IMP
2.4.0
The Integrative Modeling Platform
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#include <IMP/score_functor/Statistical.h>
Create a pairwise statistical potential from a file. The Keys passed as a template argument are used to determine how to map the names of the types as described in the loaded file to indexes. That is, if atom::ResidueKey is passed as the Keys, the potential will expect a file which has one line for each pair of residue names.
The expected file format is:
bin_width number_a number_b [offset] key_0a key_0b bin0 bin1 bin2... key_1a key_1b bin0 bin1 bin2...
The order of the lines (after the first one) does not matter. The bin_width is how much distance is allocated per bin (the distance used is that between the points). number_a and number_b are the numbers of particle types (number_b should only be specified if BIPARTITE is set). \note The values read in the file are for bins. That is, the first bin is from offset to offset+width. The second is offset+width to offset+ 2width. As a result, when interpolation is used, the function achieves the bin value at the center of the bin. \param[in] Key is an IMP::Key which maps between names and indices \param[in] BIPARTITE If true, the two sets of particles being stored are different (e.g. a protein atom and a ligand atom), otherwise they are assumed to both be the same. Appropriate values must be provided in the file. \param[in] INTERPOLATE If true, even the scores without derivatives are spline interpolated. If false, only the evaluation of derivatives is interpolated with a spline.
Definition at line 53 of file Statistical.h.
Public Member Functions | |
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 |
IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE >::Statistical | ( | IntKey | k, |
double | threshold, | ||
base::TextInput | data_file | ||
) |
[in] | k | The attribute to use for determining the particle types |
[in] | threshold | The maximum distance to score |
[in] | data_file | Where to load the file from. |
Definition at line 64 of file Statistical.h.
IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE >::Statistical | ( | IntKey | k, |
double | threshold, | ||
base::TextInput | data_file, | ||
unsigned int | shift | ||
) |
[in] | k | The attribute to use for determining the particle types |
[in] | threshold | The maximum distance to score |
[in] | data_file | Where to load the file from. |
[in] | shift | The offset for the types of the second set of types. eg, if the score is on protein and ligand atoms, the ligand atom types start with the value shift. |
Definition at line 76 of file Statistical.h.