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 | 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, forcePDB=False) 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

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)

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    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)

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