1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
|
import os
from os.path import isfile, join
import platform
from setuptools import setup
from setuptools import Extension
import shutil
import sys
if sys.version_info[:2] < (2, 7):
sys.stderr.write('Python 2.6 and older is not supported\n')
sys.exit()
if sys.version_info[:2] == (2, 7) or sys.version_info[:2] <= (3, 5):
INSTALL_REQUIRES=['numpy>=1.10', 'biopython<=1.76', 'pyparsing', 'scipy']
else:
INSTALL_REQUIRES=['numpy>=1.10', 'biopython', 'pyparsing<=3.1.1', 'scipy', 'setuptools']
if sys.version_info[0] == 3 and sys.version_info[1] < 10:
sys.stderr.write('Python 3.9 and older is not supported\n')
sys.exit()
if os.name == 'java':
sys.stderr.write('JavaOS is not supported\n')
sys.exit()
try:
import numpy
except ImportError:
sys.stderr.write('numpy is not installed, you can find it at: '
'http://www.numpy.org/\n')
sys.exit()
if [int(dgt) for dgt in numpy.__version__.split('.')[:2]] < [1, 10]:
sys.stderr.write('numpy v1.10 or later is required, you can find it at: '
'http://www.numpy.org/\n')
sys.exit()
__version__ = ''
with open('prody/__init__.py') as inp:
for line in inp:
if line.startswith('__version__'):
exec(line.strip())
break
with open('README.rst') as inp:
long_description = inp.read()
PACKAGES = ['prody',
'prody.atomic',
'prody.database',
'prody.dynamics',
'prody.ensemble',
'prody.kdtree',
'prody.measure',
'prody.proteins',
'prody.sequence',
'prody.trajectory',
'prody.chromatin',
'prody.compounds',
'prody.domain_decomposition',
'prody.utilities',
'prody.apps',
'prody.apps.prody_apps',
'prody.apps.evol_apps',
'prody.tests',
'prody.tests.apps',
'prody.tests.atomic',
'prody.tests.datafiles',
'prody.tests.dynamics',
'prody.tests.ensemble',
'prody.tests.kdtree',
'prody.tests.measure',
'prody.tests.proteins',
'prody.tests.sequence',
'prody.tests.trajectory',
'prody.tests.utilities',]
PACKAGE_DATA = {
'prody.utilities': ['datafiles/*.dat'],
'prody.tests': ['datafiles/*.pdb',
'datafiles/*.dat',
'datafiles/*.coo',
'datafiles/dcd*.dcd',
'datafiles/xml*.xml',
'datafiles/msa*',
'datafiles/mmcif*cif',
'datafiles/*.npy',
'datafiles/*.mmtf',
'datafiles/*json'],
'prody.proteins': ['tabulated_energies.txt',
'hpb.so'],
}
PACKAGE_DIR = {}
for pkg in PACKAGES:
PACKAGE_DIR[pkg] = join(*pkg.split('.'))
from glob import glob
tntDir = join('prody', 'utilities', 'tnt')
hpbSoDir = join('prody', 'proteins', 'hpbmodule',
'hpb_Python{0}.{1}'.format(sys.version_info[0],
sys.version_info[1]))
proteinsDir = join('prody', 'proteins')
if not os.path.exists(join(proteinsDir, 'hpb.so')):
try:
shutil.copy(hpbSoDir + "/hpb.so", proteinsDir)
except FileNotFoundError:
pass
EXTENSIONS = [
Extension('prody.dynamics.rtbtools',
glob(join('prody', 'dynamics', 'rtbtools.c')),
include_dirs=[numpy.get_include()]),
Extension('prody.dynamics.smtools',
glob(join('prody', 'dynamics', 'smtools.c')),
include_dirs=[numpy.get_include()]),
# Extension('prody.dynamics.saxstools',
# glob(join('prody', 'dynamics', 'saxstools.c')),
# include_dirs=[numpy.get_include()]),
Extension('prody.sequence.msatools',
[join('prody', 'sequence', 'msatools.c'),],
include_dirs=[numpy.get_include()]),
Extension('prody.sequence.msaio',
[join('prody', 'sequence', 'msaio.c'),],
include_dirs=[numpy.get_include()]),
Extension('prody.sequence.seqtools',
[join('prody', 'sequence', 'seqtools.c'),],
include_dirs=[numpy.get_include()]),
]
# extra arguments for compiling C++ extensions on MacOSX
if platform.system() == 'Darwin':
os_ver = platform.mac_ver()[0]
os.environ['MACOSX_DEPLOYMENT_TARGET'] = os_ver
os.environ['CC'] = 'clang'
os.environ['CXX'] = 'clang++'
#extra_compile_args.append('-stdlib=libc++')
CONTRIBUTED = [
Extension('prody.kdtree._CKDTree',
[join('prody', 'kdtree', 'KDTree.c'),
join('prody', 'kdtree', 'KDTreemodule.c')],
include_dirs=[numpy.get_include()]),
Extension('prody.proteins.ccealign',
[join('prody', 'proteins', 'ccealign', 'ccealignmodule.cpp')],
include_dirs=[tntDir], language='c++'),
]
for ext in CONTRIBUTED:
if all([isfile(src) for src in ext.sources]):
EXTENSIONS.append(ext)
# SCRIPTS = ['scripts/prody', 'scripts/evol']
# if (platform.system() == 'Windows' or
# len(sys.argv) > 1 and sys.argv[1] not in ('build', 'install')):
# for script in list(SCRIPTS):
# SCRIPTS.append(script + '.bat')
SCRIPTS = ['prody=prody.apps:prody_main', 'evol=prody.apps:evol_main']
setup(
name='ProDy',
version=__version__,
author='James Krieger, Karolina Mikulska-Ruminska, She Zhang, Hongchun Li, Cihan Kaya, Ahmet Bakan, and others',
author_email='jamesmkrieger@gmail.com',
description='A Python Package for Protein Dynamics Analysis',
long_description=long_description,
url='http://www.csb.pitt.edu/ProDy',
packages=PACKAGES,
#package_dir=PACKAGE_DIR,
package_data=PACKAGE_DATA,
ext_modules=EXTENSIONS,
license='MIT License',
keywords=('protein, dynamics, elastic network model, '
'Gaussian network model, anisotropic network model, '
'essential dynamics analysis, principal component analysis, '
'Protein Data Bank, PDB, GNM, ANM, SM, PCA'),
classifiers=[
'Development Status :: 5 - Production/Stable',
'Intended Audience :: Education',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: MIT License',
'Operating System :: MacOS',
'Operating System :: POSIX',
'Programming Language :: Python',
'Programming Language :: Python :: 3',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Chemistry',
],
#scripts=SCRIPTS,
entry_points = {
'console_scripts': SCRIPTS,
},
install_requires=INSTALL_REQUIRES,
#provides=['ProDy ({0:s})'.format(__version__)]
)
|
