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IMP Reference Guide  2.7.0
The Integrative Modeling Platform
MarginalNOERestraint.h
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1 /**
2  * \file IMP/isd/MarginalNOERestraint.h
3  * \brief A lognormal restraint that uses the ISPA model to model NOE-derived
4  * distance fit.
5  *
6  * Copyright 2007-2017 IMP Inventors. All rights reserved.
7  *
8  */
9 
10 #ifndef IMPISD_MARGINAL_NOE_RESTRAINT_H
11 #define IMPISD_MARGINAL_NOE_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 an NOE distance restraint between two particles.
20 /** Marginal of the NOE lognormal model. Since restraint is complicated,
21  pass individual particles to add_contribution() command. Supports
22  ambiguous NOEs and derivatives.
23 
24  \f[p(D|X,I) = SS^{-\frac{N-1}{2}} \quad
25  SS = \sum_{i=1}^N \log^2\left(\frac{V_i^{exp}}{d_i^{-6}(X)
26  \hat{\gamma}}\right) \quad
27  \hat{\gamma} = \left(\prod_{i=1}^N \frac{V_i^{exp}}{d_i^{-6}}\right)^{1/N}
28  \f]
29  */
30 class IMPISDEXPORT MarginalNOERestraint : public Restraint {
31  PairContainers contribs_;
32  std::vector<double> volumes_;
33  double loggammahat_;
34  void set_log_gammahat(double loggammahat) { loggammahat_ = loggammahat; }
35  double SS_;
36  void set_SS(double SS) { SS_ = SS; }
37 
38  public:
39  //! Create the restraint.
41  : Restraint(m, "MarginalNOERestraint%1%") {};
42 
43  // add a contribution: simple case
44  void add_contribution(Particle *p1, Particle *p2,
45  double Iexp);
46 
47  // add a contribution: general case
48  void add_contribution(PairContainer *pc, double Iexp);
49 
50  // return the estimate of gamma given the current structure.
51  double get_log_gammahat() const { return loggammahat_; }
52 
53  // return the sum of squares wrt current structure.
54  double get_SS() const { return SS_; }
55 
56  unsigned get_number_of_contributions() const { return volumes_.size(); }
57 
58  /* call for probability */
59  double get_probability() const { return exp(-unprotected_evaluate(nullptr)); }
60 
61  virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum)
62  const IMP_OVERRIDE;
65 };
66 
67 IMPISD_END_NAMESPACE
68 
69 #endif /* IMPISD_MARGINAL_NOE_RESTRAINT_H */
A shared container for Pairs.
Definition: PairContainer.h:37
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition: object_macros.h:25
MarginalNOERestraint(Model *m)
Create the restraint.
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72
A container for Pairs.
Class to handle individual particles of a Model object.
Definition: Particle.h:41
Abstract base class for all restraints.
Apply an NOE distance restraint between two particles.
virtual ModelObjectsTemp do_get_inputs() const =0
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Class for adding derivatives from restraints to the model.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52