IMP  2.2.1
The Integrative Modeling Platform
MarginalHBondRestraint.h
Go to the documentation of this file.
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 2007-2014 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/kernel/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 kernel::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.
38  /** kernel::Restraints should store the particles they are to act on,
39  preferably in a Singleton or PairContainer as appropriate.
40  */
42  : Restraint(m, "MarginalHBondRestraint%1%") {};
43 
44  // add a contribution: simple case
45  void add_contribution(kernel::Particle *p1, kernel::Particle *p2,
46  double Iexp);
47 
48  // add a contribution: general case
49  void add_contribution(PairContainer *pc, double Iexp);
50 
51  // return the sum inside the parentheses
52  double get_logsquares() const { return logsquares_; }
53 
54  unsigned get_number_of_contributions() const { return volumes_.size(); }
55 
56  /* call for probability */
57  double get_probability() const { return exp(-unprotected_evaluate(nullptr)); }
58 
59  /** This macro declares the basic needed methods: evaluate and show
60  */
61  virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum)
62  const IMP_OVERRIDE;
63  virtual IMP::kernel::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
65 };
66 
67 IMPISD_END_NAMESPACE
68 
69 #endif /* IMPISD_MARGINAL_HBOND_RESTRAINT_H */
Class for adding derivatives from restraints to the model.
A shared container for Pairs.
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.
Apply a lognormal distance restraint between two particles.
virtual ModelObjectsTemp do_get_inputs() const =0
MarginalHBondRestraint(kernel::Model *m)
Create the restraint.
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:72