SMILES to InChi?

I'm using JChem for Excel 5.6.0.482 with Excel 2007. I would like to convert a column of SMILES to InChi. I've tried using the Convert to menu to convert the SMILES to InChi and nothing appears to happen. Is it possible to do this?

Yes, it is.

The screen shot you pasted, there is a root menu above Convert From Text/SMILES,

and then when you got JChemExcel strucures you should repeat your selection and say

Convert ToText/Inchi as you did.

Viktor

Hello Viktor,

I've tried and I can't get it to work. I can convert the SMILES to a Structure, but it won't covert to InChi or any other format except back to SMILES.

Thanks

Mick

Hi,

let me give me a structure with which it is working:

C=C => structure => InChI=1S/C2H4/c1-2/h1-2H2

then now please send us 2 structures you have problems with.

Thanks,

Viktor

I can convert C=C to every other available format except for InChi. When I try and convert it, I can the strcuture flicker for a second but the it remains as a structure. The cell formula contains the following after I try and convert it to InChi:

=JCSYSStructure("48D24555FEF64C7A98D6B597B3C9E2FE")

InChi isn't working at all for me, even with a such a simple compound. :(

Could you please send some log files?

https://www.chemaxon.com/jchem4excel/adminguide/logging.html

Viktor

Here's the log file where I'm trying to convert C=C to InChi, I set logging to ALL.

The log does not contain any error text refering to incorrect load of Inchi .

Yes I noticed that. Maybe it's because it's not converting anything to InChi?

These are the steps I followed:

• I closed Excel.


• I renamed the Log File Directory (in case there's sensitive information in the log files).


• I reopened the excel spreadsheet which has one cell with C=C.


• I converted the cell to a structure.


• I tied to convert the cell to InChi.


• I saved the file and exited Excel.

I then compressed the log file. I will test on another system to see if can duplicate the problem.

Please suggest what I should do next or if I am missing step.

Everything was correct what steps you took. Inchi loading issue I think we face, maybe the error is not reported properly outside.

I tried on another system, WInXP with Excel 2007, and see the same behaviour.

It is something new we have never met,

in January we will investigate it more.

For the tim ebeing please try to upgrade to 5.7.1 Marvin and JChemExcel.

Thanks. Please inform us if the problem still persists.

I see the same behaviour. :(

Mick,

in the meantime we started dealing with the issue.

Unfortunatelly the problem is somewhere in the basic library , for any reason the inchi dll is not present in your running environment. WIth the missing dll we could reproduce a similar behavour.

Gabor is working on the issue, will contact you once he finds a workaround or a good explanation.

We also try to enhance logging on this area to see more details why the file cannot be generated ....

(This is a rare issue, 1 occasion I could recall, when on a Windows server the process wanted to use this dll, but it could not be create for security reasons - impersonation, lack of temp directory/)

Viktor

Hi Mick,

Before I continue the analysis in this way, please check the following file if it exists in your environment:

<your user home>/chemaxon/lib/inchi-1_3jni/inchi.dll

or is there any subfolder or file in

<your user home>/chemaxon/lib 

folder?

Thank you,

Gabor Vasko

<your user home>/chemaxon/lib/inchi-1_3jni/inchi.dll

<your user home>/chemaxon/lib 

Hello Gabot,

I was unable to find the inchi.dll file in my user's home directory nor in "E:\Program Files\ChemAxon\JChem for Excel" where JChem for Excel is installed.

I did find it in "C:\Documents and Settings\chemaxon\lib\inchi-1_3jni" which seems like an unusual place for it to be. I copied the dll to my home directory and I am now able to convert to InChi (see the screenshot).

I tested with a Benzene ring, and in the final result, what is the AuxInfo (see the screenshot)?


Thanks

Mick

Hi Mick,

sorry I am not able to give you more support on this specific area,
this is field of chemists so please try to keep yourself infromed from here:

http://www.inchi-trust.org/sites/default/files/inchi-1.04/InChI_UserGuide.pdf

Auxiliary Information Output
A variety of additional information is optionally provided along with the Identifier: a
mapping of canonical identification atom numbers on original atom numbers,
constitutional equivalence, inverted sp3 stereo and its numbering, isotopic and fixed-H
layer information, and „reversibility‟ information which allows the redrawing of the
original structure and recalculation of the identifier. This additional analysis information
is shown in the line that starts with AuxInfo=
AuxInfo=
{version}1
/{normalization_type}
Main part
/N:{original_atom_numbers}
/E:{atom_equivalence}
/gE:{group_equivalence}
/it:{abs_stereo_inverted:sp3}
/iN:{abs_stereo_inverted:original_atom_numbers}
Isotopic part
/I:{isotopic:original_atom_numbers}*
/E:{isotopic:atom_equivalence}
/gE{isotopic:group_equivalence}

One thing I managed to double checked with collegues, this Auxinfo should be meant together with Inchi code.

Viktor

Viktor,

Thanks for the reply, I wasn't sure of the Auxinfo should have there or not, thank you for clearing that up.

Mick