Export of enumerated Markush structures

Hi,





I have created a R-group file (see attachment) that enumerates to 10000 distinct structures.





In order to export the structures to smiles-format, I choose:





File->Save Selection





In the text-box that pops up, I enter 1-10000 in order to export all structures.


I choose smiles-format for export.





Now msketch freezes and the export stops after 4 (!!) molecules. This is reproducible with export to sd-files and another markush enumeration.





Any help?





Thank you,





Sebastian

When exporting to .mrv, the file also contains only 4 structures.





(see attachment)

Hi,





It is a known bug, and we will fix it ASAP. Te fixed version will be released early next week.





Until then, I recommend the following workaround.


Before you call the save command in the view table, scroll down (till the end of the table). In this case, the whole table will be saved.





Regards,


Zsolt

Thanks for the quick reply, that should do it for the moment.





I've looked around the forum a bit (though not exhaustively) and didn't find any bug reporting/tracking facility.





Is there any place where I can see if a bug has already been filed?





Keep up the good work!





Sebastian

srohrer wrote:

I've looked around the forum a bit (though not exhaustively) and didn't find any bug reporting/tracking facility. Is there any place where I can see if a bug has already been filed?

Hi,





The bugs are reported in forum posts. We (of course) have a bug tracking system, but it is not public.





Regards,


Zsolt

Hi,





unfortunately the workaround with scrolling down doesn't work.





When will the bug-fix be available? I am a little bit under time-pressure so I would be happy to try any test version...








Sebastian

Hi,





It will be available in couple of days (presumably tomorrow).





Zsolt

it's a really nice tool, I am burning to use it...

You can also use cxcalc command line application to generate the enumerated structures.

Code:

$ cxcalc enumerations -h Calculator plugin: enumerations. Markush enumerated structures. Usage:   cxcalc [general options] [input files/strings] enumerations [enumerations options] [input files/strings] enumerations options:   -h, --help          this help message   -m, --max           <count> max. number of structures to be generated                       (default: all)   -v, --valencecheck  [true|false] valence filter is on if true                       (default: true)   -a, --atoms         [atom1,atom2,atom3,...]                       (1-based) atom indexes of the atoms                       to be enumerated (default: all)   -r, --random        [true|false] random enumeration                       (default: false)   -f, --format        <output format> (default: concatenated smiles)   -C, --clean         <dim> clean dimension (default: no clean) Multiple values for the same parameter should be separated by commas (',' without space). Example:   cxcalc enumerations -f sdf -a 2,3,5 -r true -m 2000 test.mol

The output is a file that contains the enumerated structures.





Regards,


Zsolt

That did it! RTFM once again for me... ;-)