Wheelodex » Projects » bio-embeddings

bio-embeddings

View on PyPI — Reverse Dependencies (0)

0.2.2 bio_embeddings-0.2.2-py3-none-any.whl

Wheel Details

Project: bio-embeddings
Version: 0.2.2
Filename: bio_embeddings-0.2.2-py3-none-any.whl
Download: [link]
Size: 105407
MD5: 99c4277fd5b247e3904f9f4fd81c5986
SHA256: 83879950107bb51b1b592029d44ec5bc01f750618348e66f06a49835f754155e
Uploaded: 2021-09-06 04:16:15 +0000

dist-info

METADATA · WHEEL · RECORD · entry_points.txt

METADATA

Metadata-Version: 2.1
Name: bio-embeddings
Version: 0.2.2
Summary: A pipeline for protein embedding generation and visualization
Author: Christian Dallago
Author-Email: christian.dallago[at]tum.de
Maintainer: Rostlab
Maintainer-Email: admin[at]rostlab.org
Project-Url: homepage, https://visualize.protein.properties
Project-Url: issues, https://github.com/sacdallago/bio_embeddings/issues
Project-Url: repository, https://github.com/sacdallago/bio_embeddings
License: MIT
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.7.1,<3.10
Requires-Dist: appdirs (<2.0.0,>=1.4.4)
Requires-Dist: atomicwrites (<2.0.0,>=1.4.0)
Requires-Dist: bio-embeddings-allennlp (==0.9.2); extra == "seqvec" or extra == "all"
Requires-Dist: bio-embeddings-bepler (==0.0.1); extra == "bepler" or extra == "all"
Requires-Dist: bio-embeddings-cpcprot (==0.0.1); extra == "cpcprot" or extra == "all"
Requires-Dist: bio-embeddings-deepblast (==0.1.0); extra == "deepblast" or extra == "all"
Requires-Dist: bio-embeddings-plus (==0.1.1); extra == "plus" or extra == "all"
Requires-Dist: bio-embeddings-tape-proteins (==0.5); extra == "cpcprot" or extra == "all"
Requires-Dist: biopython (<2.0,>=1.79)
Requires-Dist: fair-esm (==0.4.0); extra == "esm" or extra == "all"
Requires-Dist: flask (<3.0.0,>=2.0.0); extra == "webserver"
Requires-Dist: fsspec (==0.8.5); extra == "deepblast"
Requires-Dist: gensim (<4.0.0,>=3.8.2)
Requires-Dist: h5py (<4.0.0,>=3.2.1)
Requires-Dist: humanize (<4.0.0,>=3.2.0)
Requires-Dist: importlib_metadata (<5.0.0,>=4.6.1)
Requires-Dist: jax-unirep (<2.0.0,>=1.0.0); extra == "unirep" or extra == "all"
Requires-Dist: jaxlib (<0.2.0,>=0.1.71); extra == "unirep"
Requires-Dist: lock (<2019.0.0,>=2018.3.25)
Requires-Dist: matplotlib (<4.0.0,>=3.2.1)
Requires-Dist: numpy (<2.0.0,>=1.18.3)
Requires-Dist: pandas (<2.0.0,>=1.2.0)
Requires-Dist: plotly (<6.0.0,>=5.1.0)
Requires-Dist: pymongo (<4.0.0,>=3.11.2); extra == "webserver"
Requires-Dist: python-slugify (<6.0.0,>=5.0.2)
Requires-Dist: ruamel.yaml (<0.18.0,>=0.17.10)
Requires-Dist: scikit-learn (<0.25.0,>=0.24.0)
Requires-Dist: scipy (<2.0.0,>=1.4.1)
Requires-Dist: sentry-sdk[flask] (<2.0.0,>=1.0.0); extra == "webserver"
Requires-Dist: torch (<=1.10.0,>=1.8.0)
Requires-Dist: tqdm (<5.0.0,>=4.45.0)
Requires-Dist: transformers (<5.0.0,>=4.5.0); extra == "transformers" or extra == "all"
Requires-Dist: umap-learn (<0.6.0,>=0.5.1)
Provides-Extra: all
Provides-Extra: bepler
Provides-Extra: cpcprot
Provides-Extra: deepblast
Provides-Extra: esm
Provides-Extra: plus
Provides-Extra: seqvec
Provides-Extra: transformers
Provides-Extra: unirep
Provides-Extra: webserver
Description-Content-Type: text/markdown
[Description omitted; length: 10363 characters]

WHEEL

Wheel-Version: 1.0
Generator: poetry 1.0.4
Root-Is-Purelib: true
Tag: py3-none-any

RECORD

Path Digest Size
LICENSE.md sha256=g-ugNA9Aq4lLzjwwT6peZBgMFHidkqKGyMa4QmQpPvQ 1094
README.md sha256=GpWlePqJtLZD7QhCTc7t4cw3LJHuhN3OUM93-yxYOcg 10365
bio_embeddings/__init__.py sha256=Bf8GfWrn10HNPbhFA2-0n1zIQivYeFCMHdODw_Ils2E 450
bio_embeddings/align/__init__.py sha256=fsgRmMB3RhMrHoVG3IRfpCC7_0rcMqNf2iM09zeOn5M 103
bio_embeddings/align/deepblast.py sha256=YU_hslGpuNe818Tmb1s15BWLOHDutL_20VKY22TbOrM 1994
bio_embeddings/align/pipeline.py sha256=ZB-LaFe8ouoaTH3MT6vewnW0gocQxhn4bkjq7wA2tyk 7667
bio_embeddings/bio_embeddings_schema.json sha256=eWgkXQuEFQKoP4hFT8j1mT9LKx1baW8v5xw8Kj5vG3s 11845
bio_embeddings/embed/__init__.py sha256=prEYxgzFje_Tiif3tmVag6L3teHrj0l6QRrHhHx2Lbc 8728
bio_embeddings/embed/bepler_embedder.py sha256=nSCfuhnT8zH3oElLKbAUML6TsFFjr8Q_xzVSlAjxyv4 5047
bio_embeddings/embed/cpcprot_embedder.py sha256=-JKsOQTEqO5ruzj1iGtCjb6ZmRcBFnHEjxb9SyEbbFI 2533
bio_embeddings/embed/embedder_interfaces.py sha256=5aTcEUVzgSYfDSRAx_CBgAlk3e73wPvKP_xFn72Xa0M 7549
bio_embeddings/embed/esm_embedder.py sha256=QyXAqpo23AJu5Yokf48pkzy-m2tU_07b8D0cUWP8J9A 5348
bio_embeddings/embed/fasttext_embedder.py sha256=sj22XjsahUy4VOODbfzFtWks7gd3UOg8eESI7zJNA8o 2192
bio_embeddings/embed/glove_embedder.py sha256=fkPY9nyFeD3A7s1ImNG3m0OGt_X7wEPJC4TGaanbwHI 2185
bio_embeddings/embed/one_hot_encoding_embedder.py sha256=uc0jsda0tpLTmOXx0RkzNHOcU5iWBLR8m22B2az9SVc 1120
bio_embeddings/embed/pipeline.py sha256=ZT6T1-yqMjyn48R-YswFtm1BzBLbFCuhWzr_soHuMp4 15548
bio_embeddings/embed/plus_rnn_embedder.py sha256=04fRvM4ri1dMxNPZI3ih-BiCgnYzXV1pU80nZwD6SiM 3286
bio_embeddings/embed/prottrans_albert_bfd_embedder.py sha256=zdulUloW424cGZhBZaK7gsAmxZkd80jR2qlxMSPNnLw 1792
bio_embeddings/embed/prottrans_base_embedder.py sha256=5vNYZ-4VwJIgVBENCxBb1t-41-iUoKQXwxLvPIgP524 2451
bio_embeddings/embed/prottrans_bert_bfd_embedder.py sha256=Qg8xi0XlQYzTOJ2AyS80Ws1H8d2GwEbfy5nNkLTSwDo 1793
bio_embeddings/embed/prottrans_t5_embedder.py sha256=GPA-NE1a2N7Y9Zs1Jl4uAuNmlsJfgInaW3QODuvgLSA 6763
bio_embeddings/embed/prottrans_xlnet_uniref100_embedder.py sha256=YBeBXl5wgbj1pFMaM0Xo-GKDXER47IaItCKbrN9LQdw 3519
bio_embeddings/embed/seqvec_embedder.py sha256=FSUM-bEAYXyvEHmeCUvXOjL-9sutbZwFt982pbTdWfc 4125
bio_embeddings/embed/unirep_embedder.py sha256=xYMDSHw6JlO7aSWy0mf-cvo2GfCTAIfWoMCtmXSo20Y 2741
bio_embeddings/embed/word2vec_embedder.py sha256=QKPkQw_i2MzM0Zos4Prpmr3jDzvgmUvpI7WQoTEhn4A 2179
bio_embeddings/extract/__init__.py sha256=E0QlS7Sd210eR2MZEwNJkHppf-94_pUNm4RpT3_YTZw 550
bio_embeddings/extract/annotations/BindingResidues.py sha256=JBPiSrLofUUdC8EaJ9gQHtSBGHlFGN46HpB9CRMuAXg 549
bio_embeddings/extract/annotations/Conservation.py sha256=sX7ix_v09YqwYFbNFxHTy-IhF6KpgNhSKmH48gav5DM 1043
bio_embeddings/extract/annotations/Disorder.py sha256=yFCcae8A2rpgVyEzBBW1naLTRZ5TC79YLwu7wzUfkpw 330
bio_embeddings/extract/annotations/Location.py sha256=3Hp5B1Rp6iv_kgS-ul0S9NS5eFHerO6-n8H4hSNWhuY 1069
bio_embeddings/extract/annotations/Membrane.py sha256=IOEE3uNwGCBTn7ts2DGtBJ-TtrmBmAZG4A7ljAKbiaU 363
bio_embeddings/extract/annotations/SecondaryStructure.py sha256=t9vKElSGgmfjCxHBUyORg-Oc0b17WQk0mNYH1ePCJAE 852
bio_embeddings/extract/annotations/__init__.py sha256=1-yhgZ0LuHu3AGm1sFHNPggkH0y_dGAcuuYQPkhOIoU 538
bio_embeddings/extract/basic/BasicAnnotationExtractor.py sha256=GBAMd7WZdBzDguvaS7tMu1nD8gdESc4JS5eXPucLxcU 8215
bio_embeddings/extract/basic/__init__.py sha256=X3Qv7hjrO1rItvloTtspDZKhUTy5FIudzQr8wiIOXug 200
bio_embeddings/extract/basic/annotation_inference_models.py sha256=YiEFoJF-n1urxoTbESCAo-WfY5nd7ld1q3irEKzcOis 2152
bio_embeddings/extract/bindEmbed21DL/__init__.py sha256=IZJ2N530TsRmxiQOYhpy7SVKXlvZ7Ns0e6RN-L6VpBQ 174
bio_embeddings/extract/bindEmbed21DL/bindEmbed21DL_annotation_extractor.py sha256=0kTReHMvJP_spi7kQLIbmo5giG5Jtt6wp2pDKOuiHT0 5783
bio_embeddings/extract/bindEmbed21DL/binding_residues_cnn.py sha256=iEWSyB7k2n7vaKCjqUMqL66PWmmsJ_9NZkUjcd44h2w 1549
bio_embeddings/extract/light_attention/LightAttentionAnnotationExtractor.py sha256=9eTxW00CQ4z5PJBFo4rIXs-9f7ZR7zgrSFnvYZcC_Js 4320
bio_embeddings/extract/light_attention/__init__.py sha256=ouM5z-dFlnQ70oxJ1xBG68ElgSFhrFHcmG_3WDo6C8M 119
bio_embeddings/extract/light_attention/light_attention_model.py sha256=8G6ZpYmId-Or5OlcQ6CRNoE2l4LpHNc6dbSMrvoN3Rg 2131
bio_embeddings/extract/pipeline.py sha256=-zFce3HMxiCQGbFfM2nHluqYRTZV3MhVRKRIB2f89fk 25087
bio_embeddings/extract/prott5cons/__init__.py sha256=kCe1yqwAnBlcGJgElMnX85aIM8aWVH5mOjY_ozZEu6k 110
bio_embeddings/extract/prott5cons/conservation_cnn.py sha256=gVMosRDHF2f52spQZGTwqC9NBsK0w-7_8AK-8_RAxDE 1255
bio_embeddings/extract/prott5cons/prot_t5_cons_annotation_extractor.py sha256=fzqpWZHZyux5e1LUB8hhXTxyAB0vpYHOZJRTPdDQzUc 3467
bio_embeddings/extract/unsupervised_utilities.py sha256=3kgSxSH7zwXKc25gd0ZGD5Cn8iKgxkcfOPhsEOnqgMw 3349
bio_embeddings/mutagenesis/__init__.py sha256=HGF8o1X-JN6oGVeCjJzDq5JJt_n3_zq_dMhSe9Cm5JQ 539
bio_embeddings/mutagenesis/constants.py sha256=LDiOwL8RW5VQra-2RKFuNwcfo5bdxLxJqU8m3jJmK8c 159
bio_embeddings/mutagenesis/pipeline.py sha256=tF6a_weMBXkhYEKAX7Y-z_uWjyD79Npq8SHW1Ztx9PY 4324
bio_embeddings/mutagenesis/protbert_bfd.py sha256=XLNCZq1KQqh6qAF7s3oG8ghZKUgErw3tOAjOmC7iXPE 5562
bio_embeddings/project/__init__.py sha256=ZPLwZLnefVtqDoKWYpB0pWiUDPa0YaeiRQMovnF_bvA 372
bio_embeddings/project/pb_tucker.py sha256=VI3lAtBY0Ym0upP8oyOW3Uh41ZZpgjKT-KoZcNnsNbs 1723
bio_embeddings/project/pipeline.py sha256=1XBynJQ32UDmRg-XJ2aVINjzRQDlFirfrl6hsC9aD0U 6988
bio_embeddings/project/tsne.py sha256=ujaZkPcvJd-pf-bgvskjlq3F_kM6TJXrthTA_wha9QY 712
bio_embeddings/project/umap.py sha256=TFty5akvB6eDusyM5L1Peqd2EYnox0ulfaBik2SBEis 690
bio_embeddings/utilities/__init__.py sha256=eimzYjmMxhwm5oW3zr4JgTCVAQWD2KpLYJ0ym4z-70g 810
bio_embeddings/utilities/backports.py sha256=zVpDkqn36HjwHRmUbfMDXO5SJjEYHZK0s-b133oToFU 667
bio_embeddings/utilities/bisect_embedder_ram.py sha256=6YbHbqv2YIZNgIblV-2ntBlflP2xUdlvFca1kG_-Ysw 2889
bio_embeddings/utilities/cli.py sha256=FvrigxJXHH_db1Mukizlku4qn36XYFwKDMpNwrGKtSk 1004
bio_embeddings/utilities/config.py sha256=TwnjRTJuJyY8gCvuli0MLSuj9rgOWc1l4K1FHWAYCa8 2360
bio_embeddings/utilities/defaults.yml sha256=I_dgiE7ZmNewhHGuOv_JCAA9L6-1Qx8zrJk5lDimQV0 5384
bio_embeddings/utilities/exceptions.py sha256=oFLOtZ1CgMKQpn0MgJapnVBSaANckP2QkrUM20wwC_U 1202
bio_embeddings/utilities/filemanagers/FileManagerInterface.py sha256=l1M3BXV8ZOpLcOdBDLkwMMKA_Jvz5dY2sYsdupXwD20 875
bio_embeddings/utilities/filemanagers/FileSystemFileManager.py sha256=5bNQGV6-EW1_oDAkKOfa8MValtZYBxt5GQojZkbAapI 2734
bio_embeddings/utilities/filemanagers/__init__.py sha256=6-fl_vh4symqi_-AUmbjxUsHUHv6BAl5GDX-yvKt4Rs 429
bio_embeddings/utilities/helpers.py sha256=B9XyRphE0omG9cBoAGYs1pnxL1sWnKmGauPk9A7DO8g 8588
bio_embeddings/utilities/model_size_impl.py sha256=tdVKnXarDBFOVh6a69UYyjyFY9AgXuBgftz_PSHJCP0 2031
bio_embeddings/utilities/model_size_main.py sha256=uSOFrXEkeVX_rMfgDLD6Lk2NwJCwNTw4v6qLsADN7_g 2013
bio_embeddings/utilities/model_size_old.py sha256=Q-4j3o9GeXxxxdV59MjY8xh2N2ib76SgGGXMhuwoxac 1695
bio_embeddings/utilities/pipeline.py sha256=LpB2CrgNEA4CU9NrORdRuWiIa0tvrZ6QoDX0oQg9imc 13611
bio_embeddings/utilities/remote_file_retriever.py sha256=zbsHIHzyajvhOoq2ci7R10uSQUgByqQHv050zQREOKo 4516
bio_embeddings/visualize/__init__.py sha256=1ecDmL6QwZCpz0O7SJAX0Bm-dLu6dmDmRbvecRxkrXw 407
bio_embeddings/visualize/mutagenesis.py sha256=KJmpwyRjI9zRc_VI_3-iLps2Ld4oyfGNKCvl1_2Y-Bw 2707
bio_embeddings/visualize/pipeline.py sha256=l7U0a3JA7y0BHC8xwIWRDGNE37RcoaCKTmUNW8MR5Nw 8003
bio_embeddings/visualize/plotly_plots.py sha256=p5nAVDkgrq1Lsd4meZ6TpFZEuwWSeBYQJk1XyIEjK5Q 4270
pyproject.toml sha256=7KuhS4WMgKE-Of1GLGu5fgwAJ3Z59kSwKCCNphoLZhU 4644
bio_embeddings-0.2.2.dist-info/entry_points.txt sha256=ahGBOXbAGfUjeOLSkWO9qgicfx-_e_CxwzNy1xmmp5o 68
bio_embeddings-0.2.2.dist-info/LICENSE.md sha256=g-ugNA9Aq4lLzjwwT6peZBgMFHidkqKGyMa4QmQpPvQ 1094
bio_embeddings-0.2.2.dist-info/WHEEL sha256=N0LZrBtofpkS5mJXgVHTCEy52Sam4D6PHQWC8HnMeTs 83
bio_embeddings-0.2.2.dist-info/METADATA sha256=Hs7IYIWh93zAwevCGEVTiRgGzt8Y3nOj8OQB8mHrPJA 13465
bio_embeddings-0.2.2.dist-info/RECORD — —

entry_points.txt

[console_scripts]
bio_embeddings = bio_embeddings.utilities.cli:main