I think we should assume each leave has a radii, because less complex code probably means faster :) in my option, read_pdb should add a radius by default and then if someone want to overwrite the values he can in a update_radii function. On Nov 1, 2010, at 1:06 PM, Javier Velazquez wrote:
> How about a parameter add_radii (true/false)? > > On 10/31/10 4:30 PM, Daniel Russel wrote: >> If people are going to have to make a decision about radii or not, >> they might as well do it by calling add_radii after read_pdb. That >> is more general and avoids doubling the number of read_pdb >> functions (and read_mol2 functions). >> >> But if almost everyone who calls read_pdb call add_radii >> afterwards, we might as well save them the trouble of learning two >> functions (and avoid the mistake of trying to perform excluded >> volume computations with points, which I have done various times >> and I have seen others do many times too). If we added the radii, >> we could then assume that leaves in the hierarchy always have radii >> which would make various code less complex. >> >> A perhaps bigger issue is that we don't always know what radii to >> add, but I think we can provide a good enough guess for almost >> anything. >> >> On Oct 31, 2010, at 3:19 PM, Dina Schneidman wrote: >> >>> I think we can simply add additional function: >>> read_pdb_and_add_radii >>> that will do what the name suggests :) >>> >>> On Sat, Oct 30, 2010 at 6:45 PM, Daniel Russeldrussel@gmail.com >>> wrote: >>>> Hmmm, good point. Not sure supporting static executables is >>>> something to use to guide interface changes. We could just have >>>> read_pdb catch the exception as a hack to deal with incomplete >>>> IMP setups. BTW, there is now a function to set set search path >>>> for data at run time. >>>> >>>> >>>> On Oct 30, 2010, at 11:12 AM, Dina Schneidman wrote: >>>> >>>>> In that case any application will require the parameter files and >>>>> handling the paths to them. >>>>> I specifically added another way of adding radii to avoid >>>>> dealing with >>>>> those files (applications/saxs/profile.cpp). >>>>> >>>>> On Sat, Oct 30, 2010 at 9:31 AM, Daniel >>>>> Russeldrussel@gmail.com wrote: >>>>>> Given that >>>>>> - doing almost anything useful requires adding radii to atoms >>>>>> - we currently have only one way to do that >>>>>> - it generally doesn't matter what radii we use for atoms for >>>>>> most of what we do >>>>>> - one can always overwrite the radii with other values if one >>>>>> wants other values >>>>>> I propose the read_pdb function add radii to the atoms it >>>>>> creates. >>>>>> >>>>>> Comments? >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > -- > Javier Velazquez > Postdoc at Salilab, UCSF > 1700 4th st. Byers Hall, office 503. > 94158 San Francsico > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev