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)