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869 discussions

How to use ScoreState ?
by Javier Ángel Velázquez Muriel 11 Oct '09

11 Oct '09

After consulting the help, I can't figure out the use of ScoreState. I does not seem to have a set_model function, as Restraint has. Is there any way of assigning ScoreStates to Restraints or Models ? Thanks

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Proposed change to checks and asserts
by Daniel Russel 11 Oct '09

11 Oct '09

This proposal tries to address two problems: - for implementers: it is no clear what the difference between IMP_check and IMP_assert is and when one should be used and not the other - for users: getting nice feedback about incorrect usage of IMP also turns on all sorts of (slow) checks of various internal implementation details. To address this, I propose: - provide IMP_implementation_check and IMP_usage_check macros - provide a methods to turn on and off the two different types of checks independently - remove the concept of check levels To implement the proposal I would do: - replace all IMP_assert with IMP_implemenetation_check - replace all IMP_check with IMP_usage_check - debug mode, by default, has both sorts of checks enabled - release mode has just usage checks - fast mode has none

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This week in IMP
by Daniel Russel 10 Oct '09

10 Oct '09

IMP::ScoreState and IMP::Restraint now better track the set of particles that they use and the dependencies between the particles. To this end, a new base class IMP::Interaction has been added with methods to get the inter-particle interactions and the set of particles used. .cpp, .h, .py and SConscript files which contain the string "DO NOT COMMIT" will be rejected on checkin. Use this to mark experimental or debugging changes you are making so you don't accidentally commit them. The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly. The PDB reader does not throw an exception if the pdb file contains a ligand.

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track changes
by Keren Lasker 09 Oct '09

09 Oct '09

hello, As we all know there are many changes to IMP code, and it is very hard to keep track of all of them. "IMP this week" is good for getting an overview of changes, but it does not cover everything. Is there a way to subscribe to get a notification for changes made on specific files ? thanks, Keren.

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Fwd: design discussions
by Javier Ángel Velázquez Muriel 09 Oct '09

09 Oct '09

2009/10/9 Daniel Russel <drussel(a)gmail.com> > nt of the cases, or even 100% (why should I call get_is_molecule() if I >> know that is going to be true all the time ? ). It is far more difficult, >> but far more useful, to agree of what we expect to get after a PDB, and how >> we are going to organize our structures in IMP into hierarchies. >> > You need some way of traversing the resulting hierarchy and telling what > you are looking at. Say read_pdb returns a Hierarchy. You then have to go > through the children of the node and determine which is a protein and which > is a ligand if you want to do much useful with it. The docs for the read_pdb > function can't possibly specify the answer. If you are writing code that > knows the pdb that is being loaded, then you can hard code it, but that is > not always possible (say you are writing something like modpipe or an > application to handle fitting into em maps). > > Or you load a protein and decide you want to define subdomains. You then > modify the hierarchy to have a node corresponding to the structure. Some > code which alter traverses the hierarchy (such as code to build a simplified > representation), may need to know when it has gotten to the atoms or > residues (it can't assume a constant structure). > Then you're simply talking about labeling the contents of the Hierarchy. But again, far more useful is to agree on how we are going to organize Hierarchies and how everybody thinks we should treat atomic structures, or structures in general. > > Together with Keren, I can give suggestions for low resolution structures. >> > Looking forwards to it. > > We'll do > _______________________________________________ > IMP-dev mailing list > IMP-dev(a)salilab.org > https://salilab.org/mailman/listinfo/imp-dev >

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Multichain proteins
by Daniel Russel 09 Oct '09

09 Oct '09

Does it make sense to talk about a protein which consists of more than one chain? I've heard people use the words that way (and there are google hits, but not a huge number), but it was suggested that this is a misuse of the words. It would make the atom hierarchy a bit simpler to say a protein is a single chain and has HierarchyType PROTEIN (and to remove the CHAIN type). Authoritative answers? Votes?

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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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