molconvert inchikey conversion with mixtures (issue)

User 677b9c22ff

12-05-2010 22:07:16

Hi,

MVIEW 5.3.2 here.

This is just for the records. so other people who run into the same problem may circumvent it.

If an SDF file contains mixtures InChiKey can be created with the current version,

molconvert will correctly alert that it can not convert the file

molconvert inchikey corrupt-water.sdf
corrupt-water.sdf: cannot convert molecule 1 to inchikey: The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file 'C:\temp\temp_java_inchi126431168742458367log'
Opened output file 'C:\temp\temp_java_inchi8777732362466598149in'
Opened problem file 'C:\temp\temp_java_inchi1759192548892501757prb'

NOW

If I use the -g option (assume I use an script or workflow I dont want to break it will convert "something"

molconvert -g inchikey corrupt-water.sdf
corrupt-water.sdf: cannot convert molecule 1 to inchikey: The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file 'C:\temp\temp_java_inchi6196373287612794185log'
Opened output file 'C:\temp\temp_java_inchi4010697477936633274in'
Opened problem file 'C:\temp\temp_java_inchi4770773726302138062prb'

InChIKey=MOSFIJXAXDLOML-UHFFFAOYSA-N
corrupt-water.sdf: cannot convert molecule 2 to inchikey: The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file 'C:\temp\temp_java_inchi3659061117279103766log'
Opened output file 'C:\temp\temp_java_inchi3558279485631806373in'
Opened problem file 'C:\temp\temp_java_inchi1572058901602774305prb'

InChIKey=MOSFIJXAXDLOML-UHFFFAOYSA-N
corrupt-water.sdf: cannot convert molecule 3 to inchikey: The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file 'C:\temp\temp_java_inchi8036349050301078733log'
Opened output file 'C:\temp\temp_java_inchi1109238055811652797in'
Opened problem file 'C:\temp\temp_java_inchi7247715186634999982prb'

InChIKey=MOSFIJXAXDLOML-UHFFFAOYSA-N

BUT the InChiKey MOSFIJXAXDLOML-UHFFFAOYSA-N does not refer to the actual substance but any given mixture.

Finally if molconvert pipes the output into a file, you will end up with 3 molecules and assume these are your hash keys, but they are not.

InChIKey=MOSFIJXAXDLOML-UHFFFAOYSA-N
InChIKey=MOSFIJXAXDLOML-UHFFFAOYSA-N
InChIKey=MOSFIJXAXDLOML-UHFFFAOYSA-N

SO the number of converted files is the same as the number of exported ones, just

MOSFIJXAXDLOML-UHFFFAOYSA-N is a place holder for non-succesful INCHIKey conversion.

Tobias