SetupPMFSF.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/
 ***********************************************************************/
 
#ifndef _RBTSETUPPMFSF_H_
#define _RBTSETUPPMFSF_H_
 
#include "rxdock/BaseInterSF.h"
 
namespace rxdock {
 
class SetupPMFSF : public BaseInterSF {
  AtomList theLigandList;   // ligand typing
  AtomList theReceptorList; // receptor typing
 
public:
  static const std::string _CT;
 
  SetupPMFSF(const std::string &strName = "setup-pmf");
  ~SetupPMFSF();
 
protected:
  virtual void SetupReceptor();
  virtual void SetupLigand();
  virtual void SetupScore();
  virtual double RawScore() const;
 
  void SetupReceptorPMFTypes(void);
  void SetupLigandPMFTypes(void);
  PMFType GetPMFfor_lC(AtomPtr); // for ligands
  PMFType GetPMFfor_lN(AtomPtr);
  PMFType GetPMFfor_lO(AtomPtr);
  PMFType GetPMFfor_lS(AtomPtr);
 
  PMFType GetPMFfor_rC(AtomPtr); // for receptor
  PMFType GetPMFfor_rN(AtomPtr);
  PMFType GetPMFfor_rO(AtomPtr);
  PMFType GetPMFfor_rS(AtomPtr);
 
  bool IsChargedNitrogen(AtomPtr); // true for guanidino or other charged
 
private:
  friend void to_json(json &j, const SetupPMFSF &pmfsf) {
    json atomList;
    for (const auto &cIter : pmfsf.theLigandList) {
      json atom = *cIter;
      atomList.push_back(atom);
    }
    json atomList2;
    for (const auto &cIter : pmfsf.theReceptorList) {
      json atom = *cIter;
      atomList2.push_back(atom);
    }
 
    j = json{{"lig-list", atomList}, {"recep-list", atomList2}};
  };
  friend void from_json(const json &j, SetupPMFSF &pmfsf) {
    pmfsf.theLigandList.clear();
    pmfsf.theLigandList.reserve(j.at("lig-list").size());
    for (auto &atom : j.at("lig-list")) {
      AtomPtr spAtom = AtomPtr(new Atom(atom));
      pmfsf.theLigandList.push_back(spAtom);
    }
    pmfsf.theReceptorList.clear();
    pmfsf.theReceptorList.reserve(j.at("recep-list").size());
    for (auto &atom : j.at("recep-list")) {
      AtomPtr spAtom = AtomPtr(new Atom(atom));
      pmfsf.theReceptorList.push_back(spAtom);
    }
  };
};
 
} // namespace rxdock
 
#endif //_RBTSETUPPMFSF_H_