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planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 |
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b2btools_single_sequence.xml script.py test-data/input.fasta test-data/random_sequence_01_consisting_of_40_residues.tsv test-data/random_sequence_01_consisting_of_40_residues_dynamine.tsv test-data/random_sequence_02_consisting_of_40_residues.tsv test-data/random_sequence_02_consisting_of_40_residues_dynamine.tsv test-data/random_sequence_03_consisting_of_30_residues.tsv test-data/random_sequence_03_consisting_of_30_residues_dynamine.tsv test-data/random_sequence_04_consisting_of_40_residues.tsv test-data/random_sequence_04_consisting_of_40_residues_dynamine.tsv test-data/random_sequence_05_consisting_of_30_residues.tsv test-data/random_sequence_05_consisting_of_30_residues_dynamine.tsv test-data/random_sequence_06_consisting_of_45_residues.tsv test-data/random_sequence_06_consisting_of_45_residues_dynamine.tsv test-data/random_sequence_07_consisting_of_30_residues.tsv test-data/random_sequence_07_consisting_of_30_residues_dynamine.tsv test-data/random_sequence_08_consisting_of_40_residues.tsv test-data/random_sequence_08_consisting_of_40_residues_dynamine.tsv test-data/random_sequence_09_consisting_of_30_residues.tsv test-data/random_sequence_09_consisting_of_30_residues_dynamine.tsv test-data/random_sequence_10_consisting_of_65_residues.tsv test-data/random_sequence_10_consisting_of_65_residues_dynamine.tsv test-data/random_sequence_11_consisting_of_30_residues.tsv test-data/random_sequence_11_consisting_of_30_residues_dynamine.tsv test-data/test_output.json test-data/test_output_dynamine.json test-data/wrong.fasta test-data/wrong.tsv |
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| diff -r 000000000000 -r b694a77ca1e8 b2btools_single_sequence.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/b2btools_single_sequence.xml Tue Aug 09 12:30:52 2022 +0000 |
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| b'@@ -0,0 +1,708 @@\n+<tool\n+ id="b2btools_single_sequence"\n+ name="b2bTools: Biophysical predictors for single sequences"\n+ version="3.0.5+galaxy0"\n+ license="GPL-3.0"\n+ python_template_version="3.5"\n+ profile="21.05">\n+ <description>from their amino-acid sequences</description>\n+ <xrefs>\n+ <xref type="bio.tools">b2btools</xref>\n+ </xrefs>\n+ <requirements>\n+ <requirement type="package" version="3.0.5">b2btools</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+mkdir -p ./tabular ./plots &&\n+python \'$__tool_directory__/script.py\' --file \'$input\' --output ./tabular --json \'$predictions_output\'\n+ $section_predictors.dynamine\n+ $section_predictors.disomine\n+ $section_predictors.efoldmine\n+ $section_predictors.agmata\n+#if $section_plot.plot == \'--plot\' or $section_plot.plot_all == \'--plot_all\':\n+ --plot-output ./plots\n+#end if\n+ $section_plot.plot\n+ $section_plot.plot_all\n+ $section_plot.highlight\n+ ]]></command>\n+ <inputs>\n+ <param type="data" name="input" format="fasta" label="Protein sequences in FASTA format" help="FASTA file of protein sequences"/>\n+ <section name="section_predictors" title="Biophyisical predictors" help="Configure this section to select the predictions to be executed">\n+ <param\n+ argument="--dynamine"\n+ type="boolean"\n+ checked="true"\n+ truevalue="--dynamine"\n+ falsevalue=""\n+ label="DynaMine: Prediction of protein backbone dynamics from sequence only"\n+ help="Fast predictor of protein backbone dynamics using only sequence information as input. The version here also predicts side-chain dynamics and secondary structure predictors using the same principle." />\n+ <param\n+ argument="--disomine"\n+ type="boolean"\n+ checked="true"\n+ truevalue="--disomine"\n+ falsevalue=""\n+ label="DisoMine: Prediction of protein disorder from sequence only"\n+ help="Predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure and early folding."/>\n+ <param\n+ argument="--efoldmine"\n+ type="boolean"\n+ checked="true"\n+ truevalue="--efoldmine"\n+ falsevalue=""\n+ label="EFoldMine: Prediction of protein early folding regions from sequence only"\n+ help="Predicts from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events."/>\n+ <param\n+ argument="--agmata"\n+ type="boolean"\n+ checked="true"\n+ truevalue="--agmata"\n+ falsevalue=""\n+ label="Agmata: Prediction of protein regions that are likely to cause beta-aggregation"\n+ help="Agmata is a single-sequence based predictor of protein regions that are likely to cause beta-aggregation. It is based on a model that uses the biophysical predictions of protein behaviour, not on amino acid codes directly."/>\n+ </section>\n+ <section name="section_plot" title="Plot options" help="Configure plot output">\n+ <param\n+ name="plot"\n+ argument="--plot"\n+ type="boolean"\n+ label="Plot predicted values by sequence"\n+ truevalue="--plot"\n+ falsevalue=""\n+ help="This option plots predicted values in different files"/>\n+ <param\n+ name="plot_all"\n+ argument="--plot_all"\n+ type="boolean"\n+ label="Plot all sequences together"\n+ trueva'..b'oil`` plot\n+ - ``sequence_01_disoMine`` plot\n+ - ``sequence_01_earlyFolding`` plot\n+ - ``sequence_01_helix`` plot\n+ - ``sequence_01_ppII`` plot\n+ - ``sequence_01_sheet`` plot\n+ - ``sequence_01_sidechain`` plot\n+ - ...\n+ - ``sequence_11_sidechain`` plot\n+\n+- Checking **Plot all** parameter implies that all the input sequences will be plotted together in order to compare predicted features.\n+ - 9 predicted features = 9 plots in PNG format\n+ - **agmata plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+ - **backbone plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+ - **coil plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+ - **disoMine plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+ - **earlyFolding plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+ - **helix plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+ - **ppII plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+ - **sheet plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+ - **sidechain plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)\n+\n+About Bio2Byte\n+--------------\n+\n+**We research the relation between protein sequence and biophysical behavior.**\n+\n+Proteins are the molecular machines that make cells work.\n+They perform a wide variety of functions through interactions with each other and many additional molecules.\n+Traditionally, proteins are described in a single static state (a picture).\n+It is now increasingly recognized that many proteins can adopt multiple states and move between these conformational states dynamically (a movie).\n+\n+We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.\n+Underlying physical and chemical principles are computationally unraveled through data integration,\n+analysis and machine learning, so connecting them to biological events and improving our understanding of the way proteins work.\n+\n+Visit our website for further information: https://bio2byte.be\n+\n+About Bio2Byte tools\n+\'\'\'\'\'\'\'\'\'\'\'\'\'\'\'\'\'\'\'\'\n+The software suite "Bio2byte tools", known as ``b2btools`` offers a set of biophysical predictions for both single protein sequences and MSA input files.\n+\n+**Useful links:**\n+\n+``B2bTools`` is also available on the *Python Package Index* (``PyPI``) https://pypi.org/project/b2bTools/, as well as on *Bioconda* https://bioconda.github.io/recipes/b2btools/README.html.\n+We also provide a set of online examples in Jupyter Notebook format that are available to run on the Google Colab platform on https://github.com/Bio2Byte/public_notebooks.\n+\n+ ]]>\n+ </help>\n+ <creator>\n+ <organization name="bio2Byte" url="https://bio2byte.be" email="Wim.Vranken@vub.be"/>\n+ <organization name="Vrije Universiteit Brussel" url="https://vub.be" alternateName="VUB"/>\n+ <person honorificPrefix="Prof." givenName="Wim" familyName="Vranken" email="Wim.Vranken@vub.be" identifier="http://orcid.org/0000-0001-7470-4324" />\n+ <person givenName="Jose" familyName="Gavalda-Garcia" email="Jose.Gavalda.Garcia@vub.be" identifier="http://orcid.org/0000-0001-6431-3442" />\n+ <person givenName="Adrian" familyName="Diaz" email="Adrian.Diaz@vub.be" identifier="http://orcid.org/0000-0003-0165-1318" />\n+ </creator>\n+ <citations>\n+ <citation type="doi">10.1038/ncomms3741</citation>\n+ <citation type="doi">10.1101/2020.05.25.115253</citation>\n+ <citation type="doi">10.1038/s41598-017-08366-3</citation>\n+ <citation type="doi">10.1093/bioinformatics/btz912</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r b694a77ca1e8 script.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/script.py Tue Aug 09 12:30:52 2022 +0000 |
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| b'@@ -0,0 +1,307 @@\n+import json\n+import optparse\n+import os.path\n+import re\n+import unicodedata\n+\n+import matplotlib.pyplot as plt\n+import numpy as np\n+import pandas as pd\n+from b2bTools import SingleSeq\n+\n+\n+def slugify(value):\n+ """\n+ From https://github.com/django/django/blob/master/django/utils/text.py\n+ Convert to ASCII if \'allow_unicode\'. Convert spaces or repeated\n+ dashes to single dashes. Remove characters that aren\'t alphanumerics,\n+ underscores, or hyphens. Convert to lowercase. Also strip leading and\n+ trailing whitespace, dashes, and underscores.\n+ """\n+ value = str(value)\n+ value = (\n+ unicodedata.normalize("NFKD", value)\n+ .encode("ascii", "ignore")\n+ .decode("ascii")\n+ )\n+ value = re.sub(r"[^\\w\\s-]", "", value.lower())\n+ return re.sub(r"[-\\s]+", "-", value).strip("-_")\n+\n+\n+def check_min_max(predicted_values, former_min, former_max):\n+ seq_max = max(predicted_values)\n+ seq_min = min(predicted_values)\n+ if (\n+ seq_max + 0.1 > former_max\n+ and not np.isnan(seq_max)\n+ and not np.isinf(seq_max)\n+ ):\n+ former_max = seq_max + 0.1\n+ if (\n+ seq_min - 0.1 < former_min\n+ and not np.isnan(seq_min)\n+ and not np.isinf(seq_min)\n+ ):\n+ former_min = seq_min - 0.1\n+ return former_min, former_max\n+\n+\n+def plot_prediction(pred_name, hlighting_regions, predicted_values, seq_name):\n+ thresholds_dict = {\n+ "backbone": {\n+ "membrane spanning": [1.0, 1.5],\n+ "rigid": [0.8, 1.0],\n+ "context-dependent": [0.69, 0.8],\n+ "flexible": [-1.0, 0.69],\n+ },\n+ "earlyFolding": {\n+ "early folds": [0.169, 2.0],\n+ "late folds": [-1.0, 0.169],\n+ },\n+ "disoMine": {"ordered": [-1.0, 0.5], "disordered": [0.5, 2.0]},\n+ }\n+ ordered_regions_dict = {\n+ "backbone": [\n+ "flexible",\n+ "context-dependent",\n+ "rigid",\n+ "membrane spanning",\n+ ],\n+ "earlyFolding": ["late folds", "early folds"],\n+ "disoMine": ["ordered", "disordered"],\n+ }\n+ colors = ["yellow", "orange", "pink", "red"]\n+ ranges_dict = {\n+ "backbone": [-0.2, 1.2],\n+ "sidechain": [-0.2, 1.2],\n+ "ppII": [-0.2, 1.2],\n+ "earlyFolding": [-0.2, 1.2],\n+ "disoMine": [-0.2, 1.2],\n+ "agmata": [-0.2, 1.2],\n+ "helix": [-1.0, 1.0],\n+ "sheet": [-1.0, 1.0],\n+ "coil": [-1.0, 1.0],\n+ }\n+ fig, ax = plt.subplots(1, 1)\n+ fig.set_figwidth(10)\n+ fig.set_figheight(5)\n+ ax.set_title(pred_name + " " + "prediction")\n+ min_value, max_value = ranges_dict[pred_name]\n+ if seq_name == "all":\n+ max_len = 0\n+ for seq in predicted_values.keys():\n+ predictions = predicted_values[seq]\n+ min_value, max_value = check_min_max(\n+ predictions, min_value, max_value\n+ )\n+ ax.plot(range(len(predictions)), predictions, label=seq)\n+ if len(predictions) > max_len:\n+ max_len = len(predictions)\n+ ax.set_xlim([0, max_len - 1])\n+ else:\n+ predictions = predicted_values\n+ min_value, max_value = check_min_max(predictions, min_value, max_value)\n+ ax.plot(range(len(predictions)), predictions, label=seq_name)\n+ ax.set_xlim([0, len(predictions) - 1])\n+ legend_lines = plt.legend(\n+ bbox_to_anchor=(1.04, 1), loc="upper left", fancybox=True, shadow=True\n+ )\n+ ax.add_artist(legend_lines)\n+ # Define regions\n+ if hlighting_regions:\n+ if pred_name in ordered_regions_dict.keys():\n+ for i, prediction in enumerate(ordered_regions_dict[pred_name]):\n+ lower = thresholds_dict[pred_name][prediction][0]\n+ upper = thresholds_dict[pred_name][prediction][1]\n+ color = colors[i]\n+ ax.axhspan(\n+ lower, upper, alpha=0.3, '..b' with open(options.json_output, "w") as f:\n+ f.write(results_json)\n+ first_sequence_key = next(iter(predictions))\n+ prediction_keys = predictions[first_sequence_key].keys()\n+ # Sort column names\n+ tsv_column_names = list(prediction_keys)\n+ tsv_column_names.remove("seq")\n+ tsv_column_names = [\'residue\', *sorted(tsv_column_names)]\n+\n+ df_dictionary = {}\n+ for sequence_key, seq_preds in predictions.items():\n+ residues = seq_preds["seq"]\n+ residues_count = len(residues)\n+ sequence_df = pd.DataFrame(\n+ columns=prediction_keys, index=range(residues_count)\n+ )\n+ sequence_df.index.name = "residue_index"\n+ for predictor in prediction_keys:\n+ sequence_df[predictor] = seq_preds[predictor]\n+ sequence_df = sequence_df.rename(columns={"seq": "residue"})\n+ sequence_df = sequence_df.round(decimals=3)\n+ filename = f"{options.output}/{slugify(sequence_key)}.tsv"\n+ df_dictionary[sequence_key] = filename\n+ sequence_df.to_csv(\n+ filename,\n+ header=True,\n+ columns=tsv_column_names,\n+ sep="\\t"\n+ )\n+ # Plot each individual plot (compatible with plot all)\n+ if options.plot:\n+ for predictor in prediction_keys:\n+ if predictor != "seq":\n+ plot_prediction(\n+ pred_name=predictor,\n+ hlighting_regions=True,\n+ predicted_values=seq_preds[predictor],\n+ seq_name=sequence_key,\n+ )\n+ # Plot all together (compatible with plot individual)\n+ if options.plot_all:\n+ for predictor in prediction_keys:\n+ if predictor != "seq":\n+ results_dictionary = df_dict_to_dict_of_values(\n+ df_dictionary, predictor\n+ )\n+ plot_prediction(\n+ pred_name=predictor,\n+ hlighting_regions=True,\n+ predicted_values=results_dictionary,\n+ seq_name="all",\n+ )\n+\n+\n+if __name__ == "__main__":\n+ parser = optparse.OptionParser()\n+ parser.add_option(\n+ "--dynamine",\n+ action="store_true"\n+ )\n+ parser.add_option(\n+ "--disomine",\n+ action="store_true"\n+ )\n+ parser.add_option(\n+ "--efoldmine",\n+ action="store_true"\n+ )\n+ parser.add_option(\n+ "--agmata",\n+ action="store_true"\n+ )\n+ parser.add_option(\n+ "--file",\n+ dest="input_fasta",\n+ type="string"\n+ )\n+ parser.add_option(\n+ "--output",\n+ dest="output",\n+ type="string"\n+ )\n+ parser.add_option(\n+ "--plot-output",\n+ type="string",\n+ dest="plot_output"\n+ )\n+ parser.add_option(\n+ "--json",\n+ dest="json_output",\n+ type="string"\n+ )\n+ parser.add_option(\n+ "--plot",\n+ action="store_true"\n+ )\n+ parser.add_option(\n+ "--plot_all",\n+ action="store_true"\n+ )\n+ parser.add_option(\n+ "--highlight",\n+ action="store_true"\n+ )\n+ try:\n+ options, args = parser.parse_args()\n+ if not (options.dynamine or options.disomine or options.efoldmine or options.agmata):\n+ parser.error(\'At least one predictor is required\')\n+ if not options.input_fasta:\n+ parser.error(\'Input file not given (--file)\')\n+ if not options.output:\n+ parser.error(\'Output directory not given (--output)\')\n+ if (options.plot or options.plot_all) and not options.plot_output:\n+ parser.error(\'Plot output directory not given (--plot-output)\')\n+ if not options.json_output:\n+ parser.error(\'Json output file not given (--json)\')\n+ main(options)\n+ except optparse.OptionError as exc:\n+ raise RuntimeError(f"Invalid arguments: {args}") from exc\n' |
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| diff -r 000000000000 -r b694a77ca1e8 test-data/input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Tue Aug 09 12:30:52 2022 +0000 |
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| @@ -0,0 +1,32 @@ +>random_sequence_01_consisting_of_40_residues +MDRHDPVQKSMMMDRHDPVQKMDRHDPVQKSDRHDPVQKS + +>random_sequence_02_consisting_of_40_residues +MWSMWRAMWSSQRAMWSMWRAMWSMSQRAMWSMWRAMWSM + +>random_sequence_03_consisting_of_30_residues +YSWTHYELKAVWCELTYWRSWTHYELKAVV + +>random_sequence_04_consisting_of_40_residues +SWTHYEYSWTHYELKAVWCELTYWRSWTHYELKAVVLKAV + +>random_sequence_05_consisting_of_30_residues +NCPIEHHLCANKMDLHHHHLCAHHLPEDQY + +>random_sequence_06_consisting_of_45_residues +YACLFQKPYIHHLCANKMDLHHNKMDLHHHHLCAHHLHHLCAHHL + +>random_sequence_07_consisting_of_30_residues +FHHLCANKMDLHHHHLCAHHLVPGKQEPDS + +>random_sequence_08_consisting_of_40_residues +HHLCANKMDLHHHHLCAHHLCANKMDLNKMDLLCANKMDL + +>random_sequence_09_consisting_of_30_residues +GNKTPFMKMHGGNKTPFMKMHNKTPFMKMH + +>random_sequence_10_consisting_of_65_residues +LDNSKMWQLDNPMPMSKMWQLDNSKMWQLDNLDNSKMWQLDNPMPMSKMWQLDNSKMWQLDNAAA + +>random_sequence_11_consisting_of_30_residues +PMSKMWQLDNMSKMWQLDNPMSKMWQLDNA |
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| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_01_consisting_of_40_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_01_consisting_of_40_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
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| @@ -0,0 +1,41 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 M 0.0 0.703 0.493 0.943 0.043 0.282 0.1 0.119 0.493 +1 D 0.001 0.708 0.542 0.964 0.048 0.235 0.115 0.073 0.287 +2 R 0.001 0.721 0.553 0.971 0.082 0.237 0.119 0.043 0.321 +3 H 0.001 0.73 0.545 0.974 0.126 0.209 0.121 0.058 0.497 +4 D 0.004 0.745 0.51 0.978 0.095 0.254 0.128 0.076 0.291 +5 P 0.045 0.731 0.444 0.979 0.135 0.345 0.131 0.106 0.489 +6 V 0.709 0.733 0.403 0.98 0.252 0.416 0.113 0.136 0.508 +7 Q 5.566 0.719 0.367 0.982 0.237 0.463 0.099 0.171 0.339 +8 K 17.394 0.705 0.353 0.984 0.27 0.459 0.093 0.207 0.321 +9 S 27.544 0.683 0.368 0.986 0.32 0.449 0.094 0.22 0.493 +10 M 28.56 0.665 0.409 0.988 0.276 0.416 0.1 0.193 0.472 +11 M 23.813 0.659 0.448 0.99 0.207 0.397 0.107 0.138 0.442 +12 M 11.996 0.658 0.498 0.992 0.185 0.324 0.125 0.095 0.452 +13 D 1.809 0.68 0.547 0.993 0.093 0.245 0.14 0.069 0.263 +14 R 0.146 0.685 0.559 0.993 0.068 0.226 0.145 0.055 0.306 +15 H 0.185 0.711 0.544 0.993 0.105 0.202 0.133 0.078 0.482 +16 D 1.571 0.726 0.508 0.993 0.089 0.231 0.139 0.132 0.28 +17 P 8.28 0.708 0.442 0.993 0.174 0.306 0.143 0.187 0.488 +18 V 17.753 0.699 0.402 0.993 0.331 0.337 0.13 0.24 0.531 +19 Q 20.564 0.661 0.401 0.993 0.219 0.327 0.132 0.236 0.321 +20 K 19.532 0.65 0.439 0.994 0.151 0.304 0.133 0.215 0.29 +21 M 12.898 0.636 0.506 0.993 0.152 0.233 0.144 0.164 0.472 +22 D 3.45 0.647 0.55 0.994 0.056 0.194 0.156 0.097 0.264 +23 R 0.61 0.647 0.571 0.994 0.04 0.161 0.162 0.081 0.285 +24 H 0.897 0.669 0.567 0.995 0.077 0.123 0.159 0.114 0.466 +25 D 3.789 0.68 0.549 0.995 0.068 0.111 0.165 0.171 0.269 +26 P 12.356 0.656 0.499 0.995 0.102 0.175 0.173 0.216 0.471 +27 V 19.297 0.644 0.478 0.995 0.192 0.193 0.158 0.244 0.507 +28 Q 20.098 0.63 0.479 0.996 0.106 0.193 0.156 0.253 0.321 +29 K 17.286 0.622 0.506 0.996 0.082 0.163 0.155 0.227 0.302 +30 S 8.716 0.627 0.543 0.996 0.09 0.135 0.158 0.18 0.477 +31 D 1.683 0.625 0.58 0.996 0.035 0.115 0.164 0.107 0.277 +32 R 0.317 0.643 0.588 0.996 0.025 0.142 0.16 0.073 0.284 +33 H 0.708 0.666 0.568 0.996 0.057 0.126 0.158 0.102 0.471 +34 D 3.245 0.688 0.533 0.996 0.064 0.142 0.16 0.159 0.278 +35 P 13.673 0.678 0.468 0.996 0.101 0.231 0.16 0.202 0.49 +36 V 15.348 0.684 0.435 0.995 0.184 0.284 0.133 0.219 0.512 +37 Q 14.796 0.681 0.414 0.995 0.118 0.313 0.12 0.231 0.338 +38 K 12.222 0.676 0.413 0.993 0.059 0.306 0.113 0.231 0.323 +39 S 1.765 0.68 0.405 0.991 0.059 0.316 0.108 0.229 0.504 |
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| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_01_consisting_of_40_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_01_consisting_of_40_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,41 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 M 0.703 0.493 0.282 0.1 0.119 0.493 +1 D 0.708 0.542 0.235 0.115 0.073 0.287 +2 R 0.721 0.553 0.237 0.119 0.043 0.321 +3 H 0.73 0.545 0.209 0.121 0.058 0.497 +4 D 0.745 0.51 0.254 0.128 0.076 0.291 +5 P 0.731 0.444 0.345 0.131 0.106 0.489 +6 V 0.733 0.403 0.416 0.113 0.136 0.508 +7 Q 0.719 0.367 0.463 0.099 0.171 0.339 +8 K 0.705 0.353 0.459 0.093 0.207 0.321 +9 S 0.683 0.368 0.449 0.094 0.22 0.493 +10 M 0.665 0.409 0.416 0.1 0.193 0.472 +11 M 0.659 0.448 0.397 0.107 0.138 0.442 +12 M 0.658 0.498 0.324 0.125 0.095 0.452 +13 D 0.68 0.547 0.245 0.14 0.069 0.263 +14 R 0.685 0.559 0.226 0.145 0.055 0.306 +15 H 0.711 0.544 0.202 0.133 0.078 0.482 +16 D 0.726 0.508 0.231 0.139 0.132 0.28 +17 P 0.708 0.442 0.306 0.143 0.187 0.488 +18 V 0.699 0.402 0.337 0.13 0.24 0.531 +19 Q 0.661 0.401 0.327 0.132 0.236 0.321 +20 K 0.65 0.439 0.304 0.133 0.215 0.29 +21 M 0.636 0.506 0.233 0.144 0.164 0.472 +22 D 0.647 0.55 0.194 0.156 0.097 0.264 +23 R 0.647 0.571 0.161 0.162 0.081 0.285 +24 H 0.669 0.567 0.123 0.159 0.114 0.466 +25 D 0.68 0.549 0.111 0.165 0.171 0.269 +26 P 0.656 0.499 0.175 0.173 0.216 0.471 +27 V 0.644 0.478 0.193 0.158 0.244 0.507 +28 Q 0.63 0.479 0.193 0.156 0.253 0.321 +29 K 0.622 0.506 0.163 0.155 0.227 0.302 +30 S 0.627 0.543 0.135 0.158 0.18 0.477 +31 D 0.625 0.58 0.115 0.164 0.107 0.277 +32 R 0.643 0.588 0.142 0.16 0.073 0.284 +33 H 0.666 0.568 0.126 0.158 0.102 0.471 +34 D 0.688 0.533 0.142 0.16 0.159 0.278 +35 P 0.678 0.468 0.231 0.16 0.202 0.49 +36 V 0.684 0.435 0.284 0.133 0.219 0.512 +37 Q 0.681 0.414 0.313 0.12 0.231 0.338 +38 K 0.676 0.413 0.306 0.113 0.231 0.323 +39 S 0.68 0.405 0.316 0.108 0.229 0.504 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_02_consisting_of_40_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_02_consisting_of_40_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,41 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 M 0.343 0.856 0.285 0.905 0.024 0.546 0.029 0.214 0.597 +1 W 10.354 0.875 0.269 0.922 0.051 0.578 0.021 0.215 0.667 +2 S 29.308 0.893 0.251 0.918 0.218 0.641 0.011 0.195 0.608 +3 M 52.192 0.91 0.249 0.905 0.382 0.619 0.005 0.223 0.615 +4 W 67.041 0.913 0.24 0.91 0.527 0.625 0.008 0.253 0.703 +5 R 61.674 0.913 0.243 0.912 0.491 0.628 0.008 0.258 0.465 +6 A 43.584 0.907 0.272 0.914 0.454 0.579 0.015 0.243 0.641 +7 M 20.881 0.894 0.31 0.92 0.316 0.575 0.023 0.187 0.6 +8 W 5.75 0.886 0.323 0.925 0.266 0.573 0.026 0.134 0.705 +9 S 1.162 0.87 0.312 0.921 0.232 0.625 0.029 0.094 0.604 +10 S 0.363 0.858 0.314 0.92 0.311 0.642 0.033 0.078 0.594 +11 Q 0.312 0.845 0.296 0.915 0.274 0.675 0.033 0.084 0.451 +12 R 0.615 0.841 0.3 0.908 0.261 0.674 0.036 0.079 0.417 +13 A 1.372 0.849 0.308 0.901 0.283 0.651 0.036 0.118 0.614 +14 M 3.354 0.848 0.297 0.892 0.262 0.676 0.034 0.118 0.584 +15 W 7.724 0.867 0.257 0.887 0.315 0.683 0.025 0.136 0.648 +16 S 14.924 0.885 0.238 0.875 0.322 0.702 0.014 0.156 0.615 +17 M 23.673 0.883 0.239 0.87 0.41 0.72 0.016 0.143 0.608 +18 W 32.028 0.899 0.226 0.869 0.543 0.692 0.015 0.194 0.686 +19 R 33.228 0.891 0.228 0.873 0.5 0.673 0.02 0.204 0.449 +20 A 27.414 0.887 0.26 0.877 0.459 0.649 0.017 0.196 0.641 +21 M 18.263 0.874 0.296 0.886 0.397 0.605 0.027 0.201 0.586 +22 W 7.952 0.875 0.306 0.899 0.362 0.594 0.029 0.161 0.696 +23 S 2.298 0.866 0.3 0.906 0.23 0.63 0.026 0.118 0.596 +24 M 0.581 0.855 0.323 0.91 0.228 0.67 0.027 0.056 0.578 +25 S 0.225 0.852 0.316 0.915 0.322 0.674 0.031 0.064 0.577 +26 Q 0.271 0.837 0.298 0.919 0.341 0.679 0.039 0.072 0.488 +27 R 0.556 0.846 0.305 0.919 0.282 0.679 0.033 0.088 0.381 +28 A 1.626 0.848 0.305 0.918 0.268 0.673 0.038 0.095 0.599 +29 M 5.417 0.865 0.284 0.918 0.294 0.682 0.03 0.117 0.584 +30 W 13.924 0.884 0.259 0.922 0.383 0.669 0.02 0.156 0.678 +31 S 23.797 0.884 0.235 0.919 0.372 0.709 0.017 0.166 0.588 +32 M 30.221 0.893 0.223 0.921 0.448 0.702 0.012 0.173 0.606 +33 W 31.827 0.89 0.224 0.923 0.523 0.678 0.02 0.189 0.677 +34 R 26.628 0.897 0.241 0.927 0.481 0.662 0.016 0.208 0.448 +35 A 19.599 0.879 0.261 0.928 0.396 0.669 0.021 0.175 0.615 +36 M 12.278 0.871 0.291 0.946 0.368 0.63 0.024 0.17 0.57 +37 W 6.829 0.866 0.308 0.958 0.417 0.57 0.024 0.185 0.67 +38 S 3.384 0.85 0.302 0.967 0.078 0.566 0.027 0.184 0.575 +39 M 0.209 0.832 0.326 0.968 0.061 0.548 0.032 0.16 0.557 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_02_consisting_of_40_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_02_consisting_of_40_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,41 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 M 0.856 0.285 0.546 0.029 0.214 0.597 +1 W 0.875 0.269 0.578 0.021 0.215 0.667 +2 S 0.893 0.251 0.641 0.011 0.195 0.608 +3 M 0.91 0.249 0.619 0.005 0.223 0.615 +4 W 0.913 0.24 0.625 0.008 0.253 0.703 +5 R 0.913 0.243 0.628 0.008 0.258 0.465 +6 A 0.907 0.272 0.579 0.015 0.243 0.641 +7 M 0.894 0.31 0.575 0.023 0.187 0.6 +8 W 0.886 0.323 0.573 0.026 0.134 0.705 +9 S 0.87 0.312 0.625 0.029 0.094 0.604 +10 S 0.858 0.314 0.642 0.033 0.078 0.594 +11 Q 0.845 0.296 0.675 0.033 0.084 0.451 +12 R 0.841 0.3 0.674 0.036 0.079 0.417 +13 A 0.849 0.308 0.651 0.036 0.118 0.614 +14 M 0.848 0.297 0.676 0.034 0.118 0.584 +15 W 0.867 0.257 0.683 0.025 0.136 0.648 +16 S 0.885 0.238 0.702 0.014 0.156 0.615 +17 M 0.883 0.239 0.72 0.016 0.143 0.608 +18 W 0.899 0.226 0.692 0.015 0.194 0.686 +19 R 0.891 0.228 0.673 0.02 0.204 0.449 +20 A 0.887 0.26 0.649 0.017 0.196 0.641 +21 M 0.874 0.296 0.605 0.027 0.201 0.586 +22 W 0.875 0.306 0.594 0.029 0.161 0.696 +23 S 0.866 0.3 0.63 0.026 0.118 0.596 +24 M 0.855 0.323 0.67 0.027 0.056 0.578 +25 S 0.852 0.316 0.674 0.031 0.064 0.577 +26 Q 0.837 0.298 0.679 0.039 0.072 0.488 +27 R 0.846 0.305 0.679 0.033 0.088 0.381 +28 A 0.848 0.305 0.673 0.038 0.095 0.599 +29 M 0.865 0.284 0.682 0.03 0.117 0.584 +30 W 0.884 0.259 0.669 0.02 0.156 0.678 +31 S 0.884 0.235 0.709 0.017 0.166 0.588 +32 M 0.893 0.223 0.702 0.012 0.173 0.606 +33 W 0.89 0.224 0.678 0.02 0.189 0.677 +34 R 0.897 0.241 0.662 0.016 0.208 0.448 +35 A 0.879 0.261 0.669 0.021 0.175 0.615 +36 M 0.871 0.291 0.63 0.024 0.17 0.57 +37 W 0.866 0.308 0.57 0.024 0.185 0.67 +38 S 0.85 0.302 0.566 0.027 0.184 0.575 +39 M 0.832 0.326 0.548 0.032 0.16 0.557 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_03_consisting_of_30_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_03_consisting_of_30_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 Y 0.012 0.818 0.376 0.783 0.031 0.262 0.074 0.295 0.624 +1 S 0.08 0.833 0.373 0.818 0.05 0.253 0.07 0.33 0.59 +2 W 0.119 0.87 0.361 0.772 0.061 0.27 0.057 0.341 0.696 +3 T 0.154 0.906 0.336 0.641 0.064 0.334 0.037 0.341 0.665 +4 H 0.2 0.945 0.295 0.596 0.099 0.421 0.017 0.324 0.673 +5 Y 0.34 0.969 0.261 0.583 0.15 0.47 0.015 0.339 0.644 +6 E 1.023 0.967 0.251 0.534 0.187 0.494 0.024 0.354 0.438 +7 L 4.084 0.959 0.247 0.441 0.291 0.481 0.025 0.382 0.677 +8 K 12.328 0.972 0.237 0.355 0.294 0.464 0.024 0.429 0.449 +9 A 20.723 0.974 0.239 0.273 0.274 0.442 0.026 0.436 0.685 +10 V 25.866 0.984 0.233 0.231 0.336 0.415 0.028 0.45 0.684 +11 W 24.864 1.016 0.222 0.193 0.408 0.412 0.023 0.471 0.722 +12 C 17.51 1.014 0.229 0.174 0.426 0.396 0.016 0.479 0.747 +13 E 9.32 0.997 0.241 0.155 0.261 0.434 0.016 0.456 0.403 +14 L 3.591 0.99 0.255 0.142 0.259 0.443 0.012 0.422 0.704 +15 T 1.559 0.977 0.277 0.138 0.278 0.45 0.019 0.379 0.72 +16 Y 0.64 0.969 0.299 0.134 0.282 0.428 0.025 0.353 0.656 +17 W 0.221 0.976 0.317 0.135 0.262 0.415 0.027 0.328 0.704 +18 R 0.084 0.957 0.331 0.132 0.147 0.41 0.029 0.295 0.462 +19 S 0.038 0.956 0.342 0.148 0.142 0.393 0.028 0.289 0.627 +20 W 0.031 0.947 0.355 0.182 0.178 0.379 0.031 0.304 0.71 +21 T 0.035 0.964 0.333 0.205 0.187 0.393 0.023 0.305 0.705 +22 H 0.052 0.976 0.286 0.228 0.19 0.451 0.013 0.309 0.663 +23 Y 0.159 0.967 0.268 0.229 0.185 0.503 0.016 0.296 0.635 +24 E 1.115 0.949 0.26 0.226 0.187 0.528 0.022 0.319 0.385 +25 L 7.747 0.929 0.243 0.215 0.261 0.519 0.023 0.358 0.649 +26 K 8.329 0.924 0.225 0.253 0.247 0.487 0.023 0.405 0.399 +27 A 8.214 0.906 0.22 0.313 0.25 0.452 0.031 0.451 0.606 +28 V 7.259 0.89 0.218 0.405 0.076 0.443 0.042 0.455 0.607 +29 V 0.608 0.871 0.242 0.605 0.029 0.418 0.051 0.426 0.596 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_03_consisting_of_30_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_03_consisting_of_30_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 Y 0.818 0.376 0.262 0.074 0.295 0.624 +1 S 0.833 0.373 0.253 0.07 0.33 0.59 +2 W 0.87 0.361 0.27 0.057 0.341 0.696 +3 T 0.906 0.336 0.334 0.037 0.341 0.665 +4 H 0.945 0.295 0.421 0.017 0.324 0.673 +5 Y 0.969 0.261 0.47 0.015 0.339 0.644 +6 E 0.967 0.251 0.494 0.024 0.354 0.438 +7 L 0.959 0.247 0.481 0.025 0.382 0.677 +8 K 0.972 0.237 0.464 0.024 0.429 0.449 +9 A 0.974 0.239 0.442 0.026 0.436 0.685 +10 V 0.984 0.233 0.415 0.028 0.45 0.684 +11 W 1.016 0.222 0.412 0.023 0.471 0.722 +12 C 1.014 0.229 0.396 0.016 0.479 0.747 +13 E 0.997 0.241 0.434 0.016 0.456 0.403 +14 L 0.99 0.255 0.443 0.012 0.422 0.704 +15 T 0.977 0.277 0.45 0.019 0.379 0.72 +16 Y 0.969 0.299 0.428 0.025 0.353 0.656 +17 W 0.976 0.317 0.415 0.027 0.328 0.704 +18 R 0.957 0.331 0.41 0.029 0.295 0.462 +19 S 0.956 0.342 0.393 0.028 0.289 0.627 +20 W 0.947 0.355 0.379 0.031 0.304 0.71 +21 T 0.964 0.333 0.393 0.023 0.305 0.705 +22 H 0.976 0.286 0.451 0.013 0.309 0.663 +23 Y 0.967 0.268 0.503 0.016 0.296 0.635 +24 E 0.949 0.26 0.528 0.022 0.319 0.385 +25 L 0.929 0.243 0.519 0.023 0.358 0.649 +26 K 0.924 0.225 0.487 0.023 0.405 0.399 +27 A 0.906 0.22 0.452 0.031 0.451 0.606 +28 V 0.89 0.218 0.443 0.042 0.455 0.607 +29 V 0.871 0.242 0.418 0.051 0.426 0.596 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_04_consisting_of_40_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_04_consisting_of_40_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,41 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 S 0.01 0.759 0.429 0.718 0.037 0.172 0.096 0.312 0.566 +1 W 0.077 0.791 0.417 0.677 0.042 0.183 0.085 0.332 0.675 +2 T 0.159 0.82 0.393 0.468 0.034 0.231 0.07 0.328 0.63 +3 H 0.246 0.848 0.368 0.317 0.053 0.292 0.057 0.339 0.644 +4 Y 0.369 0.868 0.337 0.209 0.078 0.345 0.052 0.344 0.628 +5 E 0.426 0.883 0.329 0.143 0.075 0.332 0.056 0.369 0.425 +6 Y 0.414 0.884 0.349 0.127 0.089 0.301 0.062 0.352 0.655 +7 S 0.366 0.883 0.357 0.149 0.088 0.293 0.061 0.357 0.603 +8 W 0.253 0.895 0.355 0.14 0.092 0.291 0.051 0.356 0.709 +9 T 0.147 0.92 0.331 0.135 0.094 0.348 0.038 0.348 0.682 +10 H 0.107 0.95 0.293 0.108 0.121 0.423 0.022 0.333 0.675 +11 Y 0.172 0.968 0.268 0.087 0.162 0.45 0.021 0.345 0.634 +12 E 0.546 0.965 0.251 0.072 0.192 0.478 0.028 0.371 0.426 +13 L 2.173 0.968 0.238 0.057 0.319 0.466 0.024 0.413 0.689 +14 K 6.595 0.974 0.221 0.048 0.299 0.465 0.026 0.455 0.457 +15 A 11.129 0.972 0.231 0.042 0.282 0.45 0.025 0.446 0.688 +16 V 13.752 0.989 0.225 0.042 0.339 0.424 0.024 0.463 0.687 +17 W 13.197 1.012 0.22 0.04 0.401 0.419 0.023 0.468 0.719 +18 C 9.285 1.014 0.229 0.043 0.429 0.396 0.016 0.479 0.747 +19 E 4.889 0.997 0.241 0.043 0.263 0.434 0.016 0.456 0.403 +20 L 1.951 0.99 0.255 0.044 0.261 0.443 0.012 0.422 0.704 +21 T 0.9 0.977 0.277 0.049 0.281 0.45 0.019 0.379 0.72 +22 Y 0.38 0.969 0.299 0.051 0.283 0.428 0.025 0.353 0.656 +23 W 0.128 0.976 0.317 0.053 0.266 0.415 0.027 0.328 0.704 +24 R 0.04 0.962 0.326 0.055 0.146 0.422 0.027 0.291 0.46 +25 S 0.01 0.96 0.336 0.062 0.135 0.415 0.025 0.276 0.626 +26 W 0.005 0.952 0.351 0.07 0.173 0.413 0.028 0.283 0.711 +27 T 0.003 0.974 0.323 0.077 0.188 0.436 0.018 0.283 0.705 +28 H 0.003 0.99 0.272 0.084 0.203 0.502 0.007 0.28 0.668 +29 Y 0.008 0.986 0.247 0.079 0.205 0.577 0.008 0.258 0.639 +30 E 0.059 0.973 0.234 0.077 0.225 0.609 0.012 0.275 0.386 +31 L 0.597 0.961 0.218 0.082 0.334 0.598 0.013 0.316 0.652 +32 K 3.975 0.969 0.182 0.087 0.323 0.593 0.011 0.367 0.415 +33 A 11.201 0.962 0.163 0.095 0.362 0.574 0.014 0.422 0.615 +34 V 19.921 0.953 0.15 0.116 0.393 0.571 0.021 0.454 0.621 +35 V 23.403 0.938 0.168 0.114 0.376 0.548 0.028 0.47 0.612 +36 L 20.107 0.917 0.188 0.14 0.279 0.522 0.029 0.438 0.605 +37 K 12.898 0.902 0.202 0.187 0.159 0.503 0.028 0.413 0.385 +38 A 4.119 0.889 0.232 0.231 0.06 0.481 0.035 0.384 0.612 +39 V 0.062 0.867 0.259 0.41 0.022 0.463 0.047 0.34 0.595 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_04_consisting_of_40_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_04_consisting_of_40_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,41 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 S 0.759 0.429 0.172 0.096 0.312 0.566 +1 W 0.791 0.417 0.183 0.085 0.332 0.675 +2 T 0.82 0.393 0.231 0.07 0.328 0.63 +3 H 0.848 0.368 0.292 0.057 0.339 0.644 +4 Y 0.868 0.337 0.345 0.052 0.344 0.628 +5 E 0.883 0.329 0.332 0.056 0.369 0.425 +6 Y 0.884 0.349 0.301 0.062 0.352 0.655 +7 S 0.883 0.357 0.293 0.061 0.357 0.603 +8 W 0.895 0.355 0.291 0.051 0.356 0.709 +9 T 0.92 0.331 0.348 0.038 0.348 0.682 +10 H 0.95 0.293 0.423 0.022 0.333 0.675 +11 Y 0.968 0.268 0.45 0.021 0.345 0.634 +12 E 0.965 0.251 0.478 0.028 0.371 0.426 +13 L 0.968 0.238 0.466 0.024 0.413 0.689 +14 K 0.974 0.221 0.465 0.026 0.455 0.457 +15 A 0.972 0.231 0.45 0.025 0.446 0.688 +16 V 0.989 0.225 0.424 0.024 0.463 0.687 +17 W 1.012 0.22 0.419 0.023 0.468 0.719 +18 C 1.014 0.229 0.396 0.016 0.479 0.747 +19 E 0.997 0.241 0.434 0.016 0.456 0.403 +20 L 0.99 0.255 0.443 0.012 0.422 0.704 +21 T 0.977 0.277 0.45 0.019 0.379 0.72 +22 Y 0.969 0.299 0.428 0.025 0.353 0.656 +23 W 0.976 0.317 0.415 0.027 0.328 0.704 +24 R 0.962 0.326 0.422 0.027 0.291 0.46 +25 S 0.96 0.336 0.415 0.025 0.276 0.626 +26 W 0.952 0.351 0.413 0.028 0.283 0.711 +27 T 0.974 0.323 0.436 0.018 0.283 0.705 +28 H 0.99 0.272 0.502 0.007 0.28 0.668 +29 Y 0.986 0.247 0.577 0.008 0.258 0.639 +30 E 0.973 0.234 0.609 0.012 0.275 0.386 +31 L 0.961 0.218 0.598 0.013 0.316 0.652 +32 K 0.969 0.182 0.593 0.011 0.367 0.415 +33 A 0.962 0.163 0.574 0.014 0.422 0.615 +34 V 0.953 0.15 0.571 0.021 0.454 0.621 +35 V 0.938 0.168 0.548 0.028 0.47 0.612 +36 L 0.917 0.188 0.522 0.029 0.438 0.605 +37 K 0.902 0.202 0.503 0.028 0.413 0.385 +38 A 0.889 0.232 0.481 0.035 0.384 0.612 +39 V 0.867 0.259 0.463 0.047 0.34 0.595 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_05_consisting_of_30_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_05_consisting_of_30_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 N 0.001 0.735 0.543 0.937 0.039 0.159 0.108 0.161 0.494 +1 C 0.004 0.747 0.514 0.956 0.044 0.154 0.121 0.204 0.634 +2 P 0.011 0.767 0.424 0.959 0.094 0.292 0.118 0.212 0.532 +3 I 0.038 0.784 0.377 0.953 0.103 0.392 0.099 0.197 0.588 +4 E 0.146 0.802 0.342 0.951 0.119 0.465 0.077 0.21 0.314 +5 H 0.42 0.818 0.317 0.932 0.246 0.489 0.055 0.239 0.565 +6 H 0.704 0.824 0.32 0.923 0.372 0.506 0.048 0.252 0.545 +7 L 0.753 0.83 0.338 0.927 0.4 0.499 0.048 0.233 0.579 +8 C 0.652 0.815 0.389 0.938 0.439 0.432 0.066 0.205 0.625 +9 A 0.376 0.771 0.438 0.94 0.305 0.403 0.082 0.149 0.538 +10 N 0.085 0.719 0.492 0.945 0.148 0.359 0.099 0.082 0.454 +11 K 0.009 0.685 0.512 0.952 0.083 0.363 0.112 0.047 0.316 +12 M 0.001 0.69 0.51 0.957 0.066 0.384 0.108 0.019 0.47 +13 D 0.0 0.687 0.519 0.966 0.037 0.395 0.115 0.007 0.261 +14 L 0.002 0.68 0.513 0.968 0.051 0.406 0.111 0.013 0.518 +15 H 0.019 0.71 0.484 0.974 0.071 0.394 0.094 0.055 0.528 +16 H 0.213 0.72 0.442 0.978 0.087 0.412 0.082 0.106 0.526 +17 H 1.621 0.752 0.404 0.98 0.152 0.408 0.073 0.183 0.555 +18 H 6.41 0.772 0.373 0.979 0.218 0.429 0.067 0.245 0.545 +19 L 11.755 0.78 0.36 0.977 0.297 0.405 0.07 0.297 0.582 +20 C 13.578 0.772 0.377 0.975 0.336 0.337 0.08 0.306 0.625 +21 A 12.579 0.74 0.402 0.975 0.204 0.314 0.093 0.276 0.558 +22 H 7.834 0.73 0.447 0.976 0.116 0.268 0.099 0.223 0.518 +23 H 2.474 0.72 0.496 0.976 0.088 0.214 0.119 0.208 0.527 +24 L 0.456 0.72 0.505 0.975 0.104 0.183 0.14 0.169 0.555 +25 P 0.049 0.726 0.492 0.97 0.077 0.257 0.145 0.12 0.505 +26 E 0.005 0.73 0.497 0.969 0.038 0.315 0.131 0.065 0.253 +27 D 0.001 0.73 0.495 0.967 0.036 0.343 0.114 0.049 0.302 +28 Q 0.0 0.727 0.456 0.962 0.034 0.364 0.103 0.099 0.363 +29 Y 0.0 0.739 0.411 0.964 0.064 0.376 0.096 0.143 0.535 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_05_consisting_of_30_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_05_consisting_of_30_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 N 0.735 0.543 0.159 0.108 0.161 0.494 +1 C 0.747 0.514 0.154 0.121 0.204 0.634 +2 P 0.767 0.424 0.292 0.118 0.212 0.532 +3 I 0.784 0.377 0.392 0.099 0.197 0.588 +4 E 0.802 0.342 0.465 0.077 0.21 0.314 +5 H 0.818 0.317 0.489 0.055 0.239 0.565 +6 H 0.824 0.32 0.506 0.048 0.252 0.545 +7 L 0.83 0.338 0.499 0.048 0.233 0.579 +8 C 0.815 0.389 0.432 0.066 0.205 0.625 +9 A 0.771 0.438 0.403 0.082 0.149 0.538 +10 N 0.719 0.492 0.359 0.099 0.082 0.454 +11 K 0.685 0.512 0.363 0.112 0.047 0.316 +12 M 0.69 0.51 0.384 0.108 0.019 0.47 +13 D 0.687 0.519 0.395 0.115 0.007 0.261 +14 L 0.68 0.513 0.406 0.111 0.013 0.518 +15 H 0.71 0.484 0.394 0.094 0.055 0.528 +16 H 0.72 0.442 0.412 0.082 0.106 0.526 +17 H 0.752 0.404 0.408 0.073 0.183 0.555 +18 H 0.772 0.373 0.429 0.067 0.245 0.545 +19 L 0.78 0.36 0.405 0.07 0.297 0.582 +20 C 0.772 0.377 0.337 0.08 0.306 0.625 +21 A 0.74 0.402 0.314 0.093 0.276 0.558 +22 H 0.73 0.447 0.268 0.099 0.223 0.518 +23 H 0.72 0.496 0.214 0.119 0.208 0.527 +24 L 0.72 0.505 0.183 0.14 0.169 0.555 +25 P 0.726 0.492 0.257 0.145 0.12 0.505 +26 E 0.73 0.497 0.315 0.131 0.065 0.253 +27 D 0.73 0.495 0.343 0.114 0.049 0.302 +28 Q 0.727 0.456 0.364 0.103 0.099 0.363 +29 Y 0.739 0.411 0.376 0.096 0.143 0.535 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_06_consisting_of_45_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_06_consisting_of_45_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,46 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 Y 0.794 0.89 0.231 0.832 0.029 0.553 0.027 0.292 0.62 +1 A 13.091 0.909 0.243 0.869 0.101 0.528 0.025 0.334 0.613 +2 C 15.911 0.92 0.278 0.89 0.456 0.5 0.021 0.322 0.685 +3 L 16.494 0.91 0.317 0.908 0.372 0.478 0.025 0.279 0.624 +4 F 15.922 0.893 0.363 0.931 0.343 0.424 0.039 0.231 0.631 +5 Q 3.807 0.88 0.386 0.934 0.216 0.381 0.059 0.231 0.46 +6 K 1.314 0.863 0.386 0.932 0.14 0.358 0.079 0.223 0.427 +7 P 1.417 0.861 0.363 0.932 0.124 0.401 0.085 0.222 0.586 +8 Y 2.541 0.868 0.366 0.929 0.141 0.434 0.076 0.227 0.601 +9 I 4.517 0.875 0.346 0.927 0.206 0.451 0.058 0.249 0.651 +10 H 5.996 0.899 0.312 0.916 0.271 0.491 0.034 0.277 0.595 +11 H 6.189 0.905 0.305 0.906 0.323 0.516 0.024 0.287 0.589 +12 L 5.073 0.892 0.328 0.887 0.368 0.491 0.031 0.281 0.639 +13 C 2.949 0.857 0.368 0.868 0.338 0.462 0.053 0.226 0.657 +14 A 1.149 0.814 0.39 0.869 0.19 0.457 0.061 0.157 0.559 +15 N 0.272 0.749 0.439 0.891 0.101 0.426 0.082 0.096 0.459 +16 K 0.044 0.719 0.468 0.912 0.06 0.43 0.094 0.073 0.331 +17 M 0.012 0.704 0.481 0.903 0.048 0.397 0.103 0.056 0.468 +18 D 0.007 0.716 0.49 0.9 0.028 0.403 0.11 0.056 0.271 +19 L 0.009 0.727 0.478 0.892 0.039 0.421 0.097 0.052 0.537 +20 H 0.013 0.739 0.479 0.897 0.063 0.385 0.085 0.072 0.532 +21 H 0.014 0.715 0.502 0.901 0.059 0.347 0.09 0.082 0.51 +22 N 0.015 0.678 0.531 0.9 0.04 0.296 0.108 0.081 0.452 +23 K 0.013 0.668 0.518 0.906 0.026 0.313 0.117 0.085 0.312 +24 M 0.015 0.681 0.489 0.934 0.022 0.36 0.112 0.083 0.469 +25 D 0.026 0.669 0.492 0.953 0.014 0.365 0.119 0.081 0.253 +26 L 0.061 0.649 0.493 0.961 0.019 0.368 0.12 0.085 0.511 +27 H 0.181 0.682 0.472 0.967 0.022 0.383 0.101 0.081 0.51 +28 H 0.785 0.709 0.457 0.965 0.024 0.39 0.092 0.11 0.519 +29 H 2.843 0.729 0.432 0.962 0.036 0.397 0.086 0.136 0.531 +30 H 6.194 0.733 0.407 0.96 0.052 0.402 0.085 0.2 0.502 +31 L 7.94 0.719 0.386 0.957 0.073 0.386 0.09 0.247 0.537 +32 C 7.796 0.724 0.381 0.955 0.072 0.392 0.091 0.241 0.609 +33 A 5.902 0.715 0.391 0.953 0.039 0.424 0.089 0.181 0.534 +34 H 2.626 0.723 0.421 0.951 0.029 0.434 0.084 0.124 0.501 +35 H 0.967 0.729 0.437 0.949 0.033 0.441 0.085 0.121 0.523 +36 L 1.185 0.74 0.425 0.948 0.05 0.424 0.083 0.123 0.561 +37 H 2.593 0.763 0.4 0.951 0.062 0.443 0.073 0.161 0.532 +38 H 5.198 0.768 0.376 0.951 0.07 0.453 0.067 0.194 0.508 +39 L 7.158 0.768 0.379 0.949 0.102 0.431 0.07 0.222 0.568 +40 C 7.667 0.778 0.381 0.948 0.121 0.412 0.075 0.242 0.627 +41 A 6.139 0.78 0.377 0.96 0.081 0.416 0.073 0.215 0.556 +42 H 3.423 0.786 0.382 0.964 0.066 0.429 0.06 0.183 0.536 +43 H 1.252 0.79 0.381 0.97 0.037 0.441 0.058 0.189 0.548 +44 L 0.058 0.777 0.379 0.971 0.048 0.419 0.063 0.188 0.559 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_06_consisting_of_45_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_06_consisting_of_45_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,46 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 Y 0.89 0.231 0.553 0.027 0.292 0.62 +1 A 0.909 0.243 0.528 0.025 0.334 0.613 +2 C 0.92 0.278 0.5 0.021 0.322 0.685 +3 L 0.91 0.317 0.478 0.025 0.279 0.624 +4 F 0.893 0.363 0.424 0.039 0.231 0.631 +5 Q 0.88 0.386 0.381 0.059 0.231 0.46 +6 K 0.863 0.386 0.358 0.079 0.223 0.427 +7 P 0.861 0.363 0.401 0.085 0.222 0.586 +8 Y 0.868 0.366 0.434 0.076 0.227 0.601 +9 I 0.875 0.346 0.451 0.058 0.249 0.651 +10 H 0.899 0.312 0.491 0.034 0.277 0.595 +11 H 0.905 0.305 0.516 0.024 0.287 0.589 +12 L 0.892 0.328 0.491 0.031 0.281 0.639 +13 C 0.857 0.368 0.462 0.053 0.226 0.657 +14 A 0.814 0.39 0.457 0.061 0.157 0.559 +15 N 0.749 0.439 0.426 0.082 0.096 0.459 +16 K 0.719 0.468 0.43 0.094 0.073 0.331 +17 M 0.704 0.481 0.397 0.103 0.056 0.468 +18 D 0.716 0.49 0.403 0.11 0.056 0.271 +19 L 0.727 0.478 0.421 0.097 0.052 0.537 +20 H 0.739 0.479 0.385 0.085 0.072 0.532 +21 H 0.715 0.502 0.347 0.09 0.082 0.51 +22 N 0.678 0.531 0.296 0.108 0.081 0.452 +23 K 0.668 0.518 0.313 0.117 0.085 0.312 +24 M 0.681 0.489 0.36 0.112 0.083 0.469 +25 D 0.669 0.492 0.365 0.119 0.081 0.253 +26 L 0.649 0.493 0.368 0.12 0.085 0.511 +27 H 0.682 0.472 0.383 0.101 0.081 0.51 +28 H 0.709 0.457 0.39 0.092 0.11 0.519 +29 H 0.729 0.432 0.397 0.086 0.136 0.531 +30 H 0.733 0.407 0.402 0.085 0.2 0.502 +31 L 0.719 0.386 0.386 0.09 0.247 0.537 +32 C 0.724 0.381 0.392 0.091 0.241 0.609 +33 A 0.715 0.391 0.424 0.089 0.181 0.534 +34 H 0.723 0.421 0.434 0.084 0.124 0.501 +35 H 0.729 0.437 0.441 0.085 0.121 0.523 +36 L 0.74 0.425 0.424 0.083 0.123 0.561 +37 H 0.763 0.4 0.443 0.073 0.161 0.532 +38 H 0.768 0.376 0.453 0.067 0.194 0.508 +39 L 0.768 0.379 0.431 0.07 0.222 0.568 +40 C 0.778 0.381 0.412 0.075 0.242 0.627 +41 A 0.78 0.377 0.416 0.073 0.215 0.556 +42 H 0.786 0.382 0.429 0.06 0.183 0.536 +43 H 0.79 0.381 0.441 0.058 0.189 0.548 +44 L 0.777 0.379 0.419 0.063 0.188 0.559 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_07_consisting_of_30_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_07_consisting_of_30_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 F 0.005 0.806 0.308 0.91 0.029 0.477 0.05 0.232 0.6 +1 H 0.127 0.824 0.296 0.934 0.069 0.495 0.038 0.263 0.575 +2 H 0.189 0.831 0.306 0.95 0.373 0.501 0.036 0.268 0.549 +3 L 0.2 0.835 0.334 0.96 0.418 0.48 0.038 0.257 0.58 +4 C 0.195 0.822 0.395 0.969 0.457 0.413 0.055 0.223 0.648 +5 A 0.074 0.778 0.446 0.972 0.294 0.371 0.072 0.155 0.546 +6 N 0.011 0.721 0.502 0.973 0.124 0.331 0.092 0.079 0.446 +7 K 0.001 0.684 0.526 0.976 0.065 0.337 0.107 0.041 0.314 +8 M 0.0 0.687 0.52 0.979 0.061 0.361 0.107 0.022 0.466 +9 D 0.0 0.702 0.516 0.982 0.036 0.392 0.11 0.021 0.259 +10 L 0.0 0.705 0.502 0.983 0.05 0.405 0.105 0.022 0.524 +11 H 0.001 0.732 0.469 0.985 0.089 0.399 0.089 0.066 0.536 +12 H 0.017 0.752 0.424 0.987 0.11 0.427 0.073 0.126 0.543 +13 H 0.151 0.758 0.403 0.988 0.162 0.42 0.07 0.178 0.552 +14 H 0.887 0.777 0.37 0.988 0.218 0.435 0.065 0.241 0.54 +15 L 3.284 0.783 0.352 0.989 0.264 0.419 0.071 0.291 0.584 +16 C 7.432 0.776 0.363 0.99 0.294 0.375 0.078 0.301 0.623 +17 A 13.487 0.745 0.363 0.99 0.207 0.362 0.086 0.305 0.561 +18 H 16.924 0.731 0.389 0.992 0.176 0.311 0.086 0.287 0.525 +19 H 15.936 0.723 0.423 0.993 0.167 0.256 0.102 0.323 0.525 +20 L 12.029 0.706 0.461 0.994 0.167 0.142 0.132 0.319 0.544 +21 V 5.86 0.693 0.498 0.995 0.111 0.068 0.163 0.301 0.517 +22 P 1.686 0.648 0.525 0.996 0.058 0.048 0.191 0.239 0.476 +23 G 0.277 0.609 0.579 0.996 0.028 0.018 0.2 0.171 0.43 +24 K 0.027 0.599 0.631 0.996 0.015 -0.015 0.196 0.128 0.297 +25 Q 0.004 0.609 0.632 0.996 0.014 -0.053 0.198 0.143 0.316 +26 E 0.001 0.642 0.613 0.996 0.017 -0.002 0.193 0.139 0.268 +27 P 0.0 0.655 0.566 0.995 0.018 0.113 0.18 0.11 0.481 +28 D 0.0 0.667 0.55 0.994 0.018 0.197 0.155 0.07 0.256 +29 S 0.0 0.645 0.505 0.993 0.069 0.257 0.139 0.087 0.456 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_07_consisting_of_30_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_07_consisting_of_30_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 F 0.806 0.308 0.477 0.05 0.232 0.6 +1 H 0.824 0.296 0.495 0.038 0.263 0.575 +2 H 0.831 0.306 0.501 0.036 0.268 0.549 +3 L 0.835 0.334 0.48 0.038 0.257 0.58 +4 C 0.822 0.395 0.413 0.055 0.223 0.648 +5 A 0.778 0.446 0.371 0.072 0.155 0.546 +6 N 0.721 0.502 0.331 0.092 0.079 0.446 +7 K 0.684 0.526 0.337 0.107 0.041 0.314 +8 M 0.687 0.52 0.361 0.107 0.022 0.466 +9 D 0.702 0.516 0.392 0.11 0.021 0.259 +10 L 0.705 0.502 0.405 0.105 0.022 0.524 +11 H 0.732 0.469 0.399 0.089 0.066 0.536 +12 H 0.752 0.424 0.427 0.073 0.126 0.543 +13 H 0.758 0.403 0.42 0.07 0.178 0.552 +14 H 0.777 0.37 0.435 0.065 0.241 0.54 +15 L 0.783 0.352 0.419 0.071 0.291 0.584 +16 C 0.776 0.363 0.375 0.078 0.301 0.623 +17 A 0.745 0.363 0.362 0.086 0.305 0.561 +18 H 0.731 0.389 0.311 0.086 0.287 0.525 +19 H 0.723 0.423 0.256 0.102 0.323 0.525 +20 L 0.706 0.461 0.142 0.132 0.319 0.544 +21 V 0.693 0.498 0.068 0.163 0.301 0.517 +22 P 0.648 0.525 0.048 0.191 0.239 0.476 +23 G 0.609 0.579 0.018 0.2 0.171 0.43 +24 K 0.599 0.631 -0.015 0.196 0.128 0.297 +25 Q 0.609 0.632 -0.053 0.198 0.143 0.316 +26 E 0.642 0.613 -0.002 0.193 0.139 0.268 +27 P 0.655 0.566 0.113 0.18 0.11 0.481 +28 D 0.667 0.55 0.197 0.155 0.07 0.256 +29 S 0.645 0.505 0.257 0.139 0.087 0.456 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_08_consisting_of_40_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_08_consisting_of_40_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,41 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 H 0.76 0.77 0.333 0.917 0.02 0.482 0.056 0.191 0.542 +1 H 11.154 0.781 0.334 0.946 0.046 0.487 0.052 0.222 0.527 +2 L 14.412 0.799 0.348 0.954 0.143 0.475 0.051 0.223 0.568 +3 C 14.784 0.791 0.398 0.95 0.174 0.409 0.065 0.211 0.618 +4 A 14.062 0.756 0.443 0.958 0.111 0.375 0.078 0.155 0.539 +5 N 3.675 0.704 0.491 0.96 0.048 0.336 0.096 0.09 0.445 +6 K 0.419 0.672 0.514 0.965 0.026 0.338 0.11 0.055 0.308 +7 M 0.049 0.677 0.515 0.971 0.021 0.363 0.109 0.026 0.465 +8 D 0.015 0.692 0.529 0.973 0.013 0.358 0.117 0.026 0.262 +9 L 0.029 0.708 0.518 0.973 0.018 0.376 0.109 0.028 0.532 +10 H 0.164 0.741 0.479 0.97 0.03 0.385 0.088 0.06 0.538 +11 H 0.947 0.762 0.429 0.968 0.043 0.422 0.072 0.112 0.546 +12 H 3.826 0.783 0.392 0.965 0.066 0.464 0.059 0.158 0.577 +13 H 10.168 0.802 0.36 0.964 0.096 0.502 0.054 0.194 0.559 +14 L 16.389 0.826 0.324 0.966 0.137 0.524 0.049 0.229 0.585 +15 C 19.357 0.831 0.319 0.968 0.179 0.512 0.052 0.239 0.642 +16 A 19.008 0.813 0.311 0.97 0.149 0.545 0.055 0.218 0.587 +17 H 13.948 0.817 0.315 0.973 0.126 0.575 0.046 0.174 0.561 +18 H 8.242 0.818 0.329 0.975 0.141 0.595 0.048 0.165 0.552 +19 L 4.665 0.829 0.326 0.978 0.211 0.564 0.05 0.161 0.579 +20 C 2.152 0.838 0.35 0.98 0.258 0.547 0.054 0.155 0.623 +21 A 0.852 0.815 0.385 0.982 0.23 0.501 0.067 0.129 0.554 +22 N 0.201 0.794 0.423 0.985 0.142 0.482 0.071 0.072 0.486 +23 K 0.024 0.8 0.439 0.987 0.097 0.503 0.073 0.039 0.355 +24 M 0.003 0.821 0.428 0.987 0.106 0.515 0.066 0.019 0.511 +25 D 0.001 0.846 0.43 0.987 0.098 0.567 0.064 0.006 0.336 +26 L 0.003 0.847 0.414 0.986 0.169 0.583 0.056 0.003 0.586 +27 N 0.014 0.853 0.386 0.984 0.204 0.594 0.045 0.017 0.5 +28 K 0.114 0.855 0.348 0.982 0.237 0.629 0.044 0.068 0.362 +29 M 0.973 0.88 0.316 0.981 0.312 0.649 0.035 0.113 0.548 +30 D 4.805 0.914 0.271 0.981 0.36 0.69 0.029 0.171 0.357 +31 L 8.996 0.923 0.226 0.983 0.5 0.722 0.019 0.217 0.599 +32 L 9.857 0.923 0.219 0.984 0.624 0.686 0.011 0.234 0.615 +33 C 9.098 0.903 0.255 0.986 0.623 0.641 0.017 0.227 0.668 +34 A 5.276 0.878 0.313 0.988 0.489 0.598 0.027 0.157 0.588 +35 N 1.078 0.851 0.362 0.989 0.295 0.583 0.038 0.097 0.514 +36 K 0.119 0.84 0.391 0.991 0.223 0.553 0.045 0.067 0.373 +37 M 0.018 0.848 0.392 0.991 0.208 0.53 0.04 0.075 0.518 +38 D 0.006 0.845 0.382 0.991 0.041 0.537 0.047 0.098 0.32 +39 L 0.001 0.826 0.359 0.989 0.064 0.538 0.049 0.114 0.581 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_08_consisting_of_40_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_08_consisting_of_40_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,41 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 H 0.77 0.333 0.482 0.056 0.191 0.542 +1 H 0.781 0.334 0.487 0.052 0.222 0.527 +2 L 0.799 0.348 0.475 0.051 0.223 0.568 +3 C 0.791 0.398 0.409 0.065 0.211 0.618 +4 A 0.756 0.443 0.375 0.078 0.155 0.539 +5 N 0.704 0.491 0.336 0.096 0.09 0.445 +6 K 0.672 0.514 0.338 0.11 0.055 0.308 +7 M 0.677 0.515 0.363 0.109 0.026 0.465 +8 D 0.692 0.529 0.358 0.117 0.026 0.262 +9 L 0.708 0.518 0.376 0.109 0.028 0.532 +10 H 0.741 0.479 0.385 0.088 0.06 0.538 +11 H 0.762 0.429 0.422 0.072 0.112 0.546 +12 H 0.783 0.392 0.464 0.059 0.158 0.577 +13 H 0.802 0.36 0.502 0.054 0.194 0.559 +14 L 0.826 0.324 0.524 0.049 0.229 0.585 +15 C 0.831 0.319 0.512 0.052 0.239 0.642 +16 A 0.813 0.311 0.545 0.055 0.218 0.587 +17 H 0.817 0.315 0.575 0.046 0.174 0.561 +18 H 0.818 0.329 0.595 0.048 0.165 0.552 +19 L 0.829 0.326 0.564 0.05 0.161 0.579 +20 C 0.838 0.35 0.547 0.054 0.155 0.623 +21 A 0.815 0.385 0.501 0.067 0.129 0.554 +22 N 0.794 0.423 0.482 0.071 0.072 0.486 +23 K 0.8 0.439 0.503 0.073 0.039 0.355 +24 M 0.821 0.428 0.515 0.066 0.019 0.511 +25 D 0.846 0.43 0.567 0.064 0.006 0.336 +26 L 0.847 0.414 0.583 0.056 0.003 0.586 +27 N 0.853 0.386 0.594 0.045 0.017 0.5 +28 K 0.855 0.348 0.629 0.044 0.068 0.362 +29 M 0.88 0.316 0.649 0.035 0.113 0.548 +30 D 0.914 0.271 0.69 0.029 0.171 0.357 +31 L 0.923 0.226 0.722 0.019 0.217 0.599 +32 L 0.923 0.219 0.686 0.011 0.234 0.615 +33 C 0.903 0.255 0.641 0.017 0.227 0.668 +34 A 0.878 0.313 0.598 0.027 0.157 0.588 +35 N 0.851 0.362 0.583 0.038 0.097 0.514 +36 K 0.84 0.391 0.553 0.045 0.067 0.373 +37 M 0.848 0.392 0.53 0.04 0.075 0.518 +38 D 0.845 0.382 0.537 0.047 0.098 0.32 +39 L 0.826 0.359 0.538 0.049 0.114 0.581 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_09_consisting_of_30_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_09_consisting_of_30_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 G 0.0 0.658 0.55 0.91 0.039 0.127 0.138 0.102 0.443 +1 N 0.004 0.672 0.585 0.923 0.028 0.086 0.138 0.122 0.471 +2 K 0.039 0.703 0.535 0.922 0.054 0.071 0.136 0.207 0.358 +3 T 0.648 0.728 0.441 0.91 0.14 0.147 0.129 0.301 0.581 +4 P 6.077 0.746 0.347 0.913 0.224 0.277 0.116 0.357 0.558 +5 F 11.819 0.751 0.337 0.916 0.303 0.346 0.094 0.361 0.572 +6 M 13.024 0.744 0.352 0.924 0.377 0.331 0.084 0.367 0.54 +7 K 12.527 0.732 0.395 0.93 0.237 0.283 0.087 0.328 0.353 +8 M 7.11 0.698 0.467 0.933 0.17 0.206 0.108 0.253 0.527 +9 H 1.364 0.677 0.525 0.936 0.111 0.152 0.133 0.159 0.54 +10 G 0.122 0.644 0.572 0.936 0.045 0.095 0.164 0.099 0.461 +11 G 0.019 0.632 0.629 0.942 0.026 0.013 0.182 0.078 0.433 +12 N 0.13 0.636 0.647 0.944 0.028 -0.028 0.177 0.111 0.467 +13 K 1.504 0.685 0.545 0.951 0.045 0.029 0.154 0.218 0.354 +14 T 6.09 0.719 0.428 0.962 0.131 0.153 0.136 0.32 0.582 +15 P 10.104 0.729 0.338 0.975 0.192 0.282 0.125 0.364 0.555 +16 F 10.718 0.735 0.335 0.981 0.224 0.368 0.103 0.332 0.566 +17 M 9.456 0.736 0.346 0.983 0.253 0.376 0.092 0.321 0.537 +18 K 4.88 0.729 0.375 0.984 0.2 0.349 0.096 0.273 0.339 +19 M 0.858 0.735 0.425 0.983 0.183 0.336 0.09 0.223 0.52 +20 H 0.124 0.731 0.486 0.983 0.184 0.276 0.095 0.158 0.541 +21 N 0.014 0.744 0.535 0.983 0.127 0.231 0.101 0.137 0.497 +22 K 0.015 0.764 0.516 0.982 0.082 0.219 0.114 0.143 0.356 +23 T 0.072 0.769 0.457 0.977 0.149 0.249 0.117 0.188 0.577 +24 P 0.249 0.771 0.374 0.972 0.204 0.366 0.108 0.222 0.541 +25 F 0.47 0.765 0.351 0.969 0.29 0.442 0.089 0.238 0.55 +26 M 0.476 0.763 0.343 0.975 0.347 0.439 0.075 0.26 0.527 +27 K 0.417 0.755 0.343 0.979 0.259 0.44 0.072 0.244 0.348 +28 M 0.239 0.766 0.345 0.977 0.091 0.454 0.064 0.229 0.528 +29 H 0.016 0.761 0.35 0.977 0.06 0.43 0.07 0.205 0.561 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_09_consisting_of_30_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_09_consisting_of_30_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 G 0.658 0.55 0.127 0.138 0.102 0.443 +1 N 0.672 0.585 0.086 0.138 0.122 0.471 +2 K 0.703 0.535 0.071 0.136 0.207 0.358 +3 T 0.728 0.441 0.147 0.129 0.301 0.581 +4 P 0.746 0.347 0.277 0.116 0.357 0.558 +5 F 0.751 0.337 0.346 0.094 0.361 0.572 +6 M 0.744 0.352 0.331 0.084 0.367 0.54 +7 K 0.732 0.395 0.283 0.087 0.328 0.353 +8 M 0.698 0.467 0.206 0.108 0.253 0.527 +9 H 0.677 0.525 0.152 0.133 0.159 0.54 +10 G 0.644 0.572 0.095 0.164 0.099 0.461 +11 G 0.632 0.629 0.013 0.182 0.078 0.433 +12 N 0.636 0.647 -0.028 0.177 0.111 0.467 +13 K 0.685 0.545 0.029 0.154 0.218 0.354 +14 T 0.719 0.428 0.153 0.136 0.32 0.582 +15 P 0.729 0.338 0.282 0.125 0.364 0.555 +16 F 0.735 0.335 0.368 0.103 0.332 0.566 +17 M 0.736 0.346 0.376 0.092 0.321 0.537 +18 K 0.729 0.375 0.349 0.096 0.273 0.339 +19 M 0.735 0.425 0.336 0.09 0.223 0.52 +20 H 0.731 0.486 0.276 0.095 0.158 0.541 +21 N 0.744 0.535 0.231 0.101 0.137 0.497 +22 K 0.764 0.516 0.219 0.114 0.143 0.356 +23 T 0.769 0.457 0.249 0.117 0.188 0.577 +24 P 0.771 0.374 0.366 0.108 0.222 0.541 +25 F 0.765 0.351 0.442 0.089 0.238 0.55 +26 M 0.763 0.343 0.439 0.075 0.26 0.527 +27 K 0.755 0.343 0.44 0.072 0.244 0.348 +28 M 0.766 0.345 0.454 0.064 0.229 0.528 +29 H 0.761 0.35 0.43 0.07 0.205 0.561 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_10_consisting_of_65_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_10_consisting_of_65_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,66 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 L 0.002 0.762 0.394 0.752 0.025 0.469 0.069 0.082 0.581 +1 D 0.026 0.772 0.45 0.808 0.048 0.472 0.071 0.034 0.329 +2 N 0.123 0.759 0.466 0.8 0.147 0.473 0.065 0.017 0.522 +3 S 1.154 0.753 0.451 0.742 0.199 0.464 0.064 0.058 0.519 +4 K 7.768 0.76 0.414 0.689 0.172 0.482 0.062 0.11 0.388 +5 M 22.441 0.777 0.375 0.629 0.289 0.45 0.063 0.179 0.54 +6 W 29.162 0.785 0.339 0.521 0.447 0.416 0.069 0.246 0.632 +7 Q 28.544 0.789 0.34 0.476 0.37 0.417 0.071 0.24 0.422 +8 L 21.947 0.79 0.412 0.395 0.305 0.366 0.08 0.164 0.595 +9 D 7.251 0.785 0.505 0.366 0.137 0.306 0.095 0.105 0.334 +10 N 0.434 0.761 0.559 0.346 0.101 0.28 0.11 0.031 0.552 +11 P 0.02 0.738 0.546 0.333 0.067 0.34 0.121 -0.024 0.532 +12 M 0.004 0.744 0.54 0.328 0.067 0.374 0.124 -0.038 0.523 +13 P 0.032 0.734 0.494 0.341 0.085 0.436 0.121 -0.012 0.531 +14 M 0.297 0.74 0.458 0.35 0.156 0.46 0.097 0.039 0.526 +15 S 2.08 0.751 0.411 0.348 0.185 0.504 0.08 0.079 0.521 +16 K 7.151 0.765 0.366 0.315 0.183 0.495 0.068 0.14 0.365 +17 M 9.106 0.786 0.34 0.274 0.273 0.489 0.067 0.186 0.54 +18 W 9.174 0.796 0.31 0.24 0.354 0.516 0.064 0.199 0.65 +19 Q 7.418 0.811 0.299 0.219 0.34 0.552 0.06 0.191 0.424 +20 L 2.347 0.816 0.334 0.192 0.371 0.588 0.054 0.091 0.609 +21 D 0.365 0.816 0.374 0.184 0.256 0.623 0.052 0.041 0.363 +22 N 0.038 0.794 0.423 0.166 0.332 0.622 0.048 -0.043 0.552 +23 S 0.132 0.786 0.408 0.153 0.323 0.659 0.048 -0.04 0.541 +24 K 2.276 0.781 0.373 0.14 0.328 0.623 0.056 0.002 0.392 +25 M 7.556 0.791 0.337 0.136 0.466 0.596 0.052 0.082 0.533 +26 W 10.153 0.803 0.301 0.137 0.593 0.563 0.059 0.183 0.643 +27 Q 10.272 0.802 0.294 0.14 0.545 0.551 0.062 0.207 0.422 +28 L 8.137 0.806 0.334 0.139 0.5 0.522 0.061 0.164 0.587 +29 D 2.856 0.798 0.387 0.154 0.268 0.509 0.066 0.112 0.336 +30 N 0.252 0.785 0.452 0.164 0.268 0.5 0.063 0.004 0.553 +31 L 0.012 0.785 0.463 0.177 0.214 0.545 0.066 -0.061 0.592 +32 D 0.002 0.792 0.486 0.195 0.182 0.557 0.068 -0.086 0.334 +33 N 0.024 0.782 0.466 0.198 0.288 0.55 0.059 -0.042 0.532 +34 S 0.534 0.772 0.441 0.196 0.361 0.537 0.059 0.024 0.521 +35 K 4.659 0.781 0.403 0.191 0.313 0.543 0.058 0.097 0.409 +36 M 9.18 0.793 0.352 0.2 0.387 0.499 0.056 0.162 0.541 +37 W 9.871 0.804 0.321 0.206 0.483 0.488 0.062 0.204 0.626 +38 Q 9.389 0.81 0.317 0.231 0.466 0.476 0.064 0.215 0.445 +39 L 5.265 0.812 0.376 0.237 0.374 0.466 0.069 0.119 0.599 +40 D 0.743 0.803 0.474 0.252 0.217 0.384 0.088 0.063 0.333 +41 N 0.03 0.779 0.527 0.257 0.159 0.372 0.102 -0.001 0.569 +42 P 0.001 0.752 0.537 0.267 0.099 0.408 0.114 -0.075 0.523 +43 M 0.001 0.756 0.517 0.255 0.095 0.455 0.114 -0.076 0.532 +44 P 0.011 0.747 0.471 0.262 0.119 0.506 0.11 -0.069 0.527 +45 M 0.113 0.754 0.437 0.257 0.207 0.527 0.084 -0.01 0.526 +46 S 0.854 0.756 0.401 0.254 0.264 0.54 0.074 0.042 0.517 +47 K 3.084 0.765 0.361 0.237 0.219 0.533 0.069 0.095 0.372 +48 M 4.185 0.782 0.343 0.224 0.274 0.529 0.067 0.126 0.529 +49 W 4.23 0.791 0.317 0.219 0.365 0.526 0.066 0.158 0.647 +50 Q 3.501 0.808 0.302 0.222 0.355 0.568 0.058 0.148 0.422 +51 L 1.272 0.816 0.333 0.227 0.381 0.571 0.058 0.082 0.612 +52 D 0.161 0.816 0.378 0.249 0.249 0.621 0.056 0.02 0.361 +53 N 0.022 0.8 0.406 0.272 0.329 0.616 0.048 -0.039 0.559 +54 S 0.132 0.787 0.391 0.282 0.34 0.65 0.048 -0.024 0.526 +55 K 1.325 0.786 0.35 0.286 0.313 0.647 0.049 -0.003 0.39 +56 M 3.025 0.802 0.311 0.298 0.445 0.644 0.042 0.059 0.544 +57 W 3.505 0.81 0.275 0.327 0.579 0.627 0.048 0.139 0.639 +58 Q 3.435 0.813 0.266 0.341 0.574 0.624 0.049 0.148 0.427 +59 L 2.251 0.811 0.296 0.371 0.513 0.636 0.046 0.093 0.589 +60 D 0.56 0.803 0.343 0.395 0.301 0.645 0.047 0.035 0.325 +61 N 0.077 0.778 0.38 0.473 0.285 0.627 0.045 -0.026 0.546 +62 A 0.026 0.755 0.365 0.576 0.255 0.639 0.055 -0.024 0.565 +63 A 0.015 0.743 0.346 0.625 0.067 0.653 0.059 -0.018 0.553 +64 A 0.005 0.748 0.325 0.724 0.077 0.63 0.057 0.024 0.56 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_10_consisting_of_65_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_10_consisting_of_65_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,66 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 L 0.762 0.394 0.469 0.069 0.082 0.581 +1 D 0.772 0.45 0.472 0.071 0.034 0.329 +2 N 0.759 0.466 0.473 0.065 0.017 0.522 +3 S 0.753 0.451 0.464 0.064 0.058 0.519 +4 K 0.76 0.414 0.482 0.062 0.11 0.388 +5 M 0.777 0.375 0.45 0.063 0.179 0.54 +6 W 0.785 0.339 0.416 0.069 0.246 0.632 +7 Q 0.789 0.34 0.417 0.071 0.24 0.422 +8 L 0.79 0.412 0.366 0.08 0.164 0.595 +9 D 0.785 0.505 0.306 0.095 0.105 0.334 +10 N 0.761 0.559 0.28 0.11 0.031 0.552 +11 P 0.738 0.546 0.34 0.121 -0.024 0.532 +12 M 0.744 0.54 0.374 0.124 -0.038 0.523 +13 P 0.734 0.494 0.436 0.121 -0.012 0.531 +14 M 0.74 0.458 0.46 0.097 0.039 0.526 +15 S 0.751 0.411 0.504 0.08 0.079 0.521 +16 K 0.765 0.366 0.495 0.068 0.14 0.365 +17 M 0.786 0.34 0.489 0.067 0.186 0.54 +18 W 0.796 0.31 0.516 0.064 0.199 0.65 +19 Q 0.811 0.299 0.552 0.06 0.191 0.424 +20 L 0.816 0.334 0.588 0.054 0.091 0.609 +21 D 0.816 0.374 0.623 0.052 0.041 0.363 +22 N 0.794 0.423 0.622 0.048 -0.043 0.552 +23 S 0.786 0.408 0.659 0.048 -0.04 0.541 +24 K 0.781 0.373 0.623 0.056 0.002 0.392 +25 M 0.791 0.337 0.596 0.052 0.082 0.533 +26 W 0.803 0.301 0.563 0.059 0.183 0.643 +27 Q 0.802 0.294 0.551 0.062 0.207 0.422 +28 L 0.806 0.334 0.522 0.061 0.164 0.587 +29 D 0.798 0.387 0.509 0.066 0.112 0.336 +30 N 0.785 0.452 0.5 0.063 0.004 0.553 +31 L 0.785 0.463 0.545 0.066 -0.061 0.592 +32 D 0.792 0.486 0.557 0.068 -0.086 0.334 +33 N 0.782 0.466 0.55 0.059 -0.042 0.532 +34 S 0.772 0.441 0.537 0.059 0.024 0.521 +35 K 0.781 0.403 0.543 0.058 0.097 0.409 +36 M 0.793 0.352 0.499 0.056 0.162 0.541 +37 W 0.804 0.321 0.488 0.062 0.204 0.626 +38 Q 0.81 0.317 0.476 0.064 0.215 0.445 +39 L 0.812 0.376 0.466 0.069 0.119 0.599 +40 D 0.803 0.474 0.384 0.088 0.063 0.333 +41 N 0.779 0.527 0.372 0.102 -0.001 0.569 +42 P 0.752 0.537 0.408 0.114 -0.075 0.523 +43 M 0.756 0.517 0.455 0.114 -0.076 0.532 +44 P 0.747 0.471 0.506 0.11 -0.069 0.527 +45 M 0.754 0.437 0.527 0.084 -0.01 0.526 +46 S 0.756 0.401 0.54 0.074 0.042 0.517 +47 K 0.765 0.361 0.533 0.069 0.095 0.372 +48 M 0.782 0.343 0.529 0.067 0.126 0.529 +49 W 0.791 0.317 0.526 0.066 0.158 0.647 +50 Q 0.808 0.302 0.568 0.058 0.148 0.422 +51 L 0.816 0.333 0.571 0.058 0.082 0.612 +52 D 0.816 0.378 0.621 0.056 0.02 0.361 +53 N 0.8 0.406 0.616 0.048 -0.039 0.559 +54 S 0.787 0.391 0.65 0.048 -0.024 0.526 +55 K 0.786 0.35 0.647 0.049 -0.003 0.39 +56 M 0.802 0.311 0.644 0.042 0.059 0.544 +57 W 0.81 0.275 0.627 0.048 0.139 0.639 +58 Q 0.813 0.266 0.624 0.049 0.148 0.427 +59 L 0.811 0.296 0.636 0.046 0.093 0.589 +60 D 0.803 0.343 0.645 0.047 0.035 0.325 +61 N 0.778 0.38 0.627 0.045 -0.026 0.546 +62 A 0.755 0.365 0.639 0.055 -0.024 0.565 +63 A 0.743 0.346 0.653 0.059 -0.018 0.553 +64 A 0.748 0.325 0.63 0.057 0.024 0.56 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_11_consisting_of_30_residues.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_11_consisting_of_30_residues.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain +0 P 0.01 0.746 0.394 0.881 0.022 0.444 0.101 0.093 0.531 +1 M 0.184 0.754 0.398 0.927 0.036 0.501 0.08 0.08 0.533 +2 S 0.686 0.773 0.385 0.933 0.156 0.497 0.067 0.126 0.514 +3 K 1.695 0.791 0.348 0.919 0.16 0.511 0.056 0.153 0.395 +4 M 2.641 0.818 0.315 0.922 0.245 0.522 0.044 0.186 0.55 +5 W 2.788 0.833 0.294 0.915 0.403 0.516 0.05 0.229 0.629 +6 Q 2.318 0.845 0.288 0.913 0.423 0.553 0.051 0.225 0.435 +7 L 1.316 0.841 0.326 0.913 0.389 0.566 0.049 0.139 0.607 +8 D 0.364 0.843 0.381 0.919 0.232 0.591 0.047 0.061 0.323 +9 N 0.054 0.816 0.417 0.923 0.241 0.603 0.048 0.015 0.542 +10 M 0.14 0.794 0.399 0.918 0.296 0.609 0.048 0.014 0.545 +11 S 1.191 0.788 0.367 0.916 0.361 0.613 0.054 0.068 0.513 +12 K 5.499 0.804 0.329 0.897 0.354 0.572 0.053 0.152 0.394 +13 M 10.239 0.813 0.303 0.852 0.42 0.542 0.051 0.184 0.571 +14 W 11.072 0.828 0.296 0.826 0.538 0.491 0.05 0.247 0.635 +15 Q 10.045 0.833 0.315 0.847 0.455 0.477 0.059 0.241 0.414 +16 L 5.734 0.823 0.393 0.889 0.358 0.438 0.072 0.154 0.605 +17 D 0.982 0.828 0.471 0.911 0.153 0.392 0.079 0.083 0.348 +18 N 0.032 0.803 0.493 0.936 0.108 0.419 0.093 0.004 0.541 +19 P 0.004 0.784 0.455 0.944 0.103 0.497 0.094 -0.019 0.539 +20 M 0.043 0.776 0.441 0.943 0.153 0.548 0.082 -0.012 0.528 +21 S 0.734 0.782 0.399 0.938 0.22 0.551 0.068 0.048 0.505 +22 K 7.138 0.787 0.35 0.938 0.242 0.537 0.061 0.133 0.385 +23 M 12.833 0.811 0.317 0.926 0.369 0.509 0.049 0.212 0.548 +24 W 13.89 0.829 0.276 0.922 0.435 0.526 0.049 0.261 0.628 +25 Q 13.294 0.829 0.27 0.923 0.43 0.527 0.056 0.272 0.414 +26 L 6.891 0.834 0.321 0.943 0.418 0.499 0.053 0.219 0.607 +27 D 1.193 0.818 0.371 0.949 0.194 0.511 0.057 0.142 0.327 +28 N 0.095 0.797 0.405 0.952 0.058 0.516 0.055 0.071 0.532 +29 A 0.001 0.77 0.402 0.956 0.062 0.514 0.064 0.052 0.552 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/random_sequence_11_consisting_of_30_residues_dynamine.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_sequence_11_consisting_of_30_residues_dynamine.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +residue_index residue backbone coil helix ppII sheet sidechain +0 P 0.746 0.394 0.444 0.101 0.093 0.531 +1 M 0.754 0.398 0.501 0.08 0.08 0.533 +2 S 0.773 0.385 0.497 0.067 0.126 0.514 +3 K 0.791 0.348 0.511 0.056 0.153 0.395 +4 M 0.818 0.315 0.522 0.044 0.186 0.55 +5 W 0.833 0.294 0.516 0.05 0.229 0.629 +6 Q 0.845 0.288 0.553 0.051 0.225 0.435 +7 L 0.841 0.326 0.566 0.049 0.139 0.607 +8 D 0.843 0.381 0.591 0.047 0.061 0.323 +9 N 0.816 0.417 0.603 0.048 0.015 0.542 +10 M 0.794 0.399 0.609 0.048 0.014 0.545 +11 S 0.788 0.367 0.613 0.054 0.068 0.513 +12 K 0.804 0.329 0.572 0.053 0.152 0.394 +13 M 0.813 0.303 0.542 0.051 0.184 0.571 +14 W 0.828 0.296 0.491 0.05 0.247 0.635 +15 Q 0.833 0.315 0.477 0.059 0.241 0.414 +16 L 0.823 0.393 0.438 0.072 0.154 0.605 +17 D 0.828 0.471 0.392 0.079 0.083 0.348 +18 N 0.803 0.493 0.419 0.093 0.004 0.541 +19 P 0.784 0.455 0.497 0.094 -0.019 0.539 +20 M 0.776 0.441 0.548 0.082 -0.012 0.528 +21 S 0.782 0.399 0.551 0.068 0.048 0.505 +22 K 0.787 0.35 0.537 0.061 0.133 0.385 +23 M 0.811 0.317 0.509 0.049 0.212 0.548 +24 W 0.829 0.276 0.526 0.049 0.261 0.628 +25 Q 0.829 0.27 0.527 0.056 0.272 0.414 +26 L 0.834 0.321 0.499 0.053 0.219 0.607 +27 D 0.818 0.371 0.511 0.057 0.142 0.327 +28 N 0.797 0.405 0.516 0.055 0.071 0.532 +29 A 0.77 0.402 0.514 0.064 0.052 0.552 |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/test_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output.json Tue Aug 09 12:30:52 2022 +0000 |
| [ |
| b'@@ -0,0 +1,4444 @@\n+{\n+ "random_sequence_01_consisting_of_40_residues": {\n+ "agmata": [\n+ 0.0,\n+ 0.001,\n+ 0.001,\n+ 0.001,\n+ 0.004,\n+ 0.045,\n+ 0.709,\n+ 5.566,\n+ 17.394,\n+ 27.544,\n+ 28.56,\n+ 23.813,\n+ 11.996,\n+ 1.809,\n+ 0.146,\n+ 0.185,\n+ 1.571,\n+ 8.28,\n+ 17.753,\n+ 20.564,\n+ 19.532,\n+ 12.898,\n+ 3.45,\n+ 0.61,\n+ 0.897,\n+ 3.789,\n+ 12.356,\n+ 19.297,\n+ 20.098,\n+ 17.286,\n+ 8.716,\n+ 1.683,\n+ 0.317,\n+ 0.708,\n+ 3.245,\n+ 13.673,\n+ 15.348,\n+ 14.796,\n+ 12.222,\n+ 1.765\n+ ],\n+ "backbone": [\n+ 0.703,\n+ 0.708,\n+ 0.721,\n+ 0.73,\n+ 0.745,\n+ 0.731,\n+ 0.733,\n+ 0.719,\n+ 0.705,\n+ 0.683,\n+ 0.665,\n+ 0.659,\n+ 0.658,\n+ 0.68,\n+ 0.685,\n+ 0.711,\n+ 0.726,\n+ 0.708,\n+ 0.699,\n+ 0.661,\n+ 0.65,\n+ 0.636,\n+ 0.647,\n+ 0.647,\n+ 0.669,\n+ 0.68,\n+ 0.656,\n+ 0.644,\n+ 0.629,\n+ 0.622,\n+ 0.627,\n+ 0.625,\n+ 0.643,\n+ 0.666,\n+ 0.688,\n+ 0.678,\n+ 0.684,\n+ 0.681,\n+ 0.676,\n+ 0.68\n+ ],\n+ "coil": [\n+ 0.493,\n+ 0.542,\n+ 0.553,\n+ 0.545,\n+ 0.51,\n+ 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0.791,\n+ 0.818,\n+ 0.833,\n+ 0.845,\n+ 0.841,\n+ 0.843,\n+ 0.816,\n+ 0.794,\n+ 0.788,\n+ 0.804,\n+ 0.813,\n+ 0.828,\n+ 0.833,\n+ 0.823,\n+ 0.828,\n+ 0.803,\n+ 0.784,\n+ 0.776,\n+ 0.782,\n+ 0.787,\n+ 0.811,\n+ 0.829,\n+ 0.829,\n+ 0.834,\n+ 0.818,\n+ 0.797,\n+ 0.77\n+ ],\n+ "coil": [\n+ 0.394,\n+ 0.398,\n+ 0.385,\n+ 0.348,\n+ 0.315,\n+ 0.294,\n+ 0.288,\n+ 0.326,\n+ 0.381,\n+ 0.417,\n+ 0.399,\n+ 0.367,\n+ 0.329,\n+ 0.303,\n+ 0.296,\n+ 0.315,\n+ 0.393,\n+ 0.471,\n+ 0.493,\n+ 0.455,\n+ 0.441,\n+ 0.399,\n+ 0.35,\n+ 0.317,\n+ 0.276,\n+ 0.27,\n+ 0.321,\n+ 0.371,\n+ 0.405,\n+ 0.402\n+ ],\n+ "disoMine": [\n+ 0.881,\n+ 0.927,\n+ 0.933,\n+ 0.919,\n+ 0.922,\n+ 0.915,\n+ 0.913,\n+ 0.913,\n+ 0.919,\n+ 0.923,\n+ 0.918,\n+ 0.916,\n+ 0.897,\n+ 0.852,\n+ 0.826,\n+ 0.847,\n+ 0.889,\n+ 0.911,\n+ 0.936,\n+ 0.944,\n+ 0.943,\n+ 0.938,\n+ 0.938,\n+ 0.926,\n+ 0.922,\n+ 0.923,\n+ 0.943,\n+ 0.949,\n+ 0.952,\n+ 0.956\n+ ],\n+ "earlyFolding": [\n+ 0.022,\n+ 0.036,\n+ 0.156,\n+ 0.16,\n+ 0.245,\n+ 0.403,\n+ 0.423,\n+ 0.389,\n+ 0.232,\n+ 0.241,\n+ 0.296,\n+ 0.361,\n+ 0.354,\n+ 0.42,\n+ 0.538,\n+ 0.455,\n+ 0.358,\n+ 0.153,\n+ 0.108,\n+ 0.103,\n+ 0.153,\n+ 0.22,\n+ 0.242,\n+ 0.369,\n+ 0.435,\n+ 0.43,\n+ 0.418,\n+ 0.194,\n+ 0.058,\n+ 0.062\n+ ],\n+ "helix": [\n+ 0.444,\n+ 0.501,\n+ 0.497,\n+ 0.511,\n+ 0.522,\n+ 0.516,\n+ 0.553,\n+ 0.566,\n+ 0.591,\n+ 0.603,\n+ 0.609,\n+ 0.613,\n+ 0.572,\n+ 0.542,\n+ 0.491,\n+ 0.477,\n+ 0.438,\n+ 0.392,\n+ 0.419,\n+ 0.497,\n+ 0.548,\n+ 0.551,\n+ 0.537,\n+ 0.509,\n+ 0.526,\n+ 0.527,\n+ 0.499,\n+ 0.511,\n+ 0.516,\n+ 0.514\n+ ],\n+ "ppII": [\n+ 0.101,\n+ 0.08,\n+ 0.067,\n+ 0.056,\n+ 0.044,\n+ 0.05,\n+ 0.051,\n+ 0.049,\n+ 0.047,\n+ 0.048,\n+ 0.048,\n+ 0.054,\n+ 0.053,\n+ 0.051,\n+ 0.05,\n+ 0.059,\n+ 0.072,\n+ 0.079,\n+ 0.093,\n+ 0.094,\n+ 0.082,\n+ 0.068,\n+ 0.061,\n+ 0.049,\n+ 0.049,\n+ 0.056,\n+ 0.053,\n+ 0.057,\n+ 0.055,\n+ 0.064\n+ ],\n+ "seq": [\n+ "P",\n+ "M",\n+ "S",\n+ "K",\n+ "M",\n+ "W",\n+ "Q",\n+ "L",\n+ "D",\n+ "N",\n+ "M",\n+ "S",\n+ "K",\n+ "M",\n+ "W",\n+ "Q",\n+ "L",\n+ "D",\n+ "N",\n+ "P",\n+ "M",\n+ "S",\n+ "K",\n+ "M",\n+ "W",\n+ "Q",\n+ "L",\n+ "D",\n+ "N",\n+ "A"\n+ ],\n+ "sheet": [\n+ 0.093,\n+ 0.08,\n+ 0.126,\n+ 0.153,\n+ 0.186,\n+ 0.229,\n+ 0.225,\n+ 0.139,\n+ 0.061,\n+ 0.015,\n+ 0.014,\n+ 0.068,\n+ 0.152,\n+ 0.184,\n+ 0.247,\n+ 0.241,\n+ 0.154,\n+ 0.083,\n+ 0.004,\n+ -0.019,\n+ -0.012,\n+ 0.048,\n+ 0.133,\n+ 0.212,\n+ 0.261,\n+ 0.272,\n+ 0.219,\n+ 0.142,\n+ 0.071,\n+ 0.052\n+ ],\n+ "sidechain": [\n+ 0.531,\n+ 0.533,\n+ 0.514,\n+ 0.395,\n+ 0.55,\n+ 0.629,\n+ 0.435,\n+ 0.607,\n+ 0.323,\n+ 0.542,\n+ 0.545,\n+ 0.513,\n+ 0.394,\n+ 0.571,\n+ 0.635,\n+ 0.414,\n+ 0.605,\n+ 0.348,\n+ 0.541,\n+ 0.539,\n+ 0.528,\n+ 0.505,\n+ 0.385,\n+ 0.548,\n+ 0.628,\n+ 0.414,\n+ 0.607,\n+ 0.327,\n+ 0.532,\n+ 0.552\n+ ]\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/test_output_dynamine.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output_dynamine.json Tue Aug 09 12:30:52 2022 +0000 |
| [ |
| b'@@ -0,0 +1,3118 @@\n+{\n+ "random_sequence_01_consisting_of_40_residues": {\n+ "backbone": [\n+ 0.703,\n+ 0.708,\n+ 0.721,\n+ 0.73,\n+ 0.745,\n+ 0.731,\n+ 0.733,\n+ 0.719,\n+ 0.705,\n+ 0.683,\n+ 0.665,\n+ 0.659,\n+ 0.658,\n+ 0.68,\n+ 0.685,\n+ 0.711,\n+ 0.726,\n+ 0.708,\n+ 0.699,\n+ 0.661,\n+ 0.65,\n+ 0.636,\n+ 0.647,\n+ 0.647,\n+ 0.669,\n+ 0.68,\n+ 0.656,\n+ 0.644,\n+ 0.629,\n+ 0.622,\n+ 0.627,\n+ 0.625,\n+ 0.643,\n+ 0.666,\n+ 0.688,\n+ 0.678,\n+ 0.684,\n+ 0.681,\n+ 0.676,\n+ 0.68\n+ ],\n+ "coil": [\n+ 0.493,\n+ 0.542,\n+ 0.553,\n+ 0.545,\n+ 0.51,\n+ 0.444,\n+ 0.403,\n+ 0.367,\n+ 0.353,\n+ 0.368,\n+ 0.409,\n+ 0.448,\n+ 0.498,\n+ 0.547,\n+ 0.559,\n+ 0.544,\n+ 0.508,\n+ 0.442,\n+ 0.402,\n+ 0.401,\n+ 0.439,\n+ 0.506,\n+ 0.55,\n+ 0.571,\n+ 0.567,\n+ 0.549,\n+ 0.499,\n+ 0.478,\n+ 0.479,\n+ 0.506,\n+ 0.543,\n+ 0.58,\n+ 0.588,\n+ 0.568,\n+ 0.533,\n+ 0.468,\n+ 0.435,\n+ 0.414,\n+ 0.413,\n+ 0.405\n+ ],\n+ "helix": [\n+ 0.282,\n+ 0.235,\n+ 0.237,\n+ 0.209,\n+ 0.254,\n+ 0.345,\n+ 0.416,\n+ 0.463,\n+ 0.459,\n+ 0.449,\n+ 0.416,\n+ 0.397,\n+ 0.324,\n+ 0.245,\n+ 0.226,\n+ 0.202,\n+ 0.231,\n+ 0.306,\n+ 0.337,\n+ 0.327,\n+ 0.304,\n+ 0.233,\n+ 0.194,\n+ 0.161,\n+ 0.123,\n+ 0.111,\n+ 0.175,\n+ 0.193,\n+ 0.193,\n+ 0.163,\n+ 0.135,\n+ 0.115,\n+ 0.142,\n+ 0.126,\n+ 0.142,\n+ 0.231,\n+ 0.284,\n+ 0.313,\n+ 0.306,\n+ 0.316\n+ ],\n+ "ppII": [\n+ 0.1,\n+ 0.115,\n+ 0.119,\n+ 0.121,\n+ 0.128,\n+ 0.131,\n+ 0.113,\n+ 0.099,\n+ 0.093,\n+ 0.094,\n+ 0.1,\n+ 0.107,\n+ 0.125,\n+ 0.14,\n+ 0.145,\n+ 0.133,\n+ 0.139,\n+ 0.143,\n+ 0.13,\n+ 0.132,\n+ 0.133,\n+ 0.144,\n+ 0.156,\n+ 0.162,\n+ 0.159,\n+ 0.165,\n+ 0.173,\n+ 0.158,\n+ 0.156,\n+ 0.155,\n+ 0.158,\n+ 0.164,\n+ 0.16,\n+ 0.158,\n+ 0.16,\n+ 0.16,\n+ 0.133,\n+ 0.12,\n+ 0.113,\n+ 0.108\n+ ],\n+ "seq": [\n+ "M",\n+ "D",\n+ "R",\n+ "H",\n+ "D",\n+ "P",\n+ "V",\n+ "Q",\n+ "K",\n+ "S",\n+ "M",\n+ "M",\n+ "M",\n+ "D",\n+ "R",\n+ "H",\n+ "D",\n+ "P",\n+ "V",\n+ "Q",\n+ "K",\n+ "M",\n+ "D",\n+ "R",\n+ "H",\n+ "D",\n+ "P",\n+ "V",\n+ "Q",\n+ "K",\n+ "S",\n+ "D",\n+ "R",\n+ "H",\n+ "D",\n+ "P",\n+ "V",\n+ "Q",\n+ "K",\n+ "S"\n+ ],\n+ "sheet": [\n+ 0.119,\n+ 0.073,\n+ 0.043,\n+ 0.058,\n+ 0.076,\n+ 0.106,\n+ 0.136,\n+ 0.171,\n+ 0.207,\n+ 0.22,\n+ 0.193,\n+ 0.138,\n+ 0.095,\n+ 0.069,\n+ 0.055,\n+ 0.078,\n+ 0.132,\n+ 0.187,\n+ 0.24,\n+ 0.236,\n+ 0.215,\n+ 0.164,\n+ 0.097,\n+ 0.081,\n+ 0.114,\n+ 0.171,\n+ 0.216,\n+ 0.244,\n+ 0.253,\n+ 0.227,\n+ 0.18,\n+ 0.107,\n+ 0.073,\n+ 0.102,\n+ 0.159,\n+ 0.202,\n+ 0.219,\n+ 0.231,\n+ 0.231,\n+ 0.229\n+ ],\n+ "sidechain": [\n+ 0.493,\n+ 0.287,\n+ 0.321,\n+ 0.497,\n+ 0.291,\n+ 0.489,\n+ 0.508,\n+ 0.339,\n+ 0.321,\n+ 0.493,\n+ 0.472,\n+ 0.442,\n+ 0.452,\n+ 0.263,\n+ 0.306,\n+ 0.482,\n+ 0.28,\n+ 0.488,\n+ 0.531,\n+ 0.321,\n+ 0.29,\n+ 0.472,\n+ 0.264,\n+ 0.285,\n+ 0.466,\n+ 0.269,\n+ 0.471,\n+ 0.507,\n+ 0.321,\n+ 0.302,\n+ 0.477,\n+ 0.277,\n+ 0.284,\n+ 0.471,\n+ 0.278,\n+ 0.49,\n+ '..b' 0.519,\n+ 0.388,\n+ 0.54,\n+ 0.632,\n+ 0.422,\n+ 0.595,\n+ 0.334,\n+ 0.552,\n+ 0.532,\n+ 0.523,\n+ 0.531,\n+ 0.526,\n+ 0.521,\n+ 0.365,\n+ 0.539,\n+ 0.65,\n+ 0.424,\n+ 0.609,\n+ 0.363,\n+ 0.552,\n+ 0.541,\n+ 0.392,\n+ 0.533,\n+ 0.643,\n+ 0.422,\n+ 0.587,\n+ 0.336,\n+ 0.553,\n+ 0.592,\n+ 0.334,\n+ 0.532,\n+ 0.521,\n+ 0.409,\n+ 0.541,\n+ 0.626,\n+ 0.445,\n+ 0.599,\n+ 0.333,\n+ 0.569,\n+ 0.523,\n+ 0.532,\n+ 0.527,\n+ 0.526,\n+ 0.517,\n+ 0.372,\n+ 0.529,\n+ 0.647,\n+ 0.422,\n+ 0.612,\n+ 0.361,\n+ 0.559,\n+ 0.526,\n+ 0.39,\n+ 0.544,\n+ 0.639,\n+ 0.427,\n+ 0.589,\n+ 0.325,\n+ 0.546,\n+ 0.565,\n+ 0.553,\n+ 0.56\n+ ]\n+ },\n+ "random_sequence_11_consisting_of_30_residues": {\n+ "backbone": [\n+ 0.746,\n+ 0.754,\n+ 0.773,\n+ 0.791,\n+ 0.818,\n+ 0.833,\n+ 0.845,\n+ 0.841,\n+ 0.843,\n+ 0.816,\n+ 0.794,\n+ 0.788,\n+ 0.804,\n+ 0.813,\n+ 0.828,\n+ 0.833,\n+ 0.823,\n+ 0.828,\n+ 0.803,\n+ 0.784,\n+ 0.776,\n+ 0.782,\n+ 0.787,\n+ 0.811,\n+ 0.829,\n+ 0.829,\n+ 0.834,\n+ 0.818,\n+ 0.797,\n+ 0.77\n+ ],\n+ "coil": [\n+ 0.394,\n+ 0.398,\n+ 0.385,\n+ 0.348,\n+ 0.315,\n+ 0.294,\n+ 0.288,\n+ 0.326,\n+ 0.381,\n+ 0.417,\n+ 0.399,\n+ 0.367,\n+ 0.329,\n+ 0.303,\n+ 0.296,\n+ 0.315,\n+ 0.393,\n+ 0.471,\n+ 0.493,\n+ 0.455,\n+ 0.441,\n+ 0.399,\n+ 0.35,\n+ 0.317,\n+ 0.276,\n+ 0.27,\n+ 0.321,\n+ 0.371,\n+ 0.405,\n+ 0.402\n+ ],\n+ "helix": [\n+ 0.444,\n+ 0.501,\n+ 0.497,\n+ 0.511,\n+ 0.522,\n+ 0.516,\n+ 0.553,\n+ 0.566,\n+ 0.591,\n+ 0.603,\n+ 0.609,\n+ 0.613,\n+ 0.572,\n+ 0.542,\n+ 0.491,\n+ 0.477,\n+ 0.438,\n+ 0.392,\n+ 0.419,\n+ 0.497,\n+ 0.548,\n+ 0.551,\n+ 0.537,\n+ 0.509,\n+ 0.526,\n+ 0.527,\n+ 0.499,\n+ 0.511,\n+ 0.516,\n+ 0.514\n+ ],\n+ "ppII": [\n+ 0.101,\n+ 0.08,\n+ 0.067,\n+ 0.056,\n+ 0.044,\n+ 0.05,\n+ 0.051,\n+ 0.049,\n+ 0.047,\n+ 0.048,\n+ 0.048,\n+ 0.054,\n+ 0.053,\n+ 0.051,\n+ 0.05,\n+ 0.059,\n+ 0.072,\n+ 0.079,\n+ 0.093,\n+ 0.094,\n+ 0.082,\n+ 0.068,\n+ 0.061,\n+ 0.049,\n+ 0.049,\n+ 0.056,\n+ 0.053,\n+ 0.057,\n+ 0.055,\n+ 0.064\n+ ],\n+ "seq": [\n+ "P",\n+ "M",\n+ "S",\n+ "K",\n+ "M",\n+ "W",\n+ "Q",\n+ "L",\n+ "D",\n+ "N",\n+ "M",\n+ "S",\n+ "K",\n+ "M",\n+ "W",\n+ "Q",\n+ "L",\n+ "D",\n+ "N",\n+ "P",\n+ "M",\n+ "S",\n+ "K",\n+ "M",\n+ "W",\n+ "Q",\n+ "L",\n+ "D",\n+ "N",\n+ "A"\n+ ],\n+ "sheet": [\n+ 0.093,\n+ 0.08,\n+ 0.126,\n+ 0.153,\n+ 0.186,\n+ 0.229,\n+ 0.225,\n+ 0.139,\n+ 0.061,\n+ 0.015,\n+ 0.014,\n+ 0.068,\n+ 0.152,\n+ 0.184,\n+ 0.247,\n+ 0.241,\n+ 0.154,\n+ 0.083,\n+ 0.004,\n+ -0.019,\n+ -0.012,\n+ 0.048,\n+ 0.133,\n+ 0.212,\n+ 0.261,\n+ 0.272,\n+ 0.219,\n+ 0.142,\n+ 0.071,\n+ 0.052\n+ ],\n+ "sidechain": [\n+ 0.531,\n+ 0.533,\n+ 0.514,\n+ 0.395,\n+ 0.55,\n+ 0.629,\n+ 0.435,\n+ 0.607,\n+ 0.323,\n+ 0.542,\n+ 0.545,\n+ 0.513,\n+ 0.394,\n+ 0.571,\n+ 0.635,\n+ 0.414,\n+ 0.605,\n+ 0.348,\n+ 0.541,\n+ 0.539,\n+ 0.528,\n+ 0.505,\n+ 0.385,\n+ 0.548,\n+ 0.628,\n+ 0.414,\n+ 0.607,\n+ 0.327,\n+ 0.532,\n+ 0.552\n+ ]\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/wrong.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrong.fasta Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +random_sequence_01_consisting_of_40_residues +MDRHDPVQKSMMMDRHDPVQKMDRHDPVQKSDRHDPVQKS |
| b |
| diff -r 000000000000 -r b694a77ca1e8 test-data/wrong.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrong.tsv Tue Aug 09 12:30:52 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +id,sequence +TEST,MDRHDPVQKSMMMDRHDPVQKMDRHDPVQKSDRHDPVQKS |