| Previous changeset 8:ca90d17ff51b (2022-08-19) Next changeset 10:072c324f20fc (2022-09-16) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 |
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modified:
alphafold.xml gen_extra_outputs.py validate_fasta.py |
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added:
test-data/multimer.fasta test-data/multimer_exceeds_count.fasta test-data/multimer_output/model_confidence_scores.tsv test-data/multimer_output/msas/A/bfd_uniclust_hits.a3m test-data/multimer_output/msas/A/mgnify_hits.sto test-data/multimer_output/msas/A/pdb_hits.sto test-data/multimer_output/msas/A/uniprot_hits.sto test-data/multimer_output/msas/A/uniref90_hits.sto test-data/multimer_output/msas/B/bfd_uniclust_hits.a3m test-data/multimer_output/msas/B/mgnify_hits.sto test-data/multimer_output/msas/B/pdb_hits.sto test-data/multimer_output/msas/B/uniprot_hits.sto test-data/multimer_output/msas/B/uniref90_hits.sto test-data/multimer_output/msas/chain_id_map.json test-data/multimer_output/ranked_0.pdb test-data/multimer_output/ranked_1.pdb test-data/multimer_output/ranked_2.pdb test-data/multimer_output/ranked_3.pdb test-data/multimer_output/ranked_4.pdb test-data/multimer_output/ranking_debug.json test-data/multimer_output/relaxed_model_1_multimer.pdb test-data/multimer_output/relaxed_model_2_multimer.pdb test-data/multimer_output/relaxed_model_3_multimer.pdb test-data/multimer_output/relaxed_model_4_multimer.pdb test-data/multimer_output/relaxed_model_5_multimer.pdb test-data/multimer_output/timings.json test-data/multimer_output/unrelaxed_model_1_multimer.pdb test-data/multimer_output/unrelaxed_model_2_multimer.pdb test-data/multimer_output/unrelaxed_model_3_multimer.pdb test-data/multimer_output/unrelaxed_model_4_multimer.pdb test-data/multimer_output/unrelaxed_model_5_multimer.pdb |
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| diff -r ca90d17ff51b -r 3bd420ec162d alphafold.xml --- a/alphafold.xml Fri Aug 19 00:29:16 2022 +0000 +++ b/alphafold.xml Tue Sep 13 22:04:12 2022 +0000 |
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| b'@@ -2,7 +2,7 @@\n <description> - AI-guided 3D structural prediction of proteins</description>\n <macros>\n <token name="@TOOL_VERSION@">2.1.2</token>\n- <token name="@VERSION_SUFFIX@">1</token>\n+ <token name="@VERSION_SUFFIX@">2</token>\n </macros>\n <edam_topics>\n <edam_topic>topic_0082</edam_topic>\n@@ -32,6 +32,9 @@\n python3 \'$__tool_directory__/validate_fasta.py\' input.fasta\n --min_length \\${ALPHAFOLD_AA_LENGTH_MIN:-0}\n --max_length \\${ALPHAFOLD_AA_LENGTH_MAX:-0}\n+#if $multimer:\n+--multimer\n+#end if\n > alphafold.fasta &&\n \n ## env vars -------------------------------\n@@ -46,18 +49,32 @@\n --data_dir \\${ALPHAFOLD_DB:-/data}\n --uniref90_database_path \\${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta\n --mgnify_database_path \\${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa\n---pdb70_database_path \\${ALPHAFOLD_DB:-/data}/pdb70/pdb70\n---template_mmcif_dir \\${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files\n+--template_mmcif_dir \\${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files\n --obsolete_pdbs_path \\${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat\n --max_template_date=\\$DATE\n --bfd_database_path \\${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt\n --uniclust30_database_path \\${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08\n+\n ## Param introduced in AlphaFold v2.1.2:\n --use_gpu_relax=\\${ALPHAFOLD_USE_GPU:-True}\n+\n+#if $multimer:\n+--model_preset=multimer\n+--pdb_seqres_database_path=\\${ALPHAFOLD_DB:-/data}/pdb_seqres/pdb_seqres.txt\n+--uniprot_database_path=\\${ALPHAFOLD_DB:-/data}/uniprot/uniprot.fasta\n+##--num_multimer_predictions_per_model=1 ## introduced alphafold>=2.2.0\n+\n+#else\n+--pdb70_database_path \\${ALPHAFOLD_DB:-/data}/pdb70/pdb70\n+#end if\n &&\n \n ## Generate additional outputs ------------\n-python3 \'$__tool_directory__/gen_extra_outputs.py\' output/alphafold $output_plddts &&\n+python3 \'$__tool_directory__/gen_extra_outputs.py\' output/alphafold $output_plddts\n+#if $multimer:\n+--multimer\n+#end if\n+&&\n \n ## HTML output\n mkdir -p \'${ html.files_path }\' &&\n@@ -67,24 +84,34 @@\n ## This is a (hacky) fix for a bug that has appeared in multiple Pulsar servers.\n ## The working directory ends up two levels deep and the visualization html page\n ## fails to load the PDB files as static assets.\n-[ -d working ] && cp -r working/* .\n+(([ -d working ] && cp -r working/* .) || true)\n \n ]]></command>\n <inputs>\n <conditional name="fasta_or_text">\n- <param name="input_mode" type="select" label="Fasta Input" help="Single protein sequence to fold. Input can be fasta file from history, or text. Sequence must be valid IUPAC amino acid characters. Provide only 1 sequence per job.">\n+ <param name="input_mode" type="select" label="Fasta Input" help="Protein sequence(s) to fold. Input can be fasta file from history, or text. Sequence must be valid IUPAC amino acid characters. If multiple sequences FASTA file provided, multimer mode must be selected.">\n <option value="history">Use fasta from history</option>\n <option value="textbox">Paste sequence into textbox</option>\n </param>\n <when value="history">\n- <param name="fasta_file" type="data" format="fasta" label="Fasta file from history" help="Select single fasta protein sequence from your history. If you wish to fold multiple proteins, submit an individual job for each protein." />\n+ <param name="fasta_file" type="data" multiple="false" format="fasta" label="Fasta file from history" help="Select single FASTA protein file from your history. If you wish to fold multiple proteins, submit an individual job for each protein. If you wish to run AlphaFold multimer, please supply multiple sequences in this file." />\n </when>\n <when value="textbox">\n- <param name="fasta_text" type="text" area="true" value="" label="Paste sequence" help="Paste single protein sequence into t'..b'source options <https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software>`_ are available such as `AutoDock <https://autodock.scripps.edu/>`_ and `SwissDock <http://www.swissdock.ch/>`_.\n \n+ | Protein complex interactions are also commonly observed with AlphaFold\'s multimer prediction mode.\n+ |\n+ |\n+\n **Input**\n \n *Amino acid sequence*\n \n- | AlphaFold accepts a **single amino acid sequence** in FASTA format.\n+ | AlphaFold monomer (default) accepts a **single amino acid sequence** in FASTA format.\n | You can choose to input either a file from your Galaxy history or paste a sequence into a text box.\n- | Please paste only a single sequence - we can only process a single sequence per job.\n- | Multiple sequences will return an error.\n+ | If you choose the ``multimer`` option, you can supply a FASTA file containing **multiple sequences** to be folded concurrently into a multimer.\n+ |\n |\n \n **Outputs**\n \n *Visualization*\n \n- | An interactive 3D graphic of the best predicted molecular structures.\n- | This output can be opened in Galaxy to give a visual impression of the results, with different structural representations to choose from.\n- | Open the "Visualization" history output by clicking on the "view data" icon:\n- |\n+ An interactive 3D graphic of the best predicted molecular structures.\n+ This output can be opened in Galaxy to give a visual impression of the results, with different structural representations to choose from.\n+ Open the "Visualization" history output by clicking on the "view data" icon:\n \n .. image:: https://github.com/usegalaxy-au/galaxy-local-tools/blob/1a8d3e8daa7ccc5a345ca377697735ab95ed0666/tools/alphafold/static/img/alphafold-visualization.png?raw=true\n :height: 520\n@@ -225,15 +256,24 @@\n \n *Model confidence scores (optional)*\n \n- | This optional output produces a file which describes the confidence scores for each model (based on `pLDDTs <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799472/>`_) which may be useful for downstream analysis.\n- | Model confidence scores are also included as a column in the default PDB output.\n+ | This optional output produces a file which describes the confidence scores for each model (based on `pLDDTs <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799472/>`_, or the ``iptm+ptm`` score if run in multimer mode) which may be useful for downstream analysis.\n+ | Model confidence scores are also included as a column (replacing ``bFactor``) in the default PDB output.\n+ |\n+ |\n+\n+ **AlphaFold configuration**\n+\n+ | We have configured AlphaFold to run with the parameters suggested by default on `AlphaFold\'s GitHub <https://github.com/deepmind/alphafold>`_.\n+ | This means that it runs against the full database with Amber relaxation, with ``max_template_date`` set to today\'s date. If there are additonal parameters that you would like to interact with, please `send a support request to Galaxy AU <https://site.usegalaxy.org.au/request/support>`_, or open an issue on `our GitHub <https://github.com/usegalaxy-au/tools-au>`_.\n+ |\n |\n \n **External Resources**\n \n- We recommend checking out the\n+ We HIGHLY recommend checking out the\n `Alphafold Protein Structure Database <https://alphafold.ebi.ac.uk/>`_,\n- which contains predicted sequences for thousands of Human proteins. See also:\n+ which contains pre-computed structures for over 200 million known proteins.\n+ See also:\n \n - `Google Deepmind\'s article on AlphaFold <https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology>`_\n - `AlphaFold source code on GitHub <https://github.com/deepmind/alphafold>`_\n@@ -241,5 +281,6 @@\n ]]></help>\n <citations>\n <citation type="doi">https://doi.org/10.1038/s41586-021-03819-2</citation>\n+ <citation type="doi">https://doi.org/10.1101/2021.10.04.463034</citation>\n </citations>\n </tool>\n' |
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| diff -r ca90d17ff51b -r 3bd420ec162d gen_extra_outputs.py --- a/gen_extra_outputs.py Fri Aug 19 00:29:16 2022 +0000 +++ b/gen_extra_outputs.py Tue Sep 13 22:04:12 2022 +0000 |
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| @@ -1,10 +1,17 @@ - +"""Generate additional output files not produced by AlphaFold.""" import json import pickle import argparse from typing import Any, Dict, List +# Keys for accessing confidence data from JSON/pkl files +# They change depending on whether the run was monomer or multimer +CONTEXT_KEY = { + 'monomer': 'plddts', + 'multimer': 'iptm+ptm', +} + class Settings: """parses then keeps track of program settings""" @@ -12,23 +19,31 @@ self.workdir = None self.output_confidence_scores = True self.output_residue_scores = False + self.is_multimer = False def parse_settings(self) -> None: parser = argparse.ArgumentParser() parser.add_argument( - "workdir", - help="alphafold output directory", + "workdir", + help="alphafold output directory", type=str - ) + ) parser.add_argument( "-p", "--plddts", - help="output per-residue confidence scores (pLDDTs)", + help="output per-residue confidence scores (pLDDTs)", + action="store_true" + ) + parser.add_argument( + "--multimer", + help="parse output from AlphaFold multimer", action="store_true" ) args = parser.parse_args() self.workdir = args.workdir.rstrip('/') self.output_residue_scores = args.plddts + self.is_multimer = False + self.is_multimer = args.multimer class ExecutionContext: @@ -42,8 +57,13 @@ @property def model_pkls(self) -> List[str]: - return [f'{self.settings.workdir}/result_model_{i}.pkl' - for i in range(1, 6)] + ext = '.pkl' + if self.settings.is_multimer: + ext = '_multimer.pkl' + return [ + f'{self.settings.workdir}/result_model_{i}{ext}' + for i in range(1, 6) + ] @property def model_conf_score_output(self) -> str: @@ -56,18 +76,28 @@ class FileLoader: """loads file data for use by other classes""" + def __init__(self, context: ExecutionContext): self.context = context + @property + def confidence_key(self) -> str: + """Return the correct key for confidence data.""" + if self.context.settings.is_multimer: + return CONTEXT_KEY['multimer'] + return CONTEXT_KEY['monomer'] + def get_model_mapping(self) -> Dict[str, int]: data = self.load_ranking_debug() - return {name: int(rank) + 1 + return {name: int(rank) + 1 for (rank, name) in enumerate(data['order'])} def get_conf_scores(self) -> Dict[str, float]: data = self.load_ranking_debug() - return {name: float(f'{score:.2f}') - for name, score in data['plddts'].items()} + return { + name: float(f'{score:.2f}') + for name, score in data[self.confidence_key].items() + } def load_ranking_debug(self) -> Dict[str, Any]: with open(self.context.ranking_debug, 'r') as fp: @@ -76,11 +106,14 @@ def get_model_plddts(self) -> Dict[str, List[float]]: plddts: Dict[str, List[float]] = {} model_pkls = self.context.model_pkls - for i in range(5): + for i in range(len(model_pkls)): pklfile = model_pkls[i] with open(pklfile, 'rb') as fp: data = pickle.load(fp) - plddts[f'model_{i+1}'] = [float(f'{x:.2f}') for x in data['plddt']] + plddts[f'model_{i+1}'] = [ + float(f'{x:.2f}') + for x in data['plddt'] + ] return plddts @@ -94,13 +127,13 @@ scores = self.loader.get_conf_scores() ranked = list(scores.items()) ranked.sort(key=lambda x: x[1], reverse=True) - return {f'model_{mapping[name]}': score + return {f'model_{mapping[name]}': score for name, score in ranked} def gen_residue_scores(self) -> Dict[str, List[float]]: mapping = self.loader.get_model_mapping() model_plddts = self.loader.get_model_plddts() - return {f'model_{mapping[name]}': plddts + return {f'model_{mapping[name]}': plddts for name, plddts in model_plddts.items()} @@ -114,7 +147,7 @@ with open(outfile, 'w') as fp: for model, score in data.items(): fp.write(f'{model}\t{score}\n') - + def write_residue_scores(self, data: Dict[str, List[float]]) -> None: outfile = self.context.plddt_output model_plddts = list(data.items()) @@ -133,23 +166,20 @@ settings.parse_settings() context = ExecutionContext(settings) loader = FileLoader(context) - + # generate & write outputs generator = OutputGenerator(loader) writer = OutputWriter(context) - + # confidence scores conf_scores = generator.gen_conf_scores() writer.write_conf_scores(conf_scores) - + # per-residue plddts if settings.output_residue_scores: residue_scores = generator.gen_residue_scores() writer.write_residue_scores(residue_scores) - + if __name__ == '__main__': main() - - - |
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| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer.fasta Tue Sep 13 22:04:12 2022 +0000 |
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| @@ -0,0 +1,8 @@ +>NP_000549.1 hemoglobin subunit alpha [Homo sapiens] +MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA +VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK +YR +>NP_000509.1 hemoglobin subunit beta [Homo sapiens] +MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG +AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN +ALAHKYH |
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| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_exceeds_count.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_exceeds_count.fasta Tue Sep 13 22:04:12 2022 +0000 |
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| @@ -0,0 +1,44 @@ +>NP_000549.1 hemoglobin subunit alpha [Homo sapiens] +MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA +VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK +YR +>NP_000509.1 hemoglobin subunit beta [Homo sapiens] +MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG +AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN +ALAHKYH +>NP_000549.1 hemoglobin subunit alpha [Homo sapiens] +MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA +VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK +YR +>NP_000509.1 hemoglobin subunit beta [Homo sapiens] +MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG +AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN +ALAHKYH +>NP_000549.1 hemoglobin subunit alpha [Homo sapiens] +MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA +VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK +YR +>NP_000509.1 hemoglobin subunit beta [Homo sapiens] +MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG +AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN +ALAHKYH +>NP_000549.1 hemoglobin subunit alpha [Homo sapiens] +MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA +VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK +YR +>NP_000509.1 hemoglobin subunit beta [Homo sapiens] +MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG +AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN +ALAHKYH +>NP_000549.1 hemoglobin subunit alpha [Homo sapiens] +MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA +VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK +YR +>NP_000509.1 hemoglobin subunit beta [Homo sapiens] +MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG +AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN +ALAHKYH +>NP_000549.1 hemoglobin subunit alpha [Homo sapiens] +MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA +VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK +YR |
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| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/model_confidence_scores.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/model_confidence_scores.tsv Tue Sep 13 22:04:12 2022 +0000 |
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| @@ -0,0 +1,5 @@ +model_1 0.95 +model_2 0.94 +model_4 0.94 +model_3 0.94 +model_5 0.93 |
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| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/A/bfd_uniclust_hits.a3m --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/A/bfd_uniclust_hits.a3m Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,2272 @@\n+>chain_A\n+MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR\n+>tr|A0A1K0GGD5|A0A1K0GGD5_RAT Globin d1 OS=Rattus norvegicus GN=Glnd1 PE=3 SV=1\n+-----------------------MYGLEKEp-R------------ETEGClsrKLPSNLQRSSAPWRLHGFQNLLERSQGA--------QRAKPG------------HGAHSHSSVKMAL--SQTDH------------------rlvL\n+>tr|F6QUQ8|F6QUQ8_XENTR Uncharacterized protein OS=Xenopus tropicalis OX=8364 PE=3 SV=1\n+-HWTAEEKAAITSVWQKV--NLEQDGHEALTSISLTFISPLdvvwAYFKG----------AAHNK---------IKFCFNIELKQISLSFHARWKNQNPEQKLERLGEVLVIVLASKLGTAFTPQIQGAWEKFVAVLVDALSQGYN\n+>ERR1712144_198951\n+HESLWKRQVRG---evfLGESRPE-VrRDRRRSSG-qDAGGLPPDQTYFSHWaDLSPDSSQVKKHGGVIMGAVGEAVGKIDDIVGAVSNLSSCMPSSSEWTLPTS-------------------------------------------\n+>tr|A0A096M318|A0A096M318_POEFO Uncharacterized protein OS=Poecilia formosa PE=3 SV=1\n+VNH-KHDELII---tgvFFTS-------VSECVP-pVRNIYRQTTNSIENIgNFKngetfLTNPPVALYVVNMVEFTSKPLMSL-PLNGFYGILDFLKA--KRKNPNGGKLLADCLTIVIASKMGS-gFTPEIQATFQKFLAVVVSALGKQYH\n+>ERR1719244_1811598\n+--WSDDETKAIQMIWNSVD--VNELGPAALRRCLLVYPWTQRYFGKFgDIATPTAimqnpGVAQHGITVMNGLKLAGGPGGGPGNQPGGQQELWQRGKQQGQQQLWQQGQHGGKQRGqqQRQGQq-PSPRQSX------------------\n+>ERR1719167_1707907\n+VEWTDFERATIQDIFAKMP--YEEVGPAALARGLIVYPWTQRYFGNFgnLYSAStilvNPLIAKHGTTILHGLDRAMKNMDNIKETYAELSVLHSEKLHVDPDNFRLVSDCLTIVVAGKMGKDFTGEVQAAFQKFLAVVVSALGRHHH\n+>tr|A0A146QLZ2|A0A146QLZ2_FUNHE Hemoglobin subunit alpha-2 (Fragment) OS=Fundulus heteroclitus OX=8078 PE=4 SV=1\n+IILTSNYNYTFNTFFSKFSSNSYSIFSYSLSIILFFYPHTNTYFSHFnYLIPFSSPFNNHLstfiflfsxxxXXVMGGVEDDVEKIENMKEGIIRISEMNELNMRVEKEKLKIMEKKIIVV---------------------------------\n+>tr|A0A147ASE9|A0A147ASE9_FUNHE Cytoglobin (Fragment) OS=Fundulus heteroclitus PE=3 SV=1\n+EPLSDSEREIIQDTWGHVYKNCEDVGVSVLIRFFVNFPSAKQYFSQFQdMedpeeMEQSSQLRQHACRVMNAINTVVENLNDPEKVSSvlaLVGKAHAMKHKVEPIYFKILSGVILEVLSEDFPDFFTADVQLVWTKLMGALYWHVTGAY-\n+>tr|L8HUF7|L8HUF7_9CETA Hemoglobin subunit beta (Fragment) OS=Bos mutus OX=72004 GN=M91_21159 PE=3 SV=1\n+-YLTLEKKATVIDLWSKM--RVAEVGPDTVgrqvFKLLVVYPSTQRFFDYFgDCPLLIygqCFTffvsrhrfllfilvflCFKEDKMMYCFLKQFKKIKK------MIAKRNISK---------YKLRLIWVASHQYFGKEFTPEFQAACQKVVAGVVNALTYKYH\n+>tr|A0A2Y9DG99|A0A2Y9DG99_TRIMA myoglobin OS=Trichechus manatus latirostris OX=127582 GN=LOC101351845 PE=4 SV=1\n+MALSDGEWQLVLNVWGKVEADIAGHGLEVLISLFKGHPETLEKFDKFkHLKseeemKACEDLKKHGVTVLTALGGILKKKGHHQAEIQPLAQSHATKHKIPVKYLEFISEAIIHVLQSKHPGDFGADAQGAMSKALELFRNAMAANYK\n+>tr|M3YM80|M3YM80_MUSPF Myoglobin OS=Mustela putorius furo OX=9669 GN=MB PE=3 SV=1\n+MGLSDGEWQLVLNVWGKVEADLAGHGQAVLISLCQGLESRKEEKKRDpAHAcvssrrslFVSQDLLFHSDAFLVSLGHRSFLapvSGENGQSQKTQPAHHAQHHRQPWNTEKFISDAIIQVLQSKHAGDFGAEAQAAMKKALELFRNDIAAKYK\n+>tr|A0A1C4HDU6|A0A1C4HDU6_PROAN Myoglobin (Fragment) OS=Protopterus annectens OX=7888 GN=Mb6b PE=2 SV=1\n+-------MACPAKFWEEnVVPDAAEHGKNILIRLYKEDPAAQGFFSKYkDTPvselGNNADVKEQGAVVVKALGELLKLKGQHESQLHAMAESHKNTYKIPVEYFPKIFKITDAYLHEKVGAVYA-AIQAAMNVAFDQIADGLKTQYQ\n+>tr|Q9Y0D5|Q9Y0D5_MYXGL Hemoglobin OS=Myxine glutinosa GN=Hb PE=2 SV=1\n+-RTTEGERAAVRASWAVLMKDYEHAGVQILDKFFKANPAAKPFFTKMkDLHtledlASSADARWHVERIIQAVNFAVINIEDREklsNKFVKLSQDHIEEFHVtDPQYFMILSQTILDEVEKR-NGGLSGEGKSGWHKVMTIICKMLKSKY-\n+>ERR1711977_634702\n+--WTDAERAAISSVWGKID--VGEIGPQALGRLLIVYPWTQRHFSSFgNLSTpaailGNPKVAAHGKTVMAGLERAVKNMDDIKSAYSDLSRCTPRSCMWIPTTSGSWLNAspcvwlpsldvrPSTLMSRRpGRSSWLwssppwadsTTEGLKTHHNQIICSSFL-----\n+>tr|Q9U6L6|Q9U6L6_MYXGL Hemoglobin OS=Myxine glutinosa OX=7769 GN=Hb PE=2 SV=1\n+-TLSEGDKKAIRESWPQIYKNFEQNSLAVLLEFLKKFPKAQDSFPKFsakkSHLEQDPAVKLQAEVIINAVNHTIGLMDKEaamKKYLKDLSTKHSTEFQVNPDMFKELSAVFVSTMGGK----------AAYEKLFSIIATLLRSTYD\n+>ERR1719474_978995\n+---------------------------------LLQSSWKQ--FRT----------------------------------FASLSGIRQEELGAGCQHQDLP----------QIQHHLWISEPSTFQQL-------------\n+>ERR1719336_830457\n+-----------------------------------------------------------------------------SINPQSTVDLGAQYISATPLNYKNHQDIYNSLLSNG------VLVPANVSLI-------------\n+>tr|B7QI99|B7QI99_IXOSC Globin, putative OS=Ixodes scapularis OX=6945 GN=80416'..b'gdekeeaiqgFEVLLEEIGGLHRAiVPNFVPEHFIKFLAVLPTAIVTTICdkreeimpESDREMLLELWKKISAFMGFHLDAG--\n+>KNS7NT10metaT_FD_contig_41_844412_length_214_multi_3_in_0_out_0_1 # 3 # 212 # -1 # ID=205324_1;partial=11;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.619\n+--IPPKLAVLIREKWQAFLEKfptREQAGEAIYDSFMEEAPSLRPLFKTP--------RSVFGLRFIASLTNLMAVRPAGVTEEagGNHGF-----------------------PAPRLGG--------------------------\n+>tr|E5SHC1|E5SHC1_TRISP Uncharacterized protein OS=Trichinella spiralis GN=Tsp_03845 PE=3 SV=1\n+-SLSAGELKLLRWLWKQMKQVHQgLASAKLFQIIFATCPEIKRFFGLAKVS----------------DEKALIDerMRKhmlilqASKLIILFQIISSa-----------------------------------------------------\n+>SRR5690606_9602430 \n+-------------------------YRAFYPILYSSVSGAQELFEATVG-TDNRKMLQILAKLFG----FISNVNhSSEFMKsdAFIerGKYYA-DHGISETMMRGFSSALVLTLRRTLGELFTISHVRAWGIFLDTISHAL-----\n+>SRR5581483_1589235 \n+---------DIKESFHRILEQKQAVTHLFFTVALGSGHEARLLIWETEG-----------------AGCSVESTDPPQWLC------------PPFTIYAQFTNDLLQALREFHGADWNQELMEQWRMTIERVGQIIFSACR\n+>SRR5262249_34977875 \n+------------------LEQKQAVTHLFFTVALSGCHEARLIFWGTEG-----------------AGHSGEFFSSPQMLC------------APLAMYAQFTNDLLRALREFHGADWNPELTEQWRMAIERVGQAIFATYR\n+>SRR3954454_18132641 \n+----------------------WRDADRPAWAALNADPEVREFFDR--------PLTrpeADASldrfrsdLAARGWGWWAIELTATGE---------------------LIGMAGLDPTE--DDIP-VAGVEMGWRlarAHWGHGYATEA----\n+>SRR3954470_12875293 \n+----------------------WRADDLDAWAAINADPQVRAFLGG--------VLDrgqAAESirrfrtaLAARGWGWWAVELTATGE---------------------LIGIAGLDPVD--EGLP-FDGVEIGWRlarWAWGRGYATEA----\n+>tr|A0A1Q9EV88|A0A1Q9EV88_SYMMI Uncharacterized protein OS=Symbiodinium microadriaticum GN=AK812_SmicGene4882 PE=4 SV=1\n+----------------------SAFKMEVFETFFATCEQSQEYLKASNA-----KLQFIAGRILDI---MTDMFRTPQSAVkdiSALGLLHA-GYGVREELIQPFVTAFMTAVKNAC----------------------------\n+>tr|S9TGR2|S9TGR2_9TRYP Uncharacterized protein OS=Strigomonas culicis OX=28005 GN=STCU_11951 PE=4 SV=1 \n+---------TLEGCWQLLELrpqGLEEIAQAMYFYLLSHNRQLQSYFYGI-------DMEEQGRALVRMLCSTVHTYGRTqtecdpvawsnfEGYLVEMGARHR-SYGVGDNVFHEMRDAFFQQFPHFVDAnSWRI-TCREWHTLWDTIIRLLQQG--\n+>tr|A0A0A2NAV4|A0A0A2NAV4_ALCFA Uncharacterized protein OS=Alcaligenes faecalis OX=511 GN=JT27_01100 PE=4 SV=1\n+--VTDAQRDIIKTAAPLLASGDKALTTYFYELILRDSPPMSPLASQ-------------------------------------IANNHL-ALQIQPEHDPMMGTCQLQAVREELIVRMTgNKLIDGWVAAYQQLSNLLIEA--\n+>SRR3954463_13473713 \n+-RVTPDDLKHVQRSWAKLCDRRESLLAELT-VTFQSNPALQ--C----------DACCRAEWLLCAGEELVELLPAPSTLASRARVLgDRWPDPLTAPSFEIDGRAWMAAATRCSS-MWSDTIEMAWRQAWLLLSDVLA----\n+>ERR1711890_22380\n+MHLSDTEKSAVVSSWSNVNS---SLLDSVLLQLVQENADMRAAMSRGDLAedsiREQETFKADVTKLTCCITKLVTRLGNTGEVSScpATCLKNC-P-YLQPKHVPLFISSFCD------KLELTEDAKKGWKFIMEKTAERI-----\n+>tr|A0A0B2VKC9|A0A0B2VKC9_TOXCA Uncharacterized protein OS=Toxocara canis GN=Tcan_09473 PE=4 SV=1\n+--ISPQGRDIIVNCFENS---HADIGNRICMRVFERRSDYQRFILALGKE----KWSWVTNTLRDFIEEVVLRIDDLAKideLSRKYGEDHVelKPFGFKPDFWVSLADAMIVeCVVLDMASHQPTDTVAAWSQLVSLMFSSIRDGY-\n+>ERR1700761_7028990 \n+-PLDEEALRIVRHSAGRLTYVTDDFIDWLHREGVALSPEVGHSVAG--------EGWPFCERMAQALLWV-ALTDQPAGvaagVLRRVGADNW-RDGFPDAEYVSVVQALVRVLRGLSGAAQIPAMASAWISCFQWMQPYLLIG--\n+>tr|A0A2A6D1B3|A0A2A6D1B3_PRIPA Uncharacterized protein OS=Pristionchus pacificus GN=PRIPAC_35146 PE=4 SV=1\n+-TLNHQQRKLIKNGYDSWRKKsCISSGRWVHSFVSSKDDRLKEIMEGNEE-----TTRIHEETITHLLDMAVESLESLDDsLGPLLISytgpqgvFEE-KDGFDRLYWSRVSEGMCQLARNFPSKANKYETVCAWRIVVLFICNKIELGF-\n+>tr|A0A0N5AH18|A0A0N5AH18_9BILA Uncharacterized protein OS=Syphacia muris PE=4 SV=1\n+-SLTEKQKQLIKIGYKKWSEStTVTVGEWVYQYIFHKFPSVKGKFAKDEK-----SLAENQRRITDIIEMAVESVDSLDDsLGSFLVSyssengfLGE-SEGFDRGYWEIVSEALCQLSRHFPVKSHKSDTVLAWRIVILFVINKIEYGF-\n+>tr|A0A0G4IA00|A0A0G4IA00_9ALVE Uncharacterized protein OS=Chromera velia CCMP2878 OX=1169474 GN=Cvel_12404 PE=4 SV=1 \n+------------------------LAGKVFQKIITKAPSFRKLFVRPDE--------AYTKHFSVFLEQCLDYAQRPRCFWQehnDLAVKHI-IFGVGHNDITMMGRMIVEALQDIGGEGWAEDYAETWQKFWTEISRSL-----\n+>ERR1719384_273858\n+-----------LLGTTLTT-KLLSEKLSSRAGWA--QTQTSKMFSLLSFK------QGPAQFLVERFDILLNVIDDEDQLAEQLYqvaKTHK-KVGVDQSDLYSFQASFMKTLPSF-DSDFTAEVGNAWAYTLSH----------\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/A/mgnify_hits.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/A/mgnify_hits.sto Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| b'@@ -0,0 +1,94 @@\n+# STOCKHOLM 1.0\n+\n+#=GS MGYP000836687451/13-154 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000\n+#=GS MGYP000585341746/6-147 DE [subseq from] PL=10 UP=0 BIOMES=0000000000001\n+#=GS MGYP001069732337/11-152 DE [subseq from] PL=01 UP=0 BIOMES=1000000000000\n+#=GS MGYP000701481948/1-69 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP001122892151/78-175 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000539442244/1-72 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000498009340/6-38 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP000498009340/63-137 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP000607955645/4-146 DE [subseq from] PL=00 UP=1 BIOMES=0000000011000\n+#=GS MGYP000809681506/4-146 DE [subseq from] PL=00 UP=1 BIOMES=0000000011000\n+#=GS MGYP001138391873/7-146 DE [subseq from] PL=00 UP=1 BIOMES=1000000000000\n+#=GS MGYP000131797357/13-155 DE [subseq from] PL=10 UP=0 BIOMES=0000000000001\n+#=GS MGYP000536366561/97-193 DE [subseq from] PL=11 UP=0 BIOMES=0000000011000\n+#=GS MGYP000318290004/2-70 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP001111532658/13-154 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP000722267483/2-47 DE [subseq from] PL=01 UP=0 BIOMES=0101000000000\n+#=GS MGYP000079462051/73-112 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000413961247/1-72 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000729474694/1-75 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP000459697661/48-117 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP001121356039/36-177 DE [subseq from] PL=01 UP=0 BIOMES=1000000000000\n+#=GS MGYP000132531679/62-95 DE [subseq from] PL=01 UP=0 BIOMES=0101000000000\n+#=GS MGYP000427472264/214-245 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000620445737/4-47 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000\n+#=GS MGYP000639461158/65-143 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP000507092441/12-54 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP000607025940/8-103 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP000362522003/1-32 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000322610494/7-50 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000442294717/26-101 DE [subseq from] PL=10 UP=0 BIOMES=1000000000000\n+#=GS MGYP000214952500/50-125 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000321112601/3-73 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000386264740/2-52 DE [subseq from] PL=01 UP=0 BIOMES=1000000000000\n+#=GS MGYP000172242919/33-125 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP000669192840/12-82 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000212149699/2-51 DE [subseq from] PL=00 UP=0 BIOMES=0000000010100\n+#=GS MGYP000559925714/32-112 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000335830788/32-110 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000306499386/2-53 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000450732916/70-150 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP000694104832/9-83 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000114577797/2-45 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP001143026688/10-61 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000\n+#=GS MGYP000969813914/167-286 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000\n+\n+chain_A MVLSPADKTNVKAAWGKVG-A-HAGEYGAEA-LERMFLSFPTTKTYFPHF-DLS-----H-----G-----SA-----QVKGHGKKVADALTNAVAHVDDMPNALSALSDL---HAHKLRVDPVNFKLLSHCLLVTLAAH-LPAEFTPAVHASLDKFLASVSTVLTSKYR\n+MGYP000836687451/13-154 MVLSPADKTNVKAAWGKVG-A-HAGEYGAEA-LERMFLSFPTTKTYFPHF-DLS-----H-----G-----SA-----QVKGHGKKVADALTNAVAHVDDMPNALSALSDL---HAHKLRVDPVNFKLLSHCLLVTLAAH-LPAEFTPAVHASLDKFLASVSTVLTSKYR\n+MGYP000585341746/6-147 '..b'-------------------------------------------------------QLLSHCLLVTLAAR-FPADFTAEAHAAWAKFLSVVSSVLTEKYR\n+MGYP000607025940/8-103 --------------------------------LCRLLIVYPWTQRFFASFGNLS-----SATAIIG-----NP-----MVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSEL---HCDKLHVDPENFRVRCS-WLGPIPMH-LQEEILP----------------------\n+MGYP000362522003/1-32 MVLSAADKGNVKAAWGKVG-G-HAAEYGAEA-LER---------------------------------------------------------------------------------------------------------------------------------------\n+MGYP000322610494/7-50 -----------------------------------------------------------------------------------------------------------------------------SQLLAHCLLVELAIM-FPAEFTPVVHVSMDKFFAALGLALAEKYR\n+MGYP000442294717/26-101 ----------------------------------RLLVVYPWTQRFFESFGDLSTPDAVM-----G-----NP-----KVKAHGKKVLGAFSDGLAHLDNLKGTFATLSEL---HCDKLHVDPENFRV------------------------------------------\n+MGYP000214952500/50-125 ----------------------------------RLLVVYPWTQRFFESFGDLSTPDAVM-----G-----NP-----KVKAHGKKVLGAFSDGLAHLDNLKGTFATLSEL---HCDKLHVDPENFRV------------------------------------------\n+MGYP000321112601/3-73 ---------------------------------------YPWTQRFFESFGDLS-----SPDAVMG-----NP-----KVKAHGKKVLGAFSDGLAHLDNLKGTFSQLSEL---HCDKLHVDPENFRV------------------------------------------\n+MGYP000386264740/2-52 -----------------------------------------------------------------G-----NP-----KVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSEL---HCDKLHVDPENFKVS-----------------------------------------\n+MGYP000172242919/33-125 --------------------------------IDRVLIVYPWTQRYFGTFGDLS-----NAAAILG-----NA-----KVAAHGKVVLGALDKGVKNVDNVKATYTALSQL---HCLKLNVDPDNFKVNVQALC-LLGYR-TPSQ-------------------------\n+MGYP000669192840/12-82 ---------------------------------------YSWTQRFFESFGDLS-----SADAILG-----NP-----KVKAHGKKVLDSFCEGLKQLDDLKGAFASLSEL---HCDKLHVDPENFRV------------------------------------------\n+MGYP000212149699/2-51 -----------------------------------------------------------------G-----NP-----KVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSEL---HCDKLHVDPENFRV------------------------------------------\n+MGYP000559925714/32-112 --------------------------------FHRLLVVYPWTQRFFDSFGNLS-----SPSAILG-----NP-----KVKAHGKKVLTSFGDAIKNMDNLKPAFAKLSEL---HCDKLHVDPENFKVSSG---------------------------------------\n+MGYP000335830788/32-110 --------------------------------FHRLLVVYPWTQRFFDSFGNLS-----SPSAILG-----NP-----KVKAHGKKVLTSFGDAIKNMDNLKPAFAKLSEL---HCDKLHVDPENFKVS-----------------------------------------\n+MGYP000306499386/2-53 -----------------------------------------------------------------G-----NP-----KVKAHGKKVLDSFCEGLKQLDDLKGAFASLSEL---HCDKLHVDPENFRVSL----------------------------------------\n+MGYP000450732916/70-150 ----------------------------SPS-LYRLLIVYPWTQRFFASFGNLS-----SPTAILG-----NP-----MVRAHGKKVLSSFGEAVKNLDNIKNTYAKLSEL---HCDKLHVDPENFRV------------------------------------------\n+MGYP000694104832/9-83 -----------------------------------LLIVSPWTQRHFSTFGNLS-----NAAAIMG-----NA-----KVAQHGKTVMGGLDRAVKNLDDIKNTYSALSVM---HSEKLHVDPDNFRV------------------------------------------\n+MGYP000114577797/2-45 -------------------------------------------------------------------------------------KVLNAIGEAVKNIDDIRGALAKLSEL---HAYILRVDPVNFKVSGHA--------------------------------------\n+MGYP001143026688/10-61 -----------------------------------------------------------------G-----NP-----KVKAHGKKVLISFGKAVMLTDDLKGTFATLSDL---HCNKLHVDPENFLVSS----------------------------------------\n+MGYP000969813914/167-286 ----------VEETWRIVE-P-RADQLGTDF-FLRLFQRSPSLLELFSFK-DDKP---LS-----S-----SP-----RLRAHGSKVMATIANAVSGLRDLEALIPILANLAKKHA-EYGVQEEHFPYVGEALLGTLADA-LGTDWTPDVQTAW----------------\n+#=GC RF xxxxxxxxxxxxxxxxxxx.x.xxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxx.....x.....x.....xx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx\n+//\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/A/pdb_hits.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/A/pdb_hits.sto Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| b'@@ -0,0 +1,17384 @@\n+# STOCKHOLM 1.0\n+\n+#=GS 1abw_A/2-141 DE [subseq from] mol:protein length:283 HEMOGLOBIN-BASED BLOOD SUBSTITUTE\n+#=GS 1abw_A/144-283 DE [subseq from] mol:protein length:283 HEMOGLOBIN-BASED BLOOD SUBSTITUTE\n+#=GS 1aby_A/2-141 DE [subseq from] mol:protein length:283 HEMOGLOBIN\n+#=GS 1aby_A/144-283 DE [subseq from] mol:protein length:283 HEMOGLOBIN\n+#=GS 1c7c_A/2-141 DE [subseq from] mol:protein length:283 PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))\n+#=GS 1c7c_A/144-283 DE [subseq from] mol:protein length:283 PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))\n+#=GS 1o1p_A/2-141 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1o1p_A/144-283 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1c7d_A/2-141 DE [subseq from] mol:protein length:284 PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))\n+#=GS 1c7d_A/145-284 DE [subseq from] mol:protein length:284 PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))\n+#=GS 1o1n_A/2-141 DE [subseq from] mol:protein length:285 Hemoglobin Alpha chain\n+#=GS 1o1n_A/146-285 DE [subseq from] mol:protein length:285 Hemoglobin Alpha chain\n+#=GS 1o1j_A/2-141 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1o1j_A/144-283 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1o1m_A/2-141 DE [subseq from] mol:protein length:285 Hemoglobin Alpha chain\n+#=GS 1o1m_A/146-285 DE [subseq from] mol:protein length:285 Hemoglobin Alpha chain\n+#=GS 1o1l_A/2-141 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1o1l_A/144-283 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1hbr_A/2-141 DE [subseq from] mol:protein length:141 PROTEIN (HEMOGLOBIN D)\n+#=GS 1hbr_C/2-141 DE [subseq from] mol:protein length:141 PROTEIN (HEMOGLOBIN D)\n+#=GS 1gli_A/2-141 DE [subseq from] mol:protein length:141 DEOXYHEMOGLOBIN\n+#=GS 1gli_C/2-141 DE [subseq from] mol:protein length:141 DEOXYHEMOGLOBIN\n+#=GS 1bz1_A/1-142 DE [subseq from] mol:protein length:142 PROTEIN (HEMOGLOBIN ALPHA CHAIN)\n+#=GS 1bz1_C/1-142 DE [subseq from] mol:protein length:142 PROTEIN (HEMOGLOBIN ALPHA CHAIN)\n+#=GS 1y01_B/1-142 DE [subseq from] mol:protein length:142 Hemoglobin alpha chain\n+#=GS 1z8u_B/1-142 DE [subseq from] mol:protein length:142 Hemoglobin alpha chain\n+#=GS 1z8u_D/1-142 DE [subseq from] mol:protein length:142 Hemoglobin alpha chain\n+#=GS 6kye_A/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 6kye_C/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 6kye_E/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 6kye_G/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 6kye_I/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 6kye_K/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7cue_A/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7cue_C/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7k4m_A/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7k4m_C/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7k4m_E/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7k4m_G/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7k4m_I/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7vde_A/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 7vde_C/1-142 DE [subseq from] mol:protein length:142 Hemoglobin subunit alpha\n+#=GS 3ia3_B/4-145 DE [subseq from] mol:protein length:145 Hemoglobin subunit alpha\n+#=GS 3ia3_D/4-145 DE [subseq from] mol:protein length:145 Hemoglobin subunit alpha\n+#=GS 1bab_A/2-143 DE [subseq from] mol:protein length:143 HEMOGLO'..b'-....--.-.-------------------------\n+#=GR 2ypb_B/3-65 PP ..*.....*..**..*****99........8642255555.5.......................................\n+5ic1_A/131-202 ..-.....-..--..-------........---..-----.------....--.-.-------------------------\n+#=GR 5ic1_A/131-202 PP .................................................................................\n+3jd5_p/111-156 ..Q.....K..LH..VDFRNVK........LLK..QFVCA.HTGIIF....HA.P.YTGVCMKQHKKLTQAIQK-------\n+#=GR 3jd5_p/111-156 PP ..7.....9..**..*******........***..**999.999999....99.9.999999999999998865.......\n+6neq_p/111-156 ..Q.....K..LH..VDFRNVK........LLK..QFVCA.HTGIIF....HA.P.YTGVCMKQHKKLTQAIQK-------\n+#=GR 6neq_p/111-156 PP ..7.....9..**..*******........***..**999.999999....99.9.999999999999998865.......\n+6nf8_p/111-156 ..Q.....K..LH..VDFRNVK........LLK..QFVCA.HTGIIF....HA.P.YTGVCMKQHKKLTQAIQK-------\n+#=GR 6nf8_p/111-156 PP ..7.....9..**..*******........***..**999.999999....99.9.999999999999998865.......\n+1j3j_A/83-140 ..T.....N..WE..SIPKKFK........PLS..NRINV.ILSRTL....KKeD.FDEDV--------------------\n+#=GR 1j3j_A/83-140 PP ..9.....*..**..*******........***..*****.***999....7615.77665....................\n+1j3j_B/83-140 ..T.....N..WE..SIPKKFK........PLS..NRINV.ILSRTL....KKeD.FDEDV--------------------\n+#=GR 1j3j_B/83-140 PP ..9.....*..**..*******........***..*****.***999....7615.77665....................\n+5uqe_A/160-229 ..-.....-..--..-------........---..-----.------....--.-.-------------------------\n+#=GR 5uqe_A/160-229 PP .................................................................................\n+5uqe_B/160-229 ..-.....-..--..-------........---..-----.------....--.-.-------------------------\n+#=GR 5uqe_B/160-229 PP .................................................................................\n+5uqe_C/160-229 ..-.....-..--..-------........---..-----.------....--.-.-------------------------\n+#=GR 5uqe_C/160-229 PP .................................................................................\n+5uqe_D/160-229 ..-.....-..--..-------........---..-----.------....--.-.-------------------------\n+#=GR 5uqe_D/160-229 PP .................................................................................\n+5uqe_F/160-229 ..-.....-..--..-------........---..-----.------....--.-.-------------------------\n+#=GR 5uqe_F/160-229 PP .................................................................................\n+1j3k_A/83-140 ..T.....N..WE..SIPKKFK........PLS..NRINV.ILSRTL....KKeD.FDEDV--------------------\n+#=GR 1j3k_A/83-140 PP ..9.....*..**..*******........***..*****.****99....7615.77665....................\n+1j3k_B/83-140 ..T.....N..WE..SIPKKFK........PLS..NRINV.ILSRTL....KKeD.FDEDV--------------------\n+#=GR 1j3k_B/83-140 PP ..9.....*..**..*******........***..*****.****99....7615.77665....................\n+3dg8_A/83-140 ..T.....N..WE..SIPKKFK........PLS..NRINV.ILSRTL....KKeD.FDEDV--------------------\n+#=GR 3dg8_A/83-140 PP ..9.....*..**..*******........***..*****.****99....7615.77665....................\n+3dg8_B/83-140 ..T.....N..WE..SIPKKFK........PLS..NRINV.ILSRTL....KKeD.FDEDV--------------------\n+#=GR 3dg8_B/83-140 PP ..9.....*..**..*******........***..*****.****99....7615.77665....................\n+3o55_A/27-56 ..-.....-..--..-------........---..WAVLH.TLAAYY....PD.L.PTPEQQQDMAQFIHLF---------\n+#=GR 3o55_A/27-56 PP ...................................56789.9*****....**.*.*********9998765.........\n+3o55_A/50-89 ..-.....-..--..-------........---..-----.------....--.-.-------------------------\n+#=GR 3o55_A/50-89 PP .................................................................................\n+#=GC PP_cons ..9.....9..99..*******........***..*****.**99*9....99.9.**9*********************8\n+#=GC RF ..x.....x..xx..xxxxxxx........xxx..xxxxx.xxxxxx....xx.x.xxxxxxxxxxxxxxxxxxxxxxxxx\n+//\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/A/uniprot_hits.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/A/uniprot_hits.sto Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| b'@@ -0,0 +1,70492 @@\n+# STOCKHOLM 1.0\n+#=GF ID chain_A-i1\n+\n+#=GS tr|A0A4U1FNC5|A0A4U1FNC5_MONMO/2-139 DE [subseq from] Hemoglobin subunit zeta OS=Monodon monoceros OX=40151 GN=EI555_019942 PE=3 SV=1\n+#=GS tr|A0A4U1FNC5|A0A4U1FNC5_MONMO/143-271 DE [subseq from] Hemoglobin subunit zeta OS=Monodon monoceros OX=40151 GN=EI555_019942 PE=3 SV=1\n+#=GS tr|A0A4U1FNC5|A0A4U1FNC5_MONMO/277-410 DE [subseq from] Hemoglobin subunit zeta OS=Monodon monoceros OX=40151 GN=EI555_019942 PE=3 SV=1\n+#=GS tr|A0A4U1FNC5|A0A4U1FNC5_MONMO/415-555 DE [subseq from] Hemoglobin subunit zeta OS=Monodon monoceros OX=40151 GN=EI555_019942 PE=3 SV=1\n+#=GS tr|A0A4U1FNC5|A0A4U1FNC5_MONMO/623-730 DE [subseq from] Hemoglobin subunit zeta OS=Monodon monoceros OX=40151 GN=EI555_019942 PE=3 SV=1\n+#=GS tr|A0A553QH31|A0A553QH31_9TELE/3-132 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH31|A0A553QH31_9TELE/313-450 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH31|A0A553QH31_9TELE/461-597 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH31|A0A553QH31_9TELE/795-933 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH31|A0A553QH31_9TELE/941-1082 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A315V4X2|A0A315V4X2_GAMAF/4-133 DE [subseq from] Uncharacterized protein OS=Gambusia affinis OX=33528 GN=CCH79_00008190 PE=3 SV=1\n+#=GS tr|A0A315V4X2|A0A315V4X2_GAMAF/136-274 DE [subseq from] Uncharacterized protein OS=Gambusia affinis OX=33528 GN=CCH79_00008190 PE=3 SV=1\n+#=GS tr|A0A315V4X2|A0A315V4X2_GAMAF/306-387 DE [subseq from] Uncharacterized protein OS=Gambusia affinis OX=33528 GN=CCH79_00008190 PE=3 SV=1\n+#=GS tr|A0A315V4X2|A0A315V4X2_GAMAF/386-523 DE [subseq from] Uncharacterized protein OS=Gambusia affinis OX=33528 GN=CCH79_00008190 PE=3 SV=1\n+#=GS tr|A0A315V4X2|A0A315V4X2_GAMAF/526-664 DE [subseq from] Uncharacterized protein OS=Gambusia affinis OX=33528 GN=CCH79_00008190 PE=3 SV=1\n+#=GS tr|A0A835ZNR3|A0A835ZNR3_SHEEP/1-136 DE [subseq from] Uncharacterized protein OS=Ovis aries OX=9940 GN=JEQ12_012143 PE=4 SV=1\n+#=GS tr|A0A835ZNR3|A0A835ZNR3_SHEEP/142-283 DE [subseq from] Uncharacterized protein OS=Ovis aries OX=9940 GN=JEQ12_012143 PE=4 SV=1\n+#=GS tr|A0A553QH10|A0A553QH10_9TELE/3-132 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH10|A0A553QH10_9TELE/313-450 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH10|A0A553QH10_9TELE/461-597 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH10|A0A553QH10_9TELE/795-937 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH05|A0A553QH05_9TELE/3-132 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH05|A0A553QH05_9TELE/313-450 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH05|A0A553QH05_9TELE/461-597 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH05|A0A553QH05_9TELE/795-937 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH08|A0A553QH08_9TELE/3-132 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_025392 PE=3 SV=1\n+#=GS tr|A0A553QH08|A0A553QH08_9TELE/313-448 DE [subseq from] Uncharacterized protein OS=Danionella translucida OX=623744 GN=DNTS_02539'..b'A---\n+#=GR tr|A0A6M8B3U6|A0A6M8B3U6_9ANNE/25-169 PP ....*............*............*...............*............*...*.....*...*..*...*.......*...........*.**..*.*......*...*.*.*.*.*..*.*.*9.9988888.8.899.98876...\n+tr|A0A6P7EUR3|A0A6P7EUR3_SHEEP/7-126 ----F------------C------------A---------------L------------L---G-----N---M--I---L-------I-----------V-LA--T-H------F---S-K-E-F-T--P-Q-MQ-A---------------------\n+#=GR tr|A0A6P7EUR3|A0A6P7EUR3_SHEEP/7-126 PP ....9............*............*...............*............*...*.....*...*..*...*.......*...........*.**..*.*......*...*.*.*.*.*..*.9.87.6.....................\n+tr|A0A5F0K9X8|A0A5F0K9X8_9GAMM/9-120 ----Q------------F------------V---------------P------------L---K-----Q---A--L---T-------L-----------V-LA--R-R------L---G-E-Y-F-T--P-A-LA-DAWSQ-----------------\n+#=GR tr|A0A5F0K9X8|A0A5F0K9X8_9GAMM/9-120 PP ....*............*............*...............*............*...*.....*...*..*...*.......*...........*.**..*.*......*...*.*.*.*.*..*.*.87.66555.................\n+tr|A0A075W131|A0A075W131_BUNCO/6-132 ----N------------F------------K---------------L------------I---S-----E---V--I---V-------K-----------V-LA--E-K------------A-Q-I-D--G-G-TQ-EALRRVL-A-AV----------\n+#=GR tr|A0A075W131|A0A075W131_BUNCO/6-132 PP ....*............*............*...............*............*...*.....*...9..9...9.......8...........8.88..6.4............6.6.6.6..6.7.77.7777777.7.66..........\n+tr|A0A402FB38|A0A402FB38_9SAUR/33-175 ----M------------F------------Q---------------R------------L---F-----Q---S--I---L-------G-----------V-SQ--D-L------M---G-D-E-I-T--N-N-MV-VSWDKFF-E-IVY-EEITV---\n+#=GR tr|A0A402FB38|A0A402FB38_9SAUR/33-175 PP ....9............*............*...............9............9...9.....9...9..9...9.......8...........8.88..8.8......8...9.9.9.*.*..*.*.**.******9.8.887.76665...\n+tr|A0A3Q2VZ45|A0A3Q2VZ45_HAPBU/46-126 ----N------------F------------M---------------V------------C---I-----E---L--M----------------------------------------------------------------------------------\n+#=GR tr|A0A3Q2VZ45|A0A3Q2VZ45_HAPBU/46-126 PP ....*............*............8...............8............6...5.....5...4..4..................................................................................\n+tr|A0A2R9CIG8|A0A2R9CIG8_PANPA/12-133 ----Y------------F------------K---------------P------------T---G-----H---T--A---L-------F-----------G-AV--G-P------L---P-P-P-----------------------------------\n+#=GR tr|A0A2R9CIG8|A0A2R9CIG8_PANPA/12-133 PP ....*............*............*...............*............*...*.....*...*..9...9.......9...........8.88..8.8......8...7.6.4...................................\n+tr|A0A384DL92|A0A384DL92_URSMA/5-89 ---------------------------------------------------------------------------------------------------------------------------------------------------------------\n+#=GR tr|A0A384DL92|A0A384DL92_URSMA/5-89 PP ...............................................................................................................................................................\n+tr|A0A6P6N1U6|A0A6P6N1U6_CARAU/3-114 ----N------------F------------R---------------L------------I---T-----E---V--L---V-------K-----------V-MA--E-K--------------------------------------------------\n+#=GR tr|A0A6P6N1U6|A0A6P6N1U6_CARAU/3-114 PP ....*............*............*...............*............*...*.....*...9..9...8.......8...........7.77..4.3..................................................\n+#=GC PP_cons ....*............*............*...............*............*...*.....*...*..*...*.......*...........*.**..*.*......*...*.*.*.*.*..*.*.**.*******.*.*99.99999998\n+#=GC RF ....x............x............x...............x............x...x.....x...x..x...x.......x...........x.xx..x.x......x...x.x.x.x.x..x.x.xx.xxxxxxx.x.xxx.xxxxxxxx\n+//\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/A/uniref90_hits.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/A/uniref90_hits.sto Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| b"@@ -0,0 +1,13596 @@\n+# STOCKHOLM 1.0\n+\n+#=GS UniRef90_A0A4U1FNC5/2-139 DE [subseq from] Hemoglobin subunit zeta n=1 Tax=Monodon monoceros TaxID=40151 RepID=A0A4U1FNC5_MONMO\n+#=GS UniRef90_A0A4U1FNC5/143-271 DE [subseq from] Hemoglobin subunit zeta n=1 Tax=Monodon monoceros TaxID=40151 RepID=A0A4U1FNC5_MONMO\n+#=GS UniRef90_A0A4U1FNC5/277-410 DE [subseq from] Hemoglobin subunit zeta n=1 Tax=Monodon monoceros TaxID=40151 RepID=A0A4U1FNC5_MONMO\n+#=GS UniRef90_A0A4U1FNC5/415-555 DE [subseq from] Hemoglobin subunit zeta n=1 Tax=Monodon monoceros TaxID=40151 RepID=A0A4U1FNC5_MONMO\n+#=GS UniRef90_A0A4U1FNC5/623-730 DE [subseq from] Hemoglobin subunit zeta n=1 Tax=Monodon monoceros TaxID=40151 RepID=A0A4U1FNC5_MONMO\n+#=GS UniRef90_A0A553QH31/3-132 DE [subseq from] Uncharacterized protein n=4 Tax=Danionella translucida TaxID=623744 RepID=A0A553QH31_9TELE\n+#=GS UniRef90_A0A553QH31/313-450 DE [subseq from] Uncharacterized protein n=4 Tax=Danionella translucida TaxID=623744 RepID=A0A553QH31_9TELE\n+#=GS UniRef90_A0A553QH31/461-597 DE [subseq from] Uncharacterized protein n=4 Tax=Danionella translucida TaxID=623744 RepID=A0A553QH31_9TELE\n+#=GS UniRef90_A0A553QH31/795-933 DE [subseq from] Uncharacterized protein n=4 Tax=Danionella translucida TaxID=623744 RepID=A0A553QH31_9TELE\n+#=GS UniRef90_A0A553QH31/941-1082 DE [subseq from] Uncharacterized protein n=4 Tax=Danionella translucida TaxID=623744 RepID=A0A553QH31_9TELE\n+#=GS UniRef90_A0A315V4X2/4-133 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A315V4X2/136-274 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A315V4X2/306-387 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A315V4X2/386-523 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A315V4X2/526-664 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A835ZNR3/1-136 DE [subseq from] Uncharacterized protein n=3 Tax=Ovis TaxID=9935 RepID=A0A835ZNR3_SHEEP\n+#=GS UniRef90_A0A835ZNR3/142-283 DE [subseq from] Uncharacterized protein n=3 Tax=Ovis TaxID=9935 RepID=A0A835ZNR3_SHEEP\n+#=GS UniRef90_A0A212CZ96/2-99 DE [subseq from] HBA n=1 Tax=Cervus elaphus hippelaphus TaxID=46360 RepID=A0A212CZ96_CEREH\n+#=GS UniRef90_A0A212CZ96/106-238 DE [subseq from] HBA n=1 Tax=Cervus elaphus hippelaphus TaxID=46360 RepID=A0A212CZ96_CEREH\n+#=GS UniRef90_A0A212CZ96/238-372 DE [subseq from] HBA n=1 Tax=Cervus elaphus hippelaphus TaxID=46360 RepID=A0A212CZ96_CEREH\n+#=GS UniRef90_A0A6F9C0F3/2-137 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A6F9C0F3/135-240 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A6F9C0F3/271-389 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A6F9C0F3/435-565 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A6F9C0F3/706-842 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_J9NXL3/1-130 DE [subseq from] Uncharacterized protein n=1 Tax=Canis lupus familiaris TaxID=9615 RepID=J9NXL3_CANLF\n+#=GS UniRef90_J9NXL3/126-238 DE [subseq from] Uncharacterized protein n=1 Tax=Canis lupus familiaris TaxID=9615 RepID=J9NXL3_CANLF\n+#=GS UniRef90_A0A1S5UZ39/1-63 DE [subseq from] Hemoglobin subunit alpha n=2 Tax=Homo sapiens TaxID=9606 RepID=A0A1S5UZ39_HUMAN\n+#=GS UniRef90_A0A"..b'-----VIA--E-E------F-A-D--D-F-P--AE-TQ-RA-WAKLR-S-LIYSHVT----\n+UniRef90_A0A7S3WSS3/183-270 --------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+UniRef90_A0A5F4DA56/54-172 ----E--P---V-Y------------F------------K---------------I------------L----S-----G---V--I-L-------E-----------VIA--E-E------F-A-N--D-F-P--PE-TQ-RA-WAKLR-S-LIYSHVTAAY-\n+UniRef90_UPI0018EC2E9B/7-140 ----P--I---N-N------------F------------K---------------L------------I----T-----E---I--L-V-------K-----------VLE--E-K----------A--G-L-D--AA-GQ-QA-FRNVM-A-VVIADLDSKY-\n+UniRef90_UPI0010A0283C/5-135 ----P--L---V-N------------F------------K---------------I------------I----S-----D---V----I-------V-----------TVA--T-E------K-L-D--G-F-G--PD-AQ-TA-LKNVL-K------------\n+UniRef90_B7XGC1/5-114 ----G--I---N-N------------F------------K---------------L------------I----S-----E---V--I-I-------K-----------VMA--E-K------------------------------------------------\n+UniRef90_A0A3N0XJ45/362-463 ----D--P---V-Y------------F------------K---------------I------------L----A-----G---V--I-L-------E-----------VLV--E-A------F-P-Q--S-F-S--PASVQ-----------------------\n+UniRef90_A0A3P8Q4Q4/24-134 -----------V-V------------L------------Q---------------L------------L----G-----D---C--L-A-------I-----------VVA--P-Q------L-G-K--D-F-T--PE-VH-AA-FQKFL-A-VVVSSLRRQY-\n+UniRef90_A0A669B4R2/11-131 ---FP--P---V-L------------S------------E---------------I------------V----T-----F---C--V-A-------S-----------KFG--L-Q-------------V-F-A--PD-VQ-MT-WQKFL-A-VVV--------\n+UniRef90_A0A3Q3GV14/9-113 ----P--I---N-N------------F------------R---------------L------------I----S-----E---V--I-V-------K-----------VMA--E--------------------------------------------------\n+UniRef90_A0A3B3HH82/135-177 ---------------------------------------Q---------------L------------L----A-----H---C--L-Q-------V-----------VIA--N-M------F-P-K--D-F-T--PE-AH-VA-CDKFL-A-NVALALSEKYR\n+UniRef90_A7SFV0/16-159 ---LK--P---S-Y------------L------------E---------------A------------M----H-----G---A--L-M-------D-----------TLR--N-L------L-Q-S--Q-W-T--EE-TA-EA-WNKLF-S-FISTTM-----\n+UniRef90_A0A6J3ERU2/67-185 ----E--P---V-Y------------F------------K---------------I------------L----S-----G---V--I-L-------E-----------VIA--E-E------F-A-N--D-F-P--PE-TQ-RA-WAKLR-G-LIYSHVTAAY-\n+UniRef90_A0A6P3W7J0/38-144 ----S--L---N-N------------F------------K---------------L------------I----T-----A---V--I-A---------------------------------------------------------------------------\n+UniRef90_UPI00126375FA/57-133 ----G--P---V-K------------L------------Q---------------L------------L----S-----R---A--------------------------------------------------------------------------------\n+UniRef90_Q6VN46/3-114 ----A--L---N-N------------F------------R---------------L------------I----T-----E---V--L-V-------K-----------VMA--E-K------------------------------------------------\n+UniRef90_UPI00147BB24C/18-146 ----K--A---V-Y------------F------------K---------------I------------L----I-----G---A--I-L-------E-----------VLV--E-T------F-P-E--T-F-G--VE-VQ-WA-WSK----------------\n+UniRef90_A0A6J0V7X5/24-161 ----P--S---A-M------------F------------Q---------------F------------L----F-----Q---A--I-I-------C-----------TFQ--D-L------L-G-K--E-F-T--ED-IQ-VS-WEKLF-E-ALR--------\n+UniRef90_K7FYQ5/1-135 ----P--A---A-N------------F------------Q---------------K------------K----K-----G---V--I-L-------S-----------VCK--E-L------M-G-N--E-F-S--SE-VS-SA-WEKLF-R------------\n+#=GC RF ....x..x...x.x............x............x...............x............x....x.....x...x..x.x.......x...........xxx..x.x......x.x.x..x.x.x..xx.xx.xx.xxxxx.x.xxxxxxxxxxx\n+//\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/B/bfd_uniclust_hits.a3m --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/B/bfd_uniclust_hits.a3m Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,2542 @@\n+>chain_B\n+MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH\n+>ERR1719244_1811598\n+MVQWSDDETKAIQMIWNSVDVNELGPAALRRCLLVYPWTQRYFGKFGDIATPTAIMQNPGVAQHGITVMNGLKLAGGPGGGPGNQPGGQQELWQRGKQQGQQQLWQQGQHGGKQRGqqQRQGQq-PSPRQSX------------------\n+>tr|W5MMD7|W5MMD7_LEPOC Uncharacterized protein OS=Lepisosteus oculatus OX=7918 PE=3 SV=1\n+MVTLTAEDKNNIRHVWGMVYKDPEGngAVVVIRLFTDHPETKQYFKRFKNLDTLEQMQTNPRIKLHGKRVMNTLNQVIDNLDDWAavkEILTALAERHRDVHKIHIHNFKLLFDVIIKVYGEALGPAFTDAACESWSKVFQLLYSFLQSVYT\n+>tr|G3WE01|G3WE01_SARHA Hemoglobin subunit mu OS=Sarcophilus harrisii OX=9305 GN=HBM PE=3 SV=1\n+--MFSAEEQSHIVQIWNYLsgHEAIFGTELLQRLFTVYPSTKSYFPPL-IPG-----LELTQMQNHGEQILMAVGVAVDNMYDLRTALSGLADLHAYGLRVEPTNFHFLIHCFQVMLASHLQSEYTAEMHAAWDKFLTNVAVVLTEKYH\n+>tr|W5PMJ4|W5PMJ4_SHEEP Uncharacterized protein OS=Ovis aries OX=9940 PE=3 SV=1\n+--SLTRAERTIVVSMWSKIstQADVIGTETLERRVTCVSRGPA-P----GSP------QS-------rgRREAGRKGRNDLEtggqgegAGRTGQRLL-RSRLRACTLSF---PPQFLSHCLLVTLASHFPADFTADAHAAWDKFLSLVSGVLTEKYR\n+>tr|A0A1K0GGD5|A0A1K0GGD5_RAT Globin d1 OS=Rattus norvegicus GN=Glnd1 PE=3 SV=1\n+----------------------MYGLEKEp-R------------ETEGCLS---RKLPSNLQRSSAPWRLHGFQNLLERSQGA--------QRAKPG------------HGAHSHSSVKMAL--SQTDH------------------rlvL\n+>ERR1719474_978995\n+--------------------------------LLQSSWKQ--FRT----------------------------------------FASLSGIRQEELGAGCQHQDLP----------QIQHHLWISEPSTFQQLLtftrsiktftnhylnirclflqmflslrgCVNKDSASRKKH\n+>ERR1719336_830457\n+----------------------------------------------------------------------------------SINPQSTVDLGAQYISATPLNYKNHQDIYNSLLSNG------VLVPANVSLIEGMRQDRIDEGEE\n+>tr|F6XB67|F6XB67_XENTR Uncharacterized protein OS=Xenopus tropicalis PE=3 SV=1\n+-MILSEAEKAAILSLWAKAsgNVNALGAEALERILYIWQNLFSYLESP-VI---L-----KILQTGKGASVYKIR-GLDHLSTKHSILPLL-TVKKCLCLRDAGFKILLSHAIEVTLAVHFPDDFDATAQAAWDKFLAAISTALTSQYR\n+>tr|A0A1L8EXG7|A0A1L8EXG7_XENLA Uncharacterized protein OS=Xenopus laevis GN=XELAEV_18045093mg PE=3 SV=1\n+-MSLSQAEKTLILAFWNKASglINTIGPQIVNRLLLAYPQLKTHFGNF-NVTPGS-----SDLNTLGIKIITAVGGATQHMDDLPVHLAILTDLHSLTLRIDPGNYKLMIDCIVISMAASLPQDFTAEVQNAMTNFLIIIGDILASKFC\n+>SRR5260364_139532 \n+------------T----VLapDPnPTPHSASPRRMFLSFPTTKTYFPHF-DLSHGS-----AQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKVSGGPGAIWVEGRDGAFLAGQRITRvAGGVAQAAAAGLGPRPH\n+>tr|A0A096M318|A0A096M318_POEFO Uncharacterized protein OS=Poecilia formosa OX=48698 PE=3 SV=1\n+------HDELIITGVFFTSVSECVPP-----VRNIYRQTTNSIENIGNFKNGETFLTNPPVALYVVNMVEFTSKPLMS-LPLNGFYGILDFLK--AKRKNPNGGKLLADCLTIVIASKMGSGFTPEIQATFQKFLAVVVSALGKQYH\n+>tr|A0A146TSR5|A0A146TSR5_FUNHE Hemoglobin cathodic subunit beta (Fragment) OS=Fundulus heteroclitus OX=8078 PE=3 SV=1\n+IFHFIYFYLSTIHYIFSKIYSFFFFPSSLSIFLIFYPFTHIYFFIFFNLYNSSSITSNPNFSSHFNFFLSFLYKSFNNIYYINTTYKYLIFLHSYKLQFYPYNFNLLSYFLTIFLSFHIFSSFTP----------------------\n+>tr|A0A146Z291|A0A146Z291_FUNHE Hemoglobin subunit epsilon (Fragment) OS=Fundulus heteroclitus OX=8078 PE=3 SV=1\n+IFYFSYHYLIIITSIFSNLYYNYFFPNSLIIFLIFYPFTHIYFSNFFNLYNSYSINTNPNIQSHFTNFLHFLYLSFNNIYNINFTYSYFIFLHSYNLHFYPYNFNLLSYFFTIFISSNIFSVIKE----------------------\n+>tr|H3B4U9|H3B4U9_LATCH Cytoglobin OS=Latimeria chalumnae OX=7897 GN=CYGB PE=3 SV=1\n+--QLSDTEVESIRQIWSNVytNCENVGVLVLIRFFVNFPSAKQYFSQFRHLEDPLDMERSVQLRKHARRVMGAINTVVENVEDQDKiasVLAPVGKAHALKHKVEPVYFKILSGVILEILAEEYAQHFTPEVQKAWTKLMSIICCHVTATY-\n+>tr|L8HVQ9|L8HVQ9_9CETA Cytoglobin OS=Bos mutus OX=72004 GN=M91_06698 PE=3 SV=1\n+--ELSEAERKAVQATWARLyaNCEDVGVAILVRNRFWRkKRASSTLEEFQegaqgrdsslGSSQAQKQPGCPQLRKHACRVMGALNTVVENLHDPEKvssVLSLVGKAHALKHKVEPVYFKILSGVILEVIAEEFANDFPPETQRAWAKLRGLIYSHVTAAY-\n+>ERR1711977_7585\n+-MSLSAKDKTLVKKLWEKAEgkSADIGAEALGRMLVAYPQTKTYFSQWGSDLNPQ----HPQVKKHGAVIMGGVGKAVKNIDDLVRGMGALSELHAFKLRVDPANFKILAHNIIWSWPCTSLQTSPPRPTCPLTSSCRTWLWLCPRDT-\n+>tr|A0A1C4HCU8|A0A1C4HCU8_PROAN Myoglobin (Fragment) OS=Protopterus annectens OX=7888 GN=Mb3 PE=2 SV=1\n+--MASAAQWDTTLKFWEAhVagDLKKHGHEALVRLFLKNKDSQKHFPKFKDLASEAEMRGSDGLKNHGETVFTALGKALQQRDGIANELRPLAVTHSQNHKIPLEEFENICEVID'..b'_09515 PE=4 SV=1\n+--------NDLILNSFESAAesLGDITPHVYRRFFLQYPEAESLFNIK-GAQFQD--------ELKVQMVRDAIYAYLEYLETPeevEIVFKYTIPQHV-DLDIPIRYFIALLEAVADVVCDSVDDRTQADTKASWSELLQEFRQM------\n+>ERR1711865_325941\n+---------------------SQFGLNAFNRLFDTEPRSEDHFKT-SN----------A---RLSMLATKSLELSMQMYKEptrVMNEVTSLGLRYI-FPAHD-----------------------------------------------\n+>SRR2546421_6426420 \n+------------------------------XMIRRPPRstlfPYTTLFR-SDF------------ERQNKLLRHAFGLLLIFPNQartEPSVLTRVAERHSRrDLDIPRSEEHTSElqsRSDLVCRLLLEKKK-KNQV--------------------\n+>tr|A0A2C8D7D3|A0A2C8D7D3_CORDP Phenol hydroxylase P5 protein OS=Corynebacterium diphtheriae GN=mphP PE=4 SV=1\n+--------------------VTAHSIQAVADELRAHraeFIQAANQ------------------KPD-SPLADAIVQLVDHTDLdghvpesIATSWLQHAAAAE-SLGVSRDYYLTLADASRSALRHICAD--------------------------\n+>tr|D9QCQ3|D9QCQ3_CORP2 Oxidoreductase OS=Corynebacterium pseudotuberculosis (strain C231) GN=CpC231_1874 PE=4 SV=1\n+--------------------KDAFHTQVFANF--YHsnPYARATI------------------APS-EQLVPAVISLIGHLENngfisdeVKQKFLEHTKLLD-ARGF--HHYTALASAVRSALQTMCTD--------------------------\n+>ERR1719474_106261\n+----STASLELVLDFWRCTVhrlsvhdRAMMGGDLFRGMSRQDAACRALLESL--N------PTSERMDLWGLRFLDTTGWMLRRANaaDLDASLKAMGAEDR-ARGLTVAYYRVLVERLHSELAARFPTKYSETVQAAMEEVIWSFVRR------\n+>ERR1719499_858439\n+------------------------GRAIIEGMNHE-------------N------TSPNQMDMRTVRLLDTLGWMIRMSciPtmDLKVLYAAWNGMAA-EVGYSAEYHVSWIQYIEAQLTERFPSEYTDSVRSAVRELLRWSIPN------\n+>ERR1719410_2598304\n+-------------------------------------------------------------PSHALKILNVFGYVIRNLIHpsnhlkLFKQLQSLGTVHR-AHSLNNEMYEAMLKSFNYAMEEKFANHYKIRIRFCLSQLYRVIVDIMTG---\n+>ERR1719216_785110\n+-------------------------------------------------------------PKHTIKIITTFGYIIKNLIYskehtkIFKQLQSLGEMHQ-CHSMInTDIYMELLNAWHFAMEEKFQNKYKNNTRFCFNQLYRLIVDTLMG---\n+>tr|E0VF51|E0VF51_PEDHC uncharacterized protein OS=Pediculus humanus subsp. corporis OX=121224 GN=8236397 PE=3 SV=1 \n+--------VKIVTPTWESIKedFDWYCTKIEETFFQNDTTKKELFTL-PKFEeELTDDVVNKRLFKHSSAVLNFMECIVQFMNGneeTKPVLFVLGRNHY-TIGVNEKLFLEMKDAICSVIKYKIG----TENAKAWDTILQYI---------\n+>tr|A0A0M3IFG8|A0A0M3IFG8_ASCLU Uncharacterized protein OS=Ascaris lumbricoides OX=6252 PE=3 SV=1\n+-TGLSMHQKAILTARWRQLPqgiVFDLGKRVFGTLFQKDPNLLVVINL-EHLQGTDAWRDHVNFHMHAQRFTHALSQCMRHLVEpivAADRLQEFGATYAEmedsenfnRSRIPHSYWDRLISAMTSTAKEFHEnpsqksrrnslsvddalvatnerldLQIDSANISAWSALATFVSNQIRFGYE\n+>ERR1719199_711328\n+---FKPSHISLIQNQMSALIsefgsIEGAGEFLITQICALDEYVAKLFSG-AAL------------RVQGFKFLGQIARWVTYLADpetVEADLYNLGIRHL-GY-VTQQDFAKFLPaviqCMQKSLKDVLDEQWSALAAESWKMFLGYAGGH------\n+>ERR1712070_698694\n+---------------------------------------------------------------LCFIIARVIDIAAQlfvEPDVCIAEVLQLGLRHI-MYKVPADFFGPFAGIIADEIEARCD---------------------------\n+>sp|O76243|GLBB_CERLA Body wall hemoglobin OS=Cerebratulus lacteus OX=6221 PE=1 SV=3\n+-----------------------VVDAFYVELFTAHPQYQDRFA-FKGVA-LGDLKGNAAYQTQASKTVDYITAALAGSAD----AAGLASRHV-GRNVGAPEFTHAKACLAKACA-------------------------------\n+>tr|A0A2C9LKZ0|A0A2C9LKZ0_BIOGL Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106051185 PE=4 SV=1 \n+--GISLADIKVITNQWEDVLrcSDLFGKLLVLYVLDNCPKVNALHPGLHAR--LTDARD-SVEKQIGLRVIQSISCVIHNLNRapaVESMVRDTFKKLQ-QHGYTKNTILECSEAFLSFMNQYFSKRWLKQHSDAWFKVLKALL--------\n+>SRR5690606_9602430 \n+-------------------------RAFYPILYSSVSGAQELFEA--TVG------------TDNRKMLQILAKLFGfisNVNhsSefMkSDAFIERGKYYA-DHGISETMMRGFSSALVLTLRRTLGELFTISHVRAWGIFLDTISHAL-----\n+>SRR4051812_40179264 \n+-------------------------RIFFPILYSTVPSSQELIEE--AVG------------TDSIKMLQLLVKIFRiisDINhdPevMkSEAFLERGKFYA-DHNISENMLRGFNSALTLSLRRSLGERFTISHVRAWGAFLEMISHSL-----\n+>SRR5690242_7041980 \n+-------------------------RAFYPILFSTVSSSQEIFEE--HIG------------SDQTRMTETLRHVLEffiSVNlnPqiLsSDKVIERAKKYA-DLGISENMLKGFSFSFLKALKQVLGGALSAEAMREMVRLLDNISIQI-----\n+>tr|A0A0G4HHE4|A0A0G4HHE4_9ALVE Uncharacterized protein OS=Chromera velia CCMP2878 OX=1169474 GN=Cvel_6802 PE=3 SV=1 \n+-------------------------DALLGILFEASPTMRSVFVKNGDL--------------YADLIEHLLRRIIAYADDpgaLWTDDQHLALDHI-NFGMSMSDLPLFGASLMNCLAGVLGENWCDEWQRAWEKAWQICCQSL-----\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/B/mgnify_hits.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/B/mgnify_hits.sto Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| b'@@ -0,0 +1,106 @@\n+# STOCKHOLM 1.0\n+\n+#=GS MGYP000809681506/1-147 DE [subseq from] PL=00 UP=1 BIOMES=0000000011000\n+#=GS MGYP000131797357/10-156 DE [subseq from] PL=10 UP=0 BIOMES=0000000000001\n+#=GS MGYP000607955645/1-147 DE [subseq from] PL=00 UP=1 BIOMES=0000000011000\n+#=GS MGYP001138391873/1-147 DE [subseq from] PL=00 UP=1 BIOMES=1000000000000\n+#=GS MGYP001111532658/8-155 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP000442294717/26-102 DE [subseq from] PL=10 UP=0 BIOMES=1000000000000\n+#=GS MGYP000214952500/50-125 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000639461158/2-34 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP000639461158/53-143 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP000321112601/1-74 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000669192840/7-90 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000335830788/32-110 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000559925714/32-110 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000607025940/7-103 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP000450732916/72-150 DE [subseq from] PL=01 UP=0 BIOMES=0000000000001\n+#=GS MGYP001121356039/35-179 DE [subseq from] PL=01 UP=0 BIOMES=1000000000000\n+#=GS MGYP000836687451/15-153 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000\n+#=GS MGYP000172242919/33-121 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP000585341746/8-146 DE [subseq from] PL=10 UP=0 BIOMES=0000000000001\n+#=GS MGYP000306499386/1-66 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000694104832/8-83 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000212149699/1-52 DE [subseq from] PL=00 UP=0 BIOMES=0000000010100\n+#=GS MGYP000386264740/1-52 DE [subseq from] PL=01 UP=0 BIOMES=1000000000000\n+#=GS MGYP000441972666/10-52 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000304945179/1-72 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP001143026688/4-59 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000\n+#=GS MGYP000270001578/32-81 DE [subseq from] PL=01 UP=0 BIOMES=0000000010100\n+#=GS MGYP001069732337/13-151 DE [subseq from] PL=01 UP=0 BIOMES=1000000000000\n+#=GS MGYP000742755994/10-46 DE [subseq from] PL=00 UP=0 BIOMES=1000000011000\n+#=GS MGYP000713428126/1-50 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000462927881/1-41 DE [subseq from] PL=00 UP=0 BIOMES=1000000000000\n+#=GS MGYP000026201981/1-34 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000969813914/16-146 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000\n+#=GS MGYP000969813914/178-293 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000\n+#=GS MGYP000358470208/58-90 DE [subseq from] PL=00 UP=0 BIOMES=0000000010100\n+#=GS MGYP000128452298/2-38 DE [subseq from] PL=00 UP=0 BIOMES=0000000010100\n+#=GS MGYP000729474694/1-93 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP000701481948/4-73 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000539442244/4-70 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP001145220054/370-451 DE [subseq from] PL=10 UP=0 BIOMES=0110000000000\n+#=GS MGYP001145220054/517-598 DE [subseq from] PL=10 UP=0 BIOMES=0110000000000\n+#=GS MGYP001152833638/1-56 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP001132506692/1-33 DE [subseq from] PL=10 UP=0 BIOMES=0000000000001\n+#=GS MGYP000294860436/2-38 DE [subseq from] PL=00 UP=0 BIOMES=1000000000000\n+#=GS MGYP001122892151/105-179 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000413961247/1-72 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000\n+#=GS MGYP000545182717/2-32 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000\n+#=GS MGYP000536366561/122-194 DE [subseq from] PL=11 UP=0 BIOMES=0000000011000\n+#=GS MGYP000318290004/17-71 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000\n+#=GS MGYP000498009340/65-136 DE [subseq '..b'000026201981/1-34 MVHLTPEEKSAVTALWGKVN--V--DEVGGEALGRLVS-------------------------------------------------------------------------------------------------------------------------------\n+MGYP000969813914/16-146 ----------SWTSLTSVVD--L--EDFGVNVFILVVQLAPESLQLFSFKDEKAFHDSV----LVRAYGKLLMKTVG---KIINVLHDIP---ALAVMLDELAARDPGFELRPEHFPV-L-GQ-ALL---STLQNAAGGLWSPEMQAAWIAVWTEVIDLLA----\n+MGYP000969813914/178-293 ----------------------A--DQLGTDFFLRLFQRSPSLLELF-SFKD---DKPLSSSPRLRAHGSKVMATIA---NAVSGLRDLEALIPILANLAKKHA--E-YGVQEEHFPY-V-GE-ALL---GTLADALGTDWTPDVQTAWTTVWNTV---------\n+MGYP000358470208/58-90 ---------------------------------------------------------------------------------WMAHLYNLK---GTFSQLSELHC--DKLHVDPENFRV-S---------------------------------------------\n+MGYP000128452298/2-38 -----------------------------------------------------------------------------------------------------------------------------MV---IILATHFGKEFTPEVQAAWQKLVSAVAIALAHKYH\n+MGYP000729474694/1-93 -----------------------------------MLVVYPQTKTYFSHWSDIT-P----GSAPVMKHGRTVMGGVA---TAVGVIDDLI---GGLLTLSELHA--FQLRIDPANFKV-K------T---YYIAYIKGERCTCPMQFASAK--------------\n+MGYP000701481948/4-73 --------------------------------------SFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALT---NAVAHVDDMP---NALSALSDLHA--HKLRVDPVNFKV-S-GG-P----------------------------------------\n+MGYP000539442244/4-70 --------------------------------------SFPTTKTYFPHF-DLS-----HGSAQVKGHGAKVAAALT---KAVEHLDDLP---GALSELSDLHA--HKLRVDPVNFKV-S---------------------------------------------\n+MGYP001145220054/370-451 -------------------------------------------------------------------QEKKLINALQLVVSNLRNVDTLA---KALTTLGEKH---QKYGAEPDHYNA-V-AA-TLL---DVMQEFAGELWTPEVKGAWEHALNTIARVML----\n+MGYP001145220054/517-598 --------------------------------------------------------------------EKKLLNALQLVINNLRNVDTLA---KALSTLGEKHQ---QYGVLPEHYSA-A-AN-ILI---GVMKSMAGDLWTDELHSAWEHALGVVAKVMLD---\n+MGYP001152833638/1-56 -------------------------------------------------------------------------------------MDNLK---PAFAKLSELHC--DKLHVDPENFRV-SPGD-ASLFSFYFLILHFGS-FTFPGKTAV----------------\n+MGYP001132506692/1-33 MVHLTDAEKAAVSGLWGKVN--A--DEVGGEALGRLV--------------------------------------------------------------------------------------------------------------------------------\n+MGYP000294860436/2-38 -----------------------------------------------------------------------------------------------------------------------------LV---TVLAIHFGKEFTPEVQASWQKMVTAVASALSSRYH\n+MGYP001122892151/105-179 ---------------------------------PRLFLSHPQTKTYFPHF-DLS-----HGSAQVKGHGKKVADALT---NAVAHVDDMP---NALSALSDLHA--HKLRGDQVNFKV-S-GG-P----------------------------------------\n+MGYP000413961247/1-72 -----------------------------------MLVVYPQTKTYFSHWKDVSP-----GSAAIRKHGLTVMTGYM---DAVEKIDDIA---NGLLTLSELHA--FTLRVDPANFKV-C-D-------------------------------------------\n+MGYP000545182717/2-32 MVHFTAEEKAAVTSLWSKMN--V--EEAGGEALGR----------------------------------------------------------------------------------------------------------------------------------\n+MGYP000536366561/122-194 ---------------------------------PRLFLSHPQTKTYFPHF-DL-----HPGSAQLRAHGSKVVAAVG---DAVKSIDDIG---GALSKLSELHA--YILRVDPVNFKV-R-G-------------------------------------------\n+MGYP000318290004/17-71 -----------------------------------------------------------PGSAQVAAHGQKVADALS---LAVNHLDDLP---GTLSYLRELHT--HKLRVDPVFFKV-S-SR-V----------------------------------------\n+MGYP000498009340/65-136 ----------------------------------RTFLAFPATKTYFSH-LDLS-----PGSSQVRAHGQKVADALS---LAVERLDDLP---HALSALSHLHA--CQLRVDPASFQV-S-G-------------------------------------------\n+#=GC RF xxxxxxxxxxxxxxxxxxxx..x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx...xxxxxxxxxxx..xxxxxxxxxxxx.x.xx.xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx\n+//\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/B/pdb_hits.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/B/pdb_hits.sto Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| b'@@ -0,0 +1,18099 @@\n+# STOCKHOLM 1.0\n+\n+#=GS 1abw_A/2-140 DE [subseq from] mol:protein length:283 HEMOGLOBIN-BASED BLOOD SUBSTITUTE\n+#=GS 1abw_A/144-282 DE [subseq from] mol:protein length:283 HEMOGLOBIN-BASED BLOOD SUBSTITUTE\n+#=GS 1aby_A/2-140 DE [subseq from] mol:protein length:283 HEMOGLOBIN\n+#=GS 1aby_A/144-282 DE [subseq from] mol:protein length:283 HEMOGLOBIN\n+#=GS 1c7c_A/2-140 DE [subseq from] mol:protein length:283 PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))\n+#=GS 1c7c_A/144-282 DE [subseq from] mol:protein length:283 PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))\n+#=GS 1o1p_A/2-140 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1o1p_A/144-282 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1c7d_A/2-140 DE [subseq from] mol:protein length:284 PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))\n+#=GS 1c7d_A/145-283 DE [subseq from] mol:protein length:284 PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))\n+#=GS 1o1n_A/2-140 DE [subseq from] mol:protein length:285 Hemoglobin Alpha chain\n+#=GS 1o1n_A/146-284 DE [subseq from] mol:protein length:285 Hemoglobin Alpha chain\n+#=GS 1o1j_A/2-140 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1o1j_A/144-282 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1o1m_A/2-140 DE [subseq from] mol:protein length:285 Hemoglobin Alpha chain\n+#=GS 1o1m_A/146-284 DE [subseq from] mol:protein length:285 Hemoglobin Alpha chain\n+#=GS 1o1l_A/2-140 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1o1l_A/144-282 DE [subseq from] mol:protein length:283 Hemoglobin Alpha chain\n+#=GS 1hbr_B/1-146 DE [subseq from] mol:protein length:146 PROTEIN (HEMOGLOBIN D)\n+#=GS 1hbr_D/1-146 DE [subseq from] mol:protein length:146 PROTEIN (HEMOGLOBIN D)\n+#=GS 2r80_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 2r80_D/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 3dhr_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 3dhr_D/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 3dhr_F/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 3dhr_H/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 3mju_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 3eok_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 1faw_B/1-146 DE [subseq from] mol:protein length:146 HEMOGLOBIN (BETA SUBUNIT)\n+#=GS 1faw_D/1-146 DE [subseq from] mol:protein length:146 HEMOGLOBIN (BETA SUBUNIT)\n+#=GS 2qmb_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin beta chain\n+#=GS 2qmb_D/1-146 DE [subseq from] mol:protein length:146 Hemoglobin beta chain\n+#=GS 3k8b_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin beta chain\n+#=GS 3k8b_D/1-146 DE [subseq from] mol:protein length:146 Hemoglobin beta chain\n+#=GS 6zmx_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin beta chain\n+#=GS 6zmx_D/1-146 DE [subseq from] mol:protein length:146 Hemoglobin beta chain\n+#=GS 6zmy_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin beta chain\n+#=GS 6zmy_D/1-146 DE [subseq from] mol:protein length:146 Hemoglobin beta chain\n+#=GS 3mjp_B/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 3mjp_D/1-146 DE [subseq from] mol:protein length:146 Hemoglobin subunit beta\n+#=GS 1a4f_B/1-146 DE [subseq from] mol:protein length:146 HEMOGLOBIN (BETA CHAIN)\n+#=GS 1c40_B/1-146 DE [subseq from] mol:protein length:146 PROTEIN (HEMOGLOBIN (BETA CHAIN))\n+#=GS 1hv4_B/1-146 DE [subseq from] mol:protein length:146 HEMOGLOBIN BETA CHAIN\n+#=GS 1hv4_D/1-146 DE [subseq from] mol:protein length:146 HEMOGLOBIN BETA CHAIN\n+#=GS 1hv4_F/1-146 DE [subseq from] mol:protein length:146 HEMOGLOBIN BETA CHAIN\n+#=GS 1'..b'SNLA...................VL.LAQEG.....-....-.--.---------------.----------\n+#=GR 5fzq_B/37-87 PP ....99998855...................44.44433.........................................\n+5fzq_C/37-87 ....IKTLSNLA...................VL.LAQEG.....-....-.--.---------------.----------\n+#=GR 5fzq_C/37-87 PP ....99998855...................44.44433.........................................\n+2xkg_A/5-63 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 2xkg_A/5-63 PP ................................................................................\n+2xkh_A/5-63 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 2xkh_A/5-63 PP ................................................................................\n+6nqw_A/40-93 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqw_A/40-93 PP ................................................................................\n+6nqw_A/127-149 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqw_A/127-149 PP ................................................................................\n+6nqx_A/40-93 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqx_A/40-93 PP ................................................................................\n+6nqx_A/127-149 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqx_A/127-149 PP ................................................................................\n+6nqx_B/40-93 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqx_B/40-93 PP ................................................................................\n+6nqx_B/127-149 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqx_B/127-149 PP ................................................................................\n+6nqx_C/40-93 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqx_C/40-93 PP ................................................................................\n+6nqx_C/127-149 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqx_C/127-149 PP ................................................................................\n+6nqx_D/40-93 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqx_D/40-93 PP ................................................................................\n+6nqx_D/127-149 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqx_D/127-149 PP ................................................................................\n+6nqy_A/40-93 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqy_A/40-93 PP ................................................................................\n+6nqy_A/127-149 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqy_A/127-149 PP ................................................................................\n+6nqy_B/40-93 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqy_B/40-93 PP ................................................................................\n+6nqy_B/127-149 ....--------...................--.-----.....-....-.--.---------------.----------\n+#=GR 6nqy_B/127-149 PP ................................................................................\n+#=GC PP_cons ....********...................**.**99*.....9....*.99.99***9*********.*****99*99\n+#=GC RF ....xxxxxxxx...................xx.xxxxx.....x....x.xx.xxxxxxxxxxxxxxx.xxxxxxxxxx\n+//\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/B/uniprot_hits.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/B/uniprot_hits.sto Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| b"@@ -0,0 +1,76295 @@\n+# STOCKHOLM 1.0\n+#=GF ID chain_B-i1\n+\n+#=GS tr|A0A6B0S8H8|A0A6B0S8H8_9CETA/1-106 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004455 PE=3 SV=1\n+#=GS tr|A0A6B0S8H8|A0A6B0S8H8_9CETA/127-271 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004455 PE=3 SV=1\n+#=GS tr|A0A6B0S8H8|A0A6B0S8H8_9CETA/271-344 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004455 PE=3 SV=1\n+#=GS tr|A0A6B0S8H8|A0A6B0S8H8_9CETA/366-411 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004455 PE=3 SV=1\n+#=GS tr|A0A6B0S8H8|A0A6B0S8H8_9CETA/419-562 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004455 PE=3 SV=1\n+#=GS tr|A0A6B0SCY9|A0A6B0SCY9_9CETA/1-106 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004453 PE=3 SV=1\n+#=GS tr|A0A6B0SCY9|A0A6B0SCY9_9CETA/124-268 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004453 PE=3 SV=1\n+#=GS tr|A0A6B0SCY9|A0A6B0SCY9_9CETA/268-332 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004453 PE=3 SV=1\n+#=GS tr|A0A6B0SCY9|A0A6B0SCY9_9CETA/335-478 DE [subseq from] Uncharacterized protein OS=Bos mutus OX=72004 GN=E5288_WYG004453 PE=3 SV=1\n+#=GS tr|A0A835ZZF7|A0A835ZZF7_SHEEP/1-105 DE [subseq from] Uncharacterized protein OS=Ovis aries OX=9940 GN=JEQ12_006222 PE=4 SV=1\n+#=GS tr|A0A835ZZF7|A0A835ZZF7_SHEEP/143-287 DE [subseq from] Uncharacterized protein OS=Ovis aries OX=9940 GN=JEQ12_006222 PE=4 SV=1\n+#=GS tr|A0A835ZZF7|A0A835ZZF7_SHEEP/287-367 DE [subseq from] Uncharacterized protein OS=Ovis aries OX=9940 GN=JEQ12_006222 PE=4 SV=1\n+#=GS tr|A0A835ZZF7|A0A835ZZF7_SHEEP/381-521 DE [subseq from] Uncharacterized protein OS=Ovis aries OX=9940 GN=JEQ12_006222 PE=4 SV=1\n+#=GS tr|A0A7J7ET90|A0A7J7ET90_DICBM/1-145 DE [subseq from] Uncharacterized protein OS=Diceros bicornis minor OX=77932 GN=HPG69_005711 PE=3 SV=1\n+#=GS tr|A0A7J7ET90|A0A7J7ET90_DICBM/159-265 DE [subseq from] Uncharacterized protein OS=Diceros bicornis minor OX=77932 GN=HPG69_005711 PE=3 SV=1\n+#=GS tr|A0A7J7ET90|A0A7J7ET90_DICBM/266-388 DE [subseq from] Uncharacterized protein OS=Diceros bicornis minor OX=77932 GN=HPG69_005711 PE=3 SV=1\n+#=GS tr|A0A7J7ET90|A0A7J7ET90_DICBM/388-417 DE [subseq from] Uncharacterized protein OS=Diceros bicornis minor OX=77932 GN=HPG69_005711 PE=3 SV=1\n+#=GS tr|A0A7J7ET90|A0A7J7ET90_DICBM/416-458 DE [subseq from] Uncharacterized protein OS=Diceros bicornis minor OX=77932 GN=HPG69_005711 PE=3 SV=1\n+#=GS tr|A0A6F9C0F3|A0A6F9C0F3_9TELE/2-133 DE [subseq from] Uncharacterized protein OS=Coregonus sp. 'balchen' OX=861768 GN=CSTEINMANNI_LOCUS3426706 PE=3 SV=1\n+#=GS tr|A0A6F9C0F3|A0A6F9C0F3_9TELE/135-242 DE [subseq from] Uncharacterized protein OS=Coregonus sp. 'balchen' OX=861768 GN=CSTEINMANNI_LOCUS3426706 PE=3 SV=1\n+#=GS tr|A0A6F9C0F3|A0A6F9C0F3_9TELE/250-392 DE [subseq from] Uncharacterized protein OS=Coregonus sp. 'balchen' OX=861768 GN=CSTEINMANNI_LOCUS3426706 PE=3 SV=1\n+#=GS tr|A0A6F9C0F3|A0A6F9C0F3_9TELE/426-568 DE [subseq from] Uncharacterized protein OS=Coregonus sp. 'balchen' OX=861768 GN=CSTEINMANNI_LOCUS3426706 PE=3 SV=1\n+#=GS tr|A0A6F9C0F3|A0A6F9C0F3_9TELE/697-843 DE [subseq from] Uncharacterized protein OS=Coregonus sp. 'balchen' OX=861768 GN=CSTEINMANNI_LOCUS3426706 PE=3 SV=1\n+#=GS tr|A0A484GX98|A0A484GX98_SOUCH/1-145 DE [subseq from] Uncharacterized protein OS=Sousa chinensis OX=103600 GN=DBR06_SOUSAS15710078 PE=3 SV=1\n+#=GS tr|A0A484GX98|A0A484GX98_SOUCH/176-322 DE [subseq from] Uncharacterized protein OS=Sousa chinensis OX=103600 GN=DBR06_SOUSAS15710078 PE=3 SV=1\n+#=GS tr|L5KDM3|L5KDM3_PTEAL/1-134 DE [subseq from] Hemoglobin subunit beta OS=Pteropus alecto OX=9402 GN=PAL_GLEAN10003334 PE=3 SV=1\n+#=GS tr|L5KDM3|L5KDM3_PTEAL/217-363 DE [subseq from] Hemoglobin subunit beta OS=Pteropus alecto OX=9402 GN=PAL_GLEAN10003334 P"..b'...*............*...*..****.......9........9.9.8.7.54.....4666777777.6.655........\n+tr|A0A7L2H3J8|A0A7L2H3J8_SAGSE/2-107 ------L----------T-G-V-----------M------------L---E--VIAE-------E--------Y-A-N-D-FT-P-E-AHGAWTKM----------------\n+#=GR tr|A0A7L2H3J8|A0A7L2H3J8_SAGSE/2-107 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.****9987................\n+sp|B7U9B5|MYG_CAPHI/7-147 ------I----------S-D-A-----------I------------I---H--VLHA-------K--------H-P-S-D-FG-A-D-AQGAMSKALE-L-FRNDMA-AQY-\n+#=GR sp|B7U9B5|MYG_CAPHI/7-147 PP ......*..........*.*.*...........*............*...*..**88.......8........8.9.9.*.**.*.*.*******999.8.888888.776.\n+tr|A0A7K6KIA0|A0A7K6KIA0_9PASE/2-108 ------L----------T-G-V-----------M------------L---E--VIAE-------E--------Y-P-N-D-FT-P-E-AHGAWTKMK---------------\n+#=GR tr|A0A7K6KIA0|A0A7K6KIA0_9PASE/2-108 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.****99975...............\n+tr|A0A7K6X3T0|A0A7K6X3T0_9PASE/2-108 ------L----------T-G-V-----------M------------L---E--VIAE-------E--------Y-P-N-D-FT-P-E-AHGAWTKMK---------------\n+#=GR tr|A0A7K6X3T0|A0A7K6X3T0_9PASE/2-108 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.****99975...............\n+tr|A0A7K7HM72|A0A7K7HM72_9PASS/2-108 ------L----------T-G-V-----------M------------L---E--VIAE-------E--------Y-P-N-D-FT-P-E-AHGAWTKMK---------------\n+#=GR tr|A0A7K7HM72|A0A7K7HM72_9PASS/2-108 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.****99975...............\n+tr|A0A7K8WGE0|A0A7K8WGE0_9FURN/2-108 ------L----------T-G-V-----------M------------L---E--VIAE-------E--------Y-P-N-D-FT-P-E-AHGAWTKMK---------------\n+#=GR tr|A0A7K8WGE0|A0A7K8WGE0_9FURN/2-108 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.****99975...............\n+tr|A0A7L1ZZD9|A0A7L1ZZD9_LEILU/2-108 ------L----------T-G-V-----------M------------L---E--VIAE-------E--------Y-P-N-D-FT-P-E-AHGAWTKMK---------------\n+#=GR tr|A0A7L1ZZD9|A0A7L1ZZD9_LEILU/2-108 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.****99975...............\n+tr|A0A7L2MXJ3|A0A7L2MXJ3_9PASS/2-108 ------L----------T-G-V-----------M------------L---E--VIAE-------E--------Y-P-N-D-FT-P-E-AHGAWTKMK---------------\n+#=GR tr|A0A7L2MXJ3|A0A7L2MXJ3_9PASS/2-108 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.****99975...............\n+tr|A0A093CC64|A0A093CC64_TAUER/1-116 ------I----------S-E-V-----------I------------I---K--VIAE-------K--------H-P-A-D-FG-A-D-SQAAMKKALE-L-FRNDMA-SKY-\n+#=GR tr|A0A093CC64|A0A093CC64_TAUER/1-116 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.**********.*.*****9.999.\n+tr|A0A6P4YC67|A0A6P4YC67_BRABE/34-149 ------L----------G-N-V-----------L------------M---K--GLGA-------V--------L-G-A-D-FT-E-E-VQGAWAA-----------------\n+#=GR tr|A0A6P4YC67|A0A6P4YC67_BRABE/34-149 PP ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.**99865.................\n+tr|A0A1A8AJH4|A0A1A8AJH4_NOTFU/9-133 ------I----------S-E-V-----------I------------G---K--VMAE-------K--------A-G-L-D-AA-----GQQALRNVMA-V-VI---------\n+#=GR tr|A0A1A8AJH4|A0A1A8AJH4_NOTFU/9-133 PP ......*..........*.*.*...........*............*...*..****.......9........9.9.8.7.54.....4666677776.6.65.........\n+#=GC PP_cons ......*..........*.*.*...........*............*...*..****.......*........*.*.*.*.**.*.*.********9*.*.******.**99\n+#=GC RF ......x..........x.x.x...........x............x...x..xxxx.......x........x.x.x.x.xx.x.x.xxxxxxxxxx.x.xxxxxx.xxxx\n+//\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/B/uniref90_hits.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/B/uniref90_hits.sto Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| b"@@ -0,0 +1,14608 @@\n+# STOCKHOLM 1.0\n+\n+#=GS UniRef90_A0A835ZZF7/1-105 DE [subseq from] Uncharacterized protein n=1 Tax=Ovis aries TaxID=9940 RepID=A0A835ZZF7_SHEEP\n+#=GS UniRef90_A0A835ZZF7/143-287 DE [subseq from] Uncharacterized protein n=1 Tax=Ovis aries TaxID=9940 RepID=A0A835ZZF7_SHEEP\n+#=GS UniRef90_A0A835ZZF7/287-367 DE [subseq from] Uncharacterized protein n=1 Tax=Ovis aries TaxID=9940 RepID=A0A835ZZF7_SHEEP\n+#=GS UniRef90_A0A835ZZF7/381-521 DE [subseq from] Uncharacterized protein n=1 Tax=Ovis aries TaxID=9940 RepID=A0A835ZZF7_SHEEP\n+#=GS UniRef90_A0A7J7ET90/1-145 DE [subseq from] Uncharacterized protein n=4 Tax=Boreoeutheria TaxID=1437010 RepID=A0A7J7ET90_DICBM\n+#=GS UniRef90_A0A7J7ET90/159-265 DE [subseq from] Uncharacterized protein n=4 Tax=Boreoeutheria TaxID=1437010 RepID=A0A7J7ET90_DICBM\n+#=GS UniRef90_A0A7J7ET90/266-388 DE [subseq from] Uncharacterized protein n=4 Tax=Boreoeutheria TaxID=1437010 RepID=A0A7J7ET90_DICBM\n+#=GS UniRef90_A0A7J7ET90/388-417 DE [subseq from] Uncharacterized protein n=4 Tax=Boreoeutheria TaxID=1437010 RepID=A0A7J7ET90_DICBM\n+#=GS UniRef90_A0A7J7ET90/416-458 DE [subseq from] Uncharacterized protein n=4 Tax=Boreoeutheria TaxID=1437010 RepID=A0A7J7ET90_DICBM\n+#=GS UniRef90_A0A6F9C0F3/2-133 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A6F9C0F3/135-242 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A6F9C0F3/250-392 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A6F9C0F3/426-568 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A6F9C0F3/697-843 DE [subseq from] Uncharacterized protein n=1 Tax=Coregonus sp. 'balchen' TaxID=861768 RepID=A0A6F9C0F3_9TELE\n+#=GS UniRef90_A0A484GX98/1-145 DE [subseq from] Uncharacterized protein n=2 Tax=Delphinidae TaxID=9726 RepID=A0A484GX98_SOUCH\n+#=GS UniRef90_A0A484GX98/176-322 DE [subseq from] Uncharacterized protein n=2 Tax=Delphinidae TaxID=9726 RepID=A0A484GX98_SOUCH\n+#=GS UniRef90_A0A061I7G5/1-145 DE [subseq from] Olfactory receptor 52Z1-like protein n=1 Tax=Cricetulus griseus TaxID=10029 RepID=A0A061I7G5_CRIGR\n+#=GS UniRef90_A0A061I7G5/151-295 DE [subseq from] Olfactory receptor 52Z1-like protein n=1 Tax=Cricetulus griseus TaxID=10029 RepID=A0A061I7G5_CRIGR\n+#=GS UniRef90_A0A061I7G5/296-341 DE [subseq from] Olfactory receptor 52Z1-like protein n=1 Tax=Cricetulus griseus TaxID=10029 RepID=A0A061I7G5_CRIGR\n+#=GS UniRef90_A0A315V4X2/1-133 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A315V4X2/136-276 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A315V4X2/273-386 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A315V4X2/386-524 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_A0A315V4X2/525-664 DE [subseq from] Uncharacterized protein n=1 Tax=Gambusia affinis TaxID=33528 RepID=A0A315V4X2_GAMAF\n+#=GS UniRef90_B3RFA9/1-144 DE [subseq from] Uncharacterized protein SH_m009_jsmB0827r n=1 Tax=Sorex araneus TaxID=42254 RepID=B3RFA9_SORAR\n+#=GS UniRef90_B3RFA9/143-259 DE [subseq from] Uncharacterized protein SH_m009_jsmB0827r n=1 Tax=Sorex araneus TaxID=42254 RepID=B3RFA9_SORAR\n+#=GS UniRef90_B3RFA9/260-301 DE [subseq from] Uncharacterized protein SH_m009_jsmB0827r n=1 Tax=Sorex araneus TaxID=42254 RepID=B3RFA9_SORAR\n+#=GS UniRef90_A0A4U1FBG3/66-210 DE [subseq from] Uncharacterized protein n=1 Tax=Monodon monoceros T"..b' Q-T-----------I------------L---C--VFEE-------L--------L--A-D-E-FT-TE-MKLSWE---KFFD-A------------\n+UniRef90_A0A351SFX5/1-129 E-C-----------L------------I---W--TLNQ-------G--------L--G-D-E-FT-DE-LEAAWV---KTYT-A-VADVM------\n+UniRef90_UPI0019623B28/10-135 E-V-----------I------------V---T--VAAE-------K--------L--D---R-FG-PD-AKTALK---NVLK--------------\n+UniRef90_A0A091DYW0/64-173 G-V-----------I------------L---E--LIAE-------E--------C--A-N-D-FP-PE-AQRAWA---KLR---------------\n+UniRef90_UPI00083C382C/24-158 E-V-----------M------------L---D--VLRQ-------A--------L--G-R-Q-YT-PE-VAEAWR---KTL---------------\n+UniRef90_C3YSB9/38-151 N-V-----------L------------M---K--GLTA-------V--------L--G-K-D-FT-EE-VQGAW----------------------\n+UniRef90_A0A7L2H3J8/2-107 G-V-----------M------------L---E--VIAE-------E--------Y--A-N-D-FT-PE-AHGAWT---KM----------------\n+UniRef90_UPI00109FCD10/130-268 Q-T-----------I------------L---C--VFQE-------L--------L--A-D-E-FT-ND-VKLSWE---KFFD-A------------\n+UniRef90_UPI00159072DD/41-157 Q-T-----------I------------L---C--VFQE-------L--------L--E-D-E-FT-DD-MRLSWV---KFF---------------\n+UniRef90_UPI00109EFDB0/10-134 E-V-----------I------------V---A--VVAE-------K--------L--D---G-FG-PD-AQTALK---NVL---------------\n+UniRef90_A0A6P4YC67/34-149 N-V-----------L------------M---K--GLGA-------V--------L--G-A-D-FT-EE-VQGAWA---A-----------------\n+UniRef90_A0A1A8AJH4/9-133 E-V-----------I------------G---K--VMAE-------K--------A--G-L-D-AA----GQQALR---NVMA-V-VI---------\n+UniRef90_Q9PWI1/1-64 ------------------------------------------------------------------------------------------------\n+UniRef90_P04247/7-147 E-I-----------I------------I---E--VLKK-------R--------H--S-G-D-FG-AD-AQGAMS---KALE-L-FRNDIA-AKY-\n+UniRef90_Q2LC33/10-119 E-V-----------L------------V---K--VMAE-------K--------A--G-L-D-T--------------------------------\n+UniRef90_UPI001922BBBD/149-267 R-L-----------Q------------W---G--SRAA-------R--------P--G-D-E-LT-VE-THAAGD---EFLT-H-VATVLT-EKY-\n+UniRef90_A0A813QGG7/25-154 G-V-----------L------------L---D--TLSD-------G--------L--K-E-K-FT-PE-VKQAWL---KF----------------\n+UniRef90_S7Q7N2/84-223 D-S-----------I------------I---K--VLKS-------K--------L--G-G-D-FG-DD-AQGAMK---KALE-L-FRNDMA-AKY-\n+UniRef90_A0A7L2SQT0/2-75 ------------------------------------------------------------------------------------------------\n+UniRef90_C0A1I8/2-132 E-V-----------I------------V---K--HMAE-------K--------A--G-L-D-GA----GQEALR---KVMA-V-V----------\n+UniRef90_A0A3B3I7H0/21-101 N-G-----------I---------------------------------------------------------------------------------\n+UniRef90_A0A4W5MKD4/22-141 N-Q-----------A------------T---CFHITSH-------H--------H-----------------------------------------\n+UniRef90_G3UIL0/19-126 ------------------------------------------------------------------------------------------------\n+UniRef90_UPI0014555C47/35-142 G-V-----------I------------L---E--LIAE-------E--------C--A-N-D-FP-PE-AQRAWA---KLR---------------\n+UniRef90_A0A6P7NG34/11-121 V-V-----------I------------A---K--VLEE-------K--------A--G-L-D-A--------AG----------------------\n+UniRef90_P80017/12-156 K-V-----------L------------M---E--AIKA-------E--------L--G-V-G-FT-KQ-VHDAWA---KTFA-I-VQGVLI-TK--\n+UniRef90_A0A096M318/128-238 D-C-----------L------------T---I--VIAS-------K--------M--G-S-G-FT-PE-IQATFQ---KFLA-V-VVSALG-KQYH\n+UniRef90_A0A0P7UGB6/8-117 E-V-----------I------------V---K--VFAE-------K--------A--G--------------------------------------\n+#=GC RF x.x...........x............x...x..xxxx.......x........x..x.x.x.xx.xx.xxxxxx...xxxx.x.xxxxxx.xxxx\n+//\n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/msas/chain_id_map.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/msas/chain_id_map.json Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| @@ -0,0 +1,10 @@ +{ + "A": { + "description": "NP_000549.1 hemoglobin subunit alpha [Homo sapiens]", + "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR" + }, + "B": { + "description": "NP_000509.1 hemoglobin subunit beta [Homo sapiens]", + "sequence": "MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH" + } +} \ No newline at end of file |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/ranked_0.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/ranked_0.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 4.999 -14.657 8.781 1.00 67.59 N \n+ATOM 2 H MET A 1 4.287 -14.896 8.105 1.00 67.59 H \n+ATOM 3 H2 MET A 1 5.378 -15.517 9.151 1.00 67.59 H \n+ATOM 4 H3 MET A 1 5.729 -14.130 8.323 1.00 67.59 H \n+ATOM 5 CA MET A 1 4.375 -13.863 9.860 1.00 67.59 C \n+ATOM 6 HA MET A 1 5.102 -13.682 10.651 1.00 67.59 H \n+ATOM 7 C MET A 1 3.245 -14.681 10.438 1.00 67.59 C \n+ATOM 8 CB MET A 1 3.850 -12.513 9.343 1.00 67.59 C \n+ATOM 9 HB2 MET A 1 2.808 -12.372 9.633 1.00 67.59 H \n+ATOM 10 HB3 MET A 1 3.913 -12.464 8.256 1.00 67.59 H \n+ATOM 11 O MET A 1 2.464 -15.220 9.670 1.00 67.59 O \n+ATOM 12 CG MET A 1 4.678 -11.388 9.958 1.00 67.59 C \n+ATOM 13 HG2 MET A 1 4.607 -11.467 11.043 1.00 67.59 H \n+ATOM 14 HG3 MET A 1 5.725 -11.505 9.677 1.00 67.59 H \n+ATOM 15 SD MET A 1 4.142 -9.733 9.503 1.00 67.59 S \n+ATOM 16 CE MET A 1 4.799 -9.523 7.826 1.00 67.59 C \n+ATOM 17 HE1 MET A 1 5.885 -9.618 7.839 1.00 67.59 H \n+ATOM 18 HE2 MET A 1 4.368 -10.268 7.158 1.00 67.59 H \n+ATOM 19 HE3 MET A 1 4.535 -8.531 7.461 1.00 67.59 H \n+ATOM 20 N VAL A 2 3.190 -14.836 11.755 1.00 81.89 N \n+ATOM 21 H VAL A 2 3.825 -14.340 12.364 1.00 81.89 H \n+ATOM 22 CA VAL A 2 2.071 -15.538 12.392 1.00 81.89 C \n+ATOM 23 HA VAL A 2 1.695 -16.310 11.721 1.00 81.89 H \n+ATOM 24 C VAL A 2 0.952 -14.525 12.624 1.00 81.89 C \n+ATOM 25 CB VAL A 2 2.517 -16.241 13.688 1.00 81.89 C \n+ATOM 26 HB VAL A 2 2.878 -15.497 14.397 1.00 81.89 H \n+ATOM 27 O VAL A 2 1.205 -13.440 13.148 1.00 81.89 O \n+ATOM 28 CG1 VAL A 2 1.358 -17.014 14.327 1.00 81.89 C \n+ATOM 29 HG11 VAL A 2 0.562 -16.331 14.624 1.00 81.89 H \n+ATOM 30 HG12 VAL A 2 0.962 -17.753 13.631 1.00 81.89 H \n+ATOM 31 HG13 VAL A 2 1.709 -17.526 15.223 1.00 81.89 H \n+ATOM 32 CG2 VAL A 2 3.650 -17.239 13.402 1.00 81.89 C \n+ATOM 33 HG21 VAL A 2 4.540 -16.721 13.044 1.00 81.89 H \n+ATOM 34 HG22 VAL A 2 3.330 -17.972 12.660 1.00 81.89 H \n+ATOM 35 HG23 VAL A 2 3.916 -17.763 14.320 1.00 81.89 H \n+ATOM 36 N LEU A 3 -0.269 -14.863 12.208 1.00 96.41 N \n+ATOM 37 H LEU A 3 -0.403 -15.762 11.769 1.00 96.41 H \n+ATOM 38 CA LEU A 3 -1.456 -14.053 12.478 1.00 96.41 C \n+ATOM 39 HA LEU A 3 -1.199 -12.996 12.407 1.00 96.41 H \n+ATOM 40 C LEU A 3 -1.926 -14.315 13.908 1.00 96.41 C \n+ATOM 41 CB LEU A 3 -2.563 -14.363 11.453 1.00 96.41 C \n+ATOM 42 HB2 LEU A 3 -2.768 -15.433 11.477 1.00 96.41 H \n+ATOM 43 HB3 LEU A 3 -3.472 -13.843 11.753 1.00 96.41 H \n+ATOM 44 O LEU A 3 -2.304 -15.437 14.255 1.00 96.41 O \n+ATOM 45 CG LEU A 3 -2.224 -13.953 10.009 1.00 96.41 C \n+ATOM 46 HG LEU A 3 -1.272 -14.397 9.718 1.00 96.41 H \n+ATOM 47 CD1 LEU A 3 -3.303 -14.472 9.061 1.00 96.41 C \n+ATOM 48 HD11 LEU A 3 -3.030 -14.233 8.033 1.00 96.41 H \n+ATOM 49 HD12 LEU A 3 -4.264 -14.'..b' 24.725 11.426 -3.507 1.00 94.96 H \n+ATOM 4371 HD3 LYS B 145 25.178 12.240 -1.999 1.00 94.96 H \n+ATOM 4372 CE LYS B 145 24.195 13.514 -3.432 1.00 94.96 C \n+ATOM 4373 HE2 LYS B 145 23.918 13.362 -4.475 1.00 94.96 H \n+ATOM 4374 HE3 LYS B 145 23.368 14.018 -2.932 1.00 94.96 H \n+ATOM 4375 NZ LYS B 145 25.411 14.342 -3.298 1.00 94.96 N \n+ATOM 4376 HZ1 LYS B 145 25.523 14.565 -2.320 1.00 94.96 H \n+ATOM 4377 HZ2 LYS B 145 25.321 15.232 -3.768 1.00 94.96 H \n+ATOM 4378 HZ3 LYS B 145 26.243 13.845 -3.582 1.00 94.96 H \n+ATOM 4379 N TYR B 146 23.210 6.833 -1.453 1.00 94.48 N \n+ATOM 4380 H TYR B 146 22.440 6.801 -2.106 1.00 94.48 H \n+ATOM 4381 CA TYR B 146 23.626 5.571 -0.851 1.00 94.48 C \n+ATOM 4382 HA TYR B 146 24.091 5.765 0.116 1.00 94.48 H \n+ATOM 4383 C TYR B 146 24.669 4.903 -1.750 1.00 94.48 C \n+ATOM 4384 CB TYR B 146 22.408 4.669 -0.624 1.00 94.48 C \n+ATOM 4385 HB2 TYR B 146 22.775 3.664 -0.413 1.00 94.48 H \n+ATOM 4386 HB3 TYR B 146 21.826 4.602 -1.544 1.00 94.48 H \n+ATOM 4387 O TYR B 146 24.502 4.869 -2.974 1.00 94.48 O \n+ATOM 4388 CG TYR B 146 21.498 5.097 0.515 1.00 94.48 C \n+ATOM 4389 CD1 TYR B 146 21.384 4.268 1.645 1.00 94.48 C \n+ATOM 4390 HD1 TYR B 146 21.964 3.359 1.710 1.00 94.48 H \n+ATOM 4391 CD2 TYR B 146 20.777 6.309 0.466 1.00 94.48 C \n+ATOM 4392 HD2 TYR B 146 20.878 6.969 -0.383 1.00 94.48 H \n+ATOM 4393 CE1 TYR B 146 20.539 4.633 2.705 1.00 94.48 C \n+ATOM 4394 HE1 TYR B 146 20.482 3.998 3.577 1.00 94.48 H \n+ATOM 4395 CE2 TYR B 146 19.933 6.682 1.529 1.00 94.48 C \n+ATOM 4396 HE2 TYR B 146 19.390 7.615 1.506 1.00 94.48 H \n+ATOM 4397 OH TYR B 146 18.943 6.158 3.640 1.00 94.48 O \n+ATOM 4398 HH TYR B 146 18.839 5.397 4.216 1.00 94.48 H \n+ATOM 4399 CZ TYR B 146 19.800 5.832 2.642 1.00 94.48 C \n+ATOM 4400 N HIS B 147 25.726 4.372 -1.146 1.00 80.78 N \n+ATOM 4401 H HIS B 147 25.755 4.339 -0.137 1.00 80.78 H \n+ATOM 4402 CA HIS B 147 26.876 3.770 -1.817 1.00 80.78 C \n+ATOM 4403 HA HIS B 147 26.636 3.572 -2.862 1.00 80.78 H \n+ATOM 4404 C HIS B 147 27.219 2.411 -1.208 1.00 80.78 C \n+ATOM 4405 CB HIS B 147 28.060 4.749 -1.750 1.00 80.78 C \n+ATOM 4406 HB2 HIS B 147 28.248 5.012 -0.709 1.00 80.78 H \n+ATOM 4407 HB3 HIS B 147 28.948 4.246 -2.132 1.00 80.78 H \n+ATOM 4408 O HIS B 147 26.939 2.227 -0.001 1.00 80.78 O \n+ATOM 4409 CG HIS B 147 27.844 6.005 -2.557 1.00 80.78 C \n+ATOM 4410 CD2 HIS B 147 27.749 7.295 -2.104 1.00 80.78 C \n+ATOM 4411 HD2 HIS B 147 27.806 7.606 -1.072 1.00 80.78 H \n+ATOM 4412 ND1 HIS B 147 27.662 6.042 -3.916 1.00 80.78 N \n+ATOM 4413 HD1 HIS B 147 27.555 5.220 -4.493 1.00 80.78 H \n+ATOM 4414 CE1 HIS B 147 27.470 7.319 -4.279 1.00 80.78 C \n+ATOM 4415 HE1 HIS B 147 27.258 7.649 -5.285 1.00 80.78 H \n+ATOM 4416 NE2 HIS B 147 27.529 8.131 -3.213 1.00 80.78 N \n+ATOM 4417 OXT HIS B 147 27.736 1.584 -1.989 1.00 80.78 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/ranked_1.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/ranked_1.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 12.122 -10.122 -7.912 1.00 68.86 N \n+ATOM 2 H MET A 1 11.942 -9.258 -8.403 1.00 68.86 H \n+ATOM 3 H2 MET A 1 12.360 -9.912 -6.954 1.00 68.86 H \n+ATOM 4 H3 MET A 1 12.901 -10.583 -8.360 1.00 68.86 H \n+ATOM 5 CA MET A 1 10.911 -10.969 -7.977 1.00 68.86 C \n+ATOM 6 HA MET A 1 11.116 -11.934 -7.514 1.00 68.86 H \n+ATOM 7 C MET A 1 10.574 -11.207 -9.433 1.00 68.86 C \n+ATOM 8 CB MET A 1 9.721 -10.315 -7.256 1.00 68.86 C \n+ATOM 9 HB2 MET A 1 9.959 -9.288 -6.980 1.00 68.86 H \n+ATOM 10 HB3 MET A 1 8.849 -10.294 -7.909 1.00 68.86 H \n+ATOM 11 O MET A 1 10.541 -10.250 -10.196 1.00 68.86 O \n+ATOM 12 CG MET A 1 9.356 -11.108 -6.001 1.00 68.86 C \n+ATOM 13 HG2 MET A 1 9.108 -12.127 -6.298 1.00 68.86 H \n+ATOM 14 HG3 MET A 1 10.205 -11.143 -5.319 1.00 68.86 H \n+ATOM 15 SD MET A 1 7.930 -10.425 -5.138 1.00 68.86 S \n+ATOM 16 CE MET A 1 8.685 -9.182 -4.053 1.00 68.86 C \n+ATOM 17 HE1 MET A 1 7.927 -8.453 -3.764 1.00 68.86 H \n+ATOM 18 HE2 MET A 1 9.068 -9.665 -3.154 1.00 68.86 H \n+ATOM 19 HE3 MET A 1 9.494 -8.667 -4.569 1.00 68.86 H \n+ATOM 20 N VAL A 2 10.385 -12.462 -9.823 1.00 83.07 N \n+ATOM 21 H VAL A 2 10.375 -13.215 -9.149 1.00 83.07 H \n+ATOM 22 CA VAL A 2 9.994 -12.804 -11.193 1.00 83.07 C \n+ATOM 23 HA VAL A 2 10.358 -12.038 -11.878 1.00 83.07 H \n+ATOM 24 C VAL A 2 8.468 -12.819 -11.267 1.00 83.07 C \n+ATOM 25 CB VAL A 2 10.620 -14.143 -11.630 1.00 83.07 C \n+ATOM 26 HB VAL A 2 10.250 -14.940 -10.985 1.00 83.07 H \n+ATOM 27 O VAL A 2 7.812 -13.386 -10.390 1.00 83.07 O \n+ATOM 28 CG1 VAL A 2 10.265 -14.478 -13.082 1.00 83.07 C \n+ATOM 29 HG11 VAL A 2 10.748 -15.411 -13.373 1.00 83.07 H \n+ATOM 30 HG12 VAL A 2 10.600 -13.685 -13.750 1.00 83.07 H \n+ATOM 31 HG13 VAL A 2 9.189 -14.615 -13.190 1.00 83.07 H \n+ATOM 32 CG2 VAL A 2 12.152 -14.093 -11.518 1.00 83.07 C \n+ATOM 33 HG21 VAL A 2 12.461 -13.972 -10.480 1.00 83.07 H \n+ATOM 34 HG22 VAL A 2 12.550 -13.274 -12.117 1.00 83.07 H \n+ATOM 35 HG23 VAL A 2 12.576 -15.029 -11.882 1.00 83.07 H \n+ATOM 36 N LEU A 3 7.906 -12.177 -12.291 1.00 96.79 N \n+ATOM 37 H LEU A 3 8.501 -11.725 -12.970 1.00 96.79 H \n+ATOM 38 CA LEU A 3 6.470 -12.210 -12.564 1.00 96.79 C \n+ATOM 39 HA LEU A 3 5.920 -12.168 -11.624 1.00 96.79 H \n+ATOM 40 C LEU A 3 6.118 -13.532 -13.242 1.00 96.79 C \n+ATOM 41 CB LEU A 3 6.061 -11.006 -13.433 1.00 96.79 C \n+ATOM 42 HB2 LEU A 3 5.017 -11.124 -13.724 1.00 96.79 H \n+ATOM 43 HB3 LEU A 3 6.663 -11.013 -14.342 1.00 96.79 H \n+ATOM 44 O LEU A 3 6.607 -13.830 -14.335 1.00 96.79 O \n+ATOM 45 CG LEU A 3 6.221 -9.643 -12.739 1.00 96.79 C \n+ATOM 46 HG LEU A 3 7.241 -9.542 -12.369 1.00 96.79 H \n+ATOM 47 CD1 LEU A 3 5.963 -8.522 -13.742 1.00 96.79 C \n+ATOM 48 HD11 LEU A 3 6.127 -7.559 -13.258 1.00 96.79 H \n+ATOM 49 HD12 LEU A 3 6.651 -8.'..b' 9.507 -1.223 25.383 1.00 95.60 H \n+ATOM 4371 HD3 LYS B 145 9.245 -2.807 26.131 1.00 95.60 H \n+ATOM 4372 CE LYS B 145 7.750 -1.337 26.628 1.00 95.60 C \n+ATOM 4373 HE2 LYS B 145 6.744 -1.633 26.329 1.00 95.60 H \n+ATOM 4374 HE3 LYS B 145 7.814 -0.251 26.565 1.00 95.60 H \n+ATOM 4375 NZ LYS B 145 8.009 -1.828 27.998 1.00 95.60 N \n+ATOM 4376 HZ1 LYS B 145 7.792 -2.814 28.025 1.00 95.60 H \n+ATOM 4377 HZ2 LYS B 145 7.403 -1.402 28.684 1.00 95.60 H \n+ATOM 4378 HZ3 LYS B 145 8.983 -1.743 28.252 1.00 95.60 H \n+ATOM 4379 N TYR B 146 11.438 -3.170 20.905 1.00 94.88 N \n+ATOM 4380 H TYR B 146 11.054 -2.361 20.439 1.00 94.88 H \n+ATOM 4381 CA TYR B 146 12.482 -3.916 20.209 1.00 94.88 C \n+ATOM 4382 HA TYR B 146 12.443 -4.961 20.515 1.00 94.88 H \n+ATOM 4383 C TYR B 146 13.855 -3.368 20.608 1.00 94.88 C \n+ATOM 4384 CB TYR B 146 12.258 -3.855 18.692 1.00 94.88 C \n+ATOM 4385 HB2 TYR B 146 13.183 -4.167 18.207 1.00 94.88 H \n+ATOM 4386 HB3 TYR B 146 12.075 -2.823 18.391 1.00 94.88 H \n+ATOM 4387 O TYR B 146 14.034 -2.148 20.688 1.00 94.88 O \n+ATOM 4388 CG TYR B 146 11.130 -4.736 18.185 1.00 94.88 C \n+ATOM 4389 CD1 TYR B 146 11.422 -5.789 17.300 1.00 94.88 C \n+ATOM 4390 HD1 TYR B 146 12.441 -5.975 16.995 1.00 94.88 H \n+ATOM 4391 CD2 TYR B 146 9.803 -4.544 18.621 1.00 94.88 C \n+ATOM 4392 HD2 TYR B 146 9.568 -3.760 19.326 1.00 94.88 H \n+ATOM 4393 CE1 TYR B 146 10.396 -6.639 16.853 1.00 94.88 C \n+ATOM 4394 HE1 TYR B 146 10.633 -7.479 16.217 1.00 94.88 H \n+ATOM 4395 CE2 TYR B 146 8.776 -5.392 18.178 1.00 94.88 C \n+ATOM 4396 HE2 TYR B 146 7.770 -5.271 18.553 1.00 94.88 H \n+ATOM 4397 OH TYR B 146 8.064 -7.251 16.890 1.00 94.88 O \n+ATOM 4398 HH TYR B 146 7.249 -7.004 17.334 1.00 94.88 H \n+ATOM 4399 CZ TYR B 146 9.071 -6.437 17.284 1.00 94.88 C \n+ATOM 4400 N HIS B 147 14.808 -4.265 20.840 1.00 81.24 N \n+ATOM 4401 H HIS B 147 14.623 -5.242 20.662 1.00 81.24 H \n+ATOM 4402 CA HIS B 147 16.161 -3.970 21.310 1.00 81.24 C \n+ATOM 4403 HA HIS B 147 16.383 -2.913 21.164 1.00 81.24 H \n+ATOM 4404 C HIS B 147 17.206 -4.731 20.494 1.00 81.24 C \n+ATOM 4405 CB HIS B 147 16.250 -4.301 22.809 1.00 81.24 C \n+ATOM 4406 HB2 HIS B 147 15.958 -5.340 22.963 1.00 81.24 H \n+ATOM 4407 HB3 HIS B 147 17.287 -4.195 23.126 1.00 81.24 H \n+ATOM 4408 O HIS B 147 16.865 -5.822 19.984 1.00 81.24 O \n+ATOM 4409 CG HIS B 147 15.396 -3.405 23.670 1.00 81.24 C \n+ATOM 4410 CD2 HIS B 147 14.306 -3.749 24.427 1.00 81.24 C \n+ATOM 4411 HD2 HIS B 147 13.886 -4.740 24.511 1.00 81.24 H \n+ATOM 4412 ND1 HIS B 147 15.559 -2.049 23.794 1.00 81.24 N \n+ATOM 4413 HD1 HIS B 147 16.211 -1.507 23.245 1.00 81.24 H \n+ATOM 4414 CE1 HIS B 147 14.601 -1.584 24.609 1.00 81.24 C \n+ATOM 4415 HE1 HIS B 147 14.457 -0.543 24.861 1.00 81.24 H \n+ATOM 4416 NE2 HIS B 147 13.814 -2.582 25.038 1.00 81.24 N \n+ATOM 4417 OXT HIS B 147 18.319 -4.173 20.388 1.00 81.24 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/ranked_2.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/ranked_2.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 -12.058 9.891 8.144 1.00 69.17 N \n+ATOM 2 H MET A 1 -12.767 10.453 8.593 1.00 69.17 H \n+ATOM 3 H2 MET A 1 -12.193 9.907 7.143 1.00 69.17 H \n+ATOM 4 H3 MET A 1 -11.157 10.293 8.360 1.00 69.17 H \n+ATOM 5 CA MET A 1 -12.087 8.505 8.655 1.00 69.17 C \n+ATOM 6 HA MET A 1 -13.082 8.084 8.509 1.00 69.17 H \n+ATOM 7 C MET A 1 -11.782 8.580 10.144 1.00 69.17 C \n+ATOM 8 CB MET A 1 -11.058 7.651 7.894 1.00 69.17 C \n+ATOM 9 HB2 MET A 1 -10.103 7.646 8.420 1.00 69.17 H \n+ATOM 10 HB3 MET A 1 -10.891 8.081 6.906 1.00 69.17 H \n+ATOM 11 O MET A 1 -10.779 9.186 10.488 1.00 69.17 O \n+ATOM 12 CG MET A 1 -11.538 6.217 7.691 1.00 69.17 C \n+ATOM 13 HG2 MET A 1 -12.471 6.216 7.127 1.00 69.17 H \n+ATOM 14 HG3 MET A 1 -11.722 5.771 8.668 1.00 69.17 H \n+ATOM 15 SD MET A 1 -10.330 5.197 6.825 1.00 69.17 S \n+ATOM 16 CE MET A 1 -10.485 5.687 5.086 1.00 69.17 C \n+ATOM 17 HE1 MET A 1 -9.808 5.080 4.485 1.00 69.17 H \n+ATOM 18 HE2 MET A 1 -11.506 5.524 4.742 1.00 69.17 H \n+ATOM 19 HE3 MET A 1 -10.215 6.737 4.968 1.00 69.17 H \n+ATOM 20 N VAL A 2 -12.663 8.107 11.027 1.00 84.22 N \n+ATOM 21 H VAL A 2 -13.472 7.585 10.723 1.00 84.22 H \n+ATOM 22 CA VAL A 2 -12.425 8.189 12.482 1.00 84.22 C \n+ATOM 23 HA VAL A 2 -11.810 9.062 12.697 1.00 84.22 H \n+ATOM 24 C VAL A 2 -11.645 6.948 12.918 1.00 84.22 C \n+ATOM 25 CB VAL A 2 -13.740 8.364 13.272 1.00 84.22 C \n+ATOM 26 HB VAL A 2 -14.382 7.501 13.095 1.00 84.22 H \n+ATOM 27 O VAL A 2 -12.035 5.827 12.584 1.00 84.22 O \n+ATOM 28 CG1 VAL A 2 -13.487 8.491 14.779 1.00 84.22 C \n+ATOM 29 HG11 VAL A 2 -12.830 9.336 14.984 1.00 84.22 H \n+ATOM 30 HG12 VAL A 2 -14.432 8.644 15.300 1.00 84.22 H \n+ATOM 31 HG13 VAL A 2 -13.036 7.578 15.169 1.00 84.22 H \n+ATOM 32 CG2 VAL A 2 -14.485 9.629 12.819 1.00 84.22 C \n+ATOM 33 HG21 VAL A 2 -14.782 9.548 11.773 1.00 84.22 H \n+ATOM 34 HG22 VAL A 2 -15.389 9.755 13.414 1.00 84.22 H \n+ATOM 35 HG23 VAL A 2 -13.852 10.507 12.953 1.00 84.22 H \n+ATOM 36 N LEU A 3 -10.533 7.142 13.632 1.00 96.40 N \n+ATOM 37 H LEU A 3 -10.254 8.088 13.851 1.00 96.40 H \n+ATOM 38 CA LEU A 3 -9.761 6.049 14.224 1.00 96.40 C \n+ATOM 39 HA LEU A 3 -9.700 5.224 13.514 1.00 96.40 H \n+ATOM 40 C LEU A 3 -10.487 5.530 15.464 1.00 96.40 C \n+ATOM 41 CB LEU A 3 -8.335 6.514 14.570 1.00 96.40 C \n+ATOM 42 HB2 LEU A 3 -7.836 5.724 15.131 1.00 96.40 H \n+ATOM 43 HB3 LEU A 3 -8.402 7.389 15.217 1.00 96.40 H \n+ATOM 44 O LEU A 3 -10.699 6.272 16.427 1.00 96.40 O \n+ATOM 45 CG LEU A 3 -7.466 6.862 13.350 1.00 96.40 C \n+ATOM 46 HG LEU A 3 -7.983 7.599 12.734 1.00 96.40 H \n+ATOM 47 CD1 LEU A 3 -6.143 7.468 13.814 1.00 96.40 C \n+ATOM 48 HD11 LEU A 3 -6.332 8.350 14.426 1.00 96.40 H \n+ATOM 49 HD12 LEU A 3 -5.576 6.'..b' -13.667 -3.793 -24.261 1.00 94.04 H \n+ATOM 4371 HD3 LYS B 145 -12.047 -3.067 -24.218 1.00 94.04 H \n+ATOM 4372 CE LYS B 145 -12.102 -5.104 -24.925 1.00 94.04 C \n+ATOM 4373 HE2 LYS B 145 -12.613 -6.023 -24.637 1.00 94.04 H \n+ATOM 4374 HE3 LYS B 145 -11.035 -5.244 -24.752 1.00 94.04 H \n+ATOM 4375 NZ LYS B 145 -12.376 -4.797 -26.346 1.00 94.04 N \n+ATOM 4376 HZ1 LYS B 145 -12.061 -5.554 -26.937 1.00 94.04 H \n+ATOM 4377 HZ2 LYS B 145 -13.373 -4.691 -26.467 1.00 94.04 H \n+ATOM 4378 HZ3 LYS B 145 -11.928 -3.931 -26.608 1.00 94.04 H \n+ATOM 4379 N TYR B 146 -13.536 -0.258 -20.037 1.00 94.73 N \n+ATOM 4380 H TYR B 146 -12.552 -0.187 -19.819 1.00 94.73 H \n+ATOM 4381 CA TYR B 146 -14.431 0.715 -19.419 1.00 94.73 C \n+ATOM 4382 HA TYR B 146 -15.414 0.266 -19.274 1.00 94.73 H \n+ATOM 4383 C TYR B 146 -14.588 1.904 -20.376 1.00 94.73 C \n+ATOM 4384 CB TYR B 146 -13.892 1.134 -18.044 1.00 94.73 C \n+ATOM 4385 HB2 TYR B 146 -12.851 1.443 -18.139 1.00 94.73 H \n+ATOM 4386 HB3 TYR B 146 -14.453 2.012 -17.725 1.00 94.73 H \n+ATOM 4387 O TYR B 146 -13.586 2.462 -20.832 1.00 94.73 O \n+ATOM 4388 CG TYR B 146 -14.003 0.072 -16.958 1.00 94.73 C \n+ATOM 4389 CD1 TYR B 146 -14.849 0.299 -15.858 1.00 94.73 C \n+ATOM 4390 HD1 TYR B 146 -15.431 1.207 -15.802 1.00 94.73 H \n+ATOM 4391 CD2 TYR B 146 -13.288 -1.142 -17.043 1.00 94.73 C \n+ATOM 4392 HD2 TYR B 146 -12.655 -1.342 -17.895 1.00 94.73 H \n+ATOM 4393 CE1 TYR B 146 -14.966 -0.668 -14.845 1.00 94.73 C \n+ATOM 4394 HE1 TYR B 146 -15.641 -0.492 -14.020 1.00 94.73 H \n+ATOM 4395 CE2 TYR B 146 -13.405 -2.116 -16.034 1.00 94.73 C \n+ATOM 4396 HE2 TYR B 146 -12.873 -3.053 -16.104 1.00 94.73 H \n+ATOM 4397 OH TYR B 146 -14.307 -2.790 -13.931 1.00 94.73 O \n+ATOM 4398 HH TYR B 146 -14.745 -2.390 -13.176 1.00 94.73 H \n+ATOM 4399 CZ TYR B 146 -14.235 -1.873 -14.926 1.00 94.73 C \n+ATOM 4400 N HIS B 147 -15.830 2.261 -20.696 1.00 81.22 N \n+ATOM 4401 H HIS B 147 -16.602 1.823 -20.215 1.00 81.22 H \n+ATOM 4402 CA HIS B 147 -16.203 3.317 -21.640 1.00 81.22 C \n+ATOM 4403 HA HIS B 147 -15.316 3.868 -21.951 1.00 81.22 H \n+ATOM 4404 C HIS B 147 -17.115 4.352 -20.980 1.00 81.22 C \n+ATOM 4405 CB HIS B 147 -16.857 2.684 -22.879 1.00 81.22 C \n+ATOM 4406 HB2 HIS B 147 -17.305 3.478 -23.476 1.00 81.22 H \n+ATOM 4407 HB3 HIS B 147 -17.660 2.018 -22.561 1.00 81.22 H \n+ATOM 4408 O HIS B 147 -17.852 3.969 -20.044 1.00 81.22 O \n+ATOM 4409 CG HIS B 147 -15.889 1.931 -23.756 1.00 81.22 C \n+ATOM 4410 CD2 HIS B 147 -15.848 0.584 -24.007 1.00 81.22 C \n+ATOM 4411 HD2 HIS B 147 -16.515 -0.153 -23.584 1.00 81.22 H \n+ATOM 4412 ND1 HIS B 147 -14.854 2.501 -24.451 1.00 81.22 N \n+ATOM 4413 HD1 HIS B 147 -14.593 3.473 -24.375 1.00 81.22 H \n+ATOM 4414 CE1 HIS B 147 -14.204 1.529 -25.108 1.00 81.22 C \n+ATOM 4415 HE1 HIS B 147 -13.323 1.679 -25.715 1.00 81.22 H \n+ATOM 4416 NE2 HIS B 147 -14.775 0.335 -24.883 1.00 81.22 N \n+ATOM 4417 OXT HIS B 147 -17.032 5.513 -21.437 1.00 81.22 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/ranked_3.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/ranked_3.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 -9.690 7.634 -11.926 1.00 58.25 N \n+ATOM 2 H MET A 1 -9.701 8.191 -11.084 1.00 58.25 H \n+ATOM 3 H2 MET A 1 -10.178 8.148 -12.646 1.00 58.25 H \n+ATOM 4 H3 MET A 1 -8.732 7.478 -12.206 1.00 58.25 H \n+ATOM 5 CA MET A 1 -10.372 6.353 -11.648 1.00 58.25 C \n+ATOM 6 HA MET A 1 -10.462 5.774 -12.567 1.00 58.25 H \n+ATOM 7 C MET A 1 -11.759 6.682 -11.149 1.00 58.25 C \n+ATOM 8 CB MET A 1 -9.610 5.525 -10.600 1.00 58.25 C \n+ATOM 9 HB2 MET A 1 -10.263 5.276 -9.763 1.00 58.25 H \n+ATOM 10 HB3 MET A 1 -8.762 6.087 -10.210 1.00 58.25 H \n+ATOM 11 O MET A 1 -11.873 7.481 -10.233 1.00 58.25 O \n+ATOM 12 CG MET A 1 -9.108 4.224 -11.220 1.00 58.25 C \n+ATOM 13 HG2 MET A 1 -9.967 3.666 -11.593 1.00 58.25 H \n+ATOM 14 HG3 MET A 1 -8.446 4.440 -12.058 1.00 58.25 H \n+ATOM 15 SD MET A 1 -8.243 3.177 -10.038 1.00 58.25 S \n+ATOM 16 CE MET A 1 -6.500 3.563 -10.350 1.00 58.25 C \n+ATOM 17 HE1 MET A 1 -6.237 3.286 -11.371 1.00 58.25 H \n+ATOM 18 HE2 MET A 1 -6.319 4.627 -10.196 1.00 58.25 H \n+ATOM 19 HE3 MET A 1 -5.879 2.994 -9.659 1.00 58.25 H \n+ATOM 20 N VAL A 2 -12.799 6.151 -11.779 1.00 78.37 N \n+ATOM 21 H VAL A 2 -12.674 5.464 -12.509 1.00 78.37 H \n+ATOM 22 CA VAL A 2 -14.166 6.387 -11.307 1.00 78.37 C \n+ATOM 23 HA VAL A 2 -14.227 7.376 -10.853 1.00 78.37 H \n+ATOM 24 C VAL A 2 -14.479 5.354 -10.227 1.00 78.37 C \n+ATOM 25 CB VAL A 2 -15.175 6.366 -12.470 1.00 78.37 C \n+ATOM 26 HB VAL A 2 -15.169 5.381 -12.936 1.00 78.37 H \n+ATOM 27 O VAL A 2 -14.230 4.162 -10.420 1.00 78.37 O \n+ATOM 28 CG1 VAL A 2 -16.592 6.677 -11.979 1.00 78.37 C \n+ATOM 29 HG11 VAL A 2 -16.621 7.649 -11.487 1.00 78.37 H \n+ATOM 30 HG12 VAL A 2 -17.280 6.689 -12.824 1.00 78.37 H \n+ATOM 31 HG13 VAL A 2 -16.932 5.908 -11.284 1.00 78.37 H \n+ATOM 32 CG2 VAL A 2 -14.801 7.415 -13.529 1.00 78.37 C \n+ATOM 33 HG21 VAL A 2 -15.557 7.427 -14.314 1.00 78.37 H \n+ATOM 34 HG22 VAL A 2 -13.844 7.173 -13.993 1.00 78.37 H \n+ATOM 35 HG23 VAL A 2 -14.750 8.406 -13.079 1.00 78.37 H \n+ATOM 36 N LEU A 3 -14.992 5.813 -9.085 1.00 96.86 N \n+ATOM 37 H LEU A 3 -15.147 6.805 -8.984 1.00 96.86 H \n+ATOM 38 CA LEU A 3 -15.468 4.937 -8.018 1.00 96.86 C \n+ATOM 39 HA LEU A 3 -14.792 4.088 -7.915 1.00 96.86 H \n+ATOM 40 C LEU A 3 -16.839 4.385 -8.401 1.00 96.86 C \n+ATOM 41 CB LEU A 3 -15.520 5.696 -6.680 1.00 96.86 C \n+ATOM 42 HB2 LEU A 3 -16.136 6.586 -6.807 1.00 96.86 H \n+ATOM 43 HB3 LEU A 3 -16.002 5.061 -5.936 1.00 96.86 H \n+ATOM 44 O LEU A 3 -17.795 5.142 -8.583 1.00 96.86 O \n+ATOM 45 CG LEU A 3 -14.141 6.115 -6.141 1.00 96.86 C \n+ATOM 46 HG LEU A 3 -13.615 6.694 -6.899 1.00 96.86 H \n+ATOM 47 CD1 LEU A 3 -14.319 6.993 -4.904 1.00 96.86 C \n+ATOM 48 HD11 LEU A 3 -14.806 6.431 -4.108 1.00 96.86 H \n+ATOM 49 HD12 LEU A 3 -14.921 7.'..b' 21.594 -7.109 -15.490 1.00 94.41 H \n+ATOM 4371 HD3 LYS B 145 21.175 -8.384 -16.649 1.00 94.41 H \n+ATOM 4372 CE LYS B 145 22.147 -9.102 -14.868 1.00 94.41 C \n+ATOM 4373 HE2 LYS B 145 21.539 -9.900 -14.441 1.00 94.41 H \n+ATOM 4374 HE3 LYS B 145 22.656 -8.587 -14.053 1.00 94.41 H \n+ATOM 4375 NZ LYS B 145 23.096 -9.709 -15.823 1.00 94.41 N \n+ATOM 4376 HZ1 LYS B 145 22.571 -10.355 -16.394 1.00 94.41 H \n+ATOM 4377 HZ2 LYS B 145 23.509 -9.023 -16.438 1.00 94.41 H \n+ATOM 4378 HZ3 LYS B 145 23.793 -10.276 -15.362 1.00 94.41 H \n+ATOM 4379 N TYR B 146 17.162 -4.400 -16.630 1.00 93.82 N \n+ATOM 4380 H TYR B 146 17.204 -4.039 -15.688 1.00 93.82 H \n+ATOM 4381 CA TYR B 146 16.352 -3.666 -17.597 1.00 93.82 C \n+ATOM 4382 HA TYR B 146 15.989 -4.355 -18.360 1.00 93.82 H \n+ATOM 4383 C TYR B 146 17.222 -2.620 -18.291 1.00 93.82 C \n+ATOM 4384 CB TYR B 146 15.134 -3.030 -16.915 1.00 93.82 C \n+ATOM 4385 HB2 TYR B 146 14.727 -2.279 -17.592 1.00 93.82 H \n+ATOM 4386 HB3 TYR B 146 15.450 -2.505 -16.013 1.00 93.82 H \n+ATOM 4387 O TYR B 146 17.999 -1.920 -17.633 1.00 93.82 O \n+ATOM 4388 CG TYR B 146 14.028 -4.010 -16.568 1.00 93.82 C \n+ATOM 4389 CD1 TYR B 146 12.768 -3.885 -17.185 1.00 93.82 C \n+ATOM 4390 HD1 TYR B 146 12.593 -3.102 -17.907 1.00 93.82 H \n+ATOM 4391 CD2 TYR B 146 14.261 -5.071 -15.670 1.00 93.82 C \n+ATOM 4392 HD2 TYR B 146 15.231 -5.197 -15.214 1.00 93.82 H \n+ATOM 4393 CE1 TYR B 146 11.750 -4.811 -16.899 1.00 93.82 C \n+ATOM 4394 HE1 TYR B 146 10.797 -4.744 -17.403 1.00 93.82 H \n+ATOM 4395 CE2 TYR B 146 13.248 -5.999 -15.385 1.00 93.82 C \n+ATOM 4396 HE2 TYR B 146 13.447 -6.835 -14.730 1.00 93.82 H \n+ATOM 4397 OH TYR B 146 11.043 -6.789 -15.715 1.00 93.82 O \n+ATOM 4398 HH TYR B 146 11.399 -7.459 -15.127 1.00 93.82 H \n+ATOM 4399 CZ TYR B 146 11.989 -5.865 -15.996 1.00 93.82 C \n+ATOM 4400 N HIS B 147 17.076 -2.516 -19.605 1.00 78.51 N \n+ATOM 4401 H HIS B 147 16.354 -3.049 -20.070 1.00 78.51 H \n+ATOM 4402 CA HIS B 147 17.863 -1.654 -20.481 1.00 78.51 C \n+ATOM 4403 HA HIS B 147 18.355 -0.878 -19.896 1.00 78.51 H \n+ATOM 4404 C HIS B 147 16.958 -0.920 -21.470 1.00 78.51 C \n+ATOM 4405 CB HIS B 147 18.929 -2.509 -21.186 1.00 78.51 C \n+ATOM 4406 HB2 HIS B 147 19.438 -1.889 -21.924 1.00 78.51 H \n+ATOM 4407 HB3 HIS B 147 18.439 -3.325 -21.716 1.00 78.51 H \n+ATOM 4408 O HIS B 147 15.884 -1.473 -21.799 1.00 78.51 O \n+ATOM 4409 CG HIS B 147 19.964 -3.070 -20.241 1.00 78.51 C \n+ATOM 4410 CD2 HIS B 147 20.215 -4.385 -19.949 1.00 78.51 C \n+ATOM 4411 HD2 HIS B 147 19.689 -5.233 -20.362 1.00 78.51 H \n+ATOM 4412 ND1 HIS B 147 20.806 -2.318 -19.463 1.00 78.51 N \n+ATOM 4413 HD1 HIS B 147 20.741 -1.315 -19.370 1.00 78.51 H \n+ATOM 4414 CE1 HIS B 147 21.552 -3.153 -18.724 1.00 78.51 C \n+ATOM 4415 HE1 HIS B 147 22.274 -2.843 -17.983 1.00 78.51 H \n+ATOM 4416 NE2 HIS B 147 21.244 -4.431 -18.991 1.00 78.51 N \n+ATOM 4417 OXT HIS B 147 17.365 0.201 -21.842 1.00 78.51 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/ranked_4.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/ranked_4.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 -2.440 14.968 -8.662 1.00 69.85 N \n+ATOM 2 H MET A 1 -3.122 14.868 -7.924 1.00 69.85 H \n+ATOM 3 H2 MET A 1 -2.646 15.791 -9.210 1.00 69.85 H \n+ATOM 4 H3 MET A 1 -2.496 14.165 -9.273 1.00 69.85 H \n+ATOM 5 CA MET A 1 -1.072 15.039 -8.107 1.00 69.85 C \n+ATOM 6 HA MET A 1 -0.965 15.942 -7.506 1.00 69.85 H \n+ATOM 7 C MET A 1 -0.111 15.099 -9.288 1.00 69.85 C \n+ATOM 8 CB MET A 1 -0.834 13.809 -7.220 1.00 69.85 C \n+ATOM 9 HB2 MET A 1 -0.706 12.923 -7.842 1.00 69.85 H \n+ATOM 10 HB3 MET A 1 -1.712 13.656 -6.591 1.00 69.85 H \n+ATOM 11 O MET A 1 -0.246 14.264 -10.168 1.00 69.85 O \n+ATOM 12 CG MET A 1 0.370 13.962 -6.301 1.00 69.85 C \n+ATOM 13 HG2 MET A 1 0.236 14.826 -5.650 1.00 69.85 H \n+ATOM 14 HG3 MET A 1 1.260 14.114 -6.912 1.00 69.85 H \n+ATOM 15 SD MET A 1 0.620 12.494 -5.293 1.00 69.85 S \n+ATOM 16 CE MET A 1 -0.606 12.618 -3.964 1.00 69.85 C \n+ATOM 17 HE1 MET A 1 -1.613 12.599 -4.380 1.00 69.85 H \n+ATOM 18 HE2 MET A 1 -0.488 11.768 -3.293 1.00 69.85 H \n+ATOM 19 HE3 MET A 1 -0.454 13.539 -3.401 1.00 69.85 H \n+ATOM 20 N VAL A 2 0.754 16.112 -9.396 1.00 84.01 N \n+ATOM 21 H VAL A 2 0.870 16.773 -8.641 1.00 84.01 H \n+ATOM 22 CA VAL A 2 1.667 16.250 -10.550 1.00 84.01 C \n+ATOM 23 HA VAL A 2 1.187 15.837 -11.437 1.00 84.01 H \n+ATOM 24 C VAL A 2 2.936 15.436 -10.283 1.00 84.01 C \n+ATOM 25 CB VAL A 2 1.986 17.732 -10.856 1.00 84.01 C \n+ATOM 26 HB VAL A 2 2.472 18.178 -9.989 1.00 84.01 H \n+ATOM 27 O VAL A 2 3.526 15.558 -9.208 1.00 84.01 O \n+ATOM 28 CG1 VAL A 2 2.911 17.884 -12.071 1.00 84.01 C \n+ATOM 29 HG11 VAL A 2 3.084 18.941 -12.273 1.00 84.01 H \n+ATOM 30 HG12 VAL A 2 2.462 17.425 -12.952 1.00 84.01 H \n+ATOM 31 HG13 VAL A 2 3.878 17.421 -11.875 1.00 84.01 H \n+ATOM 32 CG2 VAL A 2 0.700 18.519 -11.153 1.00 84.01 C \n+ATOM 33 HG21 VAL A 2 0.178 18.079 -12.003 1.00 84.01 H \n+ATOM 34 HG22 VAL A 2 0.951 19.553 -11.393 1.00 84.01 H \n+ATOM 35 HG23 VAL A 2 0.043 18.527 -10.284 1.00 84.01 H \n+ATOM 36 N LEU A 3 3.344 14.594 -11.238 1.00 96.42 N \n+ATOM 37 H LEU A 3 2.801 14.520 -12.086 1.00 96.42 H \n+ATOM 38 CA LEU A 3 4.605 13.851 -11.168 1.00 96.42 C \n+ATOM 39 HA LEU A 3 4.739 13.463 -10.158 1.00 96.42 H \n+ATOM 40 C LEU A 3 5.773 14.794 -11.453 1.00 96.42 C \n+ATOM 41 CB LEU A 3 4.598 12.672 -12.159 1.00 96.42 C \n+ATOM 42 HB2 LEU A 3 5.599 12.243 -12.199 1.00 96.42 H \n+ATOM 43 HB3 LEU A 3 4.362 13.056 -13.152 1.00 96.42 H \n+ATOM 44 O LEU A 3 5.874 15.362 -12.544 1.00 96.42 O \n+ATOM 45 CG LEU A 3 3.607 11.550 -11.809 1.00 96.42 C \n+ATOM 46 HG LEU A 3 2.609 11.972 -11.689 1.00 96.42 H \n+ATOM 47 CD1 LEU A 3 3.567 10.531 -12.946 1.00 96.42 C \n+ATOM 48 HD11 LEU A 3 4.538 10.048 -13.055 1.00 96.42 H \n+ATOM 49 HD12 LEU A 3 2.812 9.'..b' -14.831 4.418 21.832 1.00 93.46 H \n+ATOM 4371 HD3 LYS B 145 -14.427 5.832 22.827 1.00 93.46 H \n+ATOM 4372 CE LYS B 145 -13.782 3.960 23.659 1.00 93.46 C \n+ATOM 4373 HE2 LYS B 145 -13.488 2.974 23.298 1.00 93.46 H \n+ATOM 4374 HE3 LYS B 145 -12.942 4.379 24.213 1.00 93.46 H \n+ATOM 4375 NZ LYS B 145 -14.973 3.870 24.533 1.00 93.46 N \n+ATOM 4376 HZ1 LYS B 145 -15.765 3.528 24.008 1.00 93.46 H \n+ATOM 4377 HZ2 LYS B 145 -14.785 3.271 25.324 1.00 93.46 H \n+ATOM 4378 HZ3 LYS B 145 -15.192 4.794 24.877 1.00 93.46 H \n+ATOM 4379 N TYR B 146 -14.216 7.323 17.488 1.00 93.98 N \n+ATOM 4380 H TYR B 146 -13.990 6.464 17.008 1.00 93.98 H \n+ATOM 4381 CA TYR B 146 -14.590 8.469 16.662 1.00 93.98 C \n+ATOM 4382 HA TYR B 146 -14.293 9.394 17.156 1.00 93.98 H \n+ATOM 4383 C TYR B 146 -16.116 8.460 16.518 1.00 93.98 C \n+ATOM 4384 CB TYR B 146 -13.881 8.398 15.300 1.00 93.98 C \n+ATOM 4385 HB2 TYR B 146 -14.343 9.143 14.652 1.00 93.98 H \n+ATOM 4386 HB3 TYR B 146 -14.070 7.427 14.841 1.00 93.98 H \n+ATOM 4387 O TYR B 146 -16.671 7.571 15.867 1.00 93.98 O \n+ATOM 4388 CG TYR B 146 -12.379 8.649 15.323 1.00 93.98 C \n+ATOM 4389 CD1 TYR B 146 -11.857 9.770 14.652 1.00 93.98 C \n+ATOM 4390 HD1 TYR B 146 -12.522 10.462 14.158 1.00 93.98 H \n+ATOM 4391 CD2 TYR B 146 -11.501 7.779 16.005 1.00 93.98 C \n+ATOM 4392 HD2 TYR B 146 -11.887 6.928 16.545 1.00 93.98 H \n+ATOM 4393 CE1 TYR B 146 -10.472 10.011 14.651 1.00 93.98 C \n+ATOM 4394 HE1 TYR B 146 -10.088 10.892 14.158 1.00 93.98 H \n+ATOM 4395 CE2 TYR B 146 -10.115 8.017 16.008 1.00 93.98 C \n+ATOM 4396 HE2 TYR B 146 -9.442 7.363 16.542 1.00 93.98 H \n+ATOM 4397 OH TYR B 146 -8.257 9.328 15.289 1.00 93.98 O \n+ATOM 4398 HH TYR B 146 -8.062 10.001 14.632 1.00 93.98 H \n+ATOM 4399 CZ TYR B 146 -9.597 9.129 15.321 1.00 93.98 C \n+ATOM 4400 N HIS B 147 -16.787 9.402 17.173 1.00 75.74 N \n+ATOM 4401 H HIS B 147 -16.270 10.140 17.628 1.00 75.74 H \n+ATOM 4402 CA HIS B 147 -18.242 9.556 17.196 1.00 75.74 C \n+ATOM 4403 HA HIS B 147 -18.702 8.864 16.491 1.00 75.74 H \n+ATOM 4404 C HIS B 147 -18.648 10.951 16.724 1.00 75.74 C \n+ATOM 4405 CB HIS B 147 -18.771 9.260 18.609 1.00 75.74 C \n+ATOM 4406 HB2 HIS B 147 -18.227 9.875 19.327 1.00 75.74 H \n+ATOM 4407 HB3 HIS B 147 -19.820 9.553 18.652 1.00 75.74 H \n+ATOM 4408 O HIS B 147 -17.832 11.884 16.893 1.00 75.74 O \n+ATOM 4409 CG HIS B 147 -18.673 7.810 19.006 1.00 75.74 C \n+ATOM 4410 CD2 HIS B 147 -17.969 7.277 20.051 1.00 75.74 C \n+ATOM 4411 HD2 HIS B 147 -17.355 7.839 20.738 1.00 75.74 H \n+ATOM 4412 ND1 HIS B 147 -19.293 6.771 18.363 1.00 75.74 N \n+ATOM 4413 HD1 HIS B 147 -19.788 6.865 17.488 1.00 75.74 H \n+ATOM 4414 CE1 HIS B 147 -18.972 5.635 19.003 1.00 75.74 C \n+ATOM 4415 HE1 HIS B 147 -19.280 4.647 18.694 1.00 75.74 H \n+ATOM 4416 NE2 HIS B 147 -18.179 5.887 20.059 1.00 75.74 N \n+ATOM 4417 OXT HIS B 147 -19.778 11.030 16.196 1.00 75.74 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/ranking_debug.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/ranking_debug.json Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| @@ -0,0 +1,16 @@ +{ + "iptm+ptm": { + "model_1_multimer": 0.9423862161455335, + "model_2_multimer": 0.9476096314476533, + "model_3_multimer": 0.9368871121192816, + "model_4_multimer": 0.9415689642388605, + "model_5_multimer": 0.9347000449933884 + }, + "order": [ + "model_2_multimer", + "model_1_multimer", + "model_4_multimer", + "model_3_multimer", + "model_5_multimer" + ] +} \ No newline at end of file |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/relaxed_model_1_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/relaxed_model_1_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 12.122 -10.122 -7.912 1.00 68.86 N \n+ATOM 2 H MET A 1 11.942 -9.258 -8.403 1.00 68.86 H \n+ATOM 3 H2 MET A 1 12.360 -9.912 -6.954 1.00 68.86 H \n+ATOM 4 H3 MET A 1 12.901 -10.583 -8.360 1.00 68.86 H \n+ATOM 5 CA MET A 1 10.911 -10.969 -7.977 1.00 68.86 C \n+ATOM 6 HA MET A 1 11.116 -11.934 -7.514 1.00 68.86 H \n+ATOM 7 C MET A 1 10.574 -11.207 -9.433 1.00 68.86 C \n+ATOM 8 CB MET A 1 9.721 -10.315 -7.256 1.00 68.86 C \n+ATOM 9 HB2 MET A 1 9.959 -9.288 -6.980 1.00 68.86 H \n+ATOM 10 HB3 MET A 1 8.849 -10.294 -7.909 1.00 68.86 H \n+ATOM 11 O MET A 1 10.541 -10.250 -10.196 1.00 68.86 O \n+ATOM 12 CG MET A 1 9.356 -11.108 -6.001 1.00 68.86 C \n+ATOM 13 HG2 MET A 1 9.108 -12.127 -6.298 1.00 68.86 H \n+ATOM 14 HG3 MET A 1 10.205 -11.143 -5.319 1.00 68.86 H \n+ATOM 15 SD MET A 1 7.930 -10.425 -5.138 1.00 68.86 S \n+ATOM 16 CE MET A 1 8.685 -9.182 -4.053 1.00 68.86 C \n+ATOM 17 HE1 MET A 1 7.927 -8.453 -3.764 1.00 68.86 H \n+ATOM 18 HE2 MET A 1 9.068 -9.665 -3.154 1.00 68.86 H \n+ATOM 19 HE3 MET A 1 9.494 -8.667 -4.569 1.00 68.86 H \n+ATOM 20 N VAL A 2 10.385 -12.462 -9.823 1.00 83.07 N \n+ATOM 21 H VAL A 2 10.375 -13.215 -9.149 1.00 83.07 H \n+ATOM 22 CA VAL A 2 9.994 -12.804 -11.193 1.00 83.07 C \n+ATOM 23 HA VAL A 2 10.358 -12.038 -11.878 1.00 83.07 H \n+ATOM 24 C VAL A 2 8.468 -12.819 -11.267 1.00 83.07 C \n+ATOM 25 CB VAL A 2 10.620 -14.143 -11.630 1.00 83.07 C \n+ATOM 26 HB VAL A 2 10.250 -14.940 -10.985 1.00 83.07 H \n+ATOM 27 O VAL A 2 7.812 -13.386 -10.390 1.00 83.07 O \n+ATOM 28 CG1 VAL A 2 10.265 -14.478 -13.082 1.00 83.07 C \n+ATOM 29 HG11 VAL A 2 10.748 -15.411 -13.373 1.00 83.07 H \n+ATOM 30 HG12 VAL A 2 10.600 -13.685 -13.750 1.00 83.07 H \n+ATOM 31 HG13 VAL A 2 9.189 -14.615 -13.190 1.00 83.07 H \n+ATOM 32 CG2 VAL A 2 12.152 -14.093 -11.518 1.00 83.07 C \n+ATOM 33 HG21 VAL A 2 12.461 -13.972 -10.480 1.00 83.07 H \n+ATOM 34 HG22 VAL A 2 12.550 -13.274 -12.117 1.00 83.07 H \n+ATOM 35 HG23 VAL A 2 12.576 -15.029 -11.882 1.00 83.07 H \n+ATOM 36 N LEU A 3 7.906 -12.177 -12.291 1.00 96.79 N \n+ATOM 37 H LEU A 3 8.501 -11.725 -12.970 1.00 96.79 H \n+ATOM 38 CA LEU A 3 6.470 -12.210 -12.564 1.00 96.79 C \n+ATOM 39 HA LEU A 3 5.920 -12.168 -11.624 1.00 96.79 H \n+ATOM 40 C LEU A 3 6.118 -13.532 -13.242 1.00 96.79 C \n+ATOM 41 CB LEU A 3 6.061 -11.006 -13.433 1.00 96.79 C \n+ATOM 42 HB2 LEU A 3 5.017 -11.124 -13.724 1.00 96.79 H \n+ATOM 43 HB3 LEU A 3 6.663 -11.013 -14.342 1.00 96.79 H \n+ATOM 44 O LEU A 3 6.607 -13.830 -14.335 1.00 96.79 O \n+ATOM 45 CG LEU A 3 6.221 -9.643 -12.739 1.00 96.79 C \n+ATOM 46 HG LEU A 3 7.241 -9.542 -12.369 1.00 96.79 H \n+ATOM 47 CD1 LEU A 3 5.963 -8.522 -13.742 1.00 96.79 C \n+ATOM 48 HD11 LEU A 3 6.127 -7.559 -13.258 1.00 96.79 H \n+ATOM 49 HD12 LEU A 3 6.651 -8.'..b' 9.507 -1.223 25.383 1.00 95.60 H \n+ATOM 4371 HD3 LYS B 145 9.245 -2.807 26.131 1.00 95.60 H \n+ATOM 4372 CE LYS B 145 7.750 -1.337 26.628 1.00 95.60 C \n+ATOM 4373 HE2 LYS B 145 6.744 -1.633 26.329 1.00 95.60 H \n+ATOM 4374 HE3 LYS B 145 7.814 -0.251 26.565 1.00 95.60 H \n+ATOM 4375 NZ LYS B 145 8.009 -1.828 27.998 1.00 95.60 N \n+ATOM 4376 HZ1 LYS B 145 7.792 -2.814 28.025 1.00 95.60 H \n+ATOM 4377 HZ2 LYS B 145 7.403 -1.402 28.684 1.00 95.60 H \n+ATOM 4378 HZ3 LYS B 145 8.983 -1.743 28.252 1.00 95.60 H \n+ATOM 4379 N TYR B 146 11.438 -3.170 20.905 1.00 94.88 N \n+ATOM 4380 H TYR B 146 11.054 -2.361 20.439 1.00 94.88 H \n+ATOM 4381 CA TYR B 146 12.482 -3.916 20.209 1.00 94.88 C \n+ATOM 4382 HA TYR B 146 12.443 -4.961 20.515 1.00 94.88 H \n+ATOM 4383 C TYR B 146 13.855 -3.368 20.608 1.00 94.88 C \n+ATOM 4384 CB TYR B 146 12.258 -3.855 18.692 1.00 94.88 C \n+ATOM 4385 HB2 TYR B 146 13.183 -4.167 18.207 1.00 94.88 H \n+ATOM 4386 HB3 TYR B 146 12.075 -2.823 18.391 1.00 94.88 H \n+ATOM 4387 O TYR B 146 14.034 -2.148 20.688 1.00 94.88 O \n+ATOM 4388 CG TYR B 146 11.130 -4.736 18.185 1.00 94.88 C \n+ATOM 4389 CD1 TYR B 146 11.422 -5.789 17.300 1.00 94.88 C \n+ATOM 4390 HD1 TYR B 146 12.441 -5.975 16.995 1.00 94.88 H \n+ATOM 4391 CD2 TYR B 146 9.803 -4.544 18.621 1.00 94.88 C \n+ATOM 4392 HD2 TYR B 146 9.568 -3.760 19.326 1.00 94.88 H \n+ATOM 4393 CE1 TYR B 146 10.396 -6.639 16.853 1.00 94.88 C \n+ATOM 4394 HE1 TYR B 146 10.633 -7.479 16.217 1.00 94.88 H \n+ATOM 4395 CE2 TYR B 146 8.776 -5.392 18.178 1.00 94.88 C \n+ATOM 4396 HE2 TYR B 146 7.770 -5.271 18.553 1.00 94.88 H \n+ATOM 4397 OH TYR B 146 8.064 -7.251 16.890 1.00 94.88 O \n+ATOM 4398 HH TYR B 146 7.249 -7.004 17.334 1.00 94.88 H \n+ATOM 4399 CZ TYR B 146 9.071 -6.437 17.284 1.00 94.88 C \n+ATOM 4400 N HIS B 147 14.808 -4.265 20.840 1.00 81.24 N \n+ATOM 4401 H HIS B 147 14.623 -5.242 20.662 1.00 81.24 H \n+ATOM 4402 CA HIS B 147 16.161 -3.970 21.310 1.00 81.24 C \n+ATOM 4403 HA HIS B 147 16.383 -2.913 21.164 1.00 81.24 H \n+ATOM 4404 C HIS B 147 17.206 -4.731 20.494 1.00 81.24 C \n+ATOM 4405 CB HIS B 147 16.250 -4.301 22.809 1.00 81.24 C \n+ATOM 4406 HB2 HIS B 147 15.958 -5.340 22.963 1.00 81.24 H \n+ATOM 4407 HB3 HIS B 147 17.287 -4.195 23.126 1.00 81.24 H \n+ATOM 4408 O HIS B 147 16.865 -5.822 19.984 1.00 81.24 O \n+ATOM 4409 CG HIS B 147 15.396 -3.405 23.670 1.00 81.24 C \n+ATOM 4410 CD2 HIS B 147 14.306 -3.749 24.427 1.00 81.24 C \n+ATOM 4411 HD2 HIS B 147 13.886 -4.740 24.511 1.00 81.24 H \n+ATOM 4412 ND1 HIS B 147 15.559 -2.049 23.794 1.00 81.24 N \n+ATOM 4413 HD1 HIS B 147 16.211 -1.507 23.245 1.00 81.24 H \n+ATOM 4414 CE1 HIS B 147 14.601 -1.584 24.609 1.00 81.24 C \n+ATOM 4415 HE1 HIS B 147 14.457 -0.543 24.861 1.00 81.24 H \n+ATOM 4416 NE2 HIS B 147 13.814 -2.582 25.038 1.00 81.24 N \n+ATOM 4417 OXT HIS B 147 18.319 -4.173 20.388 1.00 81.24 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/relaxed_model_2_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/relaxed_model_2_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 4.999 -14.657 8.781 1.00 67.59 N \n+ATOM 2 H MET A 1 4.287 -14.896 8.105 1.00 67.59 H \n+ATOM 3 H2 MET A 1 5.378 -15.517 9.151 1.00 67.59 H \n+ATOM 4 H3 MET A 1 5.729 -14.130 8.323 1.00 67.59 H \n+ATOM 5 CA MET A 1 4.375 -13.863 9.860 1.00 67.59 C \n+ATOM 6 HA MET A 1 5.102 -13.682 10.651 1.00 67.59 H \n+ATOM 7 C MET A 1 3.245 -14.681 10.438 1.00 67.59 C \n+ATOM 8 CB MET A 1 3.850 -12.513 9.343 1.00 67.59 C \n+ATOM 9 HB2 MET A 1 2.808 -12.372 9.633 1.00 67.59 H \n+ATOM 10 HB3 MET A 1 3.913 -12.464 8.256 1.00 67.59 H \n+ATOM 11 O MET A 1 2.464 -15.220 9.670 1.00 67.59 O \n+ATOM 12 CG MET A 1 4.678 -11.388 9.958 1.00 67.59 C \n+ATOM 13 HG2 MET A 1 4.607 -11.467 11.043 1.00 67.59 H \n+ATOM 14 HG3 MET A 1 5.725 -11.505 9.677 1.00 67.59 H \n+ATOM 15 SD MET A 1 4.142 -9.733 9.503 1.00 67.59 S \n+ATOM 16 CE MET A 1 4.799 -9.523 7.826 1.00 67.59 C \n+ATOM 17 HE1 MET A 1 5.885 -9.618 7.839 1.00 67.59 H \n+ATOM 18 HE2 MET A 1 4.368 -10.268 7.158 1.00 67.59 H \n+ATOM 19 HE3 MET A 1 4.535 -8.531 7.461 1.00 67.59 H \n+ATOM 20 N VAL A 2 3.190 -14.836 11.755 1.00 81.89 N \n+ATOM 21 H VAL A 2 3.825 -14.340 12.364 1.00 81.89 H \n+ATOM 22 CA VAL A 2 2.071 -15.538 12.392 1.00 81.89 C \n+ATOM 23 HA VAL A 2 1.695 -16.310 11.721 1.00 81.89 H \n+ATOM 24 C VAL A 2 0.952 -14.525 12.624 1.00 81.89 C \n+ATOM 25 CB VAL A 2 2.517 -16.241 13.688 1.00 81.89 C \n+ATOM 26 HB VAL A 2 2.878 -15.497 14.397 1.00 81.89 H \n+ATOM 27 O VAL A 2 1.205 -13.440 13.148 1.00 81.89 O \n+ATOM 28 CG1 VAL A 2 1.358 -17.014 14.327 1.00 81.89 C \n+ATOM 29 HG11 VAL A 2 0.562 -16.331 14.624 1.00 81.89 H \n+ATOM 30 HG12 VAL A 2 0.962 -17.753 13.631 1.00 81.89 H \n+ATOM 31 HG13 VAL A 2 1.709 -17.526 15.223 1.00 81.89 H \n+ATOM 32 CG2 VAL A 2 3.650 -17.239 13.402 1.00 81.89 C \n+ATOM 33 HG21 VAL A 2 4.540 -16.721 13.044 1.00 81.89 H \n+ATOM 34 HG22 VAL A 2 3.330 -17.972 12.660 1.00 81.89 H \n+ATOM 35 HG23 VAL A 2 3.916 -17.763 14.320 1.00 81.89 H \n+ATOM 36 N LEU A 3 -0.269 -14.863 12.208 1.00 96.41 N \n+ATOM 37 H LEU A 3 -0.403 -15.762 11.769 1.00 96.41 H \n+ATOM 38 CA LEU A 3 -1.456 -14.053 12.478 1.00 96.41 C \n+ATOM 39 HA LEU A 3 -1.199 -12.996 12.407 1.00 96.41 H \n+ATOM 40 C LEU A 3 -1.926 -14.315 13.908 1.00 96.41 C \n+ATOM 41 CB LEU A 3 -2.563 -14.363 11.453 1.00 96.41 C \n+ATOM 42 HB2 LEU A 3 -2.768 -15.433 11.477 1.00 96.41 H \n+ATOM 43 HB3 LEU A 3 -3.472 -13.843 11.753 1.00 96.41 H \n+ATOM 44 O LEU A 3 -2.304 -15.437 14.255 1.00 96.41 O \n+ATOM 45 CG LEU A 3 -2.224 -13.953 10.009 1.00 96.41 C \n+ATOM 46 HG LEU A 3 -1.272 -14.397 9.718 1.00 96.41 H \n+ATOM 47 CD1 LEU A 3 -3.303 -14.472 9.061 1.00 96.41 C \n+ATOM 48 HD11 LEU A 3 -3.030 -14.233 8.033 1.00 96.41 H \n+ATOM 49 HD12 LEU A 3 -4.264 -14.'..b' 24.725 11.426 -3.507 1.00 94.96 H \n+ATOM 4371 HD3 LYS B 145 25.178 12.240 -1.999 1.00 94.96 H \n+ATOM 4372 CE LYS B 145 24.195 13.514 -3.432 1.00 94.96 C \n+ATOM 4373 HE2 LYS B 145 23.918 13.362 -4.475 1.00 94.96 H \n+ATOM 4374 HE3 LYS B 145 23.368 14.018 -2.932 1.00 94.96 H \n+ATOM 4375 NZ LYS B 145 25.411 14.342 -3.298 1.00 94.96 N \n+ATOM 4376 HZ1 LYS B 145 25.523 14.565 -2.320 1.00 94.96 H \n+ATOM 4377 HZ2 LYS B 145 25.321 15.232 -3.768 1.00 94.96 H \n+ATOM 4378 HZ3 LYS B 145 26.243 13.845 -3.582 1.00 94.96 H \n+ATOM 4379 N TYR B 146 23.210 6.833 -1.453 1.00 94.48 N \n+ATOM 4380 H TYR B 146 22.440 6.801 -2.106 1.00 94.48 H \n+ATOM 4381 CA TYR B 146 23.626 5.571 -0.851 1.00 94.48 C \n+ATOM 4382 HA TYR B 146 24.091 5.765 0.116 1.00 94.48 H \n+ATOM 4383 C TYR B 146 24.669 4.903 -1.750 1.00 94.48 C \n+ATOM 4384 CB TYR B 146 22.408 4.669 -0.624 1.00 94.48 C \n+ATOM 4385 HB2 TYR B 146 22.775 3.664 -0.413 1.00 94.48 H \n+ATOM 4386 HB3 TYR B 146 21.826 4.602 -1.544 1.00 94.48 H \n+ATOM 4387 O TYR B 146 24.502 4.869 -2.974 1.00 94.48 O \n+ATOM 4388 CG TYR B 146 21.498 5.097 0.515 1.00 94.48 C \n+ATOM 4389 CD1 TYR B 146 21.384 4.268 1.645 1.00 94.48 C \n+ATOM 4390 HD1 TYR B 146 21.964 3.359 1.710 1.00 94.48 H \n+ATOM 4391 CD2 TYR B 146 20.777 6.309 0.466 1.00 94.48 C \n+ATOM 4392 HD2 TYR B 146 20.878 6.969 -0.383 1.00 94.48 H \n+ATOM 4393 CE1 TYR B 146 20.539 4.633 2.705 1.00 94.48 C \n+ATOM 4394 HE1 TYR B 146 20.482 3.998 3.577 1.00 94.48 H \n+ATOM 4395 CE2 TYR B 146 19.933 6.682 1.529 1.00 94.48 C \n+ATOM 4396 HE2 TYR B 146 19.390 7.615 1.506 1.00 94.48 H \n+ATOM 4397 OH TYR B 146 18.943 6.158 3.640 1.00 94.48 O \n+ATOM 4398 HH TYR B 146 18.839 5.397 4.216 1.00 94.48 H \n+ATOM 4399 CZ TYR B 146 19.800 5.832 2.642 1.00 94.48 C \n+ATOM 4400 N HIS B 147 25.726 4.372 -1.146 1.00 80.78 N \n+ATOM 4401 H HIS B 147 25.755 4.339 -0.137 1.00 80.78 H \n+ATOM 4402 CA HIS B 147 26.876 3.770 -1.817 1.00 80.78 C \n+ATOM 4403 HA HIS B 147 26.636 3.572 -2.862 1.00 80.78 H \n+ATOM 4404 C HIS B 147 27.219 2.411 -1.208 1.00 80.78 C \n+ATOM 4405 CB HIS B 147 28.060 4.749 -1.750 1.00 80.78 C \n+ATOM 4406 HB2 HIS B 147 28.248 5.012 -0.709 1.00 80.78 H \n+ATOM 4407 HB3 HIS B 147 28.948 4.246 -2.132 1.00 80.78 H \n+ATOM 4408 O HIS B 147 26.939 2.227 -0.001 1.00 80.78 O \n+ATOM 4409 CG HIS B 147 27.844 6.005 -2.557 1.00 80.78 C \n+ATOM 4410 CD2 HIS B 147 27.749 7.295 -2.104 1.00 80.78 C \n+ATOM 4411 HD2 HIS B 147 27.806 7.606 -1.072 1.00 80.78 H \n+ATOM 4412 ND1 HIS B 147 27.662 6.042 -3.916 1.00 80.78 N \n+ATOM 4413 HD1 HIS B 147 27.555 5.220 -4.493 1.00 80.78 H \n+ATOM 4414 CE1 HIS B 147 27.470 7.319 -4.279 1.00 80.78 C \n+ATOM 4415 HE1 HIS B 147 27.258 7.649 -5.285 1.00 80.78 H \n+ATOM 4416 NE2 HIS B 147 27.529 8.131 -3.213 1.00 80.78 N \n+ATOM 4417 OXT HIS B 147 27.736 1.584 -1.989 1.00 80.78 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/relaxed_model_3_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/relaxed_model_3_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 -9.690 7.634 -11.926 1.00 58.25 N \n+ATOM 2 H MET A 1 -9.701 8.191 -11.084 1.00 58.25 H \n+ATOM 3 H2 MET A 1 -10.178 8.148 -12.646 1.00 58.25 H \n+ATOM 4 H3 MET A 1 -8.732 7.478 -12.206 1.00 58.25 H \n+ATOM 5 CA MET A 1 -10.372 6.353 -11.648 1.00 58.25 C \n+ATOM 6 HA MET A 1 -10.462 5.774 -12.567 1.00 58.25 H \n+ATOM 7 C MET A 1 -11.759 6.682 -11.149 1.00 58.25 C \n+ATOM 8 CB MET A 1 -9.610 5.525 -10.600 1.00 58.25 C \n+ATOM 9 HB2 MET A 1 -10.263 5.276 -9.763 1.00 58.25 H \n+ATOM 10 HB3 MET A 1 -8.762 6.087 -10.210 1.00 58.25 H \n+ATOM 11 O MET A 1 -11.873 7.481 -10.233 1.00 58.25 O \n+ATOM 12 CG MET A 1 -9.108 4.224 -11.220 1.00 58.25 C \n+ATOM 13 HG2 MET A 1 -9.967 3.666 -11.593 1.00 58.25 H \n+ATOM 14 HG3 MET A 1 -8.446 4.440 -12.058 1.00 58.25 H \n+ATOM 15 SD MET A 1 -8.243 3.177 -10.038 1.00 58.25 S \n+ATOM 16 CE MET A 1 -6.500 3.563 -10.350 1.00 58.25 C \n+ATOM 17 HE1 MET A 1 -6.237 3.286 -11.371 1.00 58.25 H \n+ATOM 18 HE2 MET A 1 -6.319 4.627 -10.196 1.00 58.25 H \n+ATOM 19 HE3 MET A 1 -5.879 2.994 -9.659 1.00 58.25 H \n+ATOM 20 N VAL A 2 -12.799 6.151 -11.779 1.00 78.37 N \n+ATOM 21 H VAL A 2 -12.674 5.464 -12.509 1.00 78.37 H \n+ATOM 22 CA VAL A 2 -14.166 6.387 -11.307 1.00 78.37 C \n+ATOM 23 HA VAL A 2 -14.227 7.376 -10.853 1.00 78.37 H \n+ATOM 24 C VAL A 2 -14.479 5.354 -10.227 1.00 78.37 C \n+ATOM 25 CB VAL A 2 -15.175 6.366 -12.470 1.00 78.37 C \n+ATOM 26 HB VAL A 2 -15.169 5.381 -12.936 1.00 78.37 H \n+ATOM 27 O VAL A 2 -14.230 4.162 -10.420 1.00 78.37 O \n+ATOM 28 CG1 VAL A 2 -16.592 6.677 -11.979 1.00 78.37 C \n+ATOM 29 HG11 VAL A 2 -16.621 7.649 -11.487 1.00 78.37 H \n+ATOM 30 HG12 VAL A 2 -17.280 6.689 -12.824 1.00 78.37 H \n+ATOM 31 HG13 VAL A 2 -16.932 5.908 -11.284 1.00 78.37 H \n+ATOM 32 CG2 VAL A 2 -14.801 7.415 -13.529 1.00 78.37 C \n+ATOM 33 HG21 VAL A 2 -15.557 7.427 -14.314 1.00 78.37 H \n+ATOM 34 HG22 VAL A 2 -13.844 7.173 -13.993 1.00 78.37 H \n+ATOM 35 HG23 VAL A 2 -14.750 8.406 -13.079 1.00 78.37 H \n+ATOM 36 N LEU A 3 -14.992 5.813 -9.085 1.00 96.86 N \n+ATOM 37 H LEU A 3 -15.147 6.805 -8.984 1.00 96.86 H \n+ATOM 38 CA LEU A 3 -15.468 4.937 -8.018 1.00 96.86 C \n+ATOM 39 HA LEU A 3 -14.792 4.088 -7.915 1.00 96.86 H \n+ATOM 40 C LEU A 3 -16.839 4.385 -8.401 1.00 96.86 C \n+ATOM 41 CB LEU A 3 -15.520 5.696 -6.680 1.00 96.86 C \n+ATOM 42 HB2 LEU A 3 -16.136 6.586 -6.807 1.00 96.86 H \n+ATOM 43 HB3 LEU A 3 -16.002 5.061 -5.936 1.00 96.86 H \n+ATOM 44 O LEU A 3 -17.795 5.142 -8.583 1.00 96.86 O \n+ATOM 45 CG LEU A 3 -14.141 6.115 -6.141 1.00 96.86 C \n+ATOM 46 HG LEU A 3 -13.615 6.694 -6.899 1.00 96.86 H \n+ATOM 47 CD1 LEU A 3 -14.319 6.993 -4.904 1.00 96.86 C \n+ATOM 48 HD11 LEU A 3 -14.806 6.431 -4.108 1.00 96.86 H \n+ATOM 49 HD12 LEU A 3 -14.921 7.'..b' 21.594 -7.109 -15.490 1.00 94.41 H \n+ATOM 4371 HD3 LYS B 145 21.175 -8.384 -16.649 1.00 94.41 H \n+ATOM 4372 CE LYS B 145 22.147 -9.102 -14.868 1.00 94.41 C \n+ATOM 4373 HE2 LYS B 145 21.539 -9.900 -14.441 1.00 94.41 H \n+ATOM 4374 HE3 LYS B 145 22.656 -8.587 -14.053 1.00 94.41 H \n+ATOM 4375 NZ LYS B 145 23.096 -9.709 -15.823 1.00 94.41 N \n+ATOM 4376 HZ1 LYS B 145 22.571 -10.355 -16.394 1.00 94.41 H \n+ATOM 4377 HZ2 LYS B 145 23.509 -9.023 -16.438 1.00 94.41 H \n+ATOM 4378 HZ3 LYS B 145 23.793 -10.276 -15.362 1.00 94.41 H \n+ATOM 4379 N TYR B 146 17.162 -4.400 -16.630 1.00 93.82 N \n+ATOM 4380 H TYR B 146 17.204 -4.039 -15.688 1.00 93.82 H \n+ATOM 4381 CA TYR B 146 16.352 -3.666 -17.597 1.00 93.82 C \n+ATOM 4382 HA TYR B 146 15.989 -4.355 -18.360 1.00 93.82 H \n+ATOM 4383 C TYR B 146 17.222 -2.620 -18.291 1.00 93.82 C \n+ATOM 4384 CB TYR B 146 15.134 -3.030 -16.915 1.00 93.82 C \n+ATOM 4385 HB2 TYR B 146 14.727 -2.279 -17.592 1.00 93.82 H \n+ATOM 4386 HB3 TYR B 146 15.450 -2.505 -16.013 1.00 93.82 H \n+ATOM 4387 O TYR B 146 17.999 -1.920 -17.633 1.00 93.82 O \n+ATOM 4388 CG TYR B 146 14.028 -4.010 -16.568 1.00 93.82 C \n+ATOM 4389 CD1 TYR B 146 12.768 -3.885 -17.185 1.00 93.82 C \n+ATOM 4390 HD1 TYR B 146 12.593 -3.102 -17.907 1.00 93.82 H \n+ATOM 4391 CD2 TYR B 146 14.261 -5.071 -15.670 1.00 93.82 C \n+ATOM 4392 HD2 TYR B 146 15.231 -5.197 -15.214 1.00 93.82 H \n+ATOM 4393 CE1 TYR B 146 11.750 -4.811 -16.899 1.00 93.82 C \n+ATOM 4394 HE1 TYR B 146 10.797 -4.744 -17.403 1.00 93.82 H \n+ATOM 4395 CE2 TYR B 146 13.248 -5.999 -15.385 1.00 93.82 C \n+ATOM 4396 HE2 TYR B 146 13.447 -6.835 -14.730 1.00 93.82 H \n+ATOM 4397 OH TYR B 146 11.043 -6.789 -15.715 1.00 93.82 O \n+ATOM 4398 HH TYR B 146 11.399 -7.459 -15.127 1.00 93.82 H \n+ATOM 4399 CZ TYR B 146 11.989 -5.865 -15.996 1.00 93.82 C \n+ATOM 4400 N HIS B 147 17.076 -2.516 -19.605 1.00 78.51 N \n+ATOM 4401 H HIS B 147 16.354 -3.049 -20.070 1.00 78.51 H \n+ATOM 4402 CA HIS B 147 17.863 -1.654 -20.481 1.00 78.51 C \n+ATOM 4403 HA HIS B 147 18.355 -0.878 -19.896 1.00 78.51 H \n+ATOM 4404 C HIS B 147 16.958 -0.920 -21.470 1.00 78.51 C \n+ATOM 4405 CB HIS B 147 18.929 -2.509 -21.186 1.00 78.51 C \n+ATOM 4406 HB2 HIS B 147 19.438 -1.889 -21.924 1.00 78.51 H \n+ATOM 4407 HB3 HIS B 147 18.439 -3.325 -21.716 1.00 78.51 H \n+ATOM 4408 O HIS B 147 15.884 -1.473 -21.799 1.00 78.51 O \n+ATOM 4409 CG HIS B 147 19.964 -3.070 -20.241 1.00 78.51 C \n+ATOM 4410 CD2 HIS B 147 20.215 -4.385 -19.949 1.00 78.51 C \n+ATOM 4411 HD2 HIS B 147 19.689 -5.233 -20.362 1.00 78.51 H \n+ATOM 4412 ND1 HIS B 147 20.806 -2.318 -19.463 1.00 78.51 N \n+ATOM 4413 HD1 HIS B 147 20.741 -1.315 -19.370 1.00 78.51 H \n+ATOM 4414 CE1 HIS B 147 21.552 -3.153 -18.724 1.00 78.51 C \n+ATOM 4415 HE1 HIS B 147 22.274 -2.843 -17.983 1.00 78.51 H \n+ATOM 4416 NE2 HIS B 147 21.244 -4.431 -18.991 1.00 78.51 N \n+ATOM 4417 OXT HIS B 147 17.365 0.201 -21.842 1.00 78.51 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/relaxed_model_4_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/relaxed_model_4_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 -12.058 9.891 8.144 1.00 69.17 N \n+ATOM 2 H MET A 1 -12.767 10.453 8.593 1.00 69.17 H \n+ATOM 3 H2 MET A 1 -12.193 9.907 7.143 1.00 69.17 H \n+ATOM 4 H3 MET A 1 -11.157 10.293 8.360 1.00 69.17 H \n+ATOM 5 CA MET A 1 -12.087 8.505 8.655 1.00 69.17 C \n+ATOM 6 HA MET A 1 -13.082 8.084 8.509 1.00 69.17 H \n+ATOM 7 C MET A 1 -11.782 8.580 10.144 1.00 69.17 C \n+ATOM 8 CB MET A 1 -11.058 7.651 7.894 1.00 69.17 C \n+ATOM 9 HB2 MET A 1 -10.103 7.646 8.420 1.00 69.17 H \n+ATOM 10 HB3 MET A 1 -10.891 8.081 6.906 1.00 69.17 H \n+ATOM 11 O MET A 1 -10.779 9.186 10.488 1.00 69.17 O \n+ATOM 12 CG MET A 1 -11.538 6.217 7.691 1.00 69.17 C \n+ATOM 13 HG2 MET A 1 -12.471 6.216 7.127 1.00 69.17 H \n+ATOM 14 HG3 MET A 1 -11.722 5.771 8.668 1.00 69.17 H \n+ATOM 15 SD MET A 1 -10.330 5.197 6.825 1.00 69.17 S \n+ATOM 16 CE MET A 1 -10.485 5.687 5.086 1.00 69.17 C \n+ATOM 17 HE1 MET A 1 -9.808 5.080 4.485 1.00 69.17 H \n+ATOM 18 HE2 MET A 1 -11.506 5.524 4.742 1.00 69.17 H \n+ATOM 19 HE3 MET A 1 -10.215 6.737 4.968 1.00 69.17 H \n+ATOM 20 N VAL A 2 -12.663 8.107 11.027 1.00 84.22 N \n+ATOM 21 H VAL A 2 -13.472 7.585 10.723 1.00 84.22 H \n+ATOM 22 CA VAL A 2 -12.425 8.189 12.482 1.00 84.22 C \n+ATOM 23 HA VAL A 2 -11.810 9.062 12.697 1.00 84.22 H \n+ATOM 24 C VAL A 2 -11.645 6.948 12.918 1.00 84.22 C \n+ATOM 25 CB VAL A 2 -13.740 8.364 13.272 1.00 84.22 C \n+ATOM 26 HB VAL A 2 -14.382 7.501 13.095 1.00 84.22 H \n+ATOM 27 O VAL A 2 -12.035 5.827 12.584 1.00 84.22 O \n+ATOM 28 CG1 VAL A 2 -13.487 8.491 14.779 1.00 84.22 C \n+ATOM 29 HG11 VAL A 2 -12.830 9.336 14.984 1.00 84.22 H \n+ATOM 30 HG12 VAL A 2 -14.432 8.644 15.300 1.00 84.22 H \n+ATOM 31 HG13 VAL A 2 -13.036 7.578 15.169 1.00 84.22 H \n+ATOM 32 CG2 VAL A 2 -14.485 9.629 12.819 1.00 84.22 C \n+ATOM 33 HG21 VAL A 2 -14.782 9.548 11.773 1.00 84.22 H \n+ATOM 34 HG22 VAL A 2 -15.389 9.755 13.414 1.00 84.22 H \n+ATOM 35 HG23 VAL A 2 -13.852 10.507 12.953 1.00 84.22 H \n+ATOM 36 N LEU A 3 -10.533 7.142 13.632 1.00 96.40 N \n+ATOM 37 H LEU A 3 -10.254 8.088 13.851 1.00 96.40 H \n+ATOM 38 CA LEU A 3 -9.761 6.049 14.224 1.00 96.40 C \n+ATOM 39 HA LEU A 3 -9.700 5.224 13.514 1.00 96.40 H \n+ATOM 40 C LEU A 3 -10.487 5.530 15.464 1.00 96.40 C \n+ATOM 41 CB LEU A 3 -8.335 6.514 14.570 1.00 96.40 C \n+ATOM 42 HB2 LEU A 3 -7.836 5.724 15.131 1.00 96.40 H \n+ATOM 43 HB3 LEU A 3 -8.402 7.389 15.217 1.00 96.40 H \n+ATOM 44 O LEU A 3 -10.699 6.272 16.427 1.00 96.40 O \n+ATOM 45 CG LEU A 3 -7.466 6.862 13.350 1.00 96.40 C \n+ATOM 46 HG LEU A 3 -7.983 7.599 12.734 1.00 96.40 H \n+ATOM 47 CD1 LEU A 3 -6.143 7.468 13.814 1.00 96.40 C \n+ATOM 48 HD11 LEU A 3 -6.332 8.350 14.426 1.00 96.40 H \n+ATOM 49 HD12 LEU A 3 -5.576 6.'..b' -13.667 -3.793 -24.261 1.00 94.04 H \n+ATOM 4371 HD3 LYS B 145 -12.047 -3.067 -24.218 1.00 94.04 H \n+ATOM 4372 CE LYS B 145 -12.102 -5.104 -24.925 1.00 94.04 C \n+ATOM 4373 HE2 LYS B 145 -12.613 -6.023 -24.637 1.00 94.04 H \n+ATOM 4374 HE3 LYS B 145 -11.035 -5.244 -24.752 1.00 94.04 H \n+ATOM 4375 NZ LYS B 145 -12.376 -4.797 -26.346 1.00 94.04 N \n+ATOM 4376 HZ1 LYS B 145 -12.061 -5.554 -26.937 1.00 94.04 H \n+ATOM 4377 HZ2 LYS B 145 -13.373 -4.691 -26.467 1.00 94.04 H \n+ATOM 4378 HZ3 LYS B 145 -11.928 -3.931 -26.608 1.00 94.04 H \n+ATOM 4379 N TYR B 146 -13.536 -0.258 -20.037 1.00 94.73 N \n+ATOM 4380 H TYR B 146 -12.552 -0.187 -19.819 1.00 94.73 H \n+ATOM 4381 CA TYR B 146 -14.431 0.715 -19.419 1.00 94.73 C \n+ATOM 4382 HA TYR B 146 -15.414 0.266 -19.274 1.00 94.73 H \n+ATOM 4383 C TYR B 146 -14.588 1.904 -20.376 1.00 94.73 C \n+ATOM 4384 CB TYR B 146 -13.892 1.134 -18.044 1.00 94.73 C \n+ATOM 4385 HB2 TYR B 146 -12.851 1.443 -18.139 1.00 94.73 H \n+ATOM 4386 HB3 TYR B 146 -14.453 2.012 -17.725 1.00 94.73 H \n+ATOM 4387 O TYR B 146 -13.586 2.462 -20.832 1.00 94.73 O \n+ATOM 4388 CG TYR B 146 -14.003 0.072 -16.958 1.00 94.73 C \n+ATOM 4389 CD1 TYR B 146 -14.849 0.299 -15.858 1.00 94.73 C \n+ATOM 4390 HD1 TYR B 146 -15.431 1.207 -15.802 1.00 94.73 H \n+ATOM 4391 CD2 TYR B 146 -13.288 -1.142 -17.043 1.00 94.73 C \n+ATOM 4392 HD2 TYR B 146 -12.655 -1.342 -17.895 1.00 94.73 H \n+ATOM 4393 CE1 TYR B 146 -14.966 -0.668 -14.845 1.00 94.73 C \n+ATOM 4394 HE1 TYR B 146 -15.641 -0.492 -14.020 1.00 94.73 H \n+ATOM 4395 CE2 TYR B 146 -13.405 -2.116 -16.034 1.00 94.73 C \n+ATOM 4396 HE2 TYR B 146 -12.873 -3.053 -16.104 1.00 94.73 H \n+ATOM 4397 OH TYR B 146 -14.307 -2.790 -13.931 1.00 94.73 O \n+ATOM 4398 HH TYR B 146 -14.745 -2.390 -13.176 1.00 94.73 H \n+ATOM 4399 CZ TYR B 146 -14.235 -1.873 -14.926 1.00 94.73 C \n+ATOM 4400 N HIS B 147 -15.830 2.261 -20.696 1.00 81.22 N \n+ATOM 4401 H HIS B 147 -16.602 1.823 -20.215 1.00 81.22 H \n+ATOM 4402 CA HIS B 147 -16.203 3.317 -21.640 1.00 81.22 C \n+ATOM 4403 HA HIS B 147 -15.316 3.868 -21.951 1.00 81.22 H \n+ATOM 4404 C HIS B 147 -17.115 4.352 -20.980 1.00 81.22 C \n+ATOM 4405 CB HIS B 147 -16.857 2.684 -22.879 1.00 81.22 C \n+ATOM 4406 HB2 HIS B 147 -17.305 3.478 -23.476 1.00 81.22 H \n+ATOM 4407 HB3 HIS B 147 -17.660 2.018 -22.561 1.00 81.22 H \n+ATOM 4408 O HIS B 147 -17.852 3.969 -20.044 1.00 81.22 O \n+ATOM 4409 CG HIS B 147 -15.889 1.931 -23.756 1.00 81.22 C \n+ATOM 4410 CD2 HIS B 147 -15.848 0.584 -24.007 1.00 81.22 C \n+ATOM 4411 HD2 HIS B 147 -16.515 -0.153 -23.584 1.00 81.22 H \n+ATOM 4412 ND1 HIS B 147 -14.854 2.501 -24.451 1.00 81.22 N \n+ATOM 4413 HD1 HIS B 147 -14.593 3.473 -24.375 1.00 81.22 H \n+ATOM 4414 CE1 HIS B 147 -14.204 1.529 -25.108 1.00 81.22 C \n+ATOM 4415 HE1 HIS B 147 -13.323 1.679 -25.715 1.00 81.22 H \n+ATOM 4416 NE2 HIS B 147 -14.775 0.335 -24.883 1.00 81.22 N \n+ATOM 4417 OXT HIS B 147 -17.032 5.513 -21.437 1.00 81.22 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/relaxed_model_5_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/relaxed_model_5_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,4420 @@\n+ATOM 1 N MET A 1 -2.440 14.968 -8.662 1.00 69.85 N \n+ATOM 2 H MET A 1 -3.122 14.868 -7.924 1.00 69.85 H \n+ATOM 3 H2 MET A 1 -2.646 15.791 -9.210 1.00 69.85 H \n+ATOM 4 H3 MET A 1 -2.496 14.165 -9.273 1.00 69.85 H \n+ATOM 5 CA MET A 1 -1.072 15.039 -8.107 1.00 69.85 C \n+ATOM 6 HA MET A 1 -0.965 15.942 -7.506 1.00 69.85 H \n+ATOM 7 C MET A 1 -0.111 15.099 -9.288 1.00 69.85 C \n+ATOM 8 CB MET A 1 -0.834 13.809 -7.220 1.00 69.85 C \n+ATOM 9 HB2 MET A 1 -0.706 12.923 -7.842 1.00 69.85 H \n+ATOM 10 HB3 MET A 1 -1.712 13.656 -6.591 1.00 69.85 H \n+ATOM 11 O MET A 1 -0.246 14.264 -10.168 1.00 69.85 O \n+ATOM 12 CG MET A 1 0.370 13.962 -6.301 1.00 69.85 C \n+ATOM 13 HG2 MET A 1 0.236 14.826 -5.650 1.00 69.85 H \n+ATOM 14 HG3 MET A 1 1.260 14.114 -6.912 1.00 69.85 H \n+ATOM 15 SD MET A 1 0.620 12.494 -5.293 1.00 69.85 S \n+ATOM 16 CE MET A 1 -0.606 12.618 -3.964 1.00 69.85 C \n+ATOM 17 HE1 MET A 1 -1.613 12.599 -4.380 1.00 69.85 H \n+ATOM 18 HE2 MET A 1 -0.488 11.768 -3.293 1.00 69.85 H \n+ATOM 19 HE3 MET A 1 -0.454 13.539 -3.401 1.00 69.85 H \n+ATOM 20 N VAL A 2 0.754 16.112 -9.396 1.00 84.01 N \n+ATOM 21 H VAL A 2 0.870 16.773 -8.641 1.00 84.01 H \n+ATOM 22 CA VAL A 2 1.667 16.250 -10.550 1.00 84.01 C \n+ATOM 23 HA VAL A 2 1.187 15.837 -11.437 1.00 84.01 H \n+ATOM 24 C VAL A 2 2.936 15.436 -10.283 1.00 84.01 C \n+ATOM 25 CB VAL A 2 1.986 17.732 -10.856 1.00 84.01 C \n+ATOM 26 HB VAL A 2 2.472 18.178 -9.989 1.00 84.01 H \n+ATOM 27 O VAL A 2 3.526 15.558 -9.208 1.00 84.01 O \n+ATOM 28 CG1 VAL A 2 2.911 17.884 -12.071 1.00 84.01 C \n+ATOM 29 HG11 VAL A 2 3.084 18.941 -12.273 1.00 84.01 H \n+ATOM 30 HG12 VAL A 2 2.462 17.425 -12.952 1.00 84.01 H \n+ATOM 31 HG13 VAL A 2 3.878 17.421 -11.875 1.00 84.01 H \n+ATOM 32 CG2 VAL A 2 0.700 18.519 -11.153 1.00 84.01 C \n+ATOM 33 HG21 VAL A 2 0.178 18.079 -12.003 1.00 84.01 H \n+ATOM 34 HG22 VAL A 2 0.951 19.553 -11.393 1.00 84.01 H \n+ATOM 35 HG23 VAL A 2 0.043 18.527 -10.284 1.00 84.01 H \n+ATOM 36 N LEU A 3 3.344 14.594 -11.238 1.00 96.42 N \n+ATOM 37 H LEU A 3 2.801 14.520 -12.086 1.00 96.42 H \n+ATOM 38 CA LEU A 3 4.605 13.851 -11.168 1.00 96.42 C \n+ATOM 39 HA LEU A 3 4.739 13.463 -10.158 1.00 96.42 H \n+ATOM 40 C LEU A 3 5.773 14.794 -11.453 1.00 96.42 C \n+ATOM 41 CB LEU A 3 4.598 12.672 -12.159 1.00 96.42 C \n+ATOM 42 HB2 LEU A 3 5.599 12.243 -12.199 1.00 96.42 H \n+ATOM 43 HB3 LEU A 3 4.362 13.056 -13.152 1.00 96.42 H \n+ATOM 44 O LEU A 3 5.874 15.362 -12.544 1.00 96.42 O \n+ATOM 45 CG LEU A 3 3.607 11.550 -11.809 1.00 96.42 C \n+ATOM 46 HG LEU A 3 2.609 11.972 -11.689 1.00 96.42 H \n+ATOM 47 CD1 LEU A 3 3.567 10.531 -12.946 1.00 96.42 C \n+ATOM 48 HD11 LEU A 3 4.538 10.048 -13.055 1.00 96.42 H \n+ATOM 49 HD12 LEU A 3 2.812 9.'..b' -14.831 4.418 21.832 1.00 93.46 H \n+ATOM 4371 HD3 LYS B 145 -14.427 5.832 22.827 1.00 93.46 H \n+ATOM 4372 CE LYS B 145 -13.782 3.960 23.659 1.00 93.46 C \n+ATOM 4373 HE2 LYS B 145 -13.488 2.974 23.298 1.00 93.46 H \n+ATOM 4374 HE3 LYS B 145 -12.942 4.379 24.213 1.00 93.46 H \n+ATOM 4375 NZ LYS B 145 -14.973 3.870 24.533 1.00 93.46 N \n+ATOM 4376 HZ1 LYS B 145 -15.765 3.528 24.008 1.00 93.46 H \n+ATOM 4377 HZ2 LYS B 145 -14.785 3.271 25.324 1.00 93.46 H \n+ATOM 4378 HZ3 LYS B 145 -15.192 4.794 24.877 1.00 93.46 H \n+ATOM 4379 N TYR B 146 -14.216 7.323 17.488 1.00 93.98 N \n+ATOM 4380 H TYR B 146 -13.990 6.464 17.008 1.00 93.98 H \n+ATOM 4381 CA TYR B 146 -14.590 8.469 16.662 1.00 93.98 C \n+ATOM 4382 HA TYR B 146 -14.293 9.394 17.156 1.00 93.98 H \n+ATOM 4383 C TYR B 146 -16.116 8.460 16.518 1.00 93.98 C \n+ATOM 4384 CB TYR B 146 -13.881 8.398 15.300 1.00 93.98 C \n+ATOM 4385 HB2 TYR B 146 -14.343 9.143 14.652 1.00 93.98 H \n+ATOM 4386 HB3 TYR B 146 -14.070 7.427 14.841 1.00 93.98 H \n+ATOM 4387 O TYR B 146 -16.671 7.571 15.867 1.00 93.98 O \n+ATOM 4388 CG TYR B 146 -12.379 8.649 15.323 1.00 93.98 C \n+ATOM 4389 CD1 TYR B 146 -11.857 9.770 14.652 1.00 93.98 C \n+ATOM 4390 HD1 TYR B 146 -12.522 10.462 14.158 1.00 93.98 H \n+ATOM 4391 CD2 TYR B 146 -11.501 7.779 16.005 1.00 93.98 C \n+ATOM 4392 HD2 TYR B 146 -11.887 6.928 16.545 1.00 93.98 H \n+ATOM 4393 CE1 TYR B 146 -10.472 10.011 14.651 1.00 93.98 C \n+ATOM 4394 HE1 TYR B 146 -10.088 10.892 14.158 1.00 93.98 H \n+ATOM 4395 CE2 TYR B 146 -10.115 8.017 16.008 1.00 93.98 C \n+ATOM 4396 HE2 TYR B 146 -9.442 7.363 16.542 1.00 93.98 H \n+ATOM 4397 OH TYR B 146 -8.257 9.328 15.289 1.00 93.98 O \n+ATOM 4398 HH TYR B 146 -8.062 10.001 14.632 1.00 93.98 H \n+ATOM 4399 CZ TYR B 146 -9.597 9.129 15.321 1.00 93.98 C \n+ATOM 4400 N HIS B 147 -16.787 9.402 17.173 1.00 75.74 N \n+ATOM 4401 H HIS B 147 -16.270 10.140 17.628 1.00 75.74 H \n+ATOM 4402 CA HIS B 147 -18.242 9.556 17.196 1.00 75.74 C \n+ATOM 4403 HA HIS B 147 -18.702 8.864 16.491 1.00 75.74 H \n+ATOM 4404 C HIS B 147 -18.648 10.951 16.724 1.00 75.74 C \n+ATOM 4405 CB HIS B 147 -18.771 9.260 18.609 1.00 75.74 C \n+ATOM 4406 HB2 HIS B 147 -18.227 9.875 19.327 1.00 75.74 H \n+ATOM 4407 HB3 HIS B 147 -19.820 9.553 18.652 1.00 75.74 H \n+ATOM 4408 O HIS B 147 -17.832 11.884 16.893 1.00 75.74 O \n+ATOM 4409 CG HIS B 147 -18.673 7.810 19.006 1.00 75.74 C \n+ATOM 4410 CD2 HIS B 147 -17.969 7.277 20.051 1.00 75.74 C \n+ATOM 4411 HD2 HIS B 147 -17.355 7.839 20.738 1.00 75.74 H \n+ATOM 4412 ND1 HIS B 147 -19.293 6.771 18.363 1.00 75.74 N \n+ATOM 4413 HD1 HIS B 147 -19.788 6.865 17.488 1.00 75.74 H \n+ATOM 4414 CE1 HIS B 147 -18.972 5.635 19.003 1.00 75.74 C \n+ATOM 4415 HE1 HIS B 147 -19.280 4.647 18.694 1.00 75.74 H \n+ATOM 4416 NE2 HIS B 147 -18.179 5.887 20.059 1.00 75.74 N \n+ATOM 4417 OXT HIS B 147 -19.778 11.030 16.196 1.00 75.74 O \n+TER 4418 HIS B 147 \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/timings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/timings.json Tue Sep 13 22:04:12 2022 +0000 |
| b |
| @@ -0,0 +1,18 @@ +{ + "features": 10408.720210552216, + "process_features_model_1_multimer": 6.4373016357421875e-06, + "predict_and_compile_model_1_multimer": 142.2154471874237, + "relax_model_1_multimer": 31.650254011154175, + "process_features_model_2_multimer": 8.821487426757812e-06, + "predict_and_compile_model_2_multimer": 129.20519495010376, + "relax_model_2_multimer": 23.611762523651123, + "process_features_model_3_multimer": 1.0013580322265625e-05, + "predict_and_compile_model_3_multimer": 129.59484887123108, + "relax_model_3_multimer": 23.280151844024658, + "process_features_model_4_multimer": 1.4066696166992188e-05, + "predict_and_compile_model_4_multimer": 128.83590579032898, + "relax_model_4_multimer": 23.04408311843872, + "process_features_model_5_multimer": 1.1920928955078125e-05, + "predict_and_compile_model_5_multimer": 127.42200946807861, + "relax_model_5_multimer": 22.91479754447937 +} \ No newline at end of file |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/unrelaxed_model_1_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/unrelaxed_model_1_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,2211 @@\n+MODEL 1 \n+ATOM 1 N MET B 1 12.074 -10.561 -8.065 1.00 68.86 N \n+ATOM 2 CA MET B 1 10.767 -11.211 -8.110 1.00 68.86 C \n+ATOM 3 C MET B 1 10.313 -11.420 -9.551 1.00 68.86 C \n+ATOM 4 CB MET B 1 9.729 -10.386 -7.349 1.00 68.86 C \n+ATOM 5 O MET B 1 10.189 -10.460 -10.313 1.00 68.86 O \n+ATOM 6 CG MET B 1 9.220 -11.057 -6.084 1.00 68.86 C \n+ATOM 7 SD MET B 1 7.851 -10.123 -5.295 1.00 68.86 S \n+ATOM 8 CE MET B 1 8.762 -9.276 -3.974 1.00 68.86 C \n+ATOM 9 N VAL B 2 10.401 -12.352 -9.802 1.00 83.07 N \n+ATOM 10 CA VAL B 2 10.040 -12.730 -11.164 1.00 83.07 C \n+ATOM 11 C VAL B 2 8.521 -12.823 -11.290 1.00 83.07 C \n+ATOM 12 CB VAL B 2 10.691 -14.071 -11.573 1.00 83.07 C \n+ATOM 13 O VAL B 2 7.859 -13.442 -10.453 1.00 83.07 O \n+ATOM 14 CG1 VAL B 2 10.305 -14.445 -13.003 1.00 83.07 C \n+ATOM 15 CG2 VAL B 2 12.210 -13.991 -11.430 1.00 83.07 C \n+ATOM 16 N LEU B 3 7.924 -12.223 -12.239 1.00 96.79 N \n+ATOM 17 CA LEU B 3 6.495 -12.258 -12.532 1.00 96.79 C \n+ATOM 18 C LEU B 3 6.115 -13.564 -13.223 1.00 96.79 C \n+ATOM 19 CB LEU B 3 6.099 -11.068 -13.410 1.00 96.79 C \n+ATOM 20 O LEU B 3 6.609 -13.861 -14.312 1.00 96.79 O \n+ATOM 21 CG LEU B 3 6.191 -9.687 -12.761 1.00 96.79 C \n+ATOM 22 CD1 LEU B 3 5.970 -8.595 -13.803 1.00 96.79 C \n+ATOM 23 CD2 LEU B 3 5.181 -9.561 -11.625 1.00 96.79 C \n+ATOM 24 N SER B 4 5.284 -14.239 -12.544 1.00 97.73 N \n+ATOM 25 CA SER B 4 4.779 -15.464 -13.154 1.00 97.73 C \n+ATOM 26 C SER B 4 3.797 -15.158 -14.280 1.00 97.73 C \n+ATOM 27 CB SER B 4 4.103 -16.347 -12.103 1.00 97.73 C \n+ATOM 28 O SER B 4 3.275 -14.045 -14.370 1.00 97.73 O \n+ATOM 29 OG SER B 4 2.859 -15.795 -11.708 1.00 97.73 O \n+ATOM 30 N PRO B 5 3.500 -16.146 -15.168 1.00 97.29 N \n+ATOM 31 CA PRO B 5 2.475 -15.920 -16.190 1.00 97.29 C \n+ATOM 32 C PRO B 5 1.131 -15.507 -15.595 1.00 97.29 C \n+ATOM 33 CB PRO B 5 2.369 -17.278 -16.888 1.00 97.29 C \n+ATOM 34 O PRO B 5 0.416 -14.692 -16.184 1.00 97.29 O \n+ATOM 35 CG PRO B 5 3.721 -17.896 -16.730 1.00 97.29 C \n+ATOM 36 CD PRO B 5 4.266 -17.512 -15.384 1.00 97.29 C \n+ATOM 37 N ALA B 6 0.782 -16.109 -14.460 1.00 97.39 N \n+ATOM 38 CA ALA B 6 -0.463 -15.722 -13.800 1.00 97.39 C \n+ATOM 39 C ALA B 6 -0.411 -14.267 -13.343 1.00 97.39 C \n+ATOM 40 CB ALA B 6 -0.744 -16.640 -12.613 1.00 97.39 C \n+ATOM 41 O ALA B 6 -1.409 -13.547 -13.430 1.00 97.39 O \n+ATOM 42 N ASP B 7 0.796 -13.867 -12.806 1.00 98.11 N \n+ATOM 43 CA ASP B 7 0.971 -12.467 -12.432 1.00 98.11 C \n+ATOM 44 C ASP B 7 0.739 -11.546 -13.628 1.00 98.11 C \n+ATOM 45 CB ASP B 7 2.369 -12.236 -11.854 1.00 98.11 C \n+ATOM 46 O ASP B 7 0.036 -10.539 -13.515 1.00 98.11 O \n+ATOM 47 CG ASP B 7 2.544 -12.833 -10.469 1.00 98.11 C \n+ATOM 48 OD1 ASP B 7 3.675 -13.'..b'LA C 143 6.649 -1.421 17.620 1.00 96.57 N \n+ATOM 2163 CA ALA C 143 8.083 -1.675 17.509 1.00 96.57 C \n+ATOM 2164 C ALA C 143 8.843 -1.043 18.672 1.00 96.57 C \n+ATOM 2165 CB ALA C 143 8.616 -1.146 16.180 1.00 96.57 C \n+ATOM 2166 O ALA C 143 10.059 -1.210 18.791 1.00 96.57 O \n+ATOM 2167 N HIS C 144 8.139 -0.380 19.646 1.00 95.65 N \n+ATOM 2168 CA HIS C 144 8.823 0.491 20.596 1.00 95.65 C \n+ATOM 2169 C HIS C 144 9.573 -0.321 21.647 1.00 95.65 C \n+ATOM 2170 CB HIS C 144 7.827 1.434 21.272 1.00 95.65 C \n+ATOM 2171 O HIS C 144 10.539 0.165 22.240 1.00 95.65 O \n+ATOM 2172 CG HIS C 144 7.089 0.809 22.413 1.00 95.65 C \n+ATOM 2173 CD2 HIS C 144 7.281 0.897 23.751 1.00 95.65 C \n+ATOM 2174 ND1 HIS C 144 6.009 -0.027 22.232 1.00 95.65 N \n+ATOM 2175 CE1 HIS C 144 5.566 -0.427 23.413 1.00 95.65 C \n+ATOM 2176 NE2 HIS C 144 6.321 0.120 24.351 1.00 95.65 N \n+ATOM 2177 N LYS C 145 9.295 -1.572 21.797 1.00 95.60 N \n+ATOM 2178 CA LYS C 145 9.975 -2.390 22.797 1.00 95.60 C \n+ATOM 2179 C LYS C 145 10.990 -3.324 22.145 1.00 95.60 C \n+ATOM 2180 CB LYS C 145 8.962 -3.200 23.607 1.00 95.60 C \n+ATOM 2181 O LYS C 145 11.557 -4.195 22.809 1.00 95.60 O \n+ATOM 2182 CG LYS C 145 8.030 -2.352 24.459 1.00 95.60 C \n+ATOM 2183 CD LYS C 145 8.756 -1.756 25.658 1.00 95.60 C \n+ATOM 2184 CE LYS C 145 7.792 -1.044 26.599 1.00 95.60 C \n+ATOM 2185 NZ LYS C 145 8.509 -0.394 27.737 1.00 95.60 N \n+ATOM 2186 N TYR C 146 11.407 -3.157 20.919 1.00 94.88 N \n+ATOM 2187 CA TYR C 146 12.385 -3.983 20.220 1.00 94.88 C \n+ATOM 2188 C TYR C 146 13.806 -3.584 20.599 1.00 94.88 C \n+ATOM 2189 CB TYR C 146 12.198 -3.871 18.704 1.00 94.88 C \n+ATOM 2190 O TYR C 146 14.138 -2.396 20.626 1.00 94.88 O \n+ATOM 2191 CG TYR C 146 11.098 -4.750 18.161 1.00 94.88 C \n+ATOM 2192 CD1 TYR C 146 11.356 -5.685 17.162 1.00 94.88 C \n+ATOM 2193 CD2 TYR C 146 9.798 -4.646 18.645 1.00 94.88 C \n+ATOM 2194 CE1 TYR C 146 10.345 -6.496 16.657 1.00 94.88 C \n+ATOM 2195 CE2 TYR C 146 8.779 -5.452 18.148 1.00 94.88 C \n+ATOM 2196 OH TYR C 146 8.057 -7.173 16.660 1.00 94.88 O \n+ATOM 2197 CZ TYR C 146 9.062 -6.373 17.156 1.00 94.88 C \n+ATOM 2198 N HIS C 147 14.738 -4.138 20.916 1.00 81.24 N \n+ATOM 2199 CA HIS C 147 16.136 -3.934 21.279 1.00 81.24 C \n+ATOM 2200 C HIS C 147 17.056 -4.831 20.457 1.00 81.24 C \n+ATOM 2201 CB HIS C 147 16.345 -4.195 22.772 1.00 81.24 C \n+ATOM 2202 O HIS C 147 16.656 -5.919 20.038 1.00 81.24 O \n+ATOM 2203 CG HIS C 147 15.420 -3.416 23.652 1.00 81.24 C \n+ATOM 2204 CD2 HIS C 147 14.331 -3.800 24.358 1.00 81.24 C \n+ATOM 2205 ND1 HIS C 147 15.571 -2.065 23.880 1.00 81.24 N \n+ATOM 2206 CE1 HIS C 147 14.612 -1.652 24.692 1.00 81.24 C \n+ATOM 2207 NE2 HIS C 147 13.846 -2.685 24.996 1.00 81.24 N \n+TER 2208 HIS C 147 \n+ENDMDL \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/unrelaxed_model_2_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/unrelaxed_model_2_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,2211 @@\n+MODEL 1 \n+ATOM 1 N MET B 1 5.067 -14.696 9.290 1.00 67.59 N \n+ATOM 2 CA MET B 1 4.262 -13.811 10.127 1.00 67.59 C \n+ATOM 3 C MET B 1 3.020 -14.531 10.643 1.00 67.59 C \n+ATOM 4 CB MET B 1 3.856 -12.558 9.351 1.00 67.59 C \n+ATOM 5 O MET B 1 2.237 -15.067 9.857 1.00 67.59 O \n+ATOM 6 CG MET B 1 4.365 -11.264 9.965 1.00 67.59 C \n+ATOM 7 SD MET B 1 3.627 -9.776 9.185 1.00 67.59 S \n+ATOM 8 CE MET B 1 4.864 -9.442 7.900 1.00 67.59 C \n+ATOM 9 N VAL B 2 3.212 -14.853 11.626 1.00 81.89 N \n+ATOM 10 CA VAL B 2 2.115 -15.554 12.285 1.00 81.89 C \n+ATOM 11 C VAL B 2 0.991 -14.572 12.605 1.00 81.89 C \n+ATOM 12 CB VAL B 2 2.588 -16.262 13.575 1.00 81.89 C \n+ATOM 13 O VAL B 2 1.235 -13.502 13.168 1.00 81.89 O \n+ATOM 14 CG1 VAL B 2 1.424 -16.985 14.251 1.00 81.89 C \n+ATOM 15 CG2 VAL B 2 3.720 -17.239 13.263 1.00 81.89 C \n+ATOM 16 N LEU B 3 -0.219 -14.817 12.218 1.00 96.41 N \n+ATOM 17 CA LEU B 3 -1.408 -14.016 12.489 1.00 96.41 C \n+ATOM 18 C LEU B 3 -1.910 -14.253 13.909 1.00 96.41 C \n+ATOM 19 CB LEU B 3 -2.514 -14.340 11.483 1.00 96.41 C \n+ATOM 20 O LEU B 3 -2.253 -15.382 14.270 1.00 96.41 O \n+ATOM 21 CG LEU B 3 -2.250 -13.936 10.031 1.00 96.41 C \n+ATOM 22 CD1 LEU B 3 -3.323 -14.518 9.116 1.00 96.41 C \n+ATOM 23 CD2 LEU B 3 -2.194 -12.418 9.900 1.00 96.41 C \n+ATOM 24 N SER B 4 -1.907 -13.161 14.616 1.00 97.43 N \n+ATOM 25 CA SER B 4 -2.448 -13.245 15.969 1.00 97.43 C \n+ATOM 26 C SER B 4 -3.969 -13.358 15.950 1.00 97.43 C \n+ATOM 27 CB SER B 4 -2.029 -12.025 16.790 1.00 97.43 C \n+ATOM 28 O SER B 4 -4.606 -13.063 14.937 1.00 97.43 O \n+ATOM 29 OG SER B 4 -2.742 -10.871 16.376 1.00 97.43 O \n+ATOM 30 N PRO B 5 -4.600 -13.790 17.077 1.00 96.92 N \n+ATOM 31 CA PRO B 5 -6.064 -13.786 17.139 1.00 96.92 C \n+ATOM 32 C PRO B 5 -6.664 -12.416 16.832 1.00 96.92 C \n+ATOM 33 CB PRO B 5 -6.356 -14.199 18.584 1.00 96.92 C \n+ATOM 34 O PRO B 5 -7.720 -12.328 16.201 1.00 96.92 O \n+ATOM 35 CG PRO B 5 -5.193 -15.049 18.981 1.00 96.92 C \n+ATOM 36 CD PRO B 5 -3.954 -14.490 18.344 1.00 96.92 C \n+ATOM 37 N ALA B 6 -6.000 -11.360 17.345 1.00 97.18 N \n+ATOM 38 CA ALA B 6 -6.483 -10.015 17.043 1.00 97.18 C \n+ATOM 39 C ALA B 6 -6.402 -9.727 15.546 1.00 97.18 C \n+ATOM 40 CB ALA B 6 -5.686 -8.975 17.826 1.00 97.18 C \n+ATOM 41 O ALA B 6 -7.291 -9.084 14.983 1.00 97.18 O \n+ATOM 42 N ASP B 7 -5.276 -10.183 14.921 1.00 97.92 N \n+ATOM 43 CA ASP B 7 -5.162 -10.041 13.473 1.00 97.92 C \n+ATOM 44 C ASP B 7 -6.324 -10.729 12.761 1.00 97.92 C \n+ATOM 45 CB ASP B 7 -3.831 -10.613 12.981 1.00 97.92 C \n+ATOM 46 O ASP B 7 -6.933 -10.153 11.857 1.00 97.92 O \n+ATOM 47 CG ASP B 7 -2.638 -9.755 13.366 1.00 97.92 C \n+ATOM 48 OD1 ASP B 7 -1.529 -10.'..b'LA C 143 17.301 7.763 -2.211 1.00 96.00 N \n+ATOM 2163 CA ALA C 143 18.280 6.681 -2.147 1.00 96.00 C \n+ATOM 2164 C ALA C 143 19.511 7.005 -2.988 1.00 96.00 C \n+ATOM 2165 CB ALA C 143 17.653 5.368 -2.610 1.00 96.00 C \n+ATOM 2166 O ALA C 143 20.487 6.252 -2.987 1.00 96.00 O \n+ATOM 2167 N HIS C 144 19.600 8.210 -3.673 1.00 94.82 N \n+ATOM 2168 CA HIS C 144 20.589 8.432 -4.721 1.00 94.82 C \n+ATOM 2169 C HIS C 144 21.974 8.673 -4.129 1.00 94.82 C \n+ATOM 2170 CB HIS C 144 20.181 9.615 -5.601 1.00 94.82 C \n+ATOM 2171 O HIS C 144 22.986 8.452 -4.798 1.00 94.82 O \n+ATOM 2172 CG HIS C 144 20.547 10.946 -5.024 1.00 94.82 C \n+ATOM 2173 CD2 HIS C 144 21.620 11.743 -5.240 1.00 94.82 C \n+ATOM 2174 ND1 HIS C 144 19.760 11.599 -4.101 1.00 94.82 N \n+ATOM 2175 CE1 HIS C 144 20.334 12.744 -3.774 1.00 94.82 C \n+ATOM 2176 NE2 HIS C 144 21.464 12.856 -4.451 1.00 94.82 N \n+ATOM 2177 N LYS C 145 22.064 8.978 -2.871 1.00 94.96 N \n+ATOM 2178 CA LYS C 145 23.364 9.215 -2.251 1.00 94.96 C \n+ATOM 2179 C LYS C 145 23.804 8.013 -1.420 1.00 94.96 C \n+ATOM 2180 CB LYS C 145 23.321 10.469 -1.376 1.00 94.96 C \n+ATOM 2181 O LYS C 145 24.822 8.070 -0.727 1.00 94.96 O \n+ATOM 2182 CG LYS C 145 23.092 11.757 -2.152 1.00 94.96 C \n+ATOM 2183 CD LYS C 145 24.316 12.140 -2.973 1.00 94.96 C \n+ATOM 2184 CE LYS C 145 24.151 13.508 -3.621 1.00 94.96 C \n+ATOM 2185 NZ LYS C 145 25.323 13.860 -4.478 1.00 94.96 N \n+ATOM 2186 N TYR C 146 23.215 6.838 -1.488 1.00 94.48 N \n+ATOM 2187 CA TYR C 146 23.585 5.617 -0.781 1.00 94.48 C \n+ATOM 2188 C TYR C 146 24.696 4.876 -1.515 1.00 94.48 C \n+ATOM 2189 CB TYR C 146 22.368 4.701 -0.616 1.00 94.48 C \n+ATOM 2190 O TYR C 146 24.630 4.694 -2.733 1.00 94.48 O \n+ATOM 2191 CG TYR C 146 21.464 5.093 0.527 1.00 94.48 C \n+ATOM 2192 CD1 TYR C 146 21.237 4.223 1.591 1.00 94.48 C \n+ATOM 2193 CD2 TYR C 146 20.834 6.333 0.545 1.00 94.48 C \n+ATOM 2194 CE1 TYR C 146 20.402 4.579 2.645 1.00 94.48 C \n+ATOM 2195 CE2 TYR C 146 19.997 6.699 1.594 1.00 94.48 C \n+ATOM 2196 OH TYR C 146 18.962 6.175 3.680 1.00 94.48 O \n+ATOM 2197 CZ TYR C 146 19.788 5.817 2.638 1.00 94.48 C \n+ATOM 2198 N HIS C 147 25.680 4.480 -1.288 1.00 80.78 N \n+ATOM 2199 CA HIS C 147 26.823 3.775 -1.858 1.00 80.78 C \n+ATOM 2200 C HIS C 147 27.108 2.484 -1.098 1.00 80.78 C \n+ATOM 2201 CB HIS C 147 28.062 4.671 -1.854 1.00 80.78 C \n+ATOM 2202 O HIS C 147 26.844 2.394 0.103 1.00 80.78 O \n+ATOM 2203 CG HIS C 147 27.858 5.980 -2.548 1.00 80.78 C \n+ATOM 2204 CD2 HIS C 147 27.745 7.238 -2.059 1.00 80.78 C \n+ATOM 2205 ND1 HIS C 147 27.744 6.086 -3.917 1.00 80.78 N \n+ATOM 2206 CE1 HIS C 147 27.570 7.357 -4.241 1.00 80.78 C \n+ATOM 2207 NE2 HIS C 147 27.567 8.076 -3.132 1.00 80.78 N \n+TER 2208 HIS C 147 \n+ENDMDL \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/unrelaxed_model_3_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/unrelaxed_model_3_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,2211 @@\n+MODEL 1 \n+ATOM 1 N MET B 1 -10.084 7.334 -12.268 1.00 58.25 N \n+ATOM 2 CA MET B 1 -10.664 6.134 -11.671 1.00 58.25 C \n+ATOM 3 C MET B 1 -12.007 6.445 -11.020 1.00 58.25 C \n+ATOM 4 CB MET B 1 -9.709 5.531 -10.640 1.00 58.25 C \n+ATOM 5 O MET B 1 -12.078 7.247 -10.086 1.00 58.25 O \n+ATOM 6 CG MET B 1 -9.190 4.153 -11.017 1.00 58.25 C \n+ATOM 7 SD MET B 1 -8.234 3.366 -9.662 1.00 58.25 S \n+ATOM 8 CE MET B 1 -6.563 3.440 -10.365 1.00 58.25 C \n+ATOM 9 N VAL B 2 -12.695 6.226 -11.710 1.00 78.37 N \n+ATOM 10 CA VAL B 2 -14.067 6.457 -11.270 1.00 78.37 C \n+ATOM 11 C VAL B 2 -14.468 5.395 -10.248 1.00 78.37 C \n+ATOM 12 CB VAL B 2 -15.053 6.451 -12.459 1.00 78.37 C \n+ATOM 13 O VAL B 2 -14.257 4.200 -10.470 1.00 78.37 O \n+ATOM 14 CG1 VAL B 2 -16.480 6.709 -11.979 1.00 78.37 C \n+ATOM 15 CG2 VAL B 2 -14.640 7.491 -13.499 1.00 78.37 C \n+ATOM 16 N LEU B 3 -14.984 5.815 -9.138 1.00 96.86 N \n+ATOM 17 CA LEU B 3 -15.468 4.934 -8.080 1.00 96.86 C \n+ATOM 18 C LEU B 3 -16.849 4.384 -8.420 1.00 96.86 C \n+ATOM 19 CB LEU B 3 -15.517 5.678 -6.743 1.00 96.86 C \n+ATOM 20 O LEU B 3 -17.803 5.148 -8.584 1.00 96.86 O \n+ATOM 21 CG LEU B 3 -14.170 6.090 -6.147 1.00 96.86 C \n+ATOM 22 CD1 LEU B 3 -14.380 7.000 -4.942 1.00 96.86 C \n+ATOM 23 CD2 LEU B 3 -13.358 4.859 -5.759 1.00 96.86 C \n+ATOM 24 N SER B 4 -16.847 3.093 -8.475 1.00 97.59 N \n+ATOM 25 CA SER B 4 -18.135 2.450 -8.716 1.00 97.59 C \n+ATOM 26 C SER B 4 -19.010 2.480 -7.467 1.00 97.59 C \n+ATOM 27 CB SER B 4 -17.935 1.005 -9.175 1.00 97.59 C \n+ATOM 28 O SER B 4 -18.514 2.703 -6.361 1.00 97.59 O \n+ATOM 29 OG SER B 4 -17.513 0.189 -8.096 1.00 97.59 O \n+ATOM 30 N PRO B 5 -20.340 2.231 -7.625 1.00 97.69 N \n+ATOM 31 CA PRO B 5 -21.192 2.141 -6.437 1.00 97.69 C \n+ATOM 32 C PRO B 5 -20.709 1.088 -5.442 1.00 97.69 C \n+ATOM 33 CB PRO B 5 -22.559 1.762 -7.012 1.00 97.69 C \n+ATOM 34 O PRO B 5 -20.812 1.287 -4.229 1.00 97.69 O \n+ATOM 35 CG PRO B 5 -22.571 2.348 -8.387 1.00 97.69 C \n+ATOM 36 CD PRO B 5 -21.191 2.232 -8.967 1.00 97.69 C \n+ATOM 37 N ALA B 6 -20.214 -0.016 -5.957 1.00 97.77 N \n+ATOM 38 CA ALA B 6 -19.679 -1.044 -5.068 1.00 97.77 C \n+ATOM 39 C ALA B 6 -18.448 -0.536 -4.321 1.00 97.77 C \n+ATOM 40 CB ALA B 6 -19.335 -2.304 -5.858 1.00 97.77 C \n+ATOM 41 O ALA B 6 -18.261 -0.842 -3.141 1.00 97.77 O \n+ATOM 42 N ASP B 7 -17.620 0.204 -5.036 1.00 98.28 N \n+ATOM 43 CA ASP B 7 -16.469 0.818 -4.380 1.00 98.28 C \n+ATOM 44 C ASP B 7 -16.910 1.726 -3.235 1.00 98.28 C \n+ATOM 45 CB ASP B 7 -15.636 1.610 -5.389 1.00 98.28 C \n+ATOM 46 O ASP B 7 -16.354 1.663 -2.136 1.00 98.28 O \n+ATOM 47 CG ASP B 7 -14.848 0.721 -6.336 1.00 98.28 C \n+ATOM 48 OD1 ASP B 7 -14.591 1.'..b'LA C 143 14.831 -5.213 -11.139 1.00 95.97 N \n+ATOM 2163 CA ALA C 143 14.832 -4.267 -12.252 1.00 95.97 C \n+ATOM 2164 C ALA C 143 16.250 -4.021 -12.761 1.00 95.97 C \n+ATOM 2165 CB ALA C 143 14.184 -2.950 -11.832 1.00 95.97 C \n+ATOM 2166 O ALA C 143 16.446 -3.317 -13.755 1.00 95.97 O \n+ATOM 2167 N HIS C 144 17.294 -4.631 -12.190 1.00 94.23 N \n+ATOM 2168 CA HIS C 144 18.676 -4.226 -12.417 1.00 94.23 C \n+ATOM 2169 C HIS C 144 19.151 -4.641 -13.806 1.00 94.23 C \n+ATOM 2170 CB HIS C 144 19.592 -4.826 -11.348 1.00 94.23 C \n+ATOM 2171 O HIS C 144 20.025 -3.993 -14.387 1.00 94.23 O \n+ATOM 2172 CG HIS C 144 20.069 -6.206 -11.672 1.00 94.23 C \n+ATOM 2173 CD2 HIS C 144 21.184 -6.634 -12.309 1.00 94.23 C \n+ATOM 2174 ND1 HIS C 144 19.360 -7.337 -11.331 1.00 94.23 N \n+ATOM 2175 CE1 HIS C 144 20.021 -8.405 -11.745 1.00 94.23 C \n+ATOM 2176 NE2 HIS C 144 21.131 -8.006 -12.342 1.00 94.23 N \n+ATOM 2177 N LYS C 145 18.464 -5.545 -14.434 1.00 94.41 N \n+ATOM 2178 CA LYS C 145 18.889 -6.000 -15.754 1.00 94.41 C \n+ATOM 2179 C LYS C 145 17.993 -5.425 -16.848 1.00 94.41 C \n+ATOM 2180 CB LYS C 145 18.885 -7.528 -15.823 1.00 94.41 C \n+ATOM 2181 O LYS C 145 18.091 -5.823 -18.011 1.00 94.41 O \n+ATOM 2182 CG LYS C 145 19.922 -8.190 -14.928 1.00 94.41 C \n+ATOM 2183 CD LYS C 145 21.331 -8.011 -15.477 1.00 94.41 C \n+ATOM 2184 CE LYS C 145 22.351 -8.806 -14.672 1.00 94.41 C \n+ATOM 2185 NZ LYS C 145 23.743 -8.579 -15.165 1.00 94.41 N \n+ATOM 2186 N TYR C 146 17.195 -4.407 -16.612 1.00 93.82 N \n+ATOM 2187 CA TYR C 146 16.322 -3.765 -17.589 1.00 93.82 C \n+ATOM 2188 C TYR C 146 17.090 -2.746 -18.421 1.00 93.82 C \n+ATOM 2189 CB TYR C 146 15.141 -3.085 -16.889 1.00 93.82 C \n+ATOM 2190 O TYR C 146 17.858 -1.946 -17.880 1.00 93.82 O \n+ATOM 2191 CG TYR C 146 14.005 -4.024 -16.563 1.00 93.82 C \n+ATOM 2192 CD1 TYR C 146 12.724 -3.797 -17.059 1.00 93.82 C \n+ATOM 2193 CD2 TYR C 146 14.211 -5.139 -15.758 1.00 93.82 C \n+ATOM 2194 CE1 TYR C 146 11.673 -4.659 -16.760 1.00 93.82 C \n+ATOM 2195 CE2 TYR C 146 13.168 -6.007 -15.452 1.00 93.82 C \n+ATOM 2196 OH TYR C 146 10.870 -6.616 -15.657 1.00 93.82 O \n+ATOM 2197 CZ TYR C 146 11.905 -5.759 -15.957 1.00 93.82 C \n+ATOM 2198 N HIS C 147 17.171 -2.566 -19.450 1.00 78.51 N \n+ATOM 2199 CA HIS C 147 17.829 -1.663 -20.388 1.00 78.51 C \n+ATOM 2200 C HIS C 147 16.830 -1.074 -21.378 1.00 78.51 C \n+ATOM 2201 CB HIS C 147 18.945 -2.392 -21.139 1.00 78.51 C \n+ATOM 2202 O HIS C 147 15.818 -1.705 -21.695 1.00 78.51 O \n+ATOM 2203 CG HIS C 147 19.938 -3.057 -20.240 1.00 78.51 C \n+ATOM 2204 CD2 HIS C 147 20.133 -4.363 -19.942 1.00 78.51 C \n+ATOM 2205 ND1 HIS C 147 20.879 -2.352 -19.521 1.00 78.51 N \n+ATOM 2206 CE1 HIS C 147 21.613 -3.200 -18.818 1.00 78.51 C \n+ATOM 2207 NE2 HIS C 147 21.180 -4.426 -19.056 1.00 78.51 N \n+TER 2208 HIS C 147 \n+ENDMDL \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/unrelaxed_model_4_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/unrelaxed_model_4_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,2211 @@\n+MODEL 1 \n+ATOM 1 N MET B 1 -12.379 9.544 8.236 1.00 69.17 N \n+ATOM 2 CA MET B 1 -12.120 8.226 8.806 1.00 69.17 C \n+ATOM 3 C MET B 1 -11.700 8.338 10.268 1.00 69.17 C \n+ATOM 4 CB MET B 1 -11.039 7.496 8.007 1.00 69.17 C \n+ATOM 5 O MET B 1 -10.744 9.045 10.591 1.00 69.17 O \n+ATOM 6 CG MET B 1 -11.434 6.091 7.582 1.00 69.17 C \n+ATOM 7 SD MET B 1 -10.054 5.183 6.784 1.00 69.17 S \n+ATOM 8 CE MET B 1 -10.420 5.512 5.038 1.00 69.17 C \n+ATOM 9 N VAL B 2 -12.630 8.224 11.101 1.00 84.22 N \n+ATOM 10 CA VAL B 2 -12.431 8.294 12.545 1.00 84.22 C \n+ATOM 11 C VAL B 2 -11.720 7.033 13.031 1.00 84.22 C \n+ATOM 12 CB VAL B 2 -13.770 8.474 13.294 1.00 84.22 C \n+ATOM 13 O VAL B 2 -12.118 5.917 12.687 1.00 84.22 O \n+ATOM 14 CG1 VAL B 2 -13.540 8.550 14.802 1.00 84.22 C \n+ATOM 15 CG2 VAL B 2 -14.495 9.723 12.797 1.00 84.22 C \n+ATOM 16 N LEU B 3 -10.542 7.123 13.622 1.00 96.40 N \n+ATOM 17 CA LEU B 3 -9.786 6.029 14.222 1.00 96.40 C \n+ATOM 18 C LEU B 3 -10.485 5.508 15.473 1.00 96.40 C \n+ATOM 19 CB LEU B 3 -8.367 6.487 14.570 1.00 96.40 C \n+ATOM 20 O LEU B 3 -10.715 6.263 16.421 1.00 96.40 O \n+ATOM 21 CG LEU B 3 -7.455 6.823 13.389 1.00 96.40 C \n+ATOM 22 CD1 LEU B 3 -6.159 7.456 13.884 1.00 96.40 C \n+ATOM 23 CD2 LEU B 3 -7.165 5.574 12.563 1.00 96.40 C \n+ATOM 24 N SER B 4 -10.807 4.258 15.369 1.00 97.30 N \n+ATOM 25 CA SER B 4 -11.399 3.623 16.542 1.00 97.30 C \n+ATOM 26 C SER B 4 -10.355 3.392 17.630 1.00 97.30 C \n+ATOM 27 CB SER B 4 -12.052 2.294 16.161 1.00 97.30 C \n+ATOM 28 O SER B 4 -9.153 3.433 17.363 1.00 97.30 O \n+ATOM 29 OG SER B 4 -11.070 1.308 15.895 1.00 97.30 O \n+ATOM 30 N PRO B 5 -10.801 3.140 18.891 1.00 96.74 N \n+ATOM 31 CA PRO B 5 -9.830 2.792 19.932 1.00 96.74 C \n+ATOM 32 C PRO B 5 -8.967 1.591 19.555 1.00 96.74 C \n+ATOM 33 CB PRO B 5 -10.711 2.474 21.143 1.00 96.74 C \n+ATOM 34 O PRO B 5 -7.776 1.556 19.877 1.00 96.74 O \n+ATOM 35 CG PRO B 5 -11.940 3.303 20.950 1.00 96.74 C \n+ATOM 36 CD PRO B 5 -12.253 3.357 19.483 1.00 96.74 C \n+ATOM 37 N ALA B 6 -9.595 0.644 18.908 1.00 97.04 N \n+ATOM 38 CA ALA B 6 -8.820 -0.513 18.466 1.00 97.04 C \n+ATOM 39 C ALA B 6 -7.775 -0.109 17.429 1.00 97.04 C \n+ATOM 40 CB ALA B 6 -9.744 -1.586 17.896 1.00 97.04 C \n+ATOM 41 O ALA B 6 -6.653 -0.620 17.438 1.00 97.04 O \n+ATOM 42 N ASP B 7 -8.178 0.762 16.524 1.00 97.79 N \n+ATOM 43 CA ASP B 7 -7.214 1.283 15.559 1.00 97.79 C \n+ATOM 44 C ASP B 7 -6.029 1.937 16.266 1.00 97.79 C \n+ATOM 45 CB ASP B 7 -7.885 2.287 14.619 1.00 97.79 C \n+ATOM 46 O ASP B 7 -4.874 1.697 15.906 1.00 97.79 O \n+ATOM 47 CG ASP B 7 -8.803 1.628 13.606 1.00 97.79 C \n+ATOM 48 OD1 ASP B 7 -9.799 2.'..b'LA C 143 -8.810 -2.166 -16.933 1.00 95.71 N \n+ATOM 2163 CA ALA C 143 -9.705 -1.020 -17.064 1.00 95.71 C \n+ATOM 2164 C ALA C 143 -9.899 -0.639 -18.529 1.00 95.71 C \n+ATOM 2165 CB ALA C 143 -9.163 0.171 -16.276 1.00 95.71 C \n+ATOM 2166 O ALA C 143 -10.680 0.262 -18.845 1.00 95.71 O \n+ATOM 2167 N HIS C 144 -9.293 -1.351 -19.528 1.00 94.10 N \n+ATOM 2168 CA HIS C 144 -9.209 -0.871 -20.902 1.00 94.10 C \n+ATOM 2169 C HIS C 144 -10.558 -0.974 -21.606 1.00 94.10 C \n+ATOM 2170 CB HIS C 144 -8.150 -1.654 -21.680 1.00 94.10 C \n+ATOM 2171 O HIS C 144 -10.843 -0.206 -22.527 1.00 94.10 O \n+ATOM 2172 CG HIS C 144 -8.659 -2.933 -22.266 1.00 94.10 C \n+ATOM 2173 CD2 HIS C 144 -9.131 -3.218 -23.502 1.00 94.10 C \n+ATOM 2174 ND1 HIS C 144 -8.723 -4.107 -21.547 1.00 94.10 N \n+ATOM 2175 CE1 HIS C 144 -9.213 -5.062 -22.319 1.00 94.10 C \n+ATOM 2176 NE2 HIS C 144 -9.469 -4.549 -23.510 1.00 94.10 N \n+ATOM 2177 N LYS C 145 -11.434 -1.773 -21.078 1.00 94.04 N \n+ATOM 2178 CA LYS C 145 -12.737 -1.921 -21.721 1.00 94.04 C \n+ATOM 2179 C LYS C 145 -13.802 -1.100 -20.999 1.00 94.04 C \n+ATOM 2180 CB LYS C 145 -13.150 -3.393 -21.765 1.00 94.04 C \n+ATOM 2181 O LYS C 145 -14.982 -1.158 -21.352 1.00 94.04 O \n+ATOM 2182 CG LYS C 145 -12.271 -4.256 -22.657 1.00 94.04 C \n+ATOM 2183 CD LYS C 145 -12.522 -3.973 -24.132 1.00 94.04 C \n+ATOM 2184 CE LYS C 145 -11.749 -4.932 -25.027 1.00 94.04 C \n+ATOM 2185 NZ LYS C 145 -11.924 -4.604 -26.473 1.00 94.04 N \n+ATOM 2186 N TYR C 146 -13.483 -0.233 -20.038 1.00 94.73 N \n+ATOM 2187 CA TYR C 146 -14.411 0.644 -19.333 1.00 94.73 C \n+ATOM 2188 C TYR C 146 -14.757 1.865 -20.178 1.00 94.73 C \n+ATOM 2189 CB TYR C 146 -13.819 1.089 -17.992 1.00 94.73 C \n+ATOM 2190 O TYR C 146 -13.875 2.474 -20.789 1.00 94.73 O \n+ATOM 2191 CG TYR C 146 -13.970 0.065 -16.893 1.00 94.73 C \n+ATOM 2192 CD1 TYR C 146 -14.738 0.337 -15.763 1.00 94.73 C \n+ATOM 2193 CD2 TYR C 146 -13.345 -1.174 -16.982 1.00 94.73 C \n+ATOM 2194 CE1 TYR C 146 -14.878 -0.602 -14.746 1.00 94.73 C \n+ATOM 2195 CE2 TYR C 146 -13.479 -2.121 -15.971 1.00 94.73 C \n+ATOM 2196 OH TYR C 146 -14.382 -2.759 -13.856 1.00 94.73 O \n+ATOM 2197 CZ TYR C 146 -14.247 -1.826 -14.859 1.00 94.73 C \n+ATOM 2198 N HIS C 147 -15.698 2.211 -20.847 1.00 81.22 N \n+ATOM 2199 CA HIS C 147 -16.156 3.334 -21.657 1.00 81.22 C \n+ATOM 2200 C HIS C 147 -17.126 4.215 -20.877 1.00 81.22 C \n+ATOM 2201 CB HIS C 147 -16.818 2.834 -22.942 1.00 81.22 C \n+ATOM 2202 O HIS C 147 -17.836 3.732 -19.992 1.00 81.22 O \n+ATOM 2203 CG HIS C 147 -15.926 1.976 -23.782 1.00 81.22 C \n+ATOM 2204 CD2 HIS C 147 -15.915 0.638 -23.987 1.00 81.22 C \n+ATOM 2205 ND1 HIS C 147 -14.891 2.490 -24.531 1.00 81.22 N \n+ATOM 2206 CE1 HIS C 147 -14.280 1.502 -25.164 1.00 81.22 C \n+ATOM 2207 NE2 HIS C 147 -14.882 0.368 -24.850 1.00 81.22 N \n+TER 2208 HIS C 147 \n+ENDMDL \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d test-data/multimer_output/unrelaxed_model_5_multimer.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multimer_output/unrelaxed_model_5_multimer.pdb Tue Sep 13 22:04:12 2022 +0000 |
| b |
| b'@@ -0,0 +1,2211 @@\n+MODEL 1 \n+ATOM 1 N MET B 1 -2.206 15.182 -8.354 1.00 69.85 N \n+ATOM 2 CA MET B 1 -0.812 14.991 -7.966 1.00 69.85 C \n+ATOM 3 C MET B 1 0.097 14.981 -9.190 1.00 69.85 C \n+ATOM 4 CB MET B 1 -0.646 13.689 -7.180 1.00 69.85 C \n+ATOM 5 O MET B 1 -0.136 14.227 -10.136 1.00 69.85 O \n+ATOM 6 CG MET B 1 0.520 13.705 -6.205 1.00 69.85 C \n+ATOM 7 SD MET B 1 0.701 12.120 -5.299 1.00 69.85 S \n+ATOM 8 CE MET B 1 -0.392 12.431 -3.886 1.00 69.85 C \n+ATOM 9 N VAL B 2 0.755 16.134 -9.558 1.00 84.01 N \n+ATOM 10 CA VAL B 2 1.665 16.323 -10.682 1.00 84.01 C \n+ATOM 11 C VAL B 2 2.973 15.579 -10.419 1.00 84.01 C \n+ATOM 12 CB VAL B 2 1.946 17.820 -10.940 1.00 84.01 C \n+ATOM 13 O VAL B 2 3.545 15.684 -9.331 1.00 84.01 O \n+ATOM 14 CG1 VAL B 2 2.897 17.995 -12.123 1.00 84.01 C \n+ATOM 15 CG2 VAL B 2 0.640 18.573 -11.185 1.00 84.01 C \n+ATOM 16 N LEU B 3 3.364 14.582 -11.223 1.00 96.42 N \n+ATOM 17 CA LEU B 3 4.627 13.855 -11.156 1.00 96.42 C \n+ATOM 18 C LEU B 3 5.803 14.779 -11.456 1.00 96.42 C \n+ATOM 19 CB LEU B 3 4.622 12.681 -12.139 1.00 96.42 C \n+ATOM 20 O LEU B 3 5.881 15.359 -12.542 1.00 96.42 O \n+ATOM 21 CG LEU B 3 3.661 11.535 -11.821 1.00 96.42 C \n+ATOM 22 CD1 LEU B 3 3.595 10.559 -12.991 1.00 96.42 C \n+ATOM 23 CD2 LEU B 3 4.085 10.819 -10.543 1.00 96.42 C \n+ATOM 24 N SER B 4 6.614 14.892 -10.450 1.00 97.35 N \n+ATOM 25 CA SER B 4 7.826 15.680 -10.648 1.00 97.35 C \n+ATOM 26 C SER B 4 8.825 14.945 -11.535 1.00 97.35 C \n+ATOM 27 CB SER B 4 8.475 16.014 -9.303 1.00 97.35 C \n+ATOM 28 O SER B 4 8.718 13.732 -11.726 1.00 97.35 O \n+ATOM 29 OG SER B 4 9.079 14.863 -8.738 1.00 97.35 O \n+ATOM 30 N PRO B 5 9.831 15.649 -12.117 1.00 96.94 N \n+ATOM 31 CA PRO B 5 10.872 14.960 -12.883 1.00 96.94 C \n+ATOM 32 C PRO B 5 11.561 13.857 -12.084 1.00 96.94 C \n+ATOM 33 CB PRO B 5 11.856 16.081 -13.227 1.00 96.94 C \n+ATOM 34 O PRO B 5 11.906 12.811 -12.640 1.00 96.94 O \n+ATOM 35 CG PRO B 5 11.022 17.321 -13.270 1.00 96.94 C \n+ATOM 36 CD PRO B 5 9.960 17.219 -12.214 1.00 96.94 C \n+ATOM 37 N ALA B 6 11.763 14.123 -10.795 1.00 97.25 N \n+ATOM 38 CA ALA B 6 12.365 13.093 -9.953 1.00 97.25 C \n+ATOM 39 C ALA B 6 11.454 11.874 -9.842 1.00 97.25 C \n+ATOM 40 CB ALA B 6 12.673 13.651 -8.566 1.00 97.25 C \n+ATOM 41 O ALA B 6 11.927 10.735 -9.847 1.00 97.25 O \n+ATOM 42 N ASP B 7 10.144 12.158 -9.691 1.00 97.81 N \n+ATOM 43 CA ASP B 7 9.184 11.058 -9.672 1.00 97.81 C \n+ATOM 44 C ASP B 7 9.278 10.226 -10.949 1.00 97.81 C \n+ATOM 45 CB ASP B 7 7.761 11.591 -9.495 1.00 97.81 C \n+ATOM 46 O ASP B 7 9.295 8.994 -10.893 1.00 97.81 O \n+ATOM 47 CG ASP B 7 7.492 12.112 -8.094 1.00 97.81 C \n+ATOM 48 OD1 ASP B 7 6.684 13.'..b'LA C 143 -10.282 3.390 15.259 1.00 95.26 N \n+ATOM 2163 CA ALA C 143 -11.267 4.393 14.863 1.00 95.26 C \n+ATOM 2164 C ALA C 143 -12.554 4.247 15.670 1.00 95.26 C \n+ATOM 2165 CB ALA C 143 -11.565 4.284 13.369 1.00 95.26 C \n+ATOM 2166 O ALA C 143 -13.477 5.052 15.530 1.00 95.26 O \n+ATOM 2167 N HIS C 144 -12.694 3.257 16.650 1.00 93.99 N \n+ATOM 2168 CA HIS C 144 -13.971 2.887 17.250 1.00 93.99 C \n+ATOM 2169 C HIS C 144 -14.468 3.971 18.201 1.00 93.99 C \n+ATOM 2170 CB HIS C 144 -13.849 1.554 17.991 1.00 93.99 C \n+ATOM 2171 O HIS C 144 -15.673 4.100 18.426 1.00 93.99 O \n+ATOM 2172 CG HIS C 144 -13.270 1.682 19.364 1.00 93.99 C \n+ATOM 2173 CD2 HIS C 144 -13.867 1.813 20.572 1.00 93.99 C \n+ATOM 2174 ND1 HIS C 144 -11.913 1.687 19.602 1.00 93.99 N \n+ATOM 2175 CE1 HIS C 144 -11.700 1.815 20.901 1.00 93.99 C \n+ATOM 2176 NE2 HIS C 144 -12.870 1.893 21.512 1.00 93.99 N \n+ATOM 2177 N LYS C 145 -13.639 4.838 18.618 1.00 93.46 N \n+ATOM 2178 CA LYS C 145 -14.061 5.890 19.539 1.00 93.46 C \n+ATOM 2179 C LYS C 145 -14.270 7.212 18.806 1.00 93.46 C \n+ATOM 2180 CB LYS C 145 -13.032 6.068 20.657 1.00 93.46 C \n+ATOM 2181 O LYS C 145 -14.539 8.239 19.432 1.00 93.46 O \n+ATOM 2182 CG LYS C 145 -12.912 4.868 21.584 1.00 93.46 C \n+ATOM 2183 CD LYS C 145 -14.119 4.749 22.506 1.00 93.46 C \n+ATOM 2184 CE LYS C 145 -13.930 3.644 23.536 1.00 93.46 C \n+ATOM 2185 NZ LYS C 145 -15.153 3.453 24.373 1.00 93.46 N \n+ATOM 2186 N TYR C 146 -14.257 7.309 17.424 1.00 93.98 N \n+ATOM 2187 CA TYR C 146 -14.481 8.511 16.628 1.00 93.98 C \n+ATOM 2188 C TYR C 146 -15.971 8.791 16.470 1.00 93.98 C \n+ATOM 2189 CB TYR C 146 -13.827 8.372 15.250 1.00 93.98 C \n+ATOM 2190 O TYR C 146 -16.730 7.920 16.039 1.00 93.98 O \n+ATOM 2191 CG TYR C 146 -12.343 8.649 15.251 1.00 93.98 C \n+ATOM 2192 CD1 TYR C 146 -11.810 9.700 14.508 1.00 93.98 C \n+ATOM 2193 CD2 TYR C 146 -11.471 7.861 15.995 1.00 93.98 C \n+ATOM 2194 CE1 TYR C 146 -10.444 9.959 14.505 1.00 93.98 C \n+ATOM 2195 CE2 TYR C 146 -10.103 8.110 15.999 1.00 93.98 C \n+ATOM 2196 OH TYR C 146 -8.245 9.411 15.253 1.00 93.98 O \n+ATOM 2197 CZ TYR C 146 -9.599 9.160 15.253 1.00 93.98 C \n+ATOM 2198 N HIS C 147 -16.808 9.138 17.204 1.00 75.74 N \n+ATOM 2199 CA HIS C 147 -18.225 9.485 17.171 1.00 75.74 C \n+ATOM 2200 C HIS C 147 -18.425 10.943 16.771 1.00 75.74 C \n+ATOM 2201 CB HIS C 147 -18.873 9.220 18.531 1.00 75.74 C \n+ATOM 2202 O HIS C 147 -17.554 11.782 17.009 1.00 75.74 O \n+ATOM 2203 CG HIS C 147 -18.739 7.804 18.993 1.00 75.74 C \n+ATOM 2204 CD2 HIS C 147 -17.985 7.257 19.975 1.00 75.74 C \n+ATOM 2205 ND1 HIS C 147 -19.437 6.764 18.418 1.00 75.74 N \n+ATOM 2206 CE1 HIS C 147 -19.117 5.636 19.029 1.00 75.74 C \n+ATOM 2207 NE2 HIS C 147 -18.237 5.908 19.978 1.00 75.74 N \n+TER 2208 HIS C 147 \n+ENDMDL \n+END \n' |
| b |
| diff -r ca90d17ff51b -r 3bd420ec162d validate_fasta.py --- a/validate_fasta.py Fri Aug 19 00:29:16 2022 +0000 +++ b/validate_fasta.py Tue Sep 13 22:04:12 2022 +0000 |
| [ |
| @@ -5,6 +5,8 @@ import argparse from typing import List +MULTIMER_MAX_SEQUENCE_COUNT = 10 + class Fasta: def __init__(self, header_str: str, seq_str: str): @@ -72,12 +74,12 @@ class FastaValidator: def __init__( self, - fasta_list: List[Fasta], min_length=None, - max_length=None): + max_length=None, + multiple=False): + self.multiple = multiple self.min_length = min_length self.max_length = max_length - self.fasta_list = fasta_list self.iupac_characters = { 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', @@ -85,27 +87,49 @@ 'Y', 'Z', '-' } - def validate(self): + def validate(self, fasta_list: List[Fasta]): """Perform FASTA validation.""" + self.fasta_list = fasta_list self.validate_num_seqs() self.validate_length() self.validate_alphabet() - # not checking for 'X' nucleotides at the moment. # alphafold can throw an error if it doesn't like it. # self.validate_x() + return self.fasta_list def validate_num_seqs(self) -> None: """Assert that only one sequence has been provided.""" - if len(self.fasta_list) > 1: - sys.stderr.write( - 'WARNING: More than 1 sequence detected.' - ' Using first FASTA sequence as input.\n') - self.fasta_list = self.fasta_list[:1] - elif len(self.fasta_list) == 0: - raise ValueError( - 'Error encountered validating FASTA:\n' - ' input file has no FASTA sequences') + fasta_count = len(self.fasta_list) + + if self.multiple: + if fasta_count < 2: + raise ValueError( + 'Error encountered validating FASTA:\n' + 'Multimer mode requires multiple input sequence.' + f' Only {fasta_count} sequences were detected in' + ' the provided file.') + self.fasta_list = self.fasta_list + + elif fasta_count > MULTIMER_MAX_SEQUENCE_COUNT: + sys.stderr.write( + f'WARNING: detected {fasta_count} sequences but the' + f' maximum allowed is {MULTIMER_MAX_SEQUENCE_COUNT}' + ' sequences. The last' + f' {fasta_count - MULTIMER_MAX_SEQUENCE_COUNT} sequence(s)' + ' have been discarded.\n') + self.fasta_list = self.fasta_list[:MULTIMER_MAX_SEQUENCE_COUNT] + else: + if fasta_count > 1: + sys.stderr.write( + 'WARNING: More than 1 sequence detected.' + ' Using first FASTA sequence as input.\n') + self.fasta_list = self.fasta_list[:1] + + elif len(self.fasta_list) == 0: + raise ValueError( + 'Error encountered validating FASTA:\n' + ' no FASTA sequences detected in input file.') def validate_length(self): """Confirm whether sequence length is valid.""" @@ -170,15 +194,16 @@ # validate fv = FastaValidator( - fas.fastas, min_length=args.min_length, max_length=args.max_length, + multiple=args.multimer, ) - fv.validate() + clean_fastas = fv.validate(fas.fastas) - # write cleaned version + # write clean data fw = FastaWriter() - fw.write(fas.fastas[0]) + for fas in clean_fastas: + fw.write(fas) except ValueError as exc: sys.stderr.write(f"{exc}\n\n") @@ -212,6 +237,11 @@ default=None, type=int, ) + parser.add_argument( + "--multimer", + action='store_true', + help="Require multiple input sequences", + ) return parser.parse_args() |