October 2009 - IMP-dev

IMP_check
by Keren Lasker 15 Oct '09

15 Oct '09

did it go away ? what should I use instead ??

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copyright notice check
by Keren Lasker 14 Oct '09

14 Oct '09

hi - was there any change in the copyright format? svn rejects commits due to copyright and file description errors that used to work in the past (I tried multiple files) .... thanks, keren.

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doxygen
by Daniel Russel 12 Oct '09

12 Oct '09

Doxygen is producing mostly useless documentation on the upgraded salilab linux boxes. Many functions created by macros do not show up for some reason. I don't have a good work around at this point. Sorry.

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How to iterate through the particles of a model ?
by Javier Ángel Velázquez Muriel 11 Oct '09

11 Oct '09

Could anybody provide an example of that, please? Thanks

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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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