IMP
2.0.0
The Integrative Modeling Platform
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See IMP.example Overview for more information.
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 | |
typedef IMP::base::Vector < IMP::base::Pointer < ExamplePairScore > > | ExamplePairScores |
typedef base::Vector< Pointer < ExampleRefCounted > > | ExampleRefCounteds |
typedef base::Vector < WeakPointer < ExampleRefCounted > > | ExampleRefCountedsTemp |
typedef ExampleTemplateClassD< 3 > | ExampleTemplateClass3D |
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::MonteCarloMover * | create_serial_mover (const ParticlesTemp &ps) |
std::string | get_data_path (std::string file_name) |
Return the full path to installed data. More... | |
std::string | get_example_path (std::string file_name) |
Return the path to installed example data for this module. More... | |
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=base::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) |
Store a set of objects.
Definition at line 33 of file ExamplePairScore.h.
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.
Definition at line 32 of file creating_restraints.h.
container::ClosePairContainer* IMP::example::create_excluded_volume | ( | const ParticlesTemp & | ps, |
double | k, | ||
std::string | name | ||
) |
Create an excluded-volume style ClosePairsContainer based score.
Definition at line 54 of file creating_restraints.h.
core::MonteCarloMover* IMP::example::create_serial_mover | ( | const ParticlesTemp & | ps | ) |
Create a serial mover from a list of core::XYZR particles.
std::string IMP::example::get_data_path | ( | std::string | file_name | ) |
Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data
directory of module "mymodule", do something like
This will ensure that the code works when IMP
is installed or used via the tools/imppy.sh
script.
std::string IMP::example::get_example_path | ( | std::string | file_name | ) |
Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb
located in the examples
directory of the IMP::atom module, do
This will ensure that the code works when IMP
is installed or used via the tools/imppy.sh
script.
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.
Definition at line 24 of file counting.h.
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() |
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) |
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() , |
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base::LogLevel | ll = base::DEFAULT |
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) |
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.
Definition at line 35 of file randomizing.h.