On Oct 31, 2019, at 12:49, LJ <[email protected]> wrote:
> How to find out the terminal ring (ring having no connections with any other
> ring) using SMARTS notation?
That is not possible with SMARTS.
For one, SMARTS matches a fixed substructure (possibly recursively), meaning
there is no way to match a ring of indefinite size. You can only match a ring
of a given, fixed size.
For another, you cannot express "no connections with" in SMARTS, only
"connection with something which isn't"
For example, the SMARTS "[R1]@1@[R1]@[R1]@[R1]@[R1]@[R1]1~[!R1]" will match a
6-membered ring where the atoms are only in a single SSSR ring (not in a fused
ring), and where one of the atoms is connected with something which isn't in a
ring.
However, consider "C1CCCCC1(O)c1ccccc1" where the cyclohexane is connected to
an hydroxyl and to a benzo.
The above SMARTS matches, even though there are two rings connected to each
other.
Here's one way to approach what you are looking for.
Open Babel has a way to find the smallest set of smallest rings ("SSSR"). All
disconnected rings must be in the SSSR.
The "[R1]" SMARTS pattern will find all atoms which are in only a single SSSR
ring.
The pattern "[R]!@[R]" will find all ring atoms which are connected to another
ring atom but not through a ring bond.
So, you want the SSSR rings which contain only atoms which are in a single SSSR
ring, and which are not bonded to another ring atom through a non-ring bond.
The following does something like what I think you want:
import openbabel
if openbabel.__version__.startswith("2."):
import pybel
else:
from openbabel import pybel # Use the Open Babel 3.0 API
ring_atoms_pat = pybel.Smarts("[R1]")
connected_ring_atoms_pat = pybel.Smarts("[R]!@[R]")
def find_disconnected_rings(mol):
rings = mol.sssr
# Get the atoms which are only in a single SSSR ring
single_ring_atoms = set(m[0] for m in ring_atoms_pat.findall(mol))
# Find all ring atoms which are connected to another ring
# atom through a non-ring bond.
connected_ring_atoms = set()
for m in connected_ring_atoms_pat.findall(mol):
connected_ring_atoms.add(m[0])
connected_ring_atoms.add(m[1])
# Get the rings which contain atoms which are only in a single
# SSSR ring and which are not connected to another ring.
disconnected_rings = []
for ring in rings:
if all(atom in single_ring_atoms and atom not in connected_ring_atoms
for atom in ring._path):
disconnected_rings.append(ring)
return disconnected_rings
for smiles in (
"c1ccccc1O",
"CNP",
"c1ccccc1c1ccccc1",
"C1CCCCC1(O)c1ccccc1",
"C1CCCCC1(O)Pc1ccccc1",
"C1CCCCC1(O)Pc1ccccc1-C1CCC1",
):
mol = pybel.readstring("smi", smiles)
print("SMILES:", smiles)
has_ring = False
for ring_atoms in find_disconnected_rings(mol):
print(" ", ring_atoms._path)
has_ring = True
if not has_ring:
print(" (no disconnected rings)")
The output of this is:
SMILES: c1ccccc1O
(3, 4, 5, 6, 1, 2)
SMILES: CNP
(no disconnected rings)
SMILES: c1ccccc1c1ccccc1
(no disconnected rings)
SMILES: C1CCCCC1(O)c1ccccc1
(no disconnected rings)
SMILES: C1CCCCC1(O)Pc1ccccc1
(3, 4, 5, 6, 1, 2)
(11, 12, 13, 14, 9, 10)
SMILES: C1CCCCC1(O)Pc1ccccc1-C1CCC1
(3, 4, 5, 6, 1, 2)
Andrew
[email protected]
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