Mercurial > repos > iuc > swissmodel_modelling_api
changeset 0:0c3f56c85e98 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db
| author | iuc |
|---|---|
| date | Thu, 11 Dec 2025 19:32:14 +0000 |
| parents | |
| children | |
| files | LICENSE README.rst sm_api_wrapper.py swissmodel_api.xml test-data/model_01.pdb |
| diffstat | 5 files changed, 1263 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Thu Dec 11 19:32:14 2025 +0000 @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2025 SIB, University of Basel + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Dec 11 19:32:14 2025 +0000 @@ -0,0 +1,42 @@ +============================================ +SWISS-MODEL Modelling API Galaxy integration +============================================ + +This is a wrapper for the +`SWISS-MODEL API <https://swissmodel.expasy.org/docs/help#modelling_api>`_. + +`SWISS-MODEL <https://swissmodel.expasy.org/>`_ is a web-based integrated +service dedicated to protein structure homology modelling. + +With the API wrapper, you are able to build protein models + +- fully automated (Automodel mode) +- for a specific alignment provided by the user (Alignment mode) +- based on user provider template coordinates (User template mode) + +Models can be created in ModelCIF format and legacy PDB format. + +Documentation on how to use the tool inside Galaxy is in the tool XML file. + +Installation +------------ + +Needs Python (>=3.11) and the Python requests package (2.32.5). + +Attribution +----------- + +When you publish or report results using SWISS-MODEL, please cite the relevant +publications found on https://swissmodel.expasy.org/docs/references (and on the +Galaxy tool page, once installed). + +License +------- + +License of this Galaxy tool wrapper can be found in `LICENSE <LICENSE>`_. + +Terms of use of the SWISS-MODEL server can be found at +https://swissmodel.expasy.org/docs/terms_of_use. + +Modelling results of SWISS-MODEL are licensed under the +`CC BY-SA 4.0 Creative Commons Attribution-ShareAlike 4.0 International License <https://creativecommons.org/licenses/by-sa/4.0/legalcode>`_.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sm_api_wrapper.py Thu Dec 11 19:32:14 2025 +0000 @@ -0,0 +1,428 @@ +"""Wrapper for the SWISS-MODEL API.""" + +import argparse +import json +import os +import sys +import time +from urllib.parse import urlsplit + +import requests + + +class _SmApiWhisperer: + """Parent class for talking to the SWISS-MODEL API.""" + + PROJECT_TYPE = "" + + def __init__(self, targets, token, project_title="Untitled Project"): + self.project_id = None + self.project_title = project_title + self.targets = targets + self.token = token + + def get_json_payload(self): + """Needs to be implemented per project type.""" + raise NotImplementedError + + def submit_request(self): + """Send off a request to the SM API.""" + json_payload = self.get_json_payload() + json_payload["project_title"] = self.project_title + try: + response = requests.post( + f"https://swissmodel.expasy.org/{self.PROJECT_TYPE}", + headers={"Authorization": f"Token {self.token}"}, + json=json_payload, + timeout=60, + ) + except requests.exceptions.ConnectTimeout: + print( + "SWISS-MODEL seems to temporarily unavailable", + file=sys.stderr, + ) + sys.exit(3) + if response.ok is not True: + raise RuntimeError( + f"Submitting modelling job failed ({response.status_code})" + ) + self.project_id = response.json()["project_id"] + + return response.status_code + + def wait(self): + """Poll the API for job to be finished.""" + response = None + # Wait at the end, there is a chance that this project is already + # available from cache. + while True: + # Update the status from the server + # response = requests.get( + # f"https://swissmodel.expasy.org/project/{self.project_id}/" + # + "models/summary/", + # headers={"Authorization": f"Token {self.token}"}, + # timeout=360, + # ) + response = requests.get( + f"https://swissmodel.expasy.org/project/{self.project_id}/" + + "models/full-details/", + headers={"Authorization": f"Token {self.token}"}, + timeout=360, + ) + # Update the status + status = response.json()["status"] + if status.upper() in ["COMPLETED", "FAILED"]: + break + # Wait for some time before the next request + time.sleep(17) + + return response.json() + + def fetch_results( + self, response_object, output_dir, fetch_modelcif=True, fetch_pdb=True + ): + """Get results of the modelling job.""" + + def _store_model_json(model_json, outdir): + fname = f"model_{model_json['model_id']}.json" + with open( + os.path.join(outdir, "JSON", fname), "w", encoding="utf8" + ) as jfh: + json.dump(model_json, jfh) + + def _fetch_file(url, file_type, outdir): + response = requests.get(url, timeout=360) + if response.ok is not True: + raise RuntimeError( + f"Fetching {file_type} output failed (" + + f"{response.status_code})." + ) + try: + os.mkdir(os.path.join(outdir, file_type)) + except FileExistsError: + pass + fname = f"model_{os.path.basename(urlsplit(url).path)}" + with open(os.path.join(outdir, file_type, fname), "wb") as mfh: + for chunk in response.iter_content(chunk_size=8192): + mfh.write(chunk) + + # make sure a JSON directory exists + os.mkdir(os.path.join(output_dir, "JSON")) + if response_object["status"] == "COMPLETED": + for model in response_object["models"]: + _store_model_json(model, output_dir) + if fetch_modelcif: + _fetch_file(model["modelcif_url"], "ModelCIF", output_dir) + if fetch_pdb: + _fetch_file(model["coordinates_url"], "PDB", output_dir) + + +class _AutoModelWhisperer(_SmApiWhisperer): + """SM automodel project.""" + + PROJECT_TYPE = "automodel" + + def get_json_payload(self): + """Payload for automodel mode.""" + return {"target_sequences": self.targets} + + +class _AlignmentWhisperer(_SmApiWhisperer): + """SM alignemt project.""" + + PROJECT_TYPE = "alignment" + + def __init__( + self, + targets, + token, + template_sequence, + template_seqres_offset, + pdb_id, + auth_asym_id, + assembly_id, + project_title="Untitled Project", + ): + # Not sure how to reduce the number of arguments as they are required + # by the API, so make an exception in Pylint. + # pylint: disable=too-many-arguments,too-many-positional-arguments + """Initialise alignment mode, add mode-specific info to the method.""" + super().__init__(targets, token, project_title=project_title) + self.assembly_id = assembly_id + self.auth_asym_id = auth_asym_id + self.pdb_id = pdb_id.lower() + self.template_seqres_offset = template_seqres_offset + self.template_sequence = template_sequence + + def get_json_payload(self): + """Payload for alignment mode.""" + + return { + "assembly_id": self.assembly_id, + "auth_asym_id": self.auth_asym_id, + "pdb_id": self.pdb_id, + "target_sequences": self.targets, + "template_seqres_offset": self.template_seqres_offset, + "template_sequence": self.template_sequence, + } + + +class _UserTemplateWhisperer(_SmApiWhisperer): + """SM user-template project.""" + + PROJECT_TYPE = "user_template" + + def __init__( + self, + targets, + token, + template_file, + project_title="Untitled Project", + ): + """Initialise user template mode.""" + super().__init__(targets, token, project_title=project_title) + self.template_file = template_file + + def get_json_payload(self): + """Payload for user upload mode.""" + with open(self.template_file, encoding="utf8") as tfh: + template_coordinates = tfh.read() + + return { + "project_title": self.project_title, + "target_sequences": self.targets, + "template_coordinates": template_coordinates, + } + + +def _defastarise_targets(sequences): + """In case some of the targets carry FastA headers, remove them.""" + targets = [] + for seq in sequences: + seq = seq.split(" ") + if len(seq) > 1: + if seq[0].strip().startswith((">", "__gt__")): + targets.append("".join(seq[1:])) + else: + targets.append("".join(seq)) + else: + targets.extend(seq) + + return targets + + +def _parse_args(): + """Get command line arguments.""" + parser = argparse.ArgumentParser(description=__doc__) + + parser.add_argument( + "-d", + "--project-title", + help="Title for the modelling project", + metavar="<TITLE>", + ) + parser.add_argument( + "-m", + "--no-modelcif", + help="Do not download models in ModelCIF format.", + default=False, + action="store_true", + ) + parser.add_argument( + "-l", + "--fetch-pdb", + help="Download models in PDB legacy format.", + default=False, + action="store_true", + ) + parser.add_argument( + "-t", + "--template-sequence", + help="The template sequence used for alignment mode", + metavar="<SEQUENCE>", + ) + # ToDo: do we need the offset from the user? Doesn't interactive alignment + # mode compute it? + parser.add_argument( + "-o", + "--template-seqres-offset", + help="Offset of the template sequence segment compared to the full " + + "template sequence", + metavar="<NUMBER>", + type=int, + ) + parser.add_argument( + "-p", + "--pdb-id", + help="PDB ID (SMTL ID) for the template used in alignment mode", + metavar="<PDB ID>", + ) + parser.add_argument( + "-c", + "--auth-asym-id", + help="The chain name to be used in alignment mode", + metavar="<CHAIN NAME>", + ) + parser.add_argument( + "-a", + "--assembly-id", + help="ID of the assembly of the SMTL template to be used in alignment " + + "mode", + metavar="<NUMBER>", + type=int, + ) + parser.add_argument( + "-f", + "--template-file", + help="PDB formatted file to serve as template for modelling", + metavar="<PDB FILE>", + ) + parser.add_argument( + "project_type", + choices=("alignment", "automodel", "usertemplate"), + help="Kind of project ('alignmet', 'automodel', 'usertemplate')", + metavar="<PROJECT TYPE>", + ) + metas = { + "outdir": "<OUTPUT DIRECTORY>", + "target_sequences": "<SEQUENCE[S]>", + "token": "<TOKEN>", + } + parser.add_argument( + "token", + help="Authentication token for SWISS-MODEL", + metavar=metas["token"], + ) + parser.add_argument( + "outdir", + help="Directory to store results in", + metavar=metas["outdir"], + ) + parser.add_argument( + "target_sequences", + help="Target sequence to be modelled; to add multiple sequences, " + + "delimit with a space", + metavar=metas["target_sequences"], + nargs=argparse.REMAINDER, + ) + + opts = parser.parse_args() + + # Make sure arguments for the different modelling modes are there + req_opts = { + "alignment": [ + "assembly_id", + "auth_asym_id", + "pdb_id", + "template_seqres_offset", + "template_sequence", + ], + "automodel": [], + "usertemplate": ["template_file"], + } + # check mandatory arguments + for req in req_opts[opts.project_type]: + value = getattr(opts, req) + if value is None: + print( + f"Option '--{req.replace('_', '-')}' missing for " + + f"'{opts.project_type}' mode", + file=sys.stderr, + ) + sys.exit(2) + if isinstance(value, str) and len(value) == 0: + print( + f"Option '--{req.replace('_', '-')}' can not be an empty " + + "string", + file=sys.stderr, + ) + sys.exit(2) + # check positional arguments + for req, mta in metas.items(): + value = getattr(opts, req) + if isinstance(value, str): + if len(value) == 0: + print( + f"Argument of '{mta}' can not be an empty string", + file=sys.stderr, + ) + sys.exit(2) + elif isinstance(value, list): + if len(value) == 0 or not all(value): + print( + f"Argument of '{mta}' can not be an empty", + file=sys.stderr, + ) + sys.exit(2) + else: + raise RuntimeError( + f"Value with unknown type '{type(value).__name__}' found for " + + f"'{mta}'" + ) + # check optional & positional arguments + for opt in ["project_title"]: + value = getattr(opts, opt) + if value is not None and len(value) == 0: + print( + f"Option '--{opt.replace('_', '-')}' can not have an empty " + + "string as value", + file=sys.stderr, + ) + sys.exit(2) + + return opts + + +def _main(): + """Run as script.""" + opts = _parse_args() + + target_sequences = _defastarise_targets(opts.target_sequences) + # determine class + whsprr = None + if opts.project_type.lower() == "automodel": + whsprr = _AutoModelWhisperer( + target_sequences, opts.token, project_title=opts.project_title + ) + elif opts.project_type.lower() == "alignment": + template_sequence = _defastarise_targets([opts.template_sequence]) + assert len(template_sequence) == 1 + template_sequence = template_sequence[0] + whsprr = _AlignmentWhisperer( + target_sequences, + opts.token, + template_sequence, + opts.template_seqres_offset, + opts.pdb_id, + opts.auth_asym_id, + opts.assembly_id, + project_title=opts.project_title, + ) + elif opts.project_type.lower() == "usertemplate": + whsprr = _UserTemplateWhisperer( + target_sequences, + opts.token, + opts.template_file, + project_title=opts.project_title, + ) + else: + raise RuntimeError( + f"Not a suitable project type: '{opts.project_type}'" + ) + # run the modelling job and wait for it to finish + whsprr.submit_request() + response = whsprr.wait() + whsprr.fetch_results( + response, + opts.outdir, + fetch_modelcif=not opts.no_modelcif, + fetch_pdb=opts.fetch_pdb, + ) + + sys.exit(0) + + +if __name__ == "__main__": + _main() + +# LocalWords: Pylint
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/swissmodel_api.xml Thu Dec 11 19:32:14 2025 +0000 @@ -0,0 +1,390 @@ +<tool name="SWISS-MODEL Modelling API" id="swissmodel_modelling_api" profile="21.05" version="2.0.0"> + <description> + Fully automated protein structure homology-modelling + </description> + <xrefs> + <xref type="bio.tools">swiss_model</xref> + </xrefs> + <requirements> + <requirement type="package" version="3.11">python</requirement> + <requirement type="package" version="2.32.5">requests</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ +mkdir -p 'output_dir/' +&& python3 '$__tool_directory__/sm_api_wrapper.py' + $output_format.modelcif + $output_format.pdb + #if $project_title + --project-title '${project_title}' + #end if + #if $project_type == 'alignment' + --assembly-id '${assembly_id}' + --auth-asym-id '${auth_asym_id}' + --pdb-id '${pdb_id}' + --template-seqres-offset '${template_seqres_offset}' + --template-sequence '${template_sequence}' + #elif $project_type == 'usertemplate' + --template-file '${template_file}' + #end if + '${project.project_type}' + '${token}' output_dir + #if $project_type == 'alignment' + '${target_sequence}' + #else + #for $i in $target_list + '${i.sequence}' + #end for + #end if +&& find output_dir -type f -name '*.gz' -exec gzip -d {} + +]]> + </command> + <inputs> + <param name="token" type="text" optional="false" label="API token"> + <help><![CDATA[ +Token to authenticate to the SWISS-MODEL API. Can be managed on your +<a href="https://swissmodel.expasy.org/login_page" target="_blank"> SWISS-MODEL account</a> page. + ]]></help> + </param> + <param name="project_title" type="text" value="Untitled project" optional="true" label="Project title"/> + <conditional name="project"> + <param name="project_type" type="select" value="automodel" optional="false" label="Modelling setup" display="radio"> + <option value="automodel" selected="true">Automodel mode</option> + <option value="alignment">Alignment mode</option> + <option value="usertemplate">User template mode</option> + </param> + <!-- AutoModel Mode Options --> + <when value="automodel"> + <repeat name="target_list" min="1" + help="Sequence(s) to be modelled. Add multiple sequences for hetero modelling." title="Target sequence"> + <param name="sequence" type="text" optional="false" + label="Sequence"/> + </repeat> + </when> + <!-- Alignment Mode Options --> + <when value="alignment"> + <param name="target_sequence" type="text" optional="false" + label="Target sequence" + help="Target sequence as part of the alignment"/> + <param name="pdb_id" type="text" optional="false" + label="PDB/ SMTL ID"> + <help><![CDATA[ +PDB ID of the template SMTL entry as found in the +<a href="https://swissmodel.expasy.org/templates/" target="_blank"> SWISS-MODEL +Template Library</a>. + ]]></help> + <validator type="regex" message="Only PDB-like IDs allowed, e.g. '1crn'.">^\d[A-Za-z0-9]{3}$</validator> + </param> + <param name="assembly_id" type="integer" min="0" value="0" optional="false" + label="Assembly ID"> + <help><![CDATA[ +Assembly ID of the template as found in the +<a href="https://swissmodel.expasy.org/templates/" target="_blank"> SWISS-MODEL +Template Library</a>. + ]]></help> + </param> + <param name="auth_asym_id" type="text" optional="false" + label="Chain name"> + <help><![CDATA[ +Chain name in the template assembly as found in the +<a href="https://swissmodel.expasy.org/templates/" target="_blank"> SWISS-MODEL +Template Library</a>. + ]]></help> + </param> + <param name="template_sequence" type="text" optional="false" + label="Template sequence" + help="Template sequence as part of the alignment"/> + <param name="template_seqres_offset" type="integer" value="0" optional="false" label="Template sequence offset"> + <help><![CDATA[ +Offset of the template sequence segment with respect to the full template +sequence. + ]]></help> + </param> + </when> + <!-- User Template Mode Options --> + <when value="usertemplate"> + <repeat name="target_list" min="1" + help="Sequence(s) to be modelled. Add multiple sequences for hetero modelling." title="Target sequence"> + <param name="sequence" type="text" optional="false" + label="Sequence"/> + </repeat> + <param name="template_file" type="data" format="txt" optional="false" label="Template coordinates file" + help="File with template coordinaqtes in PDB legacy format."/> + </when> + </conditional> + <section name="output_format" title="Output format options"> + <param name="modelcif" type="boolean" truevalue="" falsevalue="--no-modelcif" checked="true" label="ModelCIF format"/> + <param name="pdb" type="boolean" truevalue="--fetch-pdb" falsevalue="" checked="false" label="PDB legacy format"/> + </section> + </inputs> + <outputs> + <collection name="json_collection" type="list" + label="Metadata files for $project_title"> + <discover_datasets directory="output_dir/JSON" format="json" pattern="(?P<name>.+)\.json$"/> + </collection> + <collection name="pdb_collection" type="list" + label="PDB files for $project_title"> + <discover_datasets directory="output_dir/PDB" format="pdb" pattern="(?P<name>.+)\.pdb$"/> + <filter>output_format['pdb'] == True</filter> + </collection> + <collection name="modelcif_collection" type="list" + label="ModelCIF files for $project_title"> + <discover_datasets directory="output_dir/ModelCIF" format="cif" pattern="(?P<name>.+)\.cif$"/> + <filter>output_format['modelcif'] == True</filter> + </collection> + </outputs> + <tests> + <!-- w/o params, all will be empty strings, fail --> + <test expect_exit_code="2" expect_failure="true"> + <assert_stderr> + <has_line line="Argument of '<SEQUENCE[S]>' can not be an empty"/> + </assert_stderr> + </test> + <!-- with sequences, everything else empty, fail --> + <test expect_exit_code="2" expect_failure="true"> + <conditional name="project"> + <repeat name="target_list"> + <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/> + </repeat> + <repeat name="target_list"> + <param name="sequence" value="AKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKE"/> + </repeat> + </conditional> + <assert_stderr> + <has_line line="Argument of '<TOKEN>' can not be an empty string"/> + </assert_stderr> + </test> + <!-- sequence and token (complete automodel job), fail (no real token) --> + <test expect_exit_code="1" expect_failure="true"> + <conditional name="project"> + <repeat name="target_list"> + <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/> + </repeat> + </conditional> + <param name="token" value="NOTAVALIDTOKEN"/> + <assert_stderr> + <has_line line="RuntimeError: Submitting modelling job failed (401)"/> + </assert_stderr> + </test> + <!-- alignment mode tests, as few params as possible, fail --> + <test expect_exit_code="2" expect_failure="true"> + <conditional name="project"> + <param name="project_type" value="alignment"/> + <param name="assembly_id" value="0"/> + <param name="template_seqres_offset" value="0"/> + </conditional> + <assert_stderr> + <has_line line="Option '--auth-asym-id' can not be an empty string"/> + </assert_stderr> + </test> + <!-- alignment mode tests, with auth_asym_id, fail --> + <test expect_exit_code="2" expect_failure="true"> + <conditional name="project"> + <param name="assembly_id" value="0"/> + <param name="auth_asym_id" value="A"/> + <param name="project_type" value="alignment"/> + <param name="template_seqres_offset" value="0"/> + </conditional> + <assert_stderr> + <has_line line="Option '--pdb-id' can not be an empty string"/> + </assert_stderr> + </test> + <!-- alignment mode tests, with pdb_id, fail --> + <test expect_exit_code="2" expect_failure="true"> + <conditional name="project"> + <param name="assembly_id" value="0"/> + <param name="auth_asym_id" value="A"/> + <param name="pdb_id" value="1AKE"/> + <param name="project_type" value="alignment"/> + <param name="template_seqres_offset" value="0"/> + </conditional> + <assert_stderr> + <has_line line="Option '--template-sequence' can not be an empty string"/> + </assert_stderr> + </test> + <!-- alignment mode tests, with template_sequence, fail --> + <test expect_exit_code="2" expect_failure="true"> + <conditional name="project"> + <param name="assembly_id" value="0"/> + <param name="auth_asym_id" value="A"/> + <param name="pdb_id" value="1AKE"/> + <param name="project_type" value="alignment"/> + <param name="template_seqres_offset" value="0"/> + <param name="template_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPV"/> + </conditional> + <assert_stderr> + <has_line line="Argument of '<SEQUENCE[S]>' can not be an empty"/> + </assert_stderr> + </test> + <!-- alignment mode tests, with sequence, fail --> + <test expect_exit_code="2" expect_failure="true"> + <conditional name="project"> + <param name="assembly_id" value="0"/> + <param name="auth_asym_id" value="A"/> + <param name="pdb_id" value="1AKE"/> + <param name="project_type" value="alignment"/> + <param name="target_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSG"/> + <param name="template_seqres_offset" value="0"/> + <param name="template_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPV"/> + </conditional> + <assert_stderr> + <has_line line="Argument of '<TOKEN>' can not be an empty string"/> + </assert_stderr> + </test> + <!-- alignment mode tests, with token, fail --> + <test expect_exit_code="1" expect_failure="true"> + <conditional name="project"> + <param name="assembly_id" value="0"/> + <param name="auth_asym_id" value="A"/> + <param name="pdb_id" value="1AKE"/> + <param name="project_type" value="alignment"/> + <param name="target_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSG"/> + <param name="template_seqres_offset" value="0"/> + <param name="template_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPV"/> + </conditional> + <param name="token" value="NOTAVALIDTOKEN"/> + <assert_stderr> + <has_line line="RuntimeError: Submitting modelling job failed (401)"/> + </assert_stderr> + </test> + <!-- usertemplate mode tests, as few params as possible, fail --> + <test expect_exit_code="2" expect_failure="true"> + <conditional name="project"> + <param name="project_type" value="usertemplate"/> + <param name="template_file" value="model_01.pdb"/> + </conditional> + <assert_stderr> + <has_line line="Argument of '<SEQUENCE[S]>' can not be an empty"/> + </assert_stderr> + </test> + <!-- usertemplate mode tests, with sequence, fail --> + <test expect_exit_code="2" expect_failure="true"> + <conditional name="project"> + <param name="project_type" value="usertemplate"/> + <param name="template_file" value="model_01.pdb"/> + <repeat name="target_list"> + <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/> + </repeat> + <repeat name="target_list"> + <param name="sequence" value="AKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKE"/> + </repeat> + </conditional> + <assert_stderr> + <has_line line="Argument of '<TOKEN>' can not be an empty string"/> + </assert_stderr> + </test> + <!-- usertemplate mode tests, with token, fail --> + <test expect_exit_code="1" expect_failure="true"> + <conditional name="project"> + <param name="project_type" value="usertemplate"/> + <param name="template_file" value="model_01.pdb"/> + <repeat name="target_list"> + <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/> + </repeat> + <repeat name="target_list"> + <param name="sequence" value="AKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKE"/> + </repeat> + </conditional> + <param name="token" value="NOTAVALIDTOKEN"/> + <assert_stderr> + <has_line line="RuntimeError: Submitting modelling job failed (401)"/> + </assert_stderr> + </test> + </tests> + <help><![CDATA[ +The SWISS-MODEL Modelling API tool gives you convenient access to homology models build by `SWISS-MODEL <https://swissmodel.expasy.org>`_ via our `API <https://swissmodel.expasy.org/docs/help#modelling_api>`_. + +By default, the tool fetches model coordinates in ModelCIF format from the SWISS-MODEL API. SWISS-MODEL enriches its ModelCIF files with lots of extra information, essential for later reproduction of the computational experiment and enabling for easy deposition at archiving sites, like `Model Archive <https://modelarchive.org>`_. Output format can be toggled in the *Output format options* section for legacy PDB format, in case you are dealing with old-school tools in your workflows. Regardless of the format, output file names follow the pattern ``model_<N>.[cif|pdb]``. + +The SWISS-MODEL API provides three major modelling modes: Automodel, alignment and template upload mode. + +Automodel mode +-------------- + +This mode corresponds to the "Sequence(s)" input mode and just hitting the "Build Model" button on our `web page <https://swissmodel.expasy.org/interactive>`_. + +Automodel goes from sequence(s) to structural model. A single sequence for input leads to monomers or homomers. Multiple sequences for input produces heteromers, incorporating all target sequences. Multiple sequences input is sometimes mistaken for multi-model modelling tasks but its not, to produce models for more than one target sequence, you need to run the tool for each sequence separately. + +Inside an automodel job, the following happens: + +1. Template search in `PDB <https://www.rcsb.org>`_ and AlphaFold DB v4 sequences +2. Template selection by estimated quality and target sequence coverage + + - gain high model confidence + - cover as much of the target sequence, maybe by different models per region + - employ models for equal regions if structurally diverse + +3. Build models + +Automodel options +~~~~~~~~~~~~~~~~~ + +Only one or more sequences required, that's all! Single sequence produces monomers and/ or homomers. Multiple sequences produces heteromers. + + +Alignment mode +-------------- + +This mode corresponds to the "Target-Template Alignment" input mode on our `web page <https://swissmodel.expasy.org/interactive#alignment>`_. + +The alignment mode still builds a model for a target sequence and a template from the `SWISS-MODEL template library <https://swissmodel.expasy.org/templates/>`_ (**SMTL**). But instead of creating the alignment from its own template search run, SWISS-MODEL will use an alignment provided by yourself. The alignment will be mapped onto the template sequence and then a structural model will be build. + +To properly map a your alignment within the SMTL, you need to provide some extra information. SWISS-MODEL needs the identifier of the template. That's a common PDB ID, it just needs to exist in the SMTL. Then you need to identify the biological assembly of the entry you want your model to be based on... which can be easily done from the SMTL page. The assembly ID comes with the SMTL ID, its the number after the PDB ID and alternative assemblies of an entry can be found at the bottom of an entry page. The last component is the chain name you used for the alignment. Be aware, the SMTL uses its own chain names, so the original PDB chain name may not work. A mapping of chain names is provided on SMTL entry pages. + +Alignment mode options +~~~~~~~~~~~~~~~~~~~~~~ + +- Target sequence: first part of the alignment +- Template sequence: second sequence of the alignment +- Template sequence offset: position the template sequence starts at with respect to the full sequence; When using only a sub-sequence of the full sequence, it may be hard to automatically map to the right region in case of repeats, so you need to provide the offset +- PDB/ SMTL ID: PDB ID of the SMTL entry the alignment refers to +- Assembly ID: ID of the biological assembly to be used as template +- Chain name: ID of the chain to be used for modelling, needs to be the SMTL name, not the PDB name + + +User template mode +------------------ + +This mode corresponds to the "User Template" input mode on our `web page <https://swissmodel.expasy.org/interactive#structure>`_. + +The user template mode builds a model for a target sequence and template coordinates provided by you instead of using a SMTL entry for coordinates. The sequence alignment between target and template sequence is still calculated by SWISS-MODEL using HHblits and BLAST, or local alignment algorithm if both methods fail. With the alignment, a structural model is build based on the provided template coordinates. + +Inside a user template job, the following happens: + +1. Analyse uploaded coordinates +2. Calculate alignments with HHblits & BLAST +3. Choose "better" alignment or calculate Smith-Waterman alignment +4. Build model + +User template mode options +~~~~~~~~~~~~~~~~~~~~~~~~~~ +- Target sequence: sequence to be modelled (post multiple for heteros) +- Template coordinate file: your template file, must be PDB formatted + +Attribution/ License +~~~~~~~~~~~~~~~~~~~~ + +Terms of use can be found at https://swissmodel.expasy.org/docs/terms_of_use + +Modelling results of SWISS-MODEL are licensed under the +`CC BY-SA 4.0 Creative Commons Attribution-ShareAlike 4.0 International License <https://creativecommons.org/licenses/by-sa/4.0/legalcode>`_. + +]]> + </help> + <citations> + <!-- SWISS-MODEL --> + <citation type="doi">10.1093/nar/gky427</citation> + <!-- ProMod3 --> + <citation type="doi">10.1371/journal.pcbi.1008667</citation> + <!-- QMEANDisCo --> + <citation type="doi">10.1093/bioinformatics/btz828</citation> + <!-- Quaternary Structure Prediction/ QSQE --> + <citation type="doi">10.1038/s41598-017-09654-8</citation> + <!-- lDDT --> + <citation type="doi">10.1093/bioinformatics/btt473</citation> + </citations> + <creator> + <person email="stefan.bienert@unibas.ch" familyName="Bienert" givenName="Stefan"/> + <organization name="Swiss Institute of Bioinformatics" alternateName="SIB" url="https://www.sib.swiss"/> + <organization name="Biozentrum, University of Basel" alternateName="Biozentrum" url="https://www.biozentrum.unibas.ch"/> + </creator> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model_01.pdb Thu Dec 11 19:32:14 2025 +0000 @@ -0,0 +1,382 @@ +TITLE SWISS-MODEL SERVER (https://swissmodel.expasy.org) +TITLE 2 Untitled Project +EXPDTA THEORETICAL MODEL (SWISS-MODEL SERVER) +AUTHOR SWISS-MODEL SERVER (SEE REFERENCE IN JRNL Records) +REVDAT 1 03-DEC-25 1MOD 1 14:47 +JRNL AUTH A.WATERHOUSE,M.BERTONI,S.BIENERT,G.STUDER,G.TAURIELLO, +JRNL AUTH 2 R.GUMIENNY,F.T.HEER,T.A.P.DE BEER,C.REMPFER,L.BORDOLI, +JRNL AUTH 3 R.LEPORE,T.SCHWEDE +JRNL TITL SWISS-MODEL: HOMOLOGY MODELLING OF PROTEIN STRUCTURES AND +JRNL TITL 2 COMPLEXES +JRNL REF NUCLEIC.ACIDS.RES.. V. 46 W296 2018 +JRNL PMID 29788355 +JRNL DOI 10.1093/nar/gky427 +REMARK 1 +REMARK 1 REFERENCE 1 +REMARK 1 AUTH S.BIENERT,A.WATERHOUSE,T.A.P.DE BEER,G.TAURIELLO,G.STUDER, +REMARK 1 AUTH 2 L.BORDOLI,T.SCHWEDE +REMARK 1 TITL THE SWISS-MODEL REPOSITORY - NEW FEATURES AND FUNCTIONALITY +REMARK 1 REF NUCLEIC.ACIDS.RES.. V. 45 2017 +REMARK 1 REFN ISSN 0305-1048 +REMARK 1 PMID 27899672 +REMARK 1 DOI 10.1093/nar/gkw1132 +REMARK 1 +REMARK 1 REFERENCE 2 +REMARK 1 AUTH N.GUEX,M.C.PEITSCH,T.SCHWEDE +REMARK 1 TITL AUTOMATED COMPARATIVE PROTEIN STRUCTURE MODELING WITH +REMARK 1 TITL 2 SWISS-MODEL AND SWISS-PDBVIEWER: A HISTORICAL PERSPECTIVE +REMARK 1 REF ELECTROPHORESIS V. 30 2009 +REMARK 1 REFN ISSN 0173-0835 +REMARK 1 PMID 19517507 +REMARK 1 DOI 10.1002/elps.200900140 +REMARK 1 +REMARK 1 REFERENCE 3 +REMARK 1 AUTH G.STUDER,G.TAURIELLO,S.BIENERT,M.BIASINI,N.JOHNER,T.SCHWEDE +REMARK 1 TITL PROMOD3 - A VERSATILE HOMOLOGY MODELLING TOOLBOX +REMARK 1 REF PLOS COMP. BIOL. V. 17 2021 +REMARK 1 REFN ISSN +REMARK 1 PMID 33507980 +REMARK 1 DOI 10.1371/journal.pcbi.1008667 +REMARK 1 +REMARK 1 REFERENCE 4 +REMARK 1 AUTH G.STUDER,C.REMPFER,A.WATERHOUSE,R.GUMIENNY,J.HAAS,T.SCHWEDE +REMARK 1 TITL QMEANDISCO - DISTANCE CONSTRAINTS APPLIED ON MODEL QUALITY +REMARK 1 TITL 2 ESTIMATION +REMARK 1 REF BIOINFORMATICS V. 36 2020 +REMARK 1 REFN ISSN +REMARK 1 PMID 31697312 +REMARK 1 DOI 10.1093/bioinformatics/btz828 +REMARK 1 +REMARK 1 REFERENCE 5 +REMARK 1 AUTH P.BENKERT,M.BIASINI,T.SCHWEDE +REMARK 1 TITL TOWARD THE ESTIMATION OF THE ABSOLUTE QUALITY OF INDIVIDUAL +REMARK 1 TITL 2 PROTEIN STRUCTURE MODELS +REMARK 1 REF BIOINFORMATICS V. 27 2011 +REMARK 1 REFN ISSN 1367-4803 +REMARK 1 PMID 21134891 +REMARK 1 DOI 10.1093/bioinformatics/btq662 +REMARK 1 +REMARK 1 REFERENCE 6 +REMARK 1 AUTH M.BERTONI,F.KIEFER,M.BIASINI,L.BORDOLI,T.SCHWEDE +REMARK 1 TITL MODELING PROTEIN QUATERNARY STRUCTURE OF HOMO- AND +REMARK 1 TITL 2 HETERO-OLIGOMERS BEYOND BINARY INTERACTIONS BY HOMOLOGY +REMARK 1 REF SCI.REP. V. 7 2017 +REMARK 1 REFN ISSN +REMARK 1 PMID 28874689 +REMARK 1 DOI 10.1038/s41598-017-09654-8 +REMARK 1 +REMARK 1 DISCLAIMER +REMARK 1 The SWISS-MODEL SERVER produces theoretical models for proteins. +REMARK 1 The results of any theoretical modelling procedure is +REMARK 1 NON-EXPERIMENTAL and MUST be considered with care. These models may +REMARK 1 contain significant errors. This is especially true for automated +REMARK 1 modeling since there is no human intervention during model +REMARK 1 building. Please read the header section and the logfile carefully +REMARK 1 to know what templates and alignments were used during the model +REMARK 1 building process. All information by the SWISS-MODEL SERVER is +REMARK 1 provided "AS-IS", without any warranty, expressed or implied. +REMARK 2 +REMARK 2 COPYRIGHT NOTICE +REMARK 2 This SWISS-MODEL protein model is copyright. It is produced by the +REMARK 2 SWISS-MODEL server, developed by the Computational Structural +REMARK 2 Biology Group at the SIB Swiss Institute of Bioinformatics at the +REMARK 2 Biozentrum, University of Basel (https://swissmodel.expasy.org). This +REMARK 2 model is licensed under the CC BY-SA 4.0 Creative Commons +REMARK 2 Attribution-ShareAlike 4.0 International License +REMARK 2 (https://creativecommons.org/licenses/by-sa/4.0/legalcode), i.e. you +REMARK 2 can copy and redistribute the model in any medium or format, +REMARK 2 transform and build upon the model for any purpose, even +REMARK 2 commercially, under the following terms: +REMARK 2 Attribution - You must give appropriate credit, provide a link to +REMARK 2 the license, and indicate if changes were made. You may do so in any +REMARK 2 reasonable manner, but not in any way that suggests the licensor +REMARK 2 endorses you or your use. When you publish, patent or distribute +REMARK 2 results that were fully or partially based on the model, please cite +REMARK 2 the corresponding papers mentioned under JRNL. +REMARK 2 ShareAlike - If you remix, transform, or build upon the material, +REMARK 2 you must distribute your contributions under the same license as the +REMARK 2 original. +REMARK 2 No additional restrictions - you may not apply legal terms or +REMARK 2 technological measures that legally restrict others from doing +REMARK 2 anything the license permits. +REMARK 2 Find a human-readable summary of (and not a substitute for) the +REMARK 2 CC BY-SA 4.0 license at this link: +REMARK 2 https://creativecommons.org/licenses/by-sa/4.0/ +REMARK 3 +REMARK 3 MODEL INFORMATION +REMARK 3 SMVERSN 2025-11.2 +REMARK 3 ENGIN PROMOD3 +REMARK 3 VERSN 3.6.0 +REMARK 3 OSTAT monomer +REMARK 3 OSRSN MONOMER +REMARK 3 QSPRD 0.000 +REMARK 3 GMQE 0.60 +REMARK 3 QMNV 4.5.0 +REMARK 3 QMNDG 0.50 +REMARK 3 MODT FALSE +REMARK 3 +REMARK 3 TEMPLATE 1 +REMARK 3 PDBID 9vel +REMARK 3 CHAIN r +REMARK 3 MMCIF N +REMARK 3 PDBV 2025-11-21 +REMARK 3 SMTLE 9vel.1.N +REMARK 3 SMTLV 2025-12-01 +REMARK 3 MTHD ELECTRON MICROSCOPY 0.00 A +REMARK 3 FOUND HHblits +REMARK 3 GMQE 0.85 +REMARK 3 SIM 0.63 +REMARK 3 SID 100.00 +REMARK 3 OSTAT monomer +REMARK 3 ALN N TRG RGRNPEATGDYDDHIWVTEEVEVRPLVDEV +REMARK 3 ALN N TPL RGRNPEATGDYDDHIWVTEEVEVRPLVDEV +REMARK 3 ALN N OFF 92 +ATOM 1 N ARG N 1 347.942 282.863 -68.043 1.00 0.77 N +ATOM 2 CA ARG N 1 346.686 283.693 -68.216 1.00 0.77 C +ATOM 3 C ARG N 1 346.823 285.004 -67.474 1.00 0.77 C +ATOM 4 O ARG N 1 347.536 285.033 -66.480 1.00 0.77 O +ATOM 5 CB ARG N 1 345.457 282.942 -67.613 1.00 0.77 C +ATOM 6 CG ARG N 1 345.009 281.679 -68.376 1.00 0.77 C +ATOM 7 CD ARG N 1 343.759 281.017 -67.769 1.00 0.77 C +ATOM 8 NE ARG N 1 343.440 279.801 -68.596 1.00 0.77 N +ATOM 9 CZ ARG N 1 342.675 279.792 -69.699 1.00 0.77 C +ATOM 10 NH1 ARG N 1 342.176 280.907 -70.220 1.00 0.77 N +ATOM 11 NH2 ARG N 1 342.397 278.632 -70.292 1.00 0.77 N +ATOM 12 N GLY N 2 346.176 286.100 -67.912 1.00 0.85 N +ATOM 13 CA GLY N 2 346.233 287.368 -67.207 1.00 0.85 C +ATOM 14 C GLY N 2 344.948 288.090 -67.454 1.00 0.85 C +ATOM 15 O GLY N 2 344.016 287.531 -68.035 1.00 0.85 O +ATOM 16 N ARG N 3 344.877 289.360 -67.038 1.00 0.46 N +ATOM 17 CA ARG N 3 343.712 290.199 -67.189 1.00 0.46 C +ATOM 18 C ARG N 3 344.216 291.557 -67.588 1.00 0.46 C +ATOM 19 O ARG N 3 345.277 291.981 -67.120 1.00 0.46 O +ATOM 20 CB ARG N 3 342.904 290.360 -65.873 1.00 0.46 C +ATOM 21 CG ARG N 3 342.207 289.059 -65.425 1.00 0.46 C +ATOM 22 CD ARG N 3 341.483 289.136 -64.069 1.00 0.46 C +ATOM 23 NE ARG N 3 340.328 290.095 -64.178 1.00 0.46 N +ATOM 24 CZ ARG N 3 339.076 289.778 -64.524 1.00 0.46 C +ATOM 25 NH1 ARG N 3 338.744 288.554 -64.881 1.00 0.46 N +ATOM 26 NH2 ARG N 3 338.181 290.734 -64.691 1.00 0.46 N +ATOM 27 N ASN N 4 343.491 292.250 -68.475 1.00 0.51 N +ATOM 28 CA ASN N 4 343.856 293.547 -68.987 1.00 0.51 C +ATOM 29 C ASN N 4 343.432 294.634 -67.981 1.00 0.51 C +ATOM 30 O ASN N 4 342.243 294.685 -67.666 1.00 0.51 O +ATOM 31 CB ASN N 4 343.165 293.766 -70.365 1.00 0.51 C +ATOM 32 CG ASN N 4 344.085 294.529 -71.305 1.00 0.51 C +ATOM 33 OD1 ASN N 4 345.233 294.801 -70.993 1.00 0.51 O +ATOM 34 ND2 ASN N 4 343.575 294.849 -72.519 1.00 0.51 N +ATOM 35 N PRO N 5 344.273 295.502 -67.415 1.00 0.53 N +ATOM 36 CA PRO N 5 343.868 296.476 -66.398 1.00 0.53 C +ATOM 37 C PRO N 5 342.880 297.525 -66.890 1.00 0.53 C +ATOM 38 O PRO N 5 342.084 298.021 -66.095 1.00 0.53 O +ATOM 39 CB PRO N 5 345.185 297.155 -65.974 1.00 0.53 C +ATOM 40 CG PRO N 5 346.281 296.150 -66.339 1.00 0.53 C +ATOM 41 CD PRO N 5 345.721 295.465 -67.587 1.00 0.53 C +ATOM 42 N GLU N 6 342.971 297.909 -68.177 1.00 0.53 N +ATOM 43 CA GLU N 6 342.193 298.943 -68.821 1.00 0.53 C +ATOM 44 C GLU N 6 341.153 298.433 -69.814 1.00 0.53 C +ATOM 45 O GLU N 6 340.723 299.181 -70.691 1.00 0.53 O +ATOM 46 CB GLU N 6 343.155 299.945 -69.529 1.00 0.53 C +ATOM 47 CG GLU N 6 343.966 299.439 -70.767 1.00 0.53 C +ATOM 48 CD GLU N 6 345.280 298.701 -70.496 1.00 0.53 C +ATOM 49 OE1 GLU N 6 345.541 298.322 -69.327 1.00 0.53 O +ATOM 50 OE2 GLU N 6 346.040 298.533 -71.484 1.00 0.53 O +ATOM 51 N ALA N 7 340.692 297.160 -69.695 1.00 0.55 N +ATOM 52 CA ALA N 7 339.657 296.587 -70.551 1.00 0.55 C +ATOM 53 C ALA N 7 338.387 297.428 -70.616 1.00 0.55 C +ATOM 54 O ALA N 7 337.884 297.922 -69.602 1.00 0.55 O +ATOM 55 CB ALA N 7 339.295 295.154 -70.099 1.00 0.55 C +ATOM 56 N THR N 8 337.841 297.649 -71.827 1.00 0.54 N +ATOM 57 CA THR N 8 336.755 298.606 -72.002 1.00 0.54 C +ATOM 58 C THR N 8 335.416 297.919 -71.890 1.00 0.54 C +ATOM 59 O THR N 8 334.381 298.559 -71.736 1.00 0.54 O +ATOM 60 CB THR N 8 336.790 299.355 -73.336 1.00 0.54 C +ATOM 61 OG1 THR N 8 336.652 298.493 -74.456 1.00 0.54 O +ATOM 62 CG2 THR N 8 338.143 300.067 -73.481 1.00 0.54 C +ATOM 63 N GLY N 9 335.422 296.573 -71.949 1.00 0.50 N +ATOM 64 CA GLY N 9 334.211 295.793 -71.850 1.00 0.50 C +ATOM 65 C GLY N 9 334.512 294.358 -71.536 1.00 0.50 C +ATOM 66 O GLY N 9 335.506 294.018 -70.906 1.00 0.50 O +ATOM 67 N ASP N 10 333.640 293.454 -72.014 1.00 0.45 N +ATOM 68 CA ASP N 10 333.667 292.063 -71.618 1.00 0.45 C +ATOM 69 C ASP N 10 334.439 291.198 -72.629 1.00 0.45 C +ATOM 70 O ASP N 10 334.543 289.984 -72.496 1.00 0.45 O +ATOM 71 CB ASP N 10 332.200 291.550 -71.524 1.00 0.45 C +ATOM 72 CG ASP N 10 331.360 292.224 -70.442 1.00 0.45 C +ATOM 73 OD1 ASP N 10 331.852 293.141 -69.742 1.00 0.45 O +ATOM 74 OD2 ASP N 10 330.175 291.817 -70.336 1.00 0.45 O +ATOM 75 N TYR N 11 335.013 291.822 -73.687 1.00 0.44 N +ATOM 76 CA TYR N 11 335.597 291.113 -74.819 1.00 0.44 C +ATOM 77 C TYR N 11 337.122 291.222 -74.841 1.00 0.44 C +ATOM 78 O TYR N 11 337.780 290.494 -75.580 1.00 0.44 O +ATOM 79 CB TYR N 11 335.033 291.646 -76.176 1.00 0.44 C +ATOM 80 CG TYR N 11 333.595 291.223 -76.408 1.00 0.44 C +ATOM 81 CD1 TYR N 11 332.527 291.778 -75.678 1.00 0.44 C +ATOM 82 CD2 TYR N 11 333.297 290.264 -77.395 1.00 0.44 C +ATOM 83 CE1 TYR N 11 331.205 291.371 -75.914 1.00 0.44 C +ATOM 84 CE2 TYR N 11 331.973 289.875 -77.651 1.00 0.44 C +ATOM 85 CZ TYR N 11 330.927 290.430 -76.906 1.00 0.44 C +ATOM 86 OH TYR N 11 329.588 290.068 -77.159 1.00 0.44 O +ATOM 87 N ASP N 12 337.727 292.112 -74.022 1.00 0.48 N +ATOM 88 CA ASP N 12 339.149 292.371 -73.996 1.00 0.48 C +ATOM 89 C ASP N 12 339.741 292.237 -72.585 1.00 0.48 C +ATOM 90 O ASP N 12 340.875 292.648 -72.347 1.00 0.48 O +ATOM 91 CB ASP N 12 339.431 293.771 -74.645 1.00 0.48 C +ATOM 92 CG ASP N 12 338.722 294.969 -74.009 1.00 0.48 C +ATOM 93 OD1 ASP N 12 337.659 294.802 -73.358 1.00 0.48 O +ATOM 94 OD2 ASP N 12 339.247 296.097 -74.187 1.00 0.48 O +ATOM 95 N ASP N 13 339.001 291.627 -71.620 1.00 0.49 N +ATOM 96 CA ASP N 13 339.417 291.508 -70.228 1.00 0.49 C +ATOM 97 C ASP N 13 340.450 290.388 -70.065 1.00 0.49 C +ATOM 98 O ASP N 13 341.564 290.587 -69.602 1.00 0.49 O +ATOM 99 CB ASP N 13 338.159 291.275 -69.321 1.00 0.49 C +ATOM 100 CG ASP N 13 338.382 291.574 -67.846 1.00 0.49 C +ATOM 101 OD1 ASP N 13 339.457 292.085 -67.451 1.00 0.49 O +ATOM 102 OD2 ASP N 13 337.472 291.215 -67.048 1.00 0.49 O +ATOM 103 N HIS N 14 340.128 289.163 -70.533 1.00 0.47 N +ATOM 104 CA HIS N 14 340.987 288.000 -70.371 1.00 0.47 C +ATOM 105 C HIS N 14 341.961 287.838 -71.518 1.00 0.47 C +ATOM 106 O HIS N 14 341.580 287.753 -72.683 1.00 0.47 O +ATOM 107 CB HIS N 14 340.188 286.682 -70.248 1.00 0.47 C +ATOM 108 CG HIS N 14 339.345 286.625 -69.017 1.00 0.47 C +ATOM 109 ND1 HIS N 14 338.139 287.295 -69.012 1.00 0.47 N +ATOM 110 CD2 HIS N 14 339.519 285.971 -67.847 1.00 0.47 C +ATOM 111 CE1 HIS N 14 337.601 287.036 -67.851 1.00 0.47 C +ATOM 112 NE2 HIS N 14 338.392 286.230 -67.088 1.00 0.47 N +ATOM 113 N ILE N 15 343.266 287.759 -71.196 1.00 0.45 N +ATOM 114 CA ILE N 15 344.338 287.740 -72.171 1.00 0.45 C +ATOM 115 C ILE N 15 345.403 286.751 -71.722 1.00 0.45 C +ATOM 116 O ILE N 15 345.323 286.141 -70.647 1.00 0.45 O +ATOM 117 CB ILE N 15 344.987 289.122 -72.378 1.00 0.45 C +ATOM 118 CG1 ILE N 15 345.520 289.727 -71.049 1.00 0.45 C +ATOM 119 CG2 ILE N 15 343.989 290.067 -73.096 1.00 0.45 C +ATOM 120 CD1 ILE N 15 346.472 290.913 -71.267 1.00 0.45 C +ATOM 121 N TRP N 16 346.447 286.550 -72.543 1.00 0.38 N +ATOM 122 CA TRP N 16 347.589 285.724 -72.223 1.00 0.38 C +ATOM 123 C TRP N 16 348.797 286.627 -72.212 1.00 0.38 C +ATOM 124 O TRP N 16 348.919 287.528 -73.039 1.00 0.38 O +ATOM 125 CB TRP N 16 347.791 284.576 -73.243 1.00 0.38 C +ATOM 126 CG TRP N 16 346.609 283.630 -73.292 1.00 0.38 C +ATOM 127 CD1 TRP N 16 345.436 283.762 -73.983 1.00 0.38 C +ATOM 128 CD2 TRP N 16 346.506 282.377 -72.581 1.00 0.38 C +ATOM 129 NE1 TRP N 16 344.608 282.678 -73.762 1.00 0.38 N +ATOM 130 CE2 TRP N 16 345.271 281.818 -72.904 1.00 0.38 C +ATOM 131 CE3 TRP N 16 347.411 281.723 -71.741 1.00 0.38 C +ATOM 132 CZ2 TRP N 16 344.893 280.568 -72.411 1.00 0.38 C +ATOM 133 CZ3 TRP N 16 347.037 280.464 -71.242 1.00 0.38 C +ATOM 134 CH2 TRP N 16 345.802 279.895 -71.571 1.00 0.38 C +ATOM 135 N VAL N 17 349.702 286.422 -71.243 1.00 0.39 N +ATOM 136 CA VAL N 17 350.885 287.221 -71.040 1.00 0.39 C +ATOM 137 C VAL N 17 352.040 286.258 -70.982 1.00 0.39 C +ATOM 138 O VAL N 17 351.840 285.058 -70.773 1.00 0.39 O +ATOM 139 CB VAL N 17 350.832 288.062 -69.760 1.00 0.39 C +ATOM 140 CG1 VAL N 17 349.788 289.182 -69.964 1.00 0.39 C +ATOM 141 CG2 VAL N 17 350.525 287.212 -68.499 1.00 0.39 C +ATOM 142 N THR N 18 353.264 286.762 -71.211 1.00 0.39 N +ATOM 143 CA THR N 18 354.489 285.987 -71.297 1.00 0.39 C +ATOM 144 C THR N 18 355.395 286.423 -70.167 1.00 0.39 C +ATOM 145 O THR N 18 355.400 287.603 -69.805 1.00 0.39 O +ATOM 146 CB THR N 18 355.199 286.142 -72.648 1.00 0.39 C +ATOM 147 OG1 THR N 18 356.273 285.223 -72.751 1.00 0.39 O +ATOM 148 CG2 THR N 18 355.728 287.569 -72.913 1.00 0.39 C +ATOM 149 N GLU N 19 356.150 285.487 -69.563 1.00 0.44 N +ATOM 150 CA GLU N 19 357.011 285.741 -68.430 1.00 0.44 C +ATOM 151 C GLU N 19 358.244 284.882 -68.578 1.00 0.44 C +ATOM 152 O GLU N 19 358.190 283.798 -69.161 1.00 0.44 O +ATOM 153 CB GLU N 19 356.384 285.338 -67.064 1.00 0.44 C +ATOM 154 CG GLU N 19 354.940 285.845 -66.836 1.00 0.44 C +ATOM 155 CD GLU N 19 354.356 285.465 -65.476 1.00 0.44 C +ATOM 156 OE1 GLU N 19 355.008 284.703 -64.719 1.00 0.44 O +ATOM 157 OE2 GLU N 19 353.216 285.930 -65.207 1.00 0.44 O +ATOM 158 N GLU N 20 359.373 285.336 -68.008 1.00 0.43 N +ATOM 159 CA GLU N 20 360.658 284.685 -68.114 1.00 0.43 C +ATOM 160 C GLU N 20 360.979 284.091 -66.758 1.00 0.43 C +ATOM 161 O GLU N 20 360.750 284.714 -65.718 1.00 0.43 O +ATOM 162 CB GLU N 20 361.790 285.684 -68.482 1.00 0.43 C +ATOM 163 CG GLU N 20 361.513 286.545 -69.742 1.00 0.43 C +ATOM 164 CD GLU N 20 361.573 285.730 -71.028 1.00 0.43 C +ATOM 165 OE1 GLU N 20 362.709 285.380 -71.438 1.00 0.43 O +ATOM 166 OE2 GLU N 20 360.494 285.481 -71.622 1.00 0.43 O +ATOM 167 N VAL N 21 361.514 282.862 -66.721 1.00 0.44 N +ATOM 168 CA VAL N 21 361.780 282.144 -65.491 1.00 0.44 C +ATOM 169 C VAL N 21 363.192 281.620 -65.539 1.00 0.44 C +ATOM 170 O VAL N 21 363.803 281.502 -66.601 1.00 0.44 O +ATOM 171 CB VAL N 21 360.813 280.979 -65.242 1.00 0.44 C +ATOM 172 CG1 VAL N 21 359.425 281.552 -64.881 1.00 0.44 C +ATOM 173 CG2 VAL N 21 360.742 280.031 -66.466 1.00 0.44 C +ATOM 174 N GLU N 22 363.774 281.324 -64.363 1.00 0.42 N +ATOM 175 CA GLU N 22 365.105 280.766 -64.244 1.00 0.42 C +ATOM 176 C GLU N 22 365.196 279.331 -64.773 1.00 0.42 C +ATOM 177 O GLU N 22 364.281 278.522 -64.603 1.00 0.42 O +ATOM 178 CB GLU N 22 365.553 280.821 -62.765 1.00 0.42 C +ATOM 179 CG GLU N 22 367.068 280.606 -62.518 1.00 0.42 C +ATOM 180 CD GLU N 22 367.379 280.048 -61.130 1.00 0.42 C +ATOM 181 OE1 GLU N 22 366.427 279.727 -60.370 1.00 0.42 O +ATOM 182 OE2 GLU N 22 368.584 279.872 -60.836 1.00 0.42 O +ATOM 183 N VAL N 23 366.319 278.977 -65.424 1.00 0.46 N +ATOM 184 CA VAL N 23 366.585 277.649 -65.947 1.00 0.46 C +ATOM 185 C VAL N 23 367.448 276.913 -64.948 1.00 0.46 C +ATOM 186 O VAL N 23 368.474 277.417 -64.503 1.00 0.46 O +ATOM 187 CB VAL N 23 367.278 277.717 -67.309 1.00 0.46 C +ATOM 188 CG1 VAL N 23 367.886 276.363 -67.752 1.00 0.46 C +ATOM 189 CG2 VAL N 23 366.221 278.194 -68.325 1.00 0.46 C +ATOM 190 N ARG N 24 367.046 275.684 -64.569 1.00 0.30 N +ATOM 191 CA ARG N 24 367.776 274.864 -63.627 1.00 0.30 C +ATOM 192 C ARG N 24 368.215 273.583 -64.322 1.00 0.30 C +ATOM 193 O ARG N 24 367.541 273.175 -65.271 1.00 0.30 O +ATOM 194 CB ARG N 24 366.907 274.522 -62.395 1.00 0.30 C +ATOM 195 CG ARG N 24 366.621 275.769 -61.536 1.00 0.30 C +ATOM 196 CD ARG N 24 366.063 275.436 -60.149 1.00 0.30 C +ATOM 197 NE ARG N 24 364.598 275.759 -60.147 1.00 0.30 N +ATOM 198 CZ ARG N 24 364.099 276.933 -59.739 1.00 0.30 C +ATOM 199 NH1 ARG N 24 364.868 277.919 -59.327 1.00 0.30 N +ATOM 200 NH2 ARG N 24 362.785 277.141 -59.791 1.00 0.30 N +ATOM 201 N PRO N 25 369.321 272.924 -63.955 1.00 0.53 N +ATOM 202 CA PRO N 25 369.676 271.601 -64.466 1.00 0.53 C +ATOM 203 C PRO N 25 368.613 270.528 -64.254 1.00 0.53 C +ATOM 204 O PRO N 25 368.025 270.474 -63.174 1.00 0.53 O +ATOM 205 CB PRO N 25 370.980 271.224 -63.728 1.00 0.53 C +ATOM 206 CG PRO N 25 371.503 272.543 -63.148 1.00 0.53 C +ATOM 207 CD PRO N 25 370.225 273.337 -62.881 1.00 0.53 C +ATOM 208 N LEU N 26 368.358 269.654 -65.251 1.00 0.52 N +ATOM 209 CA LEU N 26 367.525 268.469 -65.109 1.00 0.52 C +ATOM 210 C LEU N 26 368.129 267.397 -64.206 1.00 0.52 C +ATOM 211 O LEU N 26 367.440 266.776 -63.411 1.00 0.52 O +ATOM 212 CB LEU N 26 367.241 267.855 -66.504 1.00 0.52 C +ATOM 213 CG LEU N 26 366.189 268.640 -67.314 1.00 0.52 C +ATOM 214 CD1 LEU N 26 366.233 268.223 -68.793 1.00 0.52 C +ATOM 215 CD2 LEU N 26 364.775 268.424 -66.738 1.00 0.52 C +ATOM 216 N VAL N 27 369.451 267.160 -64.334 1.00 0.58 N +ATOM 217 CA VAL N 27 370.172 266.141 -63.592 1.00 0.58 C +ATOM 218 C VAL N 27 371.467 266.789 -63.162 1.00 0.58 C +ATOM 219 O VAL N 27 372.085 267.489 -63.964 1.00 0.58 O +ATOM 220 CB VAL N 27 370.488 264.906 -64.453 1.00 0.58 C +ATOM 221 CG1 VAL N 27 371.424 263.911 -63.724 1.00 0.58 C +ATOM 222 CG2 VAL N 27 369.163 264.201 -64.811 1.00 0.58 C +ATOM 223 N ASP N 28 371.888 266.585 -61.896 1.00 0.39 N +ATOM 224 CA ASP N 28 373.170 267.026 -61.398 1.00 0.39 C +ATOM 225 C ASP N 28 373.599 266.019 -60.323 1.00 0.39 C +ATOM 226 O ASP N 28 372.984 265.957 -59.262 1.00 0.39 O +ATOM 227 CB ASP N 28 373.037 268.472 -60.835 1.00 0.39 C +ATOM 228 CG ASP N 28 374.385 269.159 -60.717 1.00 0.39 C +ATOM 229 OD1 ASP N 28 375.418 268.496 -60.981 1.00 0.39 O +ATOM 230 OD2 ASP N 28 374.383 270.374 -60.388 1.00 0.39 O +ATOM 231 N GLU N 29 374.627 265.180 -60.590 1.00 0.60 N +ATOM 232 CA GLU N 29 375.059 264.105 -59.708 1.00 0.60 C +ATOM 233 C GLU N 29 376.577 264.061 -59.759 1.00 0.60 C +ATOM 234 O GLU N 29 377.188 264.450 -60.759 1.00 0.60 O +ATOM 235 CB GLU N 29 374.515 262.702 -60.120 1.00 0.60 C +ATOM 236 CG GLU N 29 372.971 262.538 -60.018 1.00 0.60 C +ATOM 237 CD GLU N 29 372.417 262.498 -58.591 1.00 0.60 C +ATOM 238 OE1 GLU N 29 373.169 262.152 -57.646 1.00 0.60 O +ATOM 239 OE2 GLU N 29 371.191 262.758 -58.462 1.00 0.60 O +ATOM 240 N VAL N 30 377.215 263.603 -58.669 1.00 0.58 N +ATOM 241 CA VAL N 30 378.653 263.539 -58.481 1.00 0.58 C +ATOM 242 C VAL N 30 378.983 262.061 -58.132 1.00 0.58 C +ATOM 243 O VAL N 30 378.044 261.296 -57.778 1.00 0.58 O +ATOM 244 CB VAL N 30 379.117 264.538 -57.396 1.00 0.58 C +ATOM 245 CG1 VAL N 30 380.652 264.558 -57.224 1.00 0.58 C +ATOM 246 CG2 VAL N 30 378.659 265.964 -57.780 1.00 0.58 C +ATOM 247 OXT VAL N 30 380.169 261.655 -58.258 1.00 0.58 O +TER 248 VAL N 30 +END