[Solved] Bug/Feature ? SDF Export

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[Solved] Bug/Feature ? SDF Export

Postby alesser » Wed Feb 23, 2011 7:46 pm

I've noticed that when "SDF export" is used, the SDF file only has one structure in it, even if multiple structures are selected in the list. This is inconsistent with the behavior of the other "save" button right next to it, which exports ALL the values in the table.

Furthermore, since the developers of AutoDock4 have taken away the ability to easily extract docking poses into a PDB file (there's no more "get-docking" script distributed w/ ADT), it would be very valuable for lots of people to be able to use PyRx as an "extraction tool".

If the SDF export were to export all the poses in the docking table to one file, with all of the energies listed, it would be very useful for importing into other programs (such as Maestro, MOE, etc) ! As it is, I can do this, but I have to do one at a time import / export, which is particularly painful (seems like something a computer should be automated to do !)

Would it be possible to enable this feature or fix the bug if this is what's meant to happen ?
Last edited by alesser on Wed Feb 23, 2011 10:15 pm, edited 1 time in total.
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Re: Bug/Feature ? SDF Export

Postby sargis » Wed Feb 23, 2011 8:02 pm

Thank you for the message Adam! There is so called "Number of Poses to Retain" preference accessible through Edit > Preferences > Open Babel > AutoDock Ligand. Please change the default from 1 to 0 to retain all the poses. I'll change this default to 0 in the next release. Thanks!
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Re: Bug/Feature ? SDF Export

Postby alesser » Wed Feb 23, 2011 8:08 pm

DUH ! Thanks !

But one minor question remains.. it still only exports binding energy.. is there a way to get the SDF file to include the other energies as well ?

Also, not to glom too much into one request, but you might want to add a "Cluster number" to the docking table so that you can view/sort by clusterings.
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Re: Bug/Feature ? SDF Export

Postby sargis » Wed Feb 23, 2011 8:16 pm

alesser wrote:DUH ! Thanks !

But one minor question remains.. it still only exports binding energy.. is there a way to get the SDF file to include the other energies as well ?

Also, not to glom too much into one request, but you might want to add a "Cluster number" to the docking table so that you can view/sort by clusterings.


Thanks. Adding other energies that we get from dlg would be easy to implement. "Cluster number" would require extra computation, but shouldn't be a problem. Thanks!
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