diff --git a/docker/Dockerfile b/docker/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..cc3c2b143c81f29db6f7d553968cab0831b90f33
--- /dev/null
+++ b/docker/Dockerfile
@@ -0,0 +1,64 @@
+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
diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
new file mode 100644
index 0000000000000000000000000000000000000000..20874f8b156d3b6b168a2fb40d7ec8a13a7ac4a8
--- /dev/null
+++ b/docker/entrypoint.sh
@@ -0,0 +1,29 @@
+#!/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
diff --git a/docker/requirements.txt b/docker/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2abd7d3a956e774cb5b3d3765de5e9b9d66f2d96
--- /dev/null
+++ b/docker/requirements.txt
@@ -0,0 +1,2 @@
+requests
+ujson
diff --git a/projects/pointmutations-haddock/convert2modelcif.py b/projects/pointmutations-haddock/convert2modelcif.py
new file mode 100644
index 0000000000000000000000000000000000000000..4ccafd331823670334ea496bfba83ca49cc2f5c4
--- /dev/null
+++ b/projects/pointmutations-haddock/convert2modelcif.py
@@ -0,0 +1,92 @@
+#! /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()
diff --git a/projects/pointmutations-haddock/template.json b/projects/pointmutations-haddock/template.json
new file mode 100644
index 0000000000000000000000000000000000000000..a404f34d99fbb79a3593359ae2976b1150320204
--- /dev/null
+++ b/projects/pointmutations-haddock/template.json
@@ -0,0 +1,185 @@
+{
+ "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"
+}