Package AutoDockTools :: Module autogpfCommands

Module autogpfCommands

This Module facilitates producing a grid parameter file for AutoGrid. The steps in this process are:

* 'Macromolecule': Selecting the macromolecule:
The user can select the macromolecule for autogpf in two ways:
- it can be chosen from molecules previously added to the moleculeViewer
- it can be read in from a file:

o Choose Macromol...

o Read Macromolecule

* 'Set Map Types': Setting the types of maps to generate:

o Set Map Types Directly

o By Choosing Ligand

o By Reading Formatted File

The user can change the types of maps to be calculated.
He decides which types of possible hydrogen bonding he wishes to model.
For instance, IF hydrogens are present AND nitrogens, oxygens and /or sulfurs,
the user can decide to model N-H bonds, O-H bonds and/or S-H bonds.
He sets which type of dielectric to use:
-distance-dependent dielectric
-constant dielectric
(Other ligand-related commands allow the user to set energy parameters for new
atom types or to set up a specialized 'covalent' grid-map.)

* 'Set Grid': The user positions the grid and sets its dimensions by:

o Setting the center of the grid maps:

- by picking an atom or

- by entering the full-name of an atom or

- by entering the desired coordinates in entries 'x center', 'y center',
'z center' (NB: ALL entries must be 'activated' by a 'Return')

- by choosing the 'Center on Macromolecule' option which sets the
center of the grid to the geometric center of the macromolecule (obtained by
averaging all its coordinates)

- by choosing the 'Center on Ligand' option which sets the center of
the grid to the geometric center of the ligand (obtained by averaging all its
coordinates)

o Setting the number of grid points in each direction (which has to be an
even number) and the spacing between the points. This is done by using the
corresponding scale widgets.

o Adjusting the position of the grid using scales for x-offset, y-offset
and z-offset. These scales allow the user to move the grid box up to 10 angstroms
in any direction along any of the three axes.
(NOTE that the units of these scales are tenths of Angstroms and the new coordinates
of the center are reflected in the x-center, y-center, z-center entries)

* 'Set Other Options': The user adjusts these additional parameters:

o the smoothing factor can be changed from its default 0.5Angstrom value.
This changes the radius of the area within which the minimum energy is stored.
o electrostatic potential map may or may not be generated by AutoGrid

o floating point potential map may or may not be generated

o the user may decide whether or not to use the default distance dependent
dielectric constant. If not, he can enter his desired dielectric constant or use
the default value, 40. It should be noted that this entered value is multiplied
by 0.1146 by the program for input to AutoGrid.

* 'Write GPF': The results of the previous steps are written to a file.
The user selects a filename via a filebrowser. By convention, the file should
have a .gpf extension. If no macromolecule has been selected, it is not possible
to write a grid parameter file and the user gets a warning message to that effect.
Likewise, the types of the maps to be calculated must be set before the grid
parameter file is written and a warning message to this effect appears if the
types have not been set.

* 'Edit GPF': Allows user to edit a grid parameter file. If one has been
written, it is automatically loaded. Otherwise, the user can select any *.gpf
file to edit from a file browser.

Classes

[hide private]

GpfSetGpo
Command to set values in gpo object using gui input results

GpfLoadDefaults
allows user to select a file containing a set of defaults

GpfMacroInit
AD3 receptor is initialized as specified in parameters: autodock_element field added whether receptor is a protein is determined if molecule is lacking charges or if charges are all 0.

CheckMacroAtomTypes
detect types of atoms in receptor; ...

GpfMacroReader
allows user to select the receptor via a file browser

GpfMacroChooser
allows user to choose a molecule already present for the receptor

GpfAddSol
allows user to add solvation parameters to a receptor

GpfInitLigand
initializes the ligand:...

GpfLigandChooser
allows user to choose a molecule already present for the ligand

GpfLigReader
allows user to choose a ligand file via a file browser

GpfEditor
allows user to edit current output file and write it

GpfWriter
allows user to choose an output filename and write it

SelectCenter
allows user to pick an atom to be the center of the grid

SetMapTypes
allows user to enter types of maps to be calculated, directly

SetUpCovalentMap

DefineNewAtomParms

SetBoxParameters
allows user to set center, spacing, and extent of grids (number of pts in each dimension) to be calculated

SetOtherOptions
allows user to set smooth factor, whether to calculate floating point and electrostatic maps AND whether to use a constant or a distance-dependent dielectric constant

Gpf4ParameterFileSelector
allows user to select a filename for the parameter file

GpfMergeNonPolarHs
this command is left here until everyone can update his scripts

Gpf4SetMapTypes
allows user to enter types of maps to be calculated, directly

Gpf4SetAtomTypes
command to set AutoDock4 atom types for a molecule autodock_element is set...

Gpf4MacroInit
receptor is initialized as specified in parameters: whether receptor is a protein is determined if molecule is lacking charges or if charges are all 0.

Gpf4MacroReader
allows user to select the receptor via a file browser

Gpf4MacroChooser
allows user to choose a molecule already present for the receptor

Gpf4InitLigand
initializes the ligand for AutoGrid4:...

Gpf4LigandChooser
allows user to choose a molecule already present for the ligand

Gpf4LigReader
allows user to choose a ligand file via a file browser

Gpf4FlexResChooser
allows user to choose a molecule already present for the flexible residues

Gpf4FlexResReader
allows user to get types for a FlexRes file via a file browser

Gpf4Writer
allows user to choose an output filename and write it

Functions

[hide private]

check_autogpf_geoms(VFGUI)

checkHasGpo(vf)

setAutoDockElements(mol)

getSideLengths(mol, spacing)

checkFile(vf, filename)

initModule(vf)

Variables

[hide private]

cenSph = <DejaVu.Spheres.Spheres> autogpf_cenSph with 1 vertices

cenCross = <DejaVu.Points.CrossSet> autogpf_cenCross with 0 ver...

face = ((0, 3, 2, 1), (3, 7, 6, 2), (7, 4, 5, 6), (0, 1, 5,...

coords = ((1, 1, -1), (-1, 1, -1), (-1, -1, -1), (1, -1, -1),...

materials = ((0, 0, 1), (0, 1, 0), (0, 0, 1), (0, 1, 0), (1, 0, ...

box = <DejaVu.IndexedPolygons.IndexedPolygons> box with 8 ...

menuText = {'AddSol': 'Add Solvent Parameters...(AG3)', 'ReadMa...

gridOpts = {'AsFacesLabel': 'As Faces', 'YOffsetLabel': 'y offs...

messages = {'unknownExt': 'unknown file extension: must be pdbq...

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

autodockElementDict = {'c': 'Cl', 'b': 'Br', 'l': 'Xx', 'f': 'Fe'}

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

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

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

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

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

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

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

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

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

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

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

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

Gpf4ParameterFileSelectorGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4SetMapTypesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4SetAtomTypesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4MacroReaderGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4MacroChooserGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4LigandChooserGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4LigReaderGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4FlexResChooserGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4FlexResReaderGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

Gpf4WriterGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

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

Function Details

[hide private]

check_autogpf_geoms(VFGUI)

source code

None

checkHasGpo(vf)

source code

None

setAutoDockElements(mol)

source code

None

getSideLengths(mol, spacing)

source code

None

checkFile(vf, filename)

source code

None

initModule(vf)

source code

None

Variables Details

[hide private]

cenSph

None

Value:

<DejaVu.Spheres.Spheres> autogpf_cenSph with 1 vertices

cenCross

None

Value:

<DejaVu.Points.CrossSet> autogpf_cenCross with 0 vertices

face

None

Value:

((0, 3, 2, 1),
 (3, 7, 6, 2),
 (7, 4, 5, 6),
 (0, 1, 5, 4),
 (1, 2, 6, 5),
 (0, 4, 7, 3))

coords

None

Value:

((1, 1, -1),
 (-1, 1, -1),
 (-1, -1, -1),
 (1, -1, -1),
 (1, 1, 1),
 (-1, 1, 1),
 (-1, -1, 1),
 (1, -1, 1))

materials

None

Value:

((0, 0, 1), (0, 1, 0), (0, 0, 1), (0, 1, 0), (1, 0, 0), (1, 0, 0))

box

None

Value:

<DejaVu.IndexedPolygons.IndexedPolygons> box with 8 vertices and 6 fac
es

menuText

None

Value:

{'AddSol': 'Add Solvent Parameters...(AG3)',
 'AutoGpfMB': 'Grid',
 'ByChoosingFlexRes4': 'Choose FlexRes Molecule...',
 'ByChoosingLigand': 'Choose Ligand...(AG3)',
 'ByChoosingLigand4': 'Choose Ligand...',
 'ByReadingFile': 'Open Ligand...(AG3)',
 'ByReadingFile4': 'Open Ligand...',
 'ByReadingFlexResFile4': 'Open Flexible Residues...',
...

gridOpts

None

Value:

{'AcceptBut': 'Accept',
 'AsFacesLabel': 'As Faces',
 'AsLinesLabel': 'As Lines',
 'CenterGridBoxLabel': 'Center Grid Box:                  <offset>    
   ',
 'CenterLigand': 'on Ligand',
 'CenterMacro': "on Macromolecule\n('auto' option)",
 'CloseBut': 'Close',
...

messages

None

Value:

{'addSolExt': "for addsol: macromolecule type must be 'pdbq'",
 'mergeNPHSReqExt': "for GpfMergeNonPolarHs: macromolecule typemust be
 'pdbqs' or 'pdbq'",
 'multipleFlexRes': 'more than one flexible residue molecules in file'
,
 'multipleLigs': 'more than one ligand in file',
 'multipleMols': 'more than one molecule in file',
 'noNonPolarHs': 'No NonPolarHydrogens Found',
...

GpfLoadDefaultsGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb743ceac>

autodockElementDict

None

Value:

{'c': 'Cl', 'b': 'Br', 'l': 'Xx', 'f': 'Fe'}

GpfMacroReaderGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb743cf2c>

GpfMacroChooserGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb743cf8c>

GpfAddSolGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd02c>

GpfLigandChooserGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd12c>

GpfLigReaderGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd18c>

GpfEditorGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd20c>

GpfWriterGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd26c>

SetMapTypesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd36c>

SetUpCovalentMapGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd4ac>

DefineNewAtomParmsGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd52c>

SetBoxParametersGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd80c>

SetOtherOptionsGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd8ec>

Gpf4ParameterFileSelectorGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfd94c>

Gpf4SetMapTypesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfda4c>

Gpf4SetAtomTypesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfdaac>

Gpf4MacroReaderGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfdb4c>

Gpf4MacroChooserGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfdbec>

Gpf4LigandChooserGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfdcac>

Gpf4LigReaderGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfdd0c>

Gpf4FlexResChooserGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfddac>

Gpf4FlexResReaderGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfde0c>

Gpf4WriterGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb7bfde6c>

commandList

None

Value:

[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb743ceac>
,
  'name': 'ADgpf_readGPF'},
 {'gui': None, 'cmd': self., 'name': 'ADgpf_initLigand'},
 {'gui': None, 'cmd': self., 'name': 'ADgpf_initMacro'},
 {'gui': None, 'cmd': self., 'name': 'ADgpf4_initLigand'},
 {'gui': None, 'cmd': self., 'name': 'ADgpf4_initMacro'},
...