I have an sd file with around twenty five thousand entries in it. I have imported data of this file in Instant Jchem and now wish to query it only on the basis of the unique id that is assigned to every molecule. Since I need to query using a list of these ids, I am not quite sure how can this be implemented using the Query builder. Is there a command line interface which can be used to retrieve information of only those ids?
No, I don't think command line will help you here.
So you have a series of IDs (a few 10's or maybe even 100's?) and you want to just see those compounds?
If so then your best bet it probably to make a permanat list contianing those IDs and then just apply the list which will then show just those compounds. List management is described here:
Alternatively you can run a query using the 'In List' operator and specify the values as comma separated values. This would be simple enough for a small number of values, but for larger numbers using list management would be better.