Negative unit test for bad patches

source/src/core/chemical/ResidueType.cc

@@ -62,6 +62,7 @@
 
 // C++ headers
 #include <algorithm>
+#include <sstream>      // std::stringstream
 
 #ifdef    SERIALIZATION
 #include <core/chemical/rotamers/RotamerLibrarySpecification.hh>
@@ -1150,6 +1151,16 @@ ResidueType::setup_atom_ordering( MutableResidueType const & mrt )
 		first_sidechain_hydrogen_ = attached_H_begin_[n_backbone_heavyatoms_+1];
 	}
 
+	if ( atom_order.size() != natoms_  ) {
+		std::stringstream ss;
+		ss << "atom_order.size() = " << atom_order.size() << '\n';
+		ss << "natoms_ = " << natoms_ << '\n';
+		ss << "This mismatch is expected to give a segfault down the line. The mismatch can be caused by:\n";
+		ss << " - Using an invalid patch that has heavy/virtual atoms downstream of hydrogens.\n";
+		ss << " - Maybe other reasons? Add them here if you find more please!";
+		utility_exit_with_message( ss.str() );
+	}
+
 	return atom_order;
 }
 

source/test/core.test.settings

@@ -760,6 +760,7 @@ testinputfiles = [
 	"chemical/atom_properties.txt",
 	"chemical/ASX.params", # remove if the database version gets permanently enabled
 	"chemical/LYX.params", # remove if the database version gets permanently enabled
+	"chemical/bad_atom_ordering.patch",
 	"chemical/conflict_patch.txt",
 	"chemical/conn.pdb",
 	"chemical/carbohydrates/amylopectin_fragment.pdb",

source/test/core/chemical/ResidueTypeTests.cxxtest.hh

@@ -33,10 +33,15 @@
 #include <core/chemical/residue_io.hh>
 #include <core/chemical/util.hh>
 #include <core/chemical/residue_support.hh>
+#include <core/chemical/Patch.hh>
 
 #include <core/chemical/sdf/mol_writer.hh>
 
+#include <core/conformation/Residue.hh>
+#include <core/conformation/ResidueFactory.hh>
+
 #include <core/pose/Pose.hh>
+#include <core/pose/annotated_sequence.hh>
 
 #include <core/kinematics/Stub.hh>
 
@@ -657,4 +662,17 @@ public:
 
 	}
 
+	void test_bad_atom_ordering(){
+		core::pose::Pose pose;
+		core::pose::make_pose_from_sequence( pose, "TESTMYIDEAPLEASE", "fa_standard" );
+		core::Size const resid = 4;
+		core::conformation::Residue const & r = pose.residue(resid);
+		core::chemical::Patch patch;
+		patch.read_file( "core/chemical/bad_atom_ordering.patch" );
+		utility::vector1< core::chemical::VariantType > types;
+		patch.types( types );
+		auto mutable_type = patch.apply( r.type() );
+		TS_ASSERT_THROWS_ANYTHING( auto res_type = core::chemical::ResidueType::make( *mutable_type ); )
+	}
+
 };

source/test/core/chemical/bad_atom_ordering.patch

@@ -0,0 +1,25 @@
+NAME AddVirtualAtoms
+TYPES ADD_VIRTUAL_ATOMS
+BEGIN_SELECTOR
+# This patch can be applied to any residue type
+END_SELECTOR
+BEGIN_CASE
+BEGIN_SELECTOR
+# This case applies to all residues
+END_SELECTOR
+ADD_ATOM  V0  VIRT VIRT 0.00
+ADD_BOND  OG1  V0
+SET_ICOOR  V0   1.00000000  1.00000000  1.00000000   OG1   CB    CA
+ADD_ATOM  V1  VIRT VIRT 0.00
+ADD_BOND  N    V1
+SET_ICOOR  V1   1.00000000  1.00000000  1.00000000   N     CA    C 
+ADD_ATOM  V2  VIRT VIRT 0.00
+ADD_BOND  O    V2
+SET_ICOOR  V2   1.00000000  1.00000000  1.00000000   O     C     CA
+ADD_ATOM  V3  VIRT VIRT 0.00
+ADD_BOND  C    V3
+SET_ICOOR  V3   1.00000000  1.00000000  1.00000000   C     CA    N 
+ADD_ATOM  V4  VIRT VIRT 0.00
+ADD_BOND 1HG2  V4
+SET_ICOOR  V4   1.00000000  1.00000000  1.00000000  1HG2   CG2   CB
+END_CASE