[gmx-developers] Some thoughts about new trajectory analisys api

[Alexey Shvetsov]

В письме от 4 февраля 2013 10:51:29 пользователь Roland Schulz написал:
> On Mon, Feb 4, 2013 at 4:00 AM, Alexey Shvetsov 
<alexxy at omrb.pnpi.spb.ru>wrote:
> > Hi all!
> > 
> > Well, new trajectory analisys api looks good, but it has some caveates.
> > 1. Its incompatible with most functions in old gmxlib (e.g. Cannot use
> > functions like reset_x, do_fit, calc_xcm etc.).
> 
> You can convert sel to atom_id by:
> sel_[i].atomIndices().data()

Aha ok then.
> 
> > 2. It may be easyer to work with atomdata if selections will not be marked
> > static. E.g. sel.position(i).x()
> 
> I suppose you mean const? I think it makes sense that they are const. I
> think you should make a copy of them before modifying them.
>

Ghmm may be there should be some kind of helper function to copy sel class?
 
> > For #1 may be its time to reimplement needed functions using new api.
> 
> Any help with that is greatly appreciated :-)
Well I'll reimplement some needed functions like i did in 
https://gerrit.gromacs.org/#/c/2108/
> 
> > Is there a way to mark output or input files non optional with predefined
> > value
> > like it was possible with old api?
> 
> See defaultBasename and required
> 
> Roland
> 

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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