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.
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On Tue, Nov 28, 2023 at 7:35 PM 李大舟 <lidaz...@syuct.edu.cn> 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
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