From 8bcd3d2f99fdca25f6ccd6252455b73bc0dd0d2d Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 23 Jul 2024 12:29:44 +0000
Subject: [PATCH] Fix _fetch_upkb_cached in translate2modelcif.py
---
.../PP2A-B55-design/translate2modelcif.py | 21 ++++++++-----------
1 file changed, 9 insertions(+), 12 deletions(-)
diff --git a/projects/PP2A-B55-design/translate2modelcif.py b/projects/PP2A-B55-design/translate2modelcif.py
index 5db56f0..045c8df 100644
--- a/projects/PP2A-B55-design/translate2modelcif.py
+++ b/projects/PP2A-B55-design/translate2modelcif.py
@@ -363,19 +363,24 @@ def _check_sequence(up_ac, sequence):
# for cache below
upkb_entry_cache = {} # key = (up_ac, up_version, mdl_sequence)
def _fetch_upkb_cached(sqe, up_ac, up_version=None):
- """Get versioned UniProtKB entry (version=None means latest).
+ """Get best matching UniProtKB entry for sequence sqe.
Get it from cache if already fetched.
- Return None if failed to parse entry.
+ up_version defines starting version in UP to check.
+ Note that the returned UP entry may be a different version than the one in up_version.
+ Returned UP data includes result of _align_sequences.
+ If no perfect match found, it prints a warning.
"""
# check if in cache already
cache_key = (up_ac, up_version, sqe)
if cache_key in upkb_entry_cache:
return upkb_entry_cache[cache_key]
- # fetch and parse
+ # fetch and parse first guess
if up_version is None:
up_data = _fetch_upkb_entry(up_ac)
+ else:
+ up_data = _fetch_unisave_entry(up_ac, up_version)
+ # find best match starting from first guess
min_up_data = None
-
while True:
mismatches, up_range, mdl_range, covered_aln, mdl_seqres = _align_sequences(
sqe, up_data["up_sequence"], atomseq_aln=False)
@@ -415,14 +420,6 @@ def _fetch_upkb_cached(sqe, up_ac, up_version=None):
_warn_msg(msg)
# raise RuntimeError(msg)
break
- '''else:
- try:
- # note: can fail to parse very old UP versions...
- up_data = _fetch_unisave_entry(up_ac, up_version)
- except RuntimeError as ex:
- #_warn_msg(f"Error in parsing v{next_v} of {up_ac}:\n{ex}")
- up_data = None
- '''
# keep in cache
upkb_entry_cache[cache_key] = up_data
--
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