Opened 8 years ago

Closed 8 years ago

#652 closed defect (fixed)

infinite loop in PDB reader

Reported by: Greg Couch Owned by: Eric Pettersen
Priority: blocker Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The PDB reader goes into an infinite loop when trying to open 5a8l. The top of the stack is as follows:

#0  0x00007fae5ccf20fd in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) () from /home/socr/a/gregc/chimerax/bin/../lib/libatomstruct.so
#1  0x00007fae5ccf2a77 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) () from /home/socr/a/gregc/chimerax/bin/../lib/libatomstruct.so
#2  0x00007fae5ccf2a77 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) () from /home/socr/a/gregc/chimerax/bin/../lib/libatomstruct.so
#3  0x00007fae5ccf2a77 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) () from /home/socr/a/gregc/chimerax/bin/../lib/libatomstruct.so
#4  0x00007fae5ccf2711 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) () from /home/socr/a/gregc/chimerax/bin/../lib/libatomstruct.so
#5  0x00007fae5ccf3a26 in atomstruct::constrained_match(std::vector<char, std::allocator<char> > const&, atomstruct::StructureSeq const&, atomstruct::AssocParams const&, unsigned int) () from /home/socr/a/gregc/chimerax/bin/../lib/libatomstruct.so
#6  0x00007fae5ccf4faf in atomstruct::try_assoc(atomstruct::Sequence const&, atomstruct::StructureSeq const&, atomstruct::AssocParams const&, unsigned int) ()
   from /home/socr/a/gregc/chimerax/bin/../lib/libatomstruct.so
#7  0x00007fae5ccc177d in atomstruct::AtomicStructure::make_chains() const () from /home/socr/a/gregc/chimerax/bin/../lib/libatomstruct.so
#8  0x00007fae5cd91f62 in structure_num_chains () from /home/socr/a/gregc/chimerax/lib/python3.6/site-packages/chimerax/core/atomic/libmolc.so
#9  0x00007fadd15822be in ffi_call_unix64 () at /tmp/chx-develop.FKY5Cc/build/tmp/Python-3.6.1/Modules/_ctypes/libffi/src/x86/unix64.S:76

Change History (2)

comment:1 by Eric Pettersen, 8 years ago

Status: assigned → accepted

comment:2 by Eric Pettersen, 8 years ago

Resolution: → fixed
Status: accepted → closed

Translation of SEQRES records wasn't stripping spaces from residue names.

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