Re: [Rdkit-discuss] Request for Assistance: Understanding InChI to Mol Conversion Issue in RDKit

[Jan H. J. <ja...@bi...>]

You can also cross-check with standard InChI to see if this is an RDKit 
issue or a more general InChI issue. To convert InChI strings (and 
optionally AuxInfo) to SDF format with the standard inchi-1 executable, 
put the InChI string and AuxInfo into a text file and convert it like this.

P:\Projects\RInChI\INCHI-1-BIN__V1.06\windows\32bit>*type test.txt*
InChI=1/Ca.2H
AuxInfo=1/0/N:1;2;3/rA:3Ca0H0H0/rB:;;/rC:;;;

P:\Projects\RInChI\INCHI-1-BIN__V1.06\windows\32bit>*inchi-1.exe 
/InChI2Struct /OutputSDF test.txt*
InChI version 1, Software v. 1.06 (inchi-1 executable)
Windows 32-bit Build (MS VS 2015) of Dec 18 2020 20:45:14

Opened log file 'test.txt.log'
Opened input file 'test.txt'
Opened output file 'test.txt.txt'
Opened problem file 'test.txt.prb'
The command line used:
"inchi-1.exe /InChI2Struct /OutputSDF test.txt"
Converting InChI(s) to structure(s) in MOL format
Output SDfile only without stereochemical information and atom coordinates
Input format: InChI (plain identifier)
Output format: SDfile only (without stereochemical info and atom 
coordinates)
Timeout per structure: 60000 msec
Up to 1024 atoms per structure


Finished processing 1 structure: 0 errors, processing time 0:00:00.00

Elapsed walltime: 15 msec.

P:\Projects\RInChI\INCHI-1-BIN__V1.06\windows\32bit>type test.txt.txt
Structure #1.
   InChIV10

   3  0  0  0  0  0  0  0  0  0  1 V2000
     0.0000    0.0000    0.0000 Ca  0  0  0     0 15  0  0  0  0
     0.0000    0.0000    0.0000 H   0  0  0     0 15  0  0  0  0
     0.0000    0.0000    0.0000 H   0  0  0     0 15  0  0  0  0
M  END
$$$$

P:\Projects\RInChI\INCHI-1-BIN__V1.06\windows\32bit>

Cheers
-- Jan

On 2023-12-12 07:59, S Joshua Swamidass wrote:
> Perhaps provide some examples were this failure happens.
>
> Sent from Gmail Mobile
>
>
> On Tue, Nov 28, 2023 at 7:35 PM 李大舟 <lid...@sy...> wrote:
>
>     Dear RDKit Developers and Maintainers,
>
>     I hope this email finds you well. My name is Dr. Dazhou Li, and I
>     am a researcher working on the development of a tool for
>     extracting chemical compound structures recognized by OCR (Optical
>     Character Recognition) technology. I have been using the RDKit
>     library for a crucial step in this process, specifically the
>     rdkit.Chem.inchi.MolFromInchi() function, to convert InChI-format
>     strings into Mol format representations.
>
>     Firstly, I would like to express my gratitude for the excellent
>     work you have done in developing and maintaining the RDKit
>     library, which has been an invaluable resource in my research. The
>     library has consistently delivered high-quality results in various
>     aspects of chemical informatics, and I appreciate your dedication
>     to its development.
>
>     However, I have encountered a specific issue with the
>     rdkit.Chem.inchi.MolFromInchi() function that I hope you can help
>     me understand and resolve. When attempting to convert InChI-format
>     strings generated by my tool, some of them fail with an error
>     message reporting "NaN." Since the rdkit.Chem.inchi.MolFromInchi()
>     function calls C++ code, I am unable to directly inspect its
>     execution or source code to diagnose the issue.
>
>     My primary request is for assistance in understanding the internal
>     workings of the rdkit.Chem.inchi.MolFromInchi() function,
>     specifically the checking process or generation step that leads to
>     the "NaN" error when certain InChI-format strings are processed.
>     It is crucial for my research to determine at which point in the
>     execution of this function my generated InChI-formatted strings
>     are considered unreasonable, as this information will help me
>     refine my tool's output to be compatible with RDKit.
>
>     I understand that the RDKit library is a complex and comprehensive
>     toolkit, and I appreciate the complexity involved in diagnosing
>     such issues. However, any insights or guidance you can provide
>     regarding the problematic cases and the internal processes of the
>     rdkit.Chem.inchi.MolFromInchi() function would be immensely
>     valuable to me and would help me ensure the compatibility of my
>     tool with RDKit.
>
>     If possible, I would be grateful for access to relevant
>     documentation or insights into the specific error conditions that
>     may lead to the "NaN" result. Additionally, any suggestions or
>     best practices for generating InChI-format strings that are more
>     likely to be successfully processed by RDKit would be greatly
>     appreciated.
>
>     Thank you for your time and consideration. I look forward to your
>     response and hope that we can collaborate to resolve this issue
>     and enhance the compatibility of my tool with the RDKit library.
>
>     Please feel free to reach out to me if you require any additional
>     information or if there are specific details about my tool or the
>     InChI-format strings that would aid in diagnosing the issue.
>
>     Best regards,
>
>     Dr. Dazhou Li
>     Shenyang University of Chemical Technology
>     _______________________________________________
>     Rdkit-discuss mailing list
>     Rdk...@li...
>     https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>