Improve usability of itp2rtp

[recombinatrix]

Currently, renaming atoms with ITP2RTP requires that we specify the atom number, then the new atom name.

For batch projects, this is not ideal.

Consider a use case where I have fifteen molecules, and in each molecule I want to rename the atom with name CD1 to have the new name -C1. Currently, if I want to automate this process, I have to first look up the rank order of CD1 in every single ITP, then write a custom printf input string for each monomer.

A more desirable behaviour would be to be able to specify the atom by name. This should be fine. In cases where there is ambiguity in the names due to multiple atoms with the same name, the itp is already a disaster. Some mild error handling should be fine.