Merge pull request #106 from glycojones/update-cglycan-diag

update diagnostic for cglycans

.github/workflows/backend.yml

@@ -5,12 +5,12 @@ on:
   push:
     branches: [ "webapp" ]
     paths: 
-      - src/privateer/cpp/privateer-bind.cpp
+      - src/privateer/cpp/*
 
   pull_request:
     branches: [ "webapp" ]
     paths: 
-      - src/privateer/cpp/privateer-bind.cpp
+      - src/privateer/cpp/*
 
 jobs:
   build:

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.conformation_name() == "4c1" )
+                    {
+                        sugar.override_conformation_diag ( false );
+                    }
+                    if (sugar.type().trim() == "BMA")
+                    {
+                        sugar.override_anomer_diag( false );
+                    }
 
                     clipper::MAtom o5 = sugar.ring_members()[0];              // O5
                     clipper::MAtom c1 = sugar.ring_members()[1];              // C1

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; }

src/privateer/cpp/privateer-lib.cpp

@@ -1072,6 +1072,14 @@ void privateer::util::print_monosaccharide_summary (bool batch, bool showGeom, i
                 {
                     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 );
+                }
                 fprintf ( output, "\t(c) " );
             }
             else if ( ligandList[index].second.get_context() == "o-glycan" )
@@ -1171,6 +1179,14 @@ void privateer::util::print_monosaccharide_summary (bool batch, bool showGeom, i
                 {
                     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 );
+                }
                 std::cout << "\t(c) ";
             }
             else if ( ligandList[index].second.get_context() == "o-glycan" )
@@ -1289,6 +1305,14 @@ void privateer::util::print_monosaccharide_summary_python (bool batch, bool show
             {
                 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 );
+            }
             std::cout << "\t(c) ";
         }
         else if ( ligandList[index].second.get_context() == "o-glycan" )

src/privateer/cpp/privateer-lib.h

@@ -112,6 +112,14 @@ namespace privateer
                 {
                     sugar.override_conformation_diag ( true );
                 }
+                if ( sugar.conformation_name() == "4c1" )
+                {
+                    sugar.override_conformation_diag ( false );
+                }
+                if (sugar.type().trim() == "BMA")
+                {
+                    sugar.override_anomer_diag( false );
+                }
                 if ( sugar.ok_with_conformation() && sugar.ok_with_anomer() &&
                      sugar.ok_with_chirality() && sugar.ok_with_puckering() )
                     str << "<tspan>No issues have been detected.</tspan>";
@@ -155,9 +163,20 @@ namespace privateer
         {
 
             GlycanErrorCount err; 
-                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.conformation_name() == "4c1" )
+                    {
+                        sugar.override_conformation_diag ( false );
+                    }
+                    if (sugar.type().trim() == "BMA")
+                    {
+                        sugar.override_anomer_diag( false );
+                    }
                 }
                 if ( ! sugar.ok_with_anomer() ) {
                     err.anomer_err++; 
@@ -180,10 +199,22 @@ 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" )
+            {
+                if ((sugar.type().trim() == "MAN" ) && (sugar.conformation_name() == "1c4"))
                 {
                     sugar.override_conformation_diag ( true );
                 }
+                if ( sugar.conformation_name() == "4c1" )
+                {
+                    sugar.override_conformation_diag ( false );
+                }
+                if (sugar.type().trim() == "BMA")
+                {
+                    sugar.override_anomer_diag( false );
+
+                }
+            }
             if ( sugar.ok_with_conformation() && sugar.ok_with_anomer() &&
                     sugar.ok_with_chirality() && sugar.ok_with_puckering() )
                 return false;