On Feb 2, 2009, at 1:43 AM, Daniel Russel wrote:
> > On Feb 2, 2009, at 1:40 AM, Keren Lasker wrote: > >> >> On Feb 2, 2009, at 1:39 AM, Daniel Russel wrote: >> >>> >>> On Feb 2, 2009, at 1:23 AM, Keren Lasker wrote: >>> >>>> I see your point, but when you write a pdb file after reading it >>>> - sometime you want to keep the same atom indexes for analysis - >>>> can it be an option when reading a pdb file to store the indexes >>>> as well ? ( like in modeller) >>> Easy enough to add although it might be good enough to ensure that >>> the hierarchy is traversed for writing in the same order in which >>> it is read from the file. >>> >>> Then the numbers will be the same and you don't have the issue of >>> what to do with invalid indexes. >> This is true if you do not read two pdbs separately to the same >> model and ask for the indexes of the second one. > True, but this will get screwed up on writing anyway as all the > atoms need to have distinct ids in the written pdb. Or am I > misunderstanding your scenario? yes - I was thinking of writing only mol2, by giving the Particle that represents mol2 ( regardless to mol1) - so the ids should be ok. > > > I guess I would propose having a "source_pdb_index" attribute (or > something similar) in atoms, but that it always gets ignored on > writing (since either it is already correct, in which case you might > as well ignore it, or it is incorrect, in which case you have to > ignore it). would be useful for the scenario above I think. > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev