Running cath-ssaps on files in other directories can causes errors

[tonyelewis]

Eg cath-ssap ../1c0pA01 ../1hdoA00 gives:

Cannot open file "./../1c0pA01../1hdoA00.list" for writing [ios_base::clear: unspecified iostream_category error] : No such file or directory
Whilst running program /cath-tools/ninja_clang_relwithdebinfo/cath-ssap (via a program_exception_wrapper with typeid: "N4cath30ssap_program_exception_wrapperE"), caught a boost::exception:
../source/common/file/open_fstream.hpp(72): Throw in function void cath::common::detail::open_fstream_impl(fstream_t &, const boost::filesystem::path &, const std::ios_base::openmode &, const cath::common::detail::fstream_type &) [fstream_t = std::__1::basic_ofstream<char, std::__1::char_traits<char> >]
Dynamic exception type: boost::exception_detail::clone_impl<cath::common::runtime_error_exception>
std::exception::what: Cannot open file "./../1c0pA01../1hdoA00.list" for writing [ios_base::clear: unspecified iostream_category error] 

[tonyelewis]

Implementation note:

• Remember to consider strucs_context when tackling this.

[tonyelewis]

I've made some effort towards improving the handling of names in 9831df9.

This leaves me clearer that the original cath-ssap command is in error because the positional arguments are being treated as IDs. Instead, the same could be achieved with:

cath-ssap --pdb-path .. 1c0pA01 1hdoA00

That said, cath-ssap should:

• allow the direct specification of input files (making it mirror cath-superpose once Make cath-superpose do the same ID to PDB file mapping that cath-ssap does #15 is addressed)
• warn/stop when IDs contain / characters