From 8eff857b904218d578eb40bedf7bd8435b0c7ff5 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 6 Dec 2023 11:30:29 +0100
Subject: [PATCH] Add local pLDDT from b-factors
---
projects/novelfams/translate2modelcif.py | 34 +++++++++++++++++-------
1 file changed, 25 insertions(+), 9 deletions(-)
diff --git a/projects/novelfams/translate2modelcif.py b/projects/novelfams/translate2modelcif.py
index add84bb..219f50d 100644
--- a/projects/novelfams/translate2modelcif.py
+++ b/projects/novelfams/translate2modelcif.py
@@ -165,7 +165,6 @@ def _get_ch_name(ch, use_auth=False):
return ch.name
-# ToDo: are those Ab Initio Models?
class _OST2ModelCIF(modelcif.model.AbInitioModel):
"""Map OST entity elements to ihm.model"""
@@ -210,6 +209,23 @@ class _OST2ModelCIF(modelcif.model.AbInitioModel):
occupancy=atm.occupancy,
)
+ def add_scores(self):
+ """Add QA metrics from AF2 scores."""
+ # local scores
+ i = 0
+ for chn_i in self.ost_entity.chains:
+ ch_name = _get_ch_name(chn_i, self.use_auth)
+ for res_i in chn_i.residues:
+ # local pLDDT
+ res_num = _get_res_num(res_i, self.use_auth)
+ self.qa_metrics.append(
+ _LocalPLDDT(
+ self.asym[ch_name].residue(res_num),
+ self.plddts[i],
+ )
+ )
+ i += 1
+
def _get_metadata(metadata_file):
"""Read csv file with metedata and prepare for next steps."""
@@ -535,7 +551,7 @@ def _store_as_modelcif(
scores_json=data_json,
name=mdl_name,
)
-
+ model.add_scores()
model_group = modelcif.model.ModelGroup([model])
system.model_groups.append(model_group)
@@ -700,14 +716,14 @@ def _translate2modelcif(f_name, af2_lst, opts):
# ToDo: re-enable Pylint
# pylint: disable=too-many-locals
- # skip if done already
- if opts.compress:
- cifext = "cif.gz"
- else:
- cifext = "cif"
- mdl_path = os.path.join(opts.out_dir, f"{f_name}.{cifext}")
# ToDo: re-enable for final version
- #if os.path.exists(mdl_path):
+ # skip if done already
+ # if opts.compress:
+ # cifext = "cif.gz"
+ # else:
+ # cifext = "cif"
+ # mdl_path = os.path.join(opts.out_dir, f"{f_name}.{cifext}")
+ # if os.path.exists(mdl_path):
# print(f" {f_name} already done")
# return
--
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