One Cmake call for all

pymolfile/molfile/compile-without-tng.sh

-echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
-swig -py3 -Wall -c++ -python libpymolfile.i
-echo "'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'"
-g++-7 -fPIC -Wall -Wextra -shared -g -Wunused-function -Wunused-parameter  \
-    -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/  \
-    -I./include \
-    -I./include/molfile_plugin/include \
-    -I./lib/molfile_plugin/lib \
-    -I./include/plugin_src/include \
-    -I./include/netcdf/include \
-    -I./include/expat/include \
-    -I./include/tng/include \
-    libpymolfile_wrap.cxx pymolfile.c -o _libpymolfile.so  -L. \
-    -L./lib/molfile_plugin/lib \
-    -L./lib/netcdf/lib \
-    -L./lib/expat/lib \
-    -L./lib/tng/lib \
-    lib/molfile_plugin/lib/libmolfile_plugin.a  -I/labEnv3/include/python3.6m/  \
-    -L/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib  \
-    -lpython3.6 -lnetcdf 

pymolfile/molfile/compile.sh

-echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
-swig -py3 -Wall -c++ -python libpymolfile.i
-echo "'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'"
-g++-7 -fPIC -Wall -Wextra -shared -g -Wunused-function -Wunused-parameter  \
-    -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/  \
-    -I./include \
-    -I./include/molfile_plugin/include \
-    -I./lib/molfile_plugin/lib \
-    -I./include/plugin_src/include \
-    -I./include/netcdf/include \
-    -I./include/expat/include \
-    -I./include/tng/include \
-    libpymolfile_wrap.cxx pymolfile.cxx -o _libpymolfile.so  -L. \
-    -L./lib/molfile_plugin/lib \
-    -L./lib/netcdf/lib \
-    -L./lib/expat/lib \
-    -L./lib/tng/lib \
-    lib/molfile_plugin/lib/libmolfile_plugin.a  -I/labEnv3/include/python3.6m/  \
-    -L/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib  \
-    -lpython3.6 -ltng_io -lnetcdf -lexpat

pymolfile/molfile/compile27.sh

-echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
-#swig -py3 -Wall -c++ -python libpymolfile.i
-swig -Wall -c++ -python libpymolfile.i
-echo "'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'"
-g++-7 -fPIC -Wall -Wextra -Xlinker -export-dynamic -shared -g -Wunused-function -Wunused-parameter  \
-    -I/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/ \
-    -I./include \
-    -I./include/molfile_plugin/include \
-    -I./lib/molfile_plugin/lib \
-    -I./include/plugin_src/include \
-    -I./include/netcdf/include \
-    -I./include/expat/include \
-    -I./include/tng/include \
-    libpymolfile_wrap.cxx pymolfile.c -o _libpymolfile.so  -L. \
-    -L./lib/molfile_plugin/lib \
-    -L./lib/netcdf/lib \
-    -L./lib/expat/lib \
-    -L./lib/tng/lib \
-    lib/molfile_plugin/lib/libmolfile_plugin.a  \
-    -I/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/include/python2.7/  \
-    -L/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib \
-    -lpython2.7 -ltng_io -lnetcdf -lexpat

pymolfile/molfile/external/CMakeLists.txt

@@ -2,8 +2,8 @@ cmake_minimum_required(VERSION 2.8.12)
 project(TNGBuilder)
 include(ExternalProject)
 
-set(TNG_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/external/tng")
-set(TNG_INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}/external/tng")
+set(TNG_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/tng")
+set(TNG_INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}/tng")
 set(TNG_CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${TNG_INSTALL_DIR})
 
 message("TNG_PREFIX='${TNG_PREFIX}'")
@@ -19,16 +19,16 @@ ExternalProject_Add(tng
 )
 
 
-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()
-
+#set(LIB_TNGIO_FILES
+#    "${TNG_INSTALL_DIR}/include/tng/tng_io.h")
+#
+#if (APPLE)
+#   set(LIB_TNGIO_FILES ${LIB_TNGIO_FILES} "${TNG_INSTALL_DIR}/lib/libtng_io.dylib")
+#else()
+#   set(LIB_TNGIO_FILES ${LIB_TNGIO_FILES} "${TNG_INSTALL_DIR}/lib/libtng_io.so")
+#endif()
+#
 add_custom_target(tngio_comp ALL
-                  DEPENDS ${LIB_TNGIO_FILES}
-                 )
+	          DEPENDS ${TNG_INSTALL_DIR}
+)
 

pymolfile/molfile/include/expat/include

-/usr/local/Cellar/expat/2.2.4/include/
\ No newline at end of file

pymolfile/molfile/include/molfile_plugin/include

-../../vmd_molfile_plugins/include
\ No newline at end of file

pymolfile/molfile/include/netcdf/include

-/usr/local/Cellar/netcdf/4.4.1.1_6/include/
\ No newline at end of file

pymolfile/molfile/include/plugin_src/include

-../../vmd_molfile_plugins/molfile_plugin/src/
\ No newline at end of file

pymolfile/molfile/include/tng/include

-/Users/bonat/TNG/tng/include/
\ No newline at end of file

pymolfile/molfile/lib/expat/lib

-/usr/local/Cellar/expat/2.2.4/lib
\ No newline at end of file

pymolfile/molfile/lib/molfile_plugin/lib

-../../vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/
\ No newline at end of file

pymolfile/molfile/lib/netcdf/lib

-/usr/local/Cellar/netcdf/4.4.1.1_6/lib/
\ No newline at end of file

pymolfile/molfile/lib/tng/lib

-/Users/bonat/TNG/tng/build/lib/
\ No newline at end of file

pymolfile/molfile/libpymolfile.py

-# This file was automatically generated by SWIG (http://www.swig.org).
-# Version 3.0.12
-#
-# Do not make changes to this file unless you know what you are doing--modify
-# the SWIG interface file instead.
-
-"""
-
-:Author:  Berk Onat <b.onat@warwick.ac.uk>
-:Year:    2017
-:Licence: UIUC LICENSE
-
-
-
-"""
-
-
-from sys import version_info as _swig_python_version_info
-if _swig_python_version_info >= (2, 7, 0):
-    def swig_import_helper():
-        import importlib
-        pkg = __name__.rpartition('.')[0]
-        mname = '.'.join((pkg, '_libpymolfile')).lstrip('.')
-        try:
-            return importlib.import_module(mname)
-        except ImportError:
-            return importlib.import_module('_libpymolfile')
-    _libpymolfile = swig_import_helper()
-    del swig_import_helper
-elif _swig_python_version_info >= (2, 6, 0):
-    def swig_import_helper():
-        from os.path import dirname
-        import imp
-        fp = None
-        try:
-            fp, pathname, description = imp.find_module('_libpymolfile', [dirname(__file__)])
-        except ImportError:
-            import _libpymolfile
-            return _libpymolfile
-        try:
-            _mod = imp.load_module('_libpymolfile', fp, pathname, description)
-        finally:
-            if fp is not None:
-                fp.close()
-        return _mod
-    _libpymolfile = swig_import_helper()
-    del swig_import_helper
-else:
-    import _libpymolfile
-del _swig_python_version_info
-
-try:
-    _swig_property = property
-except NameError:
-    pass  # Python < 2.2 doesn't have 'property'.
-
-try:
-    import builtins as __builtin__
-except ImportError:
-    import __builtin__
-
-def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
-    if (name == "thisown"):
-        return self.this.own(value)
-    if (name == "this"):
-        if type(value).__name__ == 'SwigPyObject':
-            self.__dict__[name] = value
-            return
-    method = class_type.__swig_setmethods__.get(name, None)
-    if method:
-        return method(self, value)
-    if (not static):
-        if _newclass:
-            object.__setattr__(self, name, value)
-        else:
-            self.__dict__[name] = value
-    else:
-        raise AttributeError("You cannot add attributes to %s" % self)
-
-
-def _swig_setattr(self, class_type, name, value):
-    return _swig_setattr_nondynamic(self, class_type, name, value, 0)
-
-
-def _swig_getattr(self, class_type, name):
-    if (name == "thisown"):
-        return self.this.own()
-    method = class_type.__swig_getmethods__.get(name, None)
-    if method:
-        return method(self)
-    raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
-
-
-def _swig_repr(self):
-    try:
-        strthis = "proxy of " + self.this.__repr__()
-    except __builtin__.Exception:
-        strthis = ""
-    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
-
-try:
-    _object = object
-    _newclass = 1
-except __builtin__.Exception:
-    class _object:
-        pass
-    _newclass = 0
-
-
-def molfile_plugin_list(maxsize: 'int') -> "PyObject *":
-    """molfile_plugin_list(maxsize) -> PyObject *"""
-    return _libpymolfile.molfile_plugin_list(maxsize)
-
-def molfile_init() -> "int":
-    """molfile_init() -> int"""
-    return _libpymolfile.molfile_init()
-
-def molfile_finish() -> "int":
-    """molfile_finish() -> int"""
-    return _libpymolfile.molfile_finish()
-
-def get_plugin(molcapsule: 'PyObject *', plug_no: 'int') -> "PyObject *":
-    """get_plugin(molcapsule, plug_no) -> PyObject *"""
-    return _libpymolfile.get_plugin(molcapsule, plug_no)
-
-def molfile_plugin_info(molcapsule: 'PyObject *', plugin_no: 'int') -> "PyObject *":
-    """molfile_plugin_info(molcapsule, plugin_no) -> PyObject *"""
-    return _libpymolfile.molfile_plugin_info(molcapsule, plugin_no)
-
-def open_file_read(molcapsule: 'PyObject *', fname: 'char *', ftype: 'char *', natoms: 'int') -> "PyObject *":
-    """open_file_read(molcapsule, fname, ftype, natoms) -> PyObject *"""
-    return _libpymolfile.open_file_read(molcapsule, fname, ftype, natoms)
-
-def close_file_read(molpack: 'PyObject *') -> "PyObject *":
-    """close_file_read(molpack) -> PyObject *"""
-    return _libpymolfile.close_file_read(molpack)
-
-def read_fill_structure(molpack: 'PyObject *', prototype: 'PyObject *') -> "PyObject *":
-    """read_fill_structure(molpack, prototype) -> PyObject *"""
-    return _libpymolfile.read_fill_structure(molpack, prototype)
-
-def read_fill_bonds(molpack: 'PyObject *') -> "PyObject *":
-    """read_fill_bonds(molpack) -> PyObject *"""
-    return _libpymolfile.read_fill_bonds(molpack)
-
-def read_fill_angles(molpack: 'PyObject *') -> "PyObject *":
-    """read_fill_angles(molpack) -> PyObject *"""
-    return _libpymolfile.read_fill_angles(molpack)
-
-def read_fill_next_timestep(molpack: 'PyObject *') -> "PyObject *":
-    """read_fill_next_timestep(molpack) -> PyObject *"""
-    return _libpymolfile.read_fill_next_timestep(molpack)
-
-def are_plugins_same(molpack_a: 'PyObject *', molpack_b: 'PyObject *') -> "PyObject *":
-    """are_plugins_same(molpack_a, molpack_b) -> PyObject *"""
-    return _libpymolfile.are_plugins_same(molpack_a, molpack_b)
-
-def are_filehandles_same(molpack_a: 'PyObject *', molpack_b: 'PyObject *') -> "PyObject *":
-    """are_filehandles_same(molpack_a, molpack_b) -> PyObject *"""
-    return _libpymolfile.are_filehandles_same(molpack_a, molpack_b)
-# This file is compatible with both classic and new-style classes.
-
-

pymolfile/molfile/molfile_plugins/Makefile

@@ -72,7 +72,7 @@ win32bins:
 
 clean:
 	find compile \( -name \*.o -o -name \*.a -o -name \*.so -o -name \*.exp -o -name \*.lib -o -name \*.h \) -print | xargs rm -f
-	find compile \( -name lib\* \) -print | xargs rm -rf
+	find compile \( -name lib_\* \) -print | xargs rm -rf
 	rm -f log.*
 	rm -f molfile_plugin/so_locations
 

pymolfile/molfile/molfile_plugins/CMakeLists.txt → pymolfile/molfile/molfile_plugins/compile/CMakeLists.txt

@@ -6,9 +6,9 @@ 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 "${TNG_INSTALL_DIR}/tng/include/tng/tng_io.h")
+if (EXISTS "${TNG_INSTALL_DIR}/lib/libtng_io.dylib"
+    OR EXISTS "${TNG_INSTALL_DIR}/lib/libtng_io.so"
+    OR EXISTS "${TNG_INSTALL_DIR}/include/tng/tng_io.h")
    set(TNGIO_FOUND TRUE)
    set(TNGIO_LIBRARIES "${TNG_INSTALL_DIR}/lib/")
    set(TNGIO_INLCUDE_DIRS "${TNG_INSTALL_DIR}/include/")
@@ -32,8 +32,8 @@ if(TARGET_ARCH MATCHES "^.*64.*$")
 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")
+    "${CMAKE_CURRENT_BINARY_DIR}/lib/libmolfile_plugins.a"
+    "${CMAKE_CURRENT_BINARY_DIR}/lib/libmolfile_plugins.h")
 
 if(UNIX AND NOT APPLE)
 	set(LINUX TRUE)
@@ -124,7 +124,7 @@ if(UNIX)
       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"
+      WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../molfile_plugin"
    ) 
 endif()
 

pymolfile/molfile/vmd_molfile_plugins-clang/LICENSE

-
-With the exception of specifically marked plugins or source files
-which have different license terms due to inclusion of source code
-or data under different restrictions, the software contained
-within the VMD plugin tree is subject to the UIUC Open Source license 
-which is included below the explicitly listed exceptions below:
-
-Specifically listed exceptions: 
-  hesstrans -- Includes the "newmat10B" free C++ matrix library by
-               Robert Davies (robert@statsresearch.co.nz)
-  intersurf -- See Intersurf INRIA license text
-     pmepot -- NAMD License
-     psfgen -- NAMD License
-      stamp -- See STAMP license
-   vmdtkcon -- See TkCon license
-
-   Prof. A. MacKerell's CHARMM Empirical Force Fields -- 
-     (excerpts included with plugins: 
-      'autoionize', 'membrane', 'readcharmmtop', 'readcharmmpar', 'solvate')
-     http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm   
-
-------------------------------------------------------------------------------
-
-University of Illinois Open Source License
-Copyright 2006 Theoretical and Computational Biophysics Group, 
-All rights reserved.
-
-Developed by:		Theoretical and Computational Biophysics Group
-			University of Illinois at Urbana-Champaign
-			http://www.ks.uiuc.edu/
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the Software), to deal with 
-the Software without restriction, including without limitation the rights to 
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 
-of the Software, and to permit persons to whom the Software is furnished to 
-do so, subject to the following conditions:
-
-Redistributions of source code must retain the above copyright notice, 
-this list of conditions and the following disclaimers.
-
-Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimers in the documentation 
-and/or other materials provided with the distribution.
-
-Neither the names of Theoretical and Computational Biophysics Group, 
-University of Illinois at Urbana-Champaign, nor the names of its contributors 
-may be used to endorse or promote products derived from this Software without 
-specific prior written permission.
-
-THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL 
-THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 
-OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 
-ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
-OTHER DEALINGS WITH THE SOFTWARE.
-