FlexAtomFactory.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/
 ***********************************************************************/
 
// FlexDataVisitor class to generate lists of fixed, tethered and free atoms
// from a model or list of models
#ifndef _RBTFLEXATOMFACTORY_H_
#define _RBTFLEXATOMFACTORY_H_
 
#include "rxdock/FlexDataVisitor.h"
#include "rxdock/Model.h"
 
#include <nlohmann/json.hpp>
 
using json = nlohmann::json;
 
namespace rxdock {
 
// The main use of FlexAtomFactory is to aid with scoring function
// performance enhancements by partitioning model atoms into subsets that are:
// - fixed (never move)
// - tethered (move, but within a predictable radius)
// - free (move freely)
//
// For receptor models, the majority of atoms are FIXED
// The flexible OH/NH3+ terminal atoms are defined as TETHERED
//
// Two categorisations are defined for ligands and solvent
// depending on the internal flexibility of the model
//
// A) If model is flexible (Model::isFlexible()), all atoms are defined as
// FREE as it is too difficult to take the impact of internal dihedral motion
// into account
//
// B) If model is not flexible (e.g. explicit solvent), the mapping is:
// transMode == FIXED && rotMode == FIXED => atoms are FIXED
// transMode == FREE => atoms are FREE
// else atoms are TETHERED
//
// On exit:
// User2Value of each tethered atom is set to the maximum displacement
// possible for translational and rotational moves. The value is a
// conservative overestimate as the allowed volume mapped on by each tethered
// atom can be complex. Here we define the sphere radius that includes all
// allowed coordinates.
// The User2Value for fixed and free atoms is set to zero.
class RBTDLL_EXPORT FlexAtomFactory : public FlexDataVisitor {
public:
  FlexAtomFactory() {}
  // Constructor accepting a single model
  FlexAtomFactory(Model *);
  // Constructor accepting a list of models
  FlexAtomFactory(ModelList);
  // Helper method to visit a single model
  void Visit(Model *);
  // Clears the partitioned atom lists
  void Clear();
  // Implement the base class abstract methods
  virtual void VisitReceptorFlexData(ReceptorFlexData *);
  virtual void VisitLigandFlexData(LigandFlexData *);
  virtual void VisitSolventFlexData(SolventFlexData *);
  // Get methods for the partitioned atom lists
  AtomRList GetFixedAtomList() const { return m_fixedAtomList; }
  AtomRList GetTetheredAtomList() const { return m_tetheredAtomList; }
  AtomRList GetFreeAtomList() const { return m_freeAtomList; }
 
  friend void to_json(json &j, const FlexAtomFactory &flexAtomFactory);
  friend void from_json(const json &j, FlexAtomFactory &flexAtomFactory);
 
private:
  AtomRList m_fixedAtomList;
  AtomRList m_tetheredAtomList;
  AtomRList m_freeAtomList;
};
 
void to_json(json &j, const FlexAtomFactory &flexAtomFactory);
void from_json(const json &j, FlexAtomFactory &flexAtomFactory);
 
} // namespace rxdock
 
#endif //_RBTFLEXATOMFACTORY_H_