> atom = IMP::atom::Atom::create(p,IMP::atom::AT_CA) > connecting this atom to a molecule ( with residue and chain of course)
I tried to do the same thing now, i.e. print single coordinate in PDB format. something that normally should take 2 lines of code and ended up with 14 lines. m = IMP.Model() rp = IMP.Particle(m) ap = IMP.Particle(m) cp = IMP.Particle(m); chain = IMP.atom.Chain.create(cp, 'A') residue = IMP.atom.Residue.create(rp) atom = IMP.atom.Atom.create(ap, IMP.atom.AT_CA) xyz = IMP.core.XYZ.create(ap) hcd = IMP.atom.Hierarchy.cast(cp) hrd = IMP.atom.Hierarchy.cast(rp) had = IMP.atom.Hierarchy.cast(ap) hcd.add_child(hrd) hrd.add_child(had) print atom.get_pdb_string()
Is there a way to make it simpler? Am I the only one who thinks it should be simpler?
Dina
> On Aug 6, 2009, at 7:05 PM, Daniel Russel wrote: > >> It should get it from the aromtype for all properly initialized atom >> types. If it isn't currently doing that blame Dina :-) we should be able to >> fix it easily. >> >> I'm not sure there is a reason to store the element in the particle rather >> than just look it up from the atomtype when get_element is called. Is there? >> >> >> >> On Aug 6, 2009, at 6:31 PM, Keren Lasker kerenl@salilab.org wrote: >> >>> seems that now element is needed for writing atoms in pdb format. >>> Would not it make sense to set the value of element in Atom::create()? >>> _______________________________________________ >>> 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 >