A command to list a summary of the secondary structure for a selection. Use like "ss my_protein" where "my_protein" is the name of the chain or structure in view.
from pymol import cmd
from pymol import stored
def ss(selection):
class SSE(object):
def __init__(self, start, typ):
self.start, self.typ = start, typ
self.end = -1
def __repr__(self):
return "%s-%s %s" % (self.start, self.end, self.typ)
stored.pairs = []
cmd.iterate("%s and n. ca" % selection, "stored.pairs.append((resi, ss))")
num, currentType = stored.pairs[0]
sses = [SSE(num, currentType)]
currentSSE = sses[0]
for resi, ssType in stored.pairs:
if ssType == currentType:
currentSSE.end = resi
else:
sses.append(SSE(resi, ssType))
currentSSE = sses[-1]
currentType = ssType
for sse in sses:
print sse
cmd.extend("ss", ss)
