From b9eef263c68b6286ee25737683e0fbf1df007f69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20Gonz=C3=A1lez=20Duque?= Date: Thu, 13 Jun 2024 11:21:01 +0200 Subject: [PATCH] Update documentation --- _sources/index.md | 6 ++++++ index.html | 4 ++++ searchindex.js | 2 +- 3 files changed, 11 insertions(+), 1 deletion(-) diff --git a/_sources/index.md b/_sources/index.md index 18e43f27..285a585e 100644 --- a/_sources/index.md +++ b/_sources/index.md @@ -13,6 +13,12 @@ Some of `poli`'s features: This documentation also discusses [`poli-baselines`](https://github.com/MachineLearningLifeScience/poli-baselines), a collection of optimizers of these discrete black box functions. +:::{admonition} We are running a benchmark! + +Using `poli` and `poli-baselines`, [we are running a benchmark comparing high-dimensional Bayesian optimization algorithms for discrete sequence](https://machinelearninglifescience.github.io/hdbo_benchmark/). + +::: + ## Getting started A good place to start is the next chapter! [Go to Getting Started](./getting_started/getting_started.md). diff --git a/index.html b/index.html index a4c107f4..d1181a6c 100644 --- a/index.html +++ b/index.html @@ -750,6 +750,10 @@

poli 🧪: a library of discrete objective functions

SMILES and SELFIES support for small molecule manipulation.

This documentation also discusses poli-baselines, a collection of optimizers of these discrete black box functions.

+
+

We are running a benchmark!

+

Using poli and poli-baselines, we are running a benchmark comparing high-dimensional Bayesian optimization algorithms for discrete sequence.

+

Getting started#

A good place to start is the next chapter! Go to Getting Started.

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429], "overrid": 9, "__repr__": 9, "__str__": 9, "arg": [9, 193, 194, 199, 200, 378, 383], "kwarg": [9, 33, 73, 193, 194, 199, 200, 378, 429], "contain": [6, 11, 12, 22, 24, 28, 44, 58, 71, 73, 77, 80, 81, 82, 84, 108, 177, 178, 195, 319, 378, 380, 383, 396, 397, 413, 429], "relat": [12, 13, 24, 45, 76, 107, 382, 422], "around": [15, 136, 145, 255, 260, 266, 381, 386, 439], "therapeut": [13, 14, 15, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332, 377, 381, 385, 386, 388, 389, 390, 392, 393, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 429], "data": [14, 15, 42, 56, 116, 131, 136, 182, 183, 189, 190, 195, 215, 224, 377, 381, 383, 385, 386, 388, 389, 390, 392, 393, 394, 395, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 429], "common": [14, 15, 105, 377, 381, 383, 385, 386, 388, 389, 390, 392, 393, 394, 398, 399, 400, 401, 402, 403, 404, 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398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "yue": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "zhao": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "yusuf": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "roohani": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "jure": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "leskovec": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "connor": [13, 15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], 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392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "zitnik": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "natur": 15, "chemic": [15, 130, 131, 132, 377, 385, 388, 389, 390, 391, 394, 399, 400, 402, 403, 404, 405, 407, 411, 412, 415, 417, 418, 420], "biologi": [15, 136, 157, 164, 170, 265, 377, 393], "18": [13, 14, 15, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332, 377], "10": [13, 14, 15, 44, 113, 120, 123, 126, 130, 131, 132, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 251, 252, 268, 269, 274, 277, 295, 322, 325, 332, 377, 379, 384, 385, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 413, 415, 417, 418, 419, 420, 422, 430, 431, 432, 433, 434, 436, 438, 439, 440, 442, 444], "octob": 15, "2022": [13, 14, 15, 78, 113, 120, 123, 126, 130, 131, 132, 135, 139, 144, 145, 215, 218, 221, 224, 227, 230, 233, 236, 237, 239, 240, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332, 377, 382, 383, 386, 391, 392, 395, 398, 401, 406, 422, 431, 440], "1033": [13, 14, 15, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332], "36": 15, "http": [13, 14, 15, 44, 55, 56, 78, 80, 113, 120, 123, 126, 130, 131, 132, 135, 136, 139, 144, 145, 215, 218, 221, 224, 227, 230, 233, 236, 237, 239, 240, 245, 248, 251, 252, 268, 269, 274, 277, 295, 297, 318, 319, 322, 325, 332, 377, 378, 379, 380, 381, 382, 383, 384, 385, 387, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 422, 426, 429, 430, 431, 433, 436, 440, 442, 444], "doi": [13, 14, 15, 113, 120, 123, 126, 130, 131, 132, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 251, 252, 268, 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325, 332], "01131": [13, 14, 15, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332], "2": [13, 14, 15, 34, 44, 78, 81, 113, 120, 123, 126, 135, 139, 144, 157, 164, 170, 177, 178, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 265, 268, 269, 274, 277, 295, 297, 313, 316, 319, 322, 325, 332, 377, 378, 380, 381, 383, 384, 385, 386, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 426, 430, 431, 432, 433, 436, 438, 440, 442, 444], "oracle_nam": [14, 140], "str": [14, 23, 26, 29, 30, 33, 34, 35, 36, 47, 48, 49, 50, 51, 53, 56, 57, 59, 62, 63, 72, 73, 75, 79, 81, 82, 83, 85, 86, 87, 107, 109, 131, 140, 158, 165, 171, 206, 283, 284, 316, 378, 383, 419, 424, 429, 433, 440], "from_smil": [140, 256, 261], "true": [33, 34, 47, 48, 49, 50, 51, 56, 79, 81, 82, 87, 107, 109, 140, 183, 200, 205, 241, 256, 261, 313, 378, 383, 396, 397, 419, 422, 424, 428, 429], "kwargs_for_oracl": 14, "repres": [26, 63, 81, 86, 140, 199, 426], "It": [33, 62, 63, 136, 336, 378, 379, 380, 383, 391, 393, 423, 426, 430], "name": [11, 14, 15, 23, 29, 30, 33, 34, 35, 36, 53, 56, 57, 73, 75, 85, 86, 87, 107, 109, 131, 140, 316, 319, 378, 379, 380, 383, 384, 395, 396, 397, 419, 422, 424, 426, 428, 429, 431, 433, 440], "comput": [25, 59, 79, 81, 83, 116, 131, 136, 157, 158, 164, 165, 167, 170, 171, 237, 239, 240, 253, 256, 261, 263, 265, 297, 377, 380, 381, 382, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 427, 430, 431, 433, 436, 440, 442, 444], "dock": [130, 131, 132, 135, 136, 139, 140, 141, 377, 381, 386, 391, 427], "score": [130, 131, 132, 158, 165, 171, 377, 381, 384, 386, 391, 392, 393, 396, 397, 406, 410, 427], "an": [6, 13, 14, 15, 21, 25, 29, 35, 36, 39, 41, 44, 47, 48, 49, 50, 51, 52, 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383, 395, 399, 400, 412, 420, 422, 427, 429, 430, 431, 433, 436, 439, 440, 442], "en": [56, 318, 385, 388, 389, 390, 391, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 422, 426, 431, 442], "authent": [56, 62, 63], "keep": [56, 83, 292, 396, 397, 436], "your": [6, 56, 136, 379, 382, 383, 384, 393, 395, 396, 397, 414, 424, 427], "account": 56, "secur": 56, "person": [56, 395], "fine": [56, 380], "grain": 56, "get_repo": 57, "release_2023_09": 57, "068441957858f786c227825d90eb2c43f4f2b000": 57, "internet": 58, "reproduc": 58, "purpos": 58, "make": [58, 292, 380, 382, 383, 384, 395, 413, 428, 429, 439], "sure": [58, 380, 382, 383, 384, 395, 413, 424, 428, 429], "malici": 58, "being": [58, 292, 382, 384, 395], "filepath": 59, "read_mod": 59, "rb": 59, "md5": [59, 384], "hex": 59, "digest": 59, "open": [59, 251, 252, 377, 383, 408, 409, 424, 431], "binari": [59, 79, 136, 158, 165, 171, 383, 395, 396, 397], "form": [11, 59, 383], "mode": [59, 80], "read": [59, 79, 190, 383, 399, 400, 412, 420, 424, 428], "hex_digest": 59, "txt": [59, 79, 83, 378, 382, 383, 395, 396, 397, 424], "d41d8cd98f00b204e9800998ecf8427": 59, "wrap": [60, 61, 429], "interprocess": [60, 61], "commun": [6, 60, 61, 62, 106, 378, 408, 409], "kwargs_for_factori": [62, 107, 109], "connect": [62, 63, 75, 199], "inter": 62, "These": [62, 378, 381, 383, 384, 386, 395, 416, 422, 424, 426], "inner": 62, "up": [62, 63, 379, 391, 393, 413, 423, 424, 429], "listen": 62, "random": [62, 97, 98, 99, 100, 107, 109, 379, 381, 392, 398, 401, 423, 426, 428, 430, 431, 432, 434, 436, 438, 439, 442, 443, 444], "subprocess": [62, 383], "expect": [6, 62, 78, 79, 80, 83, 136, 158, 165, 171, 378, 379, 381, 383, 384, 385, 387, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 424, 429, 430, 431, 433, 436, 440, 442, 444], "well": [62, 380, 383, 391, 427, 428, 432], "other": [14, 62, 113, 256, 261, 378, 379, 382, 422, 424, 427, 428, 429], "objective_factori": [62, 357, 378, 380, 395, 414, 424, 426, 428, 429, 431, 433, 440], "determin": 62, "client": 63, "get": [63, 74, 87, 378, 379, 383, 386, 399, 400, 412, 420, 423, 424, 426, 428, 429], "eoferror": 63, "host": 63, "readi": [63, 183], "yet": [63, 378, 423], "connectionrefusederror": 63, "refus": 63, "attempt": 63, "establish": [63, 75], "retri": 63, "befor": [63, 72, 379, 422, 428, 429], "conda_environ": 72, "cwd": [72, 73, 383], "activ": [72, 378, 380, 381, 395, 424, 430, 431, 433, 436, 440, 442], "ad": [72, 136, 357, 393, 424, 429], "current": [72, 399, 400, 412, 414, 420, 426, 427], "either": [14, 73, 131, 140, 270, 383, 395, 414, 424, 438], "mother": [74, 75], "receiv": 75, "wait": [75, 429], "occur": 75, "sent": 75, "back": [75, 280], "quit": [75, 378, 384, 426], "messag": [75, 107], "encod": [77, 186, 187, 199, 200, 395], "For": [77, 83, 136, 182, 237, 251, 252, 319, 364, 378, 381, 383, 393, 395, 416, 424, 426, 427, 429, 434], "amino_acid": 77, "n": [13, 77, 113, 120, 123, 126, 130, 131, 132, 144, 218, 221, 227, 230, 233, 236, 245, 248, 274, 277, 295, 319, 322, 325, 332, 377, 380, 381, 383, 385, 388, 389, 390, 391, 392, 394, 398, 399, 400, 402, 403, 404, 405, 407, 411, 412, 415, 416, 417, 418, 419, 420, 424], "d": [77, 251, 252, 297, 313, 377, 382, 384, 416, 424, 440, 442, 444], "c": [77, 130, 131, 132, 377, 380, 383, 385, 388, 389, 390, 391, 392, 394, 398, 399, 400, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 415, 417, 418, 420, 424, 427, 429, 436], "q": [77, 377, 424], "h": [77, 115, 116, 117, 285, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 424, 429], "k": [13, 14, 77, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 255, 268, 269, 274, 277, 295, 309, 322, 325, 332, 377, 424], "m": [77, 135, 188, 251, 252, 377, 383, 384, 385, 387, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 424, 430, 431, 433, 436, 440, 442, 444], "p": [77, 377, 424], "v": [77, 79, 424], "measur": [78, 113, 182, 233, 383, 408, 409], "stabil": [78, 79, 160, 164, 165, 167, 170, 251, 252, 263, 265, 377, 380, 381, 383, 386, 396, 427], "sasa": [78, 79, 153, 157, 158, 159, 167, 170, 171, 172, 263, 265, 381, 386, 396, 397], "foldxinterfac": 78, "queri": [78, 378, 379, 384, 385, 387, 388, 389, 390, 391, 392, 393, 394, 395, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 423, 429], "heavili": [6, 78, 383], "inspir": [78, 383], "wai": [21, 78, 379, 380, 383, 423, 424, 426, 427], "lambo": [78, 136, 145, 237, 239, 240, 241, 381, 383, 386, 422], "automat": [78, 109, 377, 378, 382], "acceler": [78, 145, 237, 239, 240, 377, 395, 406], "bayesian": [78, 145, 237, 239, 240, 364, 377, 379, 381, 395, 406, 423, 431, 433, 440], "biolog": [78, 145, 237, 239, 240, 377, 395, 406], "design": [13, 78, 113, 120, 123, 126, 130, 131, 132, 135, 144, 145, 199, 215, 218, 221, 224, 227, 230, 233, 236, 237, 239, 240, 245, 248, 274, 277, 295, 322, 325, 332, 377, 378, 379, 381, 382, 385, 386, 388, 389, 390, 391, 392, 394, 395, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 411, 412, 415, 417, 418, 420, 422, 423, 426, 429], "withdenois": 78, "autoencod": [78, 145, 199, 237, 239, 240, 377, 395, 406, 430, 431, 432, 436, 442, 444], "stanton": [78, 145, 237, 239, 240, 377, 382, 383, 395, 406, 422], "samuel": [78, 145, 237, 239, 240, 377, 395, 406, 440], "weslei": [78, 145, 237, 239, 240, 377, 395, 406], "maddox": [78, 145, 237, 239, 240, 377, 395, 406], "nate": [78, 145, 237, 239, 240, 377, 395, 406], "gruver": [78, 145, 237, 239, 240, 377, 395, 406], "phillip": [78, 145, 237, 239, 240, 377, 395, 406], "maffetton": [78, 145, 237, 239, 240, 377, 395, 406], "emili": [78, 145, 237, 239, 240, 377, 395, 406], "delanei": [78, 145, 237, 239, 240, 377, 395, 406], "peyton": [78, 145, 237, 239, 240, 377, 395, 406], "greensid": [78, 145, 237, 239, 240, 377, 395, 406], "andrew": [78, 145, 237, 239, 240, 377, 395, 406], "gordon": [78, 145, 237, 239, 240, 377, 395, 406], "wilson": [78, 145, 237, 239, 240, 377, 395, 406], "arxiv": [13, 78, 145, 237, 239, 240, 377, 395, 406, 433, 436], "juli": [78, 145, 237, 239, 240, 377, 395, 396, 397, 398, 401, 406], "ab": [13, 78, 145, 237, 239, 240, 377, 395, 406, 433, 436], "2203": [78, 145, 237, 239, 240, 377, 395, 406], "12742": [78, 145, 237, 239, 240, 377, 395, 406], "samuelstanton": [78, 136, 395], "working_dir": [79, 383], "interact": [79, 383], "engin": [79, 297, 416, 432], "softwar": [79, 382, 384, 385, 387, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 430, 431, 433, 436, 440, 442, 444], "where": [79, 115, 116, 117, 200, 378, 379, 381, 383, 413, 423, 427, 430, 431, 433, 436, 440, 442], "store": [79, 379, 384, 422, 427], "pdb_file": 79, "remove_and_renam": 79, "ph": [79, 383, 396, 397], "remove_heteroatom": 79, "_repair_if_necessary_and_provide_path": 79, "_simulate_mut": 79, "_read_energi": 79, "_compute_sasa": 79, "solvent": [79, 153, 158, 159, 167, 171, 172, 263, 377, 381, 383, 386], "surfac": [79, 153, 158, 159, 167, 171, 172, 263, 381, 383, 386, 396], "area": [79, 153, 158, 159, 167, 171, 172, 263, 381, 383, 386, 396], "compute_st": 79, "structur": [79, 85, 86, 87, 136, 165, 379, 383, 393, 424], "compute_sasa": 79, "compute_stability_and_sasa": 79, "singl": [79, 83, 251, 252, 297, 377, 381, 384, 386, 406, 408, 409, 416, 422, 424, 432, 438], "copy_foldx_fil": 79, "copi": [79, 378, 379, 383, 423, 439], "write_mutations_to_fil": 79, "wildtype_resiud": 79, "output_dir": 79, "write": [79, 136, 378, 380, 383, 393, 421, 424, 425, 429, 435, 437], "stdout": 79, "previou": [79, 107, 109, 383, 424, 428], "reli": [79, 357, 416, 436, 442], "rotabas": [79, 382, 383, 395, 396, 397], "longer": 79, "manipul": [80, 378, 380, 381], "accord": [80, 181, 383, 426, 429], "certain": [80, 126, 295, 322, 378, 381, 383, 390, 391, 411, 428, 442], "first": [80, 81, 83, 378, 379, 381, 383, 386, 387, 422, 423, 428, 429], "letter": [80, 83, 115, 116, 117, 381, 383, 386, 387, 429], "second": [80, 81, 83, 191, 381, 383, 386, 428, 429], "posit": [80, 81, 83, 180, 185, 379, 383, 384, 422, 423, 426], "third": [80, 83], "chain": [80, 83, 383], "fourth": [80, 83], "mutant": [80, 82, 83, 251, 252, 379, 383, 423], "foldxsuit": [80, 382, 383], "crg": [80, 382, 383], "eu": [80, 382, 383], "string_1": 81, "string_2": 81, "edit": [81, 251, 252, 384], "oper": [81, 382, 428], "assertionerror": [81, 428], "abc": 81, "abd": 81, "def": [81, 378, 379, 423, 424, 429], "wildtype_pdb_fil": [82, 396, 397], "mutated_residue_str": [82, 83], "return_hamming_dist": 82, "find": [82, 115, 116, 117, 136, 378, 384, 391, 393, 424, 426, 428, 430, 431, 433, 436, 440, 442], "closest": 82, "ham": 82, "distanc": [82, 83, 116, 384, 387], "along": 82, "best": [82, 379, 422, 423, 434, 439], "candid": [82, 379], "found": [82, 380, 383, 422, 426, 429], "bio": [83, 86, 87, 383], "individual_list": [83, 383], "levenshtein": 83, "track": [83, 377], "written": 83, "line": [83, 381, 383], "ea1r": 83, "still": [83, 378, 427], "need": [11, 83, 136, 378, 379, 382, 383, 393, 395, 396, 397, 422, 424, 428], "dummi": 83, "itself": [83, 378, 380], "ecd": 83, "acd": 83, "would": [83, 378, 379, 383, 384, 424, 429], "ea1a": 83, "load": [84, 108, 174, 182, 191, 383, 424], "them": [84, 136, 364, 378, 379, 380, 383, 384, 386, 393, 423, 426, 433, 440], "path_to_pdb": [85, 86, 87], "structure_nam": [85, 86, 87], "done": [87, 136, 383, 395, 406, 426], "quietli": 87, "some": [87, 195, 241, 364, 379, 380, 381, 383, 395, 416, 424, 426, 429], "get_structur": [87, 383], "pdbparser": [87, 383], "numpi": [99, 283, 378, 380, 381, 385, 387, 388, 389, 390, 391, 392, 393, 394, 395, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 414, 415, 416, 417, 418, 419, 420, 424, 427, 429, 430, 431, 432, 433, 436, 438, 439, 440, 441, 442, 443, 444], "obj": [], "dynam": 378, "intern": [377, 378, 398, 401, 410, 414], "constructor": [], "factory_kwarg": [], "processwrapp": 106, "how": [136, 378, 379, 380, 381, 383, 386, 422, 423, 424, 426, 428, 429], "objective_nam": [], "loop": [357, 377, 430, 431, 432, 436, 442, 444], "process_wrapp": 106, "observer_init_info": 107, "force_regist": [107, 109], "force_isol": [14, 107, 109, 131, 140, 158, 165, 171, 205, 241, 270], "instantiant": 107, "associ": [107, 377, 422, 427, 430, 444], "caller": [107, 109, 424], "forward": [107, 109, 424], "logger": [107, 109], "ask": [107, 109, 379], "confirm": [107, 109], "By": [107, 256, 261, 316, 378, 379, 396, 397, 428, 432, 438], "onc": [107, 378, 379, 413, 426, 428, 429], "round": [107, 328], "down": 107, "give": [107, 281, 364, 378, 429], "config": 108, "configpars": 108, "just": [109, 378, 395, 396, 397, 422, 424, 428, 429], "One": [109, 382, 426], "aloha": [109, 380, 381, 386, 422, 423, 426, 429, 439], "arrai": [109, 177, 178, 187, 188, 280, 283, 285, 378, 380, 381, 385, 387, 388, 389, 390, 391, 392, 393, 394, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 422, 424, 426, 427, 429, 440], "reshap": [109, 379, 406, 408, 413, 429, 430, 431, 432, 436, 438, 442, 444], "simpl": [115, 116, 117, 130, 131, 132, 181, 255, 256, 260, 261, 378, 379, 422, 423, 426, 428, 429], "goal": [115, 116, 117, 292], "o": [115, 116, 117, 377, 385, 387, 388, 389, 390, 391, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 424, 427, 429, 436], "among": [113, 115, 116, 117, 382, 383, 428], "poli__bas": [115, 315, 327], "yml": [115, 136, 315, 327, 379, 395, 429, 430, 431, 433, 436, 440, 442], "simultan": [14, 116, 131, 140, 256, 261, 270, 384], "map": [116, 131], "symbol": [116, 131], "main": 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429], "overrid": 9, "__repr__": 9, "__str__": 9, "arg": [9, 193, 194, 199, 200, 378, 383], "kwarg": [9, 33, 73, 193, 194, 199, 200, 378, 429], "contain": [6, 11, 12, 22, 24, 28, 44, 58, 71, 73, 77, 80, 81, 82, 84, 108, 177, 178, 195, 319, 378, 380, 383, 396, 397, 413, 429], "relat": [12, 13, 24, 45, 76, 107, 382, 422], "around": [15, 136, 145, 255, 260, 266, 381, 386, 439], "therapeut": [13, 14, 15, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332, 377, 381, 385, 386, 388, 389, 390, 392, 393, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 429], "data": [14, 15, 42, 56, 116, 131, 136, 182, 183, 189, 190, 195, 215, 224, 377, 381, 383, 385, 386, 388, 389, 390, 392, 393, 394, 395, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 429], "common": [14, 15, 105, 377, 381, 383, 385, 386, 388, 389, 390, 392, 393, 394, 398, 399, 400, 401, 402, 403, 404, 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398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "yue": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "zhao": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "yusuf": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "roohani": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "jure": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "leskovec": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "connor": [13, 15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], 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392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "zitnik": [15, 377, 385, 388, 389, 390, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "natur": 15, "chemic": [15, 130, 131, 132, 377, 385, 388, 389, 390, 391, 394, 399, 400, 402, 403, 404, 405, 407, 411, 412, 415, 417, 418, 420], "biologi": [15, 136, 157, 164, 170, 265, 377, 393], "18": [13, 14, 15, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332, 377], "10": [13, 14, 15, 44, 113, 120, 123, 126, 130, 131, 132, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 251, 252, 268, 269, 274, 277, 295, 322, 325, 332, 377, 379, 384, 385, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 413, 415, 417, 418, 419, 420, 422, 430, 431, 432, 433, 434, 436, 438, 439, 440, 442, 444], "octob": 15, "2022": [13, 14, 15, 78, 113, 120, 123, 126, 130, 131, 132, 135, 139, 144, 145, 215, 218, 221, 224, 227, 230, 233, 236, 237, 239, 240, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332, 377, 382, 383, 386, 391, 392, 395, 398, 401, 406, 422, 431, 440], "1033": [13, 14, 15, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332], "36": 15, "http": [13, 14, 15, 44, 55, 56, 78, 80, 113, 120, 123, 126, 130, 131, 132, 135, 136, 139, 144, 145, 215, 218, 221, 224, 227, 230, 233, 236, 237, 239, 240, 245, 248, 251, 252, 268, 269, 274, 277, 295, 297, 318, 319, 322, 325, 332, 377, 378, 379, 380, 381, 382, 383, 384, 385, 387, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 422, 426, 429, 430, 431, 433, 436, 440, 442, 444], "doi": [13, 14, 15, 113, 120, 123, 126, 130, 131, 132, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 251, 252, 268, 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325, 332], "01131": [13, 14, 15, 113, 120, 123, 126, 135, 139, 144, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 268, 269, 274, 277, 295, 322, 325, 332], "2": [13, 14, 15, 34, 44, 78, 81, 113, 120, 123, 126, 135, 139, 144, 157, 164, 170, 177, 178, 215, 218, 221, 224, 227, 230, 233, 236, 245, 248, 265, 268, 269, 274, 277, 295, 297, 313, 316, 319, 322, 325, 332, 377, 378, 380, 381, 383, 384, 385, 386, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 426, 430, 431, 432, 433, 436, 438, 440, 442, 444], "oracle_nam": [14, 140], "str": [14, 23, 26, 29, 30, 33, 34, 35, 36, 47, 48, 49, 50, 51, 53, 56, 57, 59, 62, 63, 72, 73, 75, 79, 81, 82, 83, 85, 86, 87, 107, 109, 131, 140, 158, 165, 171, 206, 283, 284, 316, 378, 383, 419, 424, 429, 433, 440], "from_smil": [140, 256, 261], "true": [33, 34, 47, 48, 49, 50, 51, 56, 79, 81, 82, 87, 107, 109, 140, 183, 200, 205, 241, 256, 261, 313, 378, 383, 396, 397, 419, 422, 424, 428, 429], "kwargs_for_oracl": 14, "repres": [26, 63, 81, 86, 140, 199, 426], "It": [33, 62, 63, 136, 336, 378, 379, 380, 383, 391, 393, 423, 426, 430], "name": [11, 14, 15, 23, 29, 30, 33, 34, 35, 36, 53, 56, 57, 73, 75, 85, 86, 87, 107, 109, 131, 140, 316, 319, 378, 379, 380, 383, 384, 395, 396, 397, 419, 422, 424, 426, 428, 429, 431, 433, 440], "comput": [25, 59, 79, 81, 83, 116, 131, 136, 157, 158, 164, 165, 167, 170, 171, 237, 239, 240, 253, 256, 261, 263, 265, 297, 377, 380, 381, 382, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 427, 430, 431, 433, 436, 440, 442, 444], "dock": [130, 131, 132, 135, 136, 139, 140, 141, 377, 381, 386, 391, 427], "score": [130, 131, 132, 158, 165, 171, 377, 381, 384, 386, 391, 392, 393, 396, 397, 406, 410, 427], "an": [6, 13, 14, 15, 21, 25, 29, 35, 36, 39, 41, 44, 47, 48, 49, 50, 51, 52, 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"do": [56, 136, 239, 240, 378, 379, 383, 395, 406, 413, 423, 427, 429], "except": [56, 63, 75, 378], "github_token_for_poli": [56, 395], "doe": [56, 239, 240, 336], "try": [56, 378, 396, 397], "without": [56, 107, 109, 336, 357, 379, 397, 423, 428, 429], "rate": 56, "limit": [56, 319, 384, 395], "60": 56, "request": [56, 383], "per": 56, "hour": 56, "anonym": [56, 395], "To": [56, 378, 380, 381, 382, 383, 406, 429], "token": [56, 188, 256, 261, 282, 284, 378, 395, 413, 426, 429, 441, 443], "like": [56, 109, 136, 306, 377, 378, 379, 382, 393, 410, 413, 416, 423, 424, 426, 427, 428, 429, 430, 431, 432, 436, 442, 444], "follow": [11, 21, 56, 77, 378, 379, 380, 382, 383, 384, 385, 387, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 422, 423, 426, 428, 429, 430, 431, 433, 436, 438, 440, 442, 444], "instruct": [56, 378, 379, 426], "here": [56, 378, 379, 381, 383, 395, 399, 400, 412, 420, 422, 427, 429, 430, 431, 433, 436, 439, 440, 442], "en": [56, 318, 385, 388, 389, 390, 391, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 422, 426, 431, 442], "authent": [56, 62, 63], "keep": [56, 83, 292, 396, 397, 436], "your": [6, 56, 136, 379, 382, 383, 384, 393, 395, 396, 397, 414, 424, 427], "account": 56, "secur": 56, "person": [56, 395], "fine": [56, 380], "grain": 56, "get_repo": 57, "release_2023_09": 57, "068441957858f786c227825d90eb2c43f4f2b000": 57, "internet": 58, "reproduc": 58, "purpos": 58, "make": [58, 292, 380, 382, 383, 384, 395, 413, 428, 429, 439], "sure": [58, 380, 382, 383, 384, 395, 413, 424, 428, 429], "malici": 58, "being": [58, 292, 382, 384, 395], "filepath": 59, "read_mod": 59, "rb": 59, "md5": [59, 384], "hex": 59, "digest": 59, "open": [59, 251, 252, 377, 383, 408, 409, 424, 431], "binari": [59, 79, 136, 158, 165, 171, 383, 395, 396, 397], "form": [11, 59, 383], "mode": [59, 80], "read": [59, 79, 190, 383, 399, 400, 412, 420, 424, 428], "hex_digest": 59, "txt": [59, 79, 83, 378, 382, 383, 395, 396, 397, 424], "d41d8cd98f00b204e9800998ecf8427": 59, "wrap": [60, 61, 429], "interprocess": [60, 61], "commun": [6, 60, 61, 62, 106, 378, 408, 409], "kwargs_for_factori": [62, 107, 109], "connect": [62, 63, 75, 199], "inter": 62, "These": [62, 378, 381, 383, 384, 386, 395, 416, 422, 424, 426], "inner": 62, "up": [62, 63, 379, 391, 393, 413, 423, 424, 429], "listen": 62, "random": [62, 97, 98, 99, 100, 107, 109, 379, 381, 392, 398, 401, 423, 426, 428, 430, 431, 432, 434, 436, 438, 439, 442, 443, 444], "subprocess": [62, 383], "expect": [6, 62, 78, 79, 80, 83, 136, 158, 165, 171, 378, 379, 381, 383, 384, 385, 387, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 424, 429, 430, 431, 433, 436, 440, 442, 444], "well": [62, 380, 383, 391, 427, 428, 432], "other": [14, 62, 113, 256, 261, 378, 379, 382, 422, 424, 427, 428, 429], "objective_factori": [62, 357, 378, 380, 395, 414, 424, 426, 428, 429, 431, 433, 440], "determin": 62, "client": 63, "get": [63, 74, 87, 378, 379, 383, 386, 399, 400, 412, 420, 423, 424, 426, 428, 429], "eoferror": 63, "host": 63, "readi": [63, 183], "yet": [63, 378, 423], "connectionrefusederror": 63, "refus": 63, "attempt": 63, "establish": [63, 75], "retri": 63, "befor": [63, 72, 379, 422, 428, 429], "conda_environ": 72, "cwd": [72, 73, 383], "activ": [72, 378, 380, 381, 395, 424, 430, 431, 433, 436, 440, 442], "ad": [72, 136, 357, 393, 424, 429], "current": [72, 399, 400, 412, 414, 420, 426, 427], "either": [14, 73, 131, 140, 270, 383, 395, 414, 424, 438], "mother": [74, 75], "receiv": 75, "wait": [75, 429], "occur": 75, "sent": 75, "back": [75, 280], "quit": [75, 378, 384, 426], "messag": [75, 107], "encod": [77, 186, 187, 199, 200, 395], "For": [77, 83, 136, 182, 237, 251, 252, 319, 364, 378, 381, 383, 393, 395, 416, 424, 426, 427, 429, 434], 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401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 424, 430, 431, 433, 436, 440, 442, 444], "p": [77, 377, 424], "v": [77, 79, 424], "measur": [78, 113, 182, 233, 383, 408, 409], "stabil": [78, 79, 160, 164, 165, 167, 170, 251, 252, 263, 265, 377, 380, 381, 383, 386, 396, 427], "sasa": [78, 79, 153, 157, 158, 159, 167, 170, 171, 172, 263, 265, 381, 386, 396, 397], "foldxinterfac": 78, "queri": [78, 378, 379, 384, 385, 387, 388, 389, 390, 391, 392, 393, 394, 395, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 423, 429], "heavili": [6, 78, 383], "inspir": [78, 383], "wai": [21, 78, 379, 380, 383, 423, 424, 426, 427], "lambo": [78, 136, 145, 237, 239, 240, 241, 381, 383, 386, 422], "automat": [78, 109, 377, 378, 382], "acceler": [78, 145, 237, 239, 240, 377, 395, 406], "bayesian": [78, 145, 237, 239, 240, 364, 377, 379, 381, 395, 406, 423, 431, 433, 440], "biolog": [78, 145, 237, 239, 240, 377, 395, 406], "design": [13, 78, 113, 120, 123, 126, 130, 131, 132, 135, 144, 145, 199, 215, 218, 221, 224, 227, 230, 233, 236, 237, 239, 240, 245, 248, 274, 277, 295, 322, 325, 332, 377, 378, 379, 381, 382, 385, 386, 388, 389, 390, 391, 392, 394, 395, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 411, 412, 415, 417, 418, 420, 422, 423, 426, 429], "withdenois": 78, "autoencod": [78, 145, 199, 237, 239, 240, 377, 395, 406, 430, 431, 432, 436, 442, 444], "stanton": [78, 145, 237, 239, 240, 377, 382, 383, 395, 406, 422], "samuel": [78, 145, 237, 239, 240, 377, 395, 406, 440], "weslei": [78, 145, 237, 239, 240, 377, 395, 406], "maddox": [78, 145, 237, 239, 240, 377, 395, 406], "nate": [78, 145, 237, 239, 240, 377, 395, 406], "gruver": [78, 145, 237, 239, 240, 377, 395, 406], "phillip": [78, 145, 237, 239, 240, 377, 395, 406], "maffetton": [78, 145, 237, 239, 240, 377, 395, 406], "emili": [78, 145, 237, 239, 240, 377, 395, 406], "delanei": [78, 145, 237, 239, 240, 377, 395, 406], "peyton": [78, 145, 237, 239, 240, 377, 395, 406], "greensid": [78, 145, 237, 239, 240, 377, 395, 406], "andrew": [78, 145, 237, 239, 240, 377, 395, 406], "gordon": [78, 145, 237, 239, 240, 377, 395, 406], "wilson": [78, 145, 237, 239, 240, 377, 395, 406], "arxiv": [13, 78, 145, 237, 239, 240, 377, 395, 406, 433, 436], "juli": [78, 145, 237, 239, 240, 377, 395, 396, 397, 398, 401, 406], "ab": [13, 78, 145, 237, 239, 240, 377, 395, 406, 433, 436], "2203": [78, 145, 237, 239, 240, 377, 395, 406], "12742": [78, 145, 237, 239, 240, 377, 395, 406], "samuelstanton": [78, 136, 395], "working_dir": [79, 383], "interact": [79, 383], "engin": [79, 297, 416, 432], "softwar": [79, 382, 384, 385, 387, 388, 389, 390, 391, 392, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 415, 416, 417, 418, 419, 420, 430, 431, 433, 436, 440, 442, 444], "where": [79, 115, 116, 117, 200, 378, 379, 381, 383, 413, 423, 427, 430, 431, 433, 436, 440, 442], "store": [79, 379, 384, 422, 427], "pdb_file": 79, "remove_and_renam": 79, "ph": [79, 383, 396, 397], "remove_heteroatom": 79, "_repair_if_necessary_and_provide_path": 79, "_simulate_mut": 79, "_read_energi": 79, "_compute_sasa": 79, "solvent": [79, 153, 158, 159, 167, 171, 172, 263, 377, 381, 383, 386], "surfac": [79, 153, 158, 159, 167, 171, 172, 263, 381, 383, 386, 396], "area": [79, 153, 158, 159, 167, 171, 172, 263, 381, 383, 386, 396], "compute_st": 79, "structur": [79, 85, 86, 87, 136, 165, 379, 383, 393, 424], "compute_sasa": 79, "compute_stability_and_sasa": 79, "singl": [79, 83, 251, 252, 297, 377, 381, 384, 386, 406, 408, 409, 416, 422, 424, 432, 438], "copy_foldx_fil": 79, "copi": [79, 378, 379, 383, 423, 439], "write_mutations_to_fil": 79, "wildtype_resiud": 79, "output_dir": 79, "write": [79, 136, 378, 380, 383, 393, 421, 424, 425, 429, 435, 437], "stdout": 79, "previou": [79, 107, 109, 383, 424, 428], "reli": [79, 357, 416, 436, 442], "rotabas": [79, 382, 383, 395, 396, 397], "longer": 79, "manipul": [80, 378, 380, 381], "accord": [80, 181, 383, 426, 429], "certain": [80, 126, 295, 322, 378, 381, 383, 390, 391, 411, 428, 442], "first": [80, 81, 83, 378, 379, 381, 383, 386, 387, 422, 423, 428, 429], "letter": [80, 83, 115, 116, 117, 381, 383, 386, 387, 429], "second": [80, 81, 83, 191, 381, 383, 386, 428, 429], "posit": [80, 81, 83, 180, 185, 379, 383, 384, 422, 423, 426], "third": [80, 83], "chain": [80, 83, 383], "fourth": [80, 83], "mutant": [80, 82, 83, 251, 252, 379, 383, 423], "foldxsuit": [80, 382, 383], "crg": [80, 382, 383], "eu": [80, 382, 383], "string_1": 81, "string_2": 81, "edit": [81, 251, 252, 384], "oper": [81, 382, 428], "assertionerror": [81, 428], "abc": 81, "abd": 81, "def": [81, 378, 379, 423, 424, 429], "wildtype_pdb_fil": [82, 396, 397], "mutated_residue_str": [82, 83], "return_hamming_dist": 82, "find": [82, 115, 116, 117, 136, 378, 384, 391, 393, 424, 426, 428, 430, 431, 433, 436, 440, 442], "closest": 82, "ham": 82, "distanc": [82, 83, 116, 384, 387], "along": 82, "best": [82, 379, 422, 423, 434, 439], "candid": [82, 379], "found": [82, 380, 383, 422, 426, 429], "bio": [83, 86, 87, 383], "individual_list": [83, 383], "levenshtein": 83, "track": [83, 377], "written": 83, "line": [83, 381, 383], "ea1r": 83, "still": [83, 378, 427], "need": [11, 83, 136, 378, 379, 382, 383, 393, 395, 396, 397, 422, 424, 428], "dummi": 83, "itself": [83, 378, 380], "ecd": 83, "acd": 83, "would": [83, 378, 379, 383, 384, 424, 429], "ea1a": 83, "load": [84, 108, 174, 182, 191, 383, 424], "them": [84, 136, 364, 378, 379, 380, 383, 384, 386, 393, 423, 426, 433, 440], "path_to_pdb": [85, 86, 87], "structure_nam": [85, 86, 87], "done": [87, 136, 383, 395, 406, 426], "quietli": 87, "some": [87, 195, 241, 364, 379, 380, 381, 383, 395, 416, 424, 426, 429], "get_structur": [87, 383], "pdbparser": [87, 383], "numpi": [99, 283, 378, 380, 381, 385, 387, 388, 389, 390, 391, 392, 393, 394, 395, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 414, 415, 416, 417, 418, 419, 420, 424, 427, 429, 430, 431, 432, 433, 436, 438, 439, 440, 441, 442, 443, 444], "obj": [], "dynam": 378, "intern": [377, 378, 398, 401, 410, 414], "constructor": [], "factory_kwarg": [], "processwrapp": 106, "how": [136, 378, 379, 380, 381, 383, 386, 422, 423, 424, 426, 428, 429], "objective_nam": [], "loop": [357, 377, 430, 431, 432, 436, 442, 444], "process_wrapp": 106, "observer_init_info": 107, "force_regist": [107, 109], "force_isol": [14, 107, 109, 131, 140, 158, 165, 171, 205, 241, 270], "instantiant": 107, "associ": [107, 377, 422, 427, 430, 444], "caller": [107, 109, 424], "forward": [107, 109, 424], "logger": [107, 109], "ask": [107, 109, 379], "confirm": [107, 109], "By": [107, 256, 261, 316, 378, 379, 396, 397, 428, 432, 438], "onc": [107, 378, 379, 413, 426, 428, 429], "round": [107, 328], "down": 107, "give": [107, 281, 364, 378, 429], "config": 108, "configpars": 108, "just": [109, 378, 395, 396, 397, 422, 424, 428, 429], "One": [109, 382, 426], "aloha": [109, 380, 381, 386, 422, 423, 426, 429, 439], "arrai": [109, 177, 178, 187, 188, 280, 283, 285, 378, 380, 381, 385, 387, 388, 389, 390, 391, 392, 393, 394, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 422, 424, 426, 427, 429, 440], "reshap": [109, 379, 406, 408, 413, 429, 430, 431, 432, 436, 438, 442, 444], "simpl": [115, 116, 117, 130, 131, 132, 181, 255, 256, 260, 261, 378, 379, 422, 423, 426, 428, 429], "goal": [115, 116, 117, 292], "o": [115, 116, 117, 377, 385, 387, 388, 389, 390, 391, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420, 424, 427, 429, 436], "among": [113, 115, 116, 117, 382, 383, 428], "poli__bas": [115, 315, 327], "yml": [115, 136, 315, 327, 379, 395, 429, 430, 431, 433, 436, 440, 442], "simultan": [14, 116, 131, 140, 256, 261, 270, 384], "map": [116, 131], "symbol": [116, 131], "main": [6, 116, 256, 261, 379, 380, 381, 382, 383, 423, 424, 429], "api": [130, 131, 132, 380, 395], "assess": [130, 131, 132, 251, 252, 381, 386], "small": [130, 131, 132, 256, 378, 380, 391, 392, 393, 410, 424, 426, 428], "protein": [130, 131, 132, 157, 164, 165, 170, 251, 252, 265, 377, 380, 382, 384, 391, 393, 426, 427], "easi": [130, 131, 132, 377, 383, 391, 426, 428], "molecular": [13, 113, 120, 123, 126, 130, 131, 132, 135, 144, 157, 164, 170, 218, 221, 227, 230, 233, 236, 245, 248, 265, 274, 277, 295, 322, 325, 332, 377, 385, 388, 389, 390, 391, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 417, 418, 420], "better": [130, 131, 132, 377, 383, 391], "benchmark": [13, 21, 113, 120, 123, 126, 130, 131, 132, 144, 218, 221, 227, 230, 233, 236, 245, 248, 274, 277, 295, 297, 315, 319, 322, 325, 332, 377, 379, 385, 386, 388, 389, 390, 391, 392, 394, 398, 399, 400, 401, 402, 403, 404, 405, 407, 410, 411, 412, 415, 416, 417, 418, 420], "ligand": [130, 131, 132, 377, 381, 386, 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