230218818/alphafill repository overview

# yarn
wget https://dl.yarnpkg.com/debian/pubkey.gpg

# components.cif
curl -L https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz | gzip -cd > /path/to/components.cif

# libzeep
git clone https://github.com/mhekkel/libzeep.git
cd libzeep
git checkout v6.0.11
cd ..

# libcif++
git clone https://github.com/PDB-REDO/libcifpp.git
cd libcifpp
git checkout v6.0.0
cd ..

# libmcfp
git clone https://github.com/mhekkel/libmcfp.git
cd libmcfp
git checkout v1.2.4
cd ..

# libpqxx
git clone https://github.com/jtv/libpqxx.git
cd libpqxx
git checkout 7.7.5
cd ..

# alphafill
git clone https://github.com/PDB-REDO/alphafill.git
cd alphafill
git checkout v2.1.1
cd ..

FROM ubuntu:24.04

ENV DEBIAN_FRONTEND=noninteractive
#ENV CMAKE_BUILD_PARALLEL_LEVEL=24

RUN apt update \
&& apt install gnupg mrc cmake pkg-config libboost-all-dev libpq-dev clang libhowardhinnant-date-dev libeigen3-dev -y

COPY pubkey.gpg /etc/apt/
RUN cat /etc/apt/pubkey.gpg | apt-key add - \
&& echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources.list.d/yarn.list \
&& apt update \
&& apt install yarn git -y \
&& rm -rf /etc/apt/*

COPY libmcfp /libmcfp
RUN cd /libmcfp \
&& mkdir build \
&& cd build \
&& cmake .. \
&& cmake --build . \
&& cmake --install .

COPY libpqxx /libpqxx
RUN cd /libpqxx \
&& cmake . -DPostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql \
&& cmake --build . \
&& cmake --install .

COPY libzeep /libzeep
RUN cd /libzeep \
&& mkdir build \
&& cd build \
&& cmake .. -DZEEP_BUILD_TESTS=ON \
&& cmake --build . \
&& cmake --install .

COPY libcifpp /libcifpp
RUN cd /libcifpp \
&& mkdir build \
&& cd build \
&& cmake -DCMAKE_INSTALL_PREFIX=/usr/local .. \
&& cmake --build . --config Release \
&& cmake --install .

COPY alphafill /alphafill
RUN cd /alphafill \
&& yarn
RUN cd /alphafill \
&& mkdir build \
&& cd build \
&& cmake .. -DCMAKE_BUILD_TYPE=Release \
&& cmake --build . \
&& cmake --install .

docker run -d --rm -v /path/to/components.cif:/usr/local/share/libcifpp/components.cif -v /path/to/pdb-redo:/pdb-redo 230218818/alphafill:2.1.1 "cd /alphafill && touch alphafill.conf && build/alphafill ..."