Dear all,
When writing a python script you can add old xplor commands by running
xplor.command('<xplor-command>'). As a result, there are tasks that can be
performed redundantly in both the xplor and Python languages:
>seed = 322111
>xplor.command('set seed = i% end' % seed) # this...
>simWorld.setRandomSeed(seed) # is equivalent to this.
However, I've noticed that for certain other tasks the xplor and Python
interfaces are invisible to each other. For example,
>from ivm import IVM
>dyn = IVM()
># set up topology here (fix, group, etc.)
>dyn.autoTorsion()
>
># The flags include xplor command doesn't work.
>#command('flags exclude * include bonds angle impr vdw rama end')
>dyn.potList().removeAll()
>dyn.potList().add( XplorPot('BOND') )
>dyn.potList().add( XplorPot('ANGL') )
>dyn.potList().add( XplorPot('IMPR') )
>dyn.potList().add( XplorPot('VDW') )
>dyn.potList().add( XplorPot('RAMA') )
>
># set up dynamics parameters here.
>dyn.run()
In the above piece of script, setting the active energy terms using the
xplor "flags include" statement has no effect (and the dynamics would run
using the terms turned on by default). In this case, the xplor commands are
"invisible" in the python interface.
Is there a clear distinction between tasks that can be performed equally by
both interfaces (like setting the seed number), and others that should be
performed by either using the xplor commands or the python interface, but
not a mixture of both?
Thanks in advance. Best regards,
Guillermo Bermejo
PhD candidate
Chemistry Dept.
Carnegie Mellon University
Pittsburgh, Pa.
