Physicochemical descriptors available from RDKIT

A set of 200 physicochemical descriptors available from the RDKIT, including molecular weight, solubility and druggability parameters. We have used the DescriptaStorus selection of RDKit descriptors for simplicity.

This model was incorporated on 2021-09-17.

Information

Identifiers

• Ersilia Identifier: eos8a4x
• Slug: rdkit-descriptors

Domain

• Task: Representation
• Subtask: Featurization
• Biomedical Area: Any
• Target Organism: Not Applicable
• Tags: Descriptor

Input

• Input: Compound
• Input Dimension: 1

Output

• Output Dimension: 200
• Output Consistency: Fixed
• Interpretation: Vector representation of small molecules

Below are the Output Columns of the model:

Name	Type	Direction	Description
balabanj	float	high	Balaban index is a topological descriptor that quantifies molecular complexity based on the graph theory
bertzct	float	high	Bertz complexity index is a topological descriptor that measures molecular complexity based on atom and bond types
chi0	float	high	Valence connectivity index of order 0 indicating molecular branching and shape
chi0n	float	high	Valence connectivity index of order 0 for non-hydrogen atoms
chi0v	float	high	Valence connectivity index of order 0 using atomic valence
chi1	float	high	Valence connectivity index of order 1 representing connections between atoms in the molecule
chi1n	float	high	Valence connectivity index of order 1 for heavy atoms only
chi1v	float	high	Valence connectivity index of order 1 using atomic valences
chi2n	float	high	Valence connectivity index of order 2 for heavy atoms in the molecule
chi2v	float	high	Valence connectivity index of order 2 based on valence structure

10 of 200 columns are shown

Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos8a4x
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos8a4x.zip

Resource Consumption

• Model Size (Mb): 1
• Environment Size (Mb): 497
• Image Size (Mb): 413.97

Computational Performance (seconds):

• One input: 30
• Ten inputs: 20.11
• Hundred inputs: 20.9

References

• Source Code: https://github.com/rdkit/rdkit
• Publication: https://www.rdkit.org/docs/RDKit_Book.html
• Publication Type: Other
• Publication Year: 2010
• Ersilia Contributor: miquelduranfrigola

License

This package is licensed under a GPL-3.0 license. The model contained within this package is licensed under a BSD-3-Clause 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 eos8a4x

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

# serve the model
ersilia serve eos8a4x
# 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

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