DejaVu.colorMap.ColorMap:
A Colormap is an object designed to provide a mapping from a
property value to an entry in a 'ramp', which is a list of
lists.
DejaVu.ColormapGui.ColorMapGUI:
The ColorMapGUI is an object providing an interface to expose
and to modify a ColorMap object.
Pmv.extruder.ExtrudeSSElt:
Class to take a shape and extrude it along the 3D path defined
by a control coordinate and torsion coordinate
Pmv.extruder.Sheet2D:
Class implementing a set of method to compute a path3D, normals,
binormals and transformation matrices given a 2 sets of control
points coordinates.
Pmv.guiTools.MoleculeChooser:
presents user w/ a list of molecules currently loaded;
mode can be 'single', 'browse', 'multiple' or 'extended'.
Pmv.guiTools.AugmentedMoleculeChooser:
presents user w/ a list of molecules currently loaded;
mode can be 'single', 'browse', 'multiple' or 'extended'.
Pmv.trajectoryCommands.TrajPlayerCached:
This player saves display lists for each frame (when the frame
is played for the first time) to be used in consequent
replays.
mglutil.alignmentEditor.AlignmentEditor:
GUI for editing sequence alignments.
Pmv.trajectoryCommands.TrajPlayerCached:
This player saves display lists for each frame (when the frame
is played for the first time) to be used in consequent
replays.
mglutil.alignmentEditor.AlignmentEditor:
GUI for editing sequence alignments.
Pmv.trajectoryCommands.TrajPlayerCached:
This player saves display lists for each frame (when the frame
is played for the first time) to be used in consequent
replays.
mglutil.alignmentEditor.AlignmentEditor:
GUI for editing sequence alignments.
Pmv.trajectoryCommands.TrajPlayerCached:
This player saves display lists for each frame (when the frame
is played for the first time) to be used in consequent
replays.
mglutil.alignmentEditor.AlignmentEditor:
GUI for editing sequence alignments.
ViewerFramework.VF.ViewerFramework:
Base class for applications providing a 3D geometry Viewer based
on a DejaVu Camera object along with support for adding GUI and
commands dynamically.
Pmv.moleculeViewer.MoleculeViewer:
package : Pmv
module : moleculeViewer
class : MoleculeViewer
description:
Class derived from the ViewerFramework base class.
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.repairCommands.CheckForCloseContactsGUICommand:
This class provides Graphical User Interface to CheckForCloseContactsCommand which is invoked by it
Package : Pmv
Module : repairCommands
Class : CheckForCloseContactsGUICommand
Command : checkForCloseContactsGC
Synopsis:
None <--- checkForCloseContactsGC(keynodes,checkNodes, percentCutoff,distanceCutoff, distSelectorString,**kw)
Required Arguments:
keyNodes --- atoms to use as reference points
checkNodes --- atoms to check to see if close to keyNodes
Optional Arguments:
percentCutoff --- vdw scaling factor
distanceCutoff --- distance for DistanceSelector
distSelectorString --- name of class of selector to use
constant --- possible constant value to be added into selection
close is defined as interatomic distance< percentCutoff*(key_radius+check_radius) where the radii depend on atom element .
Pmv.amberCommands.SetMinimOptsAmber94:
This class allows you to set minimization options of a Amber94 instance
These options include cut, nsnb, dield and verbose.
Pmv.gridCommands.AutoGridIsoSurface:
Command to create:an isosurface for a 'Grid' object ,a bounding box of the grid,and a GUI to manipulate the srf and the visibility of the box .
Pmv.displayCommands.DisplayInteractionsCommand:
The DisplayInteractionsCommand class is used to display
interactions between a 'ligand' and a 'receptor' molecule: the
ligand is displayed with a msms surface...
Pmv.amberCommands.PlayMolecularDynamicsTrjAmber94:
This class allows you to select an Amber94 instance from Amber94Config
whose keys are ids specified in setup_Amber94 for the Amber94 instances, and
a molecular dynamics trajectory file and play the trajectory.
Pmv.repairCommands.ModifyNTerminus:
This command is used to modify residues which become internal n-termini
because some residues are missing within a chain in a crystal structure.
Pmv.selectionCommands.MVDeSelectCommand:
This Command deselects the current selection
Package : Pmv
Module : selectionCommands
Class : MVDeSelectCommand
Command : deselect
Synopsis:
currentSelection <--- deselect(nodes, klass=None, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
klass --- if specified nodes are converted to a set of that type otherwise
and selection level is set to Klass.
Pmv.selectionCommands.MVXorSelectCommand:
This Command xors the current selection
Package : Pmv
Module : selectionCommands
Class : MVXorSelectCommand
Command : xorselect
Synopsis:
currentSelection <--- xorselect(nodes, klass=None, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
klass --- if specified nodes are converted to a set of that type otherwise
and selection level is set to Klass.
Pmv.selectionCommands.MVAddSelectCommand:
This Command adds to the current selection
Package : Pmv
Module : selectionCommands
Class : MVAddSelectCommand
Command : addselect
Synopsis:
currentSelection <--- addselect(nodes, klass=None, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
klass --- if specified nodes are converted to a set of that type otherwise
and selection level is set to Klass.
Pmv.fileCommands.SaveMMCIF:
This command writes macromolecular Crystallographic Information File (mmCIF).
Pmv.editCommands.FixHydrogenAtomNamesCommand:
This class checks hydrogen atom names and modifies them to conform to 'IUPAC-IUB' conventions
Package:Pmv
Module :editCommands
Class:FixHydrogenAtomNamesCommand
Command:fixHNames
Synopsis:
None <- fixHNames(nodes, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
Hydrogen names have 4 spaces:'H _ _ _', (here referred to as 1-4).
Pmv.selectionCommands.MVSelectSphericalRegion:
This Command selects nodes from a specified base within specified spherical region(s)
Package : Pmv
Module : selectionCommands
Class : MVSelectSphericalRegion
Command : selectInSphere
Synopsis:
None <- selectInSphere(centerList, radius, selList, **kw)
Required Arguments:
centerList --- specifies the centers of the selection spheres
radius --- radius of the selection spheres
selList --- specifies selection base (atoms to test)
possible selList values are ['all'], a list of sets or a list
of molecule names.
Pmv.dashboardCommands.Dashboard:
Display a widget showing a tree representation of the molecules
in the Viewer and check buttons allowing to carry out command on
parts of molecules directly.
Pmv.deleteCommands.DeleteAllMolecules:
Command to delete all molecules from the MoleculeViewer
Package : Pmv
Module : deleteCommands
Class : DeleteAllMolecules
Command : deleteAllMolecules
Synopsis:
None<---deleteAllMolecules( **kw)
Required Arguments:
It resets the undo stack automatically.
Pmv.amberCommands.FixAmberHAtomNamesGUICommand:
This class provides Graphical User Interface to FixAmberHAtomsNameCommand which is invoked by it with the current selection, if there is one.
Pmv.amberCommands.MinimizeAmber94:
This class allows you to select an Amber94 instance from Amber94Config
whose keys are ids specified in setup_Amber94 for the Amber94 instances.
Pmv.repairCommands.CheckForMissingAtoms:
This command compares atoms present in residues with those expected by the dictionary used to assign Kollman charges, qkollua.
Pmv.msmsCommands.SaveMSMS:
The SaveMSMS commands allows the user to save a chosen MSMS surface (tri-angulated solvant excluded surface) resulting from a calculation.
Pmv.repairCommands.AddOXT:
This class uses add_sp2_hydrogen method of the AddHydrogens class from the PyBabel package to compute coordinates of oxygen to be added to carbon atom.The carbon atom is bonded to another oxygen and a CA.
Pmv.amberCommands.SetupAmber94:
This command creates an instance of Amber94 class and enters it in Amber94Config dictionary with specified name as the key.
Pmv.APBSCommands.APBSSetup:
APBSSetup setups all necessary parameters for Adaptive Poisson-Boltzmann
Solver (APBS)
Package : Pmv
Module : APBSCommands
Class : APBSSetup
Command name : APBSSetup
Synopsis:
None <--- APBSSetup(**kw)
Description:
Pmv-->APBS-->Setup creates Pmw.NoteBook with three tabbed pages:
Calculation, Grid and Physics.
Pmv.repairCommands.RepairMissingAtoms:
This command compares atoms present in residues with those expected by the dictionary used to assign Kollman charges, qkollua.
Pmv.amberCommands.FixAmberHAtomNamesCommand:
This class checks hydrogen atom names and modifies them to conform to
Package : Pmv
Module : amberCommands
Class : FixAmberHAtomNamesCommand
Command : fixAmberHAtomNamesCommand
Synopsis:
None <- fixAmberHNames(nodes, **kw)
Arguments:
nodes --- TreeNodeSet holding the current selection
Amber conventions:
Single hydrogen atoms bonded to N are named 'H'.
Pmv.editCommands.AddHydrogensCommand:
This command adds hydrogen atoms to all atoms in all molecules that have at least one member (i.e atom, residue, chain, base-pair etc..) specified in the first argument.
Pmv.msmsCommands.IdentifyBuriedVertices:
This command enables finding out and tagging the vertices of a Solvent excluded surface that are buried by a set of atoms.
Pmv.splineCommands.ExtrudeSplineCommand:
The extrudeSplineCommand implements a set of method to create the
extrude Geometries DejaVu.GleExtrude resulting of the extrusion of a
shape2D along a path3D computed by the DejaVu.SplineObject using the GLE
library.
Pmv.traceCommands.CustomTraceCommand:
This command computes and extrudes Trace
Package : Pmv
Module : traceCommands
Class : CustomTraceCommand
Command : customTrace
keywords: custom trace
Synopsis:
None<---customTrace(nodes,traceName='CATrace',shape2D=None,frontCap=1, endCap=1,ctlAtmName='CA',torsAtmName='O',nbchords=4,display=1,**kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
Optional Arguments:
:
traceName --- string representing the name of the computed trace.
Pmv.displayCommands.DisplayCommand:
The DisplayCommand class is the base class from which all the
display commands implemented for PMV will derive.It implements the
general functionalities to display/undisplay parts of a geometry
representing a molecule.
Pmv.displayCommands.UndisplayCPK:
The undisplayCPK command is a picking command allowing the user to undisplay the CPK geometry representing the picked nodes when used as a picking command or the given nodes when called from the Python shell.
Pmv.sdCommands.DisplayMolIndexedPolygons:
Package : Pmv
Module : sdCommands
Class : DisplayMolIndexedPolygons
Command : displayMolIndexedPolygons
Description:
The DisplayMolIndexedPolygons is used to display MolIndexedPolygons
instances (or parts thereof) which are associated with the
selected nodes
Synopsis:
None <- displayMolIndexPolygons(nodes,name,only,negate,**kw)
nodes : nodes for which polygons will be displayed
name : name of the polygon to be displayed
only : display polygon for these atoms _only_
(i.e.
Pmv.displayCommands.UndisplayLines:
The undisplayLines command is a picking command allowing the user to undisplay the lines geometry representing the picked nodes.This command can also be called from the Python shell with a set of nodes.
Pmv.msmsCommands.DisplayMSMS:
The displayMSMS command allows the user to display/undisplay or display only the given MSMS surface corresponding to the current selection.
Pmv.displayCommands.DisplayCPKByProperty:
The displayCPKByProperty command allows the user to specify a property used to display/undisplay the given nodes using a CPK representation, where each atom is represented with a sphere whose radius is set by the particular value of the property for that atom.
Pmv.splineCommands.UndisplaySplineAsLineCommand:
UndisplaySPlineAsLineCommand calls the displaySplineAsLine command with the flag negate set to 1
Package : Pmv
Module : splineCommands
Class : UndisplaySplineAsLineSplineCommand
Command : undisplaySplineAsLineSpline
Synopsis:
None <- undisplaySplineAsLine(nodes, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection.
Pmv.secondaryStructureCommands.DisplayExtrudedSSCommand:
The DisplaySSCommand displays the geometries representing the secondary structure elements of the current selection.To execute this command use the 'Display Secondary Structure' entry under the 'Display' menu in the menu bar.
Pmv.splineCommands.DisplayExtrudedSplineCommand:
The DisplayExtrudeSplineCommand implements a set of methods to display/undisplay part of the geometries created by the ExtrudeSplineCommand.
Pmv.displayCommands.DisplayCPK:
The displayCPK command allows the user to display/undisplay the given nodes using a CPK representation, where each atom is represented with a sphere.
Pmv.splineCommands.UndisplayExtrudedSplineCommand:
UndisplayExtrudeSplineCommand is the interactive command to undisplay part of the molecule when displayed as an extruded spline.It calls the displatExtrudedSpline with negate =1
Package : Pmv
Module : splineCommands
Class : UnDisplaySplineCommand
Command : undisplaySpline
Synopsis:
None <- undisplayExtrudedSpline(nodes, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection.
Pmv.displayCommands.DisplaySticksAndBalls:
The displaySticksAndBalls command allows the user to display/undisplay
the given nodes using the sticks and balls representation, where the bonds are
represented by cylinders and the atoms by balls.The radii of the cylinders and
the balls, and the quality of the spheres are user defined.
Pmv.displayCommands.DisplaySSSB:
The displaySSSB command allows the user to display/undisplay the given chains using the sticks and balls representation for non protein chains and ribbon diagram for proteic chains.
Pmv.displayCommands.DisplayBackboneTrace:
The displayBackboneTrace command allows the user to display/undisplay the given nodes using the sticks and balls representation, where the bonds are represented by cylinders and the atoms by balls.The radii of the cylinders and the balls, and the quality of the spheres are user defined.
Pmv.displayCommands.UndisplaySticksAndBalls:
The UndisplaySticksAndBalls command is an interactive command to undisplay part of the molecule when represented as sticks and balls.
Pmv.displayCommands.DisplayLines:
The displayLines allows the user to display/undisplay the selected nodes using a lines for bonded atoms, dots for non bonded atoms and doted lines for an aromatic ring.
Pmv.displayCommands.UndisplayBackboneTrace:
The UndisplayBackboneTrace command is an interactive command to undisplay part of the molecule when represented as sticks and balls.
Pmv.traceCommands.DisplayTraceCommand:
This command allows the user to display, undisplay or display only the current selection using the extruded trace representation of the given
traceName.
Pmv.msmsCommands.UndisplayMSMS:
The undisplayMSMS command allows the user to undisplay displayedMSMS
Package : Pmv
Module : msmsCommands
Class : UndisplayMSMS
Command name : undisplayMSMS
Required Arguments:
nodes --- TreeNodeSet holding the current selection
.
Pmv.repairCommands.ModifyTermini:
This class detects residues within a chain which are not bonded to a previous
residue in the chain and those not bonded to a subsequent residue in the
chain.
Pmv.labelCommands.LabelByProperties:
selector.selection,property,textcolor,font,location,only,negate,funcItems Command to label the current selection items according to different properties of the selection level (Actually of the first item in the current selection.) Color can be specified as 'red','green','blue','white' or 'yellow'.
Pmv.labelCommands.LabelByExpression:
Command to label the current selection items according to different expressions of the selection level (Actually of the first item in the current selection.) Color can be specified as 'red','green','blue','white' or 'yellow'.
Pmv.sdCommands.ReadMolIndexedPolygons:
Package : Pmv
Module : sdCommands
Class : ReadMolIndexedPolygons
Command : readMolIndexedPolygons
Description:
Class to read two files (defining vertices and faces) to generate
a MolIndexedPolygons instance and assign it to a molecule.
Pmv.sdCommands.ReadHarmony:
Package : Pmv
Module : sdCommands
Class : ReadHarmony
Command : readHarmony
Description:
The ReadHarmony class is a subclass of ReadMolIndexedPolygons for
reading files generated by the Harmony suite (usually having the
suffix 'field'.
Pmv.sdCommands.ReadDockdata:
Package : Pmv
Module : sdCommands
Class : ReadDockdata
Command : readDockdata
Description:
The ReadDockdata class is a subclass of ReadMolIndexedPolygons for
reading dockdata files as used by surfdock.
Pmv.sdCommands.ReadBlur:
Package : Pmv
Module : sdCommands
Class : ReadBlur
Command : readBlur
Description:
The ReadHarmony class is a subclass of ReadMolIndexedPolygons for
reading files generated by the Gaussian Blur method.
Pmv.amberCommands.SetMDOptsAmber94:
This class allows you to set md options of a Amber94 instance these options include t, dt, tautp, temp0, verbose, vlimit, ntpr_md, zerov,tempi and idum.
Pmv.deleteCommands.DeleteMolecule:
Command to delete a molecule from the MoleculeViewer
Package : Pmv
Module : deleteCommands
Class : DeleteMolecule
Command : deleteMolecule
Synopsis:
None<---deleteMol(nodes, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
It resets the undo stack automatically.
Pmv.amberCommands.MolecularDynamicsAmber94:
This class allows you to select an Amber94 instance from Amber94Config whose keys are ids specified in setup_Amber94 for the Amber94 instances.You can also set md options, freeze atoms, specify constrained atoms and anchor atoms and set maxStep.
Pmv.measureCommands.MeasureAtomCommand:
Base class for commands which measure between atoms.Implements
applyTransformation, getTransformedCoords and vvmult.
Pmv.measureCommands.MeasureTorsion:
Compute the torsion between atom1, atom2, atom3, atom4.All coordinates are Cartesian; result is in degrees.
Pmv.setangleCommands.SetTorsion:
Transform the coords of atoms in subTree defined by atom1-atom2
by angle less initial torsion defined by atom0, atom1, atom2, atom3
Set the coords of these atoms to the new values and return new
coords
Pmv.setangleCommands.SetRelativeTorsion:
Transform the coords of atoms in subTree defined by atom1-atom2
Set the coords of these atoms to the new values and return new
coords
Pmv.measureCommands.MeasureAngle:
Compute the angle between atom1, atom2, atom3.All coordinates are Cartesian; result is in degrees.
Pmv.measureCommands.MeasureDistance:
Computes the distance between atom1, atom2, atom3.All coordinates are Cartesian; result is in Angstrom.
Pmv.setangleCommands.SetQuaternion:
Transform the coords by quaternion Set the coords of these atoms
to the new values and return new coords
Pmv.measureCommands.MeasureGUICommand:
Base class for commands which provide measureCommands
user-interface.Implements setLength_cb, userpref callback,
setLength, guiCallback and stopICOM
Pmv.measureCommands.MeasureAngleGUICommand:
Accumulates picked atoms.Draws fans, lines and labels labelling the angle between trios of selected atoms (color-coded orange).Userpref 'measureAngleSL' sets the 'snakeLength' which is how many angle measureDisplays can be seen at the same time.When more than that number are measured, the first angle measured is no longer labeled.
Pmv.measureCommands.MeasureTorsionGUICommand:
Label torsion between four atoms (color coded cyan) Accumulates picked atoms.Draws polygons and labels showing the torsion angle between groups of 4 selected atoms (color-coded cyan).Userpref 'measureTorsionSL' sets the 'snakeLength' which is how many torsion measureDisplays can be seen at the same time.When more than that number are measured, the first torsion measured is no longer labeled.
Pmv.secondaryStructureCommands.ExtrudeSecondaryStructureCommand:
The ExtrudeCommand allows the user to represent the secondary structure elements by extruding 2D geometries along a 3D path.To execute this command use the entry 'extrude Secondary Structure' under the 'Compute' menu in the menu bar.
Pmv.extrusionCommands.ComputeSheet2DCommand:
The ComputeSheet2DCommand class implements methods to compute the sheet2D for each chain of the contained in the current selection.
Pmv.controlPanelCommands.ControlPanel:
Display a widget showing a tree representation of the molecules
in the Viewer and check buttons allowing to carry out command on
parts of molecules directly.
Pmv.editCommands.FixHydrogenAtomNamesGUICommand:
This class provides Graphical User Interface to FixHydrogenAtomsNameCommand
which is invoked by it with the current selection, if there is one.
Pmv.bondsCommands.RemoveBondsCommand:
The RemoveBondsCommand allows the user to remove the bond existing between two given atoms (atom1 and atom2).
Pmv.colorCommands.ColorCommand:
The ColorCommand class is the base class from which all the color commands implemented for PMV will derive.
Pmv.colorCommands.ColorByProperties:
Command to color the current selection according to the integer
or float properties, or by defining a function.
Pmv.colorCommands.ColorByExpression:
The colorByExpression command allows the user to color the given geometries representing the given nodes evaluated by python function or lambda function.
Pmv.colorCommands.ColorFromPalette:
The ColorFromPalette class is the base class from which all the color commands using a colorPalette implemented for PMV will derive.
Pmv.colorCommands.ColorByChain:
The colorByChain command allows the user to color the given geometries representing the given nodes by chain.
Pmv.colorCommands.ColorByMolecule:
The colorByChain command allows the user to color the given geometries representing the given nodes by molecules.
Pmv.colorCommands.ColorShapely:
The colorByShapely command allows the user to color the given geometries representing the given nodes using the Shapely coloring scheme where each residue has a different color.
Pmv.colorCommands.ColorByDG:
The colorByDG command allows the user to color the given geometries representing the given nodes using the following David Goodsell coloring
scheme.
Pmv.colorCommands.ColorByResidueType:
The colorByResidueType command allows the user to color the given geometries representing the given nodes using the Rasmol coloring scheme.
Pmv.colorCommands.ColorByAtomType:
The colorByAtomType command allows the user to color the given geometry representing the given nodes using the atomtype coloring scheme where:N :Blue ; C : White ; O : Red ; S : Yellow ; H : Cyan; P: Magenta;UNK:green.
Pmv.colorCommands.ColorFromRamp:
The colorFromRamp class implements the functionality to color the given geometries representing the given nodes using a colorMap created from the Ramp.
Pmv.sdCommands.ColorMolIndexedPolygons:
Package : Pmv
Module : sdCommands
Class : ColorMolIndexedPolygons
Command : colorMolIndexedPolygons
Description:
The ColorMolIndexedPolygons class provides a mechanism for coloring
a MolIndexedPolygons instance according to its surface properties
(i.e.
Pmv.editCommands.ComputeGasteigerCommand:
Does work of computing gasteiger partial charges for each atom and entering each atom's charge in its '_charges' dictionary as value for key 'gasteiger' (rounded to 4 decimal places).
Pmv.editCommands.SetChargeCommand:
allows user to set string used to index into _charges dictionary
Package:Pmv
Module :editCommands
Class:SetChargeCommand
Command:setChargeSet
Synopsis:
None<---setChargeSet(nodes, key, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
key --- what charges (keyword of the _charges dictionary).
Pmv.bondsCommands.AddBondsCommand:
The AddBondsCommand is a command to connect two given atoms.This command will not allow the creation inter-molecular bonds.This command doesn't have a GUI interface and can only be called through the pyShell.
Pmv.secondaryStructureCommands.ComputeSecondaryStructureCommand:
The computeSecondaryStructure command gets the information on the secondary structure of each molecule contained in the current selection.This information is then used to create object describing the various secondary structure elements.
Pmv.hbondCommands.LimitHydrogenBonds:
This class allows user to detect pre-existing HydrogenBonds with energy values
'lower' than a designated cutoff.
Pmv.editCommands.AddKollmanChargesCommand:
Kollman united atom partial charges are added to atoms by looking up each atom's parent's type to get a dictionary of charges for specific atom names (from Pmv.qkollua).
Pmv.splineCommands.ComputeSplineCommand:
The CompueSplineCommand omplements a set of method to create an DejaVu.splineObject per chain given:a TreeNodeSet,type of control Atoms (atmtype),number of points per control point in the smooth array (nbchords),continuity of the curves (continuity).
Pmv.fileCommands.MoleculeReader:
Command to read molecule
Package : Pmv
Module : fileCommands
Class : MoleculeReader
Command :readMolecule
Synopsis:
mols <- readMolecule(filename,parser=None, **kw)
Required Arguments:
filename --- path to a file describing a molecule
parser --- you can specify the parser to use to parse the file has to be one of 'PDB', 'PDBQ', 'PDBQS','PDBQT', 'PQR', 'MOL2'.This is useful when your file doesn't have the correct extension.
Pmv.editCommands.AverageChargeErrorCommand:
Adjusts the charge on each atom in residue with non-integral overall charge so that the sum of the charge on all the atoms in the residue is an integer.
Pmv.SLCommands.SLCommand:
Command that performs Bsp tree operations such as 'union',
'difference', 'intersect'.
Pmv.editCommands.MergeLonePairsCommand:
This class merges lone-pairs and the sulfur atoms to which they are attached.There are three parts to the process:the charges of lone-pairs, if any, are added to those of the sulfurs the bond between the lone-pair and its sulfur is removed from the sulfur's bonds the lone-pair 'atoms' are deleted
Package:Pmv
Module :editCommands
Class:MergeLonePairsCommand
Command:mergeLPS
Synopsis:
None<---mergeLPS(nodes, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
NB: the lone pairs are identified by these criteria:
the element field of the lone pair 'atom' is 'Xx' and its name has a 'L'
in the first or second position.
Pmv.deleteCommands.DeleteAtomSet:
Command to remove an AtomSet from the MoleculeViewer
Package : Pmv
Module : deleteCommands
Class : DeleteAtomSet
Command : deleteAtomSet
Synopsis:
None<---deleteAtomSet(atoms, **kw)
Required Arguments:
atoms --- AtomSet to be deleted.
Pmv.deleteCommands.DeleteHydrogens:
Command to remove hydrogen atoms from the MoleculeViewer
Package : Pmv
Module : deleteCommands
Class : DeleteHydrogens
Command : deleteHydrogens
Synopsis:
None<---deleteAtomSet(atoms, **kw)
Required Arguments:
atoms --- AtomSet to be deleted.
Pmv.repairCommands.RepairMissingAtomsGUICommand:
This class provides Graphical User Interface to RepairMissingAtomsCommand which is invoked by it with the current selection, if there is one.
Pmv.editCommands.ComputeGasteigerGUICommand:
Calls computeGasteiger which does work of computing gasteiger partial charges
for each atom and entering each atom's charge in its _charges dictionary.
Pmv.selectionCommands.MVDeSelectCommand:
This Command deselects the current selection
Package : Pmv
Module : selectionCommands
Class : MVDeSelectCommand
Command : deselect
Synopsis:
currentSelection <--- deselect(nodes, klass=None, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
klass --- if specified nodes are converted to a set of that type otherwise
and selection level is set to Klass.
Pmv.selectionCommands.MVXorSelectCommand:
This Command xors the current selection
Package : Pmv
Module : selectionCommands
Class : MVXorSelectCommand
Command : xorselect
Synopsis:
currentSelection <--- xorselect(nodes, klass=None, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
klass --- if specified nodes are converted to a set of that type otherwise
and selection level is set to Klass.
Pmv.selectionCommands.MVAddSelectCommand:
This Command adds to the current selection
Package : Pmv
Module : selectionCommands
Class : MVAddSelectCommand
Command : addselect
Synopsis:
currentSelection <--- addselect(nodes, klass=None, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection
klass --- if specified nodes are converted to a set of that type otherwise
and selection level is set to Klass.
Pmv.displayCommands.DisplayCommand:
The DisplayCommand class is the base class from which all the
display commands implemented for PMV will derive.It implements the
general functionalities to display/undisplay parts of a geometry
representing a molecule.
Pmv.displayCommands.UndisplayCPK:
The undisplayCPK command is a picking command allowing the user to undisplay the CPK geometry representing the picked nodes when used as a picking command or the given nodes when called from the Python shell.
Pmv.sdCommands.DisplayMolIndexedPolygons:
Package : Pmv
Module : sdCommands
Class : DisplayMolIndexedPolygons
Command : displayMolIndexedPolygons
Description:
The DisplayMolIndexedPolygons is used to display MolIndexedPolygons
instances (or parts thereof) which are associated with the
selected nodes
Synopsis:
None <- displayMolIndexPolygons(nodes,name,only,negate,**kw)
nodes : nodes for which polygons will be displayed
name : name of the polygon to be displayed
only : display polygon for these atoms _only_
(i.e.
Pmv.displayCommands.UndisplayLines:
The undisplayLines command is a picking command allowing the user to undisplay the lines geometry representing the picked nodes.This command can also be called from the Python shell with a set of nodes.
Pmv.msmsCommands.DisplayMSMS:
The displayMSMS command allows the user to display/undisplay or display only the given MSMS surface corresponding to the current selection.
Pmv.displayCommands.DisplayCPKByProperty:
The displayCPKByProperty command allows the user to specify a property used to display/undisplay the given nodes using a CPK representation, where each atom is represented with a sphere whose radius is set by the particular value of the property for that atom.
Pmv.splineCommands.UndisplaySplineAsLineCommand:
UndisplaySPlineAsLineCommand calls the displaySplineAsLine command with the flag negate set to 1
Package : Pmv
Module : splineCommands
Class : UndisplaySplineAsLineSplineCommand
Command : undisplaySplineAsLineSpline
Synopsis:
None <- undisplaySplineAsLine(nodes, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection.
Pmv.secondaryStructureCommands.DisplayExtrudedSSCommand:
The DisplaySSCommand displays the geometries representing the secondary structure elements of the current selection.To execute this command use the 'Display Secondary Structure' entry under the 'Display' menu in the menu bar.
Pmv.splineCommands.DisplayExtrudedSplineCommand:
The DisplayExtrudeSplineCommand implements a set of methods to display/undisplay part of the geometries created by the ExtrudeSplineCommand.
Pmv.displayCommands.DisplayCPK:
The displayCPK command allows the user to display/undisplay the given nodes using a CPK representation, where each atom is represented with a sphere.
Pmv.splineCommands.UndisplayExtrudedSplineCommand:
UndisplayExtrudeSplineCommand is the interactive command to undisplay part of the molecule when displayed as an extruded spline.It calls the displatExtrudedSpline with negate =1
Package : Pmv
Module : splineCommands
Class : UnDisplaySplineCommand
Command : undisplaySpline
Synopsis:
None <- undisplayExtrudedSpline(nodes, **kw)
Required Arguments:
nodes --- TreeNodeSet holding the current selection.
Pmv.displayCommands.DisplaySticksAndBalls:
The displaySticksAndBalls command allows the user to display/undisplay
the given nodes using the sticks and balls representation, where the bonds are
represented by cylinders and the atoms by balls.The radii of the cylinders and
the balls, and the quality of the spheres are user defined.
Pmv.displayCommands.DisplaySSSB:
The displaySSSB command allows the user to display/undisplay the given chains using the sticks and balls representation for non protein chains and ribbon diagram for proteic chains.
Pmv.displayCommands.DisplayBackboneTrace:
The displayBackboneTrace command allows the user to display/undisplay the given nodes using the sticks and balls representation, where the bonds are represented by cylinders and the atoms by balls.The radii of the cylinders and the balls, and the quality of the spheres are user defined.
Pmv.displayCommands.UndisplaySticksAndBalls:
The UndisplaySticksAndBalls command is an interactive command to undisplay part of the molecule when represented as sticks and balls.
Pmv.displayCommands.DisplayLines:
The displayLines allows the user to display/undisplay the selected nodes using a lines for bonded atoms, dots for non bonded atoms and doted lines for an aromatic ring.
Pmv.displayCommands.UndisplayBackboneTrace:
The UndisplayBackboneTrace command is an interactive command to undisplay part of the molecule when represented as sticks and balls.
Pmv.traceCommands.DisplayTraceCommand:
This command allows the user to display, undisplay or display only the current selection using the extruded trace representation of the given
traceName.
Pmv.msmsCommands.UndisplayMSMS:
The undisplayMSMS command allows the user to undisplay displayedMSMS
Package : Pmv
Module : msmsCommands
Class : UndisplayMSMS
Command name : undisplayMSMS
Required Arguments:
nodes --- TreeNodeSet holding the current selection
.
Pmv.colorCommands.ColorFromPalette:
The ColorFromPalette class is the base class from which all the color commands using a colorPalette implemented for PMV will derive.
Pmv.colorCommands.ColorByChain:
The colorByChain command allows the user to color the given geometries representing the given nodes by chain.
Pmv.colorCommands.ColorByMolecule:
The colorByChain command allows the user to color the given geometries representing the given nodes by molecules.
Pmv.colorCommands.ColorShapely:
The colorByShapely command allows the user to color the given geometries representing the given nodes using the Shapely coloring scheme where each residue has a different color.
Pmv.colorCommands.ColorByDG:
The colorByDG command allows the user to color the given geometries representing the given nodes using the following David Goodsell coloring
scheme.
Pmv.colorCommands.ColorByResidueType:
The colorByResidueType command allows the user to color the given geometries representing the given nodes using the Rasmol coloring scheme.
Pmv.colorCommands.ColorByAtomType:
The colorByAtomType command allows the user to color the given geometry representing the given nodes using the atomtype coloring scheme where:N :Blue ; C : White ; O : Red ; S : Yellow ; H : Cyan; P: Magenta;UNK:green.
Pmv.colorCommands.ColorFromRamp:
The colorFromRamp class implements the functionality to color the given geometries representing the given nodes using a colorMap created from the Ramp.
Pmv.bondsCommands.AddBondsGUICommand:
The AddBondGUICommand provides an interactive way of creating bonds between two given atoms by picking on them.
Pmv.labelCommands.LabelByProperties:
selector.selection,property,textcolor,font,location,only,negate,funcItems Command to label the current selection items according to different properties of the selection level (Actually of the first item in the current selection.) Color can be specified as 'red','green','blue','white' or 'yellow'.
Pmv.labelCommands.LabelByExpression:
Command to label the current selection items according to different expressions of the selection level (Actually of the first item in the current selection.) Color can be specified as 'red','green','blue','white' or 'yellow'.
Pmv.measureCommands.MeasureGUICommand:
Base class for commands which provide measureCommands
user-interface.Implements setLength_cb, userpref callback,
setLength, guiCallback and stopICOM
Pmv.measureCommands.MeasureAngleGUICommand:
Accumulates picked atoms.Draws fans, lines and labels labelling the angle between trios of selected atoms (color-coded orange).Userpref 'measureAngleSL' sets the 'snakeLength' which is how many angle measureDisplays can be seen at the same time.When more than that number are measured, the first angle measured is no longer labeled.
Pmv.measureCommands.MeasureTorsionGUICommand:
Label torsion between four atoms (color coded cyan) Accumulates picked atoms.Draws polygons and labels showing the torsion angle between groups of 4 selected atoms (color-coded cyan).Userpref 'measureTorsionSL' sets the 'snakeLength' which is how many torsion measureDisplays can be seen at the same time.When more than that number are measured, the first torsion measured is no longer labeled.
ViewerFramework.VFCommand.InteractiveCmdCaller:
Object used to bind interactive commands to picking
operations.
Pmv.mvCommand.MVInteractiveCmdCaller:
subclass InteractiveCmdCaller to add the concept of selection
level This object holds a dictionary of commands and a level.
ViewerFramework.picker.Picker:
Base class for picker objects
Pmv.picker.AtomPicker:
This objects can be used to prompt the user for selecting a set
of atoms or starting a picker that will call a callback function
after a user- defined number of atoms have been selected
ZSI.TC.TypeCode:
The parent class for all parseable SOAP types.
Pmv.grid3DCommands.myLUT:
Extend mglutil.gui.BasicWidgets.Tk.tablemaker.LUT; removes label
to top
mglutil.gui.BasicWidgets.Tk.tablemaker.TableManager:
Class for manipulating canvas widgets(lookup table), colormap
widget and entry fields on the input form
Pmv.grid3DCommands.myTF:
Extends mglutil.gui.BasicWidgets.Tk.tablemaker.TableManager and
removes iso widget