def largest_ring_size(smiles):
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, smiles)
n_rings, parts = oechem.OEDetermineRingSystems(mol)
max_i = max(parts)
l = 0
for i in range(1, max_i + 1):
n_ring = parts.count(i)
if n_ring > l:
l = n_ring
return l
def sort_rings(tagged_smiles):
"""
Sort ring bonds for nicer plotting
Paramerts
---------
tagged_smiles: mapped SMILES for plotting
Returns
-------
ring_bonds: list of tuples of aliphatic and aromtic ring bonds atom map indices
ring_sizes: list of ring sizes
"""
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, tagged_smiles)
nringsystems, parts = oechem.OEDetermineRingSystems(mol)
aromatic_ring_bonds = []
aliphatic_ring_bonds = []
aromatic_ring_sizes = []
aliphatic_ring_sizes = []
for ring_idx in range(1, nringsystems + 1):
i = 0
j = 0
for bond in mol.GetBonds():
if bond.IsInRing():
if bond.IsAromatic():
if parts[bond.GetBgnIdx()] == ring_idx and parts[
bond.GetEndIdx()] == ring_idx:
aromatic_ring_bonds.append((bond.GetBgn().GetMapIdx(),
bond.GetEnd().GetMapIdx()))
i += 1
if not bond.IsAromatic():
if parts[bond.GetBgnIdx()] == ring_idx and parts[
bond.GetEndIdx()] == ring_idx:
aliphatic_ring_bonds.append(
(bond.GetBgn().GetMapIdx(),
bond.GetEnd().GetMapIdx()))
j += 1
if i > 0:
aromatic_ring_sizes.append(i)
if j > 0:
aliphatic_ring_sizes.append(j)
return aliphatic_ring_bonds + aromatic_ring_bonds, aliphatic_ring_sizes + aromatic_ring_sizes
def test_find_ring_systems(smiles):
from openeye import oechem
molecule = Molecule.from_smiles(smiles, allow_undefined_stereo=True)
oe_molecule = molecule.to_openeye()
_, expected = oechem.OEDetermineRingSystems(oe_molecule)
ring_systems = find_ring_systems(molecule)
for i, ring_system in enumerate(expected):
if ring_system > 0:
assert ring_systems[i] == ring_system
else:
assert i not in ring_systems
def GetSameRingAtoms(mol, atomSet):
'''
@type mol: OEGraphMol
@type atomSet: OEAtomBondSet
@return list[OEAtombase]
'''
oechem.OEFindRingAtomsAndBonds(mol)
_, ringIdxPerAtom = oechem.OEDetermineRingSystems(mol)
toKeepRings = {}
for atom in atomSet.GetAtoms():
if ringIdxPerAtom[atom.GetIdx()] > 0:
toKeepRings[ringIdxPerAtom[atom.GetIdx()]] = True
ringAtoms = []
for i in range(0, len(ringIdxPerAtom)):
if ringIdxPerAtom[i] in toKeepRings:
ringAtoms.append(mol.GetAtom(oechem.OEHasAtomIdx(i)))
return ringAtoms
def ring_size (self):
"""
Returns a dictionary, which is atom's index correspoding to the ring size the atom in.
@rtype : C{dic} of C{int} : C{int}
@return: A dictionary of atom indices correspoing to the size of the ring they are in.
"""
ring_size = {}
oechem.OEFindRingAtomsAndBonds(self._struc)
nrrings, rings = oechem.OEDetermineRingSystems(self._struc)
ring_dic = {}
for ring_idx in rings:
if not ring_dic.has_key(ring_idx):
ring_dic[ring_idx] = []
for key in ring_dic.keys():
if key > 0:
ring_dic[key] = rings.count(key)
else:
ring_dic[key] = 0
for (idx, atom) in enumerate(rings):
oe_idx = idx +1
ring_size [oe_idx] = ring_dic[atom]
return ring_size
def _tag_rings(mol):
"""
This function tags ring atom and bonds with ringsystem index
Parameters
----------
mol: OpenEye OEMolGraph
Returns
-------
tagged_rings: dict
maps ringsystem index to ring atom and bond indices
"""
tagged_rings = {}
nringsystems, parts = oechem.OEDetermineRingSystems(mol)
for ringidx in range(1, nringsystems +1):
ringidx_atoms = set()
for atom in mol.GetAtoms():
if parts[atom.GetIdx()] == ringidx:
ringidx_atoms.add(atom.GetIdx())
tag = oechem.OEGetTag('ringsystem')
atom.SetData(tag, ringidx)
# Find bonds in ring and tag
ringidx_bonds = set()
for a_idx in ringidx_atoms:
atom = mol.GetAtom(oechem.OEHasAtomIdx(a_idx))
for bond in atom.GetBonds():
nbrAtom = bond.GetNbr(atom)
nbrIdx = nbrAtom.GetIdx()
if nbrIdx in ringidx_atoms and nbrIdx != a_idx:
ringidx_bonds.add(bond.GetIdx())
tag = oechem.OEGetTag('ringsystem')
bond.SetData(tag, ringidx)
tagged_rings[ringidx] = (ringidx_atoms, ringidx_bonds)
return tagged_rings
def n_rings(smiles):
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, smiles)
n_rings, parts = oechem.OEDetermineRingSystems(mol)
return n_rings
