Dear all,
@Mila1004 and I suspect that the results generated by the ConjugatedPiSystemsDetector class might be path-dependent, especially for allenes / cumulative double bonds, i.e. they depend on how the atom indices are placed because that determines which path the algorithm takes when iterating through the molecule.
Take these examples:
SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
SmilesGenerator sg = new SmilesGenerator(SmiFlavor.Canonical);
String[] smiles = {"C=CC=C=CC=C", "C(=CC=C)=CC=C", "CC=C=CC=C", "C(=CC=C)=CC", "C=C=CC#N", "C(=C)=CC#N"};
for (String smi : smiles) {
System.out.println("\nInput : " + smi);
IAtomContainer mol = sp.parseSmiles(smi);
IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol);
for (int i = 0; i < acSet.getAtomContainerCount(); i++) {
IAtomContainer ac = acSet.getAtomContainer(i);
System.out.println("\tOuput: " + sg.create(ac));
}
}Output:
Input : C=CC=C=CC=C
Ouput: [C]=CC=C //as expected
Ouput: [C]=CC=C
Input : C(=CC=C)=CC=C //same mol as above but differently ordered SMILES code
Ouput: C(=CC=C)=CC=C //different result, the allene is now part of the conjugated system
Input : CC=C=CC=C
Ouput: [C]=CC=C //as expected
Input : C(=CC=C)=CC //same mol as above but differently ordered SMILES code
Ouput: [CH]=C=CC=C //different result, the allene is now part of the conjugated system
Input : C=C=CC#N
Ouput: [C]=CC#N //as expected
Input : C(=C)=CC#N //same mol as above but differently ordered SMILES code
Ouput: N#CC=C=C //different result, the allene is now part of the conjugated system
What do you think about this? Are we doing sth. wrong? Do you see a potential fix?
Dear all,
@Mila1004 and I suspect that the results generated by the ConjugatedPiSystemsDetector class might be path-dependent, especially for allenes / cumulative double bonds, i.e. they depend on how the atom indices are placed because that determines which path the algorithm takes when iterating through the molecule.
Take these examples:
Output:
What do you think about this? Are we doing sth. wrong? Do you see a potential fix?