error while running libmcs

Hi,


I got the following error while runnig a multisdf file in libmcs.


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[arun@localhost bin]$ ./libmcs not_in_human.sdf





Some features of Clc1ccc2n(-*)cc(-c3n(-*)n(-*)n(-*)n3-c4ccccc4)c2c1 cannot be converted to smiles/cxsmiles. Use the smarts or cxsmarts format.


java.lang.IllegalArgumentException:


Some features of Clc1ccc2n(-*)cc(-c3n(-*)n(-*)n(-*)n3-c4ccccc4)c2c1 cannot be converted to smiles/cxsmiles. Use the smarts or cxsmarts format.


at chemaxon.struc.Molecule.toFormat(Molecule.java:829)


at chemaxon.marvin.modules.CommonStructureSearch.extractSubstructure(CommonStructureSearch.java:1417)


at chemaxon.marvin.modules.CommonStructureSearch.getResultAsMolecule(CommonStructureSearch.java:627)


at chemaxon.clustering.LibraryMCS.merge(LibraryMCS.java:937)


at chemaxon.clustering.LibraryMCS.cluster(LibraryMCS.java:873)


at chemaxon.clustering.LibraryMCS.search(LibraryMCS.java:838)


at chemaxon.clustering.LibraryMCS.main(LibraryMCS.java:1864)


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Please let me know where is the problem.


Regards,


Subbarao

Hi, I tried to reproduce the same problem using the smiles string in the error message but I did not manage, libmcs worked all right.


Which version of JChem are you using?


Can you send me your test structures or those are confidential?


Regards


Miklos

Hi,


I checked the structures and I found that the input files had extra lines for lone pairs and there was no atom assigned in the Mol2 format. I made new input files and could get libmcs running without any error.


Thanks,


Subbarao