From d4dcb0b9b76205d6f44342383ad880905ffe8a47 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 4 Dec 2023 14:21:50 +0100
Subject: [PATCH] Deal with 'nan' coordinates.
---
projects/novelfams/translate2modelcif.py | 27 +++++++++++++++++++-----
1 file changed, 22 insertions(+), 5 deletions(-)
diff --git a/projects/novelfams/translate2modelcif.py b/projects/novelfams/translate2modelcif.py
index ce8456b..2abf204 100644
--- a/projects/novelfams/translate2modelcif.py
+++ b/projects/novelfams/translate2modelcif.py
@@ -261,9 +261,23 @@ def _get_sequence(chn, use_auth=False):
return sqe
+class _InvalidCoordinateError(RuntimeError):
+ """Exception for weird coordinates ina PDB file, used internally to skip
+ such PDB files."""
+
+
def _get_entities(pdb_file, fam_name):
"""Gather data for the mmCIF (target) entities."""
- ost_ent = io.LoadPDB(pdb_file)
+ try:
+ ost_ent = io.LoadPDB(pdb_file)
+ except Exception as exc:
+ if str(exc).startswith("invalid coordinate on line "):
+ _warn_msg(
+ f"PDB file '{pdb_file}' containes invalid coordinate(s)."
+ )
+ raise _InvalidCoordinateError() from exc
+ _warn_msg(f"Exception for '{pdb_file}'")
+ raise
if ost_ent.chain_count != 1:
raise RuntimeError(f"Unexpected oligomer in {pdb_file}")
chn = ost_ent.chains[0]
@@ -579,11 +593,14 @@ def _main():
print(f"Processing {n_mdls} models.")
tmstmp = s_tmstmp
for f_name in sorted(pdb_files):
- _translate2modelcif(
- f_name,
- opts,
- )
n_mdls -= 1
+ try:
+ _translate2modelcif(
+ f_name,
+ opts,
+ )
+ except _InvalidCoordinateError:
+ continue
# report progress after a bit of time
if timer() - tmstmp > 60:
--
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