From 389226b82e61679df3c8f5172fd2046d41a1265e Mon Sep 17 00:00:00 2001
From: Marcin Wojdyr <wojdyr@gmail.com>
Date: Sat, 31 Aug 2024 20:01:02 +0200
Subject: [PATCH] two more checks, in align_sequence_to_polymer and
 superpose_positions

calculate_superposition() segfaulted when called with empty ResidueSpan
---
 include/gemmi/align.hpp | 3 ++-
 include/gemmi/qcp.hpp   | 5 +++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/include/gemmi/align.hpp b/include/gemmi/align.hpp
index d50256469..ceb8327f7 100644
--- a/include/gemmi/align.hpp
+++ b/include/gemmi/align.hpp
@@ -35,12 +35,13 @@ inline std::vector<int> prepare_target_gapo(const ConstResidueSpan& polymer,
   return gaps;
 }
 
-// pre: !!polymer
 inline AlignmentResult align_sequence_to_polymer(
                                      const std::vector<std::string>& full_seq,
                                      const ConstResidueSpan& polymer,
                                      PolymerType polymer_type,
                                      const AlignmentScoring* scoring=nullptr) {
+  if (!polymer)
+    return AlignmentResult();
   std::map<std::string, std::uint8_t> encoding;
   if (!scoring)
     scoring = AlignmentScoring::partial_model();
diff --git a/include/gemmi/qcp.hpp b/include/gemmi/qcp.hpp
index 56a45abad..7e0be7a74 100644
--- a/include/gemmi/qcp.hpp
+++ b/include/gemmi/qcp.hpp
@@ -303,6 +303,11 @@ inline SupResult superpose_positions(const Position* pos1, const Position* pos2,
   result.center1 = qcp_calculate_center(pos1, len, weight);
   result.center2 = qcp_calculate_center(pos2, len, weight);
 
+  if (len == 0) {
+    result.rmsd = NAN;
+    return result;
+  }
+
   double wsum = 0.0;
   if (weight == nullptr)
     wsum = (double) len;