odachi 1.0.1
Advanced deep learning-based organic retrosynthesis engine
License: MIT
Keywords: Chemistry,Organic Chemistry,Synthesis,Retrosynthesis,Deep Learning,AI,Graph,Convolution,Graph Convolution,CNN

# Odachi

Advanced deep learning-based organic retrosynthesis engine.

# Overview

The Odachi Retrosynthesis Engine provides a platform for predicting organic retrosynthetic disconnections
using a graph convolutional network. It also exposes two custom Tensorflow layers for performing spectral
graph convolutions. The engine powers the [retrosynthesis.com](retrosynthesis.com) website, which provides a clean and intuitive interface to run retrosynthetic predictions.

## Requirements

The Odachi Engine is built in Python 3. It has only three requirements to run:

    - TensorFlow 2.x
    - Scikit-Learn
    - Numpy

# Reference

## Installation

To download dgaintel, simply use Pypi via pip.
```sh
$ pip install odachi
```

Alternatively, you could install from source.
```sh
$ git clone https://github.com/sudo-rushil/odachi
$ cd odachi
$ python setup.py install
```

Verify your installation by running
```Python
>>> import odachi
>>> odachi.engine.model.Odachi()
'<odachi.engine.model.Odachi object at 0x7f9ec80b3bd0>''
```

# Examples

### Predict bond disconnection
This is simple way of finding a retrosynthetic disconnection in a molecule. The input to the model is the SMILES string of the molecule (Ex. Aspirin).

```Python
from odachi.engine.model import Odachi

odachi = Odachi() # instantiates engine and load up TensorFlow model in backend.

results = odachi('O=C(C)Oc1ccccc1C(=O)O') # call prediction function on an input molecule.
print(results)
```
> {'bonds': [2], 'smiles': 'O=C(C)Oc1ccccc1C(=O)O', 'svg':...}


# Documentation
The Odachi package exposes four main objects: the GraphConv and ConvEmbed TensorFlow layers for spectral graph convolutions with knockdown, the Conv object for representing molecules as graphs, and the Odachi object for top-level predictions.

## Layers

### GraphConv

```Python
graph_conv = odachi.engine.layers.GraphConv(n,
                                            num_feat = 41,
                                            num_atoms = 130,
                                            activation = tf.nn.elu,
                                            knockdown = 0.1,
                                            BATCH_SIZE = 1)
```
Layer for performing single-phase spectral graph convolutions. Inherits from `tensorflow.keras.layers.Layer` and has access to all associated methods.

#### Parameters

- n - Layer index for labeling purpose.
- num_feat - Number of features for each node in graph.
- num_atoms - Maximum number of nodes over all graphs.
- activation - Activation function for layer.
- knockdown - Convolutional knockdown threshold for spectral regularization.
- BATCH_SIZE - Number of batches in input

### Call

```Python
A, X = graph_conv([A, X])
```

#### Parameters

- A - Adjacency matrix of graph. Has dimensions (BATCH_SIZE, num_atoms, num_atoms).
- X - Features matrix of graph. Has dimensions (BATCH_SIZE, num_atoms, num_feat).

#### Returns

- A - Adjacency matrix of graph. Unchanged from input.
- X - Convolved features matrix of graph.

### ConvEmbed

```Python
conv_embed = odachi.engine.layers.ConvEmbed(num_feat = 41,
                                            num_atoms = 130,
                                            depth = 10,
                                            knock = 0.2,
                                            BATCH_SIZE = 1)
```
Model object for performing stacked graph convolutions with the number of features staying constant across layers. Inherits from `tensorflow.keras.Model`.

#### Parameters

- num_feat - Number of features for each node in graph.
- num_atoms - Maximum number of nodes over all graphs.
- depth - Number of stacked convolutional layers.
- knock - Convolutional knockdown threshold.
- BATCH_SIZE - Number of batches in input.

### Call

```Python
X = conv_embed([A, X])
```

#### Parameters

- A - Initial adjacency matrix of graph. Has dimensions (BATCH_SIZE, num_atoms, num_atoms).
- X - Initial features matrix of graph. Has dimensions (BATCH_SIZE, num_atoms, num_feat).

#### Returns

- X - Fully convolved features matrix of graph.

## Molecular Graph Representation

### Conv
```Python
conv = odachi.data.conv.Conv(smiles)
```
Convolutional molecule (Conv) object for storing and representing molecules as featurized graphs upon which graph convolutional methods can be applied.

#### Parameters

- smiles - SMILES string representing the molecule to be stored as a featurized graph.

#### Attributes

- smiles - SMILES string of the molecule stored in the object.
- num_atoms - Number of atoms in the stored molecule.
- num_feat - Number of features per each atom (default 41).
- adj_matrix - Adjacency matrix of molecular graph. Padded up to 130 nodes by default.
- atom_features - Features matrix of molecular graph. Padded up to 130 nodes by default.


## Engine

### Odachi

```Python
odachi = odachi.engine.models.Odachi(knock = 0.0)
```
Engine implementation that wraps all three phases of the retrosynthetic prediction process
to allow for predictions to be made and streamed to the [retrosynthesis.com](retrosynthesis.com) website.

#### Parameters

- knock - Convolutional knockdown threshold for loading saved models.

### Call

```Python
result_dict = odachi(smiles,
                     clusters = 2,
                     version = 9)
```

#### Parameters

- smiles - SMILES string of the query target molecule.
- clusters - number of synthons to cluster the target molecule into.
- version - Version edition of the convolutional embedding to use for prediction. Latest version is 9.

#### Returns

- result_dict - Dictionary containing prediction data.
    - smiles - Original smiles string of target molecule.
    - bonds - List of bonds which are predicted to be disconnected.
    - svg - Raw SVG for rendering the predicted retrosynthetic disconnection.
    - time - Total prediction runtime.