From 34da23eb9010c6ee2a74266cef930b2942f81a3d Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Tue, 28 Mar 2023 14:08:57 +0200
Subject: [PATCH] fix: properly test for invalid residues/atoms
---
modules/mol/alg/pymod/chain_mapping.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 74dfc115f..85983ed88 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1278,7 +1278,7 @@ class ChainMapper:
ch_name = r.GetChain().GetName()
rnum = r.GetNumber()
target_r = self.target.FindResidue(ch_name, rnum)
- if target_r is None:
+ if not target_r.IsValid():
raise RuntimeError(f"substructure has residue "
f"{r.GetQualifiedName()} which is not in "
f"self.target")
@@ -1290,7 +1290,7 @@ class ChainMapper:
f"EntityHandle")
for a in r.atoms:
target_a = target_r.FindAtom(a.GetName())
- if target_a is None:
+ if not target_a.IsValid():
raise RuntimeError(f"substructure has atom "
f"{a.GetQualifiedName()} which is not "
f"in self.target")
@@ -1305,7 +1305,7 @@ class ChainMapper:
ca = r.FindAtom("CA")
c3 = r.FindAtom("C3'") # FindAtom with prime in string is tested
# and works
- if ca is None and c3 is None:
+ if not ca.IsValid() and not c3.IsValid():
raise RuntimeError("All residues in substructure must contain "
"a backbone atom named CA or C3\'")
--
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