Principal moment of inertia

KNIME Analytics Platform
#1

Hello,

I am trying to find a way of calculating the 3 principal moment of inertia of a molecule, sorting the value in ascending order  and dividing the two lower values by the biggest value. In this way I can have a descriptor that can be plotted in triangle plots . They can describe the shape of a molecule or 3-Dimensionality. Is this something that Knime already have in the set of descriptors? Or can be done easily?

 

Thanks

#2

James,

Thanks.  Unfortunately I do not have MOE and I am not sure I can make the workflow you sent working. I am trying.

 

 

#3

Hi,

The MOE nodes make pmi descriptors available in KNIME - but, of course, you need access to an installation of MOE to use them.

If you do have access to MOE, then the nice thing about these descriptors is that you save yourself a couple of (trivial) steps - because they are already ordered, and there are also pre-calculated ratios of the two smaller / biggest (npr1, npr2)!

I did something like this a while ago in KNIME - but was also trying to get a sense of conformational flexibility for the molecules, as well as shape (I guess I was actually after a shape flexibility descriptor - by looking at the spread of conformers in the npr1 and npr2 dimensions).

I have modified my workflow by including a random set of DrugBank small molecules as the input.  The 'triangle' plot is achieved with the R View (Remote) node - having installed ggplot2.  This was my first go at using R - so apologies for the very clumsy script (it sort of implements a manual 2D box-plot; instead of doing 2D variability 'properly' - I'll come back to it one day...)!

I have attached the workflow (data included), and a picture to give an idea of the sort of output.

Hope this gives some ideas / is of some use.

EDIT - I don't seem to be able to get the pic to stick!  The link is: 

http://dl.dropbox.com/u/42827374/example.png

 

Kind regards

James

#4

Hopefully someone else can point you in the right direction for an alternative way to calculate the pmi descriptors.  I realised that the picture link i had posted was not correct - I have edited the URL in my original reply - hopefully it works now(?)

 

Kind regards

James

#5

hi,

Actually in knime node the moment of inertia is not present, you can use CDKgui from Rajarshi Guha or PaDEL descriptor gui these are opensource but external to knime.

i hope this can help you

 

regards

#6

hi,

I guess you're referring to W. H. B. Sauer and M. K. Schwarz in J.
Chem. Inf. Comput. Sci., 2003, 43, 987-1003.

As James already mentioned the MOE descriptors can be used to do such an analysis in KNIME. If you have no access to MOE contact support@chemcomp.com for an evaluation copy.

Regards

Guido

#7

Trying to find the MOE nodes so that I can make the workflow by James Davidson run... any help?

#8

As Guido mentioned:

If you have no access to MOE contact support@chemcomp.com for an evaluation copy.

Best,
Ferry 

#9

Hi Joel,

I had pretty-much forgotten all about posting this workflow (it was over 5 years ago!!) and your question encouraged me to relook at the task in light of changes to KNIME between then and now.

I have reworked the workflow with the following key points:

  • The PMI calculations are now handled by an internal Vernalis PMI node
  • The conformer generation is handled by RDKit nodes
  • The R script now runs in the KNIME R View (table) node - no longer requiring an R Server
  • The points on the triangle plot are now coloured by energy instead of fraction polar surface area (this last change is partly because it could be useful, and partly because I am not aware of a free way of generating this descriptor)

As stated above, the PMI node is an internal Vernalis node that we have developed.  We have a good track record of getting our internal nodes approved for release externally - so I will if we can get this into the nightly build asap.

If/when this happens I will post back here with an update, and a copy of the workflow (as it won't be very useful to you right now...).

 

Kind regards

James

PS  As already mentioned - you can, of course, contact CCG regarding the MOE nodes and make use of the existing workflow right now

#10

Just to add to James' comment above, there is now a PMI Calculation node in the Vernalis plugin - currently only in the nightly build.  If you update to version 1.6.4 of our plugin on the nightly build then you should get the nodes.

Steve