craft-mol 1.5

CRAFT: Consistent Representational Fusion of Three Molecular Modalities.

CRAFT

CRAFT: Consistent Representational Fusion of Three Molecular Modalities

1. Environment Setup

1.1. Install Conda

wget https://repo.anaconda.com/archive/Anaconda3-2023.09-0-Linux-x86_64.sh
chmod +x Anaconda3-2023.09-0-Linux-x86_64.sh
source ~/.bashrc

1.2. Create Conda Environment

conda create -n craft python=3.10.13
conda activate craft
conda install -c conda-forge rdkit

1.3. Install Dependencies

clone the repository

git clone https://github.com/hukunhukun/CRAFT.git
cd CRAFT

pip install -r requirements.txt 

or

pip install -e .

1.4. Import the CRAFT package

pip install craft_mol

2. Model weights

Download the model weights from the huggingface and place them in the weights directory.

git lfs install
git clone https://huggingface.co/kunkunhu/craft_mol

3. Usage

Get molecular representations from three molecular modalities (SELFIES, Molecular Graph and IUPAC names)

from craft_mol.batch_feature import BatchFeature

model_path = './craft_mol/1m_checkpoint_09.pth'
config_path = './craft_mol/inference.yaml'
batch_feature = BatchFeature(model_path=model_path,config_path=config_path)

smiles = "CC(C)CC1=CC=C(C=C1)C(=O)O"
iupac_name = "4-(2-methylpropyl)benzoic acid"

mol_feature = batch_feature.get_feature_single(smiles=smiles, iupac_name=iupac_name)
print(mol_feature.shape)