My GUI Instant JChem version is 184.108.40.206 on OSX 10.10.3. My command line (jcsearch) versions are 220.127.116.11 on OsX 10.10.3 and 18.104.22.168 on Ubuntu 14.04.
The problem is that by visual inspection the and by using the default settings of the GUI version I am able to find the substructure from this smile "CCCCNCC" in this structure "CCCCN1C(Nc2ccccc2C1=O)c1ccc(OC)c(COc2ccc(NC(C)=O)cc2)c1".
However, the following command line does not produce any result on neither of the jcsearch versions mentioned above.
> jcsearch -q "CCCCNCC" "CCCCN1C(Nc2ccccc2C1=O)c1ccc(OC)c(COc2ccc(NC(C)=O)cc2)c1"
So I would like to ask:
What “–flags" should I set in any of the mentioned command line versions so their output would match the GUI's version (default settings) output?
Would it help me if I had a newer version of the command line tools and where can I get it from?
Thank you for answer in advance!