IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Score that biases particles to go down the Z axis. More...
#include <IMP/npctransport/ZBiasSingletonScore.h>
Score that biases particles to go down the Z axis.
Definition at line 22 of file ZBiasSingletonScore.h.
Public Member Functions | |
ZBiasSingletonScore (double k, double max_r=HALF_SQRT_MAX_DOUBLE) | |
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 ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const |
virtual double | evaluate_index (Model *m, ParticleIndex pi, DerivativeAccumulator *da) const |
Compute the score and the derivative if needed. More... | |
double | evaluate_indexes (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const |
Compute the score and the derivative if needed over a set. More... | |
double | get_k () const |
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... | |
void | set_k (double k) |
Public Member Functions inherited from IMP::SingletonScore | |
SingletonScore (std::string name="SingletonScore %1%") | |
Restraints | create_current_decomposition (Model *m, ParticleIndex vt) const |
virtual double | evaluate_if_good_index (Model *m, ParticleIndex 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::SingletonScore | |
typedef Particle * | Argument |
typedef ParticleIndex | IndexArgument |
typedef SingletonModifier | Modifier |
typedef Particle * | PassArgument |
typedef ParticleIndex | PassIndexArgument |
Protected Member Functions inherited from IMP::SingletonScore | |
virtual Restraints | do_create_current_decomposition (Model *m, ParticleIndex 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 () |
IMP::npctransport::ZBiasSingletonScore::ZBiasSingletonScore | ( | double | k, |
double | max_r = HALF_SQRT_MAX_DOUBLE |
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Exclude particles from the range of z coordinates [bottom_..top_] with repulsive force constant k
k | repulsive force constant |
max_r | maximal distance from origin on x,y plane (radius relative to pore axis) in which force is applied. if 0.0, no limitation |
Definition at line 38 of file ZBiasSingletonScore.h.
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Overload this method to specify the inputs.
Implements IMP::ParticleInputs.
Definition at line 81 of file ZBiasSingletonScore.h.
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Compute the score and the derivative if needed over a set, only if "good". This functions similarly to evaluate_indexes(), but may terminate the computation early if the total score is higher than max.
Reimplemented from IMP::SingletonScore.
Definition at line 86 of file ZBiasSingletonScore.h.
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Compute the score and the derivative if needed.
m | the model of vt |
vt | the index in m of an object of type Particle |
da | a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
Implements IMP::SingletonScore.
Definition at line 62 of file ZBiasSingletonScore.h.
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Compute the score and the derivative if needed over a set.
m | the model of o |
o | objects of type Particle, specified by index |
da | a derivative accumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
lower_bound | index of first item in o to evaluate |
upper_bound | index of last item in o to evaluate |
Reimplemented from IMP::SingletonScore.
Definition at line 86 of file ZBiasSingletonScore.h.
double IMP::npctransport::ZBiasSingletonScore::get_k | ( | ) | const |
returns the force constant for pulling to high z (negative = pull to low z)
Definition at line 50 of file ZBiasSingletonScore.h.
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Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 87 of file ZBiasSingletonScore.h.
void IMP::npctransport::ZBiasSingletonScore::set_k | ( | double | k | ) |
sets the force constant for pulling to high z (negative = pull to low z)
k | force contant |
Definition at line 58 of file ZBiasSingletonScore.h.