def testPolI(self):
ms = xla.get_gui().Subunits.table.modelSelect
m = chimera.openModels.list()[0]
ms.setvalue([m])
g = xla.get_gui()
g.modelSelect.doSync(ms)
xFrame = g.Xlinks
xFrame.displayDefault()
self.assertEqual(1, len(xFrame.getXlinkDataMgrs()))
xmgr = xFrame.getXlinkDataMgrs()[0]
# self.assertEqual(171, len(xmgr.pbg.pseudoBonds))
xFrame.ld_score_var.set(30.0)
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
# self.assertEqual(106, displayed)
#just test open windows
# g.configFrame.domainsButton.invoke()
# g.configFrame.subCompButton.invoke()
def setUp(self):
mPaths = ["PolI/4C3H.pdb"]
super(TestPolI, self).setUp(mPaths)
ms = xla.get_gui().Subunits.table.modelSelect
m = chimera.openModels.list()[0]
ms.setvalue([m])
self.g = xla.get_gui()
self.g.modelSelect.doSync(ms)
def setUp(self):
mPaths = ['Rvb12/yRvb12.hexamer.pdb']
cPath = 'Rvb12/Rvb12.json'
super(TestTutorial, self).setUp(mPaths, cPath)
ms = xla.get_gui().Subunits.table.modelSelect
self.model = chimera.openModels.list()[0]
ms.setvalue([self.model])
self.g = xla.get_gui()
self.g.modelSelect.doSync(ms)
def setUp(self):
mPaths = ['PolI/4C3H.pdb']
super(TestPolI, self).setUp(mPaths)
ms = xla.get_gui().Subunits.table.modelSelect
m = chimera.openModels.list()[0]
ms.setvalue([m])
self.g = xla.get_gui()
self.g.modelSelect.doSync(ms)
def setUp(self):
mPaths = ["Rvb12/yRvb12.hexamer.pdb"]
cPath = "Rvb12/Rvb12.json"
super(TestTutorial, self).setUp(mPaths, cPath)
ms = xla.get_gui().Subunits.table.modelSelect
self.model = chimera.openModels.list()[0]
ms.setvalue([self.model])
self.g = xla.get_gui()
self.g.modelSelect.doSync(ms)
def setUp(self):
mPaths = ['PolI/4C3H.pdb']
cPath = 'PolI/PolI_old_format.json'
super(TestPolI, self).setUp(mPaths, cPath)
ms = xla.get_gui().Subunits.table.modelSelect
m = chimera.openModels.list()[0]
ms.setvalue([m])
self.g = xla.get_gui()
self.g.modelSelect.doSync(ms)
def testMover(self):
m = xla.get_gui().Subunits.table.mover
self.assertEqual("move component", m.mode)
name = "A49-tWH"
xla.activateByName(name)
def onAdd(self):
if self.validate():
self.synchronize()
try:
if not self.differs:
if self.listFrame:
if type(self.data) == dict:
_type = self.fields["type"][3].get()
_type = self.typeDict[_type]
cp = deepcopy(self.data[_type])
else:
cp = deepcopy(self.data)
self.listFrame.container.addItem(cp)
self.listFrame.synchronize()
self.listFrame.toBottom()
elif self.differs:
_type = self.fields["Type"][3].get()
name = self.fields["Choose"][3].get()
pool = self.fields["Choose"][0][_type]
choice = [p for p in pool if p.name == name][0]
if self.listFrame:
self.listFrame.container.addItem(choice)
self.listFrame.synchronize()
self.listFrame.toBottom()
finally:
self.empty()
g = xlinkanalyzer.get_gui()
g.configFrame._disableHack()
def testMover(self):
m = xla.get_gui().Subunits.table.mover
self.assertEqual('move component', m.mode)
name = 'A49-tWH'
xla.activateByName(name)
def testPolI(self):
ms = xla.get_gui().Subunits.table.modelSelect
m = chimera.openModels.list()[0]
ms.setvalue([m])
g = xla.get_gui()
g.modelSelect.doSync(ms)
xFrame = g.Xlinks
xFrame.displayDefault()
self.assertEqual(1, len(xFrame.getXlinkDataMgrs()))
xmgr = xFrame.getXlinkDataMgrs()[0]
self.assertNotEqual(0, len(xmgr.pbg.pseudoBonds))
def testPolI(self):
ms = xla.get_gui().Subunits.table.modelSelect
m = chimera.openModels.list()[0]
ms.setvalue([m])
g = xla.get_gui()
g.modelSelect.doSync(ms)
xFrame = g.Xlinks
xFrame.displayDefault()
self.assertEqual(1, len(xFrame.getXlinkDataMgrs()))
xmgr = xFrame.getXlinkDataMgrs()[0]
self.assertNotEqual(0, len(xmgr.pbg.pseudoBonds))
def testLoad(self):
ms = xla.get_gui().Subunits.table.modelSelect
m = chimera.openModels.list()[0]
ms.setvalue([m])
g = xla.get_gui()
g.modelSelect.doSync(ms)
xFrame = g.Xlinks
xFrame.displayDefault()
self.assertEqual(1, len(xFrame.getXlinkDataMgrs()))
xmgr = xFrame.getXlinkDataMgrs()[0]
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(75, displayed)
def testMover(self):
m = xla.get_gui().Subunits.table.mover
self.assertEqual('move component', m.mode)
# name = 'A190'
name = 'testdom'
# name = 'testsubcomplex'
xla.activateByName(name)
def testMover(self):
m = xla.get_gui().Subunits.table.mover
self.assertEqual('move component', m.mode)
name = 'Rvb1'
# xla.activateByName(name)
# xla.activateByName(name, 'A')
xla.activateByName(name, ['A', 'B'])
def testMover(self):
m = xla.get_gui().Subunits.table.mover
self.assertEqual('move component', m.mode)
name = 'Rvb1'
# xla.activateByName(name)
# xla.activateByName(name, 'A')
xla.activateByName(name, ['A', 'B'])
def testLoad(self):
ms = xla.get_gui().Subunits.table.modelSelect
m = chimera.openModels.list()[0]
ms.setvalue([m])
g = xla.get_gui()
g.modelSelect.doSync(ms)
xFrame = g.Xlinks
xFrame.displayDefault()
self.assertEqual(1, len(xFrame.getXlinkDataMgrs()))
xmgr = xFrame.getXlinkDataMgrs()[0]
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(75, displayed)
def testMover(self):
m = xla.get_gui().Subunits.table.mover
self.assertEqual('move component', m.mode)
name = 'Rvb1'
# xla.activateByName(name)
xla.activateByName(name, 'C')
# xla.activateByName(name, ['A', 'C'])
#move around, should move
symmover = symmove.SymMover()
symmover.activate()
def setUp(self, mPaths, cPath):
mPath = xlinkanalyzer.__path__[0]
xlaTestPath = path.join(path.split(mPath)[0], 'pytests/test_data')
self.xlaTestMPaths = [path.join(xlaTestPath, _path) for _path in mPaths]
self.xlaTestCPath = path.join(xlaTestPath, cPath)
[chimera.openModels.open(_path) for _path in self.xlaTestMPaths]
self.models = chimera.openModels.list()
gui.show_dialog()
guiWin = xlinkanalyzer.get_gui()
def testMover(self):
m = xla.get_gui().Subunits.table.mover
self.assertEqual('move component', m.mode)
name = 'Rvb1'
# xla.activateByName(name)
xla.activateByName(name, 'C')
# xla.activateByName(name, ['A', 'C'])
#move around, should move
symmover = symmove.SymMover()
symmover.activate()
def setUp(self, mPaths, cPath):
mPath = xlinkanalyzer.__path__[0]
xlaTestPath = path.join(path.split(mPath)[0], 'pytests/test_data')
self.xlaTestMPaths = [
path.join(xlaTestPath, _path) for _path in mPaths
]
self.xlaTestCPath = path.join(xlaTestPath, cPath)
[chimera.openModels.open(_path) for _path in self.xlaTestMPaths]
self.models = chimera.openModels.list()
gui.show_dialog()
guiWin = xlinkanalyzer.get_gui()
def setUp(self, mPaths):
mPath = xlinkanalyzer.__path__[0]
xlaTestPath = path.join(path.split(mPath)[0], 'pytests/test_data')
self.xlaTestMPaths = [path.join(xlaTestPath, _path) for _path in mPaths]
[chimera.openModels.open(_path) for _path in self.xlaTestMPaths]
self.models = chimera.openModels.list()
gui.show_dialog()
guiWin = xlinkanalyzer.get_gui()
guiWin.configFrame.resMngr.config.loadFromStructure(self.models[-1])
guiWin.configFrame.clear()
guiWin.configFrame.update()
guiWin.configFrame.config.state = "changed"
self.config = guiWin.configFrame.config
def setUp(self, mPaths, cPath):
mPath = xlinkanalyzer.__path__[0]
xlaTestPath = path.join(path.split(mPath)[0], 'pytests/test_data')
self.xlaTestMPaths = [path.join(xlaTestPath, _path) for _path in mPaths]
self.xlaTestCPath = path.join(xlaTestPath, cPath)
[chimera.openModels.open(_path) for _path in self.xlaTestMPaths]
self.models = chimera.openModels.list()
gui.show_dialog()
guiWin = xlinkanalyzer.get_gui()
guiWin.configFrame.resMngr.loadAssembly(guiWin, self.xlaTestCPath)
guiWin.configFrame.clear()
guiWin.configFrame.update()
guiWin.configFrame.mainWindow.setTitle(guiWin.configFrame.config.file)
guiWin.configFrame.config.state = "unchanged"
self.config = guiWin.configFrame.config
def setUp(self, mPaths):
mPath = xlinkanalyzer.__path__[0]
xlaTestPath = path.join(path.split(mPath)[0], 'pytests/test_data')
self.xlaTestMPaths = [
path.join(xlaTestPath, _path) for _path in mPaths
]
[chimera.openModels.open(_path) for _path in self.xlaTestMPaths]
self.models = chimera.openModels.list()
gui.show_dialog()
guiWin = xlinkanalyzer.get_gui()
guiWin.configFrame.resMngr.config.loadFromStructure(self.models[-1])
guiWin.configFrame.clear()
guiWin.configFrame.update()
guiWin.configFrame.config.state = "changed"
self.config = guiWin.configFrame.config
def setUp(self, mPaths, cPath):
mPath = xlinkanalyzer.__path__[0]
xlaTestPath = path.join(path.split(mPath)[0], 'pytests/test_data')
self.xlaTestMPaths = [
path.join(xlaTestPath, _path) for _path in mPaths
]
self.xlaTestCPath = path.join(xlaTestPath, cPath)
[chimera.openModels.open(_path) for _path in self.xlaTestMPaths]
self.models = chimera.openModels.list()
gui.show_dialog()
guiWin = xlinkanalyzer.get_gui()
guiWin.configFrame.resMngr.loadAssembly(guiWin, self.xlaTestCPath)
guiWin.configFrame.clear()
guiWin.configFrame.update()
guiWin.configFrame.mainWindow.setTitle(guiWin.configFrame.config.file)
guiWin.configFrame.config.state = "unchanged"
self.config = guiWin.configFrame.config
def is_satisfied(b, threshold):
if b:
return b.length() < threshold
def restyleXlinks(xMgrs, threshold=None):
'''Restyle xlinks in provided XlinkDataMgr objects.'''
good_color = chimera.MaterialColor(0,0,255)
bad_color = chimera.MaterialColor(255,0,0)
for xMgr in xMgrs:
for b in xMgr.iterXlinkPseudoBonds():
if b is not None:
b.drawMode = chimera.Bond.Stick
if threshold is not None:
if is_satisfied(b, threshold):
b.color = good_color
b.radius = 0.6
else:
b.color = bad_color
b.radius = 0.6
else:
b.color = bad_color
b.radius = 0.6
chimeraModel = chimera.openModels.list()[-1]
gui = xlinkanalyzer.get_gui()
x = gui.Xlinks.getXlinkDataMgrs()
xMgrs = gui.Xlinks.getXlinkDataMgrs()
restyleXlinks(xMgrs, threshold=30)
def get_first_xlinkMgr():
gui = xla.get_gui()
xframe = gui.Xlinks
return xframe.dataMgrs[0]
import xlinkanalyzer as xla
reload(xla)
gui = xla.get_gui()
xframe = gui.Xlinks
def get_first_xlinkMgr():
gui = xla.get_gui()
xframe = gui.Xlinks
return xframe.dataMgrs[0]
xframe.getActiveData()
x = get_first_xlinkMgr()
x.countSatisfiedBetweenSelections(30, '#0:.C', '#0:.C')
x.pbg.pseudoBonds
return b.length() < threshold
def restyleXlinks(xMgrs, threshold=None):
'''Restyle xlinks in provided XlinkDataMgr objects.'''
good_color = chimera.MaterialColor(0, 0, 255)
bad_color = chimera.MaterialColor(255, 0, 0)
for xMgr in xMgrs:
for b in xMgr.iterXlinkPseudoBonds():
if b is not None:
b.drawMode = chimera.Bond.Stick
if threshold is not None:
if is_satisfied(b, threshold):
b.color = good_color
b.radius = 0.6
else:
b.color = bad_color
b.radius = 0.6
else:
b.color = bad_color
b.radius = 0.6
chimeraModel = chimera.openModels.list()[-1]
gui = xlinkanalyzer.get_gui()
x = gui.Xlinks.getXlinkDataMgrs()
xMgrs = gui.Xlinks.getXlinkDataMgrs()
restyleXlinks(xMgrs, threshold=30)
def get_first_xlinkMgr():
gui = xla.get_gui()
xframe = gui.Xlinks
return xframe.dataMgrs[0]
import xlinkanalyzer as xla
reload(xla)
gui = xla.get_gui()
xframe = gui.Xlinks
def get_first_xlinkMgr():
gui = xla.get_gui()
xframe = gui.Xlinks
return xframe.dataMgrs[0]
xframe.getActiveData()
x = get_first_xlinkMgr()
x.countSatisfiedBetweenSelections(30, '#0:.C', '#0:.C')
x.pbg.pseudoBonds