Fix atomic_lib compiler warnings

[Tom Goddard]

I get various compiler warning compiling atomic_lib on Mac ARM (XCode version 15.1). Would be nice to clean up the code so it does not give these warnings, so real problems will be more apparent.

$ cd bundles/src/atomic_lib
$ make install
PYTHONNOUSERSITE=1 /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/python3.11 -I -m chimerax.core --nogui --exit --safemode --cmd "devel install . user false exit true noDeps true"
Executing: devel install . user false exit true noDeps true
warning: /Library/Developer/CommandLineTools/usr/bin/ranlib: archive library: src/lib/libatomstruct_tmpl.a will be fat and ar(1) will not be able to operate on it
atomic_cpp/atomstruct_cpp/Structure.cpp:66:21: warning: field 'ss_ids_normalized' will be initialized after field

'_worm_ribbon' [-Wreorder-ctor]

pdb_version(0), ss_ids_normalized(false), _worm_ribbon(false)
^{~ ~
lower_case_chains(false) pdb_version(0) ss_ids_normalized(false)}

atomic_cpp/atomstruct_cpp/Structure.cpp:867:5: warning: loop will run at most once (loop increment never executed)

[-Wunreachable-code-loop-increment]

for (auto a: r->atoms())

atomic_cpp/atomstruct_cpp/Structure.cpp:1092:27: warning: add explicit braces to avoid dangling else [-Wdangling-else]

} else if (a1_last && a2_first) {

3 warnings generated.
atomic_cpp/atomstruct_cpp/Structure.cpp:66:21: warning: field 'ss_ids_normalized' will be initialized after field

'_worm_ribbon' [-Wreorder-ctor]

pdb_version(0), ss_ids_normalized(false), _worm_ribbon(false)
^{~ ~
lower_case_chains(false) pdb_version(0) ss_ids_normalized(false)}

atomic_cpp/atomstruct_cpp/Structure.cpp:867:5: warning: loop will run at most once (loop increment never executed)

[-Wunreachable-code-loop-increment]

for (auto a: r->atoms())

atomic_cpp/atomstruct_cpp/Structure.cpp:1092:27: warning: add explicit braces to avoid dangling else [-Wdangling-else]

} else if (a1_last && a2_first) {

3 warnings generated.
atomic_cpp/atomstruct_cpp/seq_assoc.cpp:453:24: warning: comparison of integers of different signs: 'int' and

'size_type' (aka 'unsigned long') [-Wsign-compare]

if (mseq_index >= num_mseq_res)

1 warning generated.
atomic_cpp/atomstruct_cpp/seq_assoc.cpp:453:24: warning: comparison of integers of different signs: 'int' and

'size_type' (aka 'unsigned long') [-Wsign-compare]

if (mseq_index >= num_mseq_res)

1 warning generated.

[pett]

Changed code and added compiler flags to eliminate the warnings.