AlphaFold 3 data was added

Author: i-l-sokolov

README.md

@@ -0,0 +1,225 @@
+name: YOUR_NAME
+channels:
+  - schrodinger
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_kmp_llvm
+  - _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
+  - alsa-lib=1.2.13=hb9d3cd8_0
+  - apbs=1.5=hd8ae8d1_0
+  - attr=2.5.1=h166bdaf_1
+  - biopython=1.85=py312h66e93f0_1
+  - blosc=1.21.6=he440d0b_1
+  - brotli-python=1.1.0=py312h2ec8cdc_2
+  - bzip2=1.0.8=h5eee18b_6
+  - c-ares=1.34.4=hb9d3cd8_0
+  - ca-certificates=2025.1.31=hbcca054_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cairo=1.18.2=h3394656_1
+  - certifi=2024.12.14=pyhd8ed1ab_0
+  - cffi=1.17.1=py312h06ac9bb_0
+  - charset-normalizer=3.4.1=pyhd8ed1ab_0
+  - collada2gltf=2.1.4=h6bb024c_0
+  - cyrus-sasl=2.1.27=h54b06d7_7
+  - dbus=1.13.6=h5008d03_3
+  - expat=2.6.4=h5888daf_0
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=h77eed37_3
+  - fontconfig=2.15.0=h7e30c49_1
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - freetype=2.12.1=h267a509_2
+  - gettext=0.22.5=he02047a_3
+  - gettext-tools=0.22.5=he02047a_3
+  - glew=2.1.0=h9c3ff4c_2
+  - glib=2.82.2=h07242d1_1
+  - glib-tools=2.82.2=h4833e2c_1
+  - graphite2=1.3.13=h59595ed_1003
+  - gst-plugins-base=1.24.7=h0a52356_0
+  - gstreamer=1.24.7=hf3bb09a_0
+  - h2=4.2.0=pyhd8ed1ab_0
+  - h5py=3.12.1=nompi_py312hedeef09_103
+  - harfbuzz=10.2.0=h4bba637_0
+  - hdf4=4.2.15=h2a13503_7
+  - hdf5=1.14.3=nompi_h2d575fe_109
+  - hpack=4.1.0=pyhd8ed1ab_0
+  - hyperframe=6.1.0=pyhd8ed1ab_0
+  - icu=75.1=he02047a_0
+  - idna=3.10=pyhd8ed1ab_1
+  - kernel-headers_linux-64=3.10.0=h57e8cba_10
+  - keyutils=1.6.1=h166bdaf_0
+  - krb5=1.21.3=h659f571_0
+  - lame=3.100=h166bdaf_1003
+  - lcms2=2.16=hb7c19ff_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=4.0.0=h27087fc_0
+  - libaec=1.1.3=h59595ed_0
+  - libasprintf=0.22.5=he8f35ee_3
+  - libasprintf-devel=0.22.5=he8f35ee_3
+  - libblas=3.9.0=28_h59b9bed_openblas
+  - libcap=2.71=h39aace5_0
+  - libcblas=3.9.0=28_he106b2a_openblas
+  - libclang-cpp19.1=19.1.7=default_hb5137d0_1
+  - libclang13=19.1.7=default_h9c6a7e4_1
+  - libcups=2.3.3=h4637d8d_4
+  - libcurl=8.11.1=h332b0f4_0
+  - libdeflate=1.23=h4ddbbb0_0
+  - libdrm=2.4.124=hb9d3cd8_0
+  - libdrm-cos7-x86_64=2.4.97=ha675448_1106
+  - libedit=3.1.20250104=pl5321h7949ede_0
+  - libegl=1.7.0=ha4b6fd6_2
+  - libev=4.33=hd590300_2
+  - libevent=2.1.12=hf998b51_1
+  - libexpat=2.6.4=h5888daf_0
+  - libffi=3.4.4=h6a678d5_1
+  - libflac=1.4.3=h59595ed_0
+  - libgcc=14.2.0=h77fa898_1
+  - libgcc-ng=14.2.0=h69a702a_1
+  - libgcrypt-lib=1.11.0=hb9d3cd8_2
+  - libgettextpo=0.22.5=he02047a_3
+  - libgettextpo-devel=0.22.5=he02047a_3
+  - libgfortran=14.2.0=h69a702a_1
+  - libgfortran-ng=14.2.0=h69a702a_1
+  - libgfortran5=14.2.0=hd5240d6_1
+  - libgl=1.7.0=ha4b6fd6_2
+  - libglib=2.82.2=h2ff4ddf_1
+  - libglu=9.0.3=h03adeef_0
+  - libglvnd=1.7.0=ha4b6fd6_2
+  - libglvnd-cos7-x86_64=1.0.1=ha675448_1106
+  - libglvnd-glx-cos7-x86_64=1.0.1=ha675448_1106
+  - libglx=1.7.0=ha4b6fd6_2
+  - libgpg-error=1.51=hbd13f7d_1
+  - libholoplaycore=0.1.0_rc4=1
+  - libiconv=1.17=hd590300_2
+  - libjpeg-turbo=3.0.0=hd590300_1
+  - liblapack=3.9.0=28_h7ac8fdf_openblas
+  - libllvm19=19.1.7=ha7bfdaf_1
+  - liblzma=5.6.4=hb9d3cd8_0
+  - libnetcdf=4.9.2=nompi_h80fb2b6_111
+  - libnghttp2=1.64.0=h161d5f1_0
+  - libnsl=2.0.1=hd590300_0
+  - libntlm=1.8=hb9d3cd8_0
+  - libogg=1.3.5=h4ab18f5_0
+  - libopenblas=0.3.28=pthreads_h94d23a6_1
+  - libopus=1.3.1=h7f98852_1
+  - libpciaccess=0.18=hd590300_0
+  - libpng=1.6.46=h943b412_0
+  - libpq=17.2=h3b95a9b_1
+  - libsndfile=1.2.2=hc60ed4a_1
+  - libsqlite=3.48.0=hee588c1_1
+  - libssh2=1.11.1=hf672d98_0
+  - libstdcxx=14.2.0=hc0a3c3a_1
+  - libstdcxx-ng=14.2.0=h4852527_1
+  - libsystemd0=257.2=h3dc2cb9_0
+  - libtiff=4.7.0=hd9ff511_3
+  - libuuid=2.38.1=h0b41bf4_0
+  - libvorbis=1.3.7=h9c3ff4c_0
+  - libwebp-base=1.5.0=h851e524_0
+  - libxcb=1.17.0=h8a09558_0
+  - libxcrypt=4.4.36=hd590300_1
+  - libxkbcommon=1.8.0=hc4a0caf_0
+  - libxml2=2.13.5=h8d12d68_1
+  - libzip=1.11.2=h6991a6a_0
+  - libzlib=1.3.1=hb9d3cd8_2
+  - llvm-openmp=19.1.7=h024ca30_0
+  - lz4-c=1.10.0=h5888daf_1
+  - mengine=1=h14c3975_1
+  - mesa-libgl-cos7-x86_64=18.3.4=ha675448_1106
+  - mesa-libglapi-cos7-x86_64=18.3.4=ha675448_1106
+  - mmcif_pdbx=2.0.1=pyhd8ed1ab_1
+  - mpeg_encode=1=h14c3975_1
+  - mpg123=1.32.9=hc50e24c_0
+  - mtz2ccp4_px=1.1=h3218e01_0
+  - mysql-common=9.0.1=h266115a_4
+  - mysql-libs=9.0.1=he0572af_4
+  - ncurses=6.5=h2d0b736_3
+  - nlohmann_json=3.11.3=he02047a_1
+  - nspr=4.36=h5888daf_0
+  - nss=3.108=h159eef7_0
+  - numpy=1.26.4=py312heda63a1_0
+  - openjpeg=2.5.3=h5fbd93e_0
+  - openldap=2.6.9=he970967_0
+  - openssl=3.4.0=h7b32b05_1
+  - pandas=2.2.2=py312h1d6d2e6_1
+  - pcre2=10.44=hba22ea6_2
+  - pdb2pqr=3.6.1=pyhd8ed1ab_1
+  - pip=24.0=py312h06a4308_0
+  - pixman=0.44.2=h29eaf8c_0
+  - ply=3.11=pyhd8ed1ab_3
+  - pmw=2.0.1=py312h7900ff3_1008
+  - propka=3.5.1=pyhecae5ae_2
+  - pthread-stubs=0.4=hb9d3cd8_1002
+  - pulseaudio-client=17.0=hb77b528_0
+  - pycollada=0.8=pyhd8ed1ab_1
+  - pycparser=2.22=pyh29332c3_1
+  - pykerberos=1.2.4=py312h3770eae_6
+  - pymol=3.1.3.1=py312h2dc6bc7_0
+  - pymol-bundle=3.1.3.1=0
+  - pymol-web-examples=2.4=1
+  - pyqt=5.15.9=py312h949fe66_5
+  - pyqt5-sip=12.12.2=py312h30efb56_5
+  - pysocks=1.7.1=pyha55dd90_7
+  - python=3.12.8=h9e4cc4f_1_cpython
+  - python-dateutil=2.9.0post0=py312h06a4308_2
+  - python-tzdata=2025.1=pyhd8ed1ab_0
+  - python_abi=3.12=5_cp312
+  - qt-main=5.15.15=hc3cb62f_2
+  - readline=8.2=h5eee18b_0
+  - requests=2.32.3=pyhd8ed1ab_1
+  - rigimol=1.5=h3fd9d12_2
+  - setuptools=69.5.1=py312h06a4308_0
+  - sip=6.7.12=py312h30efb56_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - slm_x509=2024.3=h9bf148f_3
+  - snappy=1.2.1=h8bd8927_1
+  - sysroot_linux-64=2.17=h57e8cba_10
+  - tk=8.6.13=noxft_h4845f30_101
+  - toml=0.10.2=pyhd8ed1ab_1
+  - tomli=2.2.1=pyhd8ed1ab_1
+  - urllib3=2.3.0=pyhd8ed1ab_0
+  - vtk-m=1.8.0=h3fd9d12_2
+  - wheel=0.43.0=py312h06a4308_0
+  - xcb-util=0.4.1=hb711507_2
+  - xcb-util-image=0.4.0=hb711507_2
+  - xcb-util-keysyms=0.4.1=hb711507_0
+  - xcb-util-renderutil=0.3.10=hb711507_0
+  - xcb-util-wm=0.4.2=hb711507_0
+  - xkeyboard-config=2.43=hb9d3cd8_0
+  - xorg-libice=1.1.2=hb9d3cd8_0
+  - xorg-libsm=1.2.5=he73a12e_0
+  - xorg-libx11=1.8.11=h4f16b4b_0
+  - xorg-libxau=1.0.12=hb9d3cd8_0
+  - xorg-libxdamage=1.1.6=hb9d3cd8_0
+  - xorg-libxdmcp=1.1.5=hb9d3cd8_0
+  - xorg-libxext=1.3.6=hb9d3cd8_0
+  - xorg-libxfixes=6.0.1=hb9d3cd8_0
+  - xorg-libxrender=0.9.12=hb9d3cd8_0
+  - xorg-libxxf86vm=1.1.6=hb9d3cd8_0
+  - xz=5.4.6=h5eee18b_1
+  - zstandard=0.23.0=py312hef9b889_1
+  - zstd=1.5.6=ha6fb4c9_0
+  - pip:
+    - astunparse==1.6.3
+    - biopandas==0.4.1
+    - colorama==0.4.6
+    - contourpy==1.2.1
+    - cycler==0.12.1
+    - fonttools==4.53.0
+    - kiwisolver==1.4.5
+    - matplotlib==3.9.0
+    - mdtraj==1.10.0
+    - packaging==24.1
+    - pandas-parallel-apply==2.2
+    - pillow==10.3.0
+    - pyparsing==3.1.2
+    - pytz==2024.1
+    - scipy==1.13.1
+    - seaborn==0.13.2
+    - tqdm==4.66.4
+    - tzdata==2024.1
+prefix: YOUR_PATH

data/df_input.csv

@@ -1,4 +1,10 @@
 The results we obtained after executing the script with this command:
+
+For full dataset:
+```
+python main.py --ncores 25 --threshold 0.45 --scheme closest-heavy --dataset full
+```
+For sample dataset:
+```
+python main.py --ncores 14 --threshold 0.45 --scheme closest-heavy --dataset sample
 ```
-python main.py --ncores 25 --seed 42 --threshold 0.45 --scheme closest-heavy
-```