Jason, what pitfalls? Are they still present in this script? http://pymolwiki.org/index.php/Get_raw_distances
Cheers, Thomas On 02/01/2012 04:01 PM, Jason Vertrees wrote: > Takanori, > > This is a very clever script -- well done! There are some pitfalls, > but in general this should work well. > > Cheers, > > -- Jason > > On Tue, Jan 31, 2012 at 6:01 PM, Takanori Nakane > <t.nak...@mail.mfour.med.kyoto-u.ac.jp> wrote: >> Hi Abhinav and Jason, >> >>> The underlying C-object for a measurement does not support >>> iterate/alter. This is rather silly; PyMOL should be able to tell you >>> what's in the object. >> >> As an ad-hoc hack, I wrote a Python script to access internal C-object >> of distance representation and convert it to atom name. >> >> Save the script to somewhere and >> >> run script_name.py >> list_dist >> >> will do the job. >> >> Takanori Nakane >> >> === Script start === >> >> from pymol import cmd >> >> def parseDistObj(obj): >> if (obj[5][0][3][10] != 1): # 'show dashed' flag >> return "" >> points = obj[5][2][0][1] >> ret = [] >> for i in range(len(points) / 6): >> ret.append([(points[i * 6], points[i * 6 + 1], points[i * 6 + 2]), >> (points[i * 6 + 3], points[i * 6 + 4], points[i * 6 >> + 5])]) >> return ret >> >> def list_dist(): >> names = cmd.get_session()['names'] >> >> dist_pairs = [] >> for obj in names: >> if (obj == None): >> continue >> if (obj[1] == 0 and obj[4] == 4): >> dist_pairs += parseDistObj(obj) >> >> namespace = {'dict': {}, 'a': 1} >> dict = {} >> cmd.iterate_state(1, 'all', 'dict[x,y,z] = >> chain+"/"+resn+resi+"/"+name' , space=namespace) >> >> dict = namespace['dict'] >> for pair in dist_pairs: >> print dict.get(pair[0], '?') + " - " + dict.get(pair[1], '?') >> >> cmd.extend('list_dist', list_dist) -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net