Distinguish between two types of Markush structures

Hi all,

I need to distinguish between two types of Markush structures. First type is a molecule with undefined R-group on the defined position (see example in Octanoyl.svg) and second type is a molecule with undefined position of defined substituent (see example in Hydroxy-magnolin.svg). I can see that there's a way to decide between those two by analysing mol files as long as the second type has $RGP section in molfile and the first type doesn't (files Hydroxy-magnolin.mol and Octanoyl.mol). But I wonder if there is some JChem function to do it?

alena

We do not have a specific tool for this, but you can use molconvert to convert the molecule to SMILES format and see if it succeeds. Undefined R-atoms are represented by a star ('*') charactes in SMILES, while R-group definitions cannot be described in SMILES and therefore conversion produces an error message in this case.

With your example molecules:

molconvert smiles Octanoyl.mol 

CCCCCCCC(
)=O



molconvert smiles Hydroxy-magnolin.mol 

Hydroxy-magnolin.mol: cannot convert molecule 1 to smiles: 

Some features of [#6]OC1=CC(=CC(O[#6])=C1O[#6])[C@H]1OCC2C1CO[C@@H]2C1=C(
)C(
)=C(O[#6])C(O[#6])=C1
 cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.

If you want to use our JChem Java API, then you can import the molecule, check if it is an RgMolecule designed to store R-group definitions, and then list the R-group IDs with definitions. The attached example code RTest.java uses getRgroupId(int i) to get the R-group ID for R-group definition with index i. The number of R-group definitions is returned by getRgroupCount().

With your example molecules:

java RTest Octanoyl.mol 

Molecule@b37c60d[10a,9b]

Molecule does not contain R-group definitions.



java RTest Hydroxy-magnolin.mol 

RgMolecule@10eb017e[33a,36b,R1]

R1 is an R-group with definition.

Nora, 

Thanks a lot! That helped.

alena