def is_n_terminus(self, mol, atom):
""" Determine if an atom is an N-terminus
Args:
mol (:obj:`openbabel.OBMol`): molecule
atom (:obj:`openbabel.OBAtom`): atom
Returns:
:obj:`bool`: :obj:`True` if the atom is an N-terminus
"""
if atom is None:
return False
# check atom is nitrogen
if atom.GetAtomicNum() != 7:
return False
# check atom has charge 0 or +1
if atom.GetFormalCharge() < 0:
return False
# check atom is single-bonded to at least 1 carbon
has_single_c = False
for bond in openbabel.OBAtomBondIter(atom):
other_atom = bond.GetBeginAtom()
if other_atom == atom:
other_atom = bond.GetEndAtom()
if bond.GetBondOrder() == 1 and other_atom.GetAtomicNum() == 6:
has_single_c = True
if not has_single_c:
return False
# check atom can form another bond
other_atoms = [
other_atom.GetAtomicNum()
for other_atom in openbabel.OBAtomAtomIter(atom)
]
tot_bond_order = sum(
[bond.GetBondOrder() for bond in openbabel.OBAtomBondIter(atom)])
other_atoms += [1] * (3 + atom.GetFormalCharge() - tot_bond_order)
n_charge = atom.GetFormalCharge()
n_h = other_atoms.count(1)
if not ((n_charge == 1 and n_h >= 2) or
(n_charge == 0 and (n_h >= 1 or len(other_atoms) <= 2))):
return False
# return True
return True
def adjust_info(self, obatom):
'''
If a atom is bonded to polarhydrogen or heteroatom
:param obatom: openbabel OBAtom istance
:return: bond_2_hd, bond_2_hetero : boolean
'''
bonds = list(openbabel.OBAtomBondIter(obatom))
atom_id = obatom.GetId()
bond_2_hd = False
bond_2_hetero = False
for bond in bonds:
begin = bond.GetBeginAtom().GetId()
end = bond.GetEndAtom().GetId()
if atom_id == begin:
link_atom = bond.GetEndAtom()
elif atom_id == end:
link_atom = bond.GetBeginAtom()
else:
raise Exception("Wrong bond")
if link_atom.IsHydrogen():
# all the remained hydrogen is polarhydrogen
bond_2_hd = True
if link_atom.IsHeteroatom():
bond_2_hetero = True
return bond_2_hd, bond_2_hetero
def get_torsion(mol, ob_atom_idx_0, ob_atom_idx_1):
"""Get torsion between the two coupled atoms. The function is relevant for
atoms in a 3J coupling
Arguments:
mol {OBMol} -- OpenBabel molecule object
ob_atom_idx_0 {int} -- index of atom 0 in OpenBabel
ob_atom_idx_1 {int} -- index of atom 1 in OpenBabel
Returns:
float -- torsion value for the coupled pair
"""
atom_0 = mol.GetAtom(ob_atom_idx_0)
atom_1 = mol.GetAtom(ob_atom_idx_1)
for bond in ob.OBAtomBondIter(atom_0):
end_atom_idx = bond.GetEndAtomIdx()
if end_atom_idx == atom_0.GetIdx():
pivot_1 = bond.GetBeginAtom()
else:
pivot_1 = bond.GetEndAtom()
pivot_2 = get_torsion_pivot(mol, atom_1.GetIdx(), pivot_1.GetIdx())
if pivot_2:
return mol.GetTorsion(atom_0, pivot_1, pivot_2, atom_1)
return 0
def get_angle(mol, ob_atom_idx_0, ob_atom_idx_1):
"""Get the angle between two atoms. The function is relevant for atoms in
a 2J coupling
Arguments:
mol {OBMol} -- OpenBabel molecule object
ob_atom_idx_0 {int} -- index of atom 0 in OpenBabel
ob_atom_idx_1 {int} -- index of atom 1 in OpenBabel
Returns:
float -- value of angle between coupled atoms
"""
atom_0 = mol.GetAtom(ob_atom_idx_0)
atom_1 = mol.GetAtom(ob_atom_idx_1)
for bond in ob.OBAtomBondIter(atom_0):
end_atom_idx = bond.GetEndAtomIdx()
if end_atom_idx == atom_0.GetIdx():
pivot_atom = bond.GetBeginAtom()
else:
pivot_atom = bond.GetEndAtom()
missing_bond = atom_1.GetBond(pivot_atom)
if missing_bond:
return mol.GetAngle(atom_0, pivot_atom, atom_1)
return 0
def get_torsion_pivot(mol, ob_atom_idx_0, ob_atom_idx_1):
"""Find pivot atom of a torsion
Arguments:
mol {OBMol} -- OpenBabel molecule object
ob_atom_idx_0 {int} -- index of atom 0 in OpenBabel
ob_atom_idx_1 {int} -- index of atom 1 in OpenBabel
Returns:
OBAtom -- torsion pivot atom
"""
atom_0 = mol.GetAtom(ob_atom_idx_0)
atom_1 = mol.GetAtom(ob_atom_idx_1)
for bond in ob.OBAtomBondIter(atom_0):
end_atom_idx = bond.GetEndAtomIdx()
if end_atom_idx == atom_0.GetIdx():
pivot_atom = bond.GetBeginAtom()
else:
pivot_atom = bond.GetEndAtom()
missing_bond = atom_1.GetBond(pivot_atom)
if missing_bond:
return pivot_atom
return None
def Torsion3J(molname, AtomId1, AtomId2, mol, debug=False):
mol, firstAtom, lastAtom = Atoms(molname, AtomId1, AtomId2, mol)
if debug: print(molname, mol.GetFormula())
if debug:
print(firstAtom.GetType(), firstAtom.GetId(), ':', lastAtom.GetType(),
lastAtom.GetId())
for b in openbabel.OBAtomBondIter(firstAtom): # all bonds for first atom
secondAtom = SecondAtom(b, firstAtom)
for b2 in openbabel.OBAtomBondIter(
secondAtom): # all bonds for second atom
thirdAtom = SecondAtom(b2, secondAtom)
lastBond = thirdAtom.GetBond(lastAtom)
if lastBond: # found!
if debug:
print(secondAtom.GetType(), secondAtom.GetId(), '<->',
thirdAtom.GetType(), thirdAtom.GetId())
return mol.GetTorsion(firstAtom, secondAtom, thirdAtom,
lastAtom)
def findInternalRotors(self, Mol): rotor = [] for atom in openbabel.OBMolAtomIter(Mol): if not atom.IsHydrogen() and not atom.IsInRing(): for bond in openbabel.OBAtomBondIter(atom): ptr = bond.GetNbrAtom(atom) if ptr.GetId() < atom.GetId(): continue elif bond.GetBO() == 1 and atom.BOSum() > 1 and ptr.BOSum() > 1 and not ptr.IsHydrogen(): idx = [int(atom.GetId())+1, int(ptr.GetId())+1] rotor.append(idx) return rotor
def getatom_b(obatom, marker):
b = str(0)
if (marker == "0"):
return '*'
if (obatom.HasSingleBond()):
b = 's'
if (obatom.HasDoubleBond()):
b = 'd'
for obbond in ob.OBAtomBondIter(obatom):
if (obbond.IsTriple()):
b = 't'
break
i = 0
for obbond in ob.OBAtomBondIter(obatom):
if (obbond.IsDouble()):
i += 1
if (i > 1):
b = 'w'
if (obatom.HasAromaticBond()):
b = 'd'
return b
def Angle2J(molname, AtomId1, AtomId2, mol, debug=False):
mol, firstAtom, lastAtom = Atoms(molname, AtomId1, AtomId2, mol)
if debug: print(mol.GetFormula())
if debug:
print(firstAtom.GetType(), firstAtom.GetId(), ':', lastAtom.GetType(),
lastAtom.GetId())
for b in openbabel.OBAtomBondIter(firstAtom): # all bonds for first atom
secondAtom = SecondAtom(b, firstAtom)
lastBond = secondAtom.GetBond(lastAtom)
if lastBond: # found!
if debug: print('middle', secondAtom.GetId(), secondAtom.GetType())
return firstAtom.GetAngle(secondAtom, lastAtom)
def _get_neighbors(self, obatom):
""" trick or treat? """
neighbors = []
for bond in ob.OBAtomBondIter(obatom):
end = bond.GetEndAtom()
bgn = bond.GetBeginAtom()
if bgn == obatom:
neighbors.append(end.GetIndex()) # Index is 0-indexed
elif end == obatom:
neighbors.append(bgn.GetIndex())
else:
raise RuntimeError
return neighbors
def get_bom(self):
"""
get connectivity table
"""
bom = np.zeros((self.na, self.na), np.int)
for i in range(1, self.na + 1):
ai = self.m.GetAtom(i)
for bond in ob.OBAtomBondIter(ai):
ia1 = bond.GetBeginAtomIdx() - 1
ia2 = bond.GetEndAtomIdx() - 1
bo = bond.GetBO()
bom[ia1, ia2] = bo
bom[ia2, ia1] = bo
return bom
def get_bom(m):
na = m.NumAtoms()
bom = np.zeros((na, na), dtype=int)
for i in range(na):
ai = m.GetAtomById(i)
for bond in ob.OBAtomBondIter(ai):
ab, ae = bond.GetBeginAtom(), bond.GetEndAtom()
ib1 = ab.GetIdx() - 1
ie1 = ae.GetIdx() - 1
#ib2 = ab.GetId(); ie2 = ae.GetId()
#print i, ' -- ', ib1,ie1, ib2,ie2
bo = bond.GetBO()
bom[ib1, ie1] = bo
bom[ie1, ib1] = bo
return bom
def test_atom_iteration(self):
mol = parse_smiles("[U](F)(F)(F)[Cl]")
atom = mol.GetAtom(1)
counts = {9: 0, 17: 0}
for bond in ob.OBAtomBondIter(atom):
xatom = bond.GetNbrAtom(atom)
n = xatom.GetAtomicNum()
counts[n] += 1
self.assertEqual(counts, {9: 3, 17: 1})
counts = {9: 0, 17: 0}
for atom in ob.OBAtomAtomIter(atom):
n = atom.GetAtomicNum()
counts[n] += 1
self.assertEqual(counts, {9: 3, 17: 1})
def perceiveBondOrders(self, Molecule, Atom):
# . generate OBMol
frag = openbabel.OBMol()
atoms = [None] + Molecule
for i in Molecule:
frag.AddAtom(Atom[i].atom)
[frag.AddBond(atoms.index(Atom[i].id), atoms.index(bond), 1) for bond in Atom[i].bonds if Atom[i].id in atoms and bond in atoms]
frag.AssignSpinMultiplicity(True)
# . find potential multi-bonds
multi = [[], []]
for atom in openbabel.OBMolAtomIter(frag):
if atom.GetSpinMultiplicity() > 0:
for bond in openbabel.OBAtomBondIter(atom):
ptr = bond.GetNbrAtom(atom)
if ptr.GetSpinMultiplicity() > 0:
aidx = atom.GetIdx();pidx = ptr.GetIdx()
bo= Atom[atoms[aidx]].bonds[atoms[pidx]]
if (pidx, aidx) in multi[1]: continue
multi[0].append(bo-1.0)
multi[1].append((aidx, pidx))
# . sort in order of decreasing bond orders
multi = sorted(zip(multi[0], multi[1]), reverse=True)
# . loop over bonds in <multi> and set multi-bonds
while multi:
bond = list(multi[0]); del multi[0]
atom = frag.GetAtom(bond[1][0])
btom = frag.GetAtom(bond[1][1])
if atom.GetSpinMultiplicity() > 0 and btom.GetSpinMultiplicity() > 0:
tmp = frag.GetBond(atom, btom)
tmp.SetBO(tmp.GetBO() +1)
atom = self.decreaseMultiplicity(Atom=atom)
atom.DecrementImplicitValence()
btom = self.decreaseMultiplicity(Atom=btom)
btom.DecrementImplicitValence()
bond[0] -= 1.0
if bond[0] > 0: multi.append(tuple(bond))
multi = sorted(multi, reverse=True)
# . return SMILES
self.conv.SetInAndOutFormats('mdl', 'can')
return self.conv.WriteString(frag).strip().replace('@@','@')
def test_rings(self):
mol = parse_smiles("C12CNCC3C1.C2CCC3")
atom = mol.GetAtom(1)
self.assertTrue(atom.IsInRing())
self.assertTrue(atom.IsInRingSize(6))
self.assertTrue(atom.IsInRingSize(7))
self.assertFalse(atom.IsInRingSize(10))
self.assertEqual(atom.MemberOfRingCount(), 2)
self.assertEqual(atom.MemberOfRingSize(), 6)
self.assertEqual(atom.CountRingBonds(), 3)
sssr = mol.GetSSSR()
self.assertEqual(len(sssr), 2)
ring_info = [(ring.Size(), ring) for ring in sssr]
ring_info.sort()
sizes = [x[0] for x in ring_info]
self.assertEqual(sizes, [6, 7])
ring = ring_info[0][1]
self.assertFalse(ring.IsAromatic())
self.assertEqual(ring.GetType(), "")
# XXX *which* of the non-carbons is the root? That isn't documented
idx = ring.GetRootAtom() # Shouldn't that be "Idx"?
# Since there's only one non-C, it must be the N
atom = mol.GetAtom(idx)
self.assertEqual(atom.GetAtomicNum(), 7)
self.assertTrue(ring.IsMember(atom))
for bond in ob.OBAtomBondIter(atom):
self.assertTrue(ring.IsMember(bond))
self.assertTrue(ring.IsInRing(idx))
lssr = mol.GetLSSR()
self.assertEqual(len(lssr), 2)
sizes = [ring.Size() for ring in lssr]
sizes.sort()
self.assertEqual(sizes, [6, 7])
def molToMat(mol):
n = mol.NumAtoms()
# mat = np.zeros((n+3, n+1), dtype=int)
mat = [[0 for _i in range(n + 1)] for _j in range(n + 3)]
for i in range(1, n + 1):
mat[i][0] = mol.GetAtom(i).GetAtomicNum()
mat[0][i] = mat[i][0]
for atom in ob.OBMolAtomIter(mol):
i = atom.GetIdx()
nBonds = 0
for bond in ob.OBAtomBondIter(atom):
nBonds += bond.GetBondOrder()
nonBondingElecs = numValenceElectron(
atom.GetAtomicNum()) - nBonds - atom.GetFormalCharge()
mat[i][i] = nonBondingElecs
mat[n + 1][i] = nBonds
mat[n + 2][i] = atom.GetFormalCharge()
for bond in ob.OBMolBondIter(mol):
i = bond.GetBeginAtomIdx()
j = bond.GetEndAtomIdx()
mat[i][j] = bond.GetBondOrder()
mat[j][i] = mat[i][j]
return mat
def get_single_bond_neighbour(ob_atom):
"""[summary]
Args:
ob_atom ([type]): [description]
Returns:
[type]: [description]
""" '''
'''
for bond in ob.OBAtomBondIter(ob_atom):
if not bond.IsSingle():
continue
current_neighbour = bond.GetNbrAtom(ob_atom)
if current_neighbour.IsHydrogen():
continue
return current_neighbour
return None
def extract_ligand(obmol, res_name='INH'):
"""
This function is used to extract the ligands which are always named 'INH'
from CSAR structures.
"""
ligand = ob.OBMol()
for residue in ob.OBResidueIter(obmol):
if residue.GetName() == res_name:
mapping = {}
# insert the ligand atoms into the new molecule
for i, atom in enumerate(ob.OBResidueAtomIter(residue), 1):
ligand.InsertAtom(atom)
mapping[atom.GetIdx()] = i
# re-create the bonds
for atom in ob.OBResidueAtomIter(residue):
for bond in ob.OBAtomBondIter(atom):
bgn_idx = mapping[bond.GetBeginAtomIdx()]
end_idx = mapping[bond.GetEndAtomIdx()]
ligand.AddBond(bgn_idx, end_idx, bond.GetBondOrder(),
bond.GetFlags())
# remove the ligand from the original structure
for atom_idx in sorted(mapping.keys(), reverse=True):
atom = obmol.GetAtom(atom_idx)
obmol.DeleteAtom(atom)
obmol.DeleteResidue(residue)
break
return pybel.Molecule(ligand)
def _bfs(mol, startatom, D):
'''
given openbabel molecule and a starting atom of type OBAtom,
finds all bonds out to degree D via a breath-first search
'''
visited_atoms = set()
atoms_to_add = []
bonds_to_add = []
queue = deque([(startatom, 0)])
while queue:
atom, depth = queue.popleft()
index = atom.GetIndex()
visited_atoms.add(index)
atomtype = atom.GetType()
if depth < D:
for bond in ob.OBAtomBondIter(atom):
if bond not in bonds_to_add:
bonds_to_add.append(bond)
if depth < D:
for atom in ob.OBAtomAtomIter(atom):
if atom.GetIndex() not in visited_atoms:
queue.append((atom, depth + 1))
return (bonds_to_add)
def make_structure(request):
def makeResidue(mol, idx, aaatoms):
res = mol.NewResidue()
res.SetNum(idx)
for atom in ob.OBMolAtomIter(mol):
if atom.GetIdx() not in aaatoms:
res.AddAtom(atom)
aminoacids = request.GET.getlist("as")
color = request.GET.get("rescol", "#3EC1CD")
mol = ob.OBMol()
conv = ob.OBConversion()
pattern = ob.OBSmartsPattern()
pattern.Init("[NX3][$([CX4H1]([*])),$([CX4H2])][CX3](=[OX1])[OX2]")
builder = ob.OBBuilder()
conv.SetInAndOutFormats("sdf", "svg")
conv.AddOption("d", ob.OBConversion.OUTOPTIONS)
conv.AddOption("b", ob.OBConversion.OUTOPTIONS, "none")
conv.ReadString(mol, str(Substrate.objects.get(pk=int(aminoacids[0])).structure))
pattern.Match(mol)
mollist = pattern.GetUMapList()[0]
oatom = mol.GetAtom(mollist[4])
catom = mol.GetAtom(mollist[2])
firstnatom = mol.GetAtom(mollist[0])
makeResidue(mol, 0, mollist)
i = 1
for aa in aminoacids[1:]:
mol2 = ob.OBMol()
conv.ReadString(mol2, str(Substrate.objects.get(pk=int(aa)).structure))
pattern.Match(mol2)
mollist = pattern.GetUMapList()[0]
makeResidue(mol2, i, mollist)
molnatoms = mol.NumAtoms()
mol += mol2
natom = mol.GetAtom(molnatoms + mol2.GetAtom(mollist[0]).GetIdx())
builder.Connect(mol, catom.GetIdx(), natom.GetIdx())
foatom = mol.GetAtom(molnatoms + mol2.GetAtom(mollist[4]).GetIdx())
catom = mol.GetAtom(molnatoms + mol2.GetAtom(mollist[2]).GetIdx())
mol.DeleteHydrogens(oatom)
mol.DeleteAtom(oatom)
natom.SetImplicitValence(3)
mol.DeleteHydrogens(natom)
mol.AddHydrogens(natom)
oatom = foatom
i += 1
nidx = firstnatom.GetIdx()
oidx = oatom.GetIdx()
builder.Build(mol)
natom = mol.GetAtom(nidx)
oatom = mol.GetAtom(oidx)
for res in ob.OBResidueIter(mol):
for atom in ob.OBResidueAtomIter(res):
for bond in ob.OBAtomBondIter(atom):
data = ob.OBPairData()
data.SetAttribute("color")
data.SetValue(color)
bond.CloneData(data)
mol.DeleteHydrogens()
gen2d = ob.OBOp.FindType("gen2d")
gen2d.Do(mol)
opp = oatom.GetY() - natom.GetY()
adj = oatom.GetX() - natom.GetX()
angle = abs(math.atan(opp / adj))
if opp > 0 and adj > 0:
pass
elif opp > 0 and adj < 0:
angle = math.pi - angle
elif opp < 0 and adj < 0:
angle = math.pi + angle
elif opp < 0 and adj > 0:
angle = 2 * math.pi - angle
angle = -angle
mol.Rotate(ob.double_array([math.cos(angle), -math.sin(angle), 0,
math.sin(angle), math.cos(angle), 0,
0, 0, 1]))
svg = conv.WriteString(mol)
# need to get rid of square aspect ratio
delstart = svg.find("width")
delend = svg.find("svg", delstart)
delend = svg.find("viewBox", delend)
svgend = svg.rfind("</g>")
svg = svg[0:delstart] + svg[delend:svgend]
return HttpResponse(svg, mimetype="image/svg+xml")
def draw(self, show=True, filename=None, update=False, usecoords=False,
method="mcdl"):
"""Create a 2D depiction of the molecule.
Optional parameters:
show -- display on screen (default is True)
filename -- write to file (default is None)
update -- update the coordinates of the atoms to those
determined by the structure diagram generator
(default is False)
usecoords -- don't calculate 2D coordinates, just use
the current coordinates (default is False)
method -- two methods are available for calculating the
2D coordinates: OpenBabel's "mcdl" (the default), or
"oasa" (from the OASA toolkit)
OASA is used for depiction. Tkinter and Python
Imaging Library are required for image display.
"""
etab = ob.OBElementTable()
if not oasa:
errormessage = ("OASA not found, but is required for depiction. "
"OASA is part of BKChem. "
"See installation instructions for more "
"information.")
raise ImportError(errormessage)
if method not in ["mcdl", "oasa"]:
raise ValueError("Method '%s' not recognised. Should be either"
" 'mcdl' or 'oasa'.")
workingmol = self
if method == "mcdl":
if not update: # Call gen2D on a clone
workingmol = Molecule(self)
if not usecoords:
_operations['gen2D'].Do(workingmol.OBMol)
usecoords = True # Use the workingmol's coordinates
mol = oasa.molecule()
for atom in workingmol.atoms:
v = mol.create_vertex()
v.symbol = etab.GetSymbol(atom.atomicnum)
v.charge = atom.formalcharge
if usecoords:
v.x, v.y, v.z = atom.coords[0] * 30., atom.coords[1] * 30., 0.0
mol.add_vertex(v)
for bond in ob.OBMolBondIter(workingmol.OBMol):
e = mol.create_edge()
e.order = bond.GetBO()
if bond.IsHash():
e.type = "h"
elif bond.IsWedge():
e.type = "w"
mol.add_edge(bond.GetBeginAtomIdx() - 1,
bond.GetEndAtomIdx() - 1,
e)
# I'm sure there's a more elegant way to do the following, but here goes...
# let's set the stereochemistry around double bonds
self.write("can") # Perceive UP/DOWNness
for bond in ob.OBMolBondIter(workingmol.OBMol):
ends = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
if bond.GetBO() == 2:
stereobonds = [[b for b in ob.OBAtomBondIter(workingmol.OBMol.GetAtom(x)) if b.GetIdx() != bond.GetIdx() and (b.IsUp() or b.IsDown())]
for x in ends]
if stereobonds[0] and stereobonds[1]: # Needs to be defined at either end
if stereobonds[0][0].IsUp() == stereobonds[1][0].IsUp():
# Either both up or both down
stereo = oasa.stereochemistry.cis_trans_stereochemistry.SAME_SIDE
else:
stereo = oasa.stereochemistry.cis_trans_stereochemistry.OPPOSITE_SIDE
atomids = [(b[0].GetBeginAtomIdx(), b[0].GetEndAtomIdx()) for b in stereobonds]
extremes = []
for id, end in zip(ends, atomids):
if end[0] == id:
extremes.append(end[1])
else:
extremes.append(end[0])
center = mol.get_edge_between(mol.atoms[ends[0] - 1], mol.atoms[ends[1] - 1])
st = oasa.stereochemistry.cis_trans_stereochemistry(
center = center, value = stereo,
references = (mol.atoms[extremes[0] - 1], mol.atoms[ends[0] - 1],
mol.atoms[ends[1] - 1], mol.atoms[extremes[1] - 1]))
mol.add_stereochemistry(st)
mol.remove_unimportant_hydrogens()
if method == "oasa" and not usecoords:
oasa.coords_generator.calculate_coords(mol, bond_length=30)
if update:
newcoords = [(v.x / 30., v.y / 30., 0.0) for v in mol.vertices]
for atom, newcoord in zip(ob.OBMolAtomIter(self.OBMol), newcoords):
atom.SetVector(*newcoord)
if filename or show:
maxx = max([v.x for v in mol.vertices])
minx = min([v.x for v in mol.vertices])
maxy = max([v.y for v in mol.vertices])
miny = min([v.y for v in mol.vertices])
maxcoord = max(maxx - minx, maxy - miny)
fontsize = 16
bondwidth = 6
linewidth = 2
if maxcoord > 270: # 300 - margin * 2
for v in mol.vertices:
v.x *= 270. / maxcoord
v.y *= 270. / maxcoord
fontsize *= math.sqrt(270. / maxcoord)
bondwidth *= math.sqrt(270. / maxcoord)
linewidth *= math.sqrt(270. / maxcoord)
if filename:
filedes = None
else:
filedes, filename = tempfile.mkstemp()
canvas = oasa.cairo_out.cairo_out()
canvas.show_hydrogens_on_hetero = True
canvas.font_size = fontsize
canvas.bond_width = bondwidth
canvas.line_width = linewidth
canvas.mol_to_cairo(mol, filename)
if show:
if not tk:
errormessage = ("Tkinter or Python Imaging "
"Library not found, but is required for image "
"display. See installation instructions for "
"more information.")
raise ImportError(errormessage)
root = tk.Tk()
root.title((hasattr(self, "title") and self.title)
or self.__str__().rstrip())
frame = tk.Frame(root, colormap="new", visual='truecolor').pack()
image = PIL.open(filename)
imagedata = piltk.PhotoImage(image)
label = tk.Label(frame, image=imagedata).pack()
quitbutton = tk.Button(root, text="Close", command=root.destroy).pack(fill=tk.X)
root.mainloop()
if filedes:
os.close(filedes)
os.remove(filename)
def atomTotalBondOrder(atom):
nBonds = 0
for bond in ob.OBAtomBondIter(atom):
nBonds += bond.GetBondOrder()
return nBonds
def set_termini(self, mol, monomer, i_n, i_c):
""" Set the C and N terminal bond atoms of a monomer
Args:
mol (:obj:`openbabel.OBMol`): molecule
monomer (:obj:`Monomer`): monomer
i_n (:obj:`int`): index of N terminus
i_c (:obj:`int`): index of C terminus
"""
if i_c:
c_atom = mol.GetAtom(i_c)
i_o = None
for bond in openbabel.OBAtomBondIter(c_atom):
if bond.GetBondOrder() != 1:
continue
o_atom = bond.GetBeginAtom()
if o_atom.GetIdx() == c_atom.GetIdx():
o_atom = bond.GetEndAtom()
if o_atom.GetAtomicNum() == 8:
other_atoms = sorted([
other_atom.GetAtomicNum()
for other_atom in openbabel.OBAtomAtomIter(o_atom)
])
if len(other_atoms) == 1 or other_atoms[-2] == 1:
i_o = o_atom.GetIdx()
break
if i_o:
monomer.r_bond_atoms.append(
Atom(Monomer, element='C', position=i_c))
if o_atom.GetFormalCharge() == 0:
monomer.r_displaced_atoms.append(
Atom(Monomer, element='O', position=i_o))
monomer.r_displaced_atoms.append(
Atom(Monomer, element='H', position=i_o))
else:
monomer.r_displaced_atoms.append(
Atom(Monomer, element='O', position=i_o, charge=-1))
if i_n:
atom = mol.GetAtom(i_n)
other_atoms = [
other_atom.GetAtomicNum()
for other_atom in openbabel.OBAtomAtomIter(atom)
]
tot_bond_order = sum([
bond.GetBondOrder() for bond in openbabel.OBAtomBondIter(atom)
])
other_atoms += [1] * (3 + atom.GetFormalCharge() - tot_bond_order)
n_charge = atom.GetFormalCharge()
n_h = other_atoms.count(1)
monomer.l_bond_atoms.append(
Atom(Monomer, element='N', position=i_n, charge=-n_charge))
if n_charge >= 0 and n_h >= 1:
monomer.l_displaced_atoms.append(
Atom(Monomer, element='H', position=i_n))
if n_charge >= 1 and n_h >= 2:
monomer.l_displaced_atoms.append(
Atom(Monomer, element='H', position=i_n, charge=1))
def is_c_terminus(self, mol, atom, residue=True, convert_to_aa=False):
""" Determine if an atom is an C-terminus
Args:
mol (:obj:`openbabel.OBMol`): molecule
atom (:obj:`openbabel.OBAtom`): atom
residue (:obj:`bool`, optional): if :obj:`True`, search for a residue (H instead of O- at C terminus)
convert_to_aa (:obj:`bool`, optional): if :obj:`True`, convert COH to COOH
Returns:
:obj:`bool`: :obj:`True` if the atom is an C-terminus
"""
if atom is None:
return False
# check atom is carbon
if atom.GetAtomicNum() != 6:
return False
# check atom has charge 0
if atom.GetFormalCharge() != 0:
return False
# check atom is bonded to 1 oxygen, 1 carbon, and 1 hydrogen atom (residue=True) or 1 oxygen (residue=False) atom
other_atoms = [
other_atom.GetAtomicNum()
for other_atom in openbabel.OBAtomAtomIter(atom)
]
tot_bond_order = sum(
[bond.GetBondOrder() for bond in openbabel.OBAtomBondIter(atom)])
other_atoms += [1] * (4 + atom.GetFormalCharge() - tot_bond_order)
other_atoms.sort()
if set(other_atoms).difference(set([1, 6, 8])):
return False
if 6 not in other_atoms or 8 not in other_atoms:
return False
if len(other_atoms) != 3:
return False
if residue and other_atoms[0] != 1:
return False
if not residue and other_atoms[1] != 8:
return False
# check bonds to carbon and hydrogen are single bonds and bond to oxygen is a double bond
o_single_bonds = []
o_double_bonds = []
for bond in openbabel.OBAtomBondIter(atom):
other_atom = bond.GetBeginAtom()
if other_atom == atom:
other_atom = bond.GetEndAtom()
if other_atom.GetAtomicNum() == 8:
if bond.GetBondOrder() == 1:
o_single_bonds.append((bond, other_atom))
elif bond.GetBondOrder() == 2:
o_double_bonds.append((bond, other_atom))
else:
return False
elif bond.GetBondOrder() != 1:
return False
if residue and (len(o_single_bonds) != 0 or len(o_double_bonds) != 1):
return False
if not residue and (len(o_single_bonds) != 1
or len(o_double_bonds) != 1):
return False
# if not residue, check that single oxygen is bound to H
if not residue:
oxygen_atom = o_single_bonds[0][1]
for bond in openbabel.OBAtomBondIter(oxygen_atom):
other_atom = bond.GetBeginAtom()
if other_atom == oxygen_atom:
other_atom = bond.GetEndAtom()
if other_atom.GetIdx() != atom.GetIdx(
) and other_atom.GetAtomicNum() != 1:
return False
# correct residue to amino acid
if convert_to_aa:
h_atom = None
for other_atom in openbabel.OBAtomAtomIter(atom):
if other_atom.GetAtomicNum() == 1:
h_atom = other_atom
break
if h_atom is not None:
h_atom.SetAtomicNum(8)
else:
o_atom = mol.NewAtom()
o_atom.SetAtomicNum(8)
o_atom.SetFormalCharge(0)
bond = openbabel.OBBond()
bond.SetBegin(atom)
bond.SetEnd(o_atom)
bond.SetBondOrder(1)
assert mol.AddBond(bond)
# return True
return True
