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#$Id: autogridPage.py 265 2016-02-14 20:36:28Z sarkiss $
"""AutoGridPage.py contains the following classes.
"""
import wx, os, glob
from wx.lib.buttons import ThemedGenBitmapTextButton
from enthought import tvtk
import runProcess
import utils
from AutoDockTools.GridParameters import GridParameters
from vsModel import autodockPreferencesPage, autodockRemotePreferencesPage
from time import strftime
scale_factor = 1.3 #used to scale the search box
class RunAutoGrid(wx.Panel):
def __init__(self, parent):
self.flagRunAutoGrid = False
wx.Panel.__init__(self, parent, -1)
sizer = wx.BoxSizer(wx.VERTICAL)
topSizer = wx.BoxSizer(wx.HORIZONTAL)
listBoxSizer = wx.BoxSizer(wx.VERTICAL)
listBoxSizer.Add(wx.StaticText(self, -1, "AutoDock Elements:"), 0, wx.LEFT, 10)
self.listBox = wx.ListBox(self, style=wx.BORDER_SUNKEN)
listBoxSizer.Add(self.listBox, 1, wx.EXPAND)
topSizer.Add(listBoxSizer, 1, wx.EXPAND)
listBoxSizer = wx.BoxSizer(wx.VERTICAL)
#listBoxSizer.Add(wx.StaticText(self, -1, "Grid Parameters:"), 0, 5, wx.ALL)
from boxUI import AutoGirdBoxUI
boxWidget = AutoGirdBoxUI()
# grid = GridUI()
# self.grid = grid
view = boxWidget.View()
boxUI = view.ui(boxWidget, self, kind='subpanel')
self.comboBox = wx.ComboBox(self, id=wx.ID_ANY, style=wx.CB_READONLY)
listBoxSizer.Add(self.comboBox, 0, wx.EXPAND)
listBoxSizer.Add(boxUI.control, 1, wx.EXPAND)
topSizer.Add(listBoxSizer, 1, wx.EXPAND)
sizer.Add(topSizer, 1, wx.EXPAND, wx.ALIGN_BOTTOM)
self.forwardButton = wx.Button(self, wx.ID_FORWARD, "")
self.backButton = wx.Button(self, wx.ID_BACKWARD, "")
bitmap = wx.ArtProvider_GetBitmap(wx.ART_EXECUTABLE_FILE, wx.ART_BUTTON)
runAutoGridButton = ThemedGenBitmapTextButton(self, -1, bitmap, "Run AutoGrid")
buttonSizer = wx.BoxSizer(wx.HORIZONTAL)
lin = wx.StaticLine(self)
buttonSizer.Add(runAutoGridButton, 0)
buttonSizer.Add((150, -1), 1, flag=wx.EXPAND | wx.ALIGN_RIGHT)
buttonSizer.Add(self.backButton, 0, wx.ALIGN_RIGHT)
buttonSizer.Add(self.forwardButton, 0, wx.ALIGN_RIGHT)
sizer.Add(lin,0,wx.EXPAND)
sizer.Add(buttonSizer, 0, wx.EXPAND|wx.ALIGN_BOTTOM)
self.SetSizer(sizer)
self.Bind(wx.EVT_BUTTON, self.Next, self.forwardButton)
self.Bind(wx.EVT_BUTTON, self.Back, self.backButton)
self.Bind(wx.EVT_BUTTON, self.Run, runAutoGridButton)
self.Bind(wx.EVT_COMBOBOX, self.OnMacromoleculeChanged, self.comboBox)
#self.Bind(wx.EVT_SHOW, self.SetActive)
self.frame = self.TopLevelParent
self.vsModel = self.frame.vsModel
boxWidget.set(interactor=self.frame.mayaviEngine.scene.interactor)
boxWidget.set(place_factor=1)
boxWidget.rotation_enabled = False
boxWidget.key_press_activation = False
boxWidget.add_observer("InteractionEvent", boxWidget.ChangeBox)
self.boxWidget = boxWidget
def SetActive(self, event):
"This method is bound to wx.EVT_SHOW, i.e., invoked when this page is shown"
#check if ligand_types are set
if not self.frame.autodockWiz.selectMoleculesPage.ligandPass or not hasattr(self.vsModel,'ligands'):
self.frame.autodockWiz.selectMoleculesPage.Next(None)
dlg = wx.MessageDialog(self, "Please select a ligand!",'A Message Box',
wx.OK| wx.ICON_EXCLAMATION)
dlg.ShowModal()
dlg.Destroy()
wx.CallAfter(self.Parent.SetSelection, 1)
return
#check if macromoleculePath is set
if not self.frame.autodockWiz.selectMoleculesPage.macromoleculePass:
dlg = wx.MessageDialog(self, "Please select macromolecule!",'A Message Box',
wx.OK| wx.ICON_EXCLAMATION)
dlg.ShowModal()
dlg.Destroy()
wx.CallAfter(self.Parent.SetSelection, 2)
return
self.comboBox.Clear() #clears drop-down menu
self.flagRunAutoGrid = False
macromoleculePaths = self.frame.autodockWiz.selectMoleculesPage.macromoleculePaths
self.macromolecules = []
for macromoleculePath in macromoleculePaths:
tmp, ext = os.path.splitext(macromoleculePath)
basePath, molName = os.path.split(tmp)
if not molName in self.frame.molNav.moleculesNames:
macromolecule = self.frame.molNav.TryOpenMolecule(macromoleculePath)[0]
else:
index = self.frame.molNav.moleculesNames.index(molName)
macromolecule = self.frame.molNav.molecules[index]
self.macromolecules.append(macromolecule)
macromolecule.receptorFolder = basePath
macromolecule.receptor_filename = molName+ext
macromolecule.receptor_filename = macromolecule.receptor_filename.encode()
macromolecule.receptor_stem = molName.encode()
flexPath = os.path.join(basePath, molName.replace("_rigid","")+"_flex.pdbqt")
if os.path.exists(flexPath): #add flex residue atom types
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
from MolKit.pdbParser import PdbqtParser
parser = PdbqtParser(flexPath)
molecules = parser.parse()
ad4_typer = AutoDock4_AtomTyper()
ad4_typer.setAutoDockElements(molecules[0])
self.vsModel.ligand_types = self.vsModel.ligand_types.union(set(molecules[0].allAtoms.autodock_element))
if not hasattr(macromolecule, 'AD_max_XDimension'): #AD_max_XDimensionr is an arbitrary attribute which is set below
center = macromolecule.getCenter()
macromolecule.box_center = center
macromolecule.X_center, macromolecule.Y_center, macromolecule.Z_center = center
macromolecule.initCenter = tuple(center)
bounds = macromolecule.assembly.GetBounds()
macromolecule.spacing = macromolecule.initSpacing = self.boxWidget.initSpacing
macromolecule.AD_X_dimension = macromolecule.AD_max_XDimension = int(abs(bounds[1]-bounds[0])/self.boxWidget.initSpacing*scale_factor)
macromolecule.AD_Y_dimension = macromolecule.AD_max_YDimension = int(abs(bounds[3]-bounds[2])/self.boxWidget.initSpacing*scale_factor)
macromolecule.AD_Z_dimension = macromolecule.AD_max_ZDimension = int(abs(bounds[5]-bounds[4])/self.boxWidget.initSpacing*scale_factor)
macromolecule.initDimension = (macromolecule.AD_X_dimension,macromolecule.AD_Y_dimension,macromolecule.AD_Z_dimension)
self.comboBox.Append(macromolecule.name, macromolecule)
#check if we have grid maps
mapFiles = glob.glob(basePath+os.sep+'*.map')
if mapFiles:
if not self.vsModel.ligand_types: #not sure if this is needed?
self.vsModel.ligand_types = set(['A', 'C', 'HD', 'NA', 'OA', 'N'])
for ligandType in self.vsModel.ligand_types:
str = os.path.join(basePath, molName+'.'+ligandType+'.map')
if not os.path.exists(str):
self.flagRunAutoGrid = True
break
gpf = os.path.join(basePath, molName+'.gpf')
if os.path.exists(gpf):
#get box dimension from the previous run
gpm = GridParameters()
gpm.read4(os.path.join(basePath, molName+'.gpf'))
gridcenter = gpm.data['gridcenter']['value']
if gridcenter != 'auto':
macromolecule.box_center = gridcenter
macromolecule.X_center, macromolecule.Y_center, macromolecule.Z_center = gridcenter
macromolecule.spacing = gpm.data['spacing']['value']
dim = gpm.data['npts']['value']
macromolecule.X_dimension = dim[0]
macromolecule.Y_dimension = dim[1]
macromolecule.Z_dimension = dim[2]
else:
self.flagRunAutoGrid = True
else:
self.flagRunAutoGrid = True
self.listBox.Set(list(self.vsModel.ligand_types))
#activate 3D Graphics tab
self.frame.view.SetSelection(self.frame.view.GetPageIndex(self.frame.canvas3D))
#select first macromolecule and setup boxWidget
self.select_macromolecule = self.macromolecules[0]
self.comboBox.SetValue(self.select_macromolecule.name)
self.boxWidget.X_center = self.select_macromolecule.X_center
self.boxWidget.Y_center = self.select_macromolecule.Y_center
self.boxWidget.Z_center = self.select_macromolecule.Z_center
self.boxWidget.X_dimension = self.select_macromolecule.AD_X_dimension
self.boxWidget.Y_dimension = self.select_macromolecule.AD_Y_dimension
self.boxWidget.Z_dimension = self.select_macromolecule.AD_Z_dimension
self.boxWidget.max_XDimension = self.select_macromolecule.AD_max_XDimension
self.boxWidget.max_YDimension = self.select_macromolecule.AD_max_YDimension
self.boxWidget.max_ZDimension = self.select_macromolecule.AD_max_ZDimension
self.boxWidget.initCenter = self.select_macromolecule.initCenter
self.boxWidget.initDimension = self.select_macromolecule.initDimension
self.boxWidget.spacing = self.select_macromolecule.spacing
self.boxWidget.enabled = True
self.frame.canvas3D.Refresh()
def OnMacromoleculeChanged(self, event):
"Called when an item on the Macromolecule ComboBox list is selected"
cb = event.GetEventObject()
data = cb.GetClientData(event.GetSelection())
self.UpdateMacromoleculeBox()
#update boxWidget with settings from currenty selected macromolecule
self.boxWidget.X_center = data.X_center
self.boxWidget.Y_center = data.Y_center
self.boxWidget.Z_center = data.Z_center
self.boxWidget.X_dimension = data.AD_X_dimension
self.boxWidget.Y_dimension = data.AD_Y_dimension
self.boxWidget.Z_dimension = data.AD_Z_dimension
self.boxWidget.initDimension = data.initDimension
self.boxWidget.spacing = data.spacing
self.select_macromolecule = data
self.boxWidget.max_XDimension = self.select_macromolecule.AD_max_XDimension
self.boxWidget.max_YDimension = self.select_macromolecule.AD_max_YDimension
self.boxWidget.max_ZDimension = self.select_macromolecule.AD_max_ZDimension
self.boxWidget.initCenter = self.select_macromolecule.initCenter
def UpdateMacromoleculeBox(self):
#copy current boxWidget's settings for previously selected macromolecule
self.select_macromolecule.X_center = self.boxWidget.X_center
self.select_macromolecule.Y_center = self.boxWidget.Y_center
self.select_macromolecule.Z_center = self.boxWidget.Z_center
self.select_macromolecule.AD_X_dimension = self.boxWidget.X_dimension
self.select_macromolecule.AD_Y_dimension = self.boxWidget.Y_dimension
self.select_macromolecule.AD_Z_dimension = self.boxWidget.Z_dimension
def Next(self, event):
"Goto next page"
self.UpdateMacromoleculeBox()
if self.flagRunAutoGrid:
self.Run(None)
else:
self.Parent.SetSelection(3)
self.boxWidget.enabled = False
def Back(self, event):
"Goto previous page"
self.Parent.SetSelection(1)
self.boxWidget.enabled = False
def Run(self, event):
self.UpdateMacromoleculeBox()
self.frame.TryCommand(self.TryRun, None)
def TryRun(self, event):
self.macromolecules_count = len(self.macromolecules)
for macromolecule in self.macromolecules:
gridParameters = {}
gridParameters['npts'] = str(macromolecule.AD_X_dimension)+','
gridParameters['npts'] += str(macromolecule.AD_Y_dimension)+','
gridParameters['npts'] += str(macromolecule.AD_Z_dimension)
gridParameters['gridcenter'] = [macromolecule.X_center,
macromolecule.Y_center,
macromolecule.Z_center]
gridParameters['spacing'] = macromolecule.spacing
executionMode = self.frame.autodockWiz.startPage.runAutoDockOptions[autodockPreferencesPage.executionMode]
if not executionMode == "Remote (Opal Web Services)" and not utils.which(autodockPreferencesPage.autogrid):
dlg = wx.MessageDialog(self, "Cannot find "+autodockPreferencesPage.autogrid+
"\n\n. Use Edit -> Preferences to set AutoGrid path.", 'Command not found.', wx.OK| wx.ICON_EXCLAMATION)
dlg.ShowModal()
dlg.Destroy()
return
self.vsModel.macromolecule = macromolecule
self.vsModel.PrepareGPF(gridParameters=gridParameters)
autodock_elements = ""
for item in list(self.vsModel.ligand_types):
autodock_elements += str(item) +" "
args = (macromolecule.name, len(macromolecule.allAtoms), strftime("%Y.%m.%d %H:%M:%S"),autodock_elements)
if not hasattr(self.frame.dbView, 'targetsTable'):
self.frame.dbView.Activate(None)
self.frame.dbView.targetsTable.AddItem(args, deleteOnFirstMatch=True)
if executionMode == "Remote (Opal Web Services)":
self.processPanel = self.frame.autodockWS.GetAutogridWSPanel(self.GrandParent, self.CheckResults)
else:
if self.Parent.GetPage(0).rb.GetSelection() == 0:
if os.path.exists(self.vsModel.glgOutput):
os.remove(self.vsModel.glgOutput)
self.processPanel = runProcess.ProcessPanel(self.GrandParent, self.vsModel.gridCommand,
macromolecule.receptorFolder, self.vsModel.glgOutput, self.CheckResults)
else:
import pbsJobs
if not pbsJobs.startAutogrid(self):
return
if macromolecule == self.macromolecules[-1]:
return
else:
continue
self.frame.view.AddPage(self.processPanel, "Run AutoGrid "+macromolecule.name, select=True)
self.processPanel.Start()
self.frame.statusBar.SetStatusText("Running AutoGrid. Please Wait...", 0)
self.frame.autodockWiz.book.Disable()
def CheckResults(self, page, outputFile=None, success=False):
self.frame.view.DeletePage(self.frame.view.GetPageIndex(page))
self.macromolecules_count -= 1
if success:
documentsView = self.frame.documentsView
documentsView.ClosePath(outputFile) #to avoid "...has been modified outside of..." message from wx.lib.docview
documentsView.OpenDocument(outputFile)
textCtrl = documentsView._docManager.GetCurrentView()._textCtrl
wx.CallAfter(textCtrl.ScrollToEnd)
if textCtrl.GetText().find("Successful Completion") == -1:
self.frame.statusBar.SetStatusText("Unsuccessful AutoGrid Completion. See Log File for Details. ", 0)
else:
self.frame.statusBar.SetStatusText("Successful AutoGrid Completion.", 0)
if self.macromolecules_count < 1:
self.Parent.SetSelection(3)
self.frame.autodockNav.RefreshMacroolecules()
self.boxWidget.enabled = False
self.frame.autodockWiz.book.Enable()
else:
self.frame.statusBar.SetStatusText("AutoGrid run terminated.", 0)
self.boxWidget.enabled = False
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