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Verified Commit 4be1cddf authored by Xavier Robin's avatar Xavier Robin
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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.
parent 58bf34cc
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...@@ -107,7 +107,7 @@ It can also be split into subsequent commands for greater controll: ...@@ -107,7 +107,7 @@ It can also be split into subsequent commands for greater controll:
API 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_hyd_atoms=True, rm_oxt_atoms=False, \
rm_zero_occ_atoms=False, colored=False, \ rm_zero_occ_atoms=False, colored=False, \
map_nonstd_res=True, assign_elem=True) map_nonstd_res=True, assign_elem=True)
......
...@@ -33,7 +33,7 @@ object MolckSettingsInitWrapper(tuple args, dict kwargs){ ...@@ -33,7 +33,7 @@ object MolckSettingsInitWrapper(tuple args, dict kwargs){
object self = args[0]; object self = args[0];
args = tuple(args.slice(1,_)); args = tuple(args.slice(1,_));
bool rm_unk_atoms = false; bool rm_unk_atoms = true;
if(kwargs.contains("rm_unk_atoms")){ if(kwargs.contains("rm_unk_atoms")){
rm_unk_atoms = extract<bool>(kwargs["rm_unk_atoms"]); rm_unk_atoms = extract<bool>(kwargs["rm_unk_atoms"]);
kwargs["rm_unk_atoms"].del(); kwargs["rm_unk_atoms"].del();
......
...@@ -45,7 +45,7 @@ struct MolckSettings{ ...@@ -45,7 +45,7 @@ struct MolckSettings{
bool map_nonstd_res; bool map_nonstd_res;
bool assign_elem; 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_non_std=false,
bool init_rm_hyd_atoms=true, bool init_rm_hyd_atoms=true,
bool init_rm_oxt_atoms=false, bool init_rm_oxt_atoms=false,
......
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