Atom Replacer Feature Request

Hi Dmitry,

I really like this Atom Replacer node for use in Murcko Scaffolds where you can replace it with an atom of your choice such as "C". However I was thinking the scope of this node could be increased for other uses.

Is it possible to make it so the user can choose from:

- Replace all Heavy Atoms (current Atom Replacer setting).

- Replace all Heavy Atoms within Highlighted Structure.

- Replace Specific Atom Type.

- Replace Specific Atom Type within Highlighted Structure.

So for example with the specific atom type, if you tick this option, then a manual entry box becomes active where you can enter in "Cl" for instance. This will then allow the user to choose to replace all Chloro atoms for Fluoro.

Another example, is the user can do a substructure search for pyridines with the substructure matcher and choose to highlight structure in output. They then use Atom Replacer node and choose "Replace Specific Atom Type within Highlighted Structure" and select to replace N for C. The effect of this is Pyridines are replaced with Phenyls.

I appreciate it is possible for a chemist to make a mess of things by replacing a N for Cl for instance and then valences are all compromised, but I would hope chemists would show some common sense.

Thanks,

Simon.

 

Hello Simon,

I have updated Indigo Nodes for Knime and improved atom replacer node is available in the nightly build 1.0.0.0001075. You can now replace only specific atom type and to replace only highlighted atoms.  

I will add a list with Heavy Atoms soon.

There is a bug there that "replace only specific atom" is turn by default and that first atom is always replaced. I have already fixed it and you can check tomorrow next nightly build.

With best regards,
Mikhail

Hi Mikhail,

Thanks for the update, this is really good :-)

It works perfectly and now it is easy to interchange between halogens (i.e. convert alkyl chlorides to alkyl bromides) for building up a list of starting materials for a general reaction, or convert a halogen to a connection point with a "*" for use in reactions and enumerations.

Its also easy to convert pyridines to phenyls too.

This is such a simple but very versatile node now, the implementation is great.

Thanks very much for this.

Simon.

Hello Simon,

Latest Atom Replacer node from the nightly build releases can now replace not only one type of atoms, but also a list of atoms types. Also you can now replace arbirary atom to R-site (R1, R2).

There are a predifined list of types: Metals, Halogens, ..., and an arbitary custom list of a user-specfied atoms. 

Presudoatoms are also supported.

Now I assume that this request is resolved. I'm looking forward receving your feedback!

Best regards,
Mikhail

Hi Mikhail,

Thanks for the further improvements to the Atom Replacer node this is really good. Is it possible to just make some minor additions to the node please?

In the "Replace Specific Atoms" dropdown list in the Atom Replacer configuration window, please can you add two extra options;

1- Any R group. This will replace all atoms with the Rx label, i.e. R1, R2, R3 etc will all be replaced. At the moment you can use Custom and type in R1 etc, but this only allows one Rx group to be replaced at a time, it would be useful to be able to replace all of them.

2 - Attachment group. So in the output from the "R Group Decomposition" node, the "R-Group #1 etc" columns show the decomposed group and the attachment point is labelled with a zigzag line on the atom. I would like the ability to convert this zigzag line into a normal atom. I believe currently this is still not possible. So essentially I want to convert the attachment point to a Bromine for instance for searching for starting materials.

Overall Mikhail, this node is really nice and it makes it really user friendly for medicinal chemists to undertake simple transformations without having to use reaction nomenclature to do this which is not often very userfriendly. So thanks very much.

Thanks,

Simon.

Hello Simon,

I will add these two additions in the next release soon. And you can write comma-separated list of atoms labels: to replace all R-groups you can write R1, R2, R3, R4, R5, R6. So request #1 is solvable now, but I will add a predefined list with R-group labels.

Best regards,
Mikhail

Hello Simon,

You can try attachment point replacer functionality in the latest nightly build release.

Best regards,
Mikhail

Hi Mikhail,

This is brilliant, this node now does everything one could need in replacing atoms. Many thanks for all the implementations, this is going to be so useful. No other node in KNIME can do these atom transformations, so its going to be really beneficial.

Thanks,

Simon.