Package AutoDockTools :: Module autotorsCommands

Module autotorsCommands


This Module facilitates selecting and formatting a ligand for a subsequent 
AutoDock run.  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.

Classes

[hide private]

AtorsMoleculeChooser
allows user to choose as ligand a molecule already in the viewer

AtorsReader
allows user to select a file for the ligand via a file browser

Ators4MoleculeChooser
allows user to choose as ligand a molecule already in the viewer

Ators4Reader
allows user to select a file for the ligand via a file browser

AtorsRefWriter
allows user to prepare a reference file for the ligand

RigidMolecule
allows user to write molecule with ROOT, ENDROOT + TORSDOF 0 added

RigidMolecule4
allows user to write molecule with ROOT, ENDROOT + TORSDOF 0 added

AUTOTORSWriter
allows user to select and write an output file for the formatted ligand for AutoDock3

AUTOTORS4Writer
allows user to select and write an output file for the formatted ligand for AutoDock4 ADD PDBQTWriter switch here-->>>

MarkRoot
shows current extent of root portion of the molecule:it includes all contiguous atoms starting with those adjacent to the designated root atom out to first active torsion

SelectRoot
allows user to pick an atom to be ROOT, the rigid portion of ligand which has rotatable BRANCHES

SetTorsionNumberGUICommand
provides gui to ADtors_setTorsionNumber to specified number to inactivate and whether to inactive those which move the fewest atoms or those which move the most

SetTorsionNumber
sets number of torsions to specified number by inactivating either those which move the fewest atoms or those which move the most.

AutoRoot
causes program to pick an atom to be ROOT: the one which has the smallest 'largest sub-tree'

SetRotatableBonds

DefiningRotatableBonds

SetBondRotatableFlag
set the flag that tells whether a bond is rotatable in aan AutoDock ligand

CheckAromatic
checks rings for planarity and changes carbons in planar rings to element type and name: 'A'

StopCheckAromatic
restores carbons in aromatic rings to element type 'C' and name: 'C...'

SetCarbonNames
toggles Carbon names between 'A' + 'C'

ChangeAromaticCutOff
allows user to change requirement for aromaticity of cycles: default is < 5 degrees between normals to adjacent atoms.

TogglerootSphere
lets user toggle rootSph visibility

AutoAutoTors
performs default actions on designated molecule

StopAutoTors
hides AutoToolsBar and makes rootSph invisible

AtorsInit
ADtors_init is DEPRECATED.

AtorsInitMol
ADtors_initLigand is DEPRECATED.

ProcessCharges
ADtors_processCharges is DEPRECATED.

ProcessBonds
ADtors_processBonds is DEPRECATED.

Functions

[hide private]

check_autotors_geoms(VFGUI)

enter_cb(event=None)

checkMolCharges(mol, vf)

set_autoMergeNPHS(name, oldval, newval)

initLPO(mol, mode='interactive', repairs="", root=0, outputfilename=None, cleanup='nphs_lps')

initLPO4(mol, mode='interactive', repairs="", root=0, outputfilename=None, cleanup='nphs_lps')

initModule(vf)

Variables

[hide private]

rootSph = <DejaVu.Spheres.Spheres> autotors_rootSph with 1 ver...

markSph = <DejaVu.Spheres.Spheres> autotors_markSph with 1 ver...

MAXTORS = 32

menuText = {'Rigid Molecule': 'Open as Rigid...(AD3)', 'MAmide'...

warningText = {'noAtorsMol': 'Sorry, you need to read or choose a ...

charge_errorfile = None

autoMergeNPHS = 1

AtorsMoleculeChooserGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AtorsReaderGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Ators4MoleculeChooserGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Ators4ReaderGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AtorsRefWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

RigidMoleculeGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

RigidMolecule4GUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AUTOTORSWriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AUTOTORS4WriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

MarkRootGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

SelectRootGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

SetTorsionNumberGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AutoRootGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

DefiningRotatableBondsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

CheckAromaticGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

StopCheckAromaticGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

SetCarbonNamesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

ChangeAromaticCutOffGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

TogglerootSphereGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AutoAutoTorsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details

[hide private]

check_autotors_geoms(VFGUI)

source code

None

enter_cb(event=None)

source code

None

checkMolCharges(mol, vf)

source code

None

set_autoMergeNPHS(name, oldval, newval)

source code

None

initLPO(mol, mode='interactive', repairs="", root=0, outputfilename=None, cleanup='nphs_lps')

source code

None

initLPO4(mol, mode='interactive', repairs="", root=0, outputfilename=None, cleanup='nphs_lps')

source code

None

initModule(vf)

source code

None

Variables Details

[hide private]

rootSph

None

Value:

<DejaVu.Spheres.Spheres> autotors_rootSph with 1 vertices

markSph

None

Value:

<DejaVu.Spheres.Spheres> autotors_markSph with 1 vertices

MAXTORS

None

Value:

menuText

None

Value:

{'AromaticCarbonsMB': 'Aromatic Carbons',
 'AutoTorsMB': 'Ligand',
 'AutomaticAutotorsSetupMB': 'Quick Setup...',
 'Automatically': 'Detect Root...',
 'ByPicking': 'Choose Root...',
 'ChangeAromaticityCriteria': 'Aromaticity Criterion...',
 'Choose Molecule': 'Choose...(AD3)',
 'Choose Molecule4': 'Choose...',
...

warningText

None

Value:

{'noAtorsMol': 'Sorry, you need to read or choose a molecule first.\n\
nUse either:\n\nLigand:\n    Input:\n      Open...\n  or\n      Choose
...',
 'noMolecule': 'Sorry, you need to read in a molecule first.\n\nUse th
e menu\n\n"Ligand:\n Input\n  :Open...".'}

charge_errorfile

None

Value:

None

autoMergeNPHS

None

Value:

AtorsMoleculeChooserGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb750fdac>

AtorsReaderGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb750fdec>

Ators4MoleculeChooserGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb750fe0c>

Ators4ReaderGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb750fe6c>

AtorsRefWriterGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb750feec>

RigidMoleculeGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb750ff4c>

RigidMolecule4GUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb750ffac>

AUTOTORSWriterGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d02c>

AUTOTORS4WriterGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d08c>

MarkRootGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d0ec>

SelectRootGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d16c>

SetTorsionNumberGUICommandGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d22c>

AutoRootGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d2ec>

DefiningRotatableBondsGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d42c>

CheckAromaticGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d4ac>

StopCheckAromaticGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d50c>

SetCarbonNamesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d58c>

ChangeAromaticCutOffGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d5ec>

TogglerootSphereGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d68c>

AutoAutoTorsGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb751d78c>

commandList

None

Value:

[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb750fe6c>
,
  'name': 'ADtors4_readLigand'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb750fe0c>
,
  'name': 'ADtors4_chooseLigand'},
...