def testMultifilesave(self):
import glob
for name in ['ala', 'gly', 'his', 'arg']:
cmd.fragment(name)
# multistate
for i in range(2, 11):
cmd.create('ala', 'ala', 1, i)
for fmt in ['{}-{:02}.cif', '{}-{state}.cif']:
with testing.mkdtemp() as dirname:
cmd.multifilesave(os.path.join(dirname, fmt), 'ala', 0)
filenames = [os.path.basename(p) for p in glob.glob(os.path.join(dirname, '*.cif'))]
self.assertEqual(len(filenames), 10)
self.assertTrue('ala-03.cif' in filenames)
with testing.mkdtemp() as dirname:
cmd.multifilesave(os.path.join(dirname, '{}.pdb'), 'a* g*')
filenames_full = sorted(glob.glob(os.path.join(dirname, '*.pdb')))
filenames = [os.path.basename(p) for p in filenames_full]
self.assertEqual(filenames, ['ala.pdb', 'arg.pdb', 'gly.pdb'])
cmd.delete('*')
cmd.load(filenames_full[0])
self.assertEqual(cmd.count_atoms(), 10)
cmd.delete('*')
cmd.load(filenames_full[1])
self.assertEqual(cmd.count_atoms(), 24)
def testMultifilesave(self):
import glob
for name in ['ala', 'gly', 'his', 'arg']:
cmd.fragment(name)
# multistate
for i in range(2, 11):
cmd.create('ala', 'ala', 1, i)
for fmt in ['{}-{:02}.cif', '{}-{state}.cif']:
with testing.mkdtemp() as dirname:
cmd.multifilesave(os.path.join(dirname, fmt), 'ala', 0)
filenames = [os.path.basename(p) for p in glob.glob(os.path.join(dirname, '*.cif'))]
self.assertEqual(len(filenames), 10)
self.assertTrue('ala-03.cif' in filenames)
with testing.mkdtemp() as dirname:
cmd.multifilesave(os.path.join(dirname, '{}.pdb'), 'a* g*')
filenames_full = sorted(glob.glob(os.path.join(dirname, '*.pdb')))
filenames = [os.path.basename(p) for p in filenames_full]
self.assertEqual(filenames, ['ala.pdb', 'arg.pdb', 'gly.pdb'])
cmd.delete('*')
cmd.load(filenames_full[0])
self.assertEqual(cmd.count_atoms(), 10)
cmd.delete('*')
cmd.load(filenames_full[1])
self.assertEqual(cmd.count_atoms(), 24)
def test_unc(self):
'''
UNC-Paths (PYMOL-2954)
'''
pymolwin = self._get_pymolwin()
with testing.mkdtemp() as base:
if base[1] != ':':
self.skipTest('no drive letter: ' + base)
return
if base.startswith('\\\\'):
uncpath = base
else:
uncpath = '\\\\localhost\\%s$%s' % (base[0], base[2:])
pml_filename = uncpath + '\\in.pml'
out_filename = uncpath + '\\out.pdb'
with open(pml_filename, 'w') as handle:
handle.write('fragment gly\n')
handle.write('save %s\n' % out_filename)
subprocess.call([pymolwin, '+2', '-kcq', pml_filename])
# wait for spawned process
time.sleep(0.5)
cmd.load(out_filename)
self.assertEqual(7, cmd.count_atoms())
def testFetchLocal(self):
try:
import urllib.parse as urlparse
except ImportError:
import urlparse
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set(
'fetch_host',
urlparse.urlunsplit(
['file', '',
self.datafile('pdb.mirror'), '', '']))
cmd.fetch('1avy', type='pdb')
names += ['1avy']
self.assertItemsEqual(cmd.get_names(), names)
cmd.fetch('1avyB', type='pdb')
names += ['1avyB']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_chains('1avyB'), ['B'])
cmd.fetch('1aq5', type='pdb', multiplex=1)
names += ['1aq5_%04d' % (i + 1) for i in range(20)]
self.assertItemsEqual(cmd.get_names(), names)
def testFetchLocal(self):
try:
import urllib.parse as urlparse
except ImportError:
import urlparse
# PyMOL 1.8.6 adds full URLs, remove them
import pymol
pdbpaths = pymol.importing.hostPaths['pdb']
pdbpaths[:] = [p for p in pdbpaths if '://' not in p]
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', urlparse.urlunsplit(['file', '',
self.datafile('pdb.mirror'), '', '']))
cmd.fetch('1avy', type='pdb')
names += ['1avy']
self.assertItemsEqual(cmd.get_names(), names)
cmd.fetch('1avyB', type='pdb')
names += ['1avyB']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_chains('1avyB'), ['B'])
cmd.fetch('1aq5', type='pdb', multiplex=1)
names += ['1aq5_%04d' % (i+1) for i in range(20)]
self.assertItemsEqual(cmd.get_names(), names)
def testFetchLocal(self):
try:
import urllib.parse as urlparse
except ImportError:
import urlparse
# PyMOL 1.8.6 adds full URLs, remove them
import pymol
pdbpaths = pymol.importing.hostPaths['pdb']
pdbpaths[:] = [p for p in pdbpaths if '://' not in p]
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set(
'fetch_host',
urlparse.urlunsplit(
['file', '',
self.datafile('pdb.mirror'), '', '']))
cmd.fetch('1avy', type='pdb')
names += ['1avy']
self.assertItemsEqual(cmd.get_names(), names)
cmd.fetch('1avyB', type='pdb')
names += ['1avyB']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_chains('1avyB'), ['B'])
cmd.fetch('1aq5', type='pdb', multiplex=1)
names += ['1aq5_%04d' % (i + 1) for i in range(20)]
self.assertItemsEqual(cmd.get_names(), names)
def test(self, use_shaders, cgo_shader_ub, rep="cartoon"):
self._setup_movie(rep)
cmd.set("use_shaders", use_shaders)
cmd.set("cgo_shader_ub_color", cgo_shader_ub)
cmd.set("cgo_shader_ub_flags", cgo_shader_ub)
cmd.set("cgo_shader_ub_normal", cgo_shader_ub)
with testing.mkdtemp() as tempdir, self.timing():
cmd.mpng(os.path.join(tempdir, "f"))
def test(self, use_shaders, cgo_shader_ub, rep="cartoon"):
self._setup_movie(rep)
cmd.set("use_shaders", use_shaders)
cmd.set("cgo_shader_ub_color", cgo_shader_ub)
cmd.set("cgo_shader_ub_flags", cgo_shader_ub)
cmd.set("cgo_shader_ub_normal", cgo_shader_ub)
with testing.mkdtemp() as tempdir, self.timing():
cmd.mpng(os.path.join(tempdir, "f"))
def testFetch(self):
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', 'pdb pdbe')
cmd.fetch('1avy', '1avy1', type='pdb1')
names += ['1avy1']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.count_states('1avy1'), 3)
cmd.fetch('1avy', type='2fofc')
names += ['1avy_2fofc']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_type('1avy_2fofc'), 'object:map')
def testFetch(self):
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', 'pdb pdbe')
cmd.fetch('1avy', '1avy1', type='pdb1')
names += ['1avy1']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.count_states('1avy1'), 3)
cmd.fetch('1avy', type='2fofc')
names += ['1avy_2fofc']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_type('1avy_2fofc'), 'object:map')
def testCdLsPwd(self):
with testing.mkdtemp() as path:
cmd.cd(path)
self.assertEqual(os.getcwd(),
os.path.realpath(path))
touch('foo1.txt')
touch('foo2.txt')
touch('foo3.bin')
cmd.feedback("disable", "python", "output")
cmd.pwd()
# no test of output possible
cmd.ls('*.txt')
def test_get_user_config(self, basename):
'''
pymolrc finding test
'''
orig = dict((key, os.getenv(key))
for key in ['HOME', 'HOMEDRIVE', 'HOMEPATH', 'PYMOL_PATH'])
with testing.mkdtemp() as tmpdir:
os.chdir(tmpdir)
os.mkdir('abc')
pwd = os.getcwd()
if sys.platform.startswith('win'):
if pwd[1] != ':':
raise ValueError('no drive letter')
os.environ.pop('HOME', None)
os.environ['HOMEDRIVE'] = pwd[:2]
os.environ['HOMEPATH'] = pwd[2:] + r'\abc'
else:
os.environ['HOME'] = pwd + '/abc'
pymolrc = os.path.join(pwd, 'abc', basename)
with open(pymolrc, 'w') as handle:
print('# hello', file=handle)
a = invocation.get_user_config()
self.assertEqual(pymolrc, os.path.normpath(a[0]))
pymolrc = os.path.join(pwd, basename)
with open(pymolrc, 'w') as handle:
print('# hello', file=handle)
a = invocation.get_user_config()
self.assertEqual(pymolrc, os.path.normpath(a[0]))
for key, value in orig.items():
if value is None:
os.environ.pop(key, None)
else:
os.environ[key] = value
def testFetchLocal(self):
import urlparse
with testing.mkdtemp() as fetch_path:
names = []
cmd.set('fetch_path', fetch_path)
cmd.set('fetch_host', urlparse.urlunsplit(['file', '',
self.datafile('pdb.mirror'), '', '']))
cmd.fetch('1avy')
names += ['1avy']
self.assertItemsEqual(cmd.get_names(), names)
cmd.fetch('1avyB')
names += ['1avyB']
self.assertItemsEqual(cmd.get_names(), names)
self.assertEqual(cmd.get_chains('1avyB'), ['B'])
cmd.fetch('1aq5', multiplex=1)
names += ['1aq5_%04d' % (i+1) for i in range(20)]
self.assertItemsEqual(cmd.get_names(), names)
def test_get_user_config(self, basename):
'''
pymolrc finding test
'''
orig = dict((key, os.getenv(key)) for key in ['HOME', 'HOMEDRIVE', 'HOMEPATH', 'PYMOL_PATH'])
with testing.mkdtemp() as tmpdir:
os.chdir(tmpdir)
os.mkdir('abc')
pwd = os.getcwd()
if sys.platform.startswith('win'):
if pwd[1] != ':':
raise ValueError('no drive letter')
os.environ.pop('HOME', None)
os.environ['HOMEDRIVE'] = pwd[:2]
os.environ['HOMEPATH'] = pwd[2:] + r'\abc'
else:
os.environ['HOME'] = pwd + '/abc'
pymolrc = os.path.join(pwd, 'abc', basename)
with open(pymolrc, 'w') as handle:
print('# hello', file=handle)
a = invocation.get_user_config()
self.assertEqual(pymolrc, os.path.normpath(a[0]))
pymolrc = os.path.join(pwd, basename)
with open(pymolrc, 'w') as handle:
print('# hello', file=handle)
a = invocation.get_user_config()
self.assertEqual(pymolrc, os.path.normpath(a[0]))
for key, value in orig.items():
if value is None:
os.environ.pop(key, None)
else:
os.environ[key] = value
def test_scenes(self):
self._load_example()
cmd.scene('s1', 'store')
cmd.enable('g1')
cmd.scene('s2', 'store')
cmd.mset('1x4')
cmd.mview('store', 1, scene='s2')
cmd.mview('store', 4, scene='s1')
with testing.mkdtemp() as tempdir:
# export
prefix = os.path.join(tempdir, 'frame')
cmd.mpng(prefix, width=100, height=100)
img = self.get_imagearray(prefix + '0002.png')
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0003.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
def testLoadPWG(self):
if sys.version_info[0] < 3:
import urllib2
else:
import urllib.request as urllib2
content_index = b'Hello World\n'
port = 8084
baseurl = 'http://localhost:%d' % port
def urlread(url):
handle = urllib2.urlopen(url, timeout=3.0)
try:
return handle.info(), handle.read()
finally:
handle.close()
with testing.mkdtemp() as rootdir:
filename = os.path.join(rootdir, 'index.html')
with open(filename, 'wb') as handle:
handle.write(content_index)
filename = os.path.join(rootdir, 'start.pwg')
with open(filename, 'w') as handle:
handle.write('root %s\n' % rootdir)
handle.write('port %d\n' % port)
handle.write('header add Test-Key Test-Value\n') # new in 2.4
cmd.load(filename)
header, content = urlread(baseurl)
self.assertEqual(header['Test-Key'], 'Test-Value')
self.assertEqual(content, content_index)
# Warning: can't call locking functions here, will dead-lock
# get_version is non-locking since 1.7.4
header, content = urlread(baseurl + '/apply/pymol.cmd.get_version')
content = content.decode('ascii', errors='ignore')
self.assertTrue(content, cmd.get_version()[0] in content)
def testMpng(self, modal):
import glob, os
shape2 = (100, 100)
cmd.mset("1x4")
cmd.mdo(1, 'bg_color red')
cmd.mdo(3, 'bg_color blue')
with testing.mkdtemp() as dirname:
cmd.mpng(os.path.join(dirname, 'image'), width=shape2[0], height=shape2[1])
filenames = glob.glob(os.path.join(dirname, 'image*.png'))
filenames.sort()
self.assertEqual(4, len(filenames))
img = self.get_imagearray(filenames[0])
self.assertEqual(img.shape[:2], shape2)
self.assertImageHasColor('red', img)
img = self.get_imagearray(filenames[-1])
self.assertEqual(img.shape[:2], shape2)
self.assertImageHasColor('blue', img)
def test_scenes(self):
self._load_example()
cmd.scene('s1', 'store')
cmd.enable('g1')
cmd.scene('s2', 'store')
cmd.mset('1x4')
cmd.mview('store', 1, scene='s2')
cmd.mview('store', 4, scene='s1')
with testing.mkdtemp() as tempdir:
# export
prefix = os.path.join(tempdir, 'frame')
cmd.mpng(prefix, width=100, height=100)
img = self.get_imagearray(prefix + '0002.png')
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0003.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
def testLoadPWG(self):
if sys.version_info[0] < 3:
import urllib2
else:
import urllib.request as urllib2
content_index = b'Hello World\n'
port = 8084
baseurl = 'http://localhost:%d' % port
def urlread(url):
handle = urllib2.urlopen(url, timeout=3.0)
try:
return handle.read()
finally:
handle.close()
with testing.mkdtemp() as rootdir:
filename = os.path.join(rootdir, 'index.html')
with open(filename, 'wb') as handle:
handle.write(content_index)
filename = os.path.join(rootdir, 'start.pwg')
with open(filename, 'w') as handle:
handle.write('root %s\n' % rootdir)
handle.write('port %d\n' % port)
cmd.load(filename)
content = urlread(baseurl)
self.assertEqual(content, content_index)
# Warning: can't call locking functions here, will dead-lock
# get_version is non-locking since 1.7.4
content = urlread(baseurl + '/apply/pymol.cmd.get_version')
content = content.decode('ascii', errors='ignore')
self.assertTrue(content, cmd.get_version()[0] in content)
def test_wchar(self):
'''
Wide-char file names
'''
pymolwin = self._get_pymolwin()
with testing.mkdtemp() as base:
dirname = u'Japanese \u65e5\u672c\u8a9e'
dirname = os.path.join(base, dirname)
os.mkdir(dirname)
out_filename = base + '\\out.pdb'
bat_filename = base + '\\in.bat'
pml_filename = dirname + u'\\in.pml'
in_filename = dirname + u'\\in.pdb'
command = u'"%s" -kcq "%s" "%s"' % (pymolwin, in_filename, pml_filename)
cmd.fragment('gly')
cmd.save(in_filename)
cmd.delete('*')
with open(pml_filename, 'w') as handle:
handle.write('save %s\n' % out_filename)
with open(bat_filename, 'wb') as handle:
handle.write(b'chcp 65001\r\n') # UTF-8 code page
handle.write(b'set PYTHONIOENCODING=UTF-8\r\n') # avoid LookupError
handle.write(command.encode('utf-8') + b'\r\n')
handle.write(b'chcp 437\r\n')
subprocess.call([bat_filename])
# wait for spawned process
time.sleep(0.5)
cmd.load(out_filename)
self.assertEqual(7, cmd.count_atoms())
def testMpng(self, modal):
import glob, os
shape2 = (100, 100)
cmd.mset("1x4")
cmd.mdo(1, 'bg_color red')
cmd.mdo(3, 'bg_color blue')
with testing.mkdtemp() as dirname:
cmd.mpng(os.path.join(dirname, 'image'),
width=shape2[0],
height=shape2[1])
filenames = glob.glob(os.path.join(dirname, 'image*.png'))
filenames.sort()
self.assertEqual(4, len(filenames))
img = self.get_imagearray(filenames[0])
self.assertEqual(img.shape[:2], shape2)
self.assertImageHasColor('red', img)
img = self.get_imagearray(filenames[-1])
self.assertEqual(img.shape[:2], shape2)
self.assertImageHasColor('blue', img)
def test_mdo(self):
self._load_example()
cmd.mset('1x3')
cmd.mdo(1, 'disable m1')
cmd.mdo(2, 'enable m1')
cmd.mdo(3, 'enable g1')
with testing.mkdtemp() as tempdir:
# export
prefix = os.path.join(tempdir, 'frame')
cmd.mpng(prefix, width=100, height=100)
img = self.get_imagearray(prefix + '0001.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0002.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0003.png')
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
def test_mdo(self):
self._load_example()
cmd.mset('1x3')
cmd.mdo(1, 'disable m1')
cmd.mdo(2, 'enable m1')
cmd.mdo(3, 'enable g1')
with testing.mkdtemp() as tempdir:
# export
prefix = os.path.join(tempdir, 'frame')
cmd.mpng(prefix, width=100, height=100)
img = self.get_imagearray(prefix + '0001.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0002.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0003.png')
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
