Python PyUtils類代碼示例

 def update(self, data = None):
     """Called whenever the curve list is updated. Make sure the curve editor list match the application curve list."""
     
     count = self._appCurveList.getCount()
     for i in range(count):
         inCurve = self._appCurveList.get(i)
         inTrajectory1d = inCurve.getTrajectory1d()
         try: 
             outTrajectory1d = self.getTrajectory(i)
             areSameObject = PyUtils.sameObject(inTrajectory1d, outTrajectory1d)
         except IndexError: 
             outTrajectory1d = None
             areSameObject = False        
         if not areSameObject:
             # Need to delete or insert
             # First, check how many curves we should delete
             delete = 1 
             try: 
                 while not PyUtils.sameObject( inTrajectory1d, self.getTrajectory(i+delete) ) :
                     delete += 1
             except IndexError:
                 delete = 0
         
             if delete > 0 :
                 # Delete the specified controllers
                 self._removeCurveEditors(i,i+delete)
             else :
                 # Insert the specified controller                                                        
                 self._insertCurveEditor(i, inCurve)
     
     # Delete any remaining controllers
     self._removeCurveEditors(count)    
     self.getParent().layout()

    def create(self):
        """Creates the instant character based on the available description. Attach a reasonable controller, if available."""       
        app = wx.GetApp()
        
        try:
            wrappedController = PyUtils.wrapCopy( app.getController(0) )
        except IndexError:
            wrappedController = None
                
        try:
            character = app.getCharacter(0)
            previousMass = character.getMass()
        except IndexError:
            previousMass = None
        
        
        app.deleteAllObjects()
        PyUtils.load( "RigidBodies.FlatGround" )
        character = self._characterDescription.createCharacter()
        character.computeMass()
        app.addCharacter(character)

        if wrappedController is not None:
            controller = wrappedController.createAndFillObject(None, character)
            if previousMass is not None:
                massRatio = character.getMass() / previousMass
                controller.scaleGains( massRatio )
            app.addController(controller)
            controller.setStance( Core.LEFT_STANCE )
            self.connectController()
        
        return character

 def load(self):
     assert not self._loaded, "Cannot load scenario twice!"
     
     self._loaded = True
     
     # Create the rigid bodies for the main staircase        
     orientation = PyUtils.angleAxisToQuaternion( (self._angle,(0,1,0)) )
     size = MathLib.Vector3d( self._staircaseWidth, self._riserHeight, self._threadDepth )
     pos = PyUtils.toPoint3d( self._position ) + MathLib.Vector3d( 0, -self._riserHeight/2.0, 0 )
     delta = MathLib.Vector3d(size)
     delta.x = 0
     delta = orientation.rotate( delta )
     for i in range(self._stepCount):
         box = PyUtils.RigidBody.createBox( size, pos = pos + delta * (i+1), locked = True, orientation=orientation )
         Physics.world().addRigidBody(box)
     
     # Create the rigid bodies for both ramps
     rampHeights = ( self._leftRampHeight, self._rightRampHeight )
     
     deltaRamp = MathLib.Vector3d(self._staircaseWidth/2.0,0,0)
     deltaRamp = orientation.rotate( deltaRamp )
     deltaRamps = (deltaRamp, deltaRamp * -1)
     for deltaRamp, rampHeight in zip( deltaRamps, rampHeights ):
         if rampHeight is None: continue
         deltaRamp.y = rampHeight/2.0
         box = PyUtils.RigidBody.createBox( (0.02,rampHeight,0.02), pos = pos + deltaRamp + delta , locked = True, orientation=orientation )
         Physics.world().addRigidBody(box)
         box = PyUtils.RigidBody.createBox( (0.02,rampHeight,0.02), pos = pos + deltaRamp + (delta * self._stepCount) , locked = True, orientation=orientation )
         Physics.world().addRigidBody(box)
         deltaRamp.y = rampHeight
         rampOrientation = orientation * PyUtils.angleAxisToQuaternion( (math.atan2(self._riserHeight, self._threadDepth), (-1,0,0)) )
         rampLen = self._stepCount * math.sqrt( self._riserHeight*self._riserHeight + self._threadDepth*self._threadDepth )
         box = PyUtils.RigidBody.createBox( (0.04,0.02,rampLen), pos = pos + deltaRamp + (delta * ((self._stepCount+1) * 0.5)) , locked = True, orientation=rampOrientation )
         Physics.world().addRigidBody(box)

    def saveController(self, event = None):
        """Save the currently selected controller"""
        controller = self._getSelectedController()
        if controller is None : return
        
        saveNumber = self._saveNumber
        if PyUtils.sameObject( self._lastSave[0], controller ) :
            if self._lastSave[2] is not None :
                saveNumber = self._lastSave[2]

        controllerName = controller.getName()
        dialogTitle = "Save %s Controller" % controllerName
        fileName = "%s_%d.py" % (controllerName, saveNumber)
        
        dialog = wx.FileDialog(self, dialogTitle, self._dirName, fileName, "*.py", wx.SAVE | wx.OVERWRITE_PROMPT )
        dialog.CenterOnScreen()
        if dialog.ShowModal() == wx.ID_OK:
            if saveNumber != self._saveNumber:
                self._lastSave = (None, None, None)
            else:
                self._lastSave = (controller, self._saveNumber, None)
                self._saveNumber += 1
            fileName=dialog.GetFilename()
            self._dirName=dialog.GetDirectory()
            pathName = os.path.join(self._dirName,fileName)
            file = open(pathName,'w')
            file.write( "from App.Proxys import *\n\ndata = %s" % PyUtils.fancify( PyUtils.serialize(controller)) )
            file.close()
        dialog.Destroy()

 def update(self, data = None):
     """Called whenever the tree is updated."""
     try: 
         tree = self._infoTree
         rootItem = tree.GetRootItem()
         nodeData = tree.GetItemPyData( rootItem )
         snapshot = nodeData.getObject().getCurrentSnapshot()
     except AttributeError: return
     
     if self._activeTreeItemId != None :
         currentSnapshot = tree.GetItemPyData( self._activeTreeItemId )
         if PyUtils.sameObject(currentSnapshot, snapshot) : return
         tree.SetItemBold( self._activeTreeItemId, False )
     
     # Look for the new item
     activeList = [tree.GetFirstChild(rootItem)[0]]
     while len(activeList) > 0 :
         treeItemId = activeList.pop()
         if not treeItemId.IsOk(): continue
         object = tree.GetItemPyData( treeItemId ).getObject()
         if PyUtils.sameObject(snapshot, object) :
             self._activeTreeItemId = treeItemId
             tree.SetItemBold( treeItemId, True )
             return
         activeList.append( tree.GetFirstChild(treeItemId)[0] )
         activeList.append( tree.GetNextSibling(treeItemId) )

    def update(self, object):
        """Adjusts the node's _subTreeItemIds list so that it matches an input object list.
        TreeItemId s will be deleted or inserted into _subTreeItemIds based on its current content and
        that of the input object list."""

        count = self._member.getCount(object)
        for i in range(count):
            inObject = self._member.getObject(object,i)
            try: 
                outObject = self.getObject(i)
                areSameObject = PyUtils.sameObject(inObject, outObject)
            except IndexError: 
                outObject = None
                areSameObject = False        
            if not areSameObject:
                # Need to delete or insert
                # First, check how many objects we should delete
                delete = 1 
                try: 
                    while not PyUtils.sameObject( inObject, self.getObject(i+delete) ) :
                        delete += 1
                except IndexError:
                    delete = 0
            
                if delete > 0 :
                    # Delete the specified objects
                    self.removeChildren(i,i+delete)
                else :
                    # Insert the specified object                                                        
                    self.insertChild(i, inObject)
        
        # Delete any remaining objects
        self.removeChildren(count)

def createBox( size=(1,1,1), position=(0,0,0), colour=(0.6,0.6,0.6) ):
    """
    Creates the mesh for a box having the specified size and a specified position.
    The size should be a 3-tuple (xSize, ySize, zSize).
    The position should be a 3-tuple.
    Colour should be a 3-tuple (R,G,B) or a 4-tuple (R,G,B,A)
    """
    
    size     = PyUtils.toVector3d(size)
    position = PyUtils.toPoint3d(position)
    vertices = []
    delta = MathLib.Vector3d()
    for repeat in range(3):
        for x in (-0.5,0.5) :
            delta.x = size.x * x
            for y in (-0.5,0.5) :
                delta.y = size.y * y
                for z in (-0.5,0.5) :
                    delta.z = size.z * z
                    vertices.append( position + delta )
    
    faces = [(0,1,3,2),(5,4,6,7),  # YZ Faces
             (9,13,15,11),(12,8,10,14),  # XY Faces
             (18,19,23,22),(17,16,20,21)]  # XZ Faces
    
    return create( vertices, faces, colour )

 def _addIndirectVar(self, varName, initialValue):
     """Add an indirect variable with the given name, as well as its getter and setter."""
     if isinstance(initialValue, _Symmetric) :
         self.__setattr__( PyUtils.getterName(varName), lambda side: self.getIndirectVarSymmetric(varName, side) )
     else:
         self.__setattr__( PyUtils.getterName(varName), lambda: self.getIndirectVar(varName) )
     self._indirectVarsAreValid = None
     self.__setattr__(varName, initialValue)

def DownloadPDBs(PDB_list_file):
    PDB_list = open(os.getcwd()+'/'+PDB_list_file,'r').readlines()
    for i in range(len(PDB_list)):
        PDBid = PDB_list[i].strip()
        PyUtils.create_folder(os.getcwd()+"/"+PDBid)
        os.chdir(PDBid)
        cmd = ["~/../scripts/pdbUtil/getPdb.pl"+" -id "+PDBid]
        subprocess.call(cmd,shell=True)
        os.chdir("..")

 def _addNativeVar(self, varName, initialValue):
     """Add a variable with he given name, as well as its getter and setter."""
     if isinstance(initialValue, _Symmetric) :
         self.__setattr__( PyUtils.getterName(varName), lambda side: self.getNativeVarSymmetric(varName, side) )
         self.__setattr__( PyUtils.setterName(varName), lambda side, value: self.setNativeVarSymmetric(varName, side, value) )
     else :
         self.__setattr__( PyUtils.getterName(varName), lambda: self.getNativeVar(varName) )
         self.__setattr__( PyUtils.setterName(varName), lambda value: self.setNativeVar(varName, value) )
     self.__setattr__( varName, initialValue )

    def __init__(self, rec, lig, cov, cov_index, HG):
        self.rec = rec
        self.lig = lig
	#self.folder = os.getcwd() + "/"
        self.folder = os.path.dirname(os.path.abspath(rec)) + "/"
        self.fixed_rec = self.folder + "rec.pdb"
        self.fixed_lig = self.folder + "xtal-lig.pdb"
        self.cov = cov
        self.cov_index = cov_index
        self.hg = HG
        PyUtils.initPythonVs()

def _createCylinder(proxy, axis, basePos, tipPos, radius, colour, moiScale, withMesh):
    """
    Private function.
    Use createCylinder() or createArticulatedCylinder() instead.
    """
    if axis != 0 and axis != 1 and axis != 2:
        raise ValueError("Axis must be 0 for x, 1 for y or 2 for z.")

    # Mesh and cdps will be set manually
    proxy.meshes = None
    proxy.cdps = None

    # Compute box moi
    moi = [0, 0, 0]
    height = math.fabs(tipPos - basePos)
    for i in range(3):
        if i == axis:
            moi[i] = proxy.mass * radius * radius / 2.0
        else:
            moi[i] = proxy.mass * (3 * radius * radius + height * height) / 12.0
        ### HACK!
        moi[i] = max(moi[i], 0.01)
    proxy.moi = PyUtils.toVector3d(moi) * moiScale

    cylinder = proxy.createAndFillObject()

    basePoint = [0, 0, 0]
    tipPoint = [0, 0, 0]
    basePoint[axis] = basePos
    tipPoint[axis] = tipPos
    basePoint3d = PyUtils.toPoint3d(basePoint)
    tipPoint3d = PyUtils.toPoint3d(tipPoint)
    baseToTipVector3d = Vector3d(basePoint3d, tipPoint3d)
    if baseToTipVector3d.isZeroVector():
        raise ValueError("Invalid points for cylinder: base and tip are equal!")
    baseToTipUnitVector3d = baseToTipVector3d.unit()

    if height <= radius * 2.0:
        cdp = Physics.SphereCDP()
        cdp.setCenter(basePoint3d + baseToTipVector3d * 0.5)
        cdp.setRadius(height / 2.0)
    else:
        cdp = Physics.CapsuleCDP()
        cdp.setPoint1(basePoint3d + baseToTipUnitVector3d * radius)
        cdp.setPoint2(tipPoint3d + baseToTipUnitVector3d * -radius)
        cdp.setRadius(radius)

    cylinder.addCollisionDetectionPrimitive(cdp)

    if withMesh:
        mesh = Mesh.createCylinder(basePoint, tipPoint, radius, colour)
        cylinder.addMesh(mesh)

    return cylinder

 def __init__(self, rec, lig, cov, cov_index, HG, tart=False):
     self.tart = bool(tart)
     self.rec = rec
     self.lig = lig
     self.folder = os.path.dirname(os.path.abspath(rec)) + "/"
     self.fixed_rec = self.folder + "rec.pdb"
     self.fixed_lig = self.folder + "xtal-lig.pdb"
     self.cov = cov
     self.cov_index = cov_index
     self.hg = HG
     PyUtils.initPythonVs()

    def __init__(self, folder_name, compound, library = False):
	self.folder = os.getcwd() + "/"
        self.name = self.folder + folder_name + "/"
        #self.compound = os.path.abspath(compound)[5:]
        self.compound = compound
        self.library = library
        PyUtils.create_folder(self.name)
        self.copyIndock()
        self.softlink()
        os.chdir(self.name)
        self.dock_command = Paths.DOCKBASE + "docking/DOCK/src/i386/dock64"
        self.DOCK()

 def poses2pdb(self):
     PyUtils.create_folder('recs')
     os.chdir('poses')
     for k in range(1, len(os.listdir(os.getcwd())) + 1):
         i = str(k) + '.mol2'
         surface = PYMOLUtils.get_surface_area(i)
         with open(i, 'r') as f_mol:
             for line in f_mol:
                 if 'SMILES' in line:
                     smile_line = line.split()[2]
                 if 'heavy atom count' in line:
                     heavy_atoms = int(line.split()[-1])
                     break
         if surface < 200 or surface / heavy_atoms < 14.5:
             self.counters.append(0)
             continue
         if '[N+](=O)[O-]' in smile_line or smile_line.count('N') + smile_line.count('O') + smile_line.count('n') + smile_line.count('o') > 4:
             self.counters.append(0)
             continue
         pdb_pose = '../recs/' + i[:-4] + 'pdb'
         subprocess.call(['convert.py', i, pdb_pose])
         hetatm = []
         with open(pdb_pose, 'r') as f_pdb:
             for line in f_pdb:
                 if 'HETATM' in line:
                     hetatm.append(line[:23] + ' -1' + line[26:])
         rec_pose = '../recs/rec_' + i[:-4] + 'pdb'
         with open(rec_pose, 'w') as f_rec:
             for line in hetatm:
                 f_rec.write(line)
             for line in self.rec_lines:
                 f_rec.write(line)
         sub_command = []
         for res_l in self.res_list:
             sub_command.append('-seed_residue')
             sub_command.append(str(res_l))
         subprocess.call(['python', Paths.SCRIPTS + 'HBonanza.py', '-trajectory_filename', rec_pose, '-hydrogen_bond_distance_cutoff', '3.0', '-hydrogen_bond_angle_cutoff', '30', '-seed_residue', '-1'] + sub_command + ['-just_immediate_connections', 'true'], stdout=open(os.devnull, 'w'))
         os.remove(rec_pose + '.average_hbonds')
         os.remove(rec_pose + '.frame_by_frame_hbonds.csv')
         if os.path.isfile(rec_pose + '.hbond_averages_in_occupancy_column.pdb'):
             os.remove(rec_pose + '.hbond_averages_in_occupancy_column.pdb')
             counter = self.countHbonds(rec_pose + '.HBonds')
         else:
             counter = 0
         self.counters.append(counter)
         os.remove(rec_pose)
     os.chdir('../')
     shutil.rmtree('recs')
     shutil.rmtree('poses')