Partial port to MSVC via cmake

Two targets had to be leaved out: protpred-Gromacs-Front and protpred-Gromacs-Sort_Method_files_by_front_domincance for the lack of an Windows implementation of opendir, dirent.h etc. at hand.

Also the function run_programs_with_pipe is not compiled on Windows, for the lack of proper Posix fork, wait, pipe etc.