The outcome of my local run appears to be incorrect

[Maoyufeiif]

Hello,
I have successfully run NPClassifier on the local server. However, for the same SMILES input, the output pathway results are different from those on the web page. Also, the "superclass" and "class" results are not outputted. After comparing the source code, I haven't found any issues. I would like to ask, from which aspects should I start to conduct further checks?
Thank you very much.

[mseok]

Dear @mwang87,

I'm trying to use NP classifier for my experiment results, and I also met this issue.
Since NP classifier keeps updating its version, the version of the model and index files is necessary for reproducibility.

Specifically, when I query the website for the smiles "CCCCCC(=O)NC@HC(C)C" to the website, I get "class_results": ["Linear peptides"], "superclass_results": ["Oligopeptides"], "pathway_results": ["Amino acids and Peptides"].
But with np classifier version 1.6, I get "class_results": [""], "superclass_results": [""], "pathway_results": ["Alkaloids"].
Please inform us about the discrepancy between local and remote and the version of the remote website.

I think this issue also seems to be related to #59

Thank you.

[mwang87]

Interesting, might be good to ask hyunwoo. What i can do is make sure ethe model we're using is uploaded publicly to make it a bit more consistent. Can you remind me when the quarter is finished or come to my office hours, happy to upload it then.

[robin1509]

Hello,
I'm also trying to use the offline version of NPClassifier described here and meet the same issue: the output is totally inconsistent with the one provided online. Do you have any news regarding the resolution of this issue ?

Thanks for your help!!

[Maoyufeiif]

Hi,

Hope you're having a great week! Just a gentle reminder about the public model upload we discussed earlier. As this is currently preventing my local environment from functioning properly, I’d be immensely grateful if the model could be shared when possible.

Thank you so much for your attention to this matter!

Best regards

[mwang87]

Thanks for reaching out, this will be a question for Hyunwoo.

[robin1509]

@mwang87 do you have any update on the resolution of this issue ? Would be super happy to be able to use this tool on my local environment !!

Thanks in advance for your help,

[mwang87]

Can you swing by my office hours, we can see what needs to be done there. Thanks!

…

On Wed, Sep 17, 2025 at 4:50 AM Robin Huber ***@***.***> wrote: *robin1509* left a comment (mwang87/NP-Classifier#63) <#63 (comment)> @mwang87 <https://github.com/mwang87> do you have any update on the resolution of this issue ? Would be super happy to be able to use this tool on my local environment !! Thanks in advance for your help, — Reply to this email directly, view it on GitHub <#63 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXSEDHB6HGHWDI6ZFBIPL3TFDJBAVCNFSM6AAAAABUG3T4YCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTGMBSGYZDMNJQGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[volvox292]

You need to concat "\n" to the SMILES when sending the request. This fixes the issue for the not working SMILES below.

COC1=CC(=CC(=C1O)OC)C=O
COc1c2ccoc2nc2c(OC)c(OCC(O)C(C)(C)O)ccc12
O=C1c2ccccc2-c2c3c(cc4ccnc1c24)OCO3

Furthermore, changing the rdkit version when attempting the rebuild will also lead to wrong results. I think a possible starting point for a new build that works would be the dockerfile below:

this contains the right rdkit 2019.09.3.0 version + python 3.8 already prebuilt I have tested it using this container as a subprocess to generate the fingerprints

FROM brsynth/rdkit:debian

Fix broken APT sources for Debian Buster

RUN sed -i 's|http://deb.debian.org/debian|http://archive.debian.org/debian|g' /etc/apt/sources.list &&
sed -i 's|http://security.debian.org/debian-security|http://archive.debian.org/debian-security|g' /etc/apt/sources.list &&
apt-get update &&
apt-get install -y build-essential libarchive-dev wget vim &&
rm -rf /var/lib/apt/lists/*

COPY requirements.txt .

RUN /bin/bash -c "pip install -r requirements.txt"

COPY . /app

WORKDIR /app