem.OEThrow.Fatal("Unable to open %s for reading." % inputFile)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % inputFile)
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Unable to read %s." % inputFile)
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
# @ <SNIPPET-ALTLOCFACT-PRIMARY>
alf = oechem.OEAltLocationFactory(mol)
if alf.GetGroupCount() != 0:
alf.MakePrimaryAltMol(mol)
# @ </SNIPPET-ALTLOCFACT-PRIMARY>
# @ <SNIPPET-PLACE-HYDROGENS-BASIC>
if oechem.OEPlaceHydrogens(mol):
# ...
# @ </SNIPPET-PLACE-HYDROGENS-BASIC>
print("success")
# @ <SNIPPET-PLACE-HYDROGENS-OPTIONS>
opt = oechem.OEPlaceHydrogensOptions()
opt.SetStandardizeBondLen(False)
# @ </SNIPPET-PLACE-HYDROGENS-OPTIONS>
# @ <SNIPPET-PLACE-HYDROGENS-DETAILS>
# given molecule mol and OEPlaceHydrogensOptions opt...
details = oechem.OEPlaceHydrogensDetails()
if oechem.OEPlaceHydrogens(mol, details, opt):
print(details.Describe())
# @ </SNIPPET-PLACE-HYDROGENS-DETAILS>
ims.close()
def CalcResCounts(mol):
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
resCt = 0
hetCt = 0
prevRes = oechem.OEResidue()
for atom in mol.GetAtoms():
thisRes = oechem.OEAtomGetResidue(atom)
if not oechem.OESameResidue(prevRes, thisRes):
resCt += 1
if thisRes.IsHetAtom():
hetCt += 1
prevRes = thisRes
print("Molecule: %s" % mol.GetTitle())
print("Residues: %d (%d hets)" % (resCt, hetCt))
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_ALTLOC)
inputFile = itf.GetString("-in")
if not ims.open(inputFile):
oechem.OEThrow.Fatal("Unable to open %s for reading." % inputFile)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % inputFile)
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Unable to read %s." % inputFile)
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
if alf.GetGroupCount() != 0:
alf.MakePrimaryAltMol(mol)
# in our example, we will select the first histidine
selectedResidue = oechem.OEResidue()
for atom in mol.GetAtoms():
res = oechem.OEAtomGetResidue(atom)
if oechem.OEGetResidueIndex(res) == oechem.OEResidueIndex_HIS:
selectedResidue = res
break
# @ <SNIPPET-PLACE-HYDROGENS-PRED>
# given predicate IsSameResidue, residue selectedResidue and molecule mol...
opt = oechem.OEPlaceHydrogensOptions()
opt.SetNoFlipPredicate(IsSameResidue(selectedResidue))
if oechem.OEPlaceHydrogens(mol, opt):
# selectedResidue will not be flipped...
# @ </SNIPPET-PLACE-HYDROGENS-PRED>
print("success")
ims.close()
def get_protein_and_ligands(protein, ligand, itf):
if (itf.HasString("-complex")):
# separate ligand and protein in complex
iname = itf.GetString("-complex")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input complex file!")
complexmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, complexmol):
oechem.OEThrow.Fatal("Unable to read complex from %s" % iname)
if not oechem.OEHasResidues(complexmol):
oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)
sopts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(sopts, itf)
if not split_complex(protein, ligand, sopts, complexmol):
oechem.OEThrow.Fatal("Cannot separate complex!")
else:
# read ligand and protein from separate files
pname = itf.GetString("-protein")
ifs = oechem.oemolistream()
if not ifs.open(pname):
oechem.OEThrow.Fatal("Cannot open input protein file!")
if not oechem.OEReadMolecule(ifs, protein):
oechem.OEThrow.Fatal("Unable to read protein from %s" % pname)
lname = itf.GetString("-ligand")
ifs = oechem.oemolistream()
if not ifs.open(lname):
oechem.OEThrow.Fatal("Cannot open input ligand file!")
if not oechem.OEReadMolecule(ifs, ligand):
oechem.OEThrow.Fatal("Unable to read ligand from %s" % lname)
return ligand.NumAtoms() != 0 and protein.NumAtoms() != 0
def PrintLocations(mol, hideAtoms):
"""list alternate location codes and atom info (unless hideAtoms is True)"""
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
print("%s" % mol.GetTitle())
print("grp-cnt=%d" % alf.GetGroupCount(), end=" ")
if alf.GetGroupCount() > 0:
print("{")
else:
print()
for grp in alf.GetGroups():
print(" grp=%d loc-cnt=%d grp-codes='%s'" %
(grp.GetGroupID(), grp.GetLocationCount(),
alf.GetLocationCodes(grp)))
for loc in grp.GetLocations():
print(" grp=%d loc=%d loc-codes='%s'" %
(loc.GetGroupID(), loc.GetLocationID(),
alf.GetLocationCodes(loc)),
end=" ")
if not hideAtoms:
print("[", end=" ")
num_atoms = 0
for atom in alf.GetAltAtoms(loc):
num_atoms += 1
if not hideAtoms:
res = oechem.OEAtomGetResidue(atom)
print("%s:%c:%s%d%c:c%cm%d;" %
(atom.GetName(), res.GetAlternateLocation(),
res.GetName(), res.GetResidueNumber(),
res.GetInsertCode(), res.GetChainID(),
res.GetModelNumber()),
end=" ")
if not hideAtoms:
print("]", end=" ")
print(num_atoms)
if alf.GetGroupCount() > 0:
print("}")
def Rename(ims, oms):
for mol in ims.GetOEGraphMols():
# @ <SNIPPET-PERCEIVE-RES>
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
# @ </SNIPPET-PERCEIVE-RES>
# @ <SNIPPET-MSE-TO-MET-CORE>
for atom in mol.GetAtoms():
thisRes = oechem.OEAtomGetResidue(atom)
if oechem.OEGetResidueIndex(thisRes) == oechem.OEResidueIndex_MSE:
thisRes.SetName("MET") # modify res properties
thisRes.SetHetAtom(False)
oechem.OEAtomSetResidue(atom, thisRes) # store updated residue
if atom.GetAtomicNum() == oechem.OEElemNo_Se:
atom.SetAtomicNum(
oechem.OEElemNo_S) # fix atom type & name
atom.SetName(" SD ")
# @ </SNIPPET-MSE-TO-MET-CORE>
oechem.OEWriteMolecule(oms, mol)
def SubSetRes(ifs, ofs, chainid, resname, resnum):
adjustHCount = True
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
hv = oechem.OEHierView(mol)
res = hv.GetResidue(chainid, resname, resnum)
if res.GetOEResidue().GetName() is None:
oechem.OEThrow.Fatal("Failed to find residue")
atomiter = res.GetAtoms()
member = oechem.OEIsAtomMember(atomiter)
resmol = oechem.OEGraphMol()
oechem.OESubsetMol(resmol, mol, member, adjustHCount)
if chainid == " ":
resmol.SetTitle("%s %d" % (resname, resnum))
else:
resmol.SetTitle("%s %s %d" % (resname, chainid, resnum))
oechem.OEWriteMolecule(ofs, resmol)
def PrintStates(mol):
"""list alternate location state information"""
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
print("%s\t%d groups" % (mol.GetTitle(), alf.GetGroupCount()), end=" ")
tot = 1
totexp = 0.0
for grp in alf.GetGroups():
tot *= grp.GetLocationCount()
totexp += math.log10(grp.GetLocationCount())
if totexp > 7.0:
print("\tover 10^%.0f states" % totexp)
print("too many states to enumerate")
else:
print("\t%d states" % tot)
locs = [grp.GetLocations() for grp in alf.GetGroups()]
EnumerateStates(alf, locs, 0, len(locs))
def __init__(self, ipf, keepAlts=F, verbose=T):
self.ipf = ipf
self.keepAlts = keepAlts
self.verbose = verbose
flavor = oechem.OEIFlavor_PDB_Default
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, flavor)
if not ims.open(self.ipf):
oechem.OEThrow.Fatal("Unable to open %s for reading." % self.ipf)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % self.ipf)
iftp = oechem.OEGetFileType(oechem.OEGetFileExtension(self.ipf))
if (iftp == oechem.OEFormat_PDB) and not self.keepAlts:
oechem.OEThrow.Verbose(
"Default processing of alt locations (keep just 'A' and ' ').")
inmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, inmol):
oechem.OEThrow.Fatal("Unable to read %s." % self.ipf)
ims.close()
if (inmol.NumAtoms() == 0):
oechem.OEThrow.Fatal("Input molecule %s contains no atoms." %
self.ipf)
if inmol.GetTitle() == "":
inmol.SetTitle(ipf[:-4])
oechem.OEThrow.Verbose("Processing %s." % inmol.GetTitle())
if not oechem.OEHasResidues(inmol):
oechem.OEPerceiveResidues(inmol, oechem.OEPreserveResInfo_All)
self.inmol = inmol
self.mol = inmol.CreateCopy()
def ShowPhiPsi(ifs):
nrmol = 0
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
nrmol += 1
print("================================================")
print("Molecule: %d Title: %s" % (nrmol, mol.GetTitle()))
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
hv = oechem.OEHierView(mol)
for res in hv.GetResidues():
if not oechem.OEIsStandardProteinResidue(res):
continue
phi = oechem.OEGetPhi(res)
psi = oechem.OEGetPsi(res)
oeres = res.GetOEResidue()
print(" %s %s %d (PHI=%.2f, PSI=%.2f)" % (oeres.GetName(),
oeres.GetChainID(),
oeres.GetResidueNumber(),
phi, psi))
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oechem.OEConfigureSplitMolComplexOptions(
itf, oechem.OESplitMolComplexSetup_LigName)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-complex")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % iname)
complexmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, complexmol):
oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname)
if not oechem.OEHasResidues(complexmol):
oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)
# Separate ligand and protein
sopts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(sopts, itf)
ligand = oechem.OEGraphMol()
protein = oechem.OEGraphMol()
water = oechem.OEGraphMol()
other = oechem.OEGraphMol()
pfilter = sopts.GetProteinFilter()
wfilter = sopts.GetWaterFilter()
sopts.SetProteinFilter(oechem.OEOrRoleSet(pfilter, wfilter))
sopts.SetWaterFilter(
oechem.OEMolComplexFilterFactory(
oechem.OEMolComplexFilterCategory_Nothing))
oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts)
if ligand.NumAtoms() == 0:
oechem.OEThrow.Fatal("Cannot separate complex!")
# Perceive interactions
asite = oechem.OEInteractionHintContainer(protein, ligand)
if not oechem.OEIsValidActiveSite(asite):
oechem.OEThrow.Fatal("Cannot initialize active site!")
oechem.OEPerceiveInteractionHints(asite)
print("Number of interactions:", asite.NumInteractions())
for itype in oechem.OEGetActiveSiteInteractionHintTypes():
numinters = asite.NumInteractions(
oechem.OEHasInteractionHintType(itype))
if numinters == 0:
continue
print("%d %s :" % (numinters, itype.GetName()))
inters = [
s for s in asite.GetInteractions(
oechem.OEHasInteractionHintType(itype))
]
print("\n".join(sorted(GetInteractionString(s) for s in inters)))
print("\nResidue interactions:")
for res in oechem.OEGetResidues(
asite.GetMolecule(oechem.OEProteinInteractionHintComponent())):
PrintResidueInteractions(asite, res)
print("\nLigand atom interactions:")
for atom in asite.GetMolecule(
oechem.OELigandInteractionHintComponent()).GetAtoms():
PrintLigandAtomInteractions(asite, atom)
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 600.0)
oedepict.OEConfigureImageHeight(itf, 600.0)
oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
oechem.OEConfigureSplitMolComplexOptions(itf, oechem.OESplitMolComplexSetup_LigName)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-complex")
oname = itf.GetString("-out")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
complexmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, complexmol):
oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname)
if not oechem.OEHasResidues(complexmol):
oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)
# Separate ligand and protein
sopts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(sopts, itf)
ligand = oechem.OEGraphMol()
protein = oechem.OEGraphMol()
water = oechem.OEGraphMol()
other = oechem.OEGraphMol()
oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts)
if ligand.NumAtoms() == 0:
oechem.OEThrow.Fatal("Cannot separate complex!")
# Calculate average BFactor of the whole complex
avgbfactor = GetAverageBFactor(complexmol)
# Calculate minimum and maximum BFactor of the ligand and its environment
minbfactor, maxbfactor = GetMinAndMaxBFactor(ligand, protein)
# Attach to each ligand atom the average BFactor of the nearby protein atoms
stag = "avg residue BFfactor"
itag = oechem.OEGetTag(stag)
SetAverageBFactorOfNearbyProteinAtoms(ligand, protein, itag)
oechem.OEThrow.Info("Average BFactor of the complex = %+.3f" % avgbfactor)
oechem.OEThrow.Info("Minimum BFactor of the ligand and its environment = %+.3f" % minbfactor)
oechem.OEThrow.Info("Maximum BFactor of the ligand and its environment = %+.3f" % maxbfactor)
# Create image
imagewidth, imageheight = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf)
image = oedepict.OEImage(imagewidth, imageheight)
mframe = oedepict.OEImageFrame(image, imagewidth,
imageheight * 0.90, oedepict.OE2DPoint(0.0, 0.0))
lframe = oedepict.OEImageFrame(image, imagewidth, imageheight * 0.10,
oedepict.OE2DPoint(0.0, imageheight * 0.90))
opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(), mframe.GetHeight(),
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
# Create BFactor color gradient
colorg = oechem.OELinearColorGradient()
colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEDarkBlue))
colorg.AddStop(oechem.OEColorStop(10.0, oechem.OELightBlue))
colorg.AddStop(oechem.OEColorStop(25.0, oechem.OEYellowTint))
colorg.AddStop(oechem.OEColorStop(50.0, oechem.OERed))
colorg.AddStop(oechem.OEColorStop(100.0, oechem.OEDarkRose))
# Prepare ligand for depiction
oegrapheme.OEPrepareDepictionFrom3D(ligand)
arcfxn = BFactorArcFxn(colorg, itag)
for atom in ligand.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(ligand, atom, arcfxn)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(ligand, opts))
# Render ligand and visualize BFactor
disp = oedepict.OE2DMolDisplay(ligand, opts)
colorbfactor = ColorLigandAtomByBFactor(colorg)
oegrapheme.OEAddGlyph(disp, colorbfactor, oechem.OEIsTrueAtom())
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(mframe, disp)
# Draw color gradient
opts = oegrapheme.OEColorGradientDisplayOptions()
opts.SetColorStopPrecision(1)
opts.AddMarkedValue(avgbfactor)
opts.SetBoxRange(minbfactor, maxbfactor)
oegrapheme.OEDrawColorGradient(lframe, colorg, opts)
oedepict.OEWriteImage(oname, image)
return 0
from openeye import oechem
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <mol-infile>" % sys.argv[0])
ims = oechem.oemolistream()
if not ims.open(sys.argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % sys.argv[1])
# @ <SNIPPET-ALTLOCFACT-MAKEALTMOL-FLAVOR>
ims.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_ALTLOC)
# @ </SNIPPET-ALTLOCFACT-MAKEALTMOL-FLAVOR>
for mol in ims.GetOEGraphMols():
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
# @ <SNIPPET-ALTLOCFACT-MAKEALTMOL-ALF>
alf = oechem.OEAltLocationFactory(mol)
# @ </SNIPPET-ALTLOCFACT-MAKEALTMOL-ALF>
print("# atoms original.. %d" % alf.GetSourceMol().GetMaxAtomIdx())
atom = alf.GetAltAtoms()
if atom.IsValid():
# @ <SNIPPET-ALTLOCFACT-MAKEALTMOL-SSMOL>
# given OEAltLocationFactory alf and OEAtomBaseIter atom ...
loc = alf.GetLocation(atom.next(), 'B')
ssmol = oechem.OEGraphMol()
if alf.MakeAltMol(ssmol, loc):
# use the subset mol...
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 900.0)
oedepict.OEConfigureImageHeight(itf, 600.0)
oedepict.OEConfigure2DMolDisplayOptions(
itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
oechem.OEConfigureSplitMolComplexOptions(
itf, oechem.OESplitMolComplexSetup_LigName)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-complex")
oname = itf.GetString("-out")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
complexmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, complexmol):
oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname)
if not oechem.OEHasResidues(complexmol):
oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)
# Separate ligand and protein
sopts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(sopts, itf)
ligand = oechem.OEGraphMol()
protein = oechem.OEGraphMol()
water = oechem.OEGraphMol()
other = oechem.OEGraphMol()
pfilter = sopts.GetProteinFilter()
wfilter = sopts.GetWaterFilter()
sopts.SetProteinFilter(oechem.OEOrRoleSet(pfilter, wfilter))
sopts.SetWaterFilter(
oechem.OEMolComplexFilterFactory(
oechem.OEMolComplexFilterCategory_Nothing))
oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts)
if ligand.NumAtoms() == 0:
oechem.OEThrow.Fatal("Cannot separate complex!")
# Perceive interactions
asite = oechem.OEInteractionHintContainer(protein, ligand)
if not asite.IsValid():
oechem.OEThrow.Fatal("Cannot initialize active site!")
asite.SetTitle(ligand.GetTitle())
oechem.OEPerceiveInteractionHints(asite)
oegrapheme.OEPrepareActiveSiteDepiction(asite)
# Depict active site with interactions
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
cframe = oedepict.OEImageFrame(image, width * 0.80, height,
oedepict.OE2DPoint(0.0, 0.0))
lframe = oedepict.OEImageFrame(image, width * 0.20, height,
oedepict.OE2DPoint(width * 0.80, 0.0))
opts = oegrapheme.OE2DActiveSiteDisplayOptions(cframe.GetWidth(),
cframe.GetHeight())
oedepict.OESetup2DMolDisplayOptions(opts, itf)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
oegrapheme.OERenderActiveSite(cframe, adisp)
lopts = oegrapheme.OE2DActiveSiteLegendDisplayOptions(10, 1)
oegrapheme.OEDrawActiveSiteLegend(lframe, adisp, lopts)
oedepict.OEWriteImage(oname, image)
return 0
