Hello everybody, this is my first post about my first python script, so I please you to forgive me if the error is stupid.
I wrote the script attached to align two dimer structures (both files are attached). Since I have problem to "reorder" the atoms in the xyz files, I used the "canonical" option of obabel on each monomer to have the atoms in each monomer sorted in the same way. At this point I merge the two monomer of the reference structure in only one object and I create two object from the second structure monomers, in order to be sure that at least in one object I have the two monomers ordered as in the reference. The problem is that when I try to run the script it works only at random (with the same file as argument). When it does not work it gets stuck taking 100% CPU on the "align.OBAling()" command. I have no idea why.... :( (Sometime it seems to be working than if you change really stupid thing (like commenting the last "print RMSD") the script gets stuck). Thank you Riccardo SI_generator.py <http://forums.openbabel.org/file/n4656488/SI_generator.py> Me-4T-Me_E.xyz <http://forums.openbabel.org/file/n4656488/Me-4T-Me_E.xyz> 4T_2aa_E-Me.xyz <http://forums.openbabel.org/file/n4656488/4T_2aa_E-Me.xyz> PS. If there is a better way to do the obtain the canonical atom order using pybel or openbabel directly form python... thank to tell me.... :) -- View this message in context: http://forums.openbabel.org/OBAlign-in-Python-works-at-random-tp4656488.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
