refactor: set rm_unk_atoms to useful default (True)

Other flags (assign_elem, rm_hyd_atoms) do not behave as expected with
rm_unk_atoms=False. Therefore False was not a useful default value.

modules/mol/alg/doc/molck.rst

@@ -107,7 +107,7 @@ It can also be split into subsequent commands for greater controll:
 API
 ###
 
-.. class:: MolckSettings(rm_unk_atoms=False, rm_non_std=False, \
+.. class:: MolckSettings(rm_unk_atoms=True, rm_non_std=False, \
                          rm_hyd_atoms=True, rm_oxt_atoms=False, \
                          rm_zero_occ_atoms=False, colored=False, \
                          map_nonstd_res=True, assign_elem=True)

modules/mol/alg/pymod/export_molck.cc

@@ -33,7 +33,7 @@ object MolckSettingsInitWrapper(tuple args, dict kwargs){
   object self = args[0];
   args = tuple(args.slice(1,_));
 
-  bool rm_unk_atoms = false;
+  bool rm_unk_atoms = true;
   if(kwargs.contains("rm_unk_atoms")){
     rm_unk_atoms = extract<bool>(kwargs["rm_unk_atoms"]);
     kwargs["rm_unk_atoms"].del();

modules/mol/alg/src/molck.hh

@@ -45,7 +45,7 @@ struct MolckSettings{
   bool map_nonstd_res;
   bool assign_elem;
 
-  MolckSettings(bool init_rm_unk_atoms=false,
+  MolckSettings(bool init_rm_unk_atoms=true,
                 bool init_rm_non_std=false,
                 bool init_rm_hyd_atoms=true,
                 bool init_rm_oxt_atoms=false,