Molecule symmetry

I'm not sure if this is the correct section but I have a symmetry API question.

I'm trying to detect symetric molecules and am using the isSymmetric() func, but it only seems to work on molecules that have multiple planes of symmetry. However it does not detect achiral symmetry such as with:

C[C@H](C[C@H](C)O)O

C1[C@@H](CC[C@H](C1)O)N

C[C@@H]1CN(C[C@@H](S1)C)C

 

Is there another symmetry function to solve this?

Molecule mol = MolImporter.importMol("C[C@H](C[C@H](C)O)O");


if (mol.isSymmetric())


	// do something

Hi,

I moved this topic to the appropriate forum.

Bye,

Robert

Hi,

Currently we do not support symmetry group calculations in molecule.

I would suggest to get the enantiomer of the molecule:

Molecule enantiomer = Stereochemistry.getEnantiomer(m);

and compare the original and the enantiomer molecules using some format, which generates unique string: inchi, inchikey or unique smiles.

How exactly does the getEnantiomer() method work?  Does it return the original molecule if the structure is achiral? What if there are two stereocenters, but only one is specified -- e.g., C[C@@H](Cl)CC(C)Br?  What if the structure is a 3D chiral conformer of an achiral compound, e.g., 1,2-ethanediol in the gauche conformation?

Hi,

getEnantiomer() returns the mirror image of the molecule.

If the structure is achiral it returns the mirror image of the achiral molecule which is the same as the original structure (it can be translated, rotated to the original structure).

If just one stereocenter defined the stereocenter is changed to the opposite value.

If 3D chiral conformer of an achiral compound is given, returns the mirror image which is a 3D achiral compound.

Thanks.  All that is the desired behavior.  Essentially, you're getting the mirror image, which will be the enantiomer only if the structure representation is chiral.

I see that Stereochemistry.getEnantiomer() takes a MoleculeGraph and returns a MoleculeGraph, which I will have to cast back to a Molecule if I want a Molecule.  Can you add a method that takes a Molecule and returns a Molecule?  If it can't have the name "getEnantiomer", I suggest "getMirror" or just "mirror".

And I *still* think that it's best to make getEnantiomer() (or getMirror()) a dynamic method in the Molecule and MoleculeGraph classes.

We will modify the method to get the same type of structure as it is given.

So if you pass a Molecule object to the method it will return Molecule.

Actually Molecule and MoleculeGraph is huge so we are focusing to shrink it.

volfi wrote:

We will modify the method to get the same type of structure as it is given. So if you pass a Molecule object to the method it will return Molecule. Actually Molecule and MoleculeGraph is huge so we are focusing to shrink it.

I understand, but I still think it's the most intuitive place for it.

A better name for the method would be mirror() or getMirrorImage().  You're not necessarily getting the enantiomer.

Thank you for the comment we will mention it on the APIdoc and later if the Molecule size is small enough we will put thi to the Molecule API.

I am trying to categorize compounds into asymmetric and symmetric.  Consider two structures:  

Structure A:  CCC(C)N1C[C@H](C)S[C@H](C)C1

Structure B:  [H][C@]12CC[C@]([H])(CC(C)C1)N2

Both molecules contain two defined stereogenic centers and one undefined stereogenic center.  For both molecules, getEnantiomer() returns a structure which is identical to the input, suggesting that they are both symmetric.   But:  Molecule A is asymmetric and only Molecule B is symmetric.

Is there a way to distinguish asymmetric structures (like A) from symmetric structures (like B)?

The way to do it is to enumerate the stereoisomers of A and see if any of them are nonidentical mirror images.  See this page.  Here's the Java code for generating the stereoisomers:

    public static Molecule[] enumerateStereo(Molecule cpd) {

        Molecule[] stereoisomers = null;

        try {

            final StereoisomerPlugin plugin = new StereoisomerPlugin();

            plugin.setMolecule(cpd);

            plugin.setStereoisomerismType(StereoisomerPlugin.BOTH);

            plugin.setProtectTetrahedralStereo(true);

            plugin.setProtectDoubleBondStereo(true);

            plugin.run();

            stereoisomers = plugin.getStereoisomers();
        } catch (PluginException e) {

            stereoisomers = new Molecule[] {cpd};

        } // try

        return stereoisomers;

    } // enumerateStereo(Molecule)

Thank you for the suggestion!  Generating the stereoisomers and then comparing them did the trick.