def _loadAnimationData(self, obj):
prot = self.protocol
animationName = obj.getFileName() # assumes that obj.getFileName is the folder of animation
animationPath = prot._getExtraPath(animationName)
#animationName = animationPath.split('animation_')[-1]
animationRoot = join(animationPath, animationName)
animationSuffixes = ['.vmd', '.pdb', 'trajectory.txt']
for s in animationSuffixes:
f = animationRoot + s
if not exists(f):
self.errorMessage('Animation file "%s" not found. ' % f)
return
# Load animation trajectory points
trajectoryPoints = np.loadtxt(animationRoot + 'trajectory.txt')
data = PathData(dim=trajectoryPoints.shape[1])
for i, row in enumerate(trajectoryPoints):
data.addPoint(Point(pointId=i+1, data=list(row), weight=1))
self.trajectoriesWindow.setPathData(data)
self.trajectoriesWindow.setAnimationName(animationName)
self.trajectoriesWindow._onUpdateClick()
def _showVmd():
vmdFn = animationRoot + '.vmd'
VmdView(' -e %s' % vmdFn).show()
self.getTkRoot().after(500, _showVmd)
def _loadAnimationData(self, obj):
prot = self.protocol
animationName = obj.getFileName(
) # assumes that obj.getFileName is the folder of animation
animationPath = prot._getExtraPath(animationName)
#animationName = animationPath.split('animation_')[-1]
animationRoot = join(animationPath, animationName)
animationSuffixes = ['.vmd', '.pdb', 'trajectory.txt']
for s in animationSuffixes:
f = animationRoot + s
if not exists(f):
self.errorMessage('Animation file "%s" not found. ' % f)
return
# Load animation trajectory points
trajectoryPoints = np.loadtxt(animationRoot + 'trajectory.txt')
data = PathData(dim=trajectoryPoints.shape[1])
for i, row in enumerate(trajectoryPoints):
data.addPoint(Point(pointId=i + 1, data=list(row), weight=1))
self.trajectoriesWindow.setPathData(data)
self.trajectoriesWindow.setAnimationName(animationName)
self.trajectoriesWindow._onUpdateClick()
def _showVmd():
vmdFn = animationRoot + '.vmd'
VmdView(' -e %s' % vmdFn).show()
self.getTkRoot().after(500, _showVmd)
def _loadData(self):
from pyworkflow.em.packages.xmipp3.nma.data import PathData
data = PathData(dim=2)
bfactorFile = self.protocol._getPath('bfactor.txt')
if os.path.exists(bfactorFile):
f = open(bfactorFile)
values = map(float, f.readline().split())
f.close()
p1 = data.createEmptyPoint()
p1.setX(values[0])
p1.setY(values[1])
data.addPoint(p1)
p2 = data.createEmptyPoint()
p2.setX(values[2])
p2.setY(values[3])
data.addPoint(p2)
data.bfactor = values[4]
else:
data.bfactor = 0
return data
def _loadData(self):
from pyworkflow.em.packages.xmipp3.nma.data import PathData
data = PathData(dim=2)
bfactorFile = self.protocol._getPath('bfactor.txt')
if os.path.exists(bfactorFile):
f = open(bfactorFile)
values = map(float, f.readline().split())
f.close()
p1 = data.createEmptyPoint()
p1.setX(values[0])
p1.setY(values[1])
data.addPoint(p1)
p2 = data.createEmptyPoint()
p2.setX(values[2])
p2.setY(values[3])
data.addPoint(p2)
data.bfactor = values[4]
else:
data.bfactor = 0
return data
