On Nov 21, 2011, at 7:47 PM, Robert DeLisle wrote:
> Getting the file to you might be a trick as it is over 4 GB compressed.
I think that's a clue.
RDKit uses tell/seek operations on the underlying file stream, like this:
ROMol *SDMolSupplier::next() {
PRECONDITION(dp_inStream,"no stream");
// set the stream to the current position
dp_inStream->seekg(d_molpos[d_last]);
d_molpos contains "std::streampos" elements,
MolSupplier.h: std::vector<std::streampos> d_molpos; // vector of positions
in the file for molecules
and I can't tell if that's a 32-bit or 64-bit value, but there's
code which assumes it's an unsigned 32-bit integer:
std::string SDMolSupplier::getItemText(unsigned int idx){
PRECONDITION(dp_inStream,"no stream");
unsigned int holder=d_last;
moveTo(idx);
unsigned int begP=d_molpos[idx];
unsigned int endP;
try {
My guess is that there's an overflow in this code, causing it to
loop from 2**32 back to 0.
Andrew
da...@dalkescientific.com
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