From 3ee8555bc713dbd4d60ce786c6658c2dcdfdd659 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 9 Mar 2023 09:44:12 +0100
Subject: [PATCH] raise Error when no chain fulfills minimum number of residues
in ChainMapper
The previous error was a selection statement with no obvious connection to
that problem. Default minimum lengths are 10 for peptide chains and 4 for
nucleotide chains
---
modules/mol/alg/pymod/chain_mapping.py | 7 +++++++
modules/mol/alg/tests/test_chain_mapping.py | 7 +++++++
2 files changed, 14 insertions(+)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 7ee8ff5fc..f5e10d58c 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1499,6 +1499,13 @@ class ChainMapper:
else:
raise RuntimeError("This shouldnt happen")
+ if len(polypep_seqs) == 0 and len(polynuc_seqs) == 0:
+ raise RuntimeError(f"No chain fulfilled minimum length requirement "
+ f"to be considered in chain mapping "
+ f"({self.min_pep_length} for peptide chains, "
+ f"{self.min_nuc_length} for nucleotide chains) "
+ f"- mapping failed")
+
# select for chains for which we actually extracted the sequence
chain_names = [s.GetAttachedView().chains[0].name for s in polypep_seqs]
chain_names += [s.GetAttachedView().chains[0].name for s in polynuc_seqs]
diff --git a/modules/mol/alg/tests/test_chain_mapping.py b/modules/mol/alg/tests/test_chain_mapping.py
index 36a633b09..8c8846aba 100644
--- a/modules/mol/alg/tests/test_chain_mapping.py
+++ b/modules/mol/alg/tests/test_chain_mapping.py
@@ -353,6 +353,13 @@ class TestChainMapper(unittest.TestCase):
aln.GetSequence(1).GetString())
+ def test_misc(self):
+
+ # check for triggered error when no chain fulfills length threshold
+ ref = _LoadFile("3l1p.1.pdb").Select("cname=A and rnum<8")
+ self.assertRaises(Exception, ChainMapper, ref)
+
+
if __name__ == "__main__":
from ost import testutils
if testutils.SetDefaultCompoundLib():
--
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