IMP  2.1.0
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 2007-2013 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/restraint_macros.h>
14 #include <IMP/isd/isd_config.h>
15 #include <IMP/kernel/Restraint.h>
16 #include <IMP/PairContainer.h>
17 
18 IMPISD_BEGIN_NAMESPACE
19 
20 //! Apply an NOE distance restraint between two particles.
21 /** Marginal of the NOE lognormal model. Since restraint is complicated,
22  pass individual particles to add_contribution() command. Supports
23  ambiguous NOEs and derivatives.
24 
25  \f[p(D|X,I) = SS^{-\frac{N-1}{2}} \quad
26  SS = \sum_{i=1}^N \log^2\left(\frac{V_i^{exp}}{d_i^{-6}(X)
27  \hat{\gamma}}\right) \quad
28  \hat{\gamma} = \left(\prod_{i=1}^N \frac{V_i^{exp}}{d_i^{-6}}\right)^{1/N}
29  \f]
30  */
31 class IMPISDEXPORT MarginalNOERestraint : public kernel::Restraint
32 {
33  PairContainers contribs_;
34  std::vector<double> volumes_;
35  double loggammahat_;
36  void set_log_gammahat(double loggammahat) {loggammahat_=loggammahat;}
37  double SS_;
38  void set_SS(double SS) {SS_=SS;}
39 
40 public:
41  //! Create the restraint.
42  /** kernel::Restraints should store the particles they are to act on,
43  preferably in a Singleton or PairContainer as appropriate.
44  */
46  Restraint(m, "MarginalNOERestraint%1%") {};
47 
48 
49  // add a contribution: simple case
50  void add_contribution(kernel::Particle *p1, kernel::Particle *p2, double
51  Iexp);
52 
53  //add a contribution: general case
54  void add_contribution(PairContainer *pc, double Iexp);
55 
56  //return the estimate of gamma given the current structure.
57  double get_log_gammahat() const {return loggammahat_;}
58 
59  //return the sum of squares wrt current structure.
60  double get_SS() const {return SS_;}
61 
62  unsigned get_number_of_contributions() const {return volumes_.size();}
63 
64  /* call for probability */
65  double get_probability() const
66  {
67  return exp(-unprotected_evaluate(nullptr));
68  }
69 
70 
71  /** This macro declares the basic needed methods: evaluate and show
72  */
73  virtual double
74  unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum)
75  const IMP_OVERRIDE;
76  virtual IMP::kernel::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
78 
79 
80 };
81 
82 IMPISD_END_NAMESPACE
83 
84 #endif /* IMPISD_MARGINAL_NOE_RESTRAINT_H */
Class for adding derivatives from restraints to the model.
IMP::base::Vector< IMP::base::WeakPointer< kernel::ModelObject > > ModelObjectsTemp
A shared container for Pairs.
Import IMP/kernel/restraint_macros.h in the namespace.
IMP::base::Vector< IMP::base::Pointer< PairContainer > > PairContainers
Import IMP/kernel/PairContainer.h in the namespace.
Abstract base class for all restraints.
A restraint is a term in an IMP ScoringFunction.
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Class to handle individual model particles.
MarginalNOERestraint(kernel::Model *m)
Create the restraint.
Apply an NOE distance restraint between two particles.
Class for storing model, its restraints, constraints, and particles.