exception handling in libmcs

Hi,


some wrong structures just create a NPE, I discovered that on my own


code, which didnt catch it. so Libmcs should throw something like





Some features of OC1C(O)C(O)C(OP(O)(=O)OCC(COC([*;R1])=O)OC([*;R1])=O)C(O)C1O cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.





chemaxon.marvin.plugin.PluginException: Calculation result is not defined


for query molecules.


or


chemaxon.marvin.plugin.PluginException: Inconsistent molecular structure.





Which is similar to cxcalc


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Instead libmcs says something about bond indices, maybe true but not helpful:





chemaxon.formats.MolFormatException: Invalid atom indices in bond definition (0, 0)


at chemaxon.marvin.io.formats.mdl.MolImport.readBondBlockV2(MolImport.java:901)


at chemaxon.marvin.io.formats.mdl.MolImport.readCtab(MolImport.java:732)


at chemaxon.marvin.io.formats.mdl.MolImport.readMol0(MolImport.java:633)


at chemaxon.marvin.io.formats.mdl.MolImport.readMol(MolImport.java:299)


at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:270)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:759)


at chemaxon.formats.MolImporter.read(MolImporter.java:624)


at chemaxon.formats.MolImporter.read(MolImporter.java:591)


at chemaxon.clustering.JKlustorImport.readNext(JKlustorImport.java:657)


at chemaxon.clustering.JKlustorImport.readStructures(JKlustorImport.java:570)


at chemaxon.clustering.LibraryMCS.main(LibraryMCS.java:1358)





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Example mols with wrong structures (mol2 is a radical or wrong SMILES)


1) OC1C(O)C(O)C(OP(O)(=O)OCC(COC([*;R1])=O)OC([*;R1])=O)C(O)C1O


2) O[N](=O)c1cccc(c1)[N](O)=O





Tobias

Hi,





the problem with the 1st example is the same as with the one in post 4118 (http://www.chemaxon.com/forum/viewtopic.php?t=4111), namely, that R-groups are not yet supported.





The 2nd one with the radicals does not crash libmcs for me, though the radicals disappear on the way, we'll investigate that.





Miklos