def SetTorsionRad(self,
torsion: list,
rad: Union[float, int]):
"""
Set the dihedral angle of the torsion in rad. The torsion can only be defined
by a chain of bonded atoms.
Args:
torsion (list): A list of four atom indexes.
degree (float, int): The dihedral angle of the torsion in rad.
"""
rdMT.SetDihedralRad(self._conf, *torsion, rad)
def genConformer_r(mol, conf, i, matches, degree, sdwriter, args, name, log):
'''recursively enumerate all angles for rotatable dihedrals. i is
which dihedral we are enumerating by degree to output conformers to out'''
rotation_count = 1
if i >= len(matches): #base case, torsions should be set in conf
#setting the metal back instead of I
if args.metal_complex == True and args.nodihedrals == True:
for atom in mol.GetAtoms():
if atom.GetIdx() in args.metal_idx:
re_symbol = args.metal_sym[args.metal_idx.index(
atom.GetIdx())]
for el in elementspt:
if el.symbol == re_symbol:
atomic_number = el.number
atom.SetAtomicNum(atomic_number)
sdwriter.write(mol, conf)
return 1
else:
#log.write(str(i)+'starting new else writing')
#incr = math.pi*degree / 180.0
total = 0
deg = 0
while deg < 360.0:
#log.write(matches[i])
rad = math.pi * deg / 180.0
#log.write(matches[i],rad)
rdMolTransforms.SetDihedralRad(mol.GetConformer(conf),
*matches[i],
value=rad)
#recalculating energies after rotation
if args.ff == "MMFF":
GetFF = Chem.MMFFGetMoleculeForceField(
mol, Chem.MMFFGetMoleculeProperties(mol), confId=conf)
elif args.ff == "UFF":
GetFF = Chem.UFFGetMoleculeForceField(mol)
else:
log.write(' Force field {} not supported!'.format(args.ff))
sys.exit()
GetFF.Initialize()
converged = GetFF.Minimize(maxIts=args.opt_steps_RDKit)
energy = GetFF.CalcEnergy()
mol.SetProp("Energy", energy)
mol.SetProp(
'_Name',
name + ' - conformer from rotation - ' + str(rotation_count))
rotation_count += 1
total += genConformer_r(mol, conf, i + 1, matches, degree,
sdwriter, args, name, log)
deg += degree
return total
def genConformer_r(mol, conf, i, matches, degree, sdwriter): '''recursively enumerate all angles for rotatable dihedrals. i is which dihedral we are enumerating by degree to output conformers to out''' if i >= len(matches): #base case, torsions should be set in conf sdwriter.write(mol,conf) return 1 else: #incr = math.pi*degree / 180.0 total = 0 deg = 0 while deg < 360.0: rad = math.pi*deg / 180.0 rdMolTransforms.SetDihedralRad(mol.GetConformer(conf),*matches[i],value=rad) total += genConformer_r(mol, conf, i+1, matches, degree, sdwriter) deg += degree return total
def testGetSetDihedral(self):
file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'MolTransforms', 'test_data',
'3-cyclohexylpyridine.mol')
m = Chem.MolFromMolFile(file, True, False)
conf = m.GetConformer()
dihedral = rdmt.GetDihedralDeg(conf, 0, 19, 21, 24)
self.failUnlessAlmostEqual(dihedral, 176.05, 2)
rdmt.SetDihedralDeg(conf, 8, 0, 19, 21, 65.0)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, 65.0, 1)
rdmt.SetDihedralDeg(conf, 8, 0, 19, 21, -130.0)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -130.0, 1)
rdmt.SetDihedralRad(conf, 21, 19, 0, 8, -2. / 3. * math.pi)
dihedral = rdmt.GetDihedralRad(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -2. / 3. * math.pi, 1)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -120.0, 1)
def genConformer_r(mol, conf, i, matches, degree, sdwriter,args,name,log):
if i >= len(matches): # base case, torsions should be set in conf
#setting the metal back instead of I
if args.metal_complex and args.nodihedrals:
set_metal_atomic_number(mol,args)
sdwriter.write(mol,conf)
return 1
else:
total = 0
deg = 0
while deg < 360.0:
rad = math.pi*deg / 180.0
rdMolTransforms.SetDihedralRad(mol.GetConformer(conf),*matches[i],value=rad)
#recalculating energies after rotation
GetFF = minimize_rdkit_energy(mol,conf,args,log)
mol.SetProp("Energy",GetFF.CalcEnergy())
mol.SetProp('_Name',name)
total += genConformer_r(mol, conf, i+1, matches, degree, sdwriter,args,name,log)
deg += degree
return total
def summ_search(mol, name,args):
'''embeds core conformers, then optimizes and filters based on RMSD. Finally the rotatable torsions are systematically rotated'''
sdwriter = Chem.SDWriter(name+output)
Chem.SanitizeMol(mol)
mol = Chem.AddHs(mol)
mol.SetProp("_Name",name);
if args.nodihedrals == False: rotmatches = getDihedralMatches(mol, args.heavyonly)
else: rotmatches = []
if len(rotmatches) > args.max_torsions:
print("x Too many torsions (%d). Skipping %s" %(len(rotmatches),(name+output)))
else:
if args.etkdg:
cids = Chem.EmbedMultipleConfs(mol, args.sample, Chem.ETKDG(),randomSeed=args.seed)
else:
cids = Chem.EmbedMultipleConfs(mol, args.sample,randomSeed=args.seed)
if args.verbose:
print("o ", len(cids),"conformers initially sampled")
#energy minimize all to get more realistic results
if args.verbose: print("o Optimizing", len(cids), "initial conformers with", args.ff)
if args.verbose: print("o Found", len(rotmatches), "rotatable torsions")
cenergy = []
for i, conf in enumerate(cids):
#identify the atoms and decide Force Field
for atom in mol.GetAtoms():
if atom.GetAtomicNum() > 36: #upto Kr for MMFF, if not use UFF
args.ff = "UFF"
#print("UFF is used because there are atoms that MMFF doesn't recognise")
if args.ff == "MMFF":
GetFF = Chem.MMFFGetMoleculeForceField(mol, Chem.MMFFGetMoleculeProperties(mol),confId=conf)
elif args.ff == "UFF":
GetFF = Chem.UFFGetMoleculeForceField(mol)
else: print(' Force field {} not supported!'.format(args.ff)); sys.exit()
GetFF.Initialize()
converged = GetFF.Minimize()
cenergy.append(GetFF.CalcEnergy())
#if args.verbose:
# print("- conformer", (i+1), "optimized: ", args.ff, "energy", GetFF.CalcEnergy())
#reduce to unique set
if args.verbose: print("o Removing duplicate conformers ( RMSD <", args.rms_threshold, ")")
sortedcids = sorted(cids,key = lambda cid: cenergy[cid])
selectedcids = []
for i, conf in enumerate(sortedcids):
#set torsions to zero
for m in rotmatches:
rdMolTransforms.SetDihedralRad(mol.GetConformer(conf),*m,value=0)
#check rmsd
for seenconf in selectedcids:
rms = get_conf_RMS(mol,seenconf,conf, args.heavyonly)
if rms < args.rms_threshold:
break
else: #loop completed normally - no break, included empty
selectedcids.append(conf)
#now exhaustively drive torsions of selected conformers
if args.verbose: print("o ", len(selectedcids),"unique (ignoring torsions) starting conformers remain")
n_confs = int(len(selectedcids) * (360 / args.degree) ** len(rotmatches))
if args.verbose: print("o Systematic generation of", n_confs, "confomers")
total = 0
for conf in selectedcids:
total += genConformer_r(mol, conf, 0, rotmatches, args.degree, sdwriter)
if args.verbose: print("o %d total conformations generated"%total)
sdwriter.close()
print len(cids),"conformers sampled"
#energy minimize all to get more realistic results
cenergy = []
for conf in cids:
#not passing confID only minimizes the first conformer
converged = not Chem.UFFOptimizeMolecule(mol,confId=conf)
cenergy.append(Chem.UFFGetMoleculeForceField(mol,confId=conf).CalcEnergy())
#reduce to unique set
sortedcids = sorted(cids,key = lambda cid: cenergy[cid])
selectedcids = []
for conf in sortedcids:
#set torsions to zero
for m in rotmatches:
rdMolTransforms.SetDihedralRad(mol.GetConformer(conf),*m,value=0)
#check rmsd
for seenconf in selectedcids:
rms = getRMS(mol,seenconf,conf)
if rms < args.rms_threshold:
break
else: #loop completed normally - no break, included empty
selectedcids.append(conf)
#now exhaustively drive torsions of selected conformers
if args.verbose:
print len(selectedcids),"unique (ignoring torsions) starting conformers"
total = 0
for conf in selectedcids:
total += genConformer_r(mol, conf, 0, rotmatches, args.degree, sdwriter)