From ed96fc9c877277cfd5497c57ef2a3273cfc78945 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 5 Dec 2023 09:59:15 +0100
Subject: [PATCH] Handle empty PDB files/ files w/o entities.
---
projects/novelfams/translate2modelcif.py | 17 +++++++++++++++--
1 file changed, 15 insertions(+), 2 deletions(-)
diff --git a/projects/novelfams/translate2modelcif.py b/projects/novelfams/translate2modelcif.py
index 2abf204..d4392f0 100644
--- a/projects/novelfams/translate2modelcif.py
+++ b/projects/novelfams/translate2modelcif.py
@@ -262,7 +262,12 @@ def _get_sequence(chn, use_auth=False):
class _InvalidCoordinateError(RuntimeError):
- """Exception for weird coordinates ina PDB file, used internally to skip
+ """Exception for weird coordinates in a PDB file, used internally to skip
+ such PDB files."""
+
+
+class _NoEntitiesError(RuntimeError):
+ """Exception for PDB files w/o entities (empty?), used internally to skip
such PDB files."""
@@ -270,6 +275,14 @@ def _get_entities(pdb_file, fam_name):
"""Gather data for the mmCIF (target) entities."""
try:
ost_ent = io.LoadPDB(pdb_file)
+ except OSError as exc:
+ if str(exc).endswith(" doesn't contain any entities"):
+ _warn_msg(
+ f"PDB file '{pdb_file}' does not have entities (maybe empty)."
+ )
+ raise _NoEntitiesError() from exc
+ _warn_msg(f"Exception for '{pdb_file}'")
+ raise
except Exception as exc:
if str(exc).startswith("invalid coordinate on line "):
_warn_msg(
@@ -599,7 +612,7 @@ def _main():
f_name,
opts,
)
- except _InvalidCoordinateError:
+ except (_InvalidCoordinateError, _NoEntitiesError):
continue
# report progress after a bit of time
--
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