Re: [PyMOL] Writing Hbond list

[Jason V. <jas...@sc...>]

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 <ma...@bl...> 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
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120