In order to study the network structure of proteins, I'm looking for software that can predict the existence of hydrogen bonds in proteins from PDB data. I'm intending on running this software for ~1000 PDB files.
After searching around with Google, there appears to be a range of software available for detecting H-bonds according to varying criteria. I have no real way to distinguish between these.
Ideally, I'm looking for something that is "safe", e.g. well-known and widely used, used by experts, and the definition it implements is fairly mainstream and uncontroversial. I.e. I'd like to minimize the possibility of others questioning the validity of my results based on the choice of software. (Also, ideally, I'd like it to be free.)
Question: What is a "safe" package for detecting hydrogen bonds in proteins from PDB data?