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amoreheadamorehead
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Replace Conda with Mamba, and add bibtex file
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‎README.md

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</div>
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## Citation
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```bibtex
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@misc{morehead2021dipsplus,
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title={DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction},
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author={Alex Morehead and Chen Chen and Ada Sedova and Jianlin Cheng},
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year={2021},
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eprint={2106.04362},
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archivePrefix={arXiv},
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primaryClass={q-bio.QM}
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}
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```
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## Versioning
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* Version 1.0.0: Initial release of DIPS-Plus and DB5-Plus (DOI: 10.5281/zenodo.4815267)
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## How to run creation tools
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First, install and configure Conda environment:
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First, download Mamba (if not already downloaded):
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```bash
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wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
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bash Mambaforge-$(uname)-$(uname -m).sh # Accept all terms and install to the default location
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rm Mambaforge-$(uname)-$(uname -m).sh # (Optionally) Remove installer after using it
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source ~/.bashrc # Alternatively, one can restart their shell session to achieve the same result
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```
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Then, create and configure Mamba environment:
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```bash
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# Clone project:
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git clone https://github.com/amorehead/DIPS-Plus
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# Change to project directory:
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cd DIPS-Plus
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# (If on HPC cluster) Download latest 64-bit Linux version of Miniconda and activate it:
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh # Specify install directory
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source miniconda/bin/activate # Assuming environment created above is called 'miniconda'
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# Create Conda environment using local 'environment.yml' file:
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conda env create --name DIPS-Plus -f environment.yml
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# Create Conda environment in a particular directory using local 'environment.yml' file:
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conda env create --prefix MY-VENV-DIR -f environment.yml
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# Activate Conda environment located in the current directory:
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conda activate DIPS-Plus
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mamba env create -f environment.yml
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conda activate DIPS-Plus # Note: One still needs to use `conda` to (de)activate environments
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# (Optional) Activate Conda environment located in another directory:
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conda activate MY-VENV-DIR
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# (Optional) Deactivate the currently-activated Conda environment:
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conda deactivate
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# Perform a full update on the Conda environment described in 'environment.yml':
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conda env update -f environment.yml --prune
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# (Optional) To remove this long prefix in your shell prompt, modify the env_prompt setting in your .condarc file with:
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conda config --set env_prompt '({name})'
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```
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(If on HPC cluster) Install all project dependencies:
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```bash
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# Install project as a pip dependency in the Conda environment currently activated:
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# Install local project as package:
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pip3 install -e .
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# Install external pip dependencies in the Conda environment currently activated:
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pip3 install -r requirements.txt
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```
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```
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## Default DIPS-Plus directory structure
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block in the Unpickler class' find_class() function
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(e.g. line 1577 of Python 3.8.5's pickle.py).
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## Citation
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If you find DIPS-Plus useful in your research, please cite:
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```bibtex
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@misc{morehead2021dipsplus,
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title={DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction},
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author={Alex Morehead and Chen Chen and Ada Sedova and Jianlin Cheng},
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year={2021},
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eprint={2106.04362},
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archivePrefix={arXiv},
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primaryClass={q-bio.QM}
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}
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```

‎citation.bib

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@misc{morehead2021dipsplus,
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title={DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction},
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author={Alex Morehead and Chen Chen and Ada Sedova and Jianlin Cheng},
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year={2021},
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eprint={2106.04362},
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archivePrefix={arXiv},
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primaryClass={q-bio.QM}
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}

‎environment.yml

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name: DIPS-Plus
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channels:
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- defaults
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- anaconda
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- conda-forge
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- bioconda
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- pytorch
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- salilab
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- dglteam
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- dglteam/label/cu116
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- nvidia
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- defaults
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- conda-forge
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dependencies:
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- python=3.8
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- pip
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- scipy
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- pandas
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- scikit-learn
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# - After creating initial Conda environment, uncomment and run the following if not already installed on your machine
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# - biopython=1.78 # For PDB parsing
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# - hhsuite=3.3.0 # For generating sequence profile HMMs
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# - msms=2.6.1 # For computing residue depths
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# - dssp=3.0.0 # For computing secondary structures
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# - pytorch # Install with 'conda install pytorch -c pytorch -c conda-forge'
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# - dgl-cudaXX.X # Replace XX.X with the version of cudatoolkit installed by 'conda install pytorch -c pytorch -c conda-forge' directly above
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- _libgcc_mutex=0.1=conda_forge
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- _openmp_mutex=4.5=2_kmp_llvm
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- appdirs=1.4.4=pyhd3eb1b0_0
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- biopython=1.78=py38h7f8727e_0
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- blas=1.0=openblas
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- bottleneck=1.3.5=py38h7deecbd_0
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- brotlipy=0.7.0=py38h27cfd23_1003
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- bzip2=1.0.8=h7b6447c_0
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- ca-certificates=2023.5.7=hbcca054_0
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- certifi=2023.5.7=py38h06a4308_0
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- cffi=1.15.1=py38h5eee18b_3
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- charset-normalizer=2.0.4=pyhd3eb1b0_0
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- colorama=0.4.6=pyhd8ed1ab_0
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- cryptography=40.0.2=py38h3d167d9_0
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- cuda=11.6.1=0
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- cuda-cccl=11.6.55=hf6102b2_0
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- cuda-command-line-tools=11.6.2=0
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- cuda-compiler=11.6.2=0
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- cuda-cudart=11.6.55=he381448_0
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- cuda-cudart-dev=11.6.55=h42ad0f4_0
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- cuda-cuobjdump=11.6.124=h2eeebcb_0
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- cuda-cupti=11.6.124=h86345e5_0
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- cuda-cuxxfilt=11.6.124=hecbf4f6_0
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- cuda-driver-dev=11.6.55=0
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- cuda-gdb=12.1.105=0
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- cuda-libraries=11.6.1=0
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- cuda-libraries-dev=11.6.1=0
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- cuda-memcheck=11.8.86=0
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- cuda-nsight=12.1.105=0
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- cuda-nsight-compute=12.1.1=0
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- cuda-nvcc=11.6.124=hbba6d2d_0
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- cuda-nvdisasm=12.1.105=0
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- cuda-nvml-dev=11.6.55=haa9ef22_0
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- cuda-nvprof=12.1.105=0
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- cuda-nvprune=11.6.124=he22ec0a_0
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- cuda-nvrtc=11.6.124=h020bade_0
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- cuda-nvrtc-dev=11.6.124=h249d397_0
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- cuda-nvtx=11.6.124=h0630a44_0
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- cuda-nvvp=12.1.105=0
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- cuda-runtime=11.6.1=0
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- cuda-samples=11.6.101=h8efea70_0
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- cuda-sanitizer-api=12.1.105=0
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- cuda-toolkit=11.6.1=0
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- cuda-tools=11.6.1=0
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- cuda-version=11.7=h67201e3_2
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- cuda-visual-tools=11.6.1=0
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- cudatoolkit=11.7.0=hd8887f6_10
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- cudnn=8.8.0.121=h0800d71_0
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- dgl=1.1.0.cu116=py38_0
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- dssp=3.0.0=h3fd9d12_4
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- ffmpeg=4.3=hf484d3e_0
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- freetype=2.12.1=hca18f0e_1
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- gds-tools=1.6.1.9=0
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- gmp=6.2.1=h58526e2_0
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- gnutls=3.6.13=h85f3911_1
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- hhsuite=3.3.0=py38pl5321hcbe9525_8
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- icu=58.2=he6710b0_3
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- idna=3.4=py38h06a4308_0
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- joblib=1.1.1=py38h06a4308_0
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- jpeg=9e=h0b41bf4_3
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- lame=3.100=h166bdaf_1003
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- lcms2=2.15=hfd0df8a_0
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- ld_impl_linux-64=2.38=h1181459_1
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- lerc=4.0.0=h27087fc_0
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- libblas=3.9.0=16_linux64_openblas
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- libboost=1.73.0=h28710b8_12
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- libcblas=3.9.0=16_linux64_openblas
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- libcublas=11.9.2.110=h5e84587_0
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- libcublas-dev=11.9.2.110=h5c901ab_0
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- libcufft=10.7.1.112=hf425ae0_0
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- libcufft-dev=10.7.1.112=ha5ce4c0_0
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- libcufile=1.6.1.9=0
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- libcufile-dev=1.6.1.9=0
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- libcurand=10.3.2.106=0
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- libcurand-dev=10.3.2.106=0
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- libcusolver=11.3.4.124=h33c3c4e_0
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- libcusparse=11.7.2.124=h7538f96_0
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- libcusparse-dev=11.7.2.124=hbbe9722_0
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- libdeflate=1.17=h0b41bf4_0
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- libffi=3.4.4=h6a678d5_0
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- libgcc-ng=12.2.0=h65d4601_19
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- libgfortran-ng=11.2.0=h00389a5_1
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- libgfortran5=11.2.0=h1234567_1
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- libgomp=12.2.0=h65d4601_19
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- libiconv=1.17=h166bdaf_0
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- liblapack=3.9.0=16_linux64_openblas
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- libnpp=11.6.3.124=hd2722f0_0
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- libnpp-dev=11.6.3.124=h3c42840_0
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- libnsl=2.0.0=h5eee18b_0
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- libnvjpeg=11.6.2.124=hd473ad6_0
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- libnvjpeg-dev=11.6.2.124=hb5906b9_0
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- libopenblas=0.3.21=h043d6bf_0
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- libpng=1.6.39=h753d276_0
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- libprotobuf=3.21.12=h3eb15da_0
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- libsqlite=3.42.0=h2797004_0
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- libstdcxx-ng=12.2.0=h46fd767_19
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- libtiff=4.5.0=h6adf6a1_2
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- libuuid=2.38.1=h0b41bf4_0
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- libwebp-base=1.3.0=h0b41bf4_0
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- libxcb=1.13=h7f98852_1004
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- libzlib=1.2.13=h166bdaf_4
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- llvm-openmp=16.0.4=h4dfa4b3_0
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- lz4-c=1.9.4=h6a678d5_0
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- magma=2.6.2=hc72dce7_0
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- mkl=2022.2.1=h84fe81f_16997
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- msms=2.6.1=h516909a_0
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- nccl=2.15.5.1=h0800d71_0
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- ncurses=6.4=h6a678d5_0
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- nettle=3.6=he412f7d_0
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- networkx=3.1=pyhd8ed1ab_0
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- ninja=1.11.1=h924138e_0
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- nsight-compute=2023.1.1.4=0
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- numexpr=2.8.4=py38hd2a5715_1
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- numpy=1.24.3=py38hf838250_0
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- numpy-base=1.24.3=py38h1e6e340_0
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- openh264=2.1.1=h780b84a_0
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- openjpeg=2.5.0=hfec8fc6_2
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- openssl=3.1.0=hd590300_3
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- packaging=23.0=py38h06a4308_0
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- pandas=1.5.3=py38h417a72b_0
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- perl=5.32.1=0_h5eee18b_perl5
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- pillow=9.4.0=py38hde6dc18_1
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- pip=23.0.1=py38h06a4308_0
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- pooch=1.4.0=pyhd3eb1b0_0
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- psutil=5.9.5=py38h1de0b5d_0
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- pthread-stubs=0.4=h36c2ea0_1001
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- pycparser=2.21=pyhd3eb1b0_0
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- pyopenssl=23.1.1=pyhd8ed1ab_0
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- pysocks=1.7.1=py38h06a4308_0
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- python=3.8.16=he550d4f_1_cpython
141+
- python-dateutil=2.8.2=pyhd3eb1b0_0
142+
- python_abi=3.8=2_cp38
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- pytorch=1.13.1=cuda112py38hd94e077_200
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- pytorch-cuda=11.6=h867d48c_1
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- pytorch-mutex=1.0=cuda
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- pytz=2022.7=py38h06a4308_0
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- readline=8.2=h5eee18b_0
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- requests=2.29.0=py38h06a4308_0
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- scikit-learn=1.2.2=py38h6a678d5_0
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- scipy=1.10.1=py38h32ae08f_1
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- six=1.16.0=pyhd3eb1b0_1
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- sleef=3.5.1=h9b69904_2
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- sqlite=3.41.2=h5eee18b_0
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- tbb=2021.7.0=h924138e_0
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- threadpoolctl=2.2.0=pyh0d69192_0
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- tk=8.6.12=h1ccaba5_0
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- torchaudio=0.13.1=py38_cu116
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- torchvision=0.14.1=py38_cu116
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- typing_extensions=4.6.0=pyha770c72_0
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- urllib3=1.26.15=py38h06a4308_0
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- wheel=0.38.4=py38h06a4308_0
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- xorg-libxau=1.0.11=hd590300_0
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- xorg-libxdmcp=1.1.3=h7f98852_0
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- xz=5.4.2=h5eee18b_0
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- zlib=1.2.13=h166bdaf_4
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- zstd=1.5.5=hc292b87_0
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- pip:
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- -e .
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- -r requirements.txt
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- alabaster==0.7.13
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- atom3-py3==0.1.9.9
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- babel==2.12.1
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- click==7.0
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- dill==0.3.3
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- docutils==0.17.1
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- easy-parallel-py3==0.1.6.4
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- h5py==3.8.0
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- imagesize==1.4.1
177+
- jinja2==2.11.3
178+
- markupsafe==1.1.1
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- multiprocess==0.70.11.1
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- pathos==0.2.7
181+
- pox==0.3.2
182+
- ppft==1.7.6.6
183+
- pygments==2.15.1
184+
- setuptools==56.2.0
185+
- snowballstemmer==2.2.0
186+
- sphinx==4.0.1
187+
- sphinxcontrib-applehelp==1.0.4
188+
- sphinxcontrib-devhelp==1.0.2
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- sphinxcontrib-htmlhelp==2.0.1
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- sphinxcontrib-jsmath==1.0.1
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- sphinxcontrib-qthelp==1.0.3
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- sphinxcontrib-serializinghtml==1.1.5
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- tqdm==4.49.0

‎requirements.txt

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