diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..a6bc05813438bab2b2b92554385905fdf5122c11
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,59 @@
+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 requirements.txt ${SRC_DIR}
+WORKDIR ${SRC_DIR}
+RUN set -e pipefail; \
+ apt-get update -y; \
+ apt-get install -y git pip; \
+ pip install -r requirements.txt; \
+ 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 ${SRC_DIR}/modelcif.git; \
+ apt-get remove -y git pip
+
+## Copy tool(s)
+COPY --chmod=755 translate2modelcif.py /usr/local/bin/translate2modelcif
+
+## 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 /
+
+USER mmcif
+
+#ENTRYPOINT ["/docker-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
diff --git a/pyproject.toml b/pyproject.toml
index b95b5ec25a2eef2ff5629d07e649ba9b7f960547..90392da16a7316df546dc4d16157320679e4943f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,11 @@
[tool.black]
line-length=80
+[tool.pylint.MASTER]
+# A comma-separated list of package or module names from where C extensions may
+# be loaded. Extensions are loading into the active Python interpreter and may
+# run arbitrary code
+extension-pkg-allow-list='ujson'
+
[tool.pylint.REPORTS]
reports='no'
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2abd7d3a956e774cb5b3d3765de5e9b9d66f2d96
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,2 @@
+requests
+ujson
diff --git a/translate2modelcif.py b/translate2modelcif.py
index a5572989bfa51aded4582e46a055180d351d9540..6a3ded6411c754526fbd519e878ef39151aab906 100644
--- a/translate2modelcif.py
+++ b/translate2modelcif.py
@@ -1,3 +1,4 @@
+#! /usr/local/bin/ost
"""Translate models from Tara/ Xabi from PDB + extra data into ModelCIF."""
import argparse
@@ -5,10 +6,14 @@ import datetime
import os
import sys
+from timeit import default_timer as timer
+import numpy as np
import requests
+import ujson as json
import ihm
import modelcif
+import modelcif.associated
import modelcif.dumper
import modelcif.model
import modelcif.reference
@@ -34,6 +39,8 @@ def _parse_args():
opts = parser.parse_args()
# check that model dir exists
+ if opts.model_dir.endswith("/"):
+ opts.model_dir = opts.model_dir[:-1]
if not os.path.exists(opts.model_dir):
_abort_msg(f"Model directory '{opts.model_dir}' does not exist.")
if not os.path.isdir(opts.model_dir):
@@ -42,12 +49,52 @@ def _parse_args():
return opts
+# pylint: disable=too-few-public-methods
+class _GlobalPTM(modelcif.qa_metric.Global, modelcif.qa_metric.PTM):
+ """Predicted accuracy according to the TM-score score in [0,1]."""
+
+ # ToDo [input]: Add software
+ name = "pTM"
+ software = None
+
+
+class _GlobalPLDDT(modelcif.qa_metric.Global, modelcif.qa_metric.PLDDT):
+ """Predicted accuracy according to the CA-only lDDT in [0,100]."""
+
+ name = "pLDDT"
+ software = None
+
+
+class _LocalPLDDT(modelcif.qa_metric.Local, modelcif.qa_metric.PLDDT):
+ """Predicted accuracy according to the CA-only lDDT in [0,100]."""
+
+ name = "pLDDT"
+ software = None
+
+
+class _PAE(modelcif.qa_metric.MetricType):
+ """Predicted aligned error (in Angstroms).
+ See :class:`MetricType` for more information."""
+
+ type = "PAE"
+ other_details = None
+
+
+class _LocalPairwisePAE(modelcif.qa_metric.LocalPairwise, _PAE):
+ """predicted aligned error (in Angstroms)."""
+
+ name = "PAE"
+ software = None
+
+
+# pylint: enable=too-few-public-methods
+
+
class _OST2ModelCIF(modelcif.model.AbInitioModel):
"""Map OST entity elements to ihm.model"""
def __init__(self, *args, **kwargs):
"""Initialise a model"""
- # check that ost_entity exists, TypeError otherwise
self.ost_entity = kwargs.pop("ost_entity")
self.asym = kwargs.pop("asym")
@@ -69,6 +116,70 @@ class _OST2ModelCIF(modelcif.model.AbInitioModel):
occupancy=atm.occupancy,
)
+ def add_scores(self, scores_json, entry_id, ac_file_prfx):
+ """Add QA metrics from AF2 scores."""
+ # global scores
+ self.qa_metrics.extend(
+ (
+ _GlobalPLDDT(np.mean(scores_json["plddt"])),
+ _GlobalPTM(scores_json["ptm"]),
+ )
+ )
+
+ # local scores
+ lpae = []
+ i = 0
+ for chn_i in self.ost_entity.chains:
+ for res_i in chn_i.residues:
+ # local pLDDT
+ self.qa_metrics.append(
+ _LocalPLDDT(
+ self.asym[chn_i.name].residue(res_i.number.num),
+ scores_json["plddt"][i],
+ )
+ )
+
+ # pairwise alignment error
+ j = 0
+ # We do a 2nd iteration over the OST entity above doing index
+ # magic because it keeps the code cleaner and is only around
+ # 0.3s slower than iterating the array directly. Majority of
+ # time goes into writing files, anyway.
+ for chn_j in self.ost_entity.chains:
+ for res_j in chn_j.residues:
+ lpae.append(
+ _LocalPairwisePAE(
+ self.asym[chn_i.name].residue(res_i.number.num),
+ self.asym[chn_j.name].residue(res_j.number.num),
+ scores_json["pae"][i][j],
+ )
+ )
+ j += 1
+
+ i += 1
+
+ self.qa_metrics.extend(lpae)
+
+ ac_file = f"{os.path.basename(ac_file_prfx)}_local_pairwise_qa.cif"
+
+ return modelcif.associated.Repository(
+ "",
+ [
+ modelcif.associated.LocalPairwiseQAScoresFile(
+ ac_file,
+ categories=["_ma_qa_metric_local_pairwise"],
+ copy_categories=["_ma_qa_metric"],
+ entry_id=entry_id,
+ entry_details="This file is an associated file consisting "
+ + "of local pairwise QA metrics. This is a partial mmCIF "
+ + "file and can be validated by merging with the main "
+ + "mmCIF file containing the model coordinates and other "
+ + "associated data.",
+ details="Predicted aligned error.",
+ )
+ ],
+ )
+
def _abort_msg(msg, exit_code=1):
"""Write error message and exit with exit_code."""
@@ -259,21 +370,35 @@ def _get_entities(pdb_file, up_acs):
return entities, ost_ent
+def _get_scores(data, prfx):
+ """Check that all files needed to process this model are present."""
+ scrs_fle = f"{prfx}_scores.json"
+ with open(scrs_fle, encoding="utf8") as jfh:
+ scrs_json = json.load(jfh)
+
+ data.update(scrs_json)
+
+
def _store_as_modelcif(interaction_name, data_json, ost_ent, file_prfx):
"""Mix all the data into a ModelCIF file."""
+ print(" generating ModelCIF objects...", end="")
+ pstart = timer()
+ # ToDo [internal]: Get protocol/ software
+ # ToDo [internal]: Get QA metrics
# create system to gather all the data
system = modelcif.System(
title=data_json["title"],
id=interaction_name.upper(),
model_details=data_json["model_details"],
)
- # create target entities, references, source, asymmetric units...
+ # create target entities, references, source, asymmetric units & assembly
# for source we assume all chains come from the same taxon
source = ihm.source.Natural(
ncbi_taxonomy_id=data_json["target_entities"][0]["up_ncbi_taxid"],
scientific_name=data_json["target_entities"][0]["up_organism"],
)
+ # create an asymmetric unit and an entity per target sequence
asym_units = {}
for cif_ent in data_json["target_entities"]:
# ToDo [input]: Get entity description
@@ -321,6 +446,14 @@ def _store_as_modelcif(interaction_name, data_json, ost_ent, file_prfx):
ost_entity=ost_ent,
name="ma_model_list.model_name",
)
+ print(f" ({timer()-pstart:.2f}s)")
+ print(" processing QA scores...", end="", flush=True)
+ pstart = timer()
+ system.repositories.append(
+ model.add_scores(data_json, system.id, file_prfx)
+ )
+ print(f" ({timer()-pstart:.2f}s)")
+
# ToDo [input]: Get name
model_group = modelcif.model.ModelGroup(
[model], name="ma_model_list.model_group_name"
@@ -328,8 +461,11 @@ def _store_as_modelcif(interaction_name, data_json, ost_ent, file_prfx):
system.model_groups.append(model_group)
# write modelcif System to file
+ print(" write to disk...", end="", flush=True)
+ pstart = timer()
with open(f"{file_prfx}.cif", "w", encoding="utf8") as mmcif_fh:
modelcif.dumper.write(mmcif_fh, [system])
+ print(f" ({timer()-pstart:.2f}s)")
def _create_interaction_json():
@@ -370,14 +506,23 @@ def _main():
# iterate PDB files
if not fle.endswith(".pdb"):
continue
+ print(f" translating {fle}...")
+ pdb_start = timer()
file_prfx, uid = _check_model_extra_files_present(opts.model_dir, fle)
fle = os.path.join(opts.model_dir, fle)
# gather data into JSON-like structure
+ print(" preparing data...", end="")
+ pstart = timer()
ost_ent = _create_model_json(mdlcf_json, fle, up_acs)
+ # read quality scores from JSON file
+ _get_scores(mdlcf_json, file_prfx)
+ print(f" ({timer()-pstart:.2f}s)")
+
_store_as_modelcif(uid, mdlcf_json, ost_ent, file_prfx)
# ToDo [internal]: wipe data or is it overwritten in mdlcf_json?
+ print(f" ... done with {fle} ({timer()-pdb_start:.2f}s).")
print(f"... done with {opts.model_dir}.")
@@ -392,4 +537,7 @@ if __name__ == "__main__":
# LocalWords: sqe olc ACDEFGHIKLMNPQRSTVWY RuntimeError upkb txt pylint iter
# LocalWords: rspns unicode startswith sline len elif NCBI TaxID ncbi taxid
# LocalWords: seqlen crc ISOFORM DT dt flds isoforms isoform ent LoadPDB ihm
-# LocalWords: mdlcf mdlcif asym AsymUnit
+# LocalWords: mdlcf mdlcif asym AsymUnit init kwargs atm pos het hetatom pTM
+# LocalWords: biso ujson GlobalPTM pLDDT ptm jfh numpy np GlobalPLDDT lDDT
+# LocalWords: plddt LocalPLDDT timeit PAE MetricType LocalPairwisePAE lpae
+# LocalWords: nd pae qa pstart