CharmmDataSource.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 providing Charmm force field data
 
#ifndef _RBTCHARMMDATASOURCE_H_
#define _RBTCHARMMDATASOURCE_H_
 
#include "rxdock/Atom.h"
#include "rxdock/Config.h"
 
#include <nlohmann/json.hpp>
 
using json = nlohmann::json;
 
namespace rxdock {
 
// Added by DM, 8 Dec 1998 for HybridState lookup method
typedef std::map<std::string, Atom::eHybridState> StringHybridStateMap;
typedef StringHybridStateMap::iterator StringHybridStateMapIter;
typedef StringHybridStateMap::const_iterator StringHybridStateMapConstIter;
 
class CharmmDataSource {
public:
  // Constructors/destructors
 
  // DM 30 Apr 1999 - pass in masses.rtf file name as parameter
  CharmmDataSource(
      const std::string &strMassesFile = GetDataFileName("data", "masses.rtf"));
 
  ~CharmmDataSource(); // Default destructor
 
  friend void to_json(json &j, const CharmmDataSource &charDatSrc);
  friend void from_json(const json &j, CharmmDataSource &charDatSrc);
 
  // Public methods
  std::string AtomTypeString(int nAtomType);
  int ImplicitHydrogens(const std::string &strFFType);
  int AtomicNumber(const std::string &strFFType);
  int FormalCharge(const std::string &strFFType); // DM 24 Mar 1999 - changed
                                                  // from double to int
  Atom::eHybridState HybridState(const std::string &strFFType); // DM 8 Dec 1998
 
protected:
  // Protected methods
 
private:
  // Private methods
 
  CharmmDataSource(
      const CharmmDataSource &); // Copy constructor disabled by default
 
  CharmmDataSource &
  operator=(const CharmmDataSource &); // Copy assignment disabled by default
 
  // DM 8 Dec 1998 Searches for Hybridisation state string in the masses.rtf
  // comment field Valid strings are (RBT::SP), (RBT::SP2), (RBT::SP3),
  // (RBT::AROM), (RBT::TRI) (brackets are important)
  Atom::eHybridState
  ConvertCommentStringToHybridState(const std::string &strComment);
 
protected:
  // Protected data
 
private:
  // Private data
  std::map<int, std::string> m_atomTypes;
  std::map<std::string, int> m_implicitHydrogens;
  std::map<std::string, int> m_atomicNumber;
  std::map<std::string, int> m_formalCharge;
  StringHybridStateMap m_hybridState; // DM 8 Dec 1998
};
 
void to_json(json &j, const CharmmDataSource &charDatSrc);
void from_json(const json &j, CharmmDataSource &charDatSrc);
 
// useful typedefs
typedef SmartPtr<CharmmDataSource> CharmmDataSourcePtr; // Smart pointer
 
} // namespace rxdock
 
#endif //_RBTCHARMMDATASOURCE_H_