any hints about fragmenter main function?

Hello, all:


I am trying to slove a fragmenter question, but seems the api or user guide is too breif to find any hints. Thanks advance for any help!!


The question is:


I want to fragment the molecule based on RECAP method, while some part of the molecule should be remain ( like keep the scaffold unchange)? I notice the recap class has the setnotlist method, but couldn't figure out how to use it( set up in XML? does the recap will take a substructure search?)? If I need extend the fragmenter class, does anyone give me a piece of code about main function in fragmenter??





Thanks again!!





Michael

Hi,

michael_luntan wrote:

Hello, all: I am trying to slove a fragmenter question, but seems the api or user guide is too breif to find any hints. Thanks advance for any help!! The question is: I want to fragment the molecule based on RECAP method, while some part of the molecule should be remain ( like keep the scaffold unchange)? I notice the recap class has the setnotlist method, but couldn't figure out how to use it( set up in XML? does the recap will take a substructure search?)? If I need extend the fragmenter class, does anyone give me a piece of code about main function in fragmenter?? Thanks again!! Michael

You can use Fragmenter from command line and from API.





If you use it from command line, then you have to put your scaffold to the Notlist section of the configuration XML.





Usage from API:





Use the ExhaustiveFragmenter class. There is a short code example in the class header, which shows how you can pass the configuration XML to ExhaustiveFragmenter:

Code:

ExhaustiveFragmenter fragmenter = new ExhaustiveFragmenter(new File("fragment.xml"));

An other option is to create an instance of the Reacap class, set the notlist with its setNotlist(Molecule[]) method and then pass this Recap object to the ExhaustiveFragmenter using the ExhaustiveFragmenter(RxnMolecule[], Standardizer, CutBondReviser) constructor of the ExhaustiveFragmenter class (Recap IS A CutBondReviser).





See Fragmenter Developer's Guide for more.





Best regards,


Zsolt

thanks Zsolt!!


Sorry I didn't put my question clearly. In advance I only know a substructure of the scaffold. If I use the default recap method to fragment the molecule, may break the scaffold. I want to fragment the molecule while a result fragment list still has a fragment is a superstucture of the notlist mol. So I am wondering whether the program fragmenter can do this? ( and also depends on the input molecule, maybe the scaffold ( superstructure of a notlist mol) are different )

Hi,





Sorry, but I don't clearly understand your requirements. Can you give me a concrete example with input molecules, scaffolds and substructures? Please describe also what do you expect as output.





Best regards,


Zsolt

thanks,


please see the attachment! It is a chemdraw file

michael_luntan wrote:

thanks, please see the attachment! It is a chemdraw file

Thanks, it's all clear.





If a structure is in the Notlist, than Fragmenter will refuse cuts that result these structures (that are specified in the Notlist), so this is not what you need. In fact Notlist means "DoNotCutIfResultIsOnTheList".





You need a "DoNotCutStructuresOnTheList" feature, but Fragmenter does not support it.





Best regards,


Zsolt