def show_stacking(self):
        """Visualizes pi-stacking interactions."""
        grp = self.getPseudoBondGroup("pi-Stacking-%i" % self.tid, associateWith=[self.model])
        grp.lineWidth = 3
        grp.lineType = self.chimera.Dash
        for i, stack in enumerate(self.plcomplex.pistacking):

            m = self.model
            r = m.newResidue("pseudoatoms", " ", 1, " ")
            centroid_prot = m.newAtom("CENTROID", self.chimera.Element("CENTROID"))
            x, y, z = stack.proteinring_center
            centroid_prot.setCoord(self.chimera.Coord(x, y, z))
            r.addAtom(centroid_prot)

            centroid_lig = m.newAtom("CENTROID", self.chimera.Element("CENTROID"))
            x, y, z = stack.ligandring_center
            centroid_lig.setCoord(self.chimera.Coord(x, y, z))
            r.addAtom(centroid_lig)

            b = grp.newPseudoBond(centroid_lig, centroid_prot)
            b.color = self.colorbyname('forest green')

            self.bs_res_ids += stack.proteinring_atoms
def show_stacking ( self ) : grp = self . getPseudoBondGroup ( "pi-Stacking-%i" % self . tid , associateWith = [ self . model ] ) grp . lineWidth = 3 grp . lineType = self . chimera . Dash for i , stack in enumerate ( self . plcomplex . pistacking ) : m = self . model r = m . newResidue ( "pseudoatoms" , " " , 1 , " " ) centroid_prot = m . newAtom ( "CENTROID" , self . chimera . Element ( "CENTROID" ) ) x , y , z = stack . proteinring_center centroid_prot . setCoord ( self . chimera . Coord ( x , y , z ) ) r . addAtom ( centroid_prot ) centroid_lig = m . newAtom ( "CENTROID" , self . chimera . Element ( "CENTROID" ) ) x , y , z = stack . ligandring_center centroid_lig . setCoord ( self . chimera . Coord ( x , y , z ) ) r . addAtom ( centroid_lig ) b = grp . newPseudoBond ( centroid_lig , centroid_prot ) b . color = self . colorbyname ( 'forest green' ) self . bs_res_ids += stack . proteinring_atoms
Visualizes pi-stacking interactions.