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

[Roland Schulz]

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()


> 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.

>
> For #1 may be its time to reimplement needed functions using new api.
>
Any help with that is greatly appreciated :-)


> 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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