diff --git a/examples/evodiff.ipynb b/examples/evodiff.ipynb index 27e2e25..5bc8fbb 100644 --- a/examples/evodiff.ipynb +++ b/examples/evodiff.ipynb @@ -36,89 +36,235 @@ "name": "stdout", "output_type": "stream", "text": [ - "Found existing installation: evodiff 0.2.3\n", - "Uninstalling evodiff-0.2.3:\n", - " Successfully uninstalled evodiff-0.2.3\n", - "Collecting evodiff==0.2.3\n", - " Obtaining dependency information for evodiff==0.2.3 from https://files.pythonhosted.org/packages/82/2f/872ed91402c7174cc1e8f542139011327963cb0d96a57db8998e3e091194/evodiff-0.2.3-py3-none-any.whl.metadata\n", - " Using cached evodiff-0.2.3-py3-none-any.whl.metadata (14 kB)\n", - "Requirement already satisfied: pandas in /Users/nityathakkar/opt/anaconda3/envs/evodiff/lib/python3.8/site-packages (from evodiff==0.2.3) (2.0.3)\n", - "Requirement already satisfied: lmdb in /Users/nityathakkar/opt/anaconda3/envs/evodiff/lib/python3.8/site-packages (from evodiff==0.2.3) (1.4.1)\n", - "Requirement already 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"Using cached werkzeug-2.3.7-py3-none-any.whl (242 kB)\n", + "Installing collected packages: pytz, pdb-tools, msgpack, lmdb, fair-esm, websocket-client, urllib3, tzdata, tqdm, threadpoolctl, tabulate, sqlparse, smmap, sequence-models, querystring-parser, pyyaml, pyparsing, pyjwt, protobuf, pillow, oauthlib, numpy, networkx, mmtf-python, MarkupSafe, kiwisolver, joblib, itsdangerous, importlib-resources, idna, gunicorn, greenlet, fonttools, fasteners, entrypoints, cycler, cloudpickle, click, charset-normalizer, certifi, blosum, blinker, Werkzeug, sqlalchemy, scipy, requests, pyarrow, pandas, mrcfile, markdown, Mako, Jinja2, gsd, gitdb, contourpy, biopython, scikit-learn, matplotlib, GridDataFormats, gitpython, Flask, docker, databricks-cli, biotite, alembic, seaborn, mlflow, mdanalysis, evodiff\n", + "Successfully installed Flask-2.3.3 GridDataFormats-1.0.1 Jinja2-3.1.2 Mako-1.2.4 MarkupSafe-2.1.3 Werkzeug-2.3.7 alembic-1.12.0 biopython-1.81 biotite-0.38.0 blinker-1.6.2 blosum-2.0.2 certifi-2023.7.22 charset-normalizer-3.2.0 click-8.1.7 cloudpickle-2.2.1 contourpy-1.1.0 cycler-0.11.0 databricks-cli-0.17.7 docker-6.1.3 entrypoints-0.4 evodiff-1.1.0 fair-esm-2.0.0 fasteners-0.18 fonttools-4.42.1 gitdb-4.0.10 gitpython-3.1.36 greenlet-2.0.2 gsd-3.1.1 gunicorn-21.2.0 idna-3.4 importlib-resources-6.0.1 itsdangerous-2.1.2 joblib-1.3.2 kiwisolver-1.4.5 lmdb-1.4.1 markdown-3.4.4 matplotlib-3.7.3 mdanalysis-2.4.3 mlflow-2.7.0 mmtf-python-1.1.3 mrcfile-1.4.3 msgpack-1.0.5 networkx-3.1 numpy-1.24.4 oauthlib-3.2.2 pandas-2.0.3 pdb-tools-2.5.0 pillow-10.0.0 protobuf-4.24.3 pyarrow-13.0.0 pyjwt-2.8.0 pyparsing-3.1.1 pytz-2023.3.post1 pyyaml-6.0.1 querystring-parser-1.2.4 requests-2.31.0 scikit-learn-1.3.0 scipy-1.10.1 seaborn-0.12.2 sequence-models-1.7.0 smmap-5.0.0 sqlalchemy-2.0.20 sqlparse-0.4.4 tabulate-0.9.0 threadpoolctl-3.2.0 tqdm-4.66.1 tzdata-2023.3 urllib3-1.26.16 websocket-client-1.6.3\n" ] } ], @@ -152,12 +298,15 @@ "output_type": "stream", "text": [ "Collecting package metadata (current_repodata.json): done\n", + "Solving environment: failed with initial frozen solve. Retrying with flexible solve.\n", + "Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.\n", + "Collecting package metadata (repodata.json): done\n", "Solving environment: done\n", "\n", "\n", "==> WARNING: A newer version of conda exists. <==\n", " current version: 22.9.0\n", - " latest version: 23.7.3\n", + " latest version: 23.7.4\n", "\n", "Please update conda by running\n", "\n", @@ -176,11 +325,97 @@ " - torchvision\n", "\n", "\n", + "The following packages will be downloaded:\n", + "\n", + " package | build\n", + " ---------------------------|-----------------\n", + " cryptography-41.0.3 | py38ha2381d6_0 1.2 MB\n", + " icu-73.1 | hcec6c5f_0 25.1 MB\n", + " libtiff-4.5.1 | hcec6c5f_0 508 KB\n", + " libxml2-2.10.4 | h1bd7e62_1 665 KB\n", + " ------------------------------------------------------------\n", + " Total: 27.4 MB\n", + "\n", + "The following NEW packages will be INSTALLED:\n", + "\n", + " blas pkgs/main/osx-64::blas-1.0-mkl None\n", + " brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py38h9ed2024_1003 None\n", + " bzip2 pkgs/main/osx-64::bzip2-1.0.8-h1de35cc_0 None\n", + " certifi pkgs/main/osx-64::certifi-2023.7.22-py38hecd8cb5_0 None\n", + " cffi pkgs/main/osx-64::cffi-1.15.1-py38hc55c11b_0 None\n", + " charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0 None\n", + " cpuonly pytorch/noarch::cpuonly-2.0-0 None\n", + " cryptography pkgs/main/osx-64::cryptography-41.0.3-py38ha2381d6_0 None\n", + " ffmpeg pytorch/osx-64::ffmpeg-4.3-h0a44026_0 None\n", + " filelock pkgs/main/osx-64::filelock-3.9.0-py38hecd8cb5_0 None\n", + " freetype pkgs/main/osx-64::freetype-2.12.1-hd8bbffd_0 None\n", + " gettext pkgs/main/osx-64::gettext-0.21.0-he85b6c0_1 None\n", + " giflib pkgs/main/osx-64::giflib-5.2.1-h6c40b1e_3 None\n", + " gmp pkgs/main/osx-64::gmp-6.2.1-he9d5cce_3 None\n", + " gmpy2 pkgs/main/osx-64::gmpy2-2.1.2-py38hd5de756_0 None\n", + " gnutls pkgs/main/osx-64::gnutls-3.6.15-hed9c0bf_0 None\n", + " icu pkgs/main/osx-64::icu-73.1-hcec6c5f_0 None\n", + " idna pkgs/main/osx-64::idna-3.4-py38hecd8cb5_0 None\n", + " intel-openmp pkgs/main/osx-64::intel-openmp-2023.1.0-ha357a0b_43547 None\n", + " jinja2 pkgs/main/osx-64::jinja2-3.1.2-py38hecd8cb5_0 None\n", + " jpeg pkgs/main/osx-64::jpeg-9e-h6c40b1e_1 None\n", + " lame pkgs/main/osx-64::lame-3.100-h1de35cc_0 None\n", + " lcms2 pkgs/main/osx-64::lcms2-2.12-hf1fd2bf_0 None\n", + " lerc pkgs/main/osx-64::lerc-3.0-he9d5cce_0 None\n", + " libdeflate pkgs/main/osx-64::libdeflate-1.17-hb664fd8_0 None\n", + " libiconv pkgs/main/osx-64::libiconv-1.16-hca72f7f_2 None\n", + " libidn2 pkgs/main/osx-64::libidn2-2.3.4-h6c40b1e_0 None\n", + " libpng pkgs/main/osx-64::libpng-1.6.39-h6c40b1e_0 None\n", + " libtasn1 pkgs/main/osx-64::libtasn1-4.19.0-h6c40b1e_0 None\n", + " libtiff pkgs/main/osx-64::libtiff-4.5.1-hcec6c5f_0 None\n", + " libunistring pkgs/main/osx-64::libunistring-0.9.10-h9ed2024_0 None\n", + " libwebp pkgs/main/osx-64::libwebp-1.2.4-hf6ce154_1 None\n", + " libwebp-base pkgs/main/osx-64::libwebp-base-1.2.4-h6c40b1e_1 None\n", + " libxml2 pkgs/main/osx-64::libxml2-2.10.4-h1bd7e62_1 None\n", + " llvm-openmp pkgs/main/osx-64::llvm-openmp-14.0.6-h0dcd299_0 None\n", + " lz4-c pkgs/main/osx-64::lz4-c-1.9.4-hcec6c5f_0 None\n", + " markupsafe pkgs/main/osx-64::markupsafe-2.1.1-py38hca72f7f_0 None\n", + " mkl pkgs/main/osx-64::mkl-2023.1.0-h8e150cf_43559 None\n", + " mkl-service pkgs/main/osx-64::mkl-service-2.4.0-py38h6c40b1e_1 None\n", + " mkl_fft pkgs/main/osx-64::mkl_fft-1.3.6-py38h07fba90_1 None\n", + " mkl_random pkgs/main/osx-64::mkl_random-1.2.2-py38h07fba90_1 None\n", + " mpc pkgs/main/osx-64::mpc-1.1.0-h6ef4df4_1 None\n", + " mpfr pkgs/main/osx-64::mpfr-4.0.2-h9066e36_1 None\n", + " mpmath pkgs/main/osx-64::mpmath-1.3.0-py38hecd8cb5_0 None\n", + " nettle pkgs/main/osx-64::nettle-3.7.3-h230ac6f_1 None\n", + " networkx pkgs/main/osx-64::networkx-3.1-py38hecd8cb5_0 None\n", + " numpy pkgs/main/osx-64::numpy-1.23.5-py38h47b59a4_1 None\n", + " numpy-base pkgs/main/osx-64::numpy-base-1.23.5-py38hcfaf2c3_1 None\n", + " openh264 pkgs/main/osx-64::openh264-2.1.1-h8346a28_0 None\n", + " pillow pkgs/main/osx-64::pillow-9.4.0-py38hcec6c5f_0 None\n", + " pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0 None\n", + " pyopenssl pkgs/main/osx-64::pyopenssl-23.2.0-py38hecd8cb5_0 None\n", + " pysocks pkgs/main/osx-64::pysocks-1.7.1-py38_1 None\n", + " pytorch pytorch/osx-64::pytorch-2.0.1-py3.8_0 None\n", + " pytorch-mutex pytorch/noarch::pytorch-mutex-1.0-cpu None\n", + " requests pkgs/main/osx-64::requests-2.31.0-py38hecd8cb5_0 None\n", + " sympy pkgs/main/osx-64::sympy-1.11.1-py38hecd8cb5_0 None\n", + " tbb pkgs/main/osx-64::tbb-2021.8.0-ha357a0b_0 None\n", + " torchaudio pytorch/osx-64::torchaudio-2.0.2-py38_cpu None\n", + " torchvision pytorch/osx-64::torchvision-0.15.2-py38_cpu None\n", + " urllib3 pkgs/main/osx-64::urllib3-1.26.16-py38hecd8cb5_0 None\n", + " zstd pkgs/main/osx-64::zstd-1.5.5-hc035e20_0 None\n", + "\n", + "The following packages will be UPDATED:\n", + "\n", + " ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hecd8cb5_0 None\n", + "\n", "The following packages will be SUPERSEDED by a higher-priority channel:\n", "\n", - " certifi conda-forge/noarch::certifi-2023.7.22~ --> pkgs/main/osx-64::certifi-2023.7.22-py38hecd8cb5_0 None\n", + " openssl conda-forge::openssl-1.1.1w-h8a1eda9_0 --> pkgs/main::openssl-1.1.1w-hca72f7f_0 None\n", + "\n", "\n", "\n", + "Downloading and Extracting Packages\n", + "libxml2-2.10.4 | 665 KB | ##################################### | 100% \n", + "cryptography-41.0.3 | 1.2 MB | ##################################### | 100% \n", + "libtiff-4.5.1 | 508 KB | ##################################### | 100% \n", + "icu-73.1 | 25.1 MB | ##################################### | 100% \n", "Preparing transaction: done\n", "Verifying transaction: done\n", "Executing transaction: done\n", @@ -207,7 +442,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": { "pycharm": { "name": "#%%\n" @@ -224,7 +459,7 @@ "\n", "==> WARNING: A newer version of conda exists. <==\n", " current version: 22.9.0\n", - " latest version: 23.7.3\n", + " latest version: 23.7.4\n", "\n", "Please update conda by running\n", "\n", @@ -232,8 +467,53 @@ "\n", "\n", "\n", - "# All requested packages already installed.\n", + "## Package Plan ##\n", + "\n", + " environment location: /Users/nityathakkar/opt/anaconda3/envs/evodiff\n", + "\n", + " added / updated specs:\n", + " - pyg\n", + "\n", + "\n", + "The following NEW packages will be INSTALLED:\n", + "\n", + " appdirs pkgs/main/noarch::appdirs-1.4.4-pyhd3eb1b0_0 None\n", + " joblib pkgs/main/osx-64::joblib-1.2.0-py38hecd8cb5_0 None\n", + " libgfortran pkgs/main/osx-64::libgfortran-5.0.0-11_3_0_hecd8cb5_28 None\n", + " libgfortran5 pkgs/main/osx-64::libgfortran5-11.3.0-h9dfd629_28 None\n", + " pooch pkgs/main/noarch::pooch-1.4.0-pyhd3eb1b0_0 None\n", + " pyg pyg/osx-64::pyg-2.3.1-py38_torch_2.0.0_cpu None\n", + " pyparsing pkgs/main/osx-64::pyparsing-3.0.9-py38hecd8cb5_0 None\n", + " scikit-learn pkgs/main/osx-64::scikit-learn-1.2.2-py38hcec6c5f_0 None\n", + " scipy pkgs/main/osx-64::scipy-1.10.1-py38hf241641_1 None\n", + " threadpoolctl pkgs/main/noarch::threadpoolctl-2.2.0-pyh0d69192_0 None\n", + " tqdm pkgs/main/osx-64::tqdm-4.65.0-py38h01d92e1_0 None\n", + "\n", + "The following packages will be UPDATED:\n", + "\n", + " ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hecd8cb5_0 None\n", + "\n", + "The following packages will be SUPERSEDED by a higher-priority channel:\n", + "\n", + " certifi conda-forge/noarch::certifi-2023.7.22~ --> pkgs/main/osx-64::certifi-2023.7.22-py38hecd8cb5_0 None\n", + " openssl conda-forge::openssl-1.1.1w-h8a1eda9_0 --> pkgs/main::openssl-1.1.1w-hca72f7f_0 None\n", + "\n", + "\n", + "Preparing transaction: done\n", + "Verifying transaction: done\n", + "Executing transaction: | \n", + "\n", + " Installed package of scikit-learn can be accelerated using scikit-learn-intelex.\n", + " More details are available here: https://intel.github.io/scikit-learn-intelex\n", + "\n", + " For example:\n", + "\n", + " $ conda install scikit-learn-intelex\n", + " $ python -m sklearnex my_application.py\n", + "\n", + " \n", "\n", + "done\n", "Retrieving notices: ...working... done\n", "\n", "Note: you may need to restart the kernel to use updated packages.\n" @@ -246,7 +526,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "metadata": { "pycharm": { "name": "#%%\n" @@ -257,13 +537,14 @@ "name": "stdout", "output_type": "stream", "text": [ - "Collecting package metadata (current_repodata.json): done\n", + "Collecting package metadata (current_repodata.json): \\ WARNING conda.models.version:get_matcher(542): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1\n", + "done\n", "Solving environment: done\n", "\n", "\n", "==> WARNING: A newer version of conda exists. <==\n", " current version: 22.9.0\n", - " latest version: 23.7.3\n", + " latest version: 23.7.4\n", "\n", "Please update conda by running\n", "\n", @@ -279,9 +560,19 @@ " - torch-scatter\n", "\n", "\n", + "The following NEW packages will be INSTALLED:\n", + "\n", + " libprotobuf pkgs/main/osx-64::libprotobuf-3.20.3-hfff2838_0 None\n", + " libuv conda-forge/osx-64::libuv-1.46.0-h0c2f820_0 None\n", + " ninja conda-forge/osx-64::ninja-1.11.1-hb8565cd_0 None\n", + " torch-scatter conda-forge/osx-64::torch-scatter-2.1.1-py38hf47b5ae_1 None\n", + "\n", "The following packages will be SUPERSEDED by a higher-priority channel:\n", "\n", + " ca-certificates pkgs/main::ca-certificates-2023.08.22~ --> conda-forge::ca-certificates-2023.7.22-h8857fd0_0 None\n", " certifi pkgs/main/osx-64::certifi-2023.7.22-p~ --> conda-forge/noarch::certifi-2023.7.22-pyhd8ed1ab_0 None\n", + " openssl pkgs/main::openssl-1.1.1w-hca72f7f_0 --> conda-forge::openssl-1.1.1w-h8a1eda9_0 None\n", + " pytorch pytorch::pytorch-2.0.1-py3.8_0 --> pkgs/main::pytorch-2.0.1-cpu_py38h77673e4_0 None\n", "\n", "\n", "Preparing transaction: done\n", @@ -316,7 +607,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 5, "metadata": { "pycharm": { "name": "#%%\n" @@ -345,7 +636,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 6, "metadata": { "pycharm": { "name": "#%%\n" @@ -356,14 +647,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "100%|█████████████████████████████████████████████████████████████████████████████████| 100/100 [00:05<00:00, 17.88it/s]" + "100%|██████████| 100/100 [00:10<00:00, 9.80it/s]" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Generated sequence: ['MKLFITAAGAAAFVAASAAAQAGPCAEGHANTHTPQSSHSPITAEVGAINFVAVPTDKLADHQGPFDEPSVQTDVVVITPNAEALTLEEAELSALIDETG']\n" + "Generated sequence: ['MLIENPSLETVCSLKSPYKLYDFELQEIRESWEYTWQVNSEEDKFKSIISGFLRFAEFYQKLVKVSADEVYKIPGELVTNFKLMWKLQAKLSKAKYEVER']\n" ] }, { @@ -397,7 +688,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 7, "metadata": { "pycharm": { "name": "#%%\n" @@ -410,6 +701,14 @@ "text": [ "sohl-dickstein\n" ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Downloading: \"https://zenodo.org/record/8045076/files/d3pm-uniform-38M.tar?download=1\" to /Users/nityathakkar/.cache/torch/hub/checkpoints/d3pm-uniform-38M.tar\n", + "100%|██████████| 434M/434M [05:46<00:00, 1.31MB/s] \n" + ] } ], "source": [ @@ -432,7 +731,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 8, "metadata": { "pycharm": { "name": "#%%\n" @@ -443,14 +742,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "100%|█████████████████████████████████████████████████████████████████████████████████| 499/499 [00:24<00:00, 20.09it/s]" + "100%|██████████| 499/499 [00:57<00:00, 8.73it/s]" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "final seq ['MKGTVNYSSSKTQIKLAQTHPDKAAMEMKTTSLKLCRHQNQLFLNRTYSTRSSTIKASRSGLLSNWGQHRRGTFSSKYDQNPNGIAPCCMTTFEHKREDR']\n" + "final seq ['MLCIRDVAHRVLHKRPAAPIQITAASAAVSLSDSHTAIAASASDAAAVFDSEDRRNRERGEAASGENTMLTVSVASIKQFSLAVGGEDISPAPESGSAPV']\n" ] }, { @@ -494,7 +793,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 18, "metadata": { "pycharm": { "name": "#%%\n" @@ -523,34 +822,27 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 19, "metadata": { "pycharm": { "name": "#%%\n" } }, "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "a3m_example/bfd_uniclust_hits.a3m\n" - ] - }, { "name": "stderr", "output_type": "stream", "text": [ - " 0%| | 0/164 [00:00\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n \n", + "application/3dmoljs_load.v0": "
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You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
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You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

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You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

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\n", "" ] @@ -914,9 +1206,9 @@ ], "metadata": { "kernelspec": { - "display_name": "omegafold", + "display_name": "evodiff", "language": "python", - "name": "omegafold" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -933,4 +1225,4 @@ }, "nbformat": 4, "nbformat_minor": 2 -} \ No newline at end of file +}