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README.md
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pip install chemical-converters
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```
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### SMILES to IUPAC
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You can choose pretrained model from table in the section "Models",
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but we recommend to use model "smiles2iupac-canonical-base".
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#### ! Preferred IUPAC style
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To choose the preferred IUPAC style, place style tokens before
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your SMILES sequence.
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#### To perform simple translation, follow the example:
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```python
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from chemicalconverters import NamesConverter
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converter = NamesConverter(model_name="smiles2iupac-canonical-
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print(converter.smiles_to_iupac('CCO'))
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print(converter.smiles_to_iupac(['<SYST>CCO', '<TRAD>CCO', '<BASE>CCO']))
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```
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#### Processing in batches:
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```python
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from chemicalconverters import NamesConverter
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converter = NamesConverter(model_name="smiles2iupac-canonical-
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print(converter.smiles_to_iupac(["<BASE>C=CC=C" for _ in range(10)], num_beams=1,
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process_in_batch=True, batch_size=1000))
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```
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and calculating Tanimoto similarity of two molecules fingerprints.
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````python
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from chemicalconverters import NamesConverter
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converter = NamesConverter(model_name="smiles2iupac-canonical-
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print(converter.smiles_to_iupac('CCO', validate=True))
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````
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````text
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['ethanol'] 1.0
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````
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The larger is Tanimoto similarity, the
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You can also process validation manually:
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```python
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```text
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1.0
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```
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!Note validation was not implemented in processing in batches.
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### IUPAC to SMILES
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You can choose pretrained model from table in the section "Models",
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but we recommend to use model "iupac2smiles-canonical-base".
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#### To perform simple translation, follow the example:
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```python
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from chemicalconverters import NamesConverter
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converter = NamesConverter(model_name="iupac2smiles-canonical-base")
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print(converter.smiles_to_iupac('ethanol'))
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print(converter.smiles_to_iupac(['ethanol', 'ethanol', 'ethanol']))
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```
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```text
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['CCO']
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['CCO', 'CCO', 'CCO']
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```
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#### Processing in batches:
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```python
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from chemicalconverters import NamesConverter
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converter = NamesConverter(model_name="smiles2iupac-canonical-base")
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print(converter.smiles_to_iupac(["buta-1,3-diene" for _ in range(10)], num_beams=1,
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process_in_batch=True, batch_size=1000))
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```
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```text
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['<SYST>C=CC=C', '<SYST>C=CC=C'...]
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```
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Our models also predict IUPAC styles from the table:
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| Style Token | Description |
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|-------------|----------------------------------------------------------------------------------------------------|
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| `<BASE>` | The most known name of the substance, sometimes is the mixture of traditional and systematic style |
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| `<SYST>` | The totally systematic style without trivial names |
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| `<TRAD>` | The style is based on trivial names of the parts of substances |
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## Bias, Risks, and Limitations
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[More Information Needed]
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### Recommendations
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<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
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Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.
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## How to Get Started with the Model
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Use the code below to get started with the model.
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[More Information Needed]
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## Training Details
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### Training Data
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<!-- This should link to a Dataset Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->
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[More Information Needed]
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### Training Procedure
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<!-- This
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#### Preprocessing [optional]
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[More Information Needed]
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#### Training Hyperparameters
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- **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision -->
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#### Speeds, Sizes, Times [optional]
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<!-- This section provides information about throughput, start/end time, checkpoint size if relevant, etc. -->
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## Evaluation
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#### Summary
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## Model Examination [optional]
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<!-- Relevant interpretability work for the model goes here -->
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[More Information Needed]
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## Environmental Impact
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<!-- Total emissions (in grams of CO2eq) and additional considerations, such as electricity usage, go here. Edit the suggested text below accordingly -->
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Carbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).
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- **Hardware Type:** [More Information Needed]
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- **Hours used:** [More Information Needed]
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- **Cloud Provider:** [More Information Needed]
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- **Compute Region:** [More Information Needed]
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- **Carbon Emitted:** [More Information Needed]
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## Technical Specifications [optional]
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### Model Architecture and Objective
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[More Information Needed]
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### Compute Infrastructure
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[More Information Needed]
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#### Hardware
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[More Information Needed]
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#### Software
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[More Information Needed]
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## Citation [optional]
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<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->
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pip install chemical-converters
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```
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### SMILES to IUPAC
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#### ! Preferred IUPAC style
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To choose the preferred IUPAC style, place style tokens before
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your SMILES sequence.
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#### To perform simple translation, follow the example:
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```python
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from chemicalconverters import NamesConverter
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converter = NamesConverter(model_name="smiles2iupac-canonical-small")
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print(converter.smiles_to_iupac('CCO'))
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print(converter.smiles_to_iupac(['<SYST>CCO', '<TRAD>CCO', '<BASE>CCO']))
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```
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#### Processing in batches:
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```python
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from chemicalconverters import NamesConverter
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converter = NamesConverter(model_name="smiles2iupac-canonical-small")
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print(converter.smiles_to_iupac(["<BASE>C=CC=C" for _ in range(10)], num_beams=1,
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process_in_batch=True, batch_size=1000))
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```
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and calculating Tanimoto similarity of two molecules fingerprints.
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````python
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from chemicalconverters import NamesConverter
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converter = NamesConverter(model_name="smiles2iupac-canonical-small")
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print(converter.smiles_to_iupac('CCO', validate=True))
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````
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````text
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['ethanol'] 1.0
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````
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The larger is Tanimoto similarity, the larger is probability, that the prediction was correct.
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You can also process validation manually:
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```python
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```text
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1.0
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```
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## Bias, Risks, and Limitations
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This model has limited accuracy in processing large molecules and currently, doesn't support isomeric and isotopic SMILES.
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### Training Procedure
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<!-- This should link to a Dataset Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->
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The model was trained on 100M examples of SMILES-IUPAC pairs with lr=0.0003, batch_size=1024 for 2 epochs.
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## Evaluation
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#### Summary
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## Model Examination [optional]
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<!-- Relevant interpretability work for the model goes here -->
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[More Information Needed]
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## Citation [optional]
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<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->
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