From a28ca7de23dfd44ac0c9a469d312298947a79252 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 4 Oct 2023 16:18:04 +0200
Subject: [PATCH] Get first protocol step
---
convert_to_modelcif.py | 37 ++++++++++++++++++++++++++++++++-----
1 file changed, 32 insertions(+), 5 deletions(-)
diff --git a/convert_to_modelcif.py b/convert_to_modelcif.py
index 3a01fc9..e90516d 100755
--- a/convert_to_modelcif.py
+++ b/convert_to_modelcif.py
@@ -246,17 +246,36 @@ def _get_modelcif_protocol_input(
return input_data
+def _get_modelcif_protocol_output(output_data_group, model):
+ """Assemble output data for a ModelCIF protocol step."""
+ if output_data_group == "model":
+ output_data = model
+ elif output_data_group == "monomer_pickle_files":
+ output_data = modelcif.data.DataGroup(
+ [
+ modelcif.data.Data(
+ "Pickle files", details="Monomer feature/ MSA pickle files"
+ )
+ ]
+ )
+ else:
+ raise RuntimeError(f"Unknown protocol output: '{output_data_group}'")
+ return output_data
+
+
def _get_modelcif_protocol(
protocol_steps, target_entities, model, sw_dict, ref_dbs
):
"""Create the protocol for the ModelCIF file."""
protocol = modelcif.protocol.Protocol()
for js_step in protocol_steps:
- # assemble input data
+ # assemble input & output data
input_data = _get_modelcif_protocol_input(
js_step["input_data_group"], target_entities, ref_dbs, model
)
-
+ output_data = _get_modelcif_protocol_output(
+ js_step["output_data_group"], model
+ )
# loop over software group and assemble software group from that
sw_grp = modelcif.SoftwareGroup()
for pss in js_step["software_group"]: # protocol step software
@@ -277,7 +296,7 @@ def _get_modelcif_protocol(
protocol.steps.append(
modelcif.protocol.Step(
input_data=input_data,
- output_data=None, # output_data,
+ output_data=output_data,
name=js_step["step_name"],
details=js_step["details"],
software=sw_grp,
@@ -285,7 +304,7 @@ def _get_modelcif_protocol(
)
print("modelcif.protocol.Step(")
print(f" input_data={input_data},")
- # output_data=output_data,
+ print(f" output_data={output_data},")
print(f" name={js_step['step_name']},")
print(f" details=\"{js_step['details']}\",")
print(f" software={sw_grp},")
@@ -697,7 +716,15 @@ def _get_software_data(meta_json: dict) -> list:
None,
cite_hhsuite,
),
- "hmmbuild": None,
+ "hmmbuild": modelcif.Software(
+ "hmmbuild",
+ "data collection",
+ "Building HMM search profiles",
+ "http://hmmer.org/",
+ "program",
+ None,
+ None,
+ ),
"hmmsearch": None,
"jackhmmer": None,
"kalign": None,
--
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