Add software to AF2 scoresD

.gitignore

 # Don't have Emac's backup files
 *~
 
+# ignore test scripts
+biop-test.py
+junk.py
+
 # ignore some files used for testing
 1ake.1.pdb
 3lre.3.A.pdb
 6xne.pdb
+cmp.cif

convert_to_modelcif.py

@@ -20,6 +20,7 @@ from Bio.PDB.Structure import Structure as BioStructure
 from absl import app, flags, logging
 import numpy as np
 
+import ihm.citations
 import modelcif
 import modelcif.associated
 import modelcif.dumper
@@ -120,8 +121,13 @@ class _Biopython2ModelCIF(modelcif.model.AbInitioModel):
                 occupancy=atm.occupancy,
             )
 
-    def add_scores(self, scores_json, entry_id, file_prefix):
+    def add_scores(self, scores_json, entry_id, file_prefix, sw_dct):
         """Add QA metrics"""
+        _GlobalPLDDT.software = sw_dct["alphafold"]
+        _GlobalPTM.software = sw_dct["alphafold"]
+        _GlobalIPTM.software = sw_dct["alphafold"]
+        _LocalPLDDT.software = sw_dct["alphafold"]
+        _LocalPairwisePAE.software = sw_dct["alphafold"]
         # global scores
         self.qa_metrics.extend(
             (
@@ -254,9 +260,14 @@ def _store_as_modelcif(
         name="ToDo: Model <N> (ranked #<M>)",
     )
 
+    # create software list from feature metadata
+    sw_dct = _get_software_data(data_json["__meta__"])
+
     # process scores
     mdl_file = os.path.splitext(os.path.basename(mdl_file))[0]
-    system.repositories.append(model.add_scores(data_json, system.id, mdl_file))
+    system.repositories.append(
+        model.add_scores(data_json, system.id, mdl_file, sw_dct)
+    )
 
     system.model_groups.append(modelcif.model.ModelGroup([model]))
 
@@ -316,9 +327,16 @@ def _compress_cif_file(cif_file):
 def _get_model_details(cmplx_name: str, data_json: dict) -> str:
     """Get the model description."""
     ap_versions = []
-    for mnmr in data_json["__meta__"]:
-        if data_json["__meta__"][mnmr]["ap_version"] not in ap_versions:
-            ap_versions.append(data_json["__meta__"][mnmr]["ap_version"])
+    for mnmr in data_json["__meta__"]:  # mnmr = monomer
+        if (
+            data_json["__meta__"][mnmr]["software"]["alphapulldown"]["version"]
+            not in ap_versions
+        ):
+            ap_versions.append(
+                data_json["__meta__"][mnmr]["software"]["alphapulldown"][
+                    "version"
+                ]
+            )
 
     # ToDo: fetch AF2 version/ have it in metadata JSON
     return (
@@ -348,7 +366,13 @@ def _get_feature_metadata(
         # ToDo: make sure that its always ASCII
         with open(feature_json, "r", encoding="ascii") as jfh:
             jdata = json.load(jfh)
-        modelcif_json["__meta__"][mnmr]["ap_version"] = jdata["version"]
+        modelcif_json["__meta__"][mnmr]["software"] = jdata["binaries"]
+        modelcif_json["__meta__"][mnmr]["software"]["alphapulldown"] = {
+            "version": jdata["version"]
+        }
+        modelcif_json["__meta__"][mnmr]["software"]["alphafold"] = {
+            "version": jdata["AlphaFold version"]
+        }
 
     return cmplx_name
 
@@ -418,7 +442,6 @@ def _get_scores(cif_json: dict, scr_file: str) -> None:
     """Add scores to JSON data."""
     with open(scr_file, "rb") as sfh:
         scr_dict = pickle.load(sfh)
-    # dict_keys(['distogram', 'experimentally_resolved', 'masked_msa', 'num_recycles', 'structure_module', 'aligned_confidence_probs', 'max_predicted_aligned_error', 'ranking_confidence'])
     # Get pLDDT as a list, the global pLDDT is the average, calculated on the
     # spot.
     cif_json["plddt"] = scr_dict["plddt"]
@@ -427,6 +450,79 @@ def _get_scores(cif_json: dict, scr_file: str) -> None:
     cif_json["pae"] = scr_dict["predicted_aligned_error"]
 
 
+def _get_software_data(meta_json: dict) -> list:
+    """Turn meta data about software into modelcif.Software objects."""
+    # {key from json: dict needed to produce sw entry plus internal key}
+    sw_data = {
+        "jackhmmer": None,
+        "hhblits": None,
+        "hhsearch": None,
+        "hmmsearch": None,
+        "hmmbuild": None,
+        "kalign": None,
+        "alphapulldown": None,
+        "alphafold": modelcif.Software(
+            "AlphaFold-Multimer",
+            "model building",
+            "Structure prediction",
+            "https://github.com/deepmind/alphafold",
+            "package",
+            None,
+            ihm.Citation(
+                pmid=None,
+                title="Protein complex prediction with AlphaFold-Multimer.",
+                journal="bioRxiv",
+                volume=None,
+                page_range=None,
+                year=2021,
+                authors=[
+                    "Evans, R.",
+                    "O'Neill, M.",
+                    "Pritzel, A.",
+                    "Antropova, N.",
+                    "Senior, A.",
+                    "Green, T.",
+                    "Zidek, 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",
+            ),
+        ),
+    }
+    for data in meta_json.values():
+        for sftwr, version in data["software"].items():
+            if sftwr not in sw_data:
+                raise RuntimeError(
+                    "Unknown software found in meta data: " + f"'{sftwr}'"
+                )
+            version = version["version"]
+            if sw_data[sftwr] is not None:
+                if sw_data[sftwr].version is not None:
+                    if sw_data[sftwr].version != version:
+                        raise RuntimeError(
+                            "Software versions differ for "
+                            + f"'{sftwr}': '{sw_data[sftwr].version}' vs. "
+                            + f"'{version}'"
+                        )
+                sw_data[sftwr].version = version
+
+    return sw_data
+
+
 def alphapulldown_model_to_modelcif(
     cmplx_name: str,
     mdl_file: str,