Iterate sses - Revision history

Bell: 3 revisions

2014-03-28T03:06:31Z

3 revisions

Pyadmin: 1 revision

2014-03-28T02:16:16Z

1 revision

New page

A slightly more complex version of [[ss]] that allows the user to pass in a function to act on the sse list. Of course, this requires the user to know about the internals of the sse class, but since this code is all open I doubt that matters..

<source lang="python">
def iterate_sses(selection, action):

class SSE(object):

def __init__(self, start, typ, sseNumber):
self.start, self.typ = start, typ
self.end = -1
self.sseNumber = sseNumber

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]

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

for sse in sses:
action(sse)

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

As an example, here is a function that makes a series of selections, one for each sse, called "H1", "E2", and so on. Use it like: "iterate_sses('my_protein', doSelect)".
<source lang="python">
def doSelect(sse):
cmd.select("%s%s" % (sse.typ, sse.sseNumber), "i. %s-%s" % (sse.start, sse.end))
</source>

[[Category:Script_Library|Iterate SSes]]
[[Category:Structural_Biology_Scripts]]

Gilleain: same change as for the ss command.

2007-10-09T16:57:18Z

same change as for the ss command.

Gilleain: New page: A slightly more complex version of ss that allows the user to pass in a function to act on the sse list. Of course, this requires the user to know about the internals of the sse class,...

2007-10-09T10:25:41Z

New page: A slightly more complex version of ss that allows the user to pass in a function to act on the sse list. Of course, this requires the user to know about the internals of the sse class,...

New page

A slightly more complex version of [[ss]] that allows the user to pass in a function to act on the sse list. Of course, this requires the user to know about the internals of the sse class, but since this code is all open I doubt that matters..

<source lang="python">
def iterate_sses(selection, action):

class SSE(object):

def __init__(self, start, typ, sseNumber):
self.start, self.typ = start, typ
self.end = -1
self.sseNumber = sseNumber

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]

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

for sse in sses:
action(sse)

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

As an example, here is a function that makes a series of selections, one for each sse, called "H1", "E2", and so on. Use it like: "iterate_sses('my_protein', doSelect)".
<source lang="python">
def doSelect(sse):
cmd.select("%s%s" % (sse.typ, sse.sseNumber), "i. %s-%s" % (sse.start, sse.end))
</source>

← Older revision	Revision as of 03:06, 28 March 2014
(No difference)

@@ Line 21: / Line 21: @@
      sses = [SSE(num, currentType, sseNumber)]
      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:
              sseNumber += 1
-             sses.append(SSE(resi, ss, sseNumber))
+             sses.append(SSE(resi, ssType, sseNumber))
              currentSSE = sses[-1]
-             currentType = ss
+             currentType = ssType
      for sse in sses: