Detailed Description

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

Note: This potential is independent of the orientation of the pairs of particles. Use OrientedSoap instead for a score that takes orientation into account.

You need to use IMP::atom::add_dope_score_data() to add the requisite atom type data to the particles being scored.

Definition at line 33 of file Soap.h.

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 ()

Constructor & Destructor Documentation

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.

Note: The full SOAP-PP score also includes a surface accessibility term, which can be applied using SingletonStatistical (but this is unnecessary for simple ranking of solutions).

Definition at line 47 of file Soap.h.

IMP::score_functor::Soap::Soap	(	double	threshold,
		TextInput	data_file
	)

Set up SOAP using an arbitrary potential file.

Definition at line 51 of file Soap.h.

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

Soap.h

Detailed Description

Public Member Functions

Static Public Member Functions

Constructor & Destructor Documentation