Hi Noel and other,
I would guess it's the MOL2 reader. If you set a breakpoint in there and
> then step through you can confirm/deny this.
>
>
Ok, you may well be right. Here is what I do:
(gdb) b OpenBabel::MOL2Format::ReadMolecule
(gdb) run
Processing 1lrh_0-NLA-1.mol2
Breakpoint 1, OpenBabel::MOL2Format::ReadMolecule (this=0x220a488,
pOb=0xbfffedb4, pConv=0xbfffebbc)
at /opt/OPENBABEL/openbabel-2.3.2/src/src/formats/mol2format.cpp:72
72 OBMol* pmol = pOb->CastAndClear<OBMol>();
(gdb) next
Program received signal SIGSEGV, Segmentation fault.
__cxxabiv1::__dynamic_cast (src_ptr=0xbfffedb4, src_type=0x442820,
dst_type=0x442fe0, src2dst=0)
at ../../../../libstdc++-v3/libsupc++/dyncast.cc:56
56 adjust_pointer <void> (src_ptr, prefix->whole_object);
(gdb) b CastAndClear<OpenBabel::OBMol> #1
(gdb) b OpenBabel::MOL2Format::ReadMolecule #2
(gdb) b OpenBabel::OBConversion::Read #3
(gdb) b OpenBabel::OBConversion::ReadFile #4
(gdb) run
[zapping prog. output and "next" command]
Processing 1lrh_0-NLA-1.mol2
Breakpoint 4, OpenBabel::OBConversion::ReadFile (this=0xbfffebbc,
pOb=0xbfffedb4, filePath="1lrh_0-NLA-1.mol2")
at /opt/OPENBABEL/openbabel-2.3.2/src/src/obconversion.cpp:980
980 if(!pInFormat) return false;
979 {
980 if(!pInFormat) return false;
983 InFilename = filePath;
986 if (pInStream && NeedToFreeInStream) {
990 ifstream *ifs = new ifstream;
991 NeedToFreeInStream = true; // make sure we free this
996 ifs->open(filePath.c_str(),imode);
991 NeedToFreeInStream = true; // make sure we free this
996 ifs->open(filePath.c_str(),imode);
997 if(!ifs || !ifs->good())
1003 return Read(pOb,ifs);
Breakpoint 3, OpenBabel::OBConversion::Read (this=0xbfffebbc,
pOb=0xbfffedb4, pin=0x80ef438)
at /opt/OPENBABEL/openbabel-2.3.2/src/src/obconversion.cpp:792
792 {
793 if(pin) {
794 pInStream=pin;
795 CheckedForGzip = false; // haven't set this stream to gzip
(yet)
798 if(!pInFormat || !pInStream) return false;
804 if (!CheckedForGzip) {
805 zIn = new zlib_stream::zip_istream(*pInStream);
806 if (zIn->is_gzip()) {
811 delete zIn;
815 InstallStreamFilter();
821 locale originalLocale = pInStream->getloc(); // save the original
815 InstallStreamFilter();
818 obLocale.SetLocale();
821 locale originalLocale = pInStream->getloc(); // save the original
700 { return _M_ios_locale; }
822 locale cNumericLocale(originalLocale, "C", locale::numeric);
823 pInStream->imbue(cNumericLocale);
825 bool success = pInFormat->ReadMolecule(pOb, this);
Breakpoint 2, OpenBabel::MOL2Format::ReadMolecule (this=0x220a488,
pOb=0xbfffedb4, pConv=0xbfffebbc)
at /opt/OPENBABEL/openbabel-2.3.2/src/src/formats/mol2format.cpp:72
72 OBMol* pmol = pOb->CastAndClear<OBMol>();
Program received signal SIGSEGV, Segmentation fault.
__cxxabiv1::__dynamic_cast (src_ptr=0xbfffedb4, src_type=0x442820,
dst_type=0x442fe0, src2dst=0)
at ../../../../libstdc++-v3/libsupc++/dyncast.cc:56
56 adjust_pointer <void> (src_ptr, prefix->whole_object);
Is there a way to go in the function "CastAndClear"?
Trying
(gdb) b CastAndClear
or
(gdb) b CastAndClear<OpenBabel::OBMol>
is saying:
Function "CastAndClear" not defined.
it is staying "pending" and does not reach the breakpoint when running.
I'll try to set some breakpoints in the program I'm running too.
Thanks,
Pascal
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