IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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#include <IMP/npctransport/linear_distance_pair_scores.h>
A soft linear attractive / repulsive score between two spheres for the backbone of a chain.
Definition at line 406 of file linear_distance_pair_scores.h.
Public Member Functions | |
LinearWellPairScore (double rest_length_factor, double k, std::string name="LinearIDPairScore%1%") | |
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 &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const |
double | evaluate_index (Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const |
Compute the score and the derivative if needed. More... | |
double | evaluate_indexes (Model *m, const ParticleIndexPairs &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 () |
double | get_rest_length_factor () 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) |
void | set_rest_length_factor (double rest_length_factor) |
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 ParticlePair & | PassArgument |
typedef const ParticleIndexPair & | PassIndexArgument |
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 () |
IMP::npctransport::LinearWellPairScore::LinearWellPairScore | ( | double | rest_length_factor, |
double | k, | ||
std::string | name = "LinearIDPairScore%1%" |
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a linear well pair potential that keeps two particles around a resting distance relative to their radii
rest_length_factor | the resting distance between particles relative to their sum of radii |
k | the force constant (attractive if beyond or repulsive if below rest length) in units kcal/mol/A |
name | the name of the score |
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Overload this method to specify the inputs.
Implements IMP::ParticleInputs.
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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::PairScore.
Definition at line 433 of file linear_distance_pair_scores.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 ParticlePair |
da | a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
Implements IMP::PairScore.
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Compute the score and the derivative if needed over a set.
m | the model of o |
o | objects of type ParticlePair, 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::PairScore.
Definition at line 433 of file linear_distance_pair_scores.h.
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Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 434 of file linear_distance_pair_scores.h.