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IMP Reference Guide
2.14.0
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
include
IMP
core
version 2.14.0
StatisticalPairScore.h
Go to the documentation of this file.
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/**
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* \file IMP/core/StatisticalPairScore.h
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* \brief Functions to read mol2s
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*
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* Copyright 2007-2020 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPCORE_STATISTICAL_PAIR_SCORE_H
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#define IMPCORE_STATISTICAL_PAIR_SCORE_H
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#include <IMP/core/core_config.h>
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#include <
IMP/generic.h
>
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#include <
IMP/Model.h
>
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#include <
IMP/score_functor/DistancePairScore.h
>
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#include <
IMP/score_functor/Statistical.h
>
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#include <
IMP/Particle.h
>
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#include <
IMP/PairScore.h
>
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#include <
IMP/algebra/Vector3D.h
>
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#include "
XYZ.h
"
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#include <
IMP/file.h
>
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#include <limits>
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IMPCORE_BEGIN_NAMESPACE
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/** Create a pairwise statistical potential from a file. The Keys passed
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as a template argument are used to determine how to map the names of
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the types as described in the loaded file to indexes. That is, if
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atom::ResidueKey is passed as the Keys, the potential will expect a file
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which has one line for each pair of residue names.
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The expected file format is:
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\verbatim
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bin_width number_a number_b [offset]
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key_0a key_0b bin0 bin1 bin2...
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key_1a key_1b bin0 bin1 bin2...
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\endverbatim
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The order of the lines (after the first one) does not matter.
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The bin_width is how much distance is allocated per bin (the distance used
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is that between the points). number_a and number_b are the numbers of
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particle types (number_b should only be specified if BIPARTITE is set).
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\note The values read in the file are for bins. That is, the first bin
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is from offset to offset+width. The second is offset+width to offset+
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2width.
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As a result, when interpolation is used, the function achieves the
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bin value at the center of the bin.
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\param[in] Key is an IMP::Key which maps between names and indices
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\param[in] BIPARTITE If true, the two sets of particles being stored are
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different (e.g. a protein atom and a ligand atom), otherwise they are
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assumed to both be the same. Appropriate values must be provided
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in the file.
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\param[in] INTERPOLATE If true, even the scores without derivatives are
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spline interpolated. If false, only the evaluation of derivatives is
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interpolated with a spline.
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*/
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template
<
class
Key,
bool
BIPARTITE,
bool
INTERPOLATE,
bool
SPARSE = false>
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class
StatisticalPairScore
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:
public
score_functor::DistancePairScore
<
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score_functor::Statistical<Key, BIPARTITE, INTERPOLATE, SPARSE> > {
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typedef
score_functor::Statistical<Key, BIPARTITE, INTERPOLATE, SPARSE>
S
;
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typedef
score_functor::DistancePairScore<S>
P
;
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public
:
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/** \param[in] k The attribute to use for determining the particle types
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\param[in] threshold The maximum distance to score
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\param[in] data_file Where to load the file from.
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*/
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StatisticalPairScore
(
IntKey
k,
double
threshold,
TextInput
data_file)
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:
P
(
S
(k, threshold, data_file)) {}
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/** \param[in] k The attribute to use for determining the particle types
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\param[in] threshold The maximum distance to score
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\param[in] data_file Where to load the file from.
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\param[in] shift The offset for the types of the second set of types.
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eg, if the score is on protein and ligand atoms, the ligand atom types
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start with the value shift.
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*/
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StatisticalPairScore
(
IntKey
k,
double
threshold,
TextInput
data_file,
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unsigned
int
shift)
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:
P
(
S
(k, threshold, data_file, shift)) {}
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};
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IMPCORE_END_NAMESPACE
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#endif
/* IMPCORE_STATISTICAL_PAIR_SCORE_H */
DistancePairScore.h
A Score on the distance between a pair of particles.
IMP::core::StatisticalPairScore::StatisticalPairScore
StatisticalPairScore(IntKey k, double threshold, TextInput data_file, unsigned int shift)
Definition:
StatisticalPairScore.h:79
Model.h
Storage of a model, its restraints, constraints and particles.
file.h
Handling of file input/output.
IMP::core::StatisticalPairScore
Definition:
StatisticalPairScore.h:59
IMP::core::StatisticalPairScore::StatisticalPairScore
StatisticalPairScore(IntKey k, double threshold, TextInput data_file)
Definition:
StatisticalPairScore.h:70
IMP::score_functor::DistancePairScore
Create efficient distance-based pair scores.
Definition:
score_functor/DistancePairScore.h:29
IMP::TextInput
Definition:
file.h:89
XYZ.h
Simple XYZ decorator.
IMP::score_functor::Statistical
Definition:
Statistical.h:53
PairScore.h
Define PairScore.
IMP::Key< 1 >
Particle.h
Classes to handle individual model particles. (Note that implementation of inline functions is in int...
Vector3D.h
Simple 3D vector class.
generic.h
Various important functionality for implementing decorators.
Statistical.h
A Score on the distance between a pair of particles.