IMP-dev

imp-dev@salilab.org

868 discussions

AnglesRestraint
by Daniel Russel 13 Feb '08

13 Feb '08

I think it would be good to have an AnglesRestraint which stores a list of chains and applies an AngleRestraint-like restraint to each triple in each chain. It is easier to set up and maintain than a whole mess of AngleRestraints and more efficient too. Comments? //! Restraint the angles between particles /** Currently the particles can be added as chains and the angle of each three successive particles in the chain is restrained. \ingroup restraint */ class IMPDLLEXPORT AnglesRestraint : public Restraint { public: //! Create the angle restraint. /** \param[in] score_func Scoring function for the restraint. */ AnglesRestraint(UnaryFunction* score_func); virtual ~AnglesRestraint(){} IMP_RESTRAINT("0.5", "Daniel Russel"); //! Add a chain of particles /** Each three successive particles are restrained*/ void add_chain(const Particles &ps); //! Clear all the store chains void clear_chains(); protected: std::auto_ptr<UnaryFunction> score_func_; std::vector<int> chain_splits_; };

2 2

Angles restraint
by Daniel Russel 13 Feb '08

13 Feb '08

I implemented a collective version of the AngleRestraint. It maintains a bunch of chains (more interesting topology can be added later) and applies the same unary function to each angle along each chain. As before, SConscript etc are not included. %pythonprepend AnglesRestraint::AnglesRestraint %{ args[0].thisown=0 %}

3 3

kernel/src/doc
by Daniel Russel 12 Feb '08

12 Feb '08

Why is it there rather than in kernel/doc? Is it used? Especially since there is not much reason otherwise to have doxygen parse kernel/ src (since such files don't define the API).

1 0

Pulling out the macros
by Daniel Russel 12 Feb '08

12 Feb '08

It appears that we don't need to have separate copies of the macros in the IMP_macros.i. I have pulled the macros out into separate headers which are then %included into that file.

1 0

pdb patch
by Daniel Russel 12 Feb '08

12 Feb '08

This patch makes IMP get the atom name from the right modeller field.

2 1

Nonbonded list try 2
by Daniel Russel 12 Feb '08

12 Feb '08

Here is the next crack at submitting the nonbonded list. Something is undoubtedly missing. The changes since the last submission include - the grid is now updated lazily. A MaxChangeScoreState is used to accomplish this. That class just keeps track of the max change of a set of variables - various bugs have been fixed Already forgot something These changes to IMP.i may or may not be needed %pythonprepend NonbondedListScoreState::add_bonded_list %{ args[1].thisown=0 %} %pythonprepend NonbondedRestraint::NonbondedRestraint %{ args[1].thisown=0 %} %pythonprepend BondDecoratorRestraint::BondDecoratorRestraint %{ args[1].thisown=0 %}

1 0

MonteCarlo
by Daniel Russel 12 Feb '08

12 Feb '08

Keren was interested in Monte Carlo optimization, so I thought I might submit the one I wrote. It is structured as an optimizer coupled with a set of Movers which propose moves. The optimizer holds a collection of Movers and a local optimizer (which can be used to mix local optimization with monte-carlo). Current movers take a set of particles and a set of attributes and perturb all of those attributes on each of the particles either uniformly in a a ball or with a normal distribution. A class called MoveGuard keeps track of the information necessary to revert if the monte carlo step is rejected. Note that as it stands, writing a Mover in Python would take noticeably more work as the macro does a good bit of work. As a note, my current implementation uses the boost random number library. I think we should probably make boost a required dependency since - it is really useful (I could easily write better iterators for various things) - all linux systems have builds these days (mostly installed by default) and we distribute mac and windows binaries (and the important boost bits are header-only affairs)

2 1

default constructor on vector3d
by Daniel Russel 12 Feb '08

12 Feb '08

1 0

ListRestraint
by Daniel Russel 12 Feb '08

12 Feb '08

Here is a restraint which applies a singleton score to a list of particles. There is also a singleton score which acts on the distance to a fixed point. This restraint should probably replace the SphericalRestraint. %pythonprepend ListRestraint::ListRestraint %{ args[1].thisown=0 %} %pythonprepend DistanceToSingletonScore::DistanceToSingletonScore %{ args[1].thisown=0 %}

1 0

ConnectivityRestraint
by Daniel Russel 12 Feb '08

12 Feb '08

Here is a new connectivity restraint and some simple tests. The following code needs to be added to IMP.i also %pythonprepend ConnectivityRestraint::ConnectivityRestraint %{ args[0].thisown=0 %}

1 0

← Newer
1
...
77
78
79
80
81
82
83
...
87
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

IMP-dev