rdkit.Chem.PyMol.MolViewer

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

source code

    object --+
             |
            MolViewer

Instance Methods | [hide private]
__init__(self, host=None, 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) blows out everything in the viewer | source code
DeleteAllExcept(self, excludes) deletes everything except the items in the provided list of arguments | source code
LoadFile(self, filename, name, showOnly=False) calls pymol's "load" command on the given filename; the loaded object... | 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) returns the selected atoms | source code
SelectAtoms(self, itemId, atomIndices, selName=`'``selection``'`) selects a set of atoms | source code
HighlightAtoms(self, indices, where, extraHighlight=False) highlights a set of atoms | source code
SetDisplayStyle(self, obj, style=`'````'`) change the display style of the specified object | source code
SelectProteinNeighborhood(self, aroundObj, inObj, distance=5.0, name=`'``neighborhood``'`, showSurface=False) selects the area of a protein around a specified object/selection name;... | source code
AddPharmacophore(self, locs, colors, label, sphereRad=0.5) adds a set of spheres | source code
SetDisplayUpdate(self, val) | source code
GetAtomCoords(self, sels) returns the coordinates of the selected atoms | 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)``'`) toggles display of h bonds between the protein and a specified molecule | source code
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 | 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=None, 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

### LoadFile(self, filename, name, showOnly=False) | source code
    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