Add Docker files and script

docker/Dockerfile

+ARG VERSION_OST="2.3.0"
+FROM registry.scicore.unibas.ch/schwede/openstructure:${VERSION_OST}
+# We need to declare ARGs again which were declared before the build stage
+# (FROM directive), otherwise they won't be available in this stage.
+ARG VERSION_OST
+
+## Set up environment
+ENV SRC_DIR="/tmp" \
+    VERSION_OST=${VERSION_OST} \
+    PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1
+
+
+LABEL org.openstructure.base-image="${VERSION_OST}"
+LABEL org.openstructure.translate2modelcif="2022-04-08.1"
+LABEL maintainer="Stefan Bienert <stefan.bienert@unibas.ch>"
+LABEL vendor1="Schwede Group (schwedelab.org)"
+LABEL vendor2="SIB - Swiss Institute of Bioinformatics (sib.swiss)"
+LABEL vendor3="Biozentrum - University of Basel (biozentrum.unibas.ch)"
+
+
+## Install python-modelcif and python-ihm
+COPY docker/requirements.txt ${SRC_DIR}
+WORKDIR ${SRC_DIR}
+RUN set -e pipefail; \
+    apt-get update -y; \
+    # for development, install venv
+    apt-get install -y git pip python3.8-venv; \
+    pip install -r requirements.txt; \
+    # for development, install black & PyLint
+    pip install black pylint; \
+    git clone https://github.com/ihmwg/python-ihm.git ihm.git; \
+    cd ihm.git; \
+    python3 setup.py build; \
+    python3 setup.py install; \
+    rm -rf ${SRC_DIR}/ihm.git; \
+    cd ${SRC_DIR}; \
+    git clone https://github.com/ihmwg/python-modelcif.git modelcif.git; \
+    cd modelcif.git; \
+    python3 setup.py build; \
+    python3 setup.py install; \
+    rm -rf /var/lib/apt/lists/*; \
+    apt-get purge -y --auto-remove git pip gcc
+
+## Add a dedicated user
+## MMCIF_USER_ID can be used to avoid file permission issues.
+ARG MMCIF_USER_ID=501
+RUN adduser --system -u ${MMCIF_USER_ID} mmcif
+
+
+COPY --chmod=755 docker/entrypoint.sh /
+
+## Copy tool(s)
+ARG CONVERTERSCRIPT=projects/pointmutations-haddock/convert2modelcif.py
+COPY --chmod=755 $CONVERTERSCRIPT /usr/local/bin/convert2modelcif
+
+USER mmcif
+
+ENTRYPOINT ["/entrypoint.sh"]
+
+# LocalWords:  ARG OST ARGs ENV SRC tmp PYTHONUNBUFFERED Schwede schwedelab py
+# LocalWords:  PYTHONDONTWRITEBYTECODE Bioinformatics sib swiss Biozentrum ihm
+# LocalWords:  modelcif txt WORKDIR pipefail chmod adduser mmcif ENTRYPOINT cd
+# LocalWords:  pylint rf entrypoint

docker/entrypoint.sh

+#!/bin/bash
+## (We use sh since Alpine does not have Bash by default)
+
+
+## exit immediately on commands with a non-zero exit status.
+set -euo pipefail
+
+## When started without any arguments, "-h", "--help", "-help" or "help", print
+## usage.
+if [ $# -eq 0 ] || [ x$1 == x"-h" ] || [ x$1 == x"--help" ] ||
+   [ x$1 == x"-help" ] || [ x$1 == x"help" ]; then
+    echo "        ModelCIF file converter"
+    echo "----------------------------------------"
+    echo "Provided by SWISS-MODEL / Schwede group"
+    echo "(swissmodel.expasy.org / schwedelab.org)"
+    echo ""
+    /usr/local/bin/convert2modelcif --help
+    exit 1
+fi
+if [ x$1 == x"convert2modelcif" ] || [ x$1 == x"2cif" ]; then
+    shift
+    # take over the process, make translate2modelcif run on PID 1
+    exec /usr/local/bin/convert2modelcif $@
+    exit $?
+fi
+
+exec "$@"
+
+#  LocalWords:  euo pipefail eq Schwede schwedelab mmcif fi

docker/requirements.txt

+requests
+ujson

projects/pointmutations-haddock/convert2modelcif.py

+#! /usr/local/bin/ost
+"""Convert point mutation/ HADDOCK models (PDB + extra data into ModelCIF)."""
+
+import argparse
+import os
+import sys
+import ujson as json
+
+import modelcif.dumper
+
+
+def _parse_args():
+    """Parse command line arguments."""
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description=__doc__,
+    )
+
+    parser.add_argument(
+        "model_list",
+        nargs="+",
+        metavar="<MODEL FILE>",
+        help="Model PDB file to be converted.",
+    )
+
+    opts = parser.parse_args()
+
+    # check arguments
+    for mfle in opts.model_list:
+        if not os.path.isfile(mfle):
+            _abort_msg(f"Model PDB file '{mfle}' does not exist.")
+        mfp = os.path.splitext(mfle)[0]
+        if not os.path.isfile(f"{mfp}.json"):
+            _abort_msg(
+                f"JSON file '{mfp}.json' for model "
+                + f"'{os.path.basename(mfp)}' does not exist."
+            )
+
+    return opts
+
+
+def _abort_msg(msg, exit_code=1):
+    """Write error message and exit with exit_code."""
+    print(f"{msg}\nAborting.", file=sys.stderr)
+    sys.exit(exit_code)
+
+
+def _get_model_json(file_prfx):
+    """Load the JSON file corresponding to a model."""
+    with open(f"{file_prfx}.json", encoding="ascii") as jfh:
+        return json.load(jfh)
+
+
+def _get_modelcif_entities(target_entities):
+    """Create ModelCIF entities."""
+    for cif_ent in target_entities:
+        print(len(cif_ent["target_sequence"]))
+
+
+def _store_as_modelcif(name, data_json, file_prfx):
+    """Mix metadata and coordinates into a ModelCIF file."""
+    # create systme to gather all data
+    system = modelcif.System(
+        title=data_json["title"],
+        id=name.upper(),
+        model_details=data_json["model_details"],
+    )
+
+    # source: syn/ nat, can be changed on object
+    _get_modelcif_entities(data_json["target_entities"])
+
+    # finally, write the ModelCIF file
+    with open(f"{file_prfx}.cif", "w", encoding="ascii") as mmcif_fh:
+        modelcif.dumper.write(mmcif_fh, [system])
+
+
+def _main():
+    """Run as script."""
+    opts = _parse_args()
+
+    for model_file in opts.model_list:
+        model_prfx = os.path.splitext(model_file)[0]
+        model_name = os.path.basename(model_prfx)
+        print(f"Working on {model_name}...", model_prfx)
+        model_json = _get_model_json(model_prfx)
+        _store_as_modelcif(model_name, model_json, model_prfx)
+
+        print(f"... done working on {model_name}.")
+
+
+if __name__ == "__main__":
+    _main()

projects/pointmutations-haddock/template.json

+{
+  "audit_authors": [
+    "Bartolec T",
+    "V\u00e1zquez-Campos X",
+    "Johnson M",
+    "Norman A",
+    "Payne R",
+    "Wilkins M",
+    "Mackay J",
+    "Low J"
+  ],
+  "max_pae": 31.75,
+  "model_details": "_struct.pdbx_model_details",
+  "model_group_name": "Crosslinked Heterodimer ALphaFold-Multimer v2 Models",
+  "protocol": [
+    {
+      "details": "Model using AlphaFold-Multimer (AlphaFold v2.2.0), without amber relaxation and producing 5 models with up to 3 recycles each, starting from paired and unparied MSAs for the dimers using MMseqs2.",
+      "input": "target_sequences",
+      "method_type": "modeling",
+      "name": "ma_protocol_step.step_name",
+      "output": "model",
+      "software": [
+        {
+          "citation": {
+            "authors": [
+              "Mirdita M",
+              "Sch\u00fctze K",
+              "Moriwaki Y",
+              "Heo L",
+              "Ovchinnikov S",
+              "Steinegger M"
+            ],
+            "doi": "10.1101\/2021.08.15.456425",
+            "journal": "bioRxiv",
+            "page_range": null,
+            "pmid": null,
+            "title": "ColabFold - Making protein folding accessible to all",
+            "volume": null,
+            "year": 2022
+          },
+          "classification": "model building",
+          "description": "software.description",
+          "location": "https:\/\/github.com\/sokrypton\/ColabFold",
+          "name": "ColabFold",
+          "type": "package",
+          "version": "1.2.0"
+        },
+        {
+          "citation": {
+            "authors": [
+              "Mirdita M",
+              "Steinegger M",
+              "S\u00f6ding J"
+            ],
+            "doi": "10.1093\/bioinformatics\/bty1057",
+            "journal": "Bioinformatics",
+            "page_range": [
+              2856,
+              2858
+            ],
+            "pmid": "30615063",
+            "title": "MMseqs2 desktop and local web server app for fast, interactive sequence searches",
+            "volume": 35,
+            "year": 2019
+          },
+          "classification": "data collection",
+          "description": "Many-against-Many sequence searching",
+          "location": "https:\/\/github.com\/soedinglab\/mmseqs2",
+          "name": "MMseqs2",
+          "type": "package",
+          "version": null
+        },
+        {
+          "citation": {
+            "authors": [
+              "Evans R",
+              "O'Neill M",
+              "Pritzel A",
+              "Antropova N",
+              "Senior A",
+              "Green T",
+              "\u017d\u00eddek A",
+              "Bates R",
+              "Blackwell S",
+              "Yim J",
+              "Ronneberger O",
+              "Bodenstein S",
+              "Zielinski M",
+              "Bridgland A",
+              "Potapenko A",
+              "Cowie A",
+              "Tunyasuvunakool K",
+              "Jain R",
+              "Clancy E",
+              "Kohli P",
+              "Jumper J",
+              "Hassabis D"
+            ],
+            "doi": "10.1101\/2021.10.04.463034",
+            "journal": "bioRxiv",
+            "page_range": null,
+            "pmid": null,
+            "title": "Protein complex prediction with AlphaFold-Multimer.",
+            "volume": null,
+            "year": 2021
+          },
+          "classification": "model building",
+          "description": "Structure prediction",
+          "location": "https:\/\/github.com\/deepmind\/alphafold",
+          "name": "AlphaFold-Multimer",
+          "type": "package",
+          "version": "2.1.1"
+        }
+      ],
+      "software_parameters": {
+        "commit": "b532e910b15434f707f0b7460abc25c70fcb9b26",
+        "host_url": "https:\/\/api.colabfold.com",
+        "keep_existing_results": true,
+        "model_order": [
+          3,
+          4,
+          5,
+          1,
+          2
+        ],
+        "model_type": "AlphaFold2-multimer-v2",
+        "msa_mode": "MMseqs2 (UniRef+Environmental)",
+        "num_models": 5,
+        "num_queries": 1,
+        "num_recycles": 3,
+        "pair_mode": "unpaired+paired",
+        "rank_by": "multimer",
+        "recompile_all_models": true,
+        "recompile_padding": 1.1,
+        "stop_at_score": 100,
+        "use_amber": false,
+        "use_templates": false,
+        "version": "1.2.0"
+      }
+    },
+    {
+      "details": "Select best model, which is either the top-ranked model as determined by the ColabFold pipeline (iptmscore*0.8+ptmscore*0.2), or else the model with best congruence with crosslinks reported in the related study.",
+      "input": "model",
+      "method_type": "model selection",
+      "name": "ma_protocol_step.step_name",
+      "output": "model",
+      "software": [],
+      "software_parameters": {}
+    }
+  ],
+  "ptm": 0.24,
+  "target_entities": [
+    {
+      "description": "Model of ZC3H11B (A0A1B0GTU1)",
+      "pdb_chain_id": "B",
+      "pdb_sequence": "MPNQGEDCYFFFYSTCTKGDSCPFRHCEAALGNETVCTLWQEGRCFRRVCRFRHMEIDKKRSEIPCYWENQPTGCQKLNCVFHHNRGRYVDGLFLPPSKSVLPTVPESPEEEVKASQLSVQQNKLSVQSNTSPQLRSVMKVESSENVPSPKHPPVVINAADDDEDDDDQFSEEGDETKTPTLQPTPEVHNGLRVTSVRKPAVNIKQGECLHFGIKTLEEIKSKKMKEKSEEQGEGSSGVSSLLLHPEPVPGPEKENVRTVVRTVTLSTKQGEEPLVRLGLTETLGKRKFSTGGDSDPPLKRSLAQRLGKKVEAPETNTDETPKKAQVSKSLKERLGMSADPNNEDATDKVNKVGEIHVKTLEEMLLERASQKHGESQTKLKTEGPSKTDDSTSGARSSSTIRIKTFSEVLAEEEHRQQEAERQKSKKDTTCIKLKTDSEIKKTVVLPPIVASKGQSEEPAGKTKSMQEVHMKTVEEIKLEKALRVQQSSESSTSSPSQHEATPGARLLLRITKRTWRKEEKKLQEGNEVDFLSRVRMEATEASVETTGVDITKIQVKRCEIMRETRMQKQQEREKSVLTPLQGDVASCNTQVAEKPVLTAVPGITWHLTKQLPTKSSQKVEVETSGIADSLLNVKWSAQTLEKRGEAKPTVNVKQSVVKVVSSPKLAPKRKAVEMHPAVTAAVKPLSSSSVLQEPPAKKAAVDAVVLLDSEDKSVTVPEAENPRDSLVLPPTQSSSDSSPPEVSGPSSSQMSMKTRRLSSASTGKPPLSVEDDFEKLTWEISGGKLEAEIDLDPGKDEDDLPLEL",
+      "up_ac": "A0A1B0GTU1",
+      "up_crc64": "2F9E1922DA454BCD",
+      "up_gn": "ZC3H11B",
+      "up_id": "ZC11B_HUMAN",
+      "up_isoform": null,
+      "up_last_mod": "2016-10-05",
+      "up_ncbi_taxid": "9606",
+      "up_organism": "Homo sapiens (Human)",
+      "up_seqlen": 805,
+      "up_sequence": "MPNQGEDCYFFFYSTCTKGDSCPFRHCEAALGNETVCTLWQEGRCFRRVCRFRHMEIDKKRSEIPCYWENQPTGCQKLNCVFHHNRGRYVDGLFLPPSKSVLPTVPESPEEEVKASQLSVQQNKLSVQSNTSPQLRSVMKVESSENVPSPKHPPVVINAADDDEDDDDQFSEEGDETKTPTLQPTPEVHNGLRVTSVRKPAVNIKQGECLHFGIKTLEEIKSKKMKEKSEEQGEGSSGVSSLLLHPEPVPGPEKENVRTVVRTVTLSTKQGEEPLVRLGLTETLGKRKFSTGGDSDPPLKRSLAQRLGKKVEAPETNTDETPKKAQVSKSLKERLGMSADPNNEDATDKVNKVGEIHVKTLEEMLLERASQKHGESQTKLKTEGPSKTDDSTSGARSSSTIRIKTFSEVLAEEEHRQQEAERQKSKKDTTCIKLKTDSEIKKTVVLPPIVASKGQSEEPAGKTKSMQEVHMKTVEEIKLEKALRVQQSSESSTSSPSQHEATPGARLLLRITKRTWRKEEKKLQEGNEVDFLSRVRMEATEASVETTGVDITKIQVKRCEIMRETRMQKQQEREKSVLTPLQGDVASCNTQVAEKPVLTAVPGITWHLTKQLPTKSSQKVEVETSGIADSLLNVKWSAQTLEKRGEAKPTVNVKQSVVKVVSSPKLAPKRKAVEMHPAVTAAVKPLSSSSVLQEPPAKKAAVDAVVLLDSEDKSVTVPEAENPRDSLVLPPTQSSSDSSPPEVSGPSSSQMSMKTRRLSSASTGKPPLSVEDDFEKLTWEISGGKLEAEIDLDPGKDEDDLPLEL"
+    },
+    {
+      "description": "Model of ZC3H11A (O75152)",
+      "pdb_chain_id": "C",
+      "pdb_sequence": "MPNQGEDCYFFFYSTCTKGDSCPFRHCEAAIGNETVCTLWQEGRCFRQVCRFRHMEIDKKRSEIPCYWENQPTGCQKLNCAFHHNRGRYVDGLFLPPSKTVLPTVPESPEEEVKASQLSVQQNKLSVQSNPSPQLRSVMKVESSENVPSPTHPPVVINAADDDEDDDDQFSEEGDETKTPTLQPTPEVHNGLRVTSVRKPAVNIKQGECLNFGIKTLEEIKSKKMKEKSKKQGEGSSGVSSLLLHPEPVPGPEKENVRTVVRTVTLSTKQGEEPLVRLSLTERLGKRKFSAGGDSDPPLKRSLAQRLGKKVEAPETNIDKTPKKAQVSKSLKERLGMSADPDNEDATDKVNKVGEIHVKTLEEILLERASQKRGELQTKLKTEGPSKTDDSTSGARSSSTIRIKTFSEVLAEKKHRQQEAERQKSKKDTTCIKLKIDSEIKKTVVLPPIVASRGQSEEPAGKTKSMQEVHIKTLEEIKLEKALRVQQSSESSTSSPSQHEATPGARRLLRITKRTGMKEEKNLQEGNEVDSQSSIRTEAKEASGETTGVDITKIQVKRCETMREKHMQKQQEREKSVLTPLRGDVASCNTQVAEKPVLTAVPGITRHLTKRLPTKSSQKVEVETSGIGDSLLNVKCAAQTLEKRGKAKPKVNVKPSVVKVVSSPKLAPKRKAVEMHAAVIAAVKPLSSSSVLQEPPAKKAAVAVVPLVSEDKSVTVPEAENPRDSLVLPPTQSSSDSSPPEVSGPSSSQMSMKTRRLSSASTGKPPLSVEDDFEKLIWEISGGKLEAEIDLDPGKDEDDLLLELSEMIDS",
+      "up_ac": "O75152",
+      "up_crc64": "9048ABC7F4A372FB",
+      "up_gn": "ZC3H11A",
+      "up_id": "ZC11A_HUMAN",
+      "up_isoform": null,
+      "up_last_mod": "2016-10-05",
+      "up_ncbi_taxid": "9606",
+      "up_organism": "Homo sapiens (Human)",
+      "up_seqlen": 810,
+      "up_sequence": "MPNQGEDCYFFFYSTCTKGDSCPFRHCEAAIGNETVCTLWQEGRCFRQVCRFRHMEIDKKRSEIPCYWENQPTGCQKLNCAFHHNRGRYVDGLFLPPSKTVLPTVPESPEEEVKASQLSVQQNKLSVQSNPSPQLRSVMKVESSENVPSPTHPPVVINAADDDEDDDDQFSEEGDETKTPTLQPTPEVHNGLRVTSVRKPAVNIKQGECLNFGIKTLEEIKSKKMKEKSKKQGEGSSGVSSLLLHPEPVPGPEKENVRTVVRTVTLSTKQGEEPLVRLSLTERLGKRKFSAGGDSDPPLKRSLAQRLGKKVEAPETNIDKTPKKAQVSKSLKERLGMSADPDNEDATDKVNKVGEIHVKTLEEILLERASQKRGELQTKLKTEGPSKTDDSTSGARSSSTIRIKTFSEVLAEKKHRQQEAERQKSKKDTTCIKLKIDSEIKKTVVLPPIVASRGQSEEPAGKTKSMQEVHIKTLEEIKLEKALRVQQSSESSTSSPSQHEATPGARRLLRITKRTGMKEEKNLQEGNEVDSQSSIRTEAKEASGETTGVDITKIQVKRCETMREKHMQKQQEREKSVLTPLRGDVASCNTQVAEKPVLTAVPGITRHLTKRLPTKSSQKVEVETSGIGDSLLNVKCAAQTLEKRGKAKPKVNVKPSVVKVVSSPKLAPKRKAVEMHAAVIAAVKPLSSSSVLQEPPAKKAAVAVVPLVSEDKSVTVPEAENPRDSLVLPPTQSSSDSSPPEVSGPSSSQMSMKTRRLSSASTGKPPLSVEDDFEKLIWEISGGKLEAEIDLDPGKDEDDLLLELSEMIDS"
+    }
+  ],
+  "title": "_struct.title"
+}