Yes. Use caspol -ap, specifying an XML file containing the permissions in the permission set. To save you some time, here is a sample file corresponding to the 'Everything' permission set - just edit to suit your needs. When you have edited the sample, add it to the range of available permission sets like this:

caspol -ap samplepermset.xml
Then, to apply the permission set to a code group, do something like this:

caspol -cg 1.3 SamplePermSet
(By default, 1.3 is the 'Internet' code group)