AutoDockTools.GridParameters.GridParameter4FileMaker:
Accept a <ligand>.pdbqt, <receptor>.pdbqt,
reference4.gpf and create <receptor>4.gpf sets gridcenter to
center of bounding box sets npts according to bounding box
AutoDockTools.GridParameters.GridParameterFileMaker:
Accept a <ligand>.pdbq , <receptor>.pdbqs,
reference.gpf and create <receptor>.gpf sets gridcenter to
center of bounding box sets npts according to bounding box
AutoDockTools.MoleculePreparation.AD4FlexibleReceptorPreparation:
Facade for preparing 'receptor' input for an AutoDock4 experiment
with flexible sidechains in the receptor in flexres_filename
rest of the receptor in the rigid_filename
This preparation involves:
1.
AutoDockTools.atomTypeTools.AromaticCarbonManager:
Used on ligands for managing names + autodock_element fields of
aromatic carbons in cycles The parameter 'rename' determines
whether aromatic carbons are named starting with 'A': 'rename' is
True for AutoDock3 ligands and False for AutoDock4 ligands whose
written files have added 'type' field.
AutoDockTools.atomTypeTools.LonepairMerger:
removes lone pair 'atoms' from an atomset;
WARNING: builds bonds if none have been built previously
This module implements a class which merges lone pair 'atoms' with the heavy
atom to which each is bound.
AutoDockTools.histogram.Histogram:
Histogram in one variable
Constructor: Histogram(|data|, |bins|, |range|=None)
Arguments:
|data| -- a sequence of data points
|bins| -- the number of bins into which the data is to be sorted
|range| -- a tuple of two values, specifying the lower and
the upper end of the interval spanned by the bins.
ViewerFramework.VFCommand.Command:
Base class for adding commands to a Viewer derived from ViewerFramework
Classes derived from that class can be added to a viewer using the
addCommand method.
Pmv.mvCommand.MVCommand:
Base class for command objects for a molecule viewer.
AutoDockTools.autogpfCommands.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.
AutoDockTools.autoanalyzeCommands.ADMakeAllGrids:
toplevel GUI with one row per grid_type allowing:loading a grid (first, then->),toggling the visiblity of its isosurface,changing sampling rate,changing isocontour isovalue,changing the render mode between LINE and FILL visibility of the grid's bounding box...
AutoDockTools.autostartCommands.AutoStarter:
Base class for AutoGridStarter and AutoDockStarter, whose
command structure is very similar with a few differences such as
programType, title for file browser, first letters of required
parameter and log file extensions and the presence or absence of
possible flags,etc
AutoDockTools.autoanalyzeCommands.ADGetAGrid:
Adds a row to the toplevel GUI of ADMakeAllGrids enabling:loading a USER grid (first, then->),toggling its visiblity,changing sampling rate,changing isocontour value,changing the render mode between lines and fill.
AutoDockTools.autogpfCommands.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
AutoDockTools.autogpfCommands.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.
AutoDockTools.autotorsCommands.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
AutoDockTools.autoanalyzeCommands.ADGetDirDLGs:
Allows the user to read all the docking logs in a chosen directory
Package : AutoDockTools
Module : autoanalyzeCommands
Class : ADGetDirDLGs
Command : ADanalyze_readAllDLGinDirectory
Synopsis:
None<---ADanalyze_readAllDLGinDirectory(dlgDir, makeOneDocking)
Required Arguments:
dlgDir --- directory containing any number of docking log files
Optional Arguments:
makeOneDocking --- whether to compile all dlg results into one Docking object with 1 list of conformations and ability to do clustering if not, a separate Docking is created for each docking logfile.