User 677b9c22ff
26-11-2008 21:31:17
Hi,
following the discussions on the unique stereoisomers and
unique smiles and speed of duplicate detection for maltotriose,
I thought I can use INCHI, but I get an error if I turn
aromatization on in the API code.
The error does not occur using the external WINDOWS InCHI software, that works fine. Only if I call the conversion from within the API.
I attached two SDF files one aromatized one non-aromatized.
To test that I converted the attached SMILES file to SDF,
on with aroma one without aroma and submitted it to the WINCHI software
without any problems.
Z:\>molconvert sdf:+a Z:\NCI-10000.smi > NCI-10000-aroma.sdf
Z:\>molconvert sdf:-a Z:\NCI-10000.smi > NCI-10000-noaroma.sdf
The aroma version gives the following error:
Attached the two SDF files and the API code
following the discussions on the unique stereoisomers and
unique smiles and speed of duplicate detection for maltotriose,
I thought I can use INCHI, but I get an error if I turn
aromatization on in the API code.
The error does not occur using the external WINDOWS InCHI software, that works fine. Only if I call the conversion from within the API.
I attached two SDF files one aromatized one non-aromatized.
To test that I converted the attached SMILES file to SDF,
on with aroma one without aroma and submitted it to the WINCHI software
without any problems.
Z:\>molconvert sdf:+a Z:\NCI-10000.smi > NCI-10000-aroma.sdf
Z:\>molconvert sdf:-a Z:\NCI-10000.smi > NCI-10000-noaroma.sdf
The aroma version gives the following error:
| Code: |
Reading molecules. Imported 9787 structures. Exception in thread "main" java.lang.IllegalArgumentException: The following error occured in the IUPAC software: InChI version 1, Software version 1.01 release 07/21/2006 Opened log file 'C:\temp\temp_java_inchi59300log' Opened output file 'C:\temp\temp_java_inchi59298in' Opened problem file 'C:\temp\temp_java_inchi59301prb' Options: Mobile H Perception ON Isotopic ON, Absolute Stereo ON Omit undefined/unknown stereogenic centers and bonds Only narrow end of wedge points to stereocenter Aux. info suppressed Issue warning on empty structure Input format: MOLfile Output format: Plain text Timeout per structure: 60.000 sec; Up to 1024 atoms per structure Error -9986 (Charges were rearranged; Cannot process aromatic bonds) structure #1 component 1. 0 msec structure #1. (1 component, 9 atoms, error=-9986). End of file detected after structure #1. Finished processing 1 structure: 1 error, processing time 0:00:00.00 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at chemaxon.marvin.util.JavaLangUtil.newThrowable(JavaLangUtil.java:76) at chemaxon.marvin.util.JavaLangUtil.newIllegalArgumentException(JavaLangUtil.java:41) at chemaxon.struc.Molecule.toFormat(Molecule.java:1270) at examples.DuplicateSearchInchi.main(DuplicateSearchInchi.java:60) Caused by: chemaxon.marvin.io.MolExportException: The following error occured in the IUPAC software: InChI version 1, Software version 1.01 release 07/21/2006 Opened log file 'C:\temp\temp_java_inchi59300log' Opened output file 'C:\temp\temp_java_inchi59298in' Opened problem file 'C:\temp\temp_java_inchi59301prb' Options: Mobile H Perception ON Isotopic ON, Absolute Stereo ON Omit undefined/unknown stereogenic centers and bonds Only narrow end of wedge points to stereocenter Aux. info suppressed Issue warning on empty structure Input format: MOLfile Output format: Plain text Timeout per structure: 60.000 sec; Up to 1024 atoms per structure Error -9986 (Charges were rearranged; Cannot process aromatic bonds) structure #1 component 1. 0 msec structure #1. (1 component, 9 atoms, error=-9986). End of file detected after structure #1. Finished processing 1 structure: 1 error, processing time 0:00:00.00 at chemaxon.marvin.io.formats.inchi.InchiExport.convert(InchiExport.java:191) at chemaxon.struc.Molecule.exportToObject(Molecule.java:1476) at chemaxon.struc.Molecule.exportToObject(Molecule.java:1441) at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1290) at chemaxon.struc.Molecule.toFormat(Molecule.java:1268) ... 1 more |
Attached the two SDF files and the API code
| Code: |
for (int i = 0; i < mols.length; i++) { // needed for search (fails if on in API, but not external with NCI-10000) mols[i].aromatize(); inchi[i] = mols[i].toFormat("inchi:AuxNone,SAbs,NEWPS"); |