do_dssp works incorrectly with unknown residues
The current realization of do_dssp correctly works only with standard amino acids residues.
If in the studied protein unknown residues meet, dssp programm ignores them,
whereas gromacs considers them hydrophilic, and besides, indexation of resudues is broken.
My improuvements also ignores unknown residues, but the result turns out incomplete whereas Gromacs yields incorrect result.
Additionally, the file transfer to dssp programm through pipe eliminating need of repeated creation and removal of files.