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IMP Reference Guide  develop.182d9373c4,2021/04/12
The Integrative Modeling Platform
IMP::npctransport::SlabWithCylindricalPorePairScore Class Reference

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#include <IMP/npctransport/SlabWithCylindricalPorePairScore.h>

+ Inheritance diagram for IMP::npctransport::SlabWithCylindricalPorePairScore:

Detailed Description

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An origin centered slab with a pore in the vertical direction, for z = [-0.5*thickness_...0.5*thickness_] Returns 0 for all particles fully beyond z range or fully within slab radius from the origin in the [X,Y] plane TODO: verify documentation

Definition at line 27 of file SlabWithCylindricalPorePairScore.h.

Public Member Functions

 SlabWithCylindricalPorePairScore (double k)
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the inputs. More...
 
double evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
 evaluate score for particle pair pip in model m More...
 
virtual double evaluate_indexes (Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
 
algebra::Vector3D get_displacement_direction (SlabWithCylindricalPore const &slab, const algebra::Vector3D &v) const
 returns the direction vector for the displacement of point v relative to the pore walls of slab More...
 
double get_displacement_magnitude (SlabWithCylindricalPore const &slab, const algebra::Vector3D &v) const
 returns the displacement magnitude of point v relative to the pore walls of slab More...
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
- Public Member Functions inherited from IMP::PairScore
 PairScore (std::string name="PairScore %1%")
 
Restraints create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
virtual double evaluate_if_good_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
 Compute the score and the derivative if needed, only if "good". More...
 
- Public Member Functions inherited from IMP::ParticleInputs
ModelObjectsTemp get_inputs (Model *m, const ParticleIndexes &pis) const
 Get the ModelObjects read when the given list of particles is used. More...
 
- Public Member Functions inherited from IMP::Object
virtual void clear_caches ()
 
CheckLevel get_check_level () const
 
LogLevel get_log_level () const
 
void set_check_level (CheckLevel l)
 
void set_log_level (LogLevel l)
 Set the logging level used in this object. More...
 
void set_was_used (bool tf) const
 
void show (std::ostream &out=std::cout) const
 
const std::string & get_name () const
 
void set_name (std::string name)
 

Additional Inherited Members

- Public Types inherited from IMP::PairScore
typedef ParticlePair Argument
 
typedef ParticleIndexPair IndexArgument
 
typedef PairModifier Modifier
 
typedef const ParticlePairPassArgument
 
typedef const ParticleIndexPairPassIndexArgument
 
- Protected Member Functions inherited from IMP::PairScore
virtual Restraints do_create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 Override this to return your own decomposition. More...
 
- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Constructor & Destructor Documentation

IMP::npctransport::SlabWithCylindricalPorePairScore::SlabWithCylindricalPorePairScore ( double  k)

Constructs a slab with specified thickness and a cylindrical pore of specified radius and repulsive force constant k

Member Function Documentation

virtual ModelObjectsTemp IMP::npctransport::SlabWithCylindricalPorePairScore::do_get_inputs ( Model m,
const ParticleIndexes pis 
) const
virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_if_good_indexes ( Model m,
const ParticleIndexPairs pips,
DerivativeAccumulator da,
double  max,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
virtual

Evaluate score for particles pis[lower_bound..upper_bound] in model m. If da is not null, use it to accumulate derivatives in model.

Abort early and return maximal double value if score is larger than max (note this assumes all score components are non-negative, which is true for slab score)

Reimplemented from IMP::PairScore.

Definition at line 88 of file SlabWithCylindricalPorePairScore.h.

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double IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_index ( Model m,
const ParticleIndexPair pip,
DerivativeAccumulator da 
) const
virtual

evaluate score for particle pair pip in model m

evaluate score for particle pair pip in model m, where the first particle is assumed to be a cylindrical slab. If da is not null, use it to accumulate derivatives in the model.

Implements IMP::PairScore.

Definition at line 153 of file SlabWithCylindricalPorePairScore.h.

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double IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_indexes ( Model m,
const ParticleIndexPairs pips,
DerivativeAccumulator da,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
virtual

evaluate score for particles pis[lower_bound..upper_bound] in model m. If da is not null, use it to accumulate derivatives in model.

Reimplemented from IMP::PairScore.

Definition at line 186 of file SlabWithCylindricalPorePairScore.h.

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algebra::Vector3D IMP::npctransport::SlabWithCylindricalPorePairScore::get_displacement_direction ( SlabWithCylindricalPore const &  slab,
const algebra::Vector3D v 
) const

returns the direction vector for the displacement of point v relative to the pore walls of slab

double IMP::npctransport::SlabWithCylindricalPorePairScore::get_displacement_magnitude ( SlabWithCylindricalPore const &  slab,
const algebra::Vector3D v 
) const

returns the displacement magnitude of point v relative to the pore walls of slab

virtual ::IMP::VersionInfo IMP::npctransport::SlabWithCylindricalPorePairScore::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 104 of file SlabWithCylindricalPorePairScore.h.


The documentation for this class was generated from the following file: