Skip to content

GitLab

Commit 1be60c10 authored by Berk Onat's avatar Berk Onat
Browse files
Options

One Cmake call for all

parent 086f4be1
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 27 additions and 11803 deletions
build/lib.macosx-10.12-x86_64-3.6/pymolfile/__init__.py deleted 100644 → 0
View file @ 086f4be1
from __future__ import absolute_import
import warnings
try:
from .molfile import libpymolfile
except ImportError:
warnings.warn("libpymolfile package not available, pymolfile does not work without its library!")
from . import plugin_list
from . import pymolfile
__all__ = [ "pymolfile" ]
from .pymolfile import OpenMolfile, list_plugins
build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/__init__.py deleted 100644 → 0
View file @ 086f4be1
# Stand-alone python bindings for libpymolfile
# Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
# Published under the UIUC OpenSource LICENSE
"""libpymolfile library.
"""
build/lib.macosx-10.12-x86_64-3.6/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.
build/lib.macosx-10.12-x86_64-3.6/pymolfile/plugin_list.py deleted 100644 → 0
View file @ 086f4be1
import warnings
import sys
from .molfile import libpymolfile
try:
from .molfile import libpymolfile
except ImportError:
warnings.warn("libpymolfile package not available, pymolfile does not work without its library!")
MAX_NUM_PLUGINS = 200
C_MOLFILE_PLUGINS = libpymolfile.molfile_plugin_list(MAX_NUM_PLUGINS)
def byte_str_decode(data, dectype=None):
try:
return data.decode(dectype).replace('\x00', '')
except AttributeError:
return data
def plugins():
""" Information on the available molfile plugins
Example tuple: ('psf', 'psf', 1, 1, 1, 0, 1, 1, 1, 0,
'CHARMM,NAMD,XPLOR PSF', 'mol file reader',
'Justin Gullingsrud, John Stone', 1, 9, 17, 1)
The fields in the tuple represent info in ordered as follows:
1: format extension
2: format name
3: read_structure is avaliable if 1
4: read_bonds is avaliable if 1
5: read_angles is avaliable if 1
6: read_next_timestep is avaliable if 1
7: write_structure is avaliable if 1
8: write_bonds is avaliable if 1
9: write_angles is avaliable if 1
10: write_timestep is avaliable if 1
11: long name of the plugin
12: type of plugin
13: authors of the plugin
14: major version of the plugin
15: minor version of the plugin
16: ABI version of the plugin
17: 1 if is reentrant (returns is_reentrant)
Returns: A list of tuples that includes the information and
capabilities of each molfile plugin. The information is
extracted from molfile_plugin_t.
"""
global C_MOLFILE_PLUGINS
numlist = libpymolfile.molfile_init()
if sys.version_info > (3,):
basestring = str
plugins_list = [
[byte_str_decode(item,
dectype="unicode_escape") for item in libpymolfile.molfile_plugin_info(
C_MOLFILE_PLUGINS, i)
] for i in range(numlist)
]
libpymolfile.molfile_finish()
return plugins_list
MOLFILE_PLUGINS = plugins()
build/lib.macosx-10.12-x86_64-3.6/pymolfile/test_libpymolfile.py deleted 100644 → 0
View file @ 086f4be1
import numpy
import molfile.libpymolfile as pym
mylist = pym.molfile_plugin_list(200)
print(mylist)
numlist = pym.molfile_init()
print(numlist)
for i in range(numlist):
testplugin = pym.molfile_plugin_info(mylist, i)
print(i, testplugin)
#splugin = pym.get_plugin(mylist, 99) #pdb
#cplugin = pym.get_plugin(mylist, 83) #trr
#cplugin = pym.get_plugin(mylist, 85) #xtc
splugin = pym.get_plugin(mylist, 105) #psf
#splugin = pym.get_plugin(mylist, 81) #gro
cplugin = pym.get_plugin(mylist, 69) #dcd
#cplugin = pym.get_plugin(mylist, 126) #nc
print(splugin)
print(cplugin)
natoms=0
#sfname="../test/DPDP.pdb"
#cfname="../test/DPDP.nc"
#sfname="../test/ala3.pdb"
sfname="../test/ala3.psf"
cfname="../test/ala3.dcd"
#sfname="../test/md.gro"
#cfname="../test/md.trr"
#cfname="../test/md.xtc"
#sfname="../test/md_1u19.gro"
#cfname="../test/md_1u19.xtc"
#sftype="pdb"
#cftype="trr"
#cftype="xtc"
sftype="psf"
#sftype="gro"
cftype="dcd"
#cftype="nc"
print("Structure plugin:")
spluginhandle = pym.open_file_read(splugin, sfname, sftype, natoms)
print("Coordinate plugin:")
cpluginhandle = pym.open_file_read(cplugin, cfname, cftype, natoms)
print(cpluginhandle)
print(cpluginhandle.natoms)
print(spluginhandle)
print(spluginhandle.natoms)
if cpluginhandle.natoms != spluginhandle.natoms:
print("Number of atoms do not match in structure and coordinate files.")
if pym.is_plugin_same(spluginhandle, cpluginhandle):
pym.close_file_read(cpluginhandle)
cpluginhandle = spluginhandle
#if 0 && vmdplugin_ABIVERSION > 17
# /* The new PDB file formats allows for much larger structures, */
# /* which can therefore require longer chain ID strings. The */
# /* new PDBx/mmCIF file formats do not have length limits on */
# /* fields, so PDB chains could be arbitrarily long strings */
# /* in such files. At present, we know we need at least 3-char */
# /* chains for existing PDBx/mmCIF files. */
# char chain[4]; /**< required chain name, or "" */
#else
# char chain[2]; /**< required chain name, or "" */
#endif
# Change 'chain', 'S4' to S2 for PDB
if 'pdb' in [sftype, cftype]:
print("file chain is set to S2")
chain_size = 'S2'
else:
chain_size = 'S4'
x = numpy.array([
('C1','C','ACE',0,'','','','',1.0,1.0,1.0,1.0,1.0,6),
('C2','C','ACE',0,'','','','',1.0,1.0,1.0,1.0,1.0,6)
],
dtype=[
('name', 'S16'), ('type', 'S16'), ('resname', 'S8'),
('resid', 'i4'), ('segid', 'S8'), ('chain', chain_size),
('altloc', 'S2'), ('insertion', 'S2'), ('occupancy', 'f4'),
('bfactor', 'f4'), ('mass', 'f4'), ('charge', 'f4'),
('radius', 'f4'), ('atomicnumber', 'i4')
]
)
y = pym.read_fill_structure(spluginhandle, x)
if y is not None:
print(y)
print(len(y))
try:
z = pym.read_fill_bonds(spluginhandle)
if z is not None:
print(z)
print(len(z))
except (AttributeError, SystemError):
pass
try:
a = pym.read_fill_angles(spluginhandle)
if a is not None:
print(a)
print(len(a))
except (AttributeError, SystemError):
pass
if pym.is_plugin_same(spluginhandle, cpluginhandle):
pass
else:
pym.close_file_read(spluginhandle)
step=0
while True:
#while False:
try:
c = pym.read_fill_next_timestep(cpluginhandle)
if c is None:
break
step=step+1
print("Step:",step)
print(c)
if c["coords"] is not None:
print(len(c["coords"]))
except (AttributeError,OSError):
pass
pym.close_file_read(cpluginhandle)
pym.molfile_finish()
pymolfile/molfile/CMakeLists.txt
View file @ 1be60c10
......@@ -3,9 +3,10 @@ cmake_minimum_required(VERSION 2.8.12)
project(molfile)
add_subdirectory(external)
add_subdirectory(molfile_plugins)
add_subdirectory(molfile_plugins/compile)
set_source_files_properties( external/tng/include/tng/tng_io.h PROPERTIES GENERATED TRUE )
#set_source_files_properties( tng/include/tng/tng_io.h PROPERTIES GENERATED TRUE )
add_dependencies( molfile_plugins_comp tngio_comp )
#add_dependencies( molfile_plugins_comp TNGBuilder )
pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Info.plist deleted 100644 → 0
View file @ 086f4be1
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>CFBundleDevelopmentRegion</key>
<string>English</string>
<key>CFBundleIdentifier</key>
<string>com.apple.xcode.dsym._libpymolfile.so</string>
<key>CFBundleInfoDictionaryVersion</key>
<string>6.0</string>
<key>CFBundlePackageType</key>
<string>dSYM</string>
<key>CFBundleSignature</key>
<string>????</string>
<key>CFBundleShortVersionString</key>
<string>1.0</string>
<key>CFBundleVersion</key>
<string>1</string>
</dict>
</plist>
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}'")
......@@ -12,23 +12,23 @@ message("TNG_CMAKE_ARGS='${TNG_CMAKE_ARGS}'")
message("GIT_EXECUTABLE='${GIT_EXECUTABLE}'")
ExternalProject_Add(tng
PREFIX ${TNG_PREFIX}
GIT_REPOSITORY https://github.com/gromacs/tng.git
INSTALL_DIR ${TNG_INSTALL_DIR}
CMAKE_ARGS ${TNG_CMAKE_ARGS}
PREFIX ${TNG_PREFIX}
GIT_REPOSITORY https://github.com/gromacs/tng.git
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()
#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