Detailed Description

Score pair of atoms based on DOPE.

See M.-y. Shen and A. Sali. Statistical potential for assessment and prediction of protein structures. Protein Science 15, 2507–2524, 2006.

DOPE should not be applied to two atoms from the same residue. You may need to use the SameResiduePairFilter to filter these out.

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

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 36 of file Dope.h.

Public Member Functions
	Dope (double threshold=std::numeric_limits< double >::max())

	Dope (double threshold, base::TextInput data_file)

Public Member Functions inherited from IMP::score_functor::Statistical< DopeType, false, true >
	Statistical (IntKey k, double threshold, base::TextInput data_file)

	Statistical (IntKey k, double threshold, base::TextInput data_file, unsigned int shift)

bool	get_is_trivially_zero (kernel::Model *m, const ParticleIndexPair &p, double squared_distance) const

double	get_maximum_range (kernel::Model *, const ParticleIndexPair &) const

double	get_score (kernel::Model *m, const ParticleIndexPair &pp, double distance) const

DerivativePair	get_score_and_derivative (kernel::Model *m, const base::Array< 2, kernel::ParticleIndex > &pp, double distance) const

Public Member Functions inherited from IMP::score_functor::Score
kernel::ModelObjectsTemp	get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

template<unsigned int D>
bool	get_is_trivially_zero (kernel::Model *m, const base::Array< D, kernel::ParticleIndex > &p, double squared_distance) const

template<unsigned int D>
double	get_maximum_range (kernel::Model *m, const base::Array< D, kernel::ParticleIndex > &p) const

template<unsigned int D>
double	get_score (kernel::Model *m, const base::Array< D, kernel::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 (kernel::Model *m, const base::Array< D, kernel::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_dope_type_key ()

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

Dope.h

Detailed Description

Public Member Functions

Static Public Member Functions