Can someone help me understand what's wrong with my searches?
I'm following the tutorial from
http://openbabel.org/wiki/Tutorial:Fingerprints
% babel Compound_09425001_09450000.sdf.fs results.sdf '-sN#Cc1ccccc1C#N' -at0.6
Segmentation fault
% cat > x.smi
N#Cc1ccccc1C#N blah
% babel Compound_09425001_09450000.sdf.fs results.sdf -Sx.ami -at5
Segmentation fault
This is all with a version of Babel I compiled from version control (since I
want the corrected MACCS definitions)
% babel --version
No output file or format spec!
Open Babel 2.3.0 -- Jan 8 2011 -- 19:52:18
(gdb) run Compound_09425001_09450000.sdf.fs results.sdf -sN#Cc1ccccc1C#N -at0.6
...
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
OpenBabel::FastSearchFormat::ObtainTarget (this=0x10148c660,
pConv=0x7fff5fbfeb00, patternMols=@0x7fff5fbfb9a0, indexname=@0x7fff5fbfbb30)
at /Users/dalke/cvses/ob/src/formats/fastsearchformat.cpp:506
506 if(vec[0][0]=='~')
(gdb)
The relevant code is
486 OBMol patternMol;
487 patternMol.SetIsPatternStructure();
488
489 const char* p = pConv->IsOption("s",OBConversion::GENOPTIONS);
490
491 bool OldSOption=false;
492 //If no -s option, make OBMol from file in -S option or -aS option
(both deprecated)
493 if(!p)
494 {
(gdb) l
495 p = pConv->IsOption("S",OBConversion::GENOPTIONS);
496 if(!p)
497 p = pConv->IsOption("S",OBConversion::INOPTIONS);//for GUI
mainly
498 OldSOption = true;
499 }
500 if(p)
501 {
502 vector<string> vec;
503 tokenize(vec, p);
504
(gdb) l
505 //ignore leading ~ (not relevant to fastsearch)
506 if(vec[0][0]=='~')
507 vec[0].erase(0,1);
and I see that p == "", which means vector<string> vect would be the empty
list, making vec[0][0] not possible.
(gdb) print p
$1 = 0x7fff705ea518 ""
Somehow the "-s" value is being removed?
Andrew
da...@dalkescientific.com
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