diff --git a/pymolfile/molfile/CMakeLists.txt b/pymolfile/molfile/CMakeLists.txt
index 953bc142d83a6c1aae6bc496b6d610c7d54b9404..899602e7ae79b82caaf31dec29ebe9ddfdfd9784 100644
--- a/pymolfile/molfile/CMakeLists.txt
+++ b/pymolfile/molfile/CMakeLists.txt
@@ -1,16 +1,11 @@
 cmake_minimum_required(VERSION 2.8.12)
 
-if(NOT DEFINED CMAKE_MACOSX_RPATH)
-    set(CMAKE_MACOSX_RPATH 0)
-endif()
-
 project(molfile)
 
-# Set source directory
-set(SOURCE_DIR "molfile")
+add_subdirectory(external)
+add_subdirectory(molfile_plugins)
 
-# Tell CMake that headers are also in SOURCE_DIR
-include_directories(${SOURCE_DIR} "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/include" "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/lib")
+set_source_files_properties( external/tng/include/tng/tng_io.h PROPERTIES GENERATED TRUE )
 
-set(SOURCES "${SOURCE_DIR}/libpymolfile_wrap.cxx" "${SOURCE_DIR}/pymolfile.c" "${SOURCE_DIR}/lib/libmolfile_plugin.a")
+add_dependencies( molfile_plugins_comp tngio_comp )
 
diff --git a/pymolfile/molfile/external/CMakeLists.txt b/pymolfile/molfile/external/CMakeLists.txt
index 8018b695940cd74cd507ef425ba4e802943b8678..fc558ad746d7dc3a0ef960669993dbbf0d3280a7 100644
--- a/pymolfile/molfile/external/CMakeLists.txt
+++ b/pymolfile/molfile/external/CMakeLists.txt
@@ -2,8 +2,8 @@ cmake_minimum_required(VERSION 2.8.12)
 project(TNGBuilder)
 include(ExternalProject)
 
-set(TNG_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/tng")
-set(TNG_INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}/tng")
+set(TNG_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/external/tng")
+set(TNG_INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}/external/tng")
 set(TNG_CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${TNG_INSTALL_DIR})
 
 message("TNG_PREFIX='${TNG_PREFIX}'")
@@ -17,3 +17,18 @@ ExternalProject_Add(tng
     INSTALL_DIR ${TNG_INSTALL_DIR}
     CMAKE_ARGS ${TNG_CMAKE_ARGS}
 )
+
+
+set(LIB_TNGIO_FILES
+    "${TNG_INSTALL_DIR}/tng/include/tng/tng_io.h")
+
+if (APPLE)
+   set(LIB_TNGIO_FILES ${LIB_TNGIO_FILES} "${TNG_INSTALL_DIR}/tng/lib/libtng_io.dylib")
+else()
+   set(LIB_TNGIO_FILES ${LIB_TNGIO_FILES} "${TNG_INSTALL_DIR}/tng/lib/libtng_io.so")
+endif()
+
+add_custom_target(tngio_comp ALL
+                  DEPENDS ${LIB_TNGIO_FILES}
+                 )
+
diff --git a/pymolfile/molfile/molfile_plugins/CMakeLists.txt b/pymolfile/molfile/molfile_plugins/CMakeLists.txt
index 0be1a4d2d95c746602fced9d07fbaeead58937ce..107afcff3c18cd2bd0620d3c34a17cf1c57a5e55 100644
--- a/pymolfile/molfile/molfile_plugins/CMakeLists.txt
+++ b/pymolfile/molfile/molfile_plugins/CMakeLists.txt
@@ -1,43 +1,168 @@
 cmake_minimum_required(VERSION 2.8.12)
-#find_package (EXPAT)
-#find_package (NetCDF)
-project(myexecutable)
-# Set source directory
-#set(SOURCE_DIR "molfile")
 
-# Tell CMake that headers are also in SOURCE_DIR
-#include_directories(${SOURCE_DIR} "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/include" "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/lib")
+project(molfileplugins)
 
-#set(SOURCES "${SOURCE_DIR}/libpymolfile_wrap.cxx" "${SOURCE_DIR}/pymolfile.c" "${SOURCE_DIR}/lib/libmolfile_plugin.a")
+find_package(EXPAT)
+find_package(NetCDF)
+find_package(TCL)
+
+if (EXISTS "${TNG_INSTALL_DIR}/tng/lib/libtng_io.dylib"
+    OR EXISTS "${TNG_INSTALL_DIR}/tng/lib/libtng_io.so"
+    OR EXISTS "${TNG_INSTALL_DIR}/tng/include/tng/tng_io.h")
+   set(TNGIO_FOUND TRUE)
+   set(TNGIO_LIBRARIES "${TNG_INSTALL_DIR}/lib/")
+   set(TNGIO_INLCUDE_DIRS "${TNG_INSTALL_DIR}/include/")
+endif()
 
 set(TARGET_ARCH_REGEX "^.*-march[= ]([^ ]+).*$")
 string(REGEX MATCH "${TARGET_ARCH_REGEX}" TARGET_ARCH_MATCH "${CMAKE_C_FLAGS}" "${CMAKE_CXX_FLAGS}")
 if (TARGET_ARCH_MATCH)
-    string(REGEX REPLACE "${TARGET_ARCH_REGEX}" "\\1" TARGET_ARCH "${CMAKE_C_FLAGS}" "${CMAKE_CXX_FLAGS}")
+	string(REGEX REPLACE "${TARGET_ARCH_REGEX}" "\\1" TARGET_ARCH "${CMAKE_C_FLAGS}" "${CMAKE_CXX_FLAGS}")
 else()
-    set(TARGET_ARCH ${CMAKE_HOST_SYSTEM_PROCESSOR})
+	set(TARGET_ARCH ${CMAKE_HOST_SYSTEM_PROCESSOR})
 endif()
 message(TARGET_ARCH= ${TARGET_ARCH})
-message(OSX= ${OSX_ARCHITECTURES})
-message(OSX= ${CMAKE_OSX_ARCHITECTURES})
 message(SYS_VER= ${CMAKE_SYSTEM_VERSION})
 message(SYS_NAME= ${CMAKE_SYSTEM_NAME})
 message(SYS_PROC= ${CMAKE_SYSTEM_PROCESSOR})
 message(SYS= ${CMAKE_SYSTEM})
-message(TARGET_ARCH_REGEX= ${TARGET_ARCH_REGEX})
-message(TARGET_ARCH_MATCH= ${TARGET_ARCH_MATCH})
-
-add_custom_command( 
-    OUTPUT vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugins.a 
-    COMMAND make MACOSXX86_64GCCTNG
-    WORKING_DIRECTORY vmd_molfile_plugins
-) 
-add_custom_target( 
-    libmolfile_plugins.a 
-    COMMAND make MACOSXX86_64GCCTNG
-    WORKING_DIRECTORY vmd_molfile_plugins
+      
+if(TARGET_ARCH MATCHES "^.*64.*$")
+	set(ARCH64BIT TRUE)
+endif()
+
+set(LIB_MOLFILE_FILES
+    "${CMAKE_CURRENT_BINARY_DIR}/molfile_plugins/compile/lib/libmolfile_plugins.a"
+    "${CMAKE_CURRENT_BINARY_DIR}/molfile_plugins/compile/lib/libmolfile_plugins.h")
+
+if(UNIX AND NOT APPLE)
+	set(LINUX TRUE)
+endif()
+
+if(WIN32)
+   if(MSVS OR MSYS)
+      set(WINCOMP TRUE)
+   endif()
+endif()
+
+if(LINUX)
+   if(CMAKE_CXX_COMPILER_ID MATCHES "^.*GNU.*$")
+      if(ARCH64BIT)
+         set(TARGET_COPT " -fPIC -m64 -o ")
+         set(TARGET_LOPT " -fPIC -m64 -lstdc++ -o ")
+	 set(TARGET_CFLAGS " -m64 -O2 -fPIC -Wall ${CMAKE_C_FLAGS}")
+	 set(TARGET_CXXFLG " -m64 -O2 -fPIC -Wall ${CMAKE_CXX_FLAGS}")
+      else()
+         set(TARGET_COPT " -fPIC -m32 -o ")
+         set(TARGET_LOPT " -fPIC -m32 -lstdc++ -o ")
+	 set(TARGET_CFLAGS " -m32 -O2 -fPIC -Wall ${CMAKE_C_FLAGS}")
+	 set(TARGET_CXXFLG " -m32 -O2 -fPIC -Wall ${CMAKE_CXX_FLAGS}")
+      endif()
+   else()
+         set(TARGET_COPT " -o ")
+         set(TARGET_LOPT " -o ")
+	 set(TARGET_CFLAGS " -O2 -Wall ${CMAKE_C_FLAGS}")
+	 set(TARGET_CXXFLG " -O2 -Wall ${CMAKE_CXX_FLAGS}")
+   endif()
+endif()
+
+if(APPLE)
+   if(CMAKE_CXX_COMPILER_ID MATCHES "^.*GNU.*$"
+      OR CMAKE_CXX_COMPILER_ID MATCHES "^(Apple)?Clang$") 
+      if(ARCH64BIT)
+         set(TARGET_COPT -m64;-fPIC;-o)
+         set(TARGET_LOPT -m64;-fPIC;-o)
+         set(TARGET_CFLAGS -m64;-Os;-Wall;-fPIC;-dynamic;${CMAKE_C_FLAGS})
+         set(TARGET_CXXFLG -m64;-Os;-Wall;-fPIC;-dynamic;${CMAKE_CXX_FLAGS})
+      else()
+         set(TARGET_COPT " -fPIC -m32 -o ")
+         set(TARGET_LOPT " -fPIC -m32 -o ")
+         set(TARGET_CFLAGS " -m32 -Os -Wall -fPIC -dynamic ${CMAKE_C_FLAGS}")
+         set(TARGET_CXXFLG " -m32 -Os -Wall -fPIC -dynamic ${CMAKE_CXX_FLAGS}")
+      endif()
+   else()
+      set(TARGET_COPT " -o ")
+      set(TARGET_LOPT " -o ")
+      set(TARGET_CFLAGS " -O2 -Wall ${CMAKE_C_FLAGS}")
+      set(TARGET_CXXFLG " -O2 -Wall ${CMAKE_CXX_FLAGS}")
+   endif()
+endif()
+
+if(UNIX)
+   set(TARGET_DEF "-D")
+   set(TARGET_SHLD ${CMAKE_CXX_COMPILER} ${CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS})
+   set(TARGET_LIBTOOL libtool;-dynamic)
+   set(TARGET_AR ${CMAKE_AR})
+   set(TARGET_NM ${CMAKE_NM};-p)
+   set(TARGET_RANLIB ${CMAKE_RANLIB})
+   set(TARGET_MOL_LIBS "")
+   if(TCL_FOUND)
+      set(TCLLDFLAGS -ltcl;-L${TCL_LIBRARY})
+      set(TCLINC "-I${TCL_INCLUDE_PATH}")
+      set(TCLLIB "-L${TCL_LIBRARY}")
+      set(TARGET_MOL_LIBS ${TARGET_MOL_LIBS} \"TCLLDFLAGS=${TCLLDFLAGS}\";\"TCLINC=${TCLINC}\";\"TCLLIB=${TCLLIB}\";)
+   endif()
+   if(EXPAT_FOUND)
+      set(EXPATLDFLAGS ${EXPAT_LIBRARIES})
+      set(EXPATINC "-I${EXPAT_INCLUDE_DIRS}")
+      set(EXPATLIB "-I${EXPAT_INCLUDE_DIRS}")
+      set(TARGET_MOL_LIBS ${TARGET_MOL_LIBS} \"EXPATLDFLAGS=${EXPATLDFLAGS}\";\"EXPATINC=${EXPATINC}\";\"EXPATLIB=${EXPATLIB}\";)
+   endif()
+   if(NETCDF_FOUND)
+      set(NETCDFLDFLAGS ${NETCDF_LIBRARY})
+      set(NETCDFINC "-I${NETCDF_INCLUDE_DIRS}")
+      set(NETCDFLIB "-I${NETCDF_INCLUDE_DIRS}")
+      set(TARGET_MOL_LIBS ${TARGET_MOL_LIBS} \"NETCDFLDFLAGS=${NETCDFLDFLAGS}\";\"NETCDFINC=${NETCDFINC}\";\"NETCDFLIB=${NETCDFLIB}\";)
+   endif()
+   if(TNGIO_FOUND)
+      set(TNGIOLDFLAGS -ltng_io)
+      set(TNGIOINC "-I${TNGIO_INCLUDE_DIRS}")
+      set(TNGIOLIB "-L${TNGIO_LIBRARIES}")
+      set(TARGET_MOL_LIBS ${TARGET_MOL_LIBS} \"TNGLDFLAGS=${TNGIOLDFLAGS}\";\"TNGINC=${TNGIOINC}\";\"TNGLIB=${TNGIOLIB}\";)
+   endif()
+   add_custom_command( 
+      OUTPUT ${LIB_MOLFILE_FILES}
+      COMMAND make dynlibs staticlibs bins \"ARCH = ${TARGET_ARCH}\" \"COPTO = ${TARGET_COPT} \" \"LOPTO = ${TARGET_LOPT} \" \"CC = ${CMAKE_C_COMPILER} \" \"CXX = ${CMAKE_CXX_COMPILER} \" \"DEF = ${TARGET_DEF}\" \"CCFLAGS = ${TARGET_CFLAGS} \" \"CXXFLAGS = ${TARGET_CXXFLG} \" \"AR = ${TARGET_AR}\" \"NM = ${TARGET_NM}\" \"RANLIB = ${TARGET_RANLIB}\" \"LIBTOOL = ${TARGET_LIBTOOL} \" ${TARGET_MOL_LIBS}
+      COMMENT "Compiling libmolfile_plugin.a"
+      WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/molfile_plugins/molfile_plugin"
+   ) 
+endif()
+
+if(WINCOMP)
+   set(TARGET_DEF "/D")
+   set(TARGET_AR "${CMAKE_AR}")
+   set(TARGET_NM "${CMAKE_NM} -p")
+   set(TARGET_RANLIB "${CMAKE_RANLIB}")
+   set(TARGET_MOL_LIBS "")
+   set(TARGET_SHLDFLAGS "/D\"VMDPLUGIN_EXPORTS\"")
+   if(MSVS)
+      set(MYMAKE nmake)
+   else()
+      set(MYMAKE make)
+   endif()
+   if(ARCH64BIT)
+      set(TARGET_SHLD "\"link /DLL /nologo /incremental:no kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib ws2_32.lib wsock32.lib /MACHINE:X64 /OPT:REF\"")
+      set(TARGET_MOL_SETTINGS "\"CC = cl.exe /nologo /MT /DWIN64\"" "\"CXX = cl.exe /nologo /MT /TP /DWIN64\"" "\"CCFLAGS =  /EHsc /Wp64 /wd4996 /O2 /D\\\"_CRT_SECURE_NO_DEPRECATE\\\"\"" "\"CXXFLAGS = /EHsc /Wp64 /wd4996 /O2 /D\\\"_CRT_SECURE_NO_DEPRECATE\\\"\"")
+   else()
+      set(TARGET_SHLD "\"link /DLL /nologo /incremental:no kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib ws2_32.lib wsock32.lib /OPT:REF\"")
+      set(TARGET_MOL_SETTINGS "\"CC = cl.exe /nologo /MT /DWIN32\"" "\"CXX = cl.exe /nologo /MT /TP /DWIN32\"" "\"CCFLAGS = /O2 /G5\"" "\"CXXFLAGS = /O2 /G5\"")
+   endif()
+   add_custom_command( 
+      OUTPUT ${LIB_MOLFILE_FILES}
+      COMMAND ${MYMAKE} dynlibs win32staticlibs "\" ARCH = ${TARGET_ARCH} \"" "\" COPTO = /Fo \"" "\" LOPTO = /OUT: \"" "\" ${TARGET_MOL_SETTINGS} \"" "\" DEF = ${TARGET_DEF} \"" "\" AR = ${TARGET_AR} \"" "\" NM = ${TARGET_NM} \"" "\" RANLIB = ${TARGET_RANLIB} \"" "\" SHLDFLAGS = ${TARGET_SHLDFLAGS} \"" "\"${TARGET_MOL_LIBS}\""
+      COMMENT "Compiling libmolfile_plugin.a"
+      WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../molfile_plugin"
+   ) 
+endif()
+
+add_custom_target(molfile_plugins_comp ALL
+    DEPENDS ${LIB_MOLFILE_FILES}
 )
-#add_executable(myexecutable myexcutable.c)
-#target_link_libraries(myexecutable vmd_molfile_plugins/compile/lib_MACOSXX86_64GCCTNG/molfile/libmolfile_plugins.a) 
-#add_dependencies(myexecutable extern_lib) 
+
+#add_library(molfile_plugins INTERFACE)
+
+#target_include_directories(molfile_plugins INTERFACE "${CMAKE_CURRENT_BINARY_DIR}/lib/") 
+#target_link_libraries(molfile_plugins INTERFACE ${MOLFILE_LIBRARIES})
+
+
 
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/LICENSE b/pymolfile/molfile/molfile_plugins/LICENSE
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/LICENSE
rename to pymolfile/molfile/molfile_plugins/LICENSE
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/Make-arch b/pymolfile/molfile/molfile_plugins/Make-arch
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/Make-arch
rename to pymolfile/molfile/molfile_plugins/Make-arch
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/Makefile b/pymolfile/molfile/molfile_plugins/Makefile
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/Makefile
rename to pymolfile/molfile/molfile_plugins/Makefile
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/README b/pymolfile/molfile/molfile_plugins/README
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/README
rename to pymolfile/molfile/molfile_plugins/README
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/create_static_header.sh b/pymolfile/molfile/molfile_plugins/create_static_header.sh
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/create_static_header.sh
rename to pymolfile/molfile/molfile_plugins/create_static_header.sh
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/CVS/Entries b/pymolfile/molfile/molfile_plugins/include/CVS/Entries
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/CVS/Entries
rename to pymolfile/molfile/molfile_plugins/include/CVS/Entries
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/CVS/Repository b/pymolfile/molfile/molfile_plugins/include/CVS/Repository
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/CVS/Repository
rename to pymolfile/molfile/molfile_plugins/include/CVS/Repository
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/CVS/Root b/pymolfile/molfile/molfile_plugins/include/CVS/Root
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/CVS/Root
rename to pymolfile/molfile/molfile_plugins/include/CVS/Root
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/import_graphics_plugin.h b/pymolfile/molfile/molfile_plugins/include/import_graphics_plugin.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/import_graphics_plugin.h
rename to pymolfile/molfile/molfile_plugins/include/import_graphics_plugin.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/molfile_plugin.h b/pymolfile/molfile/molfile_plugins/include/molfile_plugin.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/molfile_plugin.h
rename to pymolfile/molfile/molfile_plugins/include/molfile_plugin.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/vmdconio.h b/pymolfile/molfile/molfile_plugins/include/vmdconio.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/vmdconio.h
rename to pymolfile/molfile/molfile_plugins/include/vmdconio.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/vmdplugin.h b/pymolfile/molfile/molfile_plugins/include/vmdplugin.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/include/vmdplugin.h
rename to pymolfile/molfile/molfile_plugins/include/vmdplugin.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/CVS/Entries b/pymolfile/molfile/molfile_plugins/molfile_plugin/CVS/Entries
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/CVS/Entries
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/CVS/Entries
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/CVS/Repository b/pymolfile/molfile/molfile_plugins/molfile_plugin/CVS/Repository
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/CVS/Repository
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/CVS/Repository
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/CVS/Root b/pymolfile/molfile/molfile_plugins/molfile_plugin/CVS/Root
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/CVS/Root
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/CVS/Root
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/LICENSE b/pymolfile/molfile/molfile_plugins/molfile_plugin/LICENSE
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/LICENSE
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/LICENSE
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/Makefile b/pymolfile/molfile/molfile_plugins/molfile_plugin/Makefile
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/Makefile
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/Makefile
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/Makefile.orig b/pymolfile/molfile/molfile_plugins/molfile_plugin/Makefile.orig
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/Makefile.orig
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/Makefile.orig
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/Makefile.rej b/pymolfile/molfile/molfile_plugins/molfile_plugin/Makefile.rej
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/Makefile.rej
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/Makefile.rej
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/CVS/Entries b/pymolfile/molfile/molfile_plugins/molfile_plugin/doc/CVS/Entries
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/CVS/Entries
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/doc/CVS/Entries
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/CVS/Repository b/pymolfile/molfile/molfile_plugins/molfile_plugin/doc/CVS/Repository
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/CVS/Repository
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/doc/CVS/Repository
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/CVS/Root b/pymolfile/molfile/molfile_plugins/molfile_plugin/doc/CVS/Root
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/CVS/Root
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/doc/CVS/Root
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/avsplugin.html b/pymolfile/molfile/molfile_plugins/molfile_plugin/doc/avsplugin.html
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/avsplugin.html
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/doc/avsplugin.html
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/babelplugin.html b/pymolfile/molfile/molfile_plugins/molfile_plugin/doc/babelplugin.html
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/babelplugin.html
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/doc/babelplugin.html
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/bgfplugin.html b/pymolfile/molfile/molfile_plugins/molfile_plugin/doc/bgfplugin.html
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/bgfplugin.html
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/doc/bgfplugin.html
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/binposplugin.html b/pymolfile/molfile/molfile_plugins/molfile_plugin/doc/binposplugin.html
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diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/f77/f77_molfile.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/f77/f77_molfile.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/f77/f77_molfile.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/f77/f77_molfile.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/f77/tester.f b/pymolfile/molfile/molfile_plugins/molfile_plugin/f77/tester.f
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/f77/tester.f
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/f77/tester.f
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/CVS/Entries b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/CVS/Entries
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/CVS/Entries
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/CVS/Entries
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/CVS/Repository b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/CVS/Repository
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/CVS/Repository
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/CVS/Repository
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/CVS/Root b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/CVS/Root
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/CVS/Root
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/CVS/Root
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/babelplugin.dsp b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/babelplugin.dsp
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/babelplugin.dsp
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/babelplugin.dsp
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/dcdplugin.dsp b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/dcdplugin.dsp
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/dcdplugin.dsp
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/dcdplugin.dsp
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/gromacsplugin.dsp b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/gromacsplugin.dsp
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/gromacsplugin.dsp
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/gromacsplugin.dsp
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/pdbplugin.dsp b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/pdbplugin.dsp
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/pdbplugin.dsp
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/pdbplugin.dsp
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/psfplugin.dsp b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/psfplugin.dsp
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/psfplugin.dsp
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/psfplugin.dsp
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/template.dsp b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/template.dsp
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/template.dsp
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/template.dsp
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/vc60.idb b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/vc60.idb
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/vc60.idb
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/vc60.idb
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/vc60.pdb b/pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/vc60.pdb
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/msvc/vc60.pdb
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/msvc/vc60.pdb
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/.#dlpolyplugin.c.1.21 b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/.#dlpolyplugin.c.1.21
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/.#dlpolyplugin.c.1.21
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/.#dlpolyplugin.c.1.21
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/.main.c.swp b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/.main.c.swp
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/.main.c.swp
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/.main.c.swp
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/CVS/Entries b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/CVS/Entries
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/CVS/Entries
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/CVS/Entries
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/CVS/Repository b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/CVS/Repository
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/CVS/Repository
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/CVS/Repository
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/CVS/Root b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/CVS/Root
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/CVS/Root
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/CVS/Root
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/CVS/mmCIF.C,t b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/CVS/mmCIF.C,t
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/CVS/mmCIF.C,t
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/CVS/mmCIF.C,t
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/Gromacs.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/Gromacs.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/Gromacs.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/Gromacs.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ReadPARM.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/ReadPARM.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ReadPARM.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/ReadPARM.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ReadPARM7.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/ReadPARM7.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ReadPARM7.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/ReadPARM7.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/abinitplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/abinitplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/abinitplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/abinitplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/avsplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/avsplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/avsplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/avsplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/babelplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/babelplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/babelplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/babelplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/basissetplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/basissetplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/basissetplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/basissetplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/bgfplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/bgfplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/bgfplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/bgfplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/binposplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/binposplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/binposplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/binposplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/biomoccaplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/biomoccaplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/biomoccaplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/biomoccaplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/brixplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/brixplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/brixplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/brixplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/carplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/carplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/carplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/carplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ccp4plugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/ccp4plugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ccp4plugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/ccp4plugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/corplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/corplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/corplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/corplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cpmdlogplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/cpmdlogplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cpmdlogplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/cpmdlogplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cpmdplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/cpmdplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cpmdplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/cpmdplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/crdplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/crdplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/crdplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/crdplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cubeplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/cubeplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cubeplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/cubeplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dcdplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/dcdplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dcdplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/dcdplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dlpolyplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/dlpolyplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dlpolyplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/dlpolyplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dmsplugin.cxx b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/dmsplugin.cxx
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dmsplugin.cxx
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/dmsplugin.cxx
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dsn6plugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/dsn6plugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dsn6plugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/dsn6plugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.cxx b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/dtrplugin.cxx
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.cxx
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/dtrplugin.cxx
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.hxx b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/dtrplugin.hxx
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.hxx
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/dtrplugin.hxx
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dxplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/dxplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dxplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/dxplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/edmplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/edmplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/edmplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/edmplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/endianswap.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/endianswap.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/endianswap.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/endianswap.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fastio.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/fastio.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fastio.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/fastio.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fortread.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/fortread.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fortread.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/fortread.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fs4plugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/fs4plugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fs4plugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/fs4plugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gamessplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/gamessplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gamessplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/gamessplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/gaussianplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/gaussianplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/gaussianplugin.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/gaussianplugin.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/graspplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/graspplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/graspplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/graspplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/grdplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/grdplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/grdplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/grdplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gridplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/gridplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gridplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/gridplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gromacsplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/gromacsplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gromacsplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/gromacsplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hash.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/hash.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hash.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/hash.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hash.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/hash.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hash.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/hash.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hoomdplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/hoomdplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hoomdplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/hoomdplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/inthash.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/inthash.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/inthash.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/inthash.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/inthash.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/inthash.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/inthash.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/inthash.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/jsplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/jsplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/jsplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/jsplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/lammpsplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/lammpsplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/lammpsplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/lammpsplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/largefiles.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/largefiles.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/largefiles.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/largefiles.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/maeffplugin.cxx b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/maeffplugin.cxx
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/maeffplugin.cxx
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/maeffplugin.cxx
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/main.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/main.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/main.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/main.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mapplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/mapplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mapplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/mapplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mdfplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/mdfplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mdfplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/mdfplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mmcif.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/mmcif.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mmcif.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/mmcif.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mol2plugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/mol2plugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mol2plugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/mol2plugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/moldenplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/moldenplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/moldenplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/moldenplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/molemeshplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/molemeshplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/molemeshplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/molemeshplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/msmsplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/msmsplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/msmsplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/msmsplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/namdbinplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/namdbinplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/namdbinplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/namdbinplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/netcdfplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/netcdfplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/netcdfplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/netcdfplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/offplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/offplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/offplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/offplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/parm7plugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/parm7plugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/parm7plugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/parm7plugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/parmplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/parmplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/parmplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/parmplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pbeqplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/pbeqplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pbeqplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/pbeqplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pdbplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/pdbplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pdbplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/pdbplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pdbxplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/pdbxplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pdbxplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/pdbxplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/periodic_table.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/periodic_table.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/periodic_table.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/periodic_table.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/phiplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/phiplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/phiplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/phiplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pltplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/pltplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pltplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/pltplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/plugintest.x b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/plugintest.x
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/plugintest.x
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/plugintest.x
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ply.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/ply.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ply.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/ply.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ply.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/ply.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ply.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/ply.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/plyplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/plyplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/plyplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/plyplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pqrplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/pqrplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pqrplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/pqrplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/psfplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/psfplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/psfplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/psfplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/qmplugin.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/qmplugin.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/qmplugin.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/qmplugin.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/raster3dplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/raster3dplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/raster3dplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/raster3dplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/readpdb.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/readpdb.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/readpdb.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/readpdb.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/rst7plugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/rst7plugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/rst7plugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/rst7plugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/situsplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/situsplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/situsplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/situsplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/spiderplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/spiderplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/spiderplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/spiderplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/stlplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/stlplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/stlplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/stlplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/tinkerplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/tinkerplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/tinkerplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/tinkerplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/tngplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/tngplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/tngplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/tngplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/uhbdplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/uhbdplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/uhbdplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/uhbdplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/unit_conversion.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/unit_conversion.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/unit_conversion.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/unit_conversion.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspparchgplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspparchgplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspparchgplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspparchgplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspplugin.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspplugin.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspplugin.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspplugin.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspposcarplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspposcarplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspposcarplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspposcarplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspxmlplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspxmlplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspxmlplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vaspxmlplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vmddir.h b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vmddir.h
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vmddir.h
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vmddir.h
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vtfplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vtfplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vtfplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vtfplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vtkplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/vtkplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vtkplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/vtkplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/webpdbplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/webpdbplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/webpdbplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/webpdbplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xbgfplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/xbgfplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xbgfplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/xbgfplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xsfplugin.C b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/xsfplugin.C
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xsfplugin.C
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/xsfplugin.C
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xyzplugin.c b/pymolfile/molfile/molfile_plugins/molfile_plugin/src/xyzplugin.c
similarity index 100%
rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xyzplugin.c
rename to pymolfile/molfile/molfile_plugins/molfile_plugin/src/xyzplugin.c
diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/CMakeLists.txt b/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/CMakeLists.txt
deleted file mode 100644
index 031af4eaee97c665d225c6be512a7acc3dca5941..0000000000000000000000000000000000000000
--- a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/CMakeLists.txt
+++ /dev/null
@@ -1,158 +0,0 @@
-cmake_minimum_required(VERSION 2.8.12)
-
-project(molfileplugins)
-
-find_package(EXPAT)
-find_package(NetCDF)
-find_package(TCL)
-
-set(TARGET_ARCH_REGEX "^.*-march[= ]([^ ]+).*$")
-string(REGEX MATCH "${TARGET_ARCH_REGEX}" TARGET_ARCH_MATCH "${CMAKE_C_FLAGS}" "${CMAKE_CXX_FLAGS}")
-if (TARGET_ARCH_MATCH)
-	string(REGEX REPLACE "${TARGET_ARCH_REGEX}" "\\1" TARGET_ARCH "${CMAKE_C_FLAGS}" "${CMAKE_CXX_FLAGS}")
-else()
-	set(TARGET_ARCH ${CMAKE_HOST_SYSTEM_PROCESSOR})
-endif()
-message(TARGET_ARCH= ${TARGET_ARCH})
-message(SYS_VER= ${CMAKE_SYSTEM_VERSION})
-message(SYS_NAME= ${CMAKE_SYSTEM_NAME})
-message(SYS_PROC= ${CMAKE_SYSTEM_PROCESSOR})
-message(SYS= ${CMAKE_SYSTEM})
-      
-if(TARGET_ARCH MATCHES "^.*64.*$")
-	set(ARCH64BIT TRUE)
-endif()
-
-set(LIB_MOLFILE_FILES
-    "${CMAKE_CURRENT_BINARY_DIR}/lib/libmolfile_plugins.a"
-    "${CMAKE_CURRENT_BINARY_DIR}/lib/libmolfile_plugins.h")
-
-if(UNIX AND NOT APPLE)
-	set(LINUX TRUE)
-endif()
-
-if(WIN32)
-   if(MSVS OR MSYS)
-      set(WINCOMP TRUE)
-   endif()
-endif()
-
-if(LINUX)
-   if(CMAKE_CXX_COMPILER_ID MATCHES "^.*GNU.*$")
-      if(ARCH64BIT)
-         set(TARGET_COPT "-fPIC" "-m64" "-o")
-         set(TARGET_LOPT "-fPIC" "-m64" "-lstdc++" "-o")
-	 set(TARGET_CFLAGS "-m64" "-O2" "-fPIC" "-Wall" "${CMAKE_C_FLAGS}")
-	 set(TARGET_CXXFLG "-m64" "-O2" "-fPIC" "-Wall" "${CMAKE_CXX_FLAGS}")
-      else()
-         set(TARGET_COPT "-fPIC" "-m32" "-o")
-         set(TARGET_LOPT "-fPIC" "-m32" "-lstdc++" "-o")
-	 set(TARGET_CFLAGS "-m32" "-O2" "-fPIC" "-Wall" "${CMAKE_C_FLAGS}")
-	 set(TARGET_CXXFLG "-m32" "-O2" "-fPIC" "-Wall" "${CMAKE_CXX_FLAGS}")
-      endif()
-   else()
-         set(TARGET_COPT "-o ")
-         set(TARGET_LOPT "-o ")
-	 set(TARGET_CFLAGS "-O2 -Wall " "${CMAKE_C_FLAGS}")
-	 set(TARGET_CXXFLG "-O2 -Wall " "${CMAKE_CXX_FLAGS}")
-   endif()
-endif()
-
-if(APPLE)
-   if(CMAKE_CXX_COMPILER_ID MATCHES "^.*GNU.*$"
-      OR CMAKE_CXX_COMPILER_ID MATCHES "^(Apple)?Clang$") 
-      if(ARCH64BIT)
-         set(TARGET_COPT " -fPIC -m64 -o ")
-         set(TARGET_LOPT " -fPIC -m64 -o ")
-	 set(TARGET_CFLAGS " -m64 -Os -Wall -fPIC -dynamic " "${CMAKE_C_FLAGS}")
-	 set(TARGET_CXXFLG " -m64 -Os -Wall -fPIC -dynamic " "${CMAKE_CXX_FLAGS}")
-      else()
-         set(TARGET_COPT " -fPIC -m32 -o ")
-         set(TARGET_LOPT " -fPIC -m32 -o ")
-	 set(TARGET_CFLAGS " -m32 -Os -Wall -fPIC -dynamic " "${CMAKE_C_FLAGS}")
-	 set(TARGET_CXXFLG " -m32 -Os -Wall -fPIC -dynamic " "${CMAKE_CXX_FLAGS}")
-      endif()
-   else()
-      set(TARGET_COPT " -o ")
-      set(TARGET_LOPT " -o ")
-      set(TARGET_CFLAGS " -O2 -Wall " "${CMAKE_C_FLAGS}")
-      set(TARGET_CXXFLG " -O2 -Wall " "${CMAKE_CXX_FLAGS}")
-   endif()
-endif()
-
-if(UNIX)
-   set(TARGET_DEF "-D")
-   set(TARGET_SHLD "${CMAKE_CXX_COMPILER}" "${CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS}")
-   set(TARGET_LIBTOOL "libtool -dynamic")
-   set(TARGET_AR "${CMAKE_AR}")
-   set(TARGET_NM "${CMAKE_NM} -p")
-   set(TARGET_RANLIB "${CMAKE_RANLIB}")
-   set(TARGET_MOL_LIBS "")
-   if(TCL_FOUND)
-      set(TCLLDFLAGS "-l${TCL_LIBRARY}")
-      set(TCLINC "-I${TCL_INCLUDE_PATH}")
-      set(TCLLIB "-I${TCL_INCLUDE_PATH}")
-      set(TARGET_MOL_LIBS "${TARGET_MOL_LIBS}" "TCLLDFLAGS = ${TCLLDFLAGS}" "TCLINC = ${TCLINC}" "TCLLIB = ${TCLLIB}")
-   endif()
-   if(EXPAT_FOUND)
-      set(EXPATLDFLAGS "${EXPAT_LIBRARIES}")
-      set(EXPATINC "-I${EXPAT_INCLUDE_DIRS}")
-      set(EXPATLIB "-I${EXPAT_INCLUDE_DIRS}")
-      set(TARGET_MOL_LIBS "${TARGET_MOL_LIBS}" "EXPATLDFLAGS = ${EXPATLDFLAGS}" "EXPATINC = ${EXPATINC}" "EXPATLIB = ${EXPATLIB}")
-   endif()
-   if(NETCDF_FOUND)
-      set(NETCDFLDFLAGS "${NETCDF_LIBRARY}")
-      set(NETCDFINC "-I${NETCDF_INCLUDE_DIRS}")
-      set(NETCDFLIB "-I${NETCDF_INCLUDE_DIRS}")
-      set(TARGET_MOL_LIBS "${TARGET_MOL_LIBS}" "NETCDFLDFLAGS = ${NETCDFLDFLAGS}" "NETCDFINC = ${NETCDFINC}" "NETCDFLIB = ${NETCDFLIB}")
-   endif()
-   message(MOL_C= "${CMAKE_C_COMPILER}")
-   message(MOL_CXX= "${CMAKE_CXX_COMPILER}")
-   message(MOL_CFLAGS= "${CMAKE_C_FLAGS}")
-   message(MOL_CXXFLAGS= "${CMAKE_CXX_FLAGS}")
-   add_custom_command( 
-      OUTPUT ${LIB_MOLFILE_FILES}
-      COMMAND make dynlibs staticlibs "ARCH=${TARGET_ARCH}" "COPTO=${TARGET_COPT}" "LOPTO=${TARGET_LOPT}" "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" "DEF=${TARGET_DEF}" "CCFLAGS=${TARGET_CFLAGS}" "CXXFLAGS=${TARGET_CXXFLG}" "AR=${TARGET_AR}" "NM=${TARGET_NM}" "RANLIB=${TARGET_RANLIB}" "LIBTOOL=${TARGET_LIBTOOL}" "${TARGET_MOL_LIBS}"
-      COMMENT "Compiling libmolfile_plugin.a"
-      WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../molfile_plugin"
-   ) 
-endif()
-
-if(WINCOMP)
-   set(TARGET_DEF "/D")
-   set(TARGET_AR "${CMAKE_AR}")
-   set(TARGET_NM "${CMAKE_NM} -p")
-   set(TARGET_RANLIB "${CMAKE_RANLIB}")
-   set(TARGET_MOL_LIBS "")
-   set(TARGET_SHLDFLAGS "/D\"VMDPLUGIN_EXPORTS\"")
-   if(MSVS)
-      set(MYMAKE nmake)
-   else()
-      set(MYMAKE make)
-   endif()
-   if(ARCH64BIT)
-      set(TARGET_SHLD "\"link /DLL /nologo /incremental:no kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib ws2_32.lib wsock32.lib /MACHINE:X64 /OPT:REF\"")
-      set(TARGET_MOL_SETTINGS "\"CC = cl.exe /nologo /MT /DWIN64\"" "\"CXX = cl.exe /nologo /MT /TP /DWIN64\"" "\"CCFLAGS =  /EHsc /Wp64 /wd4996 /O2 /D\\\"_CRT_SECURE_NO_DEPRECATE\\\"\"" "\"CXXFLAGS = /EHsc /Wp64 /wd4996 /O2 /D\\\"_CRT_SECURE_NO_DEPRECATE\\\"\"")
-   else()
-      set(TARGET_SHLD "\"link /DLL /nologo /incremental:no kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib ws2_32.lib wsock32.lib /OPT:REF\"")
-      set(TARGET_MOL_SETTINGS "\"CC = cl.exe /nologo /MT /DWIN32\"" "\"CXX = cl.exe /nologo /MT /TP /DWIN32\"" "\"CCFLAGS = /O2 /G5\"" "\"CXXFLAGS = /O2 /G5\"")
-   endif()
-   add_custom_command( 
-      OUTPUT ${LIB_MOLFILE_FILES}
-      COMMAND ${MYMAKE} dynlibs win32staticlibs "\" ARCH = ${TARGET_ARCH} \"" "\" COPTO = /Fo \"" "\" LOPTO = /OUT: \"" "\" ${TARGET_MOL_SETTINGS} \"" "\" DEF = ${TARGET_DEF} \"" "\" AR = ${TARGET_AR} \"" "\" NM = ${TARGET_NM} \"" "\" RANLIB = ${TARGET_RANLIB} \"" "\" SHLDFLAGS = ${TARGET_SHLDFLAGS} \"" "\"${TARGET_MOL_LIBS}\""
-      COMMENT "Compiling libmolfile_plugin.a"
-      WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../molfile_plugin"
-   ) 
-endif()
-
-add_custom_target(molfile_plugins_comp ALL
-    DEPENDS ${LIB_MOLFILE_FILES}
-)
-
-add_library(molfile_plugins INTERFACE)
-
-target_include_directories(molfile_plugins INTERFACE "${CMAKE_CURRENT_BINARY_DIR}/lib/") 
-target_link_libraries(molfile_plugins INTERFACE ${MOLFILE_LIBRARIES})
-
-#add_dependencies(molfile_plugin_comp) 
-
diff --git a/setup.py b/setup.py
index 440b38dc7112bf69963219b92a6ea7c79ecfd469..c189d0fe1368971a289909ad5a51c8730ef4b77a 100644
--- a/setup.py
+++ b/setup.py
@@ -130,21 +130,18 @@ if __name__ == '__main__':
                 ],
             swig_opts=['-py3', '-Wall', '-c++'],
             library_dirs=[
-                'pymolfile/molfile/lib/',
-                'pymolfile/molfile/lib/tng/lib/'
+                'pymolfile/molfile/external/tng/lib/',
+                'pymolfile/molfile/molfile_plugins/compile/lib/'
                 ],
             libraries=['netcdf','tng_io','expat'],
             include_dirs = [
-                get_numpy_include(), 
+                get_numpy_include(),
+                get_cmake_includes(),
                 'pymolfile/molfile',
-                'pymolfile/molfile/lib/'
-                'pymolfile/molfile/include/',
-                'pymolfile/molfile/include/molfile_plugin/include',
-                'pymolfile/molfile/lib/molfile_plugin/lib',
-                'pymolfile/molfile/include/plugin_src/include',
-                #'pymolfile/molfile/include/netcdf/include',
-                #'pymolfile/molfile/include/expat/include',
-                'pymolfile/molfile/include/tng/include',
+                'pymolfile/molfile/molfile_plugins/include',
+                'pymolfile/molfile/molfile_plugins/molfile_plugin/include',
+                'pymolfile/molfile/molfile_plugins/compile/lib/',
+                'pymolfile/molfile/external/tng/include',
                 ],
             extra_compile_args = [
                 '-fPIC', '-shared', '-O2', '-w'
@@ -152,7 +149,7 @@ if __name__ == '__main__':
                 #'-fPIC', '-O2', '-w', '-fmessage-length=0'
                 ],
             extra_link_args = [
-                'pymolfile/molfile/lib/molfile_plugin/lib/libmolfile_plugin.a'
+                'pymolfile/molfile/molfile_plugins/compile/lib/libmolfile_plugin.a'
                 ],
             define_macros = largefile_macros
             )