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
def getAromaticRes(receptor):
# TODO add acids and amides?
aromatic_res = { "PHE": ["A"],
"TYR": ["A"],
"HIS": ["A", "N", "NA"],
"TRP": ["A", "N", "NA"],
"ARG": ["N", "C" , "NA"],
"DA" : ["A", "NA", "N"], # DNA
"DC" : ["A", "N", "NA"],
"DT" : ["A", "N", "NA"],
"DG" : ["A", "N", "NA"],
"A" : ["A", "NA", "N"], # DNA/RNA
"C" : ["A", "N", "NA"],
"G" : ["A", "N", "NA"],
"T" : ["A", "N", "NA"],
"U" : ["A", "N", "NA"],
}
residues = {}
special = [] # must be treated as a ligand part
for a in receptor:
a = a.strip()
rtype = a[16:21].strip().upper() # NOTE: we can recognize only all caps!
if a.startswith("HETATM"):
special.append(a)
elif a.startswith('ATOM') and rtype in aromatic_res.keys():
if hf.getAtype(a) in aromatic_res[rtype]:
res_id = hf.pmvAtomStrip(a).rsplit(":",1)[0] # A:GLY48:N -> A:GLY48
if not res_id in residues.keys():
residues[res_id] = []
residues[res_id].append(a)
if special and DEBUG:
print "found potential co-factor: %d" % len(special)
for a in special: print a
return residues, special # residues = { "A:GLY48" : [ atom, atom, atom..]}
