Learning structural motif representations for efficient protein structure search
- Download the pretrained model from https://drive.google.com/open?id=0B8bKX4poTFVta0d6QmswR3dOcms and put it under ./models
bash setup_env.shto install the required packages
- Add the variable
floatX = float32in your
~/.theanorcconfig file under the
The script provides an example of generating an embedding for a single PDB file. PDB file of any length can be used but for maximum efficiency make sure the model size can be fit in the VRAM. The script is not efficient for generating a large number of embeddings due to the overhead. For batch processing, please call the get_embedding function of a DeepFold instance inside the network module.
python ./scripts/gen_embedding.py [-h] [--model model] pdb_file output_file Create embeddings for a protein structure. Output a numpy embedding. positional arguments: pdb_file an input pdb file output_file an output numpy embedding optional arguments: -h, --help show this help message and exit --model model the network model to load