IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Score pairs of atoms based on SOAP. More...
#include <IMP/score_functor/Soap.h>
Score pairs of atoms based on SOAP.
This is a simple pairwise atomistic statistical potential. For more details, see Optimized atomic statistical potentials: Assessment of protein interfaces and loops. Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A. Bioinformatics. 2013
You need to use IMP::atom::add_dope_score_data() to add the requisite atom type data to the particles being scored.
Public Member Functions | |
Soap (double threshold=std::numeric_limits< double >::max()) | |
Set up using the default SOAP-PP potential file. More... | |
Soap (double threshold, TextInput data_file) | |
Set up SOAP using an arbitrary potential file. More... | |
Public Member Functions inherited from IMP::score_functor::Statistical< DopeType, false, false > | |
Statistical (IntKey k, double threshold, TextInput data_file) | |
Statistical (IntKey k, double threshold, TextInput data_file, unsigned int shift) | |
bool | get_is_trivially_zero (Model *m, const ParticleIndexPair &p, double squared_distance) const |
double | get_maximum_range (Model *, const ParticleIndexPair &) const |
double | get_score (Model *m, const ParticleIndexPair &pp, double distance) const |
DerivativePair | get_score_and_derivative (Model *m, const Array< 2, ParticleIndex > &pp, double distance) const |
Public Member Functions inherited from IMP::score_functor::Score | |
ModelObjectsTemp | get_inputs (Model *m, const ParticleIndexes &pis) const |
template<unsigned int D> | |
bool | get_is_trivially_zero (Model *m, const Array< D, ParticleIndex > &p, double squared_distance) const |
template<unsigned int D> | |
double | get_maximum_range (Model *m, const Array< D, ParticleIndex > &p) const |
template<unsigned int D> | |
double | get_score (Model *m, const Array< D, ParticleIndex > &p, double distance) const |
Return the score at the passed feature size (eg distance). More... | |
template<unsigned int D> | |
DerivativePair | get_score_and_derivative (Model *m, const Array< D, ParticleIndex > &p, double distance) const |
Return the score and derivative at the passed feature size (eg distance). More... | |
void | show (std::ostream &) const |
Static Public Member Functions | |
static IntKey | get_soap_type_key () |
IMP::score_functor::Soap::Soap | ( | double | threshold = std::numeric_limits<double>::max() | ) |
Set up using the default SOAP-PP potential file.
This uses soap_score.lib, which is the pairwise part of the SOAP-PP score (see https://salilab.org/SOAP/). This is designed for ranking docking solutions. The score should be applied to pairs of atoms from the two docked proteins.
IMP::score_functor::Soap::Soap | ( | double | threshold, |
TextInput | data_file | ||
) |