dear all,
we tried to set the indexes of a fragment explicitly. however, the procedure seems to be incredibly slow in the following example where we tried to add residue numbers to a particle 'frag' (set up as a fragment). somehow, the last line takes ages (dies?). any hints would be appreciated.
thanks
pia & frido
rs= IMP.Ints() for ii in (ifirst, ilast+1): rs.append(ii) tfrag = IMP.atom.Fragment(frag) tfrag.set_residue_indexes(rs)
we just found out that we created the particle as a Domain and tried to process it as a fragment. sorry about that (albeit an error message would be helpful to prevent us from posting such problems). anyways, is there any way to alter the residue range of a Domain after setting it up?
thanks
pia & friedrich
Am 19.01.2011 um 10:20 schrieb Pia Unverdorben:
> dear all, > > we tried to set the indexes of a fragment explicitly. however, the procedure seems to be incredibly slow in the following example where we tried to add residue numbers to a particle 'frag' (set up as a fragment). somehow, the last line takes ages (dies?). > any hints would be appreciated. > > thanks > > pia & frido > > rs= IMP.Ints() > for ii in (ifirst, ilast+1): > rs.append(ii) > tfrag = IMP.atom.Fragment(frag) > tfrag.set_residue_indexes(rs) > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
When running with checks turned on there should be an error message (if not, that is a bug). Are you sure checks were turned on?
On Jan 19, 2011, at 1:27 AM, Pia Unverdorben wrote:
> we just found out that we created the particle as a Domain and tried to process it as a fragment. sorry about that (albeit an error message would be helpful to prevent us from posting such problems). When running with checks turned on there should be an error message (if not, that is a bug). Are you sure checks were turned on?
> anyways, is there any way to alter the residue range of a Domain after setting it up? not a nice way at the moment. But you can set the "domain_begin" and "domain_end" int attributes of the particle until we add one.
> thanks > > pia & friedrich > > Am 19.01.2011 um 10:20 schrieb Pia Unverdorben: > >> dear all, >> >> we tried to set the indexes of a fragment explicitly. however, the procedure seems to be incredibly slow in the following example where we tried to add residue numbers to a particle 'frag' (set up as a fragment). somehow, the last line takes ages (dies?). >> any hints would be appreciated. >> >> thanks >> >> pia & frido >> >> rs= IMP.Ints() >> for ii in (ifirst, ilast+1): >> rs.append(ii) >> tfrag = IMP.atom.Fragment(frag) >> tfrag.set_residue_indexes(rs) >> _______________________________________________ >> 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
nope, checks were not turned on to keep the code fast. good that you remind us of switching it on for debugging. a neat way of changing domain residue numbers would be appreciated, albeit we changed our code meanwhile so that the need is not pressing.
tx
frido
On Wed, Jan 19, 2011 at 4:48 PM, Daniel Russel drussel@gmail.com wrote: > When running with checks turned on there should be an error message (if not, that is a bug). Are you sure checks were turned on? > > On Jan 19, 2011, at 1:27 AM, Pia Unverdorben wrote: > >> we just found out that we created the particle as a Domain and tried to process it as a fragment. sorry about that (albeit an error message would be helpful to prevent us from posting such problems). > When running with checks turned on there should be an error message (if not, that is a bug). Are you sure checks were turned on? > > >> anyways, is there any way to alter the residue range of a Domain after setting it up? > not a nice way at the moment. But you can set the "domain_begin" and "domain_end" int attributes of the particle until we add one. > >> thanks >> >> pia & friedrich >> >> Am 19.01.2011 um 10:20 schrieb Pia Unverdorben: >> >>> dear all, >>> >>> we tried to set the indexes of a fragment explicitly. however, the procedure seems to be incredibly slow in the following example where we tried to add residue numbers to a particle 'frag' (set up as a fragment). somehow, the last line takes ages (dies?). >>> any hints would be appreciated. >>> >>> thanks >>> >>> pia & frido >>> >>> rs= IMP.Ints() >>> for ii in (ifirst, ilast+1): >>> rs.append(ii) >>> tfrag = IMP.atom.Fragment(frag) >>> tfrag.set_residue_indexes(rs) >>> _______________________________________________ >>> 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 > >
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Daniel Russel -
Friedrich Foerster -
Pia Unverdorben