From 6bbd6fa7ec53e1a0971fba40c96fa971d1022f74 Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Mon, 18 Jul 2022 14:27:08 +0200
Subject: [PATCH] Minor fixes
---
translate2modelcif.py | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/translate2modelcif.py b/translate2modelcif.py
index e685cb6..50ffdbb 100644
--- a/translate2modelcif.py
+++ b/translate2modelcif.py
@@ -251,7 +251,6 @@ def _get_protocol_steps_and_software(cnfg_file):
# Must refer to existing data, so we try keywords
step["output"] = "model"
# get software
-<<<<<<< HEAD
step["software"] = [
{
"name": "ColabFold",
@@ -543,6 +542,8 @@ def _get_scores(data, prfx):
with open(scrs_fle, encoding="utf8") as jfh:
scrs_json = json.load(jfh)
+ # ToDo: is dict.update still the way to go when iterating multiple model
+ # directories? Aka, does dict.update overwrite old scores?
data.update(scrs_json)
@@ -613,11 +614,10 @@ def _get_modelcif_protocol(protocol_steps, target_entities, model):
for sft in js_step["software"]:
sftwre.append(_assemble_modelcif_software(sft))
sftwre = modelcif.SoftwareGroup(elements=sftwre)
- # ToDo [internal]: add software parameters
- if js_step['software_parameters']:
+ if js_step["software_parameters"]:
params = []
# ToDo [internal]: handle lists!
- for k, v in js_step['software_parameters'].items():
+ for k, v in js_step["software_parameters"].items():
params.append(
modelcif.SoftwareParameter(k, v)
)
@@ -630,6 +630,7 @@ def _get_modelcif_protocol(protocol_steps, target_entities, model):
if js_step["input"] == "target_sequences":
input_data = modelcif.data.DataGroup(target_entities)
+ # ToDo: Add databases + versions
elif js_step["input"] == "model":
input_data = model
else:
--
GitLab