Hi,
I have now managed to produce a nice little self-contained DLL that uses
RDKit to do substructure mapping. It receives a query and a target
molecule as two MDL molfile strings. When the inputs are valid it
behaves well and returns the atom mapping to me. Yes :-).
However, when I give it an invalid MDL molfile as input, e.g. a text
file with regular prose, MolDataStreamToMol() throws a highly unexpected
error message.
This piece of my test code:
ifstream query_file ("C:\\SubstructData\\results.txt");
auto_ptr<RWMol> query (NULL);
unsigned int line = 0;
try {
query.reset( MolDataStreamToMol(query_file, line, false, false,
false) );
} catch (std::exception& e) {
cout << "STD-ERROR: " << e.what() << endl;
return 1;
} catch (...) {
cout << "UNK-ERROR: Unknown exception." << endl;
return 1;
}
produces this output:
[00:13:24] CTAB version string invalid at line 4
STD-ERROR: *Unknown exception*
In MolFileParser.cpp line 1881 I can locate the reported error message:
std::ostringstream errout;
errout<<"*CTAB version string invalid at line* "<<line;
if(strictParsing){
if(res) delete res;
throw FileParseException(errout.str());
} else {
* BOOST_LOG(rdWarningLog) << errout.str() << std::endl;*
}
Since I run with strictParsing==false the BOOST_LOG(rdWarningLog) call
must be the one that emits the first line of output, and I assume that
the boost warning log does not throw an exception. I haven't been able
to figure out where the exception gets thrown, but that must be later in
the code.
If I switch to strict parsing (last parameter in MolDataStreamToMol()
set to true) I don't see the boost log message anymore, only the single
line "STD-ERROR: Unknown exception". So strict parsing actually yields
less error message context.
I hope the exception error message can be changed to something more
meaningful ?
Cheers
-- Jan
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