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# The base image we are going to use.
FROM nvcr.io/nvidia/pytorch:19.10-py3
#Do some basic preparations
RUN conda install -c anaconda joblib -y
RUN pip install ipython jupyter jupyter-tensorboard --upgrade && \
jupyter tensorboard enable --system
#RUN pip install packages
RUN conda install -c conda-forge rdkit=2019.09.1 -y && \
pip install \
cupy-cuda101 \
torch==1.4.0 \
torch-scatter==2.0.4 -f https://pytorch-geometric.com/whl/torch-1.4.0+cu101.html \
torch-sparse==0.6.1 -f https://pytorch-geometric.com/whl/torch-1.4.0+cu101.html \
torch-cluster==1.5.3 -f https://pytorch-geometric.com/whl/torch-1.4.0+cu101.html \
torch-spline-conv==1.2.0 -f https://pytorch-geometric.com/whl/torch-1.4.0+cu101.html \
torch_geometric==1.4.3 \
numpy==1.16.6 \
plyfile==0.7.2 \
pandas==0.25.1 \
networkx==2.5 \
scikit_learn==0.21.3 \
matplotlib \
transformers==4.2.2 \
trimesh==3.6.5 \
Biopython \
py3Dmol
WORKDIR /
RUN wget --no-check-certificate https://github.com/PyMesh/PyMesh/releases/download/v0.2.0/pymesh2-0.2.0-cp36-cp36m-linux_x86_64.whl && \
pip install pymesh2-0.2.0-cp36-cp36m-linux_x86_64.whl && \
git clone https://github.com/shenwanxiang/ChemBench.git && \
cd ChemBench && \
pip install -e .
# Install APBS, PDB2PQR and MSMSto calculate target mesh with MaSIF
# install necessary dependencies
RUN apt-get update && \
apt-get install -y wget git unzip cmake vim libgl1-mesa-glx
# DOWNLOAD/INSTALL APBS
RUN mkdir /install
WORKDIR /install
RUN git clone https://github.com/Electrostatics/apbs-pdb2pqr && \
git clone https://github.com/swig/swig.git
WORKDIR /install/swig
RUN git checkout tags/v4.0.2 && \
apt-get install -y automake && \
./autogen.sh && \
./configure && \
apt-get install -y bison flex && \
make && \
make install
WORKDIR /install/apbs-pdb2pqr
RUN git checkout b3bfeec && \
git submodule update --init --recursive && \
cmake -DGET_MSMS=ON apbs && \
make && \
make install && \
cp -r /install/apbs-pdb2pqr/apbs/externals/mesh_routines/msms/msms_i86_64Linux2_2.6.1 /root/msms/ && \
curl https://bootstrap.pypa.io/pip/3.6/get-pip.py -o get-pip.py && \
python get-pip.py
# INSTALL PDB2PQR
WORKDIR /install/apbs-pdb2pqr/pdb2pqr
RUN apt-get -y install python-dev python3-dev && \
python2.7 scons/scons.py install PREFIX="/usr/local/bin/pdb2pqr"
# Setup environment variables
ENV MSMS_BIN /usr/local/bin/msms
ENV APBS_BIN /usr/local/bin/apbs
ENV MULTIVALUE_BIN /usr/local/share/apbs/tools/bin/multivalue
ENV PDB2PQR_BIN /usr/local/bin/pdb2pqr/pdb2pqr.py
# DOWNLOAD reduce (for protonation)
WORKDIR /install
RUN git clone https://github.com/rlabduke/reduce.git && \
cd reduce && \
git checkout b3aac6e && \
make && \
apt-get install sudo -y && \
sudo make install
# Clone deepdock and install
WORKDIR /
RUN git clone https://github.com/OptiMaL-PSE-Lab/DeepDock.git && \
cd DeepDock && \
git checkout v1.0.0 && \
git submodule update --init --recursive && \
pip install -e . && \
cd data && \
wget https://ndownloader.figshare.com/files/27800817 -O dataset_CASF-2016_285.tar
# create a conda environment to run python2.7
RUN conda create -y -n python2_env \
python=2.7 \
numpy \
pandas \
scipy \
scikit-learn \
jinja2 && \
conda init bash