Handling of abnormal charges

Hi,

I've noticed some unexpected behaviour with charge handling from SMILES (could be true of other formats). These molecules are bizarre and corner cases but wanted to let you know of the perhaps unexpected handling in ChemAxon tools.

CCCC[n+251]1cccc(c1)C 24639292

is loaded in Marvin Sketch (15.3.2) as 

CCCC[n-5]1cccc(c1)C

[CH-]1[CH-][CH-][CH-][CH-]1.[CH-]1[CH-][CH-][CH-][CH-]1.[Co+10] 717961

 is interpreted as a query or markush structure by the cartridge (15.1.12):

sql> create table jc_tmp (smi clob);

sql> insert into jc_tmp (smi) values ('c1ccccc1');

-- okay (obviously)

sql> create index jctmpidx on jc_tmp (smi) indextype is jc_idxtype;

sql> insert into jc_tmp (smi) values ('[CH]1[CH][CH][CH][CH]1.[Co+10]');

-- okay

sql> insert into jc_tmp (smi) values ('[CH-]1[CH][CH][CH][CH]1.[Co+10]');

-- not-okay "Inserting a query or Markush structure is not allowed for table"

sql> insert into jc_tmp (smi) values ('[CH-]1[CH][CH][CH][CH]1');

-- okay

sql> insert into jc_tmp (smi) values ('[CH-]1[CH-][CH-][CH-][CH-]1');

-- okay

sql> insert into jc_tmp (smi) values ('[CH-]1[CH-][CH-][CH-][CH-]1.[Co+10]');

-- not-okay "Inserting a query or Markush structure is not allowed for table"

Hi John,

thank you for reporting.

Regarding the charge: we support charges only between -127 and +127, for values below and above the stored value overflows, that is why you have experienced the strange behavior.

The problem with inserting values like 

[CH-]1[CH][CH][CH][CH]1.[Co+10]

into a table is a SMILES import bug, and aliphatic query property is added during the SMILES import to an atom in the ring, that is why it is interpreted as a query molecule and thus can not be added to a molecule table. If it is a problem for you, I recommend a workaround: please, use another molecular format instead SMILES.

Best regards,

Zsuzsa