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from BALL import Atom, Path, PDBAtom, Vector3, atoms, residues
from VIEW import *
__version__ = '1.5'
"""
I. Convenience access
"""
""" Ia. Widgets """
def getDatasetControl():
return DatasetControl.getInstance(0)
def getDisplayProperties():
return DisplayProperties.getInstance(0)
def getGeometricControl():
return GeometricControl.getInstance(0)
def getLogView():
return LogView.getInstance(0)
def getMainControl():
return MainControl.getInstance(0)
def getMolecularControl():
return MolecularControl.getInstance(0)
def getMolecularStructure():
return MolecularStructure.getInstance(0)
def getScene():
return Scene.getInstance(0)
""" Ib. Second-level getters"""
def getForceField():
return getMolecularStructure().getForceField()
def getMolecularControlSelection():
return getMainControl().getMolecularControlSelection()
def getOneSystem():
"""
Returns the highlighted system. If none or multiple systems are highlighted,
this function highlights and returns the first system available.
"""
s = getMolecularControlSelection()
if len(s) != 1:
print("Warning: Excatly one System should be highlighted! Returning first system available.")
s.append(getSystems()[0])
s = s[0].getRoot()
getMolecularControl().highlight([s])
return s
def getRepresentations():
return getMainControl().getRepresentationManager().getRepresentations()
def getSelection():
return getMainControl().getSelection()
def getSystems():
return getMainControl().getCompositeManager().getComposites()
"""
II. Main control
"""
def clearSystems():
[getMainControl().remove(system) for system in getSystems()]
def clearProject():
getMainControl().clearData()
def clearRepresentations():
while len(getRepresentations()) > 0:
getMainControl().remove(getRepresentations()[0])
def hideAllRepresentations():
for i in range(len(getRepresentations())):
getRepresentations()[i].setHidden(1)
getMainControl().update(getRepresentations()[i])
def loadProject(filename):
loc = Path().find(filename)
clearProject()
return getMainControl().loadBALLViewProjectFile(loc)
def openFile(file):
return getMainControl().openFile(file)
def quickLoad():
getMainControl().quickLoad()
def quickSave():
getMainControl().quickSave()
def quitApplication():
getMainControl().quit()
def setMultithreading(mode):
getMainControl().setMultithreading(mode)
"""
III. Misc
"""
def addOptimizedHydrogens():
getMolecularControl().highlight([getOneSystem()])
setMultithreading(False)
getMolecularStructure().addHydrogens()
getMolecularControl().applySelector("element(H)")
setMultithreading(True)
getMolecularStructure().runMinimization(False)
def highlightLigand():
removeWater()
l = [r for r in residues(getOneSystem()) if not r.isAminoAcid()]
getMolecularControl().highlight(l)
return l
def printAtomTypesForHighlighted():
print("Atom types for highlighted Items:")
for r in getMolecularControlSelection():
if r.__class__ in (Atom, PDBAtom):
print(str(r.getFullName(Atom.ADD_RESIDUE_ID)) + " : " + str(r.getType()))
else:
for a in atoms(r):
print(a.getFullName(Atom.ADD_RESIDUE_ID) +" : "+str(a.getType()))
def printAtomTypesForLigands():
highlightLigand()
printAtomTypesForHighlighted()
def relaxStructure():
getMolecularControl().highlight([getOneSystem()])
getScene().optimizeStructure()
def removeWater():
getMainControl().clearSelection()
setMultithreading(False)
if getMolecularControl().applySelector("residue(HOH)") != 0:
getMolecularControl().highlightSelection()
getMolecularControl().cut()
setMultithreading(True)
def selectByExpression(expression):
getMainControl().clearSelection()
getMolecularControl().applySelector(expression)
def selectByExpressionAndSetViewPoint(expression, view_point, look_at, look_up):
setViewPoint(view_point, look_at, look_up)
selectByExpression(expression)
def setViewPoint(view_point, look_at, look_up):
getMainControl().clearSelection()
camera = getScene().getStage().getCamera()
camera.setViewPoint(Vector3(*[float(e) for e in view_point.split('|')]))
camera.setLookAtPosition(Vector3(*[float(e) for e in look_at.split('|')]))
camera.setLookUpVector(Vector3(*[float(e) for e in look_up.split('|')]))
getScene().setCamera(camera)
Scene.getInstance(0).applyStereoDefaults()
getMainControl().update(getRepresentations()[0])
def showCartoonAndLigand():
s = getOneSystem()
clearRepresentations()
highlightLigand()
getDisplayProperties().selectModel(MODEL_VDW)
getDisplayProperties().selectColoringMethod(COLORING_ELEMENT)
getDisplayProperties().apply()
getMolecularControl().highlight([s])
getMolecularControl().centerCamera()
getDisplayProperties().selectModel(MODEL_CARTOON)
getDisplayProperties().selectColoringMethod(COLORING_RESIDUE_INDEX)
getDisplayProperties().apply()
def toggleRepresentationByName(name):
for rep in getRepresentations():
if rep.getName() == name:
rep.setHidden(not rep.isHidden())
getMainControl().update(rep)
def toggleSelectionByExpression(expression):
if len(getSelection()) == 0:
getMolecularControl().applySelector(expression)
else:
getMainControl().clearSelection()
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