Hi Martin,
I can think of two ways to achieve this. You can attempt to be tricky and add
from pymol import stored
stored.outFile = open("/my/myHbons.txt", 'w')
to your script and then inside the iterate commands instead of
'print "%1s/%3s`%s/%-4s " % (chain, resn, resi, name),')
put
'stored.outFile.write("%1s/%3s`%s/%-4s " % (chain, resn, resi, name)')
Or, second, you could just use "stored" to make a few lists to save
your data and then write those lists to disk:
from pymol import stored
stored.listA = []
> for pairs in hb:
> cmd.iterate("%s and index %s" % (pairs[0][0], pairs[0][1]),
> 'stored.listA.append( "%1s/%3s`%s/%-4s " % (chain, resn, resi,
> name)')
...
then after all your lists are created,
outFile = open("/tmp/myHbonds.txt", 'w')
for curLine in stored.listA:
outFile.write(curLine + "\n")
outFile.close()
which should write to the file /tmp/myHbonds.txt with your data.
Cheers,
-- Jason
On Thu, Aug 26, 2010 at 11:07 AM, Martin Hediger <[email protected]> wrote:
> Dear all
> I am using the script of Robert Campell to collect hydrogen bonds and
> the essential part looks like this:
>
> [collect pairs in hb by cmd.find_pairs]
> for pairs in hb:
> cmd.iterate("%s and index %s" % (pairs[0][0], pairs[0][1]),
> 'print "%1s/%3s`%s/%-4s " % (chain, resn, resi, name),')
>
>
> cmd.iterate("%s and index %s" % (pairs[1][0],pairs[1][1]),
> 'print "%1s/%3s`%s/%-4s " % (chain, resn, resi, name),')
>
>
> print "%.2f" % cmd.distance(hb_list_name, "%s and index %s" %
> (pairs[0][0], pairs[0][1]), "%s and index %s" %
> (pairs[1][0],
> pairs[1][1]))
>
> This nicely lists three columns, where the interacting pairs are shown
> together with the length of the hydrogen bond.
> I have now started various unsuccessfull attempts to direct the output
> of 'cmd.iterate(...)' to a file which I would like to process further
> (sorting for largest change for two different configurations, etc.).
>
> How do I direct the output from iterate to a file?
>
> Suggestions would be appreciated.
> Martin
>
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) [email protected]
(o) +1 (603) 374-7120
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Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
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