#############################################################################
#
# Author: Ruth HUEY, Michel F. SANNER
#
# Copyright: M. Sanner TSRI 2000
#
#############################################################################
#
# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/autotors4Commands.py,v 1.3 2009/02/10 17:44:05 rhuey Exp $
#
# $Id: autotors4Commands.py,v 1.3 2009/02/10 17:44:05 rhuey Exp $
#
#
#
#
#
#
#
"""
This Module facilitates selecting and formatting a ligand for a subsequent
AutoDock4.0 calculation. The steps in this process are:
* The user selects the small molecule from a list of molecules
already in the moleculeViewer OR as a PDBQ file, a PDB file or
a MOL2 file from a fileBrowser.
* The user selects the ROOT atom of the ligand either:
o by picking it or
o by autoroot which sets the root to be the atom in the
molecule which has the smallest 'largest sub-tree.'
* Next the user decides which possible and active torsions he wants
to disallow, changing them from active to inactive. This is done by picking
an active 'green' bond which turns it inactive or 'purple'. This is
reversible. The user can also disallow all peptide backbone torsions and/or
all torsions of amide bonds.
* Carbons in cycles can be tested for aromaticity. If the angle
between the normals to adjacent atoms in the cycle is less than 7.5 Degrees,
the cycle is considered aromatic: its carbons are renamed "A.." and their
element type set to 'A'. (This is for the force-field calculations done
in AutoDock.) This Module does this conversion reversibly. Also, the user
is able to select a carbon to convert (reversibly) and he can change the
the value of the aromaticity cut-off.
* Non-polar hydrogens and lone pairs are merged which means that the charge of
each is added to its heavy atom and the hydrogen atoms themselves are not written
in the output file, thus in some sense 'removing' them from the molecule.
'Fewer' atoms simplifies the AutoDock run.
* The last function of this Module is to write a file which contains
the correctly formatted ligand atoms. The ROOT section of the molecule
expands from the selected ROOT atom out to include all atoms adjacent to it
up to the first active torsion. The active torsions set the position of
BRANCH key words in the output pdbq file (and their corresponding
ENDBRANCH key words). These keywords are nested to set up a
Breadth-First Order Traversal. Autotors also calculates the torsional degrees
of freedom (TORSDOF) which is the number of possible torsions less the number of
symmetry-equivalent torsions (such as a bond to a NH3). This key word is the
last line of the pdbq file.
"""
import Tkinter
from ViewerFramework.VFCommand import CommandGUI
from AutoDockTools.autotorsCommands import rootSph, markSph,\
menuText, AtorsMoleculeChooser, MAXTORS, AdtSetMode,\
AtorsReader, Ators4MoleculeChooser, Ators4Reader, AtorsRefWriter, \
RigidMolecule, RigidMolecule4, AUTOTORSWriter, AUTOTORS4Writer, \
MarkRoot, SelectRoot, SetTorsionNumberGUICommand, SetTorsionNumber, \
AutoRoot, SetRotatableBonds, DefiningRotatableBonds, SetBondRotatableFlag,\
CheckAromatic, StopCheckAromatic, SetCarbonNames, ChangeAromaticCutOff, \
TogglerootSphere, AutoAutoTors, StopAutoTors, AtorsInit, AtorsInitMol, \
ProcessCharges, ProcessBonds, rootSph, markSph, check_autotors_geoms,\
MAXTORS, menuText, warningText, checkMolCharges,\
autoMergeNPHS, set_autoMergeNPHS
Ators4MoleculeChooserGUI=CommandGUI()
Ators4MoleculeChooserGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'], menuText['Choose Molecule4'], cascadeName = menuText['Input Molecule'])
Ators4ReaderGUI = CommandGUI()
Ators4ReaderGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'], menuText['Read Molecule4'], cascadeName = menuText['Input Molecule'])
AtorsRefWriterGUI = CommandGUI()
AtorsRefWriterGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'], menuText['Ref Molecule'], cascadeName = menuText['Input Molecule'])
RigidMolecule4GUI = CommandGUI()
RigidMolecule4GUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'], menuText['Rigid Molecule4'], cascadeName = menuText['Input Molecule'])
AUTOTORS4WriterGUI=CommandGUI()
AUTOTORS4WriterGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'], menuText['WritePDBQTMB'],
cascadeName = menuText['WriteMB'])
MarkRootGUI=CommandGUI()
MarkRootGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'], menuText['SRA1'],
cascadeName = menuText['DefineRigidRootMB'])
SelectRootGUI=CommandGUI()
SelectRootGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['ByPicking'], cascadeName = menuText['DefineRigidRootMB'])
SetTorsionNumberGUICommandGUI=CommandGUI()
SetTorsionNumberGUICommandGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['SetTorsionNumber'], cascadeName = menuText['DefineRigidRootMB'] )
AutoRootGUI=CommandGUI()
AutoRootGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['Automatically'], cascadeName = menuText['DefineRigidRootMB'])
DefiningRotatableBondsGUI = CommandGUI()
DefiningRotatableBondsGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['DefineRotatableBonds'], cascadeName = menuText['DefineRigidRootMB'])
CheckAromaticGUI = CommandGUI()
CheckAromaticGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['RenameAromaticCarbons'], cascadeName = menuText['AromaticCarbonsMB'])
StopCheckAromaticGUI = CommandGUI()
StopCheckAromaticGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['RestoreAliphaticCarbons'], cascadeName = menuText['AromaticCarbonsMB'])
SetCarbonNamesGUI = CommandGUI()
SetCarbonNamesGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['SetCarbonNames'], cascadeName = menuText['AromaticCarbonsMB'])
ChangeAromaticCutOffGUI=CommandGUI()
ChangeAromaticCutOffGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['ChangeAromaticityCriteria'], cascadeName = menuText['AromaticCarbonsMB'])
TogglerootSphereGUI=CommandGUI()
TogglerootSphereGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'],\
menuText['ShowAutotorsRootSphMB'], cascadeName = menuText['DefineRigidRootMB'])
AutoAutoTorsGUI=CommandGUI()
AutoAutoTorsGUI.addMenuCommand('AutoTools4Bar', menuText['AutoTorsMB'], \
menuText['AutomaticAutotorsSetupMB'], cascadeName = menuText['Input Molecule'])
commandList = [
{'name':'AD4tors_readLigand','cmd':Ators4Reader(),
'gui':Ators4ReaderGUI},
{'name':'AD4tors_chooseLigand','cmd':Ators4MoleculeChooser(),
'gui':Ators4MoleculeChooserGUI},
{'name':'AD4tors_rigidLigand','cmd':RigidMolecule4(),
'gui':RigidMolecule4GUI},
{'name':'AD4tors_automaticLigandFormatting','cmd':AutoAutoTors(),
'gui':AutoAutoTorsGUI},
# {'name':'AD4tors_writeRef','cmd':AtorsRefWriter(),
# 'gui':AtorsRefWriterGUI},
{'name':'AD4tors_setRoot','cmd':SelectRoot(),'gui':SelectRootGUI},
{'name':'AD4tors_autoRoot','cmd':AutoRoot(),'gui':AutoRootGUI},
# {'name':'AD4tors_addChainToRootGC','cmd':AddChainToRootGUICommand(),
# 'gui':AddChainToRootGUICommandGUI},
# {'name':'AD4tors_addChainToRoot','cmd':AddChainToRoot(),'gui':None},
# {'name':'AD4tors_removeChainFromRootGC','cmd':RemoveChainFromRootGUICommand(),
# 'gui':RemoveChainFromRootGUICommandGUI},
# {'name':'AD4tors_removeChainFromRoot','cmd':RemoveChainFromRoot(),'gui':None},
{'name':'AD4tors_markRoot','cmd':MarkRoot(),'gui':MarkRootGUI},
{'name':'AD4tors_showRootSphere','cmd':TogglerootSphere(),
'gui':TogglerootSphereGUI},
{'name':'AD4tors_defineRotBonds', 'cmd':DefiningRotatableBonds(),
'gui':DefiningRotatableBondsGUI },
{'name':'AD4tors_limitTorsionsGC','cmd':SetTorsionNumberGUICommand(),
'gui':SetTorsionNumberGUICommandGUI},
## {'name':'AD4tors_changePlanarCarbonsToA','cmd':CheckAromatic(),
## 'gui':CheckAromaticGUI},
## {'name':'AD4tors_changeAromaticCarbonsToC','cmd':StopCheckAromatic(),
## 'gui':StopCheckAromaticGUI},
{'name':'AD4tors_setCarbonNames','cmd':SetCarbonNames(),
'gui':SetCarbonNamesGUI},
{'name':'AD4tors_changePlanarityCriteria','cmd':ChangeAromaticCutOff(),
'gui':ChangeAromaticCutOffGUI},
{'name':'AD4tors_writeFormattedPDBQT','cmd':AUTOTORS4Writer(),
'gui':AUTOTORS4WriterGUI},
]
def initModule(vf):
for dict in commandList:
vf.addCommand(dict['cmd'],dict['name'],dict['gui'])
if not hasattr(vf, 'ADTSetMode'):
vf.addCommand(AdtSetMode(), 'ADTSetMode')
if not hasattr(vf, 'ADtors_limitTorsions'):
vf.addCommand(SetTorsionNumber(), 'ADtors_limitTorsions')
if not hasattr(vf, 'ADtors_setBondRotatableFlag'):
vf.addCommand(SetBondRotatableFlag(), 'ADtors_setBondRotatableFlag')
if not hasattr(vf, 'ADtors_stop'):
vf.addCommand(StopAutoTors(), 'ADtors_stop')
if vf.hasGui:
vf.GUI.menuBars['AutoTools4Bar']._frame.config( {'background':'tan'})
for item in vf.GUI.menuBars['AutoTools4Bar'].menubuttons.values():
item.configure(background = 'tan')
if not hasattr(vf.GUI, 'adt4Bar'):
vf.GUI.adt4Bar = vf.GUI.menuBars['AutoTools4Bar']
vf.GUI.adt4Frame = vf.GUI.adt4Bar.menubuttons.values()[0].master
if not hasattr(vf.GUI, 'adt4ModeLabel'):
mbs = {}
packing_list = []
for c in vf.GUI.adt4Frame.children.values():
if isinstance(c, Tkinter.Menubutton):
mbs[c.cget('text')] = c
packing_list.append(c.cget('text'))
c.pack_forget()
vf.GUI.adt4ModeLabel=Tkinter.Label(vf.GUI.adt4Frame, text="ADT4.0", width=6,
relief='sunken', borderwidth=1, fg='DarkGreen',
bg = 'ivory',anchor='w' )
vf.GUI.adt4ModeLabel.pack(side='left')
vf.GUI.adt4ModeLabel.bind("<Double-Button-1>", vf.ADTSetMode.guiCallback())
for t in packing_list:
try:
c = mbs[t]
c.pack(side='left')
except:
pass
# if not hasattr(vf.GUI, 'ligandLabel'):
# vf.GUI.ligandLabelLabel = Tkinter.Label(vf.GUI.adtFrame, \
# text="Ligand:", bg='tan')
# vf.GUI.ligandLabelLabel.pack(side='left')
# vf.GUI.ligandLabel=Tkinter.Label(vf.GUI.adtFrame, text="None", width=4,
# relief='sunken', borderwidth=1,
# anchor='w' )
# vf.GUI.ligandLabel.pack(side='left')
