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Fix CIF rhombohedral symmetry scoring mutating imported lattice #70

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Fix CIF rhombohedral symmetry scoring mutating imported lattice #70

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122cd6e
Fix CIF rhombohedral symmetry scoring mutating imported lattice
clemisch Mar 24, 2026
7c8175c
use space_group instead of temp crystal
clemisch Mar 30, 2026
7c6bf98
More specific catch for invalid sgtbx symbols during symmetry scoring
clemisch Mar 30, 2026
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21 changes: 13 additions & 8 deletions ObjCryst/ObjCryst/CIF.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1130,20 +1130,25 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
unsigned int bestscore=0;
for(vector<string>::const_iterator posOrig=origin_list.begin();posOrig!=origin_list.end();++posOrig)
{
// The origin extension may not make sense, so we need to watch for exception
string testSymbol=hmorig + *posOrig;
string canonicalSymbol;
cctbx::sgtbx::space_group cctbxspg;
try
{
pCryst->ChangeSpaceGroup(hmorig+*posOrig);
cctbxspg = cctbx::sgtbx::space_group(cctbx::sgtbx::space_group_symbols(testSymbol));
const char ext = cctbxspg.match_tabulated_settings().extension();
canonicalSymbol = cctbxspg.match_tabulated_settings().hermann_mauguin();
if(ext!='\0') canonicalSymbol += ":" + string(1, ext);
}
catch(invalid_argument)
catch(cctbx::error)
{
continue;
}

// If the symbol is the same as before, the origin probably was not understood - no need to test
if((posOrig!=origin_list.begin())&&(pCryst->GetSpaceGroup().GetName()==bestsymbol)) continue;
if((posOrig!=origin_list.begin())&&(canonicalSymbol==bestsymbol)) continue;

unsigned int nbSymSpg=pCryst->GetSpaceGroup().GetCCTbxSpg().all_ops().size();
unsigned int nbSymSpg=cctbxspg.all_ops().size();
unsigned int nbSymCommon=0;
try
{
Expand All @@ -1153,7 +1158,7 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
posSymCIF!=pos->second.mvSymmetry_equiv_pos_as_xyz.end();++posSymCIF)
{
cctbx::sgtbx::rt_mx mx1(*posSymCIF);
cctbx::sgtbx::rt_mx mx2(pCryst->GetSpaceGroup().GetCCTbxSpg().all_ops()[i]);
cctbx::sgtbx::rt_mx mx2(cctbxspg.all_ops()[i]);
mx1.mod_positive_in_place();
mx2.mod_positive_in_place();
if(mx1==mx2)
Expand All @@ -1163,14 +1168,14 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
}
}
}
if(verbose) cout<<" Trying: "<<pCryst->GetSpaceGroup().GetName()
if(verbose) cout<<" Trying: "<<canonicalSymbol
<<" nbsym:"<<nbSymSpg<<"(cctbx), "
<<pos->second.mvSymmetry_equiv_pos_as_xyz.size()<<"(CIF)"
<<",common:"<<nbSymCommon<<endl;
if(bestscore<((nbSymSpg==pos->second.mvSymmetry_equiv_pos_as_xyz.size())*nbSymCommon))
{
bestscore=(nbSymSpg==pos->second.mvSymmetry_equiv_pos_as_xyz.size())*nbSymCommon;
bestsymbol=pCryst->GetSpaceGroup().GetName();
bestsymbol=canonicalSymbol;
}
}
catch(cctbx::error)
Expand Down