Neighborlist.txt in ward & Jarp

Hi,





1)i am not claer about the differnt columns(fields) in this neighborlist.txt. can u please expalin what it refers?


2) how the parameter -c --common <ratio> in jarp is useful?how do we need to set this value for optimal result?








see the attached file.

Hi,

Quote:

1)i am not claer about the differnt columns(fields) in this neighborlist.txt. can u please expalin what it refers?

The first column is the compound id. Then the id-s of the nearest neighbours is listed. If a compound has no nearest neighbour (according to the actual parameter setup) the line contains only the id of the input structure.

Quote:

2) how the parameter -c --common <ratio> in jarp is useful?how do we need to set this value for optimal result?

This option provides a way to create looser or tighter clusters. There's no recipe on how to set it up, it always depends on particular needs and goals, as well as the properties of objects being clustered. One has to experiment a lot to obtain best results.





Regards


Miklos