Fix undefined behavior from empty container access and other bugs

[Copilot]

Static analysis and code review identified multiple instances of undefined behavior from accessing empty containers, plus a few other bugs.

Empty container access guards

• molecule.h: is_protein() now checks atoms_->empty() before accessing [0]
• bonds.cpp: get_bonds() and update_bonds() return early on empty input
• pqr.cpp, cif.cpp, mol2.cpp: Guard molecules()[0] and atoms()[0] access
• pdb.cpp: Throw FileException when structure.models is empty

Other fixes

• ee_method.cpp: Division by zero guard in cover solver: if (charges_count[i] > 0)
• common.cpp: Early return in get_element_symbol() for empty strings
• python.cpp: Rename loop var charges → chg to avoid shadowing parameter
• options.cpp: std::print → std::println for proper newline

Example fix

// Before - UB on empty atoms
bool is_protein() const { return not(*atoms_)[0].chain_id().empty(); }

// After
bool is_protein() const { return not atoms_->empty() and not(*atoms_)[0].chain_id().empty(); }

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