fix anomer and conformation diagnostic for c-glycans in case where no…

… experimental data provided
glycojones · Aug 2, 2024 · 01c5439 · 01c5439
1 parent 93dc7c1
commit 01c5439
Showing 1 changed file with 28 additions and 5 deletions.
diff --git a/src/privateer/cpp/privateer.cpp b/src/privateer/cpp/privateer.cpp
@@ -931,9 +931,20 @@ int main(int argc, char** argv)
                             }
                             else if ( list_of_glycans[i].get_type() == "c-glycan" )
                             {
-
-                              ligandList[index].second.set_context ( "c-glycan" );
-                              fprintf ( output, "\t(c) " );
+                                if ( (ligandList[index].second.type().trim() == "MAN" ) && (ligandList[index].second.conformation_name() == "1c4"))
+                                {
+                                    ligandList[index].second.override_conformation_diag ( true );
+                                }
+                                if (ligandList[index].second.conformation_name() == "4c1")
+                                {
+                                    ligandList[index].second.override_conformation_diag ( false );
+                                }
+                                if (ligandList[index].second.type().trim() == "BMA" )
+                                {
+                                    ligandList[index].second.override_anomer_diag ( false );
+                                }
+                                ligandList[index].second.set_context ( "c-glycan" );
+                                fprintf ( output, "\t(c) " );
                             }
                             else if ( list_of_glycans[i].get_type() == "o-glycan" )
                             {
@@ -981,7 +992,7 @@ int main(int argc, char** argv)
                             {
                                 fprintf(output, "\tcheck");
                             }
-                            if ( ! ligandList[index].second.ok_with_anomer() )
+                            else if ( ! ligandList[index].second.ok_with_anomer() )
                             {
                                 fprintf(output, "\tcheck");
                             }
@@ -1074,6 +1085,18 @@ int main(int argc, char** argv)
                             }
                             else if ( list_of_glycans[i].get_type() == "c-glycan" )
                             {
+                                if ( (ligandList[index].second.type().trim() == "MAN" ) && (ligandList[index].second.conformation_name() == "1c4"))
+                                {
+                                    ligandList[index].second.override_conformation_diag ( true );
+                                }
+                                if (ligandList[index].second.conformation_name() == "4c1")
+                                {
+                                    ligandList[index].second.override_conformation_diag ( false );
+                                }
+                                if (ligandList[index].second.type().trim() == "BMA" )
+                                {
+                                    ligandList[index].second.override_anomer_diag ( false );
+                                }
                                 ligandList[index].second.set_context ( "c-glycan" );
 
                                 std::cout << "\t(c) ";
@@ -1126,7 +1149,7 @@ int main(int argc, char** argv)
                             {
                                 printf("\tcheck");
                             }
-                            if ( ! ligandList[index].second.ok_with_anomer () )
+                            else if ( ! ligandList[index].second.ok_with_anomer () )
                             {
                                 printf("\tcheck");
                             }