User 8201cee929
10-07-2007 11:40:48
Hi,
I import an sd file/structure with:
| Code: |
MolImporter oSDFileImporter = new MolImporter(sInputFile);
oMolecule = oSDFileImporter.read();
String sMolecule = oMolecule.exportToFormat("mol"); |
the resulting mol file is aromatized but I need the original mol format without any changes. There is no aromatic bond in the original sd file.
Is it possible to disable this function?
thank you,
peter
User f359e526a1
10-07-2007 20:10:46
Hello, we will check the issue - it should not happen.
User 8201cee929
11-07-2007 08:36:14
Hi,
Thank you!
I forgot to give you the version: Jchem 3.2.7
bye,
peter
User f359e526a1
16-07-2007 08:02:01
Could you please send some files (input and result files) you got since I was not able to reproduce the error.
User 8201cee929
16-07-2007 08:40:47
hi,
here you can find the sample sd file I used.
regards,
peter
ChemAxon 7c2d26e5cf
23-07-2007 22:14:00
Thanks, we will check it.
User f359e526a1
24-07-2007 07:48:04
Hello, I tried a small program (see attached code) but can not see any aromatic bond in the bond block of the generated strings. Could you please show a longer code snippet?
User 8201cee929
24-07-2007 08:19:03
hi,
I realised that bonds are aromatised when I run a structural serach:
Before I import structures into the db an optional structural search is executed.
please find attached the code.
regards,
peter
ChemAxon a3d59b832c
24-07-2007 09:05:04
Thanks, we will investigate. A quick fix is to clone the molecule and pass the clone to JChemSearch:
| Code: |
| searcher.setQueryStructure(molecule.clone()); |
Szabolcs
ChemAxon 9c0afc9aaf
25-07-2007 09:19:42
Hi,
Please see the API documentation of the method:
http://www.chemaxon.com/jchem/doc/api/chemaxon/jchem/db/JChemSearch.html#setQueryStructure(chemaxon.struc.Molecule)
It states:
| Quote: |
| NOTE: The Molecule object will be altered (standardized) at the start of the search. To keep the original form of the structure please clone it. |
When cloning a Molecule, you will have to type cast, as the clone() method always returns an Object type by definition.
The code correctly:
| Code: |
JChemSearch searcher = ... ;
searcher.setQueryStructure((Molecule)molecule.clone()); |
Best regards,
Szilard
User 8201cee929
25-07-2007 09:49:37
Hi,
I simply followed the code in the Dev. guide 'Structure Searching' but
of course I sould have checked the code in the API.
Thank you!
peter