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IMP Reference Guide  develop.cb6747d2d1,2024/03/28
The Integrative Modeling Platform
MarginalHBondRestraint.h
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1 /**
2  * \file IMP/isd/MarginalHBondRestraint.h
3  * \brief A lognormal restraint that uses the ISPA model to model HBond-derived
4  * distance fit.
5  *
6  * Copyright 2007-2022 IMP Inventors. All rights reserved.
7  *
8  */
9 
10 #ifndef IMPISD_MARGINAL_HBOND_RESTRAINT_H
11 #define IMPISD_MARGINAL_HBOND_RESTRAINT_H
12 
13 #include <IMP/isd/isd_config.h>
14 #include <IMP/Restraint.h>
15 #include <IMP/PairContainer.h>
16 
17 IMPISD_BEGIN_NAMESPACE
18 
19 //! Apply a lognormal distance restraint between two particles.
20 /** Marginal of the lognormal model for NOEs where only \f$\sigma\f$ was
21  marginalized, and \f$\gamma\f$ was set to 1.
22  Since the restraint is complicated, pass individual particles to
23  add_contribution() command.
24 
25  \f[p(D|X,I) =
26  \left(\sum_{i=1}^N \log^2\left(\frac{V_i^{exp}}
27  {d_i^{-6}(X)}\right)\right)^{-\frac{N}{2}}
28  \f]
29  */
30 class IMPISDEXPORT MarginalHBondRestraint : public Restraint {
31  PairContainers contribs_;
32  std::vector<double> volumes_;
33  double logsquares_;
34  void set_logsquares(double logsquares) { logsquares_ = logsquares; }
35 
36  public:
37  //! Create the restraint.
39  : Restraint(m, "MarginalHBondRestraint%1%") {};
40 
41  // add a contribution: simple case
42  void add_contribution(Particle *p1, Particle *p2,
43  double Iexp);
44 
45  // add a contribution: general case
46  void add_contribution(PairContainer *pc, double Iexp);
47 
48  // return the sum inside the parentheses
49  double get_logsquares() const { return logsquares_; }
50 
51  unsigned get_number_of_contributions() const { return volumes_.size(); }
52 
53  /* call for probability */
54  double get_probability() const { return exp(-unprotected_evaluate(nullptr)); }
55 
57  const override;
58  virtual IMP::ModelObjectsTemp do_get_inputs() const override;
60 };
61 
62 IMPISD_END_NAMESPACE
63 
64 #endif /* IMPISD_MARGINAL_HBOND_RESTRAINT_H */
A shared container for Pairs.
Definition: PairContainer.h:39
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition: object_macros.h:25
virtual double unprotected_evaluate(DerivativeAccumulator *da) const
Return the unweighted score for the restraint.
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
A container for Pairs.
MarginalHBondRestraint(Model *m)
Create the restraint.
Apply a lognormal distance restraint between two particles.
Class to handle individual particles of a Model object.
Definition: Particle.h:43
Abstract base class for all restraints.
virtual ModelObjectsTemp do_get_inputs() const =0
Class for adding derivatives from restraints to the model.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56