From 7edd5e7f59c18a69738269f0314784ee794e807a Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Wed, 19 Mar 2025 20:26:15 +0100
Subject: [PATCH 01/17] adding github actions

---
 .github/workflows/python-app.yml | 44 ++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 .github/workflows/python-app.yml

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
new file mode 100644
index 0000000..1540006
--- /dev/null
+++ b/.github/workflows/python-app.yml
@@ -0,0 +1,44 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches:
+      - main
+      - '**'
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest] #, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniconda-version: "latest"
+        channels: bioconda, conda-forge, defaults
+        use-only-tar-bz2: true
+        auto-update-conda: true
+        auto-activate-base: true
+    - name: Install dependencies
+      run: |
+        conda create -n test_env --file ./requirements_conda.txt      
+        conda activate test_env
+        pip install -r ./requirements_pip.txt
+    - name: Test
+      run: |
+        conda activate test_env
+        cd example
+        python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
+        python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth
+        python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -ac -m ../trained_models/rtmscore_model1.pth
+        python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -rc -m ../trained_models/rtmscore_model1.pth

From b6e48ff3aff40cfe9576b7c0149c080f8621d164 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 14:18:57 +0100
Subject: [PATCH 02/17] new reqs

---
 .github/workflows/python-app.yml |   5 +-
 requirements_conda.txt           | 330 ++-----------------------------
 requirements_pip.txt             | 208 +------------------
 3 files changed, 19 insertions(+), 524 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 1540006..5b04bad 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -31,8 +31,9 @@ jobs:
         auto-activate-base: true
     - name: Install dependencies
       run: |
-        conda create -n test_env --file ./requirements_conda.txt      
-        conda activate test_env
+        conda create -n test_env python=3.8
+	conda activate test_env
+	conda install --file=requirements_conda.txt   
         pip install -r ./requirements_pip.txt
     - name: Test
       run: |
diff --git a/requirements_conda.txt b/requirements_conda.txt
index 7001081..30717d0 100644
--- a/requirements_conda.txt
+++ b/requirements_conda.txt
@@ -1,316 +1,14 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: linux-64
-_libgcc_mutex=0.1=conda_forge
-_openmp_mutex=4.5=1_llvm
-_py-xgboost-mutex=2.0=cpu_0
-_tflow_select=2.1.0=gpu
-abseil-cpp=20210324.0=h9c3ff4c_0
-absl-py=0.13.0=pyhd8ed1ab_0
-aiohttp=3.7.4.post0=py38h497a2fe_0
-alabaster=0.7.12=py_0
-alembic=1.6.5=pyhd8ed1ab_0
-appdirs=1.4.4=pyh9f0ad1d_0
-astor=0.8.1=pyh9f0ad1d_0
-astunparse=1.6.3=pyhd8ed1ab_0
-async-timeout=3.0.1=py_1000
-attrs=21.2.0=pyhd8ed1ab_0
-babel=2.9.1=pyh44b312d_0
-backcall=0.2.0=pypi_0
-backports=1.0=py_2
-backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
-biopandas=0.2.7=pyh9f0ad1d_1
-biopython=1.79=py38h497a2fe_0
-blas=1.0=mkl
-blinker=1.4=py_1
-blosc=1.21.0=h9c3ff4c_0
-bokeh=2.4.0=py38h578d9bd_0
-boost=1.74.0=py38hc10631b_3
-boost-cpp=1.74.0=hc6e9bd1_3
-brotlipy=0.7.0=py38h497a2fe_1001
-bzip2=1.0.8=h7f98852_4
-c-ares=1.17.2=h7f98852_0
-ca-certificates=2021.5.30=ha878542_0
-cached-property=1.5.2=hd8ed1ab_1
-cached_property=1.5.2=pyha770c72_1
-cachetools=4.2.2=pyhd8ed1ab_0
-cairo=1.16.0=h6cf1ce9_1008
-catboost=0.26.1=py38h578d9bd_0
-certifi=2021.5.30=py38h578d9bd_0
-cffi=1.14.6=py38ha65f79e_0
-cftime=1.5.0=py38hb5d20a5_0
-chardet=4.0.0=py38h578d9bd_1
-charset-normalizer=2.0.0=pyhd8ed1ab_0
-chemprop=1.3.1=pyhd8ed1ab_0
-click=8.0.1=py38h578d9bd_0
-cliff=3.8.0=pyhd8ed1ab_0
-cloudpickle=1.6.0=py_0
-cmaes=0.8.2=pyh44b312d_0
-cmd2=2.1.2=py38h578d9bd_0
-colorama=0.4.4=pyh9f0ad1d_0
-colorlog=6.4.1=py38h578d9bd_0
-conda-pack=0+unknown=pypi_0
-configargparse=1.5.2=pypi_0
-cryptography=3.4.7=py38ha5dfef3_0
-cudatoolkit=11.1.1=h6406543_8
-curl=7.78.0=hea6ffbf_0
-cycler=0.10.0=py_2
-cytoolz=0.11.0=py38h497a2fe_3
-dask=2021.8.1=pyhd8ed1ab_0
-dask-core=2021.8.1=pyhd8ed1ab_0
-dataclasses=0.8=pyhc8e2a94_3
-decorator=4.4.2=py_0
-dgl-cuda11.1=0.7.0=py38_0
-dgllife=0.2.8=pypi_0
-distributed=2021.8.1=py38h06a4308_0
-docutils=0.17.1=py38h578d9bd_0
-enum34=1.1.10=py38h32f6830_2
-ffmpeg=4.3=hf484d3e_0
-fftw=3.3.9=h27cfd23_1
-filelock=3.0.12=pypi_0
-flask=2.0.1=pyhd8ed1ab_0
-fontconfig=2.13.1=hba837de_1005
-freetype=2.10.4=h0708190_1
-fsspec=2021.7.0=pyhd8ed1ab_0
-future=0.18.2=py38h578d9bd_3
-gast=0.3.3=py_0
-gettext=0.19.8.1=h0b5b191_1005
-giflib=5.2.1=h36c2ea0_2
-gmp=6.2.1=h58526e2_0
-gnutls=3.6.13=h85f3911_1
-google-auth=1.35.0=pyh6c4a22f_0
-google-auth-oauthlib=0.4.5=pyhd8ed1ab_0
-google-pasta=0.2.0=pyh8c360ce_0
-googledrivedownloader=0.4=pypi_0
-greenlet=1.1.1=py38h709712a_0
-griddataformats=0.5.0=py_0
-grpc-cpp=1.37.1=h36de60a_0
-grpcio=1.37.1=py38hdd6454d_0
-gsd=2.4.2=py38hb5d20a5_0
-h5py=2.10.0=nompi_py38h9915d05_106
-hdf4=4.2.13=h3ca952b_2
-hdf5=1.10.6=nompi_h7c3c948_1111
-heapdict=1.0.1=py_0
-hyperopt=0.2.5=pyh9f0ad1d_0
-icu=68.1=h58526e2_0
-idna=3.1=pyhd3deb0d_0
-imagecodecs-lite=2019.12.3=py38h5c078b8_3
-imageio=2.9.0=py_0
-imagesize=1.2.0=py_0
-importlib-metadata=4.6.4=py38h578d9bd_0
-intel-openmp=2021.3.0=h06a4308_3350
-ipython=7.28.0=pypi_0
-isodate=0.6.1=pypi_0
-itsdangerous=2.0.1=pyhd8ed1ab_0
-jedi=0.18.0=pypi_0
-jinja2=3.0.1=pyhd8ed1ab_0
-joblib=1.0.1=pyhd8ed1ab_0
-jpeg=9d=h36c2ea0_0
-keras-preprocessing=1.1.2=pyhd8ed1ab_0
-kiwisolver=1.3.1=py38h1fd1430_1
-krb5=1.19.2=hcc1bbae_0
-lame=3.100=h7f98852_1001
-lcms2=2.12=h3be6417_0
-ld_impl_linux-64=2.35.1=h7274673_9
-libcurl=7.78.0=h2574ce0_0
-libedit=3.1.20191231=he28a2e2_2
-libev=4.33=h516909a_1
-libffi=3.3=he6710b0_2
-libgcc-ng=11.1.0=hc902ee8_8
-libgfortran-ng=7.5.0=h14aa051_19
-libgfortran4=7.5.0=h14aa051_19
-libglib=2.68.4=h3e27bee_0
-libiconv=1.16=h516909a_0
-libnetcdf=4.6.1=h2053bdc_4
-libnghttp2=1.43.0=h812cca2_0
-libpng=1.6.37=h21135ba_2
-libprotobuf=3.15.8=h780b84a_0
-libssh2=1.9.0=ha56f1ee_6
-libstdcxx-ng=11.1.0=h56837e0_8
-libtiff=4.1.0=h2733197_1
-libuuid=2.32.1=h7f98852_1000
-libuv=1.42.0=h7f98852_0
-libxcb=1.13=h7f98852_1003
-libxgboost=1.4.0=h9c3ff4c_0
-libxml2=2.9.12=h72842e0_0
-lightgbm=3.2.1=py38h709712a_0
-llvm-openmp=12.0.1=h4bd325d_1
-locket=0.2.0=py_2
-lz4-c=1.9.3=h9c3ff4c_1
-lzo=2.10=h516909a_1000
-mako=1.1.5=pyhd8ed1ab_0
-markdown=3.3.4=pyhd8ed1ab_0
-markupsafe=2.0.1=py38h497a2fe_0
-matplotlib-base=3.4.3=py38hf4fb855_0
-matplotlib-inline=0.1.3=pypi_0
-mdanalysis=2.0.0=py38h709712a_1
-mdtraj=1.9.6=py38hf01b267_1
-meeko=0.1.dev3=pypi_0
-mkl=2021.3.0=h06a4308_520
-mkl-service=2.4.0=py38h497a2fe_0
-mkl_fft=1.3.0=py38h42c9631_2
-mkl_random=1.2.2=py38h1abd341_0
-mmtf-python=1.1.2=py_0
-mock=4.0.3=py38h578d9bd_1
-msgpack-python=1.0.2=py38h1fd1430_1
-multidict=5.1.0=py38h497a2fe_1
-mypy_extensions=0.4.3=py38h578d9bd_3
-ncurses=6.2=he6710b0_1
-netcdf4=1.5.7=py38h0a24e14_0
-nettle=3.6=he412f7d_0
-networkx=2.5.1=pyhd8ed1ab_0
-ninja=1.10.2=h4bd325d_0
-numexpr=2.7.3=py38h51da96c_0
-numpy=1.20.3=py38hf144106_0
-numpy-base=1.20.3=py38h74d4b33_0
-oauthlib=3.1.1=pyhd8ed1ab_0
-ocl-icd=2.3.1=h7f98852_0
-ocl-icd-system=1.0.0=1
-oddt=0.7=pyh500f238_0
-olefile=0.46=pyh9f0ad1d_1
-openbabel=3.1.1=py38hd2c4bc0_1
-openh264=2.1.1=h780b84a_0
-openjpeg=2.4.0=hf7af979_0
-openmm=0.2=pypi_0
-openssl=1.1.1l=h7f98852_0
-opt_einsum=3.3.0=pyhd8ed1ab_1
-optuna=2.9.1=pyhd8ed1ab_0
-packaging=21.0=pyhd8ed1ab_0
-pandas=1.0.3=pypi_0
-pandas-flavor=0.2.0=py_0
-parso=0.8.2=pypi_0
-partd=1.2.0=pyhd8ed1ab_0
-pathlib=1.0.1=py38h578d9bd_4
-patsy=0.5.1=py_0
-pbr=5.6.0=pyhd8ed1ab_0
-pcre=8.45=h9c3ff4c_0
-pdbfixer=1.7=pypi_0
-pexpect=4.8.0=pypi_0
-pickleshare=0.7.5=pypi_0
-pillow=8.3.1=py38h2c7a002_0
-pip=21.0.1=py38h06a4308_0
-pixman=0.40.0=h36c2ea0_0
-pooch=1.5.1=pyhd8ed1ab_0
-prettytable=2.1.0=pyhd8ed1ab_0
-prody=2.1.0=pypi_0
-prompt-toolkit=3.0.20=pypi_0
-protobuf=3.15.8=py38h709712a_0
-psutil=5.8.0=py38h497a2fe_1
-pthread-stubs=0.4=h36c2ea0_1001
-ptyprocess=0.7.0=pypi_0
-pubchempy=1.0.4=pypi_0
-py-xgboost=1.4.0=py38h578d9bd_0
-pyasn1=0.4.8=py_0
-pyasn1-modules=0.2.7=py_0
-pycairo=1.20.1=py38hf61ee4a_0
-pycparser=2.20=pyh9f0ad1d_2
-pydeprecate=0.3.1=pypi_0
-pygments=2.10.0=pyhd8ed1ab_0
-pyjwt=2.1.0=pyhd8ed1ab_0
-pymongo=3.12.0=py38h709712a_0
-pyopenssl=20.0.1=pyhd8ed1ab_0
-pyparsing=2.4.7=pyh9f0ad1d_0
-pyperclip=1.8.2=pyhd8ed1ab_2
-pyscreener=0+unknown=pypi_0
-pysocks=1.7.1=py38h578d9bd_3
-pytables=3.6.1=py38hc386592_3
-python=3.8.11=h12debd9_0_cpython
-python-dateutil=2.8.2=pyhd8ed1ab_0
-python-editor=1.0.4=py_0
-python-flatbuffers=1.12=pyhd8ed1ab_1
-python_abi=3.8=2_cp38
-pytorch=1.9.0=py3.8_cuda11.1_cudnn8.0.5_0
-pytorch-lightning=1.4.4=pypi_0
-pytz=2021.1=pyhd8ed1ab_0
-pyu2f=0.1.5=pyhd8ed1ab_0
-pywavelets=1.1.1=py38h5c078b8_3
-pyyaml=5.4.1=py38h497a2fe_1
-ray=1.6.0=pypi_0
-rdflib=6.1.1=pypi_0
-rdkit=2021.03.5=py38h8c3fb5a_0
-re2=2021.04.01=h9c3ff4c_0
-readline=8.1=h27cfd23_0
-redis=3.5.3=pypi_0
-reportlab=3.5.68=py38hadf75a6_0
-requests=2.26.0=pyhd8ed1ab_0
-requests-oauthlib=1.3.0=pyh9f0ad1d_0
-rsa=4.7.2=pyh44b312d_0
-scikit-image=0.18.3=py38h43a58ef_0
-scikit-learn=0.24.2=py38ha9443f7_0
-scipy=1.6.2=py38had2a1c9_1
-scopy=1.2.5=pypi_0
-seaborn=0.12.0.dev0=pypi_0
-seaborn-base=0.11.2=pyhd8ed1ab_0
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-six=1.16.0=pyh6c4a22f_0
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-statsmodels=0.12.2=py38h5c078b8_0
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-tabulate=0.8.9=pypi_0
-tblib=1.7.0=pyhd8ed1ab_0
-tensorboard=2.4.1=pyhd8ed1ab_1
-tensorboard-plugin-wit=1.8.0=pyh44b312d_0
-tensorboardx=2.4=pyhd8ed1ab_0
-tensorflow=2.4.1=py38h578d9bd_0
-tensorflow-addons=0.14.0=pypi_0
-tensorflow-base=2.4.1=py38h83f5f1d_0
-tensorflow-estimator=2.4.0=pyh9656e83_0
-tensorflow-gpu=2.4.1=h30adc30_0
-termcolor=1.1.0=py_2
-threadpoolctl=2.2.0=pyh8a188c0_0
-tifffile=2019.7.26.2=py38_0
-tk=8.6.10=hbc83047_0
-toolz=0.11.1=py_0
-torch-cluster=1.5.9=pypi_0
-torch-geometric=2.0.3=pypi_0
-torch-scatter=2.0.9=pypi_0
-torch-sparse=0.6.12=pypi_0
-torch-spline-conv=1.2.1=pypi_0
-torchmetrics=0.5.0=pypi_0
-torchvision=0.2.2=py_3
-tornado=6.1=py38h497a2fe_1
-tqdm=4.62.2=pyhd8ed1ab_0
-traitlets=5.1.0=pypi_0
-typed-argument-parser=1.7.1=pyhd8ed1ab_0
-typeguard=2.12.1=pypi_0
-typing-extensions=3.10.0.0=hd8ed1ab_0
-typing_extensions=3.10.0.0=pyha770c72_0
-typing_inspect=0.7.1=pyh6c4a22f_0
-urllib3=1.26.6=pyhd8ed1ab_0
-vina=1.2.2=pypi_0
-wcwidth=0.2.5=pyh9f0ad1d_2
-werkzeug=2.0.1=pyhd8ed1ab_0
-wheel=0.37.0=pyhd3eb1b0_0
-wrapt=1.12.1=py38h497a2fe_3
-xarray=0.19.0=pyhd8ed1ab_1
-xgboost=1.4.0=py38h578d9bd_0
-xorg-kbproto=1.0.7=h7f98852_1002
-xorg-libice=1.0.10=h7f98852_0
-xorg-libsm=1.2.3=hd9c2040_1000
-xorg-libx11=1.7.2=h7f98852_0
-xorg-libxau=1.0.9=h7f98852_0
-xorg-libxdmcp=1.1.3=h7f98852_0
-xorg-libxext=1.3.4=h7f98852_1
-xorg-libxrender=0.9.10=h7f98852_1003
-xorg-renderproto=0.11.1=h7f98852_1002
-xorg-xextproto=7.3.0=h7f98852_1002
-xorg-xproto=7.0.31=h7f98852_1007
-xz=5.2.5=h7b6447c_0
-yacs=0.1.8=pypi_0
-yaml=0.2.5=h516909a_0
-yarl=1.6.3=py38h497a2fe_2
-zict=2.0.0=py_0
-zipp=3.5.0=pyhd8ed1ab_0
-zlib=1.2.11=h7b6447c_3
-zstd=1.4.9=ha95c52a_0
+torch-scatter=2.0.9
+cudatoolkit-dev=11.1.1
+cudatoolkit=11.1.1
+openbabel
+pillow=9.2.0
+pytorch=1.9.0
+gsd=2.5.3
+mdanalysis=2.0.0
+prody=2.1.0
+rdkit=2022.03.03
+scipy=1.6.2
+seaborn=0.11.2
+matplotlib=3.4.3
+joblib=1.0.1
diff --git a/requirements_pip.txt b/requirements_pip.txt
index 9f2093c..193cefa 100644
--- a/requirements_pip.txt
+++ b/requirements_pip.txt
@@ -1,206 +1,2 @@
-absl-py @ file:///home/conda/feedstock_root/build_artifacts/absl-py_1623774798911/work
-aiohttp @ file:///home/conda/feedstock_root/build_artifacts/aiohttp_1623682244451/work
-alabaster==0.7.12
-alembic @ file:///home/conda/feedstock_root/build_artifacts/alembic_1622150326904/work
-appdirs @ file:///home/conda/feedstock_root/build_artifacts/appdirs_1603108395799/work
-astor @ file:///home/conda/feedstock_root/build_artifacts/astor_1593610464257/work
-astunparse @ file:///home/conda/feedstock_root/build_artifacts/astunparse_1610696312422/work
-async-timeout==3.0.1
-attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1620387926260/work
-Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1619719576210/work
-backcall==0.2.0
-backports.functools-lru-cache @ file:///home/conda/feedstock_root/build_artifacts/backports.functools_lru_cache_1618230623929/work
-biopandas @ file:///home/conda/feedstock_root/build_artifacts/biopandas_1596868292228/work
-biopython @ file:///home/conda/feedstock_root/build_artifacts/biopython_1622747233620/work
-blinker==1.4
-bokeh==2.4.0
-brotlipy==0.7.0
-cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work
-cachetools @ file:///home/conda/feedstock_root/build_artifacts/cachetools_1619593780156/work
-catboost @ https://pypi.org/packages/cp38/c/catboost/catboost-0.26.1-cp38-none-manylinux1_x86_64.whl
-certifi==2021.5.30
-cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1625835293160/work
-cftime @ file:///home/conda/feedstock_root/build_artifacts/cftime_1621553714314/work
-chardet @ file:///home/conda/feedstock_root/build_artifacts/chardet_1610093490430/work
-charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1626371162869/work
-chemprop @ file:///home/conda/feedstock_root/build_artifacts/chemprop_1627453600984/work
-click @ file:///home/conda/feedstock_root/build_artifacts/click_1621503718520/work
-cliff @ file:///home/conda/feedstock_root/build_artifacts/cliff_1622119770880/work
-cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1598400192773/work
-cmaes @ file:///home/conda/feedstock_root/build_artifacts/cmaes_1613785714721/work
-cmd2 @ file:///home/conda/feedstock_root/build_artifacts/cmd2_1625509081997/work
-colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1602866480661/work
-colorlog==6.4.1
-conda-pack @ file:///home/shenchao/conda-pack-master.zip
-ConfigArgParse==1.5.2
-cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography_1616851476134/work
-cycler==0.10.0
-cytoolz==0.11.0
-dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1629497402825/work
-dataclasses @ file:///home/conda/feedstock_root/build_artifacts/dataclasses_1628958434797/work
-decorator==4.4.2
-dgl==0.7.0
-dgllife==0.2.8
-distributed @ file:///tmp/build/80754af9/distributed_1630629268815/work
-docutils @ file:///home/conda/feedstock_root/build_artifacts/docutils_1618676255808/work
-filelock==3.0.12
-Flask @ file:///home/conda/feedstock_root/build_artifacts/flask_1621629915293/work
-flatbuffers @ file:///home/conda/feedstock_root/build_artifacts/python-flatbuffers_1617723079010/work
-fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1626188337504/work
-future @ file:///home/conda/feedstock_root/build_artifacts/future_1610147327521/work
-gast==0.3.3
-google-auth @ file:///home/conda/feedstock_root/build_artifacts/google-auth_1629296548061/work
-google-auth-oauthlib @ file:///home/conda/feedstock_root/build_artifacts/google-auth-oauthlib_1627588028651/work
-google-pasta==0.2.0
-googledrivedownloader @ file:///home/shenchao/test/googledrivedownloader-0.4-py2.py3-none-any.whl
-greenlet @ file:///home/conda/feedstock_root/build_artifacts/greenlet_1628272065194/work
-GridDataFormats==0.5.0
-grpcio @ file:///home/conda/feedstock_root/build_artifacts/grpcio_1619796013894/work
-gsd @ file:///home/conda/feedstock_root/build_artifacts/gsd_1618454803899/work
-h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1617739432869/work
-HeapDict==1.0.1
-hyperopt @ file:///home/conda/feedstock_root/build_artifacts/hyperopt_1602661729544/work
-idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1609836280497/work
-imagecodecs-lite @ file:///home/conda/feedstock_root/build_artifacts/imagecodecs-lite_1610557095663/work
-imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1594044661732/work
-imagesize==1.2.0
-importlib-metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1628897593933/work
-ipython==7.28.0
-isodate @ file:///home/shenchao/test/isodate-0.6.1-py2.py3-none-any.whl
-itsdangerous @ file:///home/conda/feedstock_root/build_artifacts/itsdangerous_1621360792037/work
-jedi==0.18.0
-Jinja2 @ file:///home/conda/feedstock_root/build_artifacts/jinja2_1621419064915/work
-joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1612898609989/work
-Keras-Preprocessing @ file:///home/conda/feedstock_root/build_artifacts/keras-preprocessing_1610713559828/work
-kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1610099769230/work
-lightgbm @ file:///home/conda/feedstock_root/build_artifacts/lightgbm_1618922572018/work
-locket==0.2.0
-Mako @ file:///home/conda/feedstock_root/build_artifacts/mako_1629523042001/work
-Markdown @ file:///home/conda/feedstock_root/build_artifacts/markdown_1614595805172/work
-MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1621455677251/work
-matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1628881758439/work
-matplotlib-inline==0.1.3
-MDAnalysis @ file:///home/conda/feedstock_root/build_artifacts/mdanalysis_1629624786895/work
-mdtraj @ file:///home/conda/feedstock_root/build_artifacts/mdtraj_1623425400526/work
-meeko==0.1.dev3
-mkl-fft==1.3.0
-mkl-random==1.2.2
-mkl-service==2.4.0
-mmtf-python==1.1.2
-mock @ file:///home/conda/feedstock_root/build_artifacts/mock_1610094566888/work
-msgpack @ file:///home/conda/feedstock_root/build_artifacts/msgpack-python_1610121699837/work
-multidict @ file:///home/conda/feedstock_root/build_artifacts/multidict_1610319019165/work
-mypy-extensions @ file:///home/conda/feedstock_root/build_artifacts/mypy_extensions_1610127166133/work
-netCDF4 @ file:///tmp/build/80754af9/netcdf4_1624383287733/work
-networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1617499744980/work
-numexpr @ file:///home/conda/feedstock_root/build_artifacts/numexpr_1614971340455/work
-numpy @ file:///tmp/build/80754af9/numpy_and_numpy_base_1626271506491/work
-oauthlib @ file:///home/conda/feedstock_root/build_artifacts/oauthlib_1622563202229/work
-oddt==0.7
-olefile @ file:///home/conda/feedstock_root/build_artifacts/olefile_1602866521163/work
-OpenMM==7.6.0
-opt-einsum @ file:///home/conda/feedstock_root/build_artifacts/opt_einsum_1617859230218/work
-optuna @ file:///home/conda/feedstock_root/build_artifacts/optuna_1628151932842/work
-packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1625323647219/work
-pandas==1.3.2
-pandas-flavor==0.2.0
-parso==0.8.2
-partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1617910651905/work
-patsy==0.5.1
-pbr @ file:///home/conda/feedstock_root/build_artifacts/pbr_1619460527081/work
-pdbfixer==1.7
-pexpect==4.8.0
-pickleshare==0.7.5
-Pillow @ file:///tmp/build/80754af9/pillow_1625655817137/work
-pooch @ file:///home/conda/feedstock_root/build_artifacts/pooch_1629815302302/work
-prettytable @ file:///home/conda/feedstock_root/build_artifacts/prettytable_1614725168556/work
-ProDy==2.1.0
-prompt-toolkit==3.0.20
-protobuf==3.15.8
-psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1610127095720/work
-ptyprocess==0.7.0
-PubChemPy==1.0.4
-pyasn1==0.4.8
-pyasn1-modules==0.2.7
-pycairo==1.20.1
-pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1593275161868/work
-pyDeprecate==0.3.1
-Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1629119114968/work
-PyJWT @ file:///home/conda/feedstock_root/build_artifacts/pyjwt_1619620644068/work
-pymongo @ file:///home/conda/feedstock_root/build_artifacts/pymongo_1626207954681/work
-pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1608055815057/work
-pyparsing==2.4.7
-pyperclip @ file:///home/conda/feedstock_root/build_artifacts/pyperclip_1622337600177/work
-pyscreener==0+unknown
-PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1610291447907/work
-python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work
-python-editor==1.0.4
-pytorch-lightning==1.4.4
-pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1612179539967/work
-pyu2f @ file:///home/conda/feedstock_root/build_artifacts/pyu2f_1604248910016/work
-PyWavelets @ file:///home/conda/feedstock_root/build_artifacts/pywavelets_1607290812047/work
-PyYAML==5.4.1
-ray==1.6.0
-rdflib @ file:///home/shenchao/test/rdflib-6.1.1-py3-none-any.whl
-redis==3.5.3
-reportlab==3.5.68
-requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1626393743643/work
-requests-oauthlib @ file:///home/conda/feedstock_root/build_artifacts/requests-oauthlib_1595492159598/work
-rsa @ file:///home/conda/feedstock_root/build_artifacts/rsa_1614171254180/work
-scikit-image==0.18.3
-scikit-learn @ file:///tmp/build/80754af9/scikit-learn_1621370412049/work
-scipy @ file:///tmp/build/80754af9/scipy_1618855647378/work
-scopy==1.2.5
-seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1629095986539/work
-six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
-snowballstemmer @ file:///home/conda/feedstock_root/build_artifacts/snowballstemmer_1611270869511/work
-sortedcontainers @ file:///home/conda/feedstock_root/build_artifacts/sortedcontainers_1621217038088/work
-Sphinx @ file:///home/conda/feedstock_root/build_artifacts/sphinx_1627331724246/work
-sphinxcontrib-applehelp==1.0.2
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp @ file:///home/conda/feedstock_root/build_artifacts/sphinxcontrib-htmlhelp_1621704829796/work
-sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml @ file:///home/conda/feedstock_root/build_artifacts/sphinxcontrib-serializinghtml_1621704833237/work
-SQLAlchemy @ file:///home/conda/feedstock_root/build_artifacts/sqlalchemy_1629314936610/work
-statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1612273599609/work
-stevedore @ file:///home/conda/feedstock_root/build_artifacts/stevedore_1629395109532/work
-tables @ file:///home/conda/feedstock_root/build_artifacts/pytables_1610156075390/work
-tabulate==0.8.9
-tblib @ file:///home/conda/feedstock_root/build_artifacts/tblib_1616261298899/work
-tensorboard @ file:///home/conda/feedstock_root/build_artifacts/tensorboard_1629725799390/work/tensorboard-2.4.1-py3-none-any.whl
-tensorboard-plugin-wit @ file:///home/conda/feedstock_root/build_artifacts/tensorboard-plugin-wit_1611075653546/work/tensorboard_plugin_wit-1.8.0-py3-none-any.whl
-tensorboardX @ file:///home/conda/feedstock_root/build_artifacts/tensorboardx_1628560643999/work
-tensorflow @ file:///home/conda/feedstock_root/build_artifacts/tensorflow-split_1619434534109/work/tensorflow_pkg/tensorflow-2.4.1-cp38-cp38-linux_x86_64.whl
-tensorflow-addons==0.14.0
-tensorflow-estimator @ file:///home/conda/feedstock_root/build_artifacts/tensorflow-estimator_1610655765755/work/tensorflow_estimator-2.4.0-py2.py3-none-any.whl
-termcolor==1.1.0
-threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1626092076920/work
-tifffile==2019.7.26.2
-toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1600973991856/work
-torch==1.9.0
-torch-cluster @ file:///home/shenchao/test/torch_cluster-1.5.9-cp38-cp38-linux_x86_64.whl
-torch-geometric @ file:///home/shenchao/test/torch_geometric-2.0.3.tar
-torch-scatter @ file:///home/shenchao/test/torch_scatter-2.0.9-cp38-cp38-linux_x86_64.whl
-torch-sparse @ file:///home/shenchao/test/torch_sparse-0.6.12-cp38-cp38-linux_x86_64.whl
-torch-spline-conv @ file:///home/shenchao/test/torch_spline_conv-1.2.1-cp38-cp38-linux_x86_64.whl
-torchmetrics==0.5.0
-torchvision==0.2.2
-tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1610094706440/work
-tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1629742505296/work
-traitlets==5.1.0
-typed-argument-parser @ file:///home/conda/feedstock_root/build_artifacts/typed-argument-parser_1629068416546/work
-typeguard==2.12.1
-typing-extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1622748266870/work
-typing-inspect @ file:///home/conda/feedstock_root/build_artifacts/typing_inspect_1623277617575/work
-urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1624634538755/work
-vina==1.2.2
-wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1600965781394/work
-Werkzeug @ file:///home/conda/feedstock_root/build_artifacts/werkzeug_1621518206714/work
-wrapt @ file:///home/conda/feedstock_root/build_artifacts/wrapt_1610094884173/work
-xarray @ file:///home/conda/feedstock_root/build_artifacts/xarray_1627311788418/work
-xgboost==1.4.0
-yacs @ file:///home/shenchao/test/yacs-0.1.8-py3-none-any.whl
-yarl @ file:///home/conda/feedstock_root/build_artifacts/yarl_1625232865745/work
-zict==2.0.0
-zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1625284368454/work
+dgl==0.6.1
+numpy==1.22.0

From 4e5749524c20b0fc01bbad77f35f0c1c98cd4b8f Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 14:20:29 +0100
Subject: [PATCH 03/17] new reqs

---
 .github/workflows/python-app.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 5b04bad..c99369b 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -32,8 +32,8 @@ jobs:
     - name: Install dependencies
       run: |
         conda create -n test_env python=3.8
-	conda activate test_env
-	conda install --file=requirements_conda.txt   
+        conda activate test_env
+        conda install --file=requirements_conda.txt   
         pip install -r ./requirements_pip.txt
     - name: Test
       run: |

From 657419330f24d745822fe907ecd2c45b2cbefb1e Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 14:22:18 +0100
Subject: [PATCH 04/17] new reqs

---
 .github/workflows/python-app.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index c99369b..910ef3f 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -31,6 +31,7 @@ jobs:
         auto-activate-base: true
     - name: Install dependencies
       run: |
+        conda init
         conda create -n test_env python=3.8
         conda activate test_env
         conda install --file=requirements_conda.txt   

From a8e7960d35caf3b947071b90b4c536b10c46071a Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 14:26:09 +0100
Subject: [PATCH 05/17] new reqs

---
 .github/workflows/python-app.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 910ef3f..4ff176e 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -31,14 +31,10 @@ jobs:
         auto-activate-base: true
     - name: Install dependencies
       run: |
-        conda init
-        conda create -n test_env python=3.8
-        conda activate test_env
         conda install --file=requirements_conda.txt   
         pip install -r ./requirements_pip.txt
     - name: Test
       run: |
-        conda activate test_env
         cd example
         python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth

From e44438c9b2ac6e4992ab694304eb380831820157 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 14:29:37 +0100
Subject: [PATCH 06/17] new reqs

---
 requirements_conda.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements_conda.txt b/requirements_conda.txt
index 30717d0..d54bbd7 100644
--- a/requirements_conda.txt
+++ b/requirements_conda.txt
@@ -1,3 +1,4 @@
+python=3.8
 torch-scatter=2.0.9
 cudatoolkit-dev=11.1.1
 cudatoolkit=11.1.1

From f45b7b5b7ee7bed967e0b0ad57ada20e57034634 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 16:41:20 +0100
Subject: [PATCH 07/17] new reqs

---
 .github/workflows/python-app.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 4ff176e..55ffe0c 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -22,13 +22,14 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniconda-version: "latest"
         channels: bioconda, conda-forge, defaults
         use-only-tar-bz2: true
         auto-update-conda: true
         auto-activate-base: true
+        python-version: 3.8
     - name: Install dependencies
       run: |
         conda install --file=requirements_conda.txt   

From 0596563fc5b062fceb6d2c9ab6dd751e68610938 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 16:54:04 +0100
Subject: [PATCH 08/17] new reqs

---
 .github/workflows/python-app.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 55ffe0c..ede771f 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -28,7 +28,8 @@ jobs:
         channels: bioconda, conda-forge, defaults
         use-only-tar-bz2: true
         auto-update-conda: true
-        auto-activate-base: true
+#        auto-activate-base: true
+        activate-environment: test
         python-version: 3.8
     - name: Install dependencies
       run: |

From a9d41ea1501a6e0afc56b84ff3bd534c62e4e253 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 16:55:36 +0100
Subject: [PATCH 09/17] new reqs

---
 .github/workflows/python-app.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index ede771f..fe85763 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -32,10 +32,12 @@ jobs:
         activate-environment: test
         python-version: 3.8
     - name: Install dependencies
+      shell: bash -el {0}
       run: |
         conda install --file=requirements_conda.txt   
         pip install -r ./requirements_pip.txt
     - name: Test
+      shell: bash -el {0}
       run: |
         cd example
         python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth

From b71569593d753928a73b63bf3c9f851af23610f8 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 17:03:39 +0100
Subject: [PATCH 10/17] testing only 3/4 example scripts

---
 example/run_rtmscore.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/example/run_rtmscore.sh b/example/run_rtmscore.sh
index e5cb4f0..11146ee 100644
--- a/example/run_rtmscore.sh
+++ b/example/run_rtmscore.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # input is protein (needs to be converted to pocket)
-python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
+#python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
 
 # input is pocket
 python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth

From 15b3d1ab2e45bf88a3b189842848e505e8547091 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 17:14:36 +0100
Subject: [PATCH 11/17] testing only 3/4 example scripts

---
 .github/workflows/python-app.yml | 2 +-
 example/run_rtmscore.sh          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index fe85763..386617f 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -40,7 +40,7 @@ jobs:
       shell: bash -el {0}
       run: |
         cd example
-        python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
+#        python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -ac -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -rc -m ../trained_models/rtmscore_model1.pth
diff --git a/example/run_rtmscore.sh b/example/run_rtmscore.sh
index 11146ee..e5cb4f0 100644
--- a/example/run_rtmscore.sh
+++ b/example/run_rtmscore.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # input is protein (needs to be converted to pocket)
-#python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
+python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
 
 # input is pocket
 python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth

From aa08435793b5e2669457722e25d4b394a7c05ccd Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 17:25:40 +0100
Subject: [PATCH 12/17] testing only 3/4 example scripts

---
 .github/workflows/python-app.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 386617f..361f89a 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -34,7 +34,7 @@ jobs:
     - name: Install dependencies
       shell: bash -el {0}
       run: |
-        conda install --file=requirements_conda.txt   
+        conda install --file=requirements_conda.txt
         pip install -r ./requirements_pip.txt
     - name: Test
       shell: bash -el {0}

From 9b88bd7305d8381d580e2eaecbc048f5525e369d Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 17:27:07 +0100
Subject: [PATCH 13/17] testing only 3/4 example scripts

---
 .github/workflows/python-app.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 361f89a..ced239b 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -33,9 +33,7 @@ jobs:
         python-version: 3.8
     - name: Install dependencies
       shell: bash -el {0}
-      run: |
-        conda install --file=requirements_conda.txt
-        pip install -r ./requirements_pip.txt
+      run: conda install --file=requirements_conda.txt; pip install -r ./requirements_pip.txt
     - name: Test
       shell: bash -el {0}
       run: |

From 2dfc47fb2b6e299dec51e00aff202ec71b77e2ea Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 17:28:18 +0100
Subject: [PATCH 14/17] testing only 3/4 example scripts

---
 .github/workflows/python-app.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index ced239b..ce2d643 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -33,7 +33,7 @@ jobs:
         python-version: 3.8
     - name: Install dependencies
       shell: bash -el {0}
-      run: conda install --file=requirements_conda.txt; pip install -r ./requirements_pip.txt
+      run: "conda install --file=requirements_conda.txt; pip install -r ./requirements_pip.txt"
     - name: Test
       shell: bash -el {0}
       run: |

From 3c58702c6662591b66abce3e98b583c53edc0ca0 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Fri, 21 Mar 2025 17:29:05 +0100
Subject: [PATCH 15/17] testing only 3/4 example scripts

---
 .github/workflows/python-app.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index ce2d643..da7aedb 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -38,7 +38,6 @@ jobs:
       shell: bash -el {0}
       run: |
         cd example
-#        python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -ac -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -rc -m ../trained_models/rtmscore_model1.pth

From fe403d8841e6ed77b1d38f8860cfec421b1e5192 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Mon, 24 Mar 2025 14:31:55 +0100
Subject: [PATCH 16/17] openbabel libdir set with CONDA_PREFIX

---
 .github/workflows/python-app.yml | 5 ++++-
 example/rtmscore.py              | 3 ++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index da7aedb..a758692 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -33,7 +33,9 @@ jobs:
         python-version: 3.8
     - name: Install dependencies
       shell: bash -el {0}
-      run: "conda install --file=requirements_conda.txt; pip install -r ./requirements_pip.txt"
+      run: |
+        conda install --file=requirements_conda.txt
+        pip install -r ./requirements_pip.txt"
     - name: Test
       shell: bash -el {0}
       run: |
@@ -41,3 +43,4 @@ jobs:
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -ac -m ../trained_models/rtmscore_model1.pth
         python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -rc -m ../trained_models/rtmscore_model1.pth
+        python  rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth
diff --git a/example/rtmscore.py b/example/rtmscore.py
index d914f39..76e84e7 100644
--- a/example/rtmscore.py
+++ b/example/rtmscore.py
@@ -15,7 +15,8 @@
 torch.multiprocessing.set_sharing_strategy('file_system')
 
 #you need to set the babel libdir first if you need to generate the pocket
-os.environ["BABEL_LIBDIR"] = "/home/shenchao/.conda/envs/my2/lib/openbabel/3.1.0"
+env_path=os.environ['CONDA_PREFIX']
+os.environ["BABEL_LIBDIR"] = os.path.join(env_path,"lib","openbabel","3.1.0")
 
 def Input():
 	p = argparse.ArgumentParser()

From 252fb209af14d84d5ea03d16d1f2fd3d64bfdae7 Mon Sep 17 00:00:00 2001
From: William Schueller <william.schueller@gmail.com>
Date: Mon, 24 Mar 2025 14:40:00 +0100
Subject: [PATCH 17/17] typo in actions worflow

---
 .github/workflows/python-app.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index a758692..a3a6050 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -35,7 +35,7 @@ jobs:
       shell: bash -el {0}
       run: |
         conda install --file=requirements_conda.txt
-        pip install -r ./requirements_pip.txt"
+        pip install -r ./requirements_pip.txt
     - name: Test
       shell: bash -el {0}
       run: |