It seems like obabel invoked with '--filter' option fails to parse filter
string properly.
I am running openbabel 2.3.2 compiled with gcc 4.6.3 on Ubuntu 12.04.2 LTS.
My SDF file is:
MySoft
Molecule1
5 4 0 0 0 0 0 0 0999 V2000
2.5369 0.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0739 0.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 -0.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2269 0.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8469 -0.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END
> <MyProp>
-2.0
$$$$
MySoft
Molecule2
5 4 0 0 0 0 0 0 0999 V2000
2.5369 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0739 0.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 -0.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2269 0.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8469 -0.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END
> <MyProp>
-3.0
$$$$
When I filter it by property MyProp with a command:
obabel -isdf test.sdf -osdf --filter "MyProp<-1"
it works fine (i.e. both molecules are converted).
However, invoking obabel with command:
obabel -isdf test.sdf -osdf --filter "(MyProp<-1)"
gives 0 molecules.
Having investigated the source code and done some debugging stuff, I suggest
that any filter condition other than in the very end of the filter line (so
that the next symbol is EOF) leads to it's misparsing. In the last given
example, "-1" is identified as string, not float. This is caused by broken
code in OBDescriptor::ParsePredicate. As a result, any filter string other
than a single condition without any parentheses fails to work properly.
Please try to reproduce the bug and correct me if I am wrong.
Regards,
Oleksii Balinskyi
--
View this message in context:
http://forums.openbabel.org/Molecular-descriptor-filter-does-not-work-properly-tp4656057.html
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