storing mixtures

Hi,





I have a SD file containing mixtures. Thus, their formula field is empty. jcman stops at the first such line. Is it possible to still import the full database, including mixtures? Say, by editing the SD file and passing a dummy record in the formula fields for mixtures?





Or would it be better to strip off mixtures, enter pure chemicals and then to add the rest directly in MySQL bypassing jchem?





In that I assume that jchem search would still work on the full database, although MySQL entries without formula will be skipped in chemical searches? Is it a valid assumption?

Hi,





Could you possibly attach an example file here ?


(if the structures are properietrary, you may alter them as long as they maintain the probelmatic behaviour)


Please also let me know your Jchem version.





What do you mean by "jcman stops at the first such line" ?


What operation stops, do you get an error message (if so please copy/paste) ?

Quote:

Or would it be better to strip off mixtures, enter pure chemicals and then to add the rest directly in MySQL bypassing jchem?

In general we do not recommend to externally modify JChem database objects in any situation. In such a case we may not be able to provide support for errors that are the result of such modifications.

Quote:

In that I assume that jchem search would still work on the full database, although MySQL entries without formula will be skipped in chemical searches? Is it a valid assumption?

The search process doesn't use the cd_formula field at all, so it should make no difference if it is null or not.





Best regards,





Szilard

Ok, let's give one more try.





What happens if a DBMS table contains both rows with chemical structures and without, i.e. some of the chem fields are blank? Can jchem handle this?





Thank you,


-G.

guest wrote:

Hi, I have a SD file containing mixtures. Thus, their formula field is empty. jcman stops at the first such line. Is it possible to still import the full database, including mixtures? Say, by editing the SD file and passing a dummy record in the formula fields for mixtures? Or would it be better to strip off mixtures, enter pure chemicals and then to add the rest directly in MySQL bypassing jchem? In that I assume that jchem search would still work on the full database, although MySQL entries without formula will be skipped in chemical searches? Is it a valid assumption?

Hi,





You are probably thinking about structures without structural information ("empty" structures).





JChem can optionally allow the import of empty structures.


Please look for the "Allow empty structures" checkbox in the import dialog.


From command-line you can use the "--noempty" option to skip empty structures (the import does not stop).


These instructions are based on version 3.0.12.





Best regards,





Szilard

Please note that mixture S-groups are not yet supported in JChem. They are planned to appear in a future release, together with other S-groups of polymer notation.





However, you can represent mixtures by simply drawing two or more fragments as part of the molecule. Stoichiometry may be handled using multiple groups. (Integer coefficients.)





Answering your other question: for database search we do not use the formula column, only the fingerprint, hash code and the two structure columns (cd_smiles and cd_structure). However, - as Szilard mentioned - we do not encourage the manipulation of JChem tables outside JChem, because this may violate database integrity and can cause problems.





All the best,


Szabolcs