metfish

Code for the MetFish LDRD project

Installation

The following commands will install the code in this repository in such a way that will allow one to use the tools provided by said code. With that said, the provided sequence of commands may not suit your specific needs. As this repository follows PEP 517 style packaging, there are many ways to install the software, so please use discretion and adapt as necessary.

git clone [email protected]:lbl-cbg/metfish.git
cd metfish
pip install -r requirements.txt
pip install .

Training the model

Training the modified OpenFold model requires some additional dependencies and constraints. Please follow these instructions to setup a conda environment for model training and evaluation. Note the OpenFold installation requires CUDA 11.

conda create -n metfish python=3.9
conda activate metfish
pip install torch==1.12.1+cu113 -f https://download.pytorch.org/whl/torch_stable.html  # install separately to specify with findlinks
pip install .[training,viz]

To install additional resources required by OpenFold, run this command and copy to the openfold/resources folder:

wget -N --no-check-certificate -P openfold/resources \
    https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt

To run training, use the following command, which provides several additional flags:

python train.py path/to/data path/to/output

Commands

• calc-pr: Calculate P(r) for models from a PDB or mmCIF file
• extract-seq: Extract Sequence from a PDB file.
• generate-nma-conformers: Generate conformations from normal mode analysis