def findLigandRings(atoms):
matrix = hf.getDistMatrix(atoms)
bdist = 2.0 # angstrom of bond dinstance
graph = hf.makeGraph(nodes_list = range(len(matrix)), distance_matrix = matrix, cutoff = bdist**2)
rings5,rings6 = findRings(graph)
RING = rings5+rings6
ligand_rings = {}
for r in range(len(RING)):
# res name first...
# get the first atom PDB string in the ring
atstring = atoms[RING[r][0]][2]
ringname = hf.pmvAtomStrip(atstring)
ringname_short = ringname.rsplit(":",1)[0].strip()
if ringname_short:
c = 0
while ringname_short+":"+str(c) in ligand_rings.keys():
c+=1
if c > 20:
ringname_short = None
break
if ringname_short:
lnam = ringname_short+":"+str(c)
else:
lnam = "rng:"+str(r)
ligand_rings[lnam] = []
for a in RING[r]:
ligand_rings[lnam].append(atoms[a][2])
return ligand_rings
