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nomad-lab
pymolfile
Commits
1be60c10
Commit
1be60c10
authored
Oct 24, 2017
by
Berk Onat
Browse files
One Cmake call for all
parent
086f4be1
Changes
844
Expand all
Show whitespace changes
Inline
Side-by-side
pymolfile/molfile/compile-without-tng.sh
deleted
100644 → 0
View file @
086f4be1
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
deleted
100644 → 0
View file @
086f4be1
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
deleted
100644 → 0
View file @
086f4be1
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
View file @
1be60c10
...
...
@@ -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
deleted
120000 → 0
View file @
086f4be1
/usr/local/Cellar/expat/2.2.4/include/
\ No newline at end of file
pymolfile/molfile/include/molfile_plugin/include
deleted
120000 → 0
View file @
086f4be1
../../vmd_molfile_plugins/include
\ No newline at end of file
pymolfile/molfile/include/netcdf/include
deleted
120000 → 0
View file @
086f4be1
/usr/local/Cellar/netcdf/4.4.1.1_6/include/
\ No newline at end of file
pymolfile/molfile/include/plugin_src/include
deleted
120000 → 0
View file @
086f4be1
../../vmd_molfile_plugins/molfile_plugin/src/
\ No newline at end of file
pymolfile/molfile/include/tng/include
deleted
120000 → 0
View file @
086f4be1
/Users/bonat/TNG/tng/include/
\ No newline at end of file
pymolfile/molfile/lib/expat/lib
deleted
120000 → 0
View file @
086f4be1
/usr/local/Cellar/expat/2.2.4/lib
\ No newline at end of file
pymolfile/molfile/lib/molfile_plugin/lib
deleted
120000 → 0
View file @
086f4be1
../../vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/
\ No newline at end of file
pymolfile/molfile/lib/netcdf/lib
deleted
120000 → 0
View file @
086f4be1
/usr/local/Cellar/netcdf/4.4.1.1_6/lib/
\ No newline at end of file
pymolfile/molfile/lib/tng/lib
deleted
120000 → 0
View file @
086f4be1
/Users/bonat/TNG/tng/build/lib/
\ No newline at end of file
pymolfile/molfile/libpymolfile.py
deleted
100644 → 0
View file @
086f4be1
# 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/libpymolfile_wrap.cpp
deleted
100644 → 0
View file @
086f4be1
This diff is collapsed.
Click to expand it.
pymolfile/molfile/libpymolfile_wrap.cxx
deleted
100644 → 0
View file @
086f4be1
This diff is collapsed.
Click to expand it.
pymolfile/molfile/molfile_plugins/Makefile
View file @
1be60c10
...
...
@@ -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
View file @
1be60c10
...
...
@@ -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/pymolfile.c
deleted
100644 → 0
View file @
086f4be1
This diff is collapsed.
Click to expand it.
pymolfile/molfile/vmd_molfile_plugins-clang/LICENSE
deleted
100644 → 0
View file @
086f4be1
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.
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