AromIdxSF.h

/***********************************************************************
 * The rDock program was developed from 1998 - 2006 by the software team
 * at RiboTargets (subsequently Vernalis (R&D) Ltd).
 * In 2006, the software was licensed to the University of York for
 * maintenance and distribution.
 * In 2012, Vernalis and the University of York agreed to release the
 * program as Open Source software.
 * This version is licensed under GNU-LGPL version 3.0 with support from
 * the University of Barcelona.
 * http://rdock.sourceforge.net/
 ***********************************************************************/
 
// Indexed-grid-based intermolecular aromatic scoring function
 
#ifndef _RBTAROMIDXSF_H_
#define _RBTAROMIDXSF_H_
 
#include "rxdock/AnnotationHandler.h"
#include "rxdock/BaseIdxSF.h"
#include "rxdock/BaseInterSF.h"
#include "rxdock/Plane.h"
 
#include <nlohmann/json.hpp>
 
using json = nlohmann::json;
 
namespace rxdock {
 
class AromIdxSF : public BaseInterSF,
                  public BaseIdxSF,
                  public AnnotationHandler {
public:
  // Class type string
  static const std::string _CT;
  // Parameter names
  static const std::string _INCR;
  static const std::string _R12;
  static const std::string _DR12MIN;
  static const std::string _DR12MAX;
  static const std::string _DAMIN;
  static const std::string _DAMAX;
  // DM 12 Jun 2002 - score threshold used for counting aromatic interactions
  static const std::string _THRESHOLD;
 
  AromIdxSF(const std::string &strName = "arom");
  virtual ~AromIdxSF();
 
  friend void to_json(json &j, const AromIdxSF &aromIdxSF);
  friend void from_json(const json &j, AromIdxSF &aromIdxSF);
 
  // Override BaseSF::ScoreMap to provide additional raw descriptors
  // virtual void ScoreMap(StringVariantMap& scoreMap) const;
 
protected:
  virtual void SetupReceptor();
  virtual void SetupLigand();
  virtual void SetupScore();
  virtual double RawScore() const;
 
  // Clear the receptor and ligand grids and lists respectively
  // As we are not using smart pointers, there is some memory management to do
  void ClearReceptor();
  void ClearLigand();
 
  // DM 25 Oct 2000 - track changes to parameter values in local data members
  // ParameterUpdated is invoked by ParamHandler::SetParameter
  void ParameterUpdated(const std::string &strName);
 
private:
  // DM 6 Feb 2003
  // To be consistent with the Polar score, we should really define a base
  // AromSF class which will provide the scoring function primitives, then
  // have an AromIdxSF subclass for intermolecular aromatic interactions, and
  // a AromIntraSF subclass for ligand intramolecular interactions. Currently
  // there is no AromIntraSF class so everything is contained within
  // AromIdxSF
 
  // Generic scoring function params
  struct f1prms {
    double R0, DRMin, DRMax, slope;
    f1prms(double R, double DMin, double DMax)
        : R0(R), DRMin(DMin), DRMax(DMax), slope(1.0 / (DMax - DMin)) {}
  };
 
  inline f1prms GetRprms() const { return f1prms(m_R12, m_DR12Min, m_DR12Max); }
  inline f1prms GetAprms() const { return f1prms(0.0, m_DAMin, m_DAMax); }
 
  // Generic scoring function primitive (deviation from ideal geometry)
  inline double f1(double DR, const f1prms &prms) const {
    return (DR > prms.DRMax)   ? 0.0
           : (DR > prms.DRMin) ? 1.0 - prms.slope * (DR - prms.DRMin)
                               : 1.0;
  }
 
  // The actual aromatic score, between a given interaction center and a list of
  // near neighbour centers
  double AromScore(const InteractionCenter *pIC1,
                   const InteractionCenterList &IC2List, const f1prms &Rprms,
                   const f1prms &Aprms) const;
  double PiScore(const InteractionCenter *pIC1,
                 const InteractionCenterList &IC2List) const;
  // End of section that should ultimately be moved to AromSF base class
 
  InteractionGridPtr m_spAromGrid;
  InteractionGridPtr m_spGuanGrid;
  InteractionCenterList m_recepAromList;
  InteractionCenterList m_recepGuanList;
  InteractionCenterList m_ligAromList;
  InteractionCenterList m_ligGuanList;
 
  // DM 25 Oct 2000 - local copies of params
  double m_R12;
  double m_DR12Min;
  double m_DR12Max;
  double m_DAMin;
  double m_DAMax;
 
  // DM 12 Jun 2002 - keep track of number of ligand rings and guan carbons
  // involved in non-zero arom interactions
  mutable int m_nArom;
  mutable int m_nGuan;
  mutable double m_ss; // Sigma-sigma score
  mutable double m_sp; // Sigma-pi score
  mutable double m_pp; // pi-pi score
  double m_threshold;
};
 
void to_json(json &j, const Bond &bond);
void from_json(const json &j, Bond &bond);
 
} // namespace rxdock
 
#endif //_RBTAROMIDXSF_H_