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feat: use im-rdkit-utilities instead of local rdkit_utils.py #21

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Merged
tdudgeon merged 1 commit into from
Aug 5, 2026
Merged

feat: use im-rdkit-utilities instead of local rdkit_utils.py #21

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4 changes: 2 additions & 2 deletions Dockerfile-jaqpot
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@ RUN apt-get -y update &&\
apt-get -y install procps &&\
apt-get clean

RUN pip install im-data-manager-job-utilities==1.0.1
RUN pip install im-data-manager-job-utilities==1.0.1 im-rdkit-utilities==1.0.0

ENV HOME=/code
WORKDIR ${HOME}

COPY utils.py rdkit_utils.py jaqpot*.py ./
COPY utils.py jaqpot*.py ./
3 changes: 2 additions & 1 deletion Dockerfile-moldb
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Expand Up @@ -17,7 +17,8 @@ RUN apt-get update && apt-get install -y gcc libpq-dev &&\
RUN pip install sqlalchemy==1.4.49\
psycopg2-binary==2.9.6\
im-standardize-molecule==0.1.0\
im-data-manager-job-utilities==1.0.1
im-data-manager-job-utilities==1.0.1\
im-rdkit-utilities==1.0.0

COPY *.py site_substructures.smarts ./
COPY moldb/* ./moldb/
5 changes: 3 additions & 2 deletions Dockerfile-mordred
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Expand Up @@ -13,7 +13,8 @@ WORKDIR ${HOME}
# install our requirements. RDKit is present in base container
RUN pip install mordredcommunity==2.0.4 \
im-standardize-molecule==0.1.0 \
im-data-manager-job-utilities==1.1.1
im-data-manager-job-utilities==1.1.1 \
im-rdkit-utilities==1.0.0

COPY im_mordred/descriptor_generator.py ./im_mordred/
COPY utils.py rdkit_utils.py ./
COPY utils.py ./
1 change: 1 addition & 0 deletions Dockerfile-oddt
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Expand Up @@ -16,6 +16,7 @@ WORKDIR ${HOME}

RUN pip install wheel six &&\
pip install im-data-manager-job-utilities==1.1.1\
im-rdkit-utilities==1.0.0\
git+https://github.com/oddt/oddt.git@master

COPY *.py ./
1 change: 1 addition & 0 deletions Dockerfile-prep
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Expand Up @@ -20,6 +20,7 @@ RUN pip install scikit-learn==1.2.2\
pdb2pqr==3.6.1\
im-standardize-molecule==0.1.0\
im-data-manager-job-utilities==1.1.1\
im-rdkit-utilities==1.0.0\
sigfig==1.3.19

COPY *.py fpscores.pkl.gz site_substructures.smarts ./
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