Brownbp1/pharmmap fld

apps/internal/chemistry/bcl_app_link_fragments.cpp

@@ -258,7 +258,7 @@ namespace bcl
           command::Parameter
           (
             "type", "the type of druglikenes to use",
-            command::ParameterCheckAllowed( storage::Vector< std::string>::Create( "IsConstitutionDruglike", "IsConstitutionDruglikeAndHitlike", "None")),
+            command::ParameterCheckAllowed( storage::Vector< std::string>::Create( "IsConstitutionDruglike", "IsConstitutionDruglikeAndHitlike", "Constant(1.0)")),
             "IsConstitutionDruglike"
           )
         )
@@ -1526,7 +1526,7 @@ namespace bcl
        (
          cleaner.Clean
          (
-           new_frag_v, REFERENCE, m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue()
+           new_frag_v, REFERENCE, descriptor::CheminfoProperty( m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue())
          )
        );
        return clean_frag;
@@ -1561,7 +1561,7 @@ namespace bcl
        );
        static chemistry::FragmentMapConformer conf_mapper
        (
-         m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue(),
+         descriptor::CheminfoProperty( m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue()),
          m_MDLString,
          m_PocketFilename,
          SCORER,

apps/internal/chemistry/bcl_app_molecule_mutate.cpp

@@ -13,22 +13,24 @@
 // (c)
 
 // initialize the static initialization fiasco finder, if macro ENABLE_FIASCO_FINDER is defined
-#include "command/bcl_command_parameter_check_ranged.h"
 #include "util/bcl_util_static_initialization_fiasco_finder.h"
 BCL_StaticInitializationFiascoFinder
 
 // include header of this class
-#include "app/bcl_app_apps.h"
+#include "internal/chemistry/bcl_app_molecule_mutate.h"
+
+// include bcl headers
 #include "chemistry/bcl_chemistry_fragment_feed.h"
 #include "chemistry/bcl_chemistry_fragment_mutate_interface.h"
 #include "command/bcl_command_app_default_flags.h"
 #include "command/bcl_command_flag_dynamic.h"
 #include "command/bcl_command_flag_static.h"
+#include "command/bcl_command_parameter_check_ranged.h"
 #include "command/bcl_command_parameter_check_serializable.h"
-#include "internal/chemistry/bcl_app_molecule_mutate.h"
 #include "io/bcl_io_file.h"
 #include "math/bcl_math_mutate_interface.h"
 #include "storage/bcl_storage_template_instantiations.h"
+
 namespace bcl
 {
   namespace app
@@ -83,7 +85,20 @@ namespace bcl
         new command::FlagStatic
         (
           "accumulate",
-          "accumulate mutations into one molecule; be careful"
+          "accumulate mutations at specified 'mutable_atoms' into one molecule; "
+          "only applicable if using the application-level 'mutable_atoms'; "
+          "similar behavior can be achieved using multiple implementations sequentially "
+          "with careful mutate-level atom selections."
+        )
+      ),
+      m_FinalProductOnlyFlag
+      (
+        new command::FlagStatic
+        (
+          "final_product_only",
+          "only return the product resulting from all mutates; by default a "
+          "molecule is returned after each mutation; this flag is useful if you "
+          "are only interested in the final product."
         )
       ),
       m_RecenterFlag
@@ -115,6 +130,7 @@ namespace bcl
     MoleculeMutate::MoleculeMutate( const MoleculeMutate &PARENT) :
           m_ImplementationFlag( PARENT.m_ImplementationFlag),
           m_AccumulateFlag( PARENT.m_AccumulateFlag),
+          m_FinalProductOnlyFlag( PARENT.m_FinalProductOnlyFlag),
           m_MutableAtomsFlag( PARENT.m_MutableAtomsFlag),
           m_RecenterFlag( PARENT.m_RecenterFlag),
           m_OutputFilenameFlag( PARENT.m_OutputFilenameFlag),
@@ -173,6 +189,9 @@ namespace bcl
       //! make all mutations to one molecule
       sp_cmd->AddFlag( m_AccumulateFlag);
 
+      //! only return the last molecule after all mutations have been applied
+      sp_cmd->AddFlag( m_FinalProductOnlyFlag);
+
       //! whether to recenter the molecules
       sp_cmd->AddFlag( m_RecenterFlag);
 
@@ -295,8 +314,15 @@ namespace bcl
                   current_frag = *( mutated_object.GetArgument());
                   continue;
                 }
-                chemistry::FragmentComplete fragment( *( mutated_object.GetArgument()));
-                Write( fragment);
+                if
+                (
+                    !m_FinalProductOnlyFlag->GetFlag() ||
+                    i+1 == n_mutates
+                )
+                {
+                  chemistry::FragmentComplete fragment( *( mutated_object.GetArgument()));
+                  Write( fragment);
+                }
               }
             }
           }
@@ -322,8 +348,15 @@ namespace bcl
             if( mutated_object.GetArgument().IsDefined())
             {
               current_frag = *( mutated_object.GetArgument());
-              chemistry::FragmentComplete fragment( *( mutated_object.GetArgument()));
-              Write( fragment);
+              if
+              (
+                  !m_FinalProductOnlyFlag->GetFlag() ||
+                  i+1 == n_mutates
+              )
+              {
+                chemistry::FragmentComplete fragment( *( mutated_object.GetArgument()));
+                Write( fragment);
+              }
             }
           }
         }

apps/internal/chemistry/bcl_app_molecule_mutate.h

@@ -68,6 +68,9 @@ namespace bcl
       //! accumulate all mutations onto a single molecule
       util::ShPtr< command::FlagInterface> m_AccumulateFlag;
 
+      //! only return the last molecule after all mutations have been applied
+      util::ShPtr< command::FlagInterface> m_FinalProductOnlyFlag;
+
       //! whether to recenter the molecules
       util::ShPtr< command::FlagInterface> m_RecenterFlag;
 

apps/internal/chemistry/bcl_app_reaction_combichem.cpp

@@ -203,7 +203,7 @@ namespace bcl
           command::Parameter
           (
             "type", "the type of druglikenes to use",
-            command::ParameterCheckAllowed( storage::Vector< std::string>::Create( "IsConstitutionDruglike", "IsConstitutionDruglikeAndHitlike", "None")),
+            command::ParameterCheckAllowed( storage::Vector< std::string>::Create( "IsConstitutionDruglike", "IsConstitutionDruglikeAndHitlike", "Constant(1.0)")),
             "IsConstitutionDruglike"
           )
         )
@@ -641,7 +641,7 @@ namespace bcl
               chemistry::HydrogensHandler::Remove( atoms);
               chemistry::FragmentMapConformer cleaner
               (
-                m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue(),
+                descriptor::CheminfoProperty( m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue()),
                 m_CorinaFlag->GetFlag()
               );
               util::ShPtr< chemistry::FragmentComplete> clean_mol
@@ -650,7 +650,7 @@ namespace bcl
                 (
                   atoms,
                   *ens_itr,
-                  m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue(),
+                  descriptor::CheminfoProperty( m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue()),
                   false
                 )
               );
@@ -765,17 +765,17 @@ namespace bcl
        static chemistry::FragmentMapConformer cleaner;
        if( m_CorinaFlag->GetFlag())
        {
-         cleaner = chemistry::FragmentMapConformer( "None", true);
+         cleaner = chemistry::FragmentMapConformer( descriptor::CheminfoProperty( "Constant(1.0)"), true);
        }
        else
        {
-         cleaner = chemistry::FragmentMapConformer( "None", false);
+         cleaner = chemistry::FragmentMapConformer( descriptor::CheminfoProperty( "Constant(1.0)"), false);
        }
        util::ShPtr< chemistry::FragmentComplete> clean_frag( cleaner.Clean
          (
            new_frag_v,
            REFERENCE,
-           m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue()
+           descriptor::CheminfoProperty( m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue())
          ));
        return clean_frag;
      }
@@ -811,7 +811,7 @@ namespace bcl
        );
        static chemistry::FragmentMapConformer conf_mapper
        (
-         m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue(),
+         descriptor::CheminfoProperty( m_DrugLikenessTypeFlag->GetFirstParameter()->GetValue()),
          m_MDLString,
          m_PocketFilename,
          SCORER,