Moved pdb2gmx from src/kernel/ to src/programs/pdb2gmx/.

Functionality shared with g_x2top and/or g_protonate was moved to
src/gromacs/gmxpreprocess/.

IssueID #637

diff --git a/src/kernel/fflibutil.c b/src/gromacs/gmxpreprocess/fflibutil.c
similarity index 100%
rename from src/kernel/fflibutil.c
rename to src/gromacs/gmxpreprocess/fflibutil.c

diff --git a/src/kernel/fflibutil.h b/src/gromacs/gmxpreprocess/fflibutil.h
similarity index 100%
rename from src/kernel/fflibutil.h
rename to src/gromacs/gmxpreprocess/fflibutil.h

diff --git a/src/kernel/gen_ad.c b/src/gromacs/gmxpreprocess/gen_ad.c
similarity index 100%
rename from src/kernel/gen_ad.c
rename to src/gromacs/gmxpreprocess/gen_ad.c

diff --git a/src/kernel/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
similarity index 100%
rename from src/kernel/gen_vsite.c
rename to src/gromacs/gmxpreprocess/gen_vsite.c

diff --git a/src/kernel/gen_vsite.h b/src/gromacs/gmxpreprocess/gen_vsite.h
similarity index 100%
rename from src/kernel/gen_vsite.h
rename to src/gromacs/gmxpreprocess/gen_vsite.h

diff --git a/src/kernel/genhydro.c b/src/gromacs/gmxpreprocess/genhydro.c
similarity index 100%
rename from src/kernel/genhydro.c
rename to src/gromacs/gmxpreprocess/genhydro.c

diff --git a/src/kernel/genhydro.h b/src/gromacs/gmxpreprocess/genhydro.h
similarity index 100%
rename from src/kernel/genhydro.h
rename to src/gromacs/gmxpreprocess/genhydro.h

diff --git a/src/kernel/h_db.c b/src/gromacs/gmxpreprocess/h_db.c
similarity index 100%
rename from src/kernel/h_db.c
rename to src/gromacs/gmxpreprocess/h_db.c

diff --git a/src/kernel/h_db.h b/src/gromacs/gmxpreprocess/h_db.h
similarity index 100%
rename from src/kernel/h_db.h
rename to src/gromacs/gmxpreprocess/h_db.h

diff --git a/src/kernel/hackblock.c b/src/gromacs/gmxpreprocess/hackblock.c
similarity index 100%
rename from src/kernel/hackblock.c
rename to src/gromacs/gmxpreprocess/hackblock.c

diff --git a/src/kernel/pdb2top.c b/src/gromacs/gmxpreprocess/pdb2top.c
similarity index 100%
rename from src/kernel/pdb2top.c
rename to src/gromacs/gmxpreprocess/pdb2top.c

diff --git a/src/kernel/pgutil.c b/src/gromacs/gmxpreprocess/pgutil.c
similarity index 100%
rename from src/kernel/pgutil.c
rename to src/gromacs/gmxpreprocess/pgutil.c

diff --git a/src/kernel/pgutil.h b/src/gromacs/gmxpreprocess/pgutil.h
similarity index 100%
rename from src/kernel/pgutil.h
rename to src/gromacs/gmxpreprocess/pgutil.h

diff --git a/src/kernel/resall.c b/src/gromacs/gmxpreprocess/resall.c
similarity index 100%
rename from src/kernel/resall.c
rename to src/gromacs/gmxpreprocess/resall.c

diff --git a/src/kernel/ter_db.c b/src/gromacs/gmxpreprocess/ter_db.c
similarity index 100%
rename from src/kernel/ter_db.c
rename to src/gromacs/gmxpreprocess/ter_db.c

diff --git a/src/kernel/ter_db.h b/src/gromacs/gmxpreprocess/ter_db.h
similarity index 100%
rename from src/kernel/ter_db.h
rename to src/gromacs/gmxpreprocess/ter_db.h

diff --git a/src/kernel/CMakeLists.txt b/src/kernel/CMakeLists.txt
index c045ff2b8def61daa404615e8ca74883b64f07e9..58bc9f3a9250a69624d0cd0ac1af997bcc41d55e 100644 (file)
--- a/src/kernel/CMakeLists.txt
+++ b/src/kernel/CMakeLists.txt
@@ -1,22 +1,9 @@
 include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
 
 set(GMXPREPROCESS_SOURCES 
-    gen_ad.c        
-    gen_vsite.c     
-    genhydro.c   
-    h_db.c          
-    hackblock.c             
-    hizzie.c        
     nm2type.c
-    pdb2top.c       
-    pgutil.c        
-    resall.c        
     sorting.c       
-    specbond.c      
-    ter_db.c        
-    tpbcmp.c        
-    fflibutil.c
-    xlate.c)
+    tpbcmp.c)
 
 add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
 target_link_libraries(gmxpreprocess libgromacs)
@@ -30,10 +17,6 @@ add_executable(tpbconv tpbconv.c)
 target_link_libraries(tpbconv ${GMX_EXTRA_LIBRARIES})
 set_target_properties(tpbconv PROPERTIES OUTPUT_NAME "tpbconv${GMX_BINARY_SUFFIX}")
 
-add_executable(pdb2gmx pdb2gmx.c)
-target_link_libraries(pdb2gmx ${GMX_EXTRA_LIBRARIES})
-set_target_properties(pdb2gmx PROPERTIES OUTPUT_NAME "pdb2gmx${GMX_BINARY_SUFFIX}")
-
 add_executable(g_protonate g_protonate.c)
 target_link_libraries(g_protonate ${GMX_EXTRA_LIBRARIES})
 set_target_properties(g_protonate PROPERTIES OUTPUT_NAME "g_protonate${GMX_BINARY_SUFFIX}")
@@ -57,7 +40,6 @@ set_target_properties(gmxcheck PROPERTIES OUTPUT_NAME "gmxcheck${GMX_BINARY_SUFF
 install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
 install(TARGETS 
         tpbconv
-        pdb2gmx
         g_protonate
         g_luck
         gmxdump

diff --git a/src/programs/CMakeLists.txt b/src/programs/CMakeLists.txt
index d2f0dd28919566f6bfceff78445cabb6d6e96f8a..4a7cf565cc440cabdb03a5a2aa9776620cd9fc68 100644 (file)
--- a/src/programs/CMakeLists.txt
+++ b/src/programs/CMakeLists.txt
@@ -2,4 +2,5 @@ add_subdirectory(mdrun)
 if (NOT GMX_FAHCORE)
     add_subdirectory(g_ana)
     add_subdirectory(grompp)
+    add_subdirectory(pdb2gmx)
 endif (NOT GMX_FAHCORE)

diff --git a/src/programs/pdb2gmx/CMakeLists.txt b/src/programs/pdb2gmx/CMakeLists.txt
new file mode 100644 (file)
index 0000000..a90ce45
--- /dev/null
+++ b/src/programs/pdb2gmx/CMakeLists.txt
@@ -0,0 +1,8 @@
+include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
+
+file(GLOB PDB2GMX_SOURCES *.c)
+
+add_executable(pdb2gmx ${PDB2GMX_SOURCES})
+target_link_libraries(pdb2gmx ${GMX_EXTRA_LIBRARIES} libgromacs)
+set_target_properties(pdb2gmx PROPERTIES OUTPUT_NAME "pdb2gmx${GMX_BINARY_SUFFIX}")
+install(TARGETS pdb2gmx DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)

diff --git a/src/kernel/hizzie.c b/src/programs/pdb2gmx/hizzie.c
similarity index 100%
rename from src/kernel/hizzie.c
rename to src/programs/pdb2gmx/hizzie.c

diff --git a/src/kernel/hizzie.h b/src/programs/pdb2gmx/hizzie.h
similarity index 100%
rename from src/kernel/hizzie.h
rename to src/programs/pdb2gmx/hizzie.h

diff --git a/src/kernel/pdb2gmx.c b/src/programs/pdb2gmx/pdb2gmx.c
similarity index 100%
rename from src/kernel/pdb2gmx.c
rename to src/programs/pdb2gmx/pdb2gmx.c

diff --git a/src/kernel/specbond.c b/src/programs/pdb2gmx/specbond.c
similarity index 100%
rename from src/kernel/specbond.c
rename to src/programs/pdb2gmx/specbond.c

diff --git a/src/kernel/specbond.h b/src/programs/pdb2gmx/specbond.h
similarity index 100%
rename from src/kernel/specbond.h
rename to src/programs/pdb2gmx/specbond.h

diff --git a/src/kernel/xlate.c b/src/programs/pdb2gmx/xlate.c
similarity index 100%
rename from src/kernel/xlate.c
rename to src/programs/pdb2gmx/xlate.c

diff --git a/src/kernel/xlate.h b/src/programs/pdb2gmx/xlate.h
similarity index 100%
rename from src/kernel/xlate.h
rename to src/programs/pdb2gmx/xlate.h