Ring Perception

Problem

You want to determine whether two atoms belong to the same ring. See examples in Table 1.

Ring perception is one of the fundamental algorithms when handling chemical structures. While OEChem TK does not provide a solution for SSSR (Smallest Set of Smallest Rings) it includes wide range of functions (see Table 2) that answer related questions. This recipe will illustrate how to utilize these functions to determine whether two atoms belong to the same ring.

See also

Smallest Set of Smallest Rings (SSSR) Considered Harmful section in OEChem TK manual

**Table 1. Example of depiction of atoms (pink) and those that are perceived to be in the same ring(s) (blue)**

**Table 2. Ring perception API in OEChem TK**
API	See subsection
OEFindRingAtomsAndBonds	Ring Perception section in OEChem TK
OEDetermineRingSystems	Identifying Ring Systems of a Molecule
OEDetermineAromaticRingSystems	Identifying Aromatic Ring Systems of a Molecule
OEAtomIsInRingSize / OEBondIsInRingSize	Identifying Atom in Certain Ring Size
OEAtomIsInAromaticRingSize / OEBondIsInAromaticRingSize	Identifying Atom in Certain Aromatic Ring Size
OEAtomGetSmallestRingSize / OEBondGetSmallestRingSize	Identifying Atoms’ Smallest Ring Size

Ingredients

OEChem TK - cheminformatics toolkit

Difficulty level

Download

Download code

samering.py

Solution

The algorithm implemented in AtomsInSameRing is based on a simple concept: if two atoms belong to the same ring then there has to at least two alternative ring paths between them. These paths are identified by using the OEShortestPath function.

def AtomsInSameRing(atomA, atomB):

    if not atomA.IsInRing() or not atomB.IsInRing():
        return False

    if atomA == atomB:
        return True

    firstpath = [a for a in oechem.OEShortestPath(atomA, atomB, oechem.OEAtomIsInChain())]
    firstpathlength = len(firstpath)

    if firstpathlength == 2:
        return True  # neighbors

    if firstpathlength == 0:
        return False  # not is same ring system

    smallestA = oechem.OEAtomGetSmallestRingSize(atomA)
    smallestB = oechem.OEAtomGetSmallestRingSize(atomB)

    if firstpathlength > smallestA and firstpathlength > smallestB:
        return False  # too far away

    # try to find the second shortest different path
    excludepred = ChainAtomOrAlreadyTraversed(firstpath[1:-1])
    secondpath = [a for a in oechem.OEShortestPath(atomA, atomB, excludepred)]
    secondpathlength = len(secondpath)

    if secondpathlength == 0:
        return False  # can not be in the same ring

    if secondpathlength > smallestA and secondpathlength > smallestB:
        return False  # too far away

    sumringsize = len(firstpath) + len(secondpath) - 2
    if sumringsize > smallestA and sumringsize > smallestB:
        return False

    inringA = oechem.OEAtomIsInRingSize(atomA, sumringsize)
    inringB = oechem.OEAtomIsInRingSize(atomB, sumringsize)
    return inringA and inringB

ChainAtomOrAlreadyTraversed is the atom predicate that is used with OEShortestPath to identify a second alternative path between two atoms.

class ChainAtomOrAlreadyTraversed(oechem.OEUnaryAtomPred):
    def __init__(self, exclude):
        oechem.OEUnaryAtomPred.__init__(self)
        self.exclude = exclude

    def __call__(self, atom):
        if not atom.IsInRing():
            return False
        return (atom in self.exclude)

    def CreateCopy(self):
        return ChainAtomOrAlreadyTraversed(self.exclude).__disown__()

Usage

Usage

samering.py

prompt > python3 samering.py .ism
c1ccc2c(c1)cc[nH]2

atom  0 C in the same ring as  0 C  1 C  2 C  3 C  4 C  5 C
atom  1 C in the same ring as  0 C  1 C  2 C  3 C  4 C  5 C
atom  2 C in the same ring as  0 C  1 C  2 C  3 C  4 C  5 C
atom  3 C in the same ring as  0 C  1 C  2 C  3 C  4 C  5 C  6 C  7 C  8 N
atom  4 C in the same ring as  0 C  1 C  2 C  3 C  4 C  5 C  6 C  7 C  8 N
atom  5 C in the same ring as  0 C  1 C  2 C  3 C  4 C  5 C
atom  6 C in the same ring as  3 C  4 C  6 C  7 C  8 N
atom  7 C in the same ring as  3 C  4 C  6 C  7 C  8 N
atom  8 N in the same ring as  3 C  4 C  6 C  7 C  8 N

Discussion

The following examples show how to use ring perception functions available in OEChem TK.

Identifying Ring Systems of a Molecule

nrrings, ringlist = oechem.OEDetermineRingSystems(mol)

disp = oedepict.OE2DMolDisplay(mol, opts)

highlight = oedepict.OEHighlightByLasso(oechem.OEBlack)
highlight.SetConsiderAtomLabelBoundingBox(True)

ringpred = oechem.OEPartPredAtom(ringlist)
for ringidx, color in zip(range(1, nrrings + 1), oechem.OEGetVividColors()):
    ringpred.SelectPart(ringidx)
    ringset = oechem.OEAtomBondSet(mol.GetAtoms(ringpred))
    highlight.SetColor(color)
    oedepict.OEAddHighlighting(disp, highlight, ringset)

oedepict.OERenderMolecule(image, disp)

Download code

depict-ringsystem.py

See also

OEDetermineRingSystems method

Identifying Aromatic Ring Systems of a Molecule

nrrings, ringlist = oechem.OEDetermineAromaticRingSystems(mol)

disp = oedepict.OE2DMolDisplay(mol, opts)

highlight = oedepict.OEHighlightByLasso(oechem.OEBlack)
highlight.SetConsiderAtomLabelBoundingBox(True)

ringpred = oechem.OEPartPredAtom(ringlist)
for ringidx, color in zip(range(1, nrrings + 1), oechem.OEGetVividColors()):
    ringpred.SelectPart(ringidx)
    ringset = oechem.OEAtomBondSet(mol.GetAtoms(ringpred))
    highlight.SetColor(color)
    oedepict.OEAddHighlighting(disp, highlight, ringset)

oedepict.OERenderMolecule(image, disp)

Download code

depict-aromringsystem.py

See also

OEDetermineAromaticRingSystems method

Identifying Atom in Certain Ring Size

class LabelRingSize(oedepict.OEDisplayAtomPropBase):
    def __init__(self, maxringsize):
        self.maxringsize = maxringsize
        oedepict.OEDisplayAtomPropBase.__init__(self)

    def __call__(self, atom):
        if not atom.IsInRing():
            return ""
        rings = []
        for ringsize in range(3, self.maxringsize):
            if oechem.OEAtomIsInRingSize(atom, ringsize):
                rings.append(ringsize)
        if len(rings) == 0:
            return ""
        return "(" + ",".join([str(r) for r in rings]) + ")"

    def CreateCopy(self):
        return LabelRingSize(self.maxringsize).__disown__()


scale = oedepict.OEScale_AutoScale
opts = oedepict.OE2DMolDisplayOptions(width, height, scale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
opts.SetAtomPropertyFunctor(LabelRingSize(maxringsize=10))

disp = oedepict.OE2DMolDisplay(mol, opts)

Download code

depict-ringsize.py

See also

Identifying Atom in Certain Aromatic Ring Size

class LabelAromaticRingSize(oedepict.OEDisplayAtomPropBase):
    def __init__(self, maxringsize):
        self.maxringsize = maxringsize
        oedepict.OEDisplayAtomPropBase.__init__(self)

    def __call__(self, atom):
        if not atom.IsInRing():
            return ""
        rings = []
        for ringsize in range(3, self.maxringsize):
            if oechem.OEAtomIsInAromaticRingSize(atom, ringsize):
                rings.append(ringsize)
        if len(rings) == 0:
            return ""
        return "(" + ",".join([str(r) for r in rings]) + ")"

    def CreateCopy(self):
        return LabelAromaticRingSize(self.maxringsize).__disown__()


scale = oedepict.OEScale_AutoScale
opts = oedepict.OE2DMolDisplayOptions(width, height, scale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
opts.SetAtomPropertyFunctor(LabelAromaticRingSize(maxringsize=10))

disp = oedepict.OE2DMolDisplay(mol, opts)

Download code

depict-aromringsize.py

See also

Identifying Atoms’ Smallest Ring Size

class LabelSmallestRingSize(oedepict.OEDisplayAtomPropBase):
    def __init__(self):
        oedepict.OEDisplayAtomPropBase.__init__(self)

    def __call__(self, atom):
        if not atom.IsInRing():
            return ""
        smallest = oechem.OEAtomGetSmallestRingSize(atom)
        return "(" + str(smallest) + ")"

    def CreateCopy(self):
        return LabelSmallestRingSize().__disown__()


scale = oedepict.OEScale_AutoScale
opts = oedepict.OE2DMolDisplayOptions(width, height, scale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
opts.SetAtomPropertyFunctor(LabelSmallestRingSize())

disp = oedepict.OE2DMolDisplay(mol, opts)

Download code

depict-smallestringsize.py

See also

Ring Perception

Problem

Ingredients

Difficulty level

Download

Solution

Usage

Discussion

Identifying Ring Systems of a Molecule

Identifying Aromatic Ring Systems of a Molecule

Identifying Atom in Certain Ring Size

Identifying Atom in Certain Aromatic Ring Size

Identifying Atoms’ Smallest Ring Size

See also in OEChem TK manual