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

Table 1. Example of depiction of atoms (pink) and those that are perceived to be in the same ring(s) (blue)
../_images/samering2img-01.png ../_images/samering2img-02.png ../_images/samering2img-03.png
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

Difficulty level

../_images/chilly.png ../_images/chilly.png

Download

Download code

samering.py

See also Usage subsection.

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.

 1def AtomsInSameRing(atomA, atomB):
 2
 3    if not atomA.IsInRing() or not atomB.IsInRing():
 4        return False
 5
 6    if atomA == atomB:
 7        return True
 8
 9    firstpath = [a for a in oechem.OEShortestPath(atomA, atomB, oechem.OEAtomIsInChain())]
10    firstpathlength = len(firstpath)
11
12    if firstpathlength == 2:
13        return True  # neighbors
14
15    if firstpathlength == 0:
16        return False  # not is same ring system
17
18    smallestA = oechem.OEAtomGetSmallestRingSize(atomA)
19    smallestB = oechem.OEAtomGetSmallestRingSize(atomB)
20
21    if firstpathlength > smallestA and firstpathlength > smallestB:
22        return False  # too far away
23
24    # try to find the second shortest different path
25    excludepred = ChainAtomOrAlreadyTraversed(firstpath[1:-1])
26    secondpath = [a for a in oechem.OEShortestPath(atomA, atomB, excludepred)]
27    secondpathlength = len(secondpath)
28
29    if secondpathlength == 0:
30        return False  # can not be in the same ring
31
32    if secondpathlength > smallestA and secondpathlength > smallestB:
33        return False  # too far away
34
35    sumringsize = len(firstpath) + len(secondpath) - 2
36    if sumringsize > smallestA and sumringsize > smallestB:
37        return False
38
39    inringA = oechem.OEAtomIsInRingSize(atomA, sumringsize)
40    inringB = oechem.OEAtomIsInRingSize(atomB, sumringsize)
41    return inringA and inringB

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

 1class ChainAtomOrAlreadyTraversed(oechem.OEUnaryAtomPred):
 2    def __init__(self, exclude):
 3        oechem.OEUnaryAtomPred.__init__(self)
 4        self.exclude = exclude
 5
 6    def __call__(self, atom):
 7        if not atom.IsInRing():
 8            return False
 9        return (atom in self.exclude)
10
11    def CreateCopy(self):
12        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

../_images/depict-ringsystem.png

See also

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

../_images/depict-aromringsystem.png

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

../_images/depict-ringsize.png

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

../_images/depict-aromringsize.png

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)
../_images/depict-smallestringsize.png

See also in OEChem TK manual

Theory

API