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

[Roland Schulz]

On Mon, Feb 4, 2013 at 3:41 PM, Schulz, Roland <rschulz3 at utk.edu> wrote:

>
>
>
> On Mon, Feb 4, 2013 at 2:35 PM, Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>wrote:
>
>> В письме от 4 февраля 2013 10:51:29 пользователь Roland Schulz написал:
>> > On Mon, Feb 4, 2013 at 4:00 AM, Alexey Shvetsov
>>
>
>
>> >
>>
>> > > 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?
>>
> Why would you want to copy sel? I thought it would be sufficient to copy
> x. angle.cpp has a copy_pos. It might be nice to have that in Selection,
> e.g.:
>  void copy_x(int first, int last, rvec x[]) const;
>

Actually that suggestion is very non-std like. It combines access to the
complete range of coordinates ,with the algorithm (copy), and thus is less
flexible because these two things can't be combined differently.
So it might be better to provide: "iterator xBegin()" and "iterator
xEnd()". That would allow to copy using:
"std::copy(sel.xBegin(),sel.xEnd(),out)".
But I'm not sure we discussed how much we want to make use of iterators.
Our modified version changes that mpp uses iterators and we think it got
better/more flexible by doing that. I think Teemu tried to avoid them. So
this is probably something we should discuss.

Roland



>
>> > > 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/
>>
>
>  Great! But given that those functions are general they shouldn't be in
> the ProteinFilamentGeometry class.
>
>  Roland
>
>>
>>  >
>>
>> > > 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
>>
>
>
>
>  --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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