rdkit.Chem.PyMol module — The RDKit 2016.09.1 documentation

# rdkit.Chem.PyMol module

uses pymol to interact with molecules

class `rdkit.Chem.PyMol.` `MolViewer`(host=None, port=9123, force=0, **kwargs)

  Bases: `object`

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

    adds a set of spheres

  `DeleteAll`()

    blows out everything in the viewer

  `DeleteAllExcept`(excludes)

    deletes everything except the items in the provided list of arguments

  `DisplayCollisions`(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

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

    toggles display of h bonds between the protein and a specified molecule

  `DisplayObject`(objName)
  `GetAtomCoords`(sels)

    returns the coordinates of the selected atoms

  `GetPNG`(h=None, w=None, preDelay=0)
  `GetSelectedAtoms`(whichSelection=None)

    returns the selected atoms

  `HideAll`()
  `HideObject`(objName)
  `HighlightAtoms`(indices, where, extraHighlight=False)

    highlights a set of atoms

  `InitializePyMol`()

    does some initializations to set up PyMol according to our tastes

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

    calls pymol’s “load” command on the given filename; the loaded object is assigned the name “name”

  `Redraw`()
  `SaveFile`(filename)
  `SelectAtoms`(itemId, atomIndices, selName='selection')

    selects a set of atoms

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

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

  `SetDisplayStyle`(obj, style='')

    change the display style of the specified object

  `SetDisplayUpdate`(val)
  `ShowMol`(mol, name='molecule', showOnly=True, highlightFeatures=[], molB='', confId=-1, zoom=True, forcePDB=False, showSticks=False)

    special case for displaying a molecule or mol block

  `Zoom`(objName)