Re: [rDock-list-def] rdock and the SDF property issue

[Peter S. <pet...@gm...>]

Hey, cool and thanks looking into this. It’s a bit the same for me, would be good to know more about that. 

In the two file you sent, 

the one written with Pipeline Pilot has a less extensive description of the atoms and bond order first of all, but also has different header descriptions. 
The one written with knime all fields of the mol file in v2000 are specified. 
For the descriptor part (Index) I guess both are the same even though you might want to check the newlines at the end (but I already did that in the past and it wasn’t the issue in my case). 

So I’d start to permutate a bit between both files to narrow down it’s the header / atom or bond section messing things up here. 

Cannot do this right now on my own here, but maybe some time next week.

Thanks for looking into this anyway.



Peter

> On 24 Oct 2019, at 20:32, Scott Bembenek <sbe...@de...> wrote:
> 
> Hi Peter,
> 
> Sorry to mail you directly, I am unclear what email to send it to so that it post on the forum. 
> 
> Question, that has been on mind for awhile ... 
> 
> The problem with including properties in the input SDF has been discussed. I have also run into this problem, but find that sometimes it happens and sometimes it does not. 
> 
> Doe anyone have any more insight into this? 
> 
> Here's an example where to two files written by different programs have the same properties in them, but one of them runs fine with rdock (format 2), while the other does not (format 1).
> 
> I'd be grateful if you have insight into the nature of "the property problem" since I find it is not consistent and also, it is often times nice/necessary to include at least one property in your input SDF. 
> 
> thanks! 
> 
> Scott
> <mol1_pp_format_index_format1.sdf><mol1_knime_format_index_format2.sdf>