diff --git a/translate2modelcif.py b/translate2modelcif.py
index 6222ac4c3f3b38c99b6fc6842048347f8ad391ac..bcfbed10a5cb5e257777e6b9c8767c11e1120f74 100644
--- a/translate2modelcif.py
+++ b/translate2modelcif.py
@@ -240,7 +240,10 @@ def _get_protocol_steps_and_software(cnfg_file):
step = {
"method_type": "modeling",
"name": "ma_protocol_step.step_name",
- "details": "ma_protocol_step.details",
+ "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.",
}
# get input data
# Must refer to data already in the JSON, so we try keywords
@@ -249,31 +252,99 @@ def _get_protocol_steps_and_software(cnfg_file):
# Must refer to existing data, so we try keywords
step["output"] = "model"
# get software
- step["software"] = {
- "name": "ColabFold",
- "classification": "model building",
- "description": "software.description",
- "citation": {
- "pmid": None,
- "title": "ColabFold - Making protein folding accessible to all",
- "journal": "bioRxiv",
- "volume": None,
- "page_range": None,
- "year": 2022,
- "authors": [
- "Mirdita M",
- "Schütze K",
- "Moriwaki Y",
- "Heo L",
- "Ovchinnikov S",
- "Steinegger M",
- ],
- "doi": "10.1101/2021.08.15.456425",
+ step["software"] = [
+ {
+ "name": "ColabFold",
+ "classification": "model building",
+ # ToDo: Get description for ColabFold
+ "description": "software.description",
+ "citation": {
+ "pmid": None,
+ "title": "ColabFold - Making protein folding accessible to all",
+ "journal": "bioRxiv",
+ "volume": None,
+ "page_range": None,
+ "year": 2022,
+ "authors": [
+ "Mirdita M",
+ "Schütze K",
+ "Moriwaki Y",
+ "Heo L",
+ "Ovchinnikov S",
+ "Steinegger M",
+ ],
+ "doi": "10.1101/2021.08.15.456425",
+ },
+ "location": "https://github.com/sokrypton/ColabFold",
+ "type": "package",
+ "version": "1.2.0",
},
- "location": "https://github.com/sokrypton/ColabFold",
- "type": "package",
- "version": "1.2.0",
- }
+ {
+ "name": "MMseqs2",
+ "classification": "data collection",
+ "description": "Many-against-Many sequence searching",
+ "citation": {
+ "pmid": "30615063",
+ "title": "MMseqs2 desktop and local web server app for fast, "
+ + "interactive sequence searches",
+ "journal": "Bioinformatics",
+ "volume": 35,
+ "page_range": (2856, 2858),
+ "year": 2019,
+ "authors": [
+ "Mirdita M",
+ "Steinegger M",
+ "Söding J",
+ ],
+ "doi": "10.1093/bioinformatics/bty1057",
+ },
+ "location": "https://github.com/soedinglab/mmseqs2",
+ "type": "package",
+ "version": None,
+ },
+ {
+ "name": "AlphaFold-Multimer",
+ "classification": "model building",
+ "description": "Structure prediction",
+ "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",
+ "Žídek 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",
+ },
+ "location": "https://github.com/deepmind/alphafold",
+ "type": "package",
+ "version": "2.1.1",
+ },
+ ]
# get parameters
with open(cnfg_file, encoding="utf8") as jfh:
step["software_parameters"] = json.load(jfh)
@@ -285,11 +356,14 @@ def _get_protocol_steps_and_software(cnfg_file):
step = {
"method_type": "model selection",
"name": "ma_protocol_step.step_name",
- "details": "ma_protocol_step.details",
+ "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.",
}
step["input"] = "model"
step["output"] = "model"
- step["software"] = {}
+ step["software"] = []
step["software_parameters"] = {}
protocol.append(step)
@@ -504,37 +578,46 @@ def _get_modelcif_entities(target_ents, source, asym_units, system):
system.target_entities.append(mdlcif_ent)
+def _assemble_modelcif_software(soft_dict):
+ """Create a modelcif.Software instance from dictionary."""
+ return modelcif.Software(
+ soft_dict["name"],
+ soft_dict["classification"],
+ soft_dict["description"],
+ soft_dict["location"],
+ soft_dict["type"],
+ soft_dict["version"],
+ citation=ihm.Citation(
+ pmid=soft_dict["citation"]["pmid"],
+ title=soft_dict["citation"]["title"],
+ journal=soft_dict["citation"]["journal"],
+ volume=soft_dict["citation"]["volume"],
+ page_range=soft_dict["citation"]["page_range"],
+ year=soft_dict["citation"]["year"],
+ authors=soft_dict["citation"]["authors"],
+ doi=soft_dict["citation"]["doi"],
+ ),
+ )
+
+
def _get_modelcif_protocol(protocol_steps, target_entities, model):
"""Create the protocol for the ModelCIF file."""
protocol = modelcif.protocol.Protocol()
for js_step in protocol_steps:
sftwre = None
# ToDo [input]: Turn into software group if parameters are available
- # ToDo [input]: Get software.description
if js_step["software"]:
- sftwre = modelcif.Software(
- js_step["software"]["name"],
- js_step["software"]["classification"],
- js_step["software"]["description"],
- js_step["software"]["location"],
- js_step["software"]["type"],
- js_step["software"]["version"],
- citation=ihm.Citation(
- pmid=js_step["software"]["citation"]["pmid"],
- title=js_step["software"]["citation"]["title"],
- journal=js_step["software"]["citation"]["journal"],
- volume=js_step["software"]["citation"]["volume"],
- page_range=js_step["software"]["citation"]["page_range"],
- year=js_step["software"]["citation"]["year"],
- authors=js_step["software"]["citation"]["authors"],
- doi=js_step["software"]["citation"]["doi"],
- ),
- )
+ if len(js_step["software"]) == 1:
+ sftwre = _assemble_modelcif_software(js_step["software"][0])
+ else:
+ sftwre = []
+ for sft in js_step["software"]:
+ sftwre.append(_assemble_modelcif_software(sft))
+ sftwre = modelcif.SoftwareGroup(elements=sftwre)
# if js_step['software_parameters']:
# params = []
# # ToDo [internal]: handle lists!
# for k, v in js_step['software_parameters'].items():
- # print(k, v.__class__)
# params.append(
# modelcif.SoftwareParameter(k, v)
# )
@@ -711,4 +794,4 @@ if __name__ == "__main__":
# 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
+# LocalWords: nd pae qa pstart ColabFold