def setCAlphaSizeToDefault(self):
''''
Sets the residue's C-alpha atom to the default size. This is useful if the size has been changed somewhere.
'''
try:
temp = PDBAtom('____', '9', 1, 'CA')
defaultSize = temp.getAtomRadius()
del temp
atom = self.getAtom('CA')
atom.setAtomRadius(defaultSize)
except:
pass
def setLoopAtoms(self, startIndex, endIndex):
self.engine.clearAtomList()
self.engine.clearCurrentPath()
for i in range(startIndex, endIndex + 1):
if (i in self.chain.residueRange()):
atom = self.chain[i].getAtom('CA')
if (not atom):
raw = PDBAtom(self.chain.getPdbID(),
self.chain.getChainID(), i, 'CA')
raw.setPosition(Vector3DFloat(0, 0, 0))
atom = self.calphaViewer.renderer.addAtom(raw)
atom.setVisible(False)
print atom
self.chain[i].addAtomObject(atom)
self.chain[i].setCAlphaColorToDefault()
bondBefore = None
bondAfter = None
if i - 1 in self.chain.residueRange():
prevCAlpha = self.chain[i - 1].getAtom('CA')
if prevCAlpha:
print "adding a bond before"
bondBefore = PDBBond()
bondBefore.setAtom0Ix(prevCAlpha.getHashKey())
bondBefore.setAtom1Ix(atom.getHashKey())
if i + 1 in self.chain.residueRange():
nextCAlpha = self.chain[i + 1].getAtom('CA')
if nextCAlpha:
print "adding a bond after"
bondAfter = PDBBond()
bondAfter.setAtom0Ix(nextCAlpha.getHashKey())
bondAfter.setAtom1Ix(atom.getHashKey())
if bondBefore:
self.calphaViewer.renderer.addBond(bondBefore)
if bondAfter:
self.calphaViewer.renderer.addBond(bondAfter)
self.engine.addAtom(atom.getHashKey())
if not self.calphaViewer.loaded:
self.calphaViewer.loaded = True
self.calphaViewer.emitModelLoaded()
else:
self.calphaViewer.emitModelChanged()
def redo(self):
"""
In addition to being called to redo an action, this is called the first
time the action occurs.
"""
raw = PDBAtom(self.currentChainModel.getPdbID(),
self.currentChainModel.getChainID(), self.resSeqNum,
'CA')
raw.setPosition(self.chosenCoordinates)
atom = self.viewer.renderer.addAtom(raw)
self.currentChainModel[self.resSeqNum].addAtomObject(atom)
self.currentChainModel[self.resSeqNum].setCAlphaColorToDefault()
bondBefore = None
bondAfter = None
if self.resSeqNum - 1 in self.currentChainModel.residueRange():
prevCAlpha = self.currentChainModel[self.resSeqNum -
1].getAtom('CA')
if prevCAlpha:
bondBefore = PDBBond()
bondBefore.setAtom0Ix(prevCAlpha.getHashKey())
bondBefore.setAtom1Ix(atom.getHashKey())
if self.resSeqNum + 1 in self.currentChainModel.residueRange():
nextCAlpha = self.currentChainModel[self.resSeqNum +
1].getAtom('CA')
if nextCAlpha:
bondAfter = PDBBond()
bondAfter.setAtom0Ix(nextCAlpha.getHashKey())
bondAfter.setAtom1Ix(atom.getHashKey())
if bondBefore:
self.viewer.renderer.addBond(bondBefore)
if bondAfter:
self.viewer.renderer.addBond(bondAfter)
self.viewer.emitModelChanged()
self.structureEditor.atomJustAdded = atom
if self.structureEditor.atomicBackwardRadioButton.isChecked():
self.structureEditor.atomPrevButtonPress()
elif self.structureEditor.atomicForwardRadioButton.isChecked():
self.structureEditor.atomNextButtonPress()
def setCAlphaColorToDefault(self):
''''
Sets the residue's C-alpha atom to the default color. This is useful if the color has been changed somewhere.
'''
try:
temp = PDBAtom('____', '9', 1, 'CA')
defaultColor = (temp.getColorR(), temp.getColorG(),
temp.getColorB(), temp.getColorA())
del temp
atom = self.getAtom('CA')
atom.setColor(*defaultColor)
except:
pass
#!/usr/bin/python
import sys
from libpyGORGON import PDBAtom,Vector3DFloat
from PyQt4 import QtGui, QtCore
from window_manager import WindowManager
from main_window_form import MainWindowForm
app = QtGui.QApplication(sys.argv)
window = MainWindowForm("2.0")
window.addModule(WindowManager(window))
window.showMaximized()
cAlphaViewer=window.viewers['calpha']
rawAtom=PDBAtom('AAAA', 'A', 1, 'CA')
rawAtom.setPosition(Vector3DFloat(-1, 0, 0))
rawAtom = cAlphaViewer.renderer.addAtom(rawAtom)
a = PDBAtom('AAAA', 'A', 2, 'CA')
a.setPosition(Vector3DFloat(1, 0, 0))
print 'a:', a
b = cAlphaViewer.renderer.addAtom(a)
print 'b-1:', b
if not cAlphaViewer.loaded:
cAlphaViewer.loaded = True
cAlphaViewer.emitModelLoaded()
del a #This line causes a segmentation fault later on, which is weird because we never use the atom at this location in memory after this
#Thus, unless there's a change, I'll have to be extremely careful about Python's garbage collection
rawAtom.setColor(1, 0, 0, 1) #Red
def addAtom(self,
atomName,
x,
y,
z,
element="",
serialNo=None,
occupancy=None,
tempFactor=None,
charge=""):
'''Adds a new PDBAtom to the residue.'''
residueIndex = self.chain.findIndexForRes(self)
rawAtom = PDBAtom(self.chain.getPdbID(), self.chain.getChainID(),
residueIndex, atomName)
rawAtom.setPosition(Vector3DFloat(x, y, z))
if not element:
element = atomName[0]
rawAtom.setElement(element)
if serialNo != None:
rawAtom.setSerial(serialNo)
if occupancy != None:
rawAtom.setOccupancy(occupancy)
if tempFactor != None:
rawAtom.setTempFactor(tempFactor)
if charge:
rawAtom.setCharge(charge)
self.__atoms[atomName] = rawAtom
#print "%s PDBAtom added to %s Residue" %(atomName,self)
'''
#Add atom to viewer and update --Mike's addition
#self.chain.getViewer().renderer.addAtom(rawAtom)
'''
'''
if(not self.chain.getViewer().loaded):
self.chain.getViewer().loaded = True
self.chain.getViewer().emitModelLoaded()
self.chain.getViewer().dirty = True
self.chain.getViewer().emitModelChanged()
'''
return rawAtom
from PyQt4 import QtGui
from window_manager import WindowManager
from main_window_form import MainWindowForm
from seq_model.Chain import Chain
# Create the application object required by Qt
app = QtGui.QApplication(sys.argv)
# Create Gorgon's main window and get a handle on the CAlpha Viewer
window = MainWindowForm("2.0")
window.addModule(WindowManager(window))
window.showMaximized()
cAlphaViewer = window.viewers['calpha']
# Instantiate an Atom
rawAtom = PDBAtom('AAAA', 'A', 1, 'CA')
rawAtom.setPosition(Vector3DFloat(-.5, -0.5, -0.5))
rawAtom = cAlphaViewer.renderer.addAtom(
rawAtom
) #A new PDBAtom is returned by this function, and rawAtom needs to refer to it
# Instantiate an Second Atom
rawAtom2 = PDBAtom('AAAA', 'A', 2, 'CA')
rawAtom2.setPosition(Vector3DFloat(.5, 0.5, 0.5))
rawAtom2 = cAlphaViewer.renderer.addAtom(rawAtom2)
# Confirm that these accessor functions are working
key = rawAtom2.getHashKey()
atom = cAlphaViewer.renderer.getAtom(key)
print atom.getPDBId()
print atom.getChainId()
from seq_model.findHelixCalphas import helixEndpointsToCAlphaPositions
# Create the application object required by Qt
app = QtGui.QApplication(sys.argv)
# Create Gorgon's main window and get a handle on the CAlpha Viewer
window = MainWindowForm("2.0")
window.addModule(WindowManager(window))
window.showMaximized()
cAlphaViewer = window.viewers['calpha']
startPos = (-20, -10, -5)
stopPos = (20, 10, 5)
# Instantiate an Atom
rawAtom = PDBAtom('AAAA', 'A', 1, 'CA')
rawAtom.setPosition(Vector3DFloat(*startPos))
rawAtom.setAtomRadius(2)
rawAtom.setColor(0, 1, 0, 1)
rawAtom = cAlphaViewer.renderer.addAtom(
rawAtom
) #A new PDBAtom is returned by this function, and rawAtom needs to refer to it
# Instantiate a Second Atom
rawAtom2 = PDBAtom('AAAA', 'A', 2, 'CA')
rawAtom2.setPosition(Vector3DFloat(*stopPos))
rawAtom2.setAtomRadius(2)
rawAtom2.setColor(1, 0, 0, 1)
rawAtom2 = cAlphaViewer.renderer.addAtom(rawAtom2)
# Get coordinates for helix with axis starting and ending at startPos and stopPos