Package Chem :: Module PyMol :: Class MolViewer

Class MolViewer

object --+
         |
        MolViewer

Instance Methods

[hide private]

__init__(self, host='localhost', port=9123, force=0, **kwargs)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature source code

InitializePyMol(self)
does some initializations to set up PyMol according to our...

source code

DeleteAll(self)

source code

DeleteAllExcept(self, excludes)

source code

LoadFile(self, filename, name, showOnly=False)

source code

ShowMol(self, mol, name='molecule', showOnly=True, highlightFeatures=[], molB='', confId=-1, zoom=True)
special case for displaying a molecule or mol block source code

GetSelectedAtoms(self, whichSelection=None)

source code

SelectAtoms(self, itemId, atomIndices, selName='selection') source code

HighlightAtoms(self, indices, where, extraHighlight=False)

source code

SetDisplayStyle(self, obj, style='') source code

SelectProteinNeighborhood(self, aroundObj, inObj, distance=5.0, name='neighborhood', showSurface=False) source code

AddPharmacophore(self, locs, colors, label, sphereRad=0.5)

source code

SetDisplayUpdate(self, val)

source code

GetAtomCoords(self, sels)

source code

HideAll(self)

source code

HideObject(self, objName)

source code

DisplayObject(self, objName)

source code

Redraw(self)

source code

Zoom(self, objName)

source code

DisplayHBonds(self, objName, molName, proteinName, molSelText='(%(molName)s)', proteinSelText='(%(proteinName)s and not het)') source code

DisplayCollisions(self, objName, molName, proteinName, distCutoff=3.0, color='red', molSelText='(%(molName)s)', proteinSelText='(%(proteinName)s and not het)') source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, host=`'localhost'`, port=9123, force=0, **kwargs)
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

InitializePyMol(self)

source code

does some initializations to set up PyMol according to our
tastes

Class MolViewer

__init__(self, host='localhost', port=9123, force=0, **kwargs) (Constructor)

InitializePyMol(self)

init(self, host=`'localhost'`, port=9123, force=0, **kwargs)
(Constructor)