For each bond that has been determined to be important, a line gets drawn.

def draw_hydrogen_bonds(self,color="black"):
		"""For each bond that has been determined to be important, a line gets drawn.
		"""
		self.draw_hbonds=""
		if self.hbonds!=None:
			for bond in self.hbonds.hbonds_for_drawing:
				x = str((self.molecule.x_dim-self.molecule.molsize1)/2)
				y = str((self.molecule.y_dim-self.molecule.molsize2)/2)
				self.draw_hbonds ="<g id='"+str(bond[0])+"' class='HBonds' transform='translate("+x+","+y+")' x='"+x+"' y='"+y+"'>'"
				atom = self.topology_data.universe.atoms[bond[0]-1] #zero-based index vs one-based index
				residue = (atom.resname, str(atom.resid), atom.segid)
				if bond[2] in ["N","O","H"]:
					#backbone interactions
					self.draw_hbonds=self.draw_hbonds+"<line id='"+str(bond[0])+"' class='HBonds' x1='"+str(int(self.molecule.nearest_points_coords[residue][0]))+"' y1='"+str(int(self.molecule.nearest_points_coords[residue][1]))+"' x2='"+str(float(self.molecule.ligand_atom_coords_from_diagr[bond[1]][0]))+"' y2='"+str(float(self.molecule.ligand_atom_coords_from_diagr[bond[1]][1]))+"' style='stroke:white;stroke-width:15' />"
					self.draw_hbonds=self.draw_hbonds+"<line id='"+str(bond[0])+"' class='HBonds' x1='"+str(int(self.molecule.nearest_points_coords[residue][0]))+"' y1='"+str(int(self.molecule.nearest_points_coords[residue][1]))+"' x2='"+str(float(self.molecule.ligand_atom_coords_from_diagr[bond[1]][0]))+"' y2='"+str(float(self.molecule.ligand_atom_coords_from_diagr[bond[1]][1]))+"' style='stroke:"+color+";stroke-width:4' />"
				else:
					#sidechain interactions
					self.draw_hbonds=self.draw_hbonds+"<line id='"+str(bond[0])+"' class='HBonds'  x1='"+str(int(self.molecule.nearest_points_coords[residue][0]))+"' y1='"+str(int(self.molecule.nearest_points_coords[residue][1]))+"' x2='"+str(float(self.molecule.ligand_atom_coords_from_diagr[bond[1]][0]))+"' y2='"+str(float(self.molecule.ligand_atom_coords_from_diagr[bond[1]][1]))+"' style='stroke:white;stroke-width:15' />"
					self.draw_hbonds=self.draw_hbonds+"<line id='"+str(bond[0])+"' class='HBonds' stroke-dasharray='5,5'  x1='"+str(int(self.molecule.nearest_points_coords[residue][0]))+"' y1='"+str(int(self.molecule.nearest_points_coords[residue][1]))+"' x2='"+str(float(self.molecule.ligand_atom_coords_from_diagr[bond[1]][0]))+"' y2='"+str(float(self.molecule.ligand_atom_coords_from_diagr[bond[1]][1]))+"' style='stroke:"+color+";stroke-width:4' />"
				self.draw_hbonds+="</g>"