SerConverter fails converting graphs to structures about denoptim HOT 5 CLOSED

OK, @philippba89, I think I got it. The molecular geometry you find in the dg_10.sdf shows some very wrong bond lengths and angles. This is because SerConverter is only meant to convert the serialized file containing a DENOPTIMGraph (i.e., the content of dg_10.ser) into and SDF file containing the same DENOPTIMGraph (i.e., the content of dg_10.sdf). This conversion is completely unrelated to how a DENOPTIMGraph (whether hosted in a serialized *.ser file or in a *.sdf file) is converted into a molecular geometry. In practice, the molecular geometry you see in the dg_10.sdf file is only the sum of the molecular geometries of all the fragments that are part of the graph.

That said, I agree it would be best to get the unrefined 3D geometry, i.e., a geometry where the 3D fragments are aligned according to their attachment point vectors. Therefore, I've added a new keyword, SERCONV-MAKE3DTREE, that asks SerConverted to produce SDF files that contain such unrefined geometry. Note that I say "unrefined" because there is no molecular modeling done on such geometry, so, while it is good enough for starting a conformational search, it is not an optimized geometry.

You find this fix in the latest release: https://github.com/denoptim-project/DENOPTIM/releases/tag/v2.2.4

Your suggestion was a very good, thanks!

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@philippba89 Thanks for reporting. I'm looking into this, but I want to be sure I understand what is the problem you have experienced. Could you give me an example of a "messed up" sdf file? The best would be to make me able to reproduce the issue with the PtCOLX2_FSE test case.

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Hey marco-foscato, sorry for the misunderstanding. In let the test "PtCOLX2_FSE" run. Generally one obtains the resulting .sdf files in the Folder FSENUMBER...those are all fine. What I tried to do is to convert a .ser file in one of the sub-filders, e.g. "FSE-level_0" to a .sdf file.

As mentioned before, using the SerConverter to try this at the graph dg_10.ser. Therefor I added the following lines to the "input-parameters" file (which i copied to "PtCOLX2_FSE/FSE_run_13/FSE24022021030255/FSE-Level_0"):

#SERCONVERTER
SERCONV-WORKDIR=./
SERCONV-INPFILE=dg_10.ser
SERCONV-OUTFORMAT=SDF
SERCONV-OUTFILE=dg_10.sdf

I simple run the script via" java -jar SerConverter.jar input-parameters"

The resulting dg_10.sdf is somehow not reasonable. If I directly open the dg_10.ser file with the GUI, the structure shown there is reasonable. I hope you can reproduce this error, or maybe I am doing something wrong...pls let me know :)

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closed with https://github.com/denoptim-project/DENOPTIM/releases/tag/v2.2.4

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Thank you so much, this was exactly what I was looking for!

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