Merge pull request #102 from glycojones/fix_cglycan_diagnostic

Fix cglycan diagnostic
glycojones · Aug 2, 2024 · ba14939 · ba14939
2 parents 22cfa2b + f4d4776
commit ba14939
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Showing 4 changed files with 57 additions and 4 deletions.
diff --git a/src/privateer/cpp/clipper-glyco.cpp b/src/privateer/cpp/clipper-glyco.cpp
@@ -5483,6 +5483,14 @@ void MGlycology::init ( const clipper::MiniMol& mmol, const clipper::MAtomNonBon
                     {
                         sugar.override_conformation_diag ( true );
                     }
+                    if (sugar.type().trim() == "BMA")
+                    {
+                        sugar.override_anomer_diag( false );
+                        if ( sugar.conformation_name() == "4c1" )
+                        {
+                            sugar.override_conformation_diag ( false );
+                        }
+                    }
 
                     clipper::MAtom o5 = sugar.ring_members()[0];              // O5
                     clipper::MAtom c1 = sugar.ring_members()[1];              // C1

diff --git a/src/privateer/cpp/clipper-glyco.h b/src/privateer/cpp/clipper-glyco.h
@@ -417,6 +417,8 @@ namespace clipper
 
             void override_conformation_diag ( bool is_it_ok ) { sugar_diag_conformation = is_it_ok; }
 
+            void override_anomer_diag ( bool is_it_ok ) { sugar_diag_anomer = is_it_ok; }
+
             void set_occupancy_check ( bool occupancy_check_in ) { sugar_occupancy_check = occupancy_check_in; }
 
             clipper::String get_diagnostic() const { return sugar_diagnostic; }

diff --git a/src/privateer/cpp/privateer-lib.cpp b/src/privateer/cpp/privateer-lib.cpp
@@ -1072,6 +1072,13 @@ void privateer::util::print_monosaccharide_summary (bool batch, bool showGeom, i
                 {
                     ligandList[index].second.override_conformation_diag ( true );
                 }
+                if (ligandList[index].second.type().trim() == "BMA" )
+                {
+                    ligandList[index].second.override_anomer_diag ( false );
+                    if (ligandList[index].second.conformation_name() == "4c1"){
+                        ligandList[index].second.override_conformation_diag ( false );
+                    }
+                }
                 fprintf ( output, "\t(c) " );
             }
             else if ( ligandList[index].second.get_context() == "o-glycan" )
@@ -1171,6 +1178,13 @@ void privateer::util::print_monosaccharide_summary (bool batch, bool showGeom, i
                 {
                     ligandList[index].second.override_conformation_diag ( true );
                 }
+                if (ligandList[index].second.type().trim() == "BMA" )
+                {
+                    ligandList[index].second.override_anomer_diag ( false );
+                    if (ligandList[index].second.conformation_name() == "4c1"){
+                        ligandList[index].second.override_conformation_diag ( false );
+                    }
+                }
                 std::cout << "\t(c) ";
             }
             else if ( ligandList[index].second.get_context() == "o-glycan" )
@@ -1289,6 +1303,13 @@ void privateer::util::print_monosaccharide_summary_python (bool batch, bool show
             {
                 ligandList[index].second.override_conformation_diag ( true );
             }
+            if (ligandList[index].second.type().trim() == "BMA" )
+            {
+                ligandList[index].second.override_anomer_diag ( false );
+                if (ligandList[index].second.conformation_name() == "4c1"){
+                    ligandList[index].second.override_conformation_diag ( false );
+                }
+            }
             std::cout << "\t(c) ";
         }
         else if ( ligandList[index].second.get_context() == "o-glycan" )

diff --git a/src/privateer/cpp/privateer-lib.h b/src/privateer/cpp/privateer-lib.h
@@ -108,9 +108,20 @@ namespace privateer
                 << "<tspan>Detected type: " << sugar.type_of_sugar() << ". </tspan>";
             if ( validation )
             {
-                if ( ( glycan.get_type() == "c-glycan" ) && (sugar.type().trim() == "MAN" ) && (sugar.conformation_name() == "1c4"))
+                if  ( glycan.get_type() == "c-glycan" )
                 {
-                    sugar.override_conformation_diag ( true );
+                    if ((sugar.type().trim() == "MAN" ) && (sugar.conformation_name() == "1c4"))
+                    {
+                        sugar.override_conformation_diag ( true );
+                    }
+                    if (sugar.type().trim() == "BMA")
+                    {
+                        sugar.override_anomer_diag( false );
+                        if ( sugar.conformation_name() == "4c1" )
+                        {
+                            sugar.override_conformation_diag ( false );
+                        }
+                    }
                 }
                 if ( sugar.ok_with_conformation() && sugar.ok_with_anomer() &&
                      sugar.ok_with_chirality() && sugar.ok_with_puckering() )
@@ -135,9 +146,20 @@ namespace privateer
 
         inline const bool sugar_contains_issues ( clipper::MSugar sugar, clipper::MGlycan glycan  )
         {
-            if ( ( glycan.get_type() == "c-glycan" ) && (sugar.type().trim() == "MAN" ) && (sugar.conformation_name() == "1c4"))
+            if  ( glycan.get_type() == "c-glycan" )
             {
-                sugar.override_conformation_diag ( true );
+                if ((sugar.type().trim() == "MAN" ) && (sugar.conformation_name() == "1c4"))
+                {
+                    sugar.override_conformation_diag ( true );
+                }
+                if (sugar.type().trim() == "BMA")
+                {
+                    sugar.override_anomer_diag( false );
+                    if ( sugar.conformation_name() == "4c1" )
+                    {
+                        sugar.override_conformation_diag ( false );
+                    }
+                }
             }
 
             if ( sugar.ok_with_conformation() && sugar.ok_with_anomer() &&