BaseMolecularFileSink.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/
 ***********************************************************************/
 
// Abstract base class for molecular file-based output. Provides hooks for
// handling multiple models/conformations being rendered.
// Derived classes must provide a Render method.
 
#ifndef _RBTBASEMOLECULARFILESINK_H_
#define _RBTBASEMOLECULARFILESINK_H_
 
#include "rxdock/BaseFileSink.h"
#include "rxdock/Model.h"
 
#include <nlohmann/json.hpp>
 
using json = nlohmann::json;
 
namespace rxdock {
 
class BaseMolecularFileSink : public BaseFileSink {
public:
  // Constructors/destructors
  // BaseMolecularFileSink(const char* fileName, ModelPtr spModel);
  BaseMolecularFileSink(const std::string &fileName, ModelPtr spModel,
                        bool bUseModelSegmentNames = true);
 
  virtual ~BaseMolecularFileSink(); // Default destructor
 
  friend void to_json(json &j, const BaseMolecularFileSink &baseBiMolFSink);
  friend void from_json(const json &j, BaseMolecularFileSink &baseBiMolFSink);
 
  // Public methods
 
  // Derived classes should override
  // Controls whether file type can support the writing of multiple
  // conformations/models to a single file
  virtual bool isMultiConfSupported() { return false; }
 
  // Get/set the Model that is linked to the sink
  ModelPtr GetModel() const;
  // DM 21 Apr 1999 - if bUseModelSegmentNames is true, the model segment names
  // are rendered if bUseModelSegmentNames is false, incremental numeric segment
  // IDs are rendered
  RBTDLL_EXPORT void SetModel(ModelPtr spModel,
                              bool bUseModelSegmentNames = false);
 
  // DM 21 Apr 1999 - change the segment ID counter
  // Set to nSegmentId-1 as the counter gets incremented before each Render
  void SetNextSegmentId(int nSegmentId) {
    m_nSegmentId = nSegmentId - 1;
    m_bUseModelSegmentNames = false;
  }
 
  // Get/set the multi-conformer status
  // With MultiConf = false, each call to Render should immediately Write the
  // cache to the file With MultiConf = true, each call to Render should
  // continue to fill the cache with atom records The cache is only written by
  // an explicit call to WriteMultiConf, or by the base FileSink destructor
  bool GetMultiConf() const;
  void SetMultiConf(bool bMultiConf);
  // Force writing the file following several multi-conf Renders
  void WriteMultiConf();
 
  ModelList GetSolvent() const;
  void SetSolvent(ModelList solventList);
 
protected:
  // Protected methods
  void Reset(); // Reset the atom, residue and segment numbering
 
private:
  // Private methods
 
  BaseMolecularFileSink(); // Disable default constructor
  BaseMolecularFileSink(
      const BaseMolecularFileSink &); // Copy constructor disabled by default
  BaseMolecularFileSink &operator=(
      const BaseMolecularFileSink &); // Copy assignment disabled by default
 
protected:
  // Protected data
  int m_nAtomId;    // Next available atom number
  int m_nSubunitId; // Next available subunit number
  int m_nSegmentId; // Next available segment number
  // DM 21 Apr 1999 - if true, output the atom segment names in the model
  // If false, output incremental segment IDs
  bool m_bUseModelSegmentNames;
 
private:
  // Private data
  ModelPtr m_spModel;
  ModelList m_solventList;
  bool m_bMultiConf;
};
 
void to_json(json &j, const BaseMolecularFileSink &baseBiMolFSink);
void from_json(const json &j, BaseMolecularFileSink &baseBiMolFSink);
 
// Useful typedefs
typedef SmartPtr<BaseMolecularFileSink> MolecularFileSinkPtr; // Smart pointer
 
} // namespace rxdock
 
#endif //_RBTBASEMOLECULARFILESINK_H_