ersiliaos/eos2hzy repository overview

⁠PubChem Molecular Sampler

A simple sampler of the PubChem database using their API. It looks for similar molecules (similarity 0.7) to the input molecule and returns a list of maximum 100 molecules by default. This model has been developed by Ersilia and posts queries to an online server.

This model was incorporated on 2023-08-10.Last packaged on 2026-09-14.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos2hzy
• Slug: pubchem-sampler

⁠Domain

• Task: Sampling
• Subtask: Similarity search
• Biomedical Area: Any
• Target Organism: Any
• Tags: Similarity

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 100
• Output Consistency: Fixed
• Interpretation: Up to 100 nearest molecules in PubChem (similarity >0.7)

Below are the Output Columns of the model:

10 of 100 columns are shown

⁠Source and Deployment

• Source: Online
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos2hzy⁠
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos2hzy.zip⁠

⁠Resource Consumption

• Model Size (Mb): 1
• Environment Size (Mb): 446
• Image Size (Mb): 492.53

Computational Performance (seconds):

• 10 inputs: 33.85
• 100 inputs: 463.3
• 10000 inputs: -1

⁠References

• Source Code: https://github.com/ersilia-os/chem-sampler⁠
• Publication: https://doi.org/10.1093/nar/gkac956⁠
• Publication Type: Peer reviewed
• Publication Year: 2023
• Ersilia Contributor: GemmaTuron⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a GPL-3.0-or-later⁠ license.

Notice: Ersilia grants access to models as is, directly from the original authors, please refer to the original code repository and/or publication if you use the model in your research.

⁠Use

To use this model locally, you need to have the Ersilia CLI⁠ installed. The model can be fetched using the following command:

# fetch model from the Ersilia Model Hub
ersilia fetch eos2hzy

Then, you can serve, run and close the model as follows:

# serve the model
ersilia serve eos2hzy
# generate an example file
ersilia example -n 3 -f my_input.csv
# run the model
ersilia run -i my_input.csv -o my_output.csv
# close the model
ersilia close

⁠About Ersilia

The Ersilia Open Source Initiative⁠ is a tech non-profit organization fueling sustainable research in the Global South. Please cite⁠ the Ersilia Model Hub if you've found this model to be useful. Always let us know⁠ if you experience any issues while trying to run it. If you want to contribute to our mission, consider donating⁠ to Ersilia!