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
- Run
bash setup_env.sh
to install the required packages - Add the variable
floatX = float32
in your~/.theanorc
config file under the[global]
section.
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