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IMP Reference Guide
2.20.0
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
include
IMP
atom
version 2.20.0
protein_ligand_score.h
Go to the documentation of this file.
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/**
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* \file IMP/atom/protein_ligand_score.h
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* \brief Functions to score protein-ligand interactions
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*
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* Copyright 2007-2022 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPATOM_PROTEIN_LIGAND_SCORE_H
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#define IMPATOM_PROTEIN_LIGAND_SCORE_H
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#include <IMP/atom/atom_config.h>
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#include "
Hierarchy.h
"
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#include <
IMP/core/StatisticalPairScore.h
>
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#include <
IMP/Model.h
>
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#include <
IMP/Particle.h
>
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#include <
IMP/Restraint.h
>
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#include <
IMP/PairScore.h
>
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#include <
IMP/container/PairsRestraint.h
>
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#include <
IMP/algebra/Vector3D.h
>
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#include <
IMP/file.h
>
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#include <limits>
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IMPATOM_BEGIN_NAMESPACE
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/** \name Protein-ligand scoring
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\anchor protein_ligand
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\imp provides a statistical scoring function for scoring
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protein-ligand complexes. See the
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[Ligand Score application](@ref impligand_score) for more information.
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@{
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*/
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class
ProteinLigandRestraint
;
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#ifndef SWIG
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/** The marker to identify the atom types.*/
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typedef
Key<783462>
ProteinLigandType
;
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IMP_VALUES
(
ProteinLigandType
,
ProteinLigandTypes
);
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#else
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class
ProteinLigandType
;
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#endif
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/** add_protein_ligand_score_data() must be called on the molecules
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containing the atoms before the PairScore is used in order
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to properly initialize the particles.
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The default library to use is \c protein_ligand_rank_score.lib.
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\imp also provides \c protein_ligand_pose_score.lib which can be
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found at IMP::atom::get_data_path("protein_ligand_pose_score.lib").
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*/
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class
IMPATOMEXPORT
ProteinLigandAtomPairScore
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:
public
core::StatisticalPairScore
<ProteinLigandType, true, false> {
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friend
class
ProteinLigandRestraint
;
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typedef
core::StatisticalPairScore<ProteinLigandType, true, false>
P
;
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double
threshold_;
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public
:
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ProteinLigandAtomPairScore
(
double
threshold =
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std::numeric_limits<double>::max());
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ProteinLigandAtomPairScore
(
double
threshold,
TextInput
data_file);
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double
get_maximum_distance()
const
{
return
threshold_; }
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};
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IMP_OBJECTS
(
ProteinLigandAtomPairScore
,
ProteinLigandAtomPairScores
);
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//! Score a pair of molecules.
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/** \see ProteinLigandAtomPairScore for simply scoring the atom pairs.
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*/
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class
IMPATOMEXPORT
ProteinLigandRestraint
:
public
container::PairsRestraint
{
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void
initialize(
Hierarchy
protein,
Hierarchy
ligand);
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public
:
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ProteinLigandRestraint
(
Hierarchy
protein,
Hierarchy
ligand,
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double
threshold = std::numeric_limits<double>::max());
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ProteinLigandRestraint
(
Hierarchy
protein,
Hierarchy
ligand,
double
threshold,
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TextInput
data_file);
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};
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IMP_OBJECTS
(
ProteinLigandRestraint
,
ProteinLigandRestraints
);
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/** Add the data needed to use ProteinLigandAtomPairScore with the passed
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Hierarchy.*/
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IMPATOMEXPORT
void
add_protein_ligand_score_data
(
Hierarchy
h);
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/** @} */
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IMPATOM_END_NAMESPACE
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#endif
/* IMPATOM_PROTEIN_LIGAND_SCORE_H */
PairsRestraint.h
Apply a PairScore to each Pair in a list.
Model.h
Storage of a model, its restraints, constraints and particles.
IMP::atom::ProteinLigandAtomPairScore
Definition:
protein_ligand_score.h:52
file.h
Handling of file input/output.
IMP::core::StatisticalPairScore
Definition:
StatisticalPairScore.h:59
IMP::TextInput
Definition:
file.h:89
IMP::Vector
A more IMP-like version of the std::vector.
Definition:
Vector.h:42
IMP::atom::ProteinLigandRestraint
Score a pair of molecules.
Definition:
protein_ligand_score.h:70
Hierarchy.h
Decorator for helping deal with a hierarchy of molecules.
IMP_VALUES
#define IMP_VALUES(Name, PluralName)
Define the type for storing sets of values.
Definition:
value_macros.h:23
IMP::atom::Hierarchy
The standard decorator for manipulating molecular structures.
Definition:
atom/Hierarchy.h:192
PairScore.h
Define PairScore.
IMP::Key
A base class for Keys.
Definition:
Key.h:45
IMP::atom::add_protein_ligand_score_data
void add_protein_ligand_score_data(Hierarchy h)
Particle.h
Classes to handle individual model particles. (Note that implementation of inline functions is in int...
IMP_OBJECTS
#define IMP_OBJECTS(Name, PluralName)
Define the types for storing lists of object pointers.
Definition:
object_macros.h:44
IMP::atom::ProteinLigandType
Key< 783462 > ProteinLigandType
Definition:
protein_ligand_score.h:34
Vector3D.h
Simple 3D vector class.
Restraint.h
Abstract base class for all restraints.
StatisticalPairScore.h
Functions to read mol2s.
IMP::container::PairsRestraint
Applies a PairScore to each Pair in a list.
Definition:
PairsRestraint.h:36