MdlFileSink.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/
 ***********************************************************************/
 
// Class for writing Model's to MDL SD and MOL files
 
#ifndef _RBTMDLFILESINK_H_
#define _RBTMDLFILESINK_H_
 
#include "rxdock/BaseMolecularFileSink.h"
#include "rxdock/ElementFileSource.h"
 
#include <nlohmann/json.hpp>
 
using json = nlohmann::json;
 
namespace rxdock {
 
// DM 19 June 2006
// Map to keep track of logical atom IDs as they are rendered to file
// This avoids the need for the atoms in the Model to have consecutive
// atom IDs. The rendering of enabled solvent models is now supported
// correctly.
// Key = Atom* pointer
// Value = logical atom ID as rendered to file
// Logical atom IDs are consecutive for all atoms rendered
// The actual atom ID (Atom::GetAtomId()) is unchanged
typedef std::map<Atom *, unsigned int, AtomPtrCmp_Ptr> AtomIdMap;
 
class MdlFileSink : public BaseMolecularFileSink {
public:
  // Constructors/destructors
  RBTDLL_EXPORT MdlFileSink(const std::string &fileName, ModelPtr spModel);
 
  virtual ~MdlFileSink(); // Default destructor
 
  friend void to_json(json &j, const MdlFileSink &mdlFileSink);
  friend void from_json(const json &j, MdlFileSink &mdlFileSink);
 
  // Public methods
  //
  //
  // Override public methods from BaseFileSink
  virtual void Render();
 
protected:
  // Protected methods
 
private:
  // Private methods
  void RenderAtomList(const AtomList &atomList);
  void RenderBondList(const BondList &bondList);
  void RenderData(const StringVariantMap &dataMap);
 
  MdlFileSink();                    // Disable default constructor
  MdlFileSink(const MdlFileSink &); // Copy constructor disabled by
                                    // default
  MdlFileSink &
  operator=(const MdlFileSink &); // Copy assignment disabled by default
 
protected:
  // Protected data
 
private:
  // Private data
  ElementFileSourcePtr m_spElementData;
  // DM 27 Apr 1999 - default behaviour is for the first Render to overwrite any
  // existing file then subsequent Renders to append.
  bool m_bFirstRender;
  AtomIdMap m_atomIdMap; // Keep track of logical atom IDs as rendered to
                         // file
};
 
void to_json(json &j, const MdlFileSink &mdlFileSink);
void from_json(const json &j, MdlFileSink &mdlFileSink);
 
// Useful typedefs
typedef SmartPtr<MdlFileSink> MdlFileSinkPtr; // Smart pointer
 
void RenumberScaffold(AtomList &atomList);
 
} // namespace rxdock
 
#endif //_RBTMDLFILESINK_H_