Ss - Revision history

Bell: 6 revisions

2014-03-28T03:55:50Z

6 revisions

New page

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.

<source lang="python">
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)
</source>

[[Category:Script_Library|Secondary Structure Writer]]
[[Category:Structural_Biology_Scripts]]

B5foan at 14:53, 24 October 2007

2007-10-24T14:53:46Z

Gilleain: changed a loop variable to avoid name clashes.

2007-10-09T16:56:06Z

changed a loop variable to avoid name clashes.

Gilleain: New page: 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. def ss(selectio...

2007-10-09T10:20:07Z

New page: 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. <source lang="python"> def ss(selectio...

New page

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.

<source lang="python">
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(selection, "stored.pairs.append((resi, ss))")
num, currentType = stored.pairs[0]

sses = [SSE(num, currentType)]
currentSSE = sses[0]
for resi, ss in stored.pairs:
if ss == currentType:
currentSSE.end = resi
else:
sses.append(SSE(resi, ss))
currentSSE = sses[-1]
currentType = ss

for sse in sses:
print sse

cmd.extend("ss", ss)
</source>

@@ Line 2: / Line 2: @@
 <source lang="python">
 def ss(selection):
@@ Line 14: / Line 17: @@
      stored.pairs = []
-     cmd.iterate(selection, "stored.pairs.append((resi, ss))")
+     cmd.iterate("%s and n. ca" % selection, "stored.pairs.append((resi, ss))")
      num, currentType = stored.pairs[0]

@@ Line 19: / Line 19: @@
      sses = [SSE(num, currentType)]
      currentSSE = sses[0]
-     for resi, ss in stored.pairs:
+     for resi, ssType in stored.pairs:
-         if ss == currentType:
+         if ssType == currentType:
              currentSSE.end = resi
          else:
-             sses.append(SSE(resi, ss))
+             sses.append(SSE(resi, ssType))
              currentSSE = sses[-1]
-             currentType = ss
+             currentType = ssType
      for sse in sses: