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This module provides example showing how to implement various types of objects and functionality in IMP.
The overview section of the module page can contain any doxygen markup as well as references to IMP classes such as IMP::Model. See the doxygen web site for a full description of what can be done in doxygen.
Remember to escape characters to keep python happy.
Examples:
Author(s): Daniel Russel
Version: SVN.r14091
License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Publications:
IMP and how to apply them to biological problems.Classes | |
| class | ExampleComplexRestraint |
| Restrain the diameter of a set of points. More... | |
| class | ExampleConstraint |
| A trivial constraint that just increments a counter. More... | |
| class | ExampleDecorator |
| A simple decorator which adds a name to a particle. More... | |
| class | ExamplePairScore |
| Apply a harmonic to the distance between two particles. More... | |
| class | ExampleRefCounted |
| An example simple object which is reference counted. More... | |
| class | ExampleRestraint |
| Restrain a particle to be in the x,y plane. More... | |
| class | ExampleSingletonModifier |
| An example singleton modifer. More... | |
| class | ExampleSubsetFilterTable |
| class | ExampleTemplateClassD |
| A line segment templated on the dimension. More... | |
| class | ExampleUnaryFunction |
| A simple unary function. More... | |
Typedefs | |
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typedef base::Vector< Pointer < ExampleRefCounted > > | ExampleRefCounteds |
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typedef base::Vector < WeakPointer < ExampleRefCounted > > | ExampleRefCountedsTemp |
| typedef ExampleTemplateClassD< 3 > | ExampleTemplateClass3D |
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typedef base::Vector < ExampleTemplateClassD< 3 > > | ExampleTemplateClass3Ds |
Functions | |
| Restraint * | create_chain_restraint (const ParticlesTemp &ps, double length_factor, double k, std::string name) |
| container::ClosePairContainer * | create_excluded_volume (const ParticlesTemp &ps, double k, std::string name) |
| core::Mover * | create_serial_mover (const ParticlesTemp &ps) |
| unsigned int | get_number_of_incidences (const ParticlesTemp &psa, const ParticlesTemp &psb, double point_distance) |
| void | optimize_assembly (Model *m, const ParticlesTemp &components, const RestraintsTemp &interactions, const RestraintsTemp &other_restraints, const algebra::BoundingBox3D &bb, PairScore *ev, double cutoff, const PairPredicates &excluded=PairPredicates()) |
| void | optimize_balls (const ParticlesTemp &ps, const RestraintsTemp &rs=RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), base::LogLevel ll=DEFAULT) |
| template<class ParticlesList , class BoundingVolume > | |
| void | randomize_particles (const ParticlesList &ps, const BoundingVolume &bv) |
| template<class RigidBody , class BoundingVolume > | |
| void | randomize_rigid_body (RigidBody rbi, const BoundingVolume &bv) |
| Restraint* IMP::example::create_chain_restraint | ( | const ParticlesTemp & | ps, |
| double | length_factor, | ||
| double | k, | ||
| std::string | name | ||
| ) |
Restraint the passed particles to be connected in a chain. The distance between consecutive particles is length_factor*the sum of the radii.
Note, this assumes that all such chains will be disjoint and so you can use the container::ExclusiveConsecutivePairFilter if you want to filter out all pairs of particles connected by such chain restraints.
The restraint is not added to the model.
| container::ClosePairContainer* IMP::example::create_excluded_volume | ( | const ParticlesTemp & | ps, |
| double | k, | ||
| std::string | name | ||
| ) |
Create an excluded-volume style ClosePairsContainer based score.
| core::Mover* IMP::example::create_serial_mover | ( | const ParticlesTemp & | ps | ) |
Create a serial mover from a list of core::XYZR particles.
| unsigned int IMP::example::get_number_of_incidences | ( | const ParticlesTemp & | psa, |
| const ParticlesTemp & | psb, | ||
| double | point_distance | ||
| ) |
Return the number of times particles from one set are close to those from another set.
| void IMP::example::optimize_assembly | ( | Model * | m, |
| const ParticlesTemp & | components, | ||
| const RestraintsTemp & | interactions, | ||
| const RestraintsTemp & | other_restraints, | ||
| const algebra::BoundingBox3D & | bb, | ||
| PairScore * | ev, | ||
| double | cutoff, | ||
| const PairPredicates & | excluded = PairPredicates() |
||
| ) |
Provide an example of a more involved protocol for assembly a complex. The protocol adds the particles one at a time based on how well connected they are to the already added particles (in the interaction graph). After each addition, the assembly is optimized. The protocol seems to work at assembling the residues of a protein from a truncated distance matrix.
| void IMP::example::optimize_balls | ( | const ParticlesTemp & | ps, |
| const RestraintsTemp & | rs = RestraintsTemp(), |
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| const PairPredicates & | excluded = PairPredicates(), |
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| const OptimizerStates & | opt_states = OptimizerStates(), |
||
| base::LogLevel | ll = DEFAULT |
||
| ) |
Take a set of core::XYZR particles and relax them relative to a set of restraints. Excluded volume is handle separately, so don't include it in the passed list of restraints.
| void IMP::example::randomize_particles | ( | const ParticlesList & | ps, |
| const BoundingVolume & | bv | ||
| ) |
Randomize the positions of a set of particles within a bounding volume. Rigid bodies have their orientation randomized too.