#1384 Inchi with nonstandard options generates standard InChI in CDK 1.5.14

[Nina Jeliazkova]

Using InChIGenerator with non-standard options generates standard InChI (starting with 1S/ ) with 1.5.14. The same code generated non-standard InChI in previous versions (1.5.13 and before)

List<INCHI_OPTION> options = new ArrayList<INCHI_OPTION>();
options.add(INCHI_OPTION.FixedH);
options.add(INCHI_OPTION.SAbs);
options.add(INCHI_OPTION.SAsXYZ);
options.add(INCHI_OPTION.SPXYZ);
options.add(INCHI_OPTION.FixSp3Bug);
options.add(INCHI_OPTION.AuxNone);
InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
InChIGenerator gen1 = factory.getInChIGenerator(mol1, options);

[John May]

Hmmm I did respond by EMail but looks like SF doesn't handled that anymore. Anyways there was a change here recently but adding a test case exactly as you've specfied doesn't reproduce it. Do you have a dependency conflict somewhere:

https://github.com/cdk/cdk/commit/4c2e39f1b0ee9150fa18e1cdb7a51bfab9c4037b

https://jenkins.bigcat.unimaas.nl/job/cdk/

(Will fix that other failure..)

P.S. You can now use GitHub for issues, I created one this bug out of frustation with SF.

John

[John May]

Hi Nina,

Do you have a test molecule? Also I likely know where the problem is I had
to backdoor JNIInChI to get the timeout option and KET/15T options working.

Also we're going to start using the GitHub issue tracker - I created one
for this here: https://github.com/cdk/cdk/issues/253.

John

[John May]

Resolved

[Rajesh]

Hi John , Can you please help me out in storing a structure with some text in it (read from .mol) in jpg format . I guess, (as per my knowledge) i need to set some properties for the rendering panel but i am unable to find it out

Thanks

[John May]

Yes this is possible but please post this in the appropriate place
(cdk-user mailing list) and not on a unrelated bug report.

On 25 January 2017 at 12:23, Rajesh r6174@users.sf.net wrote:

Hi John , Can you please help me out in storing a structure with some text
in it (read from .mol) in jpg format . I guess, (as per my knowledge) i
need to set some properties for the rendering panel but i am unable to find
it out

Thanks

Attachments:

• cp1.PNG
  https://sourceforge.net/p/cdk/bugs/_discuss/thread/0634dffb/6b92/attachment/cp1.PNG
  (3.0 kB; image/png)

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• [bugs:#1384] https://sourceforge.net/p/cdk/bugs/1384/ Inchi with
  nonstandard options generates standard InChI in CDK 1.5.14*

Status: closed
Group: cdk-1.6.x
Created: Sat Dec 10, 2016 05:35 PM UTC by Nina Jeliazkova
Last Updated: Sun Jan 08, 2017 04:07 PM UTC
Owner: John May

Using InChIGenerator with non-standard options generates standard InChI
(starting with 1S/ ) with 1.5.14. The same code generated non-standard
InChI in previous versions (1.5.13 and before)

List<inchi_option> options = new ArrayList<inchi_option>();
options.add(INCHI_OPTION.FixedH);
options.add(INCHI_OPTION.SAbs);
options.add(INCHI_OPTION.SAsXYZ);
options.add(INCHI_OPTION.SPXYZ);
options.add(INCHI_OPTION.FixSp3Bug);
options.add(INCHI_OPTION.AuxNone);
InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
InChIGenerator gen1 = factory.getInChIGenerator(mol1, options);</inchi_option></inchi_option>

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