IMP-dev October 2009

imp-dev@salilab.org

7 participants
26 discussions

Re: [IMP-dev] design discussions
by Javier Ángel Velázquez Muriel 08 Oct '09

08 Oct '09

> > hi, >> >> I think that it would be much more productive to have discussion on major >> design changes in IMP meeting and not via emails. >> It would be preferable to raise issues in an email before the meeting and >> write an email with conclusions after the meeting. >> > > > Yes. Also, and perhaps more importantly, now IMP is at a level of maturity > when it is used by many people in the lab, so changes in it affect others. I > think that major changes and philosophical view should be discussed previous > implementation or changed. They "already done" things show a big tendency to > stay that way even if they could be improved. > >

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Loading multiple molecules from a pdb file
by Daniel Russel 08 Oct '09

08 Oct '09

We need to clean up what happens when multiple molecules are loaded from a PDB. My current favorite is to - make the current read_pdb only support loading a single protein (chain) from the first model of a PDB file and return it as a Hierarchy with the root being a PROTEIN. It can spit out warnings if there are other molecules in there. - add a read_model_from_pdb which loads all molecules from a given model in the PDB (defaulting to the first) and which returns an array of Hierarchy decorators each of which has a root of either a PROTEIN or a MOLECULE (or some other name to specify a molecule that is not a protein or nucleic acid). Thoughts?

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Re: [IMP-dev] [IMP-commits] r3874 - trunk/kernel/src
by Dina Schneidman 08 Oct '09

08 Oct '09

atom is still looking for PairFilter build/lib/libimp_atom.so: undefined reference to `IMP::PairFilter::PairFilter(std::basic_string<char, std::char_traits<char>, std::allocator<char> >)' On Thu, Oct 8, 2009 at 3:15 PM, Notification of IMP commits <imp-commits(a)salilab.org> wrote: > Author: drussel(a)SALILAB.ORG > Date: 2009-10-08 15:15:32 -0700 (Thu, 08 Oct 2009) > New Revision: 3874 > > Modified: > trunk/kernel/src/Particle.cpp > Log: > see if it commits this time > > Modified: trunk/kernel/src/Particle.cpp > =================================================================== > --- trunk/kernel/src/Particle.cpp 2009-10-08 22:08:26 UTC (rev 3873) > +++ trunk/kernel/src/Particle.cpp 2009-10-08 22:15:32 UTC (rev 3874) > @@ -11,6 +11,15 @@ > #include "IMP/internal/utility.h" > #include "IMP/internal/PrefixStream.h" > > +IMP_BEGIN_INTERNAL_NAMESPACE > +LockedParticleException::LockedParticleException(const Particle *p): p_(p){}; > +LockedParticleException::~LockedParticleException() throw(){} > + > +ParticleStorage::~ParticleStorage(){ > + if (shadow_) internal::unref(shadow_); > +} > +IMP_END_INTERNAL_NAMESPACE > + > IMP_BEGIN_NAMESPACE > > > > _______________________________________________ > IMP-commits mailing list > IMP-commits(a)salilab.org > https://salilab.org/mailman/listinfo/imp-commits >

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Last week in IMP
by Daniel Russel 05 Oct '09

05 Oct '09

- Some support for gather statistics has been added to Model<file:///flute1/home/drussel/src/IMP/svn/debug/doc/html/classModel.html>(see Model::set_gather_statistics()). If requested, an API can be provided so that the individual data points can be returned to programs. - A class RigidBodyDistancePairScore<file:///flute1/home/drussel/src/IMP/svn/debug/doc/html/classRigidBodyDistancePairScore.html>has been added which provides accelerated computations for the distance between two rigid bodies. - The swig input files were renamed from swig.i to swig.i-in to aid in dependency tracking. - rigid bodies now have two sets of particles associated with them in the various places they are used. One is the RigidBodyMember particles, as was previously the case. The other is defined through a refiner (and could be the RigidBodyMember if a RigidMembersRefiner<file:///flute1/home/drussel/src/IMP/svn/debug/doc/html/classRigidMembersRefiner.html>is used). The idea is that you sometimes want some particles which are transformed along with the rigid body, but which are not really part of the representation of the rigid body. Examples would include marker points or multiresolution representations of proteins.The RigidMembersRefiner is generally provided as a default, so the API doesn't change.

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MaximumChange* ScoreStates
by Daniel Russel 05 Oct '09

05 Oct '09

Does anyone use them directly? If not, I propose hiding them away.

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IMP_NEW
by Keren Lasker 04 Oct '09

04 Oct '09

hi, how can i safely delete an object generated by IMP_NEW ? thanks, Keren.

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IMP-dev October 2009