Package rdkit :: Package Chem :: Module PyMol :: Class MolViewer
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Class MolViewer

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object --+
         |
        MolViewer

Instance Methods [hide private]
 
__init__(self, host=None, port=9123, force=0, **kwargs)
x.__init__(...) initializes x; see help(type(x)) for signature
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InitializePyMol(self)
does some initializations to set up PyMol according to our...
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DeleteAll(self)
blows out everything in the viewer
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DeleteAllExcept(self, excludes)
deletes everything except the items in the provided list of arguments
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LoadFile(self, filename, name, showOnly=False)
calls pymol's "load" command on the given filename; the loaded object...
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ShowMol(self, mol, name='molecule', showOnly=True, highlightFeatures=[], molB='', confId=-1, zoom=True)
special case for displaying a molecule or mol block
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GetSelectedAtoms(self, whichSelection=None)
returns the selected atoms
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SelectAtoms(self, itemId, atomIndices, selName='selection')
selects a set of atoms
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HighlightAtoms(self, indices, where, extraHighlight=False)
highlights a set of atoms
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SetDisplayStyle(self, obj, style='')
change the display style of the specified object
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SelectProteinNeighborhood(self, aroundObj, inObj, distance=5.0, name='neighborhood', showSurface=False)
selects the area of a protein around a specified object/selection name;...
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AddPharmacophore(self, locs, colors, label, sphereRad=0.5)
adds a set of spheres
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SetDisplayUpdate(self, val) source code
 
GetAtomCoords(self, sels)
returns the coordinates of the selected atoms
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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)')
toggles display of h bonds between the protein and a specified molecule
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DisplayCollisions(self, objName, molName, proteinName, distCutoff=3.0, color='red', molSelText='(%(molName)s)', proteinSelText='(%(proteinName)s and not het)')
toggles display of collisions between the protein and a specified molecule
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GetPNG(self, h=None, w=None, preDelay=0) source code

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

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, host=None, port=9123, force=0, **kwargs)
(Constructor)

source code 
x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

InitializePyMol(self)

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does some initializations to set up PyMol according to our
tastes

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

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calls pymol's "load" command on the given filename; the loaded object
is assigned the name "name"

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

source code 
selects the area of a protein around a specified object/selection name;
optionally adds a surface to that