[gmx-developers] options file handling in master

[David van der Spoel]

On 2013-11-08 18:41, Alexey Shvetsov wrote:
> Hi!
>
> David are you going to implement sfactors as xml file like it was done
> in sassena?
I have done it using xml indeed. Do you have a link for this implementation?

Anyway my collaborators have made a new polynomial representation of the 
structure factors (paper submitted). Of course you can download the 
implementation from gerrit. In fact the analysis tool does not work 
completely yet, since everything is in the new code base.

We have looked at g_sans as well and we noticed the similarities with 
g_sans (and there is even g_saxs). It would be good to collaborate to 
merge these tools as far as possible.

@Teemu: Ok I will add the xml file format. Hopefully we can move more 
stuff to XML soon.

>
> PS I wanna submit reimplementation of g_sans using new api after you
> WAXS stuff will be merged
>
> David van der Spoel писал 08-11-2013 17:47:
>> Hi,
>>
>> I'm trying to implement new analysis tools using Teemu's framework.
>> For some reason this only supports a subset of all gromacs files, and
>> uses new enumerated types to distinguish them. E.g.:
>>
>> options->addOption(FileNameOption("sfac").filetype(eftGenericData)
>>                    .inputFile().required()
>>                    .store(&fnSfactor_).defaultBasename("sfactor")
>>                    .description("Structure factors"));
>>
>> I would like this file to have the .xml extension, however in
>> options/filenameoption.cpp we only have:
>>
>> FileTypeRegistry::FileTypeRegistry()
>> {
>>     filetypes_.resize(eftOptionFileType_NR);
>>     registerType(eftTopology,    efTPS);
>>     registerType(eftTrajectory,  efTRX);
>>     registerType(eftPDB,         efPDB);
>>     registerType(eftIndex,       efNDX);
>>     registerType(eftPlot,        efXVG);
>>     registerType(eftGenericData, efDAT);
>> }
>>
>> note that the eftXXX are different from efXXX in fileio/filenm.h.
>>
>> Main question therefore is:
>> Why would we not allow all the old field types?
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se