# HG changeset patch # User iuc # Date 1660048252 0 # Node ID b694a77ca1e8d5fae687b9e1a9409a0dbd51894d planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 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 @@ -0,0 +1,708 @@ + + from their amino-acid sequences + + b2btools + + + b2btools + + + + +
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+ + + + + + + + + + + + + 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 + +There will be the next results if all the predictor tools (DynaMine, DisoMine, EFoldMine, and AgMata) are selected: + +JSON result +........... +Containing all the input sequences and their predicted features depending on the selected predictors. +:: + + { + "random_sequence_03_consisting_of_30_residues": { + "agmata": [ + 0.012, + 0.08, + 0.119, + 0.154, + 0.2, + 0.34, + 1.023, + 4.084, + 12.328, + 20.723, + 25.866, + 24.864, + 17.509, + 9.32, + 3.591, + 1.559, + 0.64, + 0.221, + 0.084, + 0.038, + 0.031, + 0.035, + 0.052, + 0.159, + 1.115, + 7.747, + 8.329, + 8.214, + 7.259, + 0.608 + ], + "backbone": [ + 0.818, + 0.833, + 0.87, + ... + ], + ... + }, + ... + } + +Tabular results +............... +There will be a tabular files (.TSV) for each sequence where each row is a residue of the sequence and the columns are the predicted features depending on the selected predictors. + +:: + + 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 + +Plots +..... + +Depending on the options selected, there will be a plot (built using ``matplotlib``) +per prediction per sequence and/or a plot per prediction for all the sequences together. + +- Checking **Plot** parameter implies that predicted features will be plotted in different files by input sequence. + - 11 input sequences x 9 predicted features = 99 plots in PNG format + - ``sequence_01_agmata`` plot + - ``sequence_01_backbone`` plot + - ``sequence_01_coil`` plot + - ``sequence_01_disoMine`` plot + - ``sequence_01_earlyFolding`` plot + - ``sequence_01_helix`` plot + - ``sequence_01_ppII`` plot + - ``sequence_01_sheet`` plot + - ``sequence_01_sidechain`` plot + - ... + - ``sequence_11_sidechain`` plot + +- Checking **Plot all** parameter implies that all the input sequences will be plotted together in order to compare predicted features. + - 9 predicted features = 9 plots in PNG format + - **agmata plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + - **backbone plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + - **coil plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + - **disoMine plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + - **earlyFolding plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + - **helix plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + - **ppII plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + - **sheet plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + - **sidechain plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``) + +About Bio2Byte +-------------- + +**We research the relation between protein sequence and biophysical behavior.** + +Proteins are the molecular machines that make cells work. +They perform a wide variety of functions through interactions with each other and many additional molecules. +Traditionally, proteins are described in a single static state (a picture). +It is now increasingly recognized that many proteins can adopt multiple states and move between these conformational states dynamically (a movie). + +We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence. +Underlying physical and chemical principles are computationally unraveled through data integration, +analysis and machine learning, so connecting them to biological events and improving our understanding of the way proteins work. + +Visit our website for further information: https://bio2byte.be + +About Bio2Byte tools +'''''''''''''''''''' +The software suite "Bio2byte tools", known as ``b2btools`` offers a set of biophysical predictions for both single protein sequences and MSA input files. + +**Useful links:** + +``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. +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. + + ]]> + + + + + + + + + + 10.1038/ncomms3741 + 10.1101/2020.05.25.115253 + 10.1038/s41598-017-08366-3 + 10.1093/bioinformatics/btz912 + + 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 @@ -0,0 +1,307 @@ +import json +import optparse +import os.path +import re +import unicodedata + +import matplotlib.pyplot as plt +import numpy as np +import pandas as pd +from b2bTools import SingleSeq + + +def slugify(value): + """ + From https://github.com/django/django/blob/master/django/utils/text.py + Convert to ASCII if 'allow_unicode'. Convert spaces or repeated + dashes to single dashes. Remove characters that aren't alphanumerics, + underscores, or hyphens. Convert to lowercase. Also strip leading and + trailing whitespace, dashes, and underscores. + """ + value = str(value) + value = ( + unicodedata.normalize("NFKD", value) + .encode("ascii", "ignore") + .decode("ascii") + ) + value = re.sub(r"[^\w\s-]", "", value.lower()) + return re.sub(r"[-\s]+", "-", value).strip("-_") + + +def check_min_max(predicted_values, former_min, former_max): + seq_max = max(predicted_values) + seq_min = min(predicted_values) + if ( + seq_max + 0.1 > former_max + and not np.isnan(seq_max) + and not np.isinf(seq_max) + ): + former_max = seq_max + 0.1 + if ( + seq_min - 0.1 < former_min + and not np.isnan(seq_min) + and not np.isinf(seq_min) + ): + former_min = seq_min - 0.1 + return former_min, former_max + + +def plot_prediction(pred_name, hlighting_regions, predicted_values, seq_name): + thresholds_dict = { + "backbone": { + "membrane spanning": [1.0, 1.5], + "rigid": [0.8, 1.0], + "context-dependent": [0.69, 0.8], + "flexible": [-1.0, 0.69], + }, + "earlyFolding": { + "early folds": [0.169, 2.0], + "late folds": [-1.0, 0.169], + }, + "disoMine": {"ordered": [-1.0, 0.5], "disordered": [0.5, 2.0]}, + } + ordered_regions_dict = { + "backbone": [ + "flexible", + "context-dependent", + "rigid", + "membrane spanning", + ], + "earlyFolding": ["late folds", "early folds"], + "disoMine": ["ordered", "disordered"], + } + colors = ["yellow", "orange", "pink", "red"] + ranges_dict = { + "backbone": [-0.2, 1.2], + "sidechain": [-0.2, 1.2], + "ppII": [-0.2, 1.2], + "earlyFolding": [-0.2, 1.2], + "disoMine": [-0.2, 1.2], + "agmata": [-0.2, 1.2], + "helix": [-1.0, 1.0], + "sheet": [-1.0, 1.0], + "coil": [-1.0, 1.0], + } + fig, ax = plt.subplots(1, 1) + fig.set_figwidth(10) + fig.set_figheight(5) + ax.set_title(pred_name + " " + "prediction") + min_value, max_value = ranges_dict[pred_name] + if seq_name == "all": + max_len = 0 + for seq in predicted_values.keys(): + predictions = predicted_values[seq] + min_value, max_value = check_min_max( + predictions, min_value, max_value + ) + ax.plot(range(len(predictions)), predictions, label=seq) + if len(predictions) > max_len: + max_len = len(predictions) + ax.set_xlim([0, max_len - 1]) + else: + predictions = predicted_values + min_value, max_value = check_min_max(predictions, min_value, max_value) + ax.plot(range(len(predictions)), predictions, label=seq_name) + ax.set_xlim([0, len(predictions) - 1]) + legend_lines = plt.legend( + bbox_to_anchor=(1.04, 1), loc="upper left", fancybox=True, shadow=True + ) + ax.add_artist(legend_lines) + # Define regions + if hlighting_regions: + if pred_name in ordered_regions_dict.keys(): + for i, prediction in enumerate(ordered_regions_dict[pred_name]): + lower = thresholds_dict[pred_name][prediction][0] + upper = thresholds_dict[pred_name][prediction][1] + color = colors[i] + ax.axhspan( + lower, upper, alpha=0.3, color=color, label=prediction + ) + included_in_regions_legend = list( + reversed( + [ + prediction + for prediction in ordered_regions_dict[pred_name] + ] + ) + ) # to sort it "from up to low" + # Get handles and labels + handles, labels = plt.gca().get_legend_handles_labels() + handles_dict = { + label: handles[idx] for idx, label in enumerate(labels) + } + # Add legend for regions, if available + region_legend = ax.legend( + [ + handles_dict[region] + for region in included_in_regions_legend + ], + [region for region in included_in_regions_legend], + fancybox=True, + shadow=True, + loc="lower left", + bbox_to_anchor=(1.04, 0), + ) + ax.add_artist(region_legend) + ax.set_ylim([min_value, max_value]) + ax.set_xlabel("residue index") + ax.set_ylabel("prediction values") + ax.grid(axis="y") + plt.savefig( + os.path.join( + options.plot_output, + "{0}_{1}.png".format(slugify(seq_name), pred_name), + ), + bbox_inches="tight", + ) + plt.close() + + +def df_dict_to_dict_of_values(df_dict, predictor): + results_dict = {} + for seq in df_dict.keys(): + df = pd.read_csv(df_dict[seq], sep="\t") + results_dict[seq] = df[predictor] + return results_dict + + +def main(options): + single_seq = SingleSeq(options.input_fasta) + b2b_tools = [] + if options.dynamine: + b2b_tools.append("dynamine") + if options.disomine: + b2b_tools.append("disomine") + if options.efoldmine: + b2b_tools.append("efoldmine") + if options.agmata: + b2b_tools.append("agmata") + single_seq.predict(b2b_tools) + predictions = single_seq.get_all_predictions() + + def rounder_function(value): + return round(float(value), 3) + + rounded_predictions = json.loads( + json.dumps(predictions), parse_float=rounder_function + ) + results_json = json.dumps(rounded_predictions, indent=2, sort_keys=True) + with open(options.json_output, "w") as f: + f.write(results_json) + first_sequence_key = next(iter(predictions)) + prediction_keys = predictions[first_sequence_key].keys() + # Sort column names + tsv_column_names = list(prediction_keys) + tsv_column_names.remove("seq") + tsv_column_names = ['residue', *sorted(tsv_column_names)] + + df_dictionary = {} + for sequence_key, seq_preds in predictions.items(): + residues = seq_preds["seq"] + residues_count = len(residues) + sequence_df = pd.DataFrame( + columns=prediction_keys, index=range(residues_count) + ) + sequence_df.index.name = "residue_index" + for predictor in prediction_keys: + sequence_df[predictor] = seq_preds[predictor] + sequence_df = sequence_df.rename(columns={"seq": "residue"}) + sequence_df = sequence_df.round(decimals=3) + filename = f"{options.output}/{slugify(sequence_key)}.tsv" + df_dictionary[sequence_key] = filename + sequence_df.to_csv( + filename, + header=True, + columns=tsv_column_names, + sep="\t" + ) + # Plot each individual plot (compatible with plot all) + if options.plot: + for predictor in prediction_keys: + if predictor != "seq": + plot_prediction( + pred_name=predictor, + hlighting_regions=True, + predicted_values=seq_preds[predictor], + seq_name=sequence_key, + ) + # Plot all together (compatible with plot individual) + if options.plot_all: + for predictor in prediction_keys: + if predictor != "seq": + results_dictionary = df_dict_to_dict_of_values( + df_dictionary, predictor + ) + plot_prediction( + pred_name=predictor, + hlighting_regions=True, + predicted_values=results_dictionary, + seq_name="all", + ) + + +if __name__ == "__main__": + parser = optparse.OptionParser() + parser.add_option( + "--dynamine", + action="store_true" + ) + parser.add_option( + "--disomine", + action="store_true" + ) + parser.add_option( + "--efoldmine", + action="store_true" + ) + parser.add_option( + "--agmata", + action="store_true" + ) + parser.add_option( + "--file", + dest="input_fasta", + type="string" + ) + parser.add_option( + "--output", + dest="output", + type="string" + ) + parser.add_option( + "--plot-output", + type="string", + dest="plot_output" + ) + parser.add_option( + "--json", + dest="json_output", + type="string" + ) + parser.add_option( + "--plot", + action="store_true" + ) + parser.add_option( + "--plot_all", + action="store_true" + ) + parser.add_option( + "--highlight", + action="store_true" + ) + try: + options, args = parser.parse_args() + if not (options.dynamine or options.disomine or options.efoldmine or options.agmata): + parser.error('At least one predictor is required') + if not options.input_fasta: + parser.error('Input file not given (--file)') + if not options.output: + parser.error('Output directory not given (--output)') + if (options.plot or options.plot_all) and not options.plot_output: + parser.error('Plot output directory not given (--plot-output)') + if not options.json_output: + parser.error('Json output file not given (--json)') + main(options) + except optparse.OptionError as exc: + raise RuntimeError(f"Invalid arguments: {args}") from exc 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -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 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