rdkit-discuss

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

[<lid...@sy...>]

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

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

[S J. S. <swa...@gm...>]

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
>

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
>