Enable NumPy code and most C code under PyPy by peterjc · Pull Request #1116 · biopython/biopython
This would address #126 (Bio.PDB under PyPy) and #953 (our NumPy code in general under PyPy).
Known issues which I believe are PyPy limitations:
PyPy cannot build Bio.trie #1114 Bio.trie does not ...