Fixes #6756 (#6780)

Code/GraphMol/FileParsers/CMakeLists.txt

@@ -118,3 +118,7 @@ rdkit_catch_test(cdxmlParserCatchTest cdxml_parser_catch.cpp
 rdkit_catch_test(molfileStereoCatchTest molfile_stereo_catch.cpp
            LINK_LIBRARIES CIPLabeler FileParsers Subgraphs)
 
+rdkit_catch_test(connectTheDotsTest connectTheDots_catch.cpp
+           LINK_LIBRARIES FileParsers)
+
+

Code/GraphMol/FileParsers/ProximityBonds.cpp

@@ -228,7 +228,8 @@ static void ConnectTheDots_Large(RWMol *mol, unsigned int flags) {
         auto *n_info =
             (AtomPDBResidueInfo *)(mol->getAtomWithIdx(*nbr)->getMonomerInfo());
         if (d < best &&
-            atom_info->getResidueNumber() == n_info->getResidueNumber()) {
+            ((!atom_info || !n_info) ||
+             atom_info->getResidueNumber() == n_info->getResidueNumber())) {
           best = d;
           best_idx = *nbr;
         }

Code/GraphMol/FileParsers/connectTheDots_catch.cpp

@@ -0,0 +1,66 @@
+//
+//  Copyright (C) 2023 Greg Landrum and other RDKit contributors
+//   @@ All Rights Reserved @@
+//  This file is part of the RDKit.
+//  The contents are covered by the terms of the BSD license
+//  which is included in the file license.txt, found at the root
+//  of the RDKit source tree.
+//
+
+#include <algorithm>
+#include <fstream>
+#include <string>
+#include <sstream>
+#include <string_view>
+#include <streambuf>
+
+#include "RDGeneral/test.h"
+#include "catch.hpp"
+#include <RDGeneral/Invariant.h>
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/FileParsers/FileParsers.h>
+#include <GraphMol/SmilesParse/SmilesParse.h>
+#include <GraphMol/FileParsers/ProximityBonds.h>
+
+using namespace RDKit;
+
+TEST_CASE(
+    "Github #6756: ConnectTheDots can segfault if atoms do not have residue info") {
+  SECTION("small molecule, was not a problem") {
+    std::string smiles =
+        "[H]C([H])=C([H])C([H])([H])[H] |(1.35283,-0.241953,-1.28693;1.35436,-0.216135,-0.201646;2.30673,-0.352635,0.30154;0.23076,-0.0239947,0.500064;0.281106,-0.00576639,1.58653;-1.11716,0.171588,-0.112486;-1.08265,0.139951,-1.20609;-1.52627,1.14083,0.188471;-1.79971,-0.611884,0.230548)|";
+    SmilesParserParams ps;
+    ps.removeHs = false;
+    std::unique_ptr<RWMol> m(SmilesToMol(smiles, ps));
+    REQUIRE(m);
+    CHECK(m->getNumBonds() == 8);
+    // start without bonds
+    m->beginBatchEdit();
+    for (auto bond : m->bonds()) {
+      m->removeBond(bond->getBeginAtomIdx(), bond->getEndAtomIdx());
+    }
+    m->commitBatchEdit();
+    CHECK(m->getNumBonds() == 0);
+    ConnectTheDots(m.get());
+    CHECK(m->getNumBonds() == 8);
+  }
+  SECTION("small molecule with bivalent H, this did crash") {
+    std::string smiles = "F[H]F |(1.1,0,0;0,0,0;-1.1,0,0)|";
+    SmilesParserParams ps;
+    ps.removeHs = false;
+    ps.sanitize = false;
+    std::unique_ptr<RWMol> m(SmilesToMol(smiles, ps));
+    REQUIRE(m);
+    m->updatePropertyCache(false);
+    CHECK(m->getNumBonds() == 2);
+    // start without bonds
+    m->beginBatchEdit();
+    for (auto bond : m->bonds()) {
+      m->removeBond(bond->getBeginAtomIdx(), bond->getEndAtomIdx());
+    }
+    m->commitBatchEdit();
+    CHECK(m->getNumBonds() == 0);
+    ConnectTheDots(m.get());
+    CHECK(m->getNumBonds() == 1);
+  }
+}