def GetDihedralHs(atom):
sp3carbonFound = False
#find the proton neigbour, check that it is sp3 carbon
for NbrAtom in OBAtomAtomIter(atom):
if NbrAtom.GetAtomicNum() == 6 and NbrAtom.GetHyb() == 3:
carbon = NbrAtom
sp3carbonFound = True
break
if not sp3carbonFound:
return 0
#find the carbon neibours, check that they are sp3 hybridized
ncarbons = []
for NbrAtom in OBAtomAtomIter(carbon):
if NbrAtom.GetAtomicNum() == 6 and NbrAtom.GetHyb() == 3:
ncarbons.append(NbrAtom)
#check that the carbon neighbours have protons and return them
nHs = []
for ncarbon in ncarbons:
for NbrAtom in OBAtomAtomIter(ncarbon):
if NbrAtom.GetAtomicNum() == 1:
nHs.append(NbrAtom.GetIdx())
if len(nHs) == 0:
return 0
else:
return nHs
def methyl_protons(file):
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, file)
methyl_protons = []
for atom in OBMolAtomIter(obmol):
count = 0
nbrprotons = []
for NbrAtom in OBAtomAtomIter(atom):
if (atom.GetAtomicNum() == 6) & (NbrAtom.GetAtomicNum() == 1):
l = NbrAtom.GetIndex()
count += 1
nbrprotons.append('H' + str(l + 1))
if count == 3:
methyl_protons.append(nbrprotons)
return methyl_protons
def remove_labile_protons(sdffile, lbls, shifts):
f = sdffile.split('.sdf')[0] + '.sdf'
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, f)
CI = []
for atom in OBMolAtomIter(obmol):
if atom.GetAtomicNum() == 1:
for NbrAtom in OBAtomAtomIter(atom):
if (NbrAtom.GetAtomicNum() == 8):
CI.append('H' + str(atom.GetIndex() + 1))
#remove these carbons
for C in CI:
ind = lbls.index(C)
lbls.remove(C)
for l in shifts:
l.pop(ind)
return lbls, shifts
def FindSubstAtoms(atom, outAtom, al):
indexes = [a.GetIdx() for a in al]
for NbrAtom in OBAtomAtomIter(atom):
if (NbrAtom.GetIdx() not in indexes) and\
(NbrAtom.GetIdx() != outAtom.GetIdx()):
al.append(NbrAtom)
FindSubstAtoms(NbrAtom, outAtom, al)
def RestoreNumsSDF(f, fold, AuxInfo):
#Read molecule from file
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, f)
#Get the atoms Hs are connected to
oldHcons = GetHcons(fold)
#translate the H connected atoms to the new numbering system
amap = GetInchiRenumMap(AuxInfo)
for i in range(0, len(oldHcons)):
oldHcons[i][1] = amap.index(oldHcons[i][1]) + 1
newHcons = []
temp = []
i = 0
for atom in OBMolAtomIter(obmol):
idx = atom.GetIdx()
anum = atom.GetAtomicNum()
#If atom is hydrogen, check what it is connected to
if anum == 1:
for NbrAtom in OBAtomAtomIter(atom):
newHcons.append([idx, NbrAtom.GetIdx()])
#Pick the temporary atom
temp.append(atom)
for i in range(0, len(newHcons)):
conatom = newHcons[i][1]
for b in range(0, len(oldHcons)):
if conatom == oldHcons[b][1]:
amap.append(oldHcons[b][0])
#remove the number, so that it doesn't get added twice
oldHcons[b][1] = 0
newmol = OBMol()
added = []
for i in range(1, len(amap) + 1):
newn = amap.index(i)
newmol.AddAtom(temp[newn])
added.append(newn)
#Final runthrough to check that all atoms have been added,
#tautomeric protons can be missed. If tautomeric proton tracking
#is implemented this can be removed
for i in range(0, len(temp)):
if not i in added:
newmol.AddAtom(temp[i])
#Restore the bonds
newmol.ConnectTheDots()
newmol.PerceiveBondOrders()
#Write renumbered molecule to file
obconversion.SetOutFormat("sdf")
obconversion.WriteFile(newmol, f)
def GetENCorrection(atom, satom):
Anum = atom.GetAtomicNum()
if Anum != 6:
return ENs[Anum - 1] - ENs[0], 0.0
else:
ENcorr = 0.0
for NbrAtom in OBAtomAtomIter(atom):
if NbrAtom.GetIdx() != satom.GetIdx():
neighbAnum = NbrAtom.GetAtomicNum()
ENcorr += ENs[neighbAnum - 1] - ENs[0]
return ENs[Anum - 1] - ENs[0], ENcorr
def GetHcons(f):
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, f)
Hcons = []
for atom in OBMolAtomIter(obmol):
idx = atom.GetIdx()
anum = atom.GetAtomicNum()
if anum == 1:
for NbrAtom in OBAtomAtomIter(atom):
Hcons.append([idx, NbrAtom.GetIdx()])
return Hcons
def labile_protons(file):
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, file)
count = 0
for atom in OBMolAtomIter(obmol):
for NbrAtom in OBAtomAtomIter(atom):
if (atom.GetAtomicNum() == 8) & (NbrAtom.GetAtomicNum() == 1):
count += 1
return count
def pication(rings, pos_charged, protcharged):
"""Return all pi-Cation interaction between aromatic rings and positively charged groups.
For tertiary and quaternary amines, check also the angle between the ring and the nitrogen.
"""
data = namedtuple(
'pication', 'ring charge distance offset type restype resnr reschain restype_l resnr_l reschain_l protcharged')
pairings = []
if len(rings) == 0 or len(pos_charged) == 0:
return pairings
for ring in rings:
c = ring.center
for p in pos_charged:
d = euclidean3d(c, p.center)
# Project the center of charge into the ring and measure distance to ring center
proj = projection(ring.normal, ring.center, p.center)
offset = euclidean3d(proj, ring.center)
if not config.MIN_DIST < d < config.PICATION_DIST_MAX or not offset < config.PISTACK_OFFSET_MAX:
continue
if type(p).__name__ == 'lcharge' and p.fgroup == 'tertamine':
# Special case here if the ligand has a tertiary amine, check an additional angle
# Otherwise, we might have have a pi-cation interaction 'through' the ligand
n_atoms = [a_neighbor for a_neighbor in OBAtomAtomIter(p.atoms[0].OBAtom)]
n_atoms_coords = [(a.x(), a.y(), a.z()) for a in n_atoms]
amine_normal = np.cross(vector(n_atoms_coords[0], n_atoms_coords[1]),
vector(n_atoms_coords[2], n_atoms_coords[0]))
b = vecangle(ring.normal, amine_normal)
# Smallest of two angles, depending on direction of normal
a = min(b, 180 - b if not 180 - b < 0 else b)
if not a > 30.0:
resnr, restype = whichresnumber(ring.atoms[0]), whichrestype(ring.atoms[0])
reschain = whichchain(ring.atoms[0])
resnr_l, restype_l = whichresnumber(p.orig_atoms[0]), whichrestype(p.orig_atoms[0])
reschain_l = whichchain(p.orig_atoms[0])
contact = data(ring=ring, charge=p, distance=d, offset=offset, type='regular',
restype=restype, resnr=resnr, reschain=reschain,
restype_l=restype_l, resnr_l=resnr_l, reschain_l=reschain_l,
protcharged=protcharged)
pairings.append(contact)
break
resnr = whichresnumber(p.atoms[0]) if protcharged else whichresnumber(ring.atoms[0])
resnr_l = whichresnumber(ring.orig_atoms[0]) if protcharged else whichresnumber(p.orig_atoms[0])
restype = whichrestype(p.atoms[0]) if protcharged else whichrestype(ring.atoms[0])
restype_l = whichrestype(ring.orig_atoms[0]) if protcharged else whichrestype(p.orig_atoms[0])
reschain = whichchain(p.atoms[0]) if protcharged else whichchain(ring.atoms[0])
reschain_l = whichchain(ring.orig_atoms[0]) if protcharged else whichchain(p.orig_atoms[0])
contact = data(ring=ring, charge=p, distance=d, offset=offset, type='regular', restype=restype,
resnr=resnr, reschain=reschain, restype_l=restype_l, resnr_l=resnr_l,
reschain_l=reschain_l, protcharged=protcharged)
pairings.append(contact)
return filter_contacts(pairings)
def FixTautProtons(f, inchi, AuxInfo):
#Get tautomeric protons and atoms they are connected to from Inchi
TautProts = GetTautProtons(inchi)
amap = GetInchiRenumMap(AuxInfo)
#get the correspondence of the Inchi numbers to the source numbers
hmap = []
for taut in TautProts:
for heavyatom in range(1, len(taut)):
hmap.append([int(taut[heavyatom]), amap[int(taut[heavyatom]) - 1]])
#Read molecule from file
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, f)
Fixprotpos = []
for heavyatom in hmap:
atom = obmol.GetAtom(heavyatom[1])
for nbratom in OBAtomAtomIter(atom):
if nbratom.GetAtomicNum() == 1:
Fixprotpos.append(heavyatom[0])
draftFH = []
for i in range(0, len(Fixprotpos)):
if Fixprotpos[i] not in [a[0] for a in draftFH]:
draftFH.append([Fixprotpos[i], Fixprotpos.count(Fixprotpos[i])])
fixedlayer = '/f/h'
for h in draftFH:
if h[1] == 1:
fixedlayer = fixedlayer + str(h[0]) + 'H,'
else:
fixedlayer = fixedlayer + str(h[0]) + 'H' + str(h[1]) + ','
resinchi = inchi + fixedlayer[:-1]
return resinchi
def neighbors(self):
return [Atom(a) for a in OBAtomAtomIter(self.OBAtom)]
def CalcJ(atom1, atom2):
#Get the 2 carbon atoms joining the protons
for NbrAtom in OBAtomAtomIter(atom1):
if NbrAtom.GetAtomicNum() == 6 and NbrAtom.GetHyb() == 3:
carbon1 = NbrAtom
break
for NbrAtom in OBAtomAtomIter(atom2):
if NbrAtom.GetAtomicNum() == 6 and NbrAtom.GetHyb() == 3:
carbon2 = NbrAtom
break
#Get the 2 planes formed by the carbons and each of the protons
normal1, d = FindPlane(carbon1, atom1, carbon2)
normal2, d = FindPlane(carbon2, atom2, carbon1)
sign = VectAngleSign(BondVect(carbon1, atom1), BondVect(carbon2, atom2),
BondVect(carbon1, carbon2))
angle = VectorAngle(normal1, normal2)
if dotproduct(BondVect(carbon1, atom1), BondVect(carbon2, atom2)) > 0 and \
angle < 0.5*pi:
dihedral = angle * sign
else:
dihedral = (pi - angle) * sign
#Count the substituents, get their electronegativities
nSubst = 0
relENs = []
ENcorrs = []
signs = []
for NbrAtom in OBAtomAtomIter(carbon1):
ANum = NbrAtom.GetAtomicNum()
if NbrAtom.GetIdx() != carbon2.GetIdx() and ANum != 1:
nSubst += 1
relEN, ENcorr = GetENCorrection(NbrAtom, carbon1)
relENs.append(relEN)
ENcorrs.append(ENcorr)
signs.append(
VectAngleSign(BondVect(carbon1, atom1),
BondVect(carbon1, NbrAtom),
BondVect(carbon1, carbon2)))
for NbrAtom in OBAtomAtomIter(carbon2):
ANum = NbrAtom.GetAtomicNum()
if NbrAtom.GetIdx() != carbon1.GetIdx() and ANum != 1:
nSubst += 1
relEN, ENcorr = GetENCorrection(NbrAtom, carbon2)
relENs.append(relEN)
ENcorrs.append(ENcorr)
signs.append(
VectAngleSign(BondVect(carbon2, atom2),
BondVect(carbon2, NbrAtom),
BondVect(carbon2, carbon1)))
SubstEffects = 0
if nSubst < 2:
for relEN, ENcorr, sign in zip(relENs, ENcorrs, signs):
corrRelEN = relEN - (Params[0][6]) * ENcorr
SubstEffects += SubstEffect(dihedral, corrRelEN, sign, 0)
J = Params[0][0] * cos(dihedral)**2 + Params[0][1] * cos(dihedral)
else:
for relEN, sign in zip(relENs, signs):
corrRelEN = relEN - (Params[nSubst - 1][6]) * ENcorr
SubstEffects += SubstEffect(dihedral, corrRelEN, sign, nSubst - 1)
J = Params[nSubst - 1][0] * cos(dihedral)**2 + Params[
nSubst - 1][1] * cos(dihedral)
return J + SubstEffects
def mol_fragments(mole,outfile):
obconv = OBConversion()
obconv.SetOutFormat("xyz")
c = 1
for atom, exp,dft,diff in zip(OBMolAtomIter(mole)):
# if this is a carbon atom start a breadth first search for other carbon atoms with depth specified
# create a new mol instance
new_mol = OBMol()
# add this atom
# new_mol.AddAtom(atom)
fragment_ind = []
l = atom.GetIndex()
fragment_ind.append(l)
# for iteration depth radius
old_queue = [atom]
for iteration in range(0, 3):
new_queue = []
for a in old_queue:
for atom2 in OBAtomAtomIter(a):
i = atom2.GetIndex()
# if the atom has not been seen before add it to the fragment ind list and to the new molecule
if i not in fragment_ind:
new_queue.append(atom2)
fragment_ind.append(i)
# new_mol.AddAtom(atom2)
old_queue = copy.copy(new_queue)
fragment_ind = [fragment_ind[0]] + sorted(fragment_ind[1:])
for i in fragment_ind:
for a in OBMolAtomIter(mole):
if a.GetIndex() == i:
new_mol.AddAtom(a)
f = open(outfile + "frag" + str(l).zfill(3) + ".xyz", "w+")
f.write(str(new_mol.NumAtoms()) + "\n\n")
i = 0
for atom in OBMolAtomIter(new_mol):
f.write(atom.GetType()[0] + " " + str(atom.GetX()) + " " + str(atom.GetY()) + " " + str(
atom.GetZ()) + "\n")
i+=1
f.close()
c += 1
def main(f, settings):
"""
Find the axis atoms
Find all the atoms to be rotated
Rotate it and the substituents to the other side of the plane
"""
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, f)
obmol.ConnectTheDots()
#Find the atoms composing furan ring
Rings = obmol.GetSSSR()
furan = []
for ring in Rings:
if len(settings.RingAtoms) == 5:
if all(x in ring._path for x in settings.RingAtoms):
furan = ring
break
else:
if ring.Size() == 5 and not ring.IsAromatic():
furan = ring
break
if furan == []:
"No five membered rings to rotate. Quitting..."
quit()
#Find the plane of the 5-membered ring and the outlying atom
norm, d, outAtom = FindFuranPlane(obmol, furan)
#Find the atoms connected to the outlying atom and sort them
#as either part of the ring(axis atoms) or as atoms to be rotated
AxisAtoms = []
RotAtoms = []
for NbrAtom in OBAtomAtomIter(outAtom):
#if NbrAtom.IsInRingSize(5):
if furan.IsInRing(NbrAtom.GetIdx()):
AxisAtoms.append(NbrAtom)
else:
RotAtoms.append(NbrAtom)
FindSubstAtoms(NbrAtom, outAtom, RotAtoms)
#Simple switch to help detect if the atoms are rotated the right way
WasAbove90 = False
angle = FindRotAngle(AxisAtoms[0], AxisAtoms[1], outAtom, norm)
if angle > 0.5 * pi:
WasAbove90 = True
rotangle = 2 * (angle - 0.5 * pi)
else:
WasAbove90 = False
rotangle = 2 * (0.5 * pi - angle)
OldAtomCoords = outAtom.GetVector()
print("Atom " + str(outAtom.GetAtomicNum()) + " will be rotated by " +\
str(rotangle*57.3) + ' degrees')
RotateAtom(outAtom, AxisAtoms[0], AxisAtoms[1], rotangle)
angle2 = FindRotAngle(AxisAtoms[0], AxisAtoms[1], outAtom, norm)
#if the atom is on the same side of the plane as it was,
# it has been rotated in the wrong direction
if ((angle2 > 0.5 * pi) and WasAbove90) or ((angle2 < 0.5 * pi)
and not WasAbove90):
#Flip the sign of the rotation angle, restore the coords
#and rotate the atom in the opposite direction
print("Atom was rotated the wrong way, switching the direction")
rotangle = -rotangle
outAtom.SetVector(OldAtomCoords)
RotateAtom(outAtom, AxisAtoms[0], AxisAtoms[1], rotangle)
RotatedAtoms = [] # Index to make sure that atoms are not rotated twice
for atom in RotAtoms:
if atom not in RotatedAtoms:
RotateAtom(atom, AxisAtoms[0], AxisAtoms[1], rotangle)
RotatedAtoms.append(atom)
else:
print("Atom already rotated, skipping")
obconversion.SetOutFormat("sdf")
obconversion.WriteFile(obmol, f[:-4] + 'rot.sdf')