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 similarity index 100% rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/binposplugin.html rename to pymolfile/molfile/molfile_plugins/molfile_plugin/doc/binposplugin.html diff --git a/pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/biomoccaplugin.html b/pymolfile/molfile/molfile_plugins/molfile_plugin/doc/biomoccaplugin.html similarity index 100% rename from pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/doc/biomoccaplugin.html rename to pymolfile/molfile/molfile_plugins/molfile_plugin/doc/biomoccaplugin.html diff --git 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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 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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 )