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Commit 68ad8fb6 authored by Bienchen's avatar Bienchen
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Add selection step

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with 53 additions and 63 deletions
translate2modelcif.py
+ 53
− 63
View file @ 68ad8fb6
......@@ -249,7 +249,6 @@ def _check_model_extra_files_present(model_dir, pdb_file):
def _get_audit_authors():
"""Return the list of authors that produced this model."""
# ToDo: tell Xabi that his name can't have a á in mmCIF
return (
"Bartolec, T.",
"Vazquez-Campos, X.",
......@@ -289,7 +288,8 @@ def _parse_colabfold_config(cnfg_file):
use_msa = False
elif cf_config["msa_mode"] == "custom":
print(
"WARNING: Custom MSA mode used. Not clear from config what to do here!"
"WARNING: Custom MSA mode used. Not clear from config what to do "
+ "here!"
)
seq_dbs = []
use_mmseqs = False
......@@ -311,63 +311,71 @@ def _parse_colabfold_config(cnfg_file):
else:
raise ValueError(f"Unknown model_type {cf_config['model_type']}")
# write description
description = f"Model generated using ColabFold v{cf_config['version']}"
# write modeling description
mdl_description = f"Model generated using ColabFold v{cf_config['version']}"
if use_multimer:
description += f" with AlphaFold-Multimer (v{multimer_version})"
mdl_description += f" with AlphaFold-Multimer (v{multimer_version})"
else:
description += " with AlphaFold"
mdl_description += " with AlphaFold"
if cf_config["stop_at_score"] < 100:
# early stopping feature of ColabFold
upto = "up to "
else:
upto = ""
description += (
mdl_description += (
f" producing {upto}{cf_config['num_models']} models"
f" with {upto}{cf_config['num_recycles']} recycles each"
)
if cf_config["use_amber"]:
description += ", with AMBER relaxation"
mdl_description += ", with AMBER relaxation"
else:
description += ", without model relaxation"
mdl_description += ", without model relaxation"
if cf_config["use_templates"]:
print(
"WARNING: ColabFold may use PDB70 or custom templates. "
"Not clear from config!"
)
description += ", using templates"
mdl_description += ", using templates"
else:
description += ", without templates"
mdl_description += ", without templates"
if cf_config["rank_by"] == "plddt":
description += ", ranked by pLDDT"
mdl_description += ", ranked by pLDDT"
elif cf_config["rank_by"] == "ptmscore":
description += ", ranked by pTM"
mdl_description += ", ranked by pTM"
elif cf_config["rank_by"] == "multimer":
description += ", ranked by ipTM*0.8+pTM*0.2"
mdl_description += ", ranked by ipTM*0.8+pTM*0.2"
else:
raise ValueError(f"Unknown rank_by {cf_config['rank_by']}")
if use_msa:
description += ", starting from"
mdl_description += ", starting from"
if use_mmseqs:
msa_type = "MSA"
else:
msa_type = "custom MSA"
if use_multimer:
if cf_config["pair_mode"] == "unpaired+paired":
description += f" paired and unpaired {msa_type}s"
mdl_description += f" paired and unpaired {msa_type}s"
elif cf_config["pair_mode"] == "paired":
description += f" paired {msa_type}s"
mdl_description += f" paired {msa_type}s"
elif cf_config["pair_mode"] == "unpaired":
description += f" unpaired {msa_type}s"
mdl_description += f" unpaired {msa_type}s"
else:
raise ValueError(f"Unknown pair_mode {cf_config['pair_mode']}")
else:
description += f" an {msa_type}"
mdl_description += f" an {msa_type}"
if use_mmseqs:
description += f" from MMseqs2 ({'+'.join(seq_dbs)})"
mdl_description += f" from MMseqs2 ({'+'.join(seq_dbs)})"
else:
description += " without an MSA"
description += "."
mdl_description += " without an MSA"
mdl_description += "."
# write selection description
slct_description = (
"Select best model, which is either the top-ranked model as "
+ "determined by the ColabFold pipeline (ipTM*0.8+pTM*0.2), or else "
+ "the model with best congruence with crosslinks reported in the "
+ "related study."
)
return {
"config": cf_config,
......@@ -376,7 +384,8 @@ def _parse_colabfold_config(cnfg_file):
"use_msa": use_msa,
"use_multimer": use_multimer,
"multimer_version": multimer_version,
"description": description,
"modeling_description": mdl_description,
"selection_description": slct_description,
}
......@@ -388,7 +397,7 @@ def _get_protocol_steps_and_software(config_data):
step = {
"method_type": "modeling",
"name": None,
"details": config_data["description"],
"details": config_data["modeling_description"],
}
# get input data
# Must refer to data already in the JSON, so we try keywords
......@@ -415,21 +424,7 @@ def _get_protocol_steps_and_software(config_data):
"classification": "data collection",
"description": "Many-against-Many sequence searching",
# ToDo: add citation to ihm.citations
"citation": ihm.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.",
"Soeding, J.",
],
doi="10.1093/bioinformatics/bty1057",
),
"citation": ihm.citations.mmseqs2,
"location": "https://github.com/soedinglab/mmseqs2",
"type": "package",
"version": None,
......@@ -496,29 +491,22 @@ def _get_protocol_steps_and_software(config_data):
protocol.append(step)
# model selection step
# ToDo [input/ internal]: model selection step on a single model is a bit
# silly, how do we get a list of models?
# GT-NOTES:
# - input/output should be ok without list of models
# - rank of model is already stored in _ma_model_list.model_name and
# _ma_data.name (in _store_as_modelcif)
# - ColabFold ranking details is already in details of step above.
# - Suggestion: add extra step only if AF-ranking was overruled and
# include it in step above.
# step = {
# "method_type": "model selection",
# "name": "ma_protocol_step.step_name",
# "details": "Select best model, which is either the top-ranked model "
# + "as determined by the ColabFold pipeline "
# + "(ipTM*0.8+pTM*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_parameters"] = {}
# protocol.append(step)
if (
"selection_description" not in config_data
or len(config_data["selection_description"]) == 0
):
return protocol
step = {
"method_type": "model selection",
"name": None,
"details": config_data["selection_description"],
}
step["input"] = "model"
step["output"] = "model"
step["software"] = []
step["software_parameters"] = {}
protocol.append(step)
return protocol
......@@ -584,7 +572,9 @@ def _fetch_upkb_entry(up_ac):
data["up_organism"] = ""
data["up_sequence"] = ""
data["up_ac"] = up_ac
rspns = requests.get(f"https://www.uniprot.org/uniprot/{up_ac}.txt")
rspns = requests.get(
f"https://www.uniprot.org/uniprot/{up_ac}.txt", timeout=180
)
for line in rspns.iter_lines(decode_unicode=True):
if line.startswith("ID "):
sline = line.split()
......
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