alias.h

Go to the documentation of this file.

/**********************************************************************
alias.h - OBGenericData class to hold alias information on atoms
Copyright (C) Copyright (C) 2007 by Chris Morley

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#ifndef OB_ALIAS_H
#define OB_ALIAS_H

#include <vector>
#include <openbabel/generic.h>
#include <openbabel/shared_ptr.h>

namespace OpenBabel
{
  class OBSmartsPattern;
  class OBMol;

// This macro is used in DLL builds. If it has not
// been set in babelconfig.h, define it as nothing.
#ifndef OBCOMMON
  #define OBCOMMON
#endif

const unsigned int AliasDataType = 0x7883;

class OBCOMMON AliasData : public OBGenericData
{
protected:
  std::string _alias;
  std::string _right_form;
  std::vector<unsigned long> _expandedatoms; //atom ids (not idxs)
  std::string _color;
public:

  AliasData(): OBGenericData("Alias", AliasDataType){ }

  virtual OBGenericData* Clone(OBBase* /*parent*/) const{return new AliasData(*this);}

  void SetAlias(const std::string& alias) {_alias = alias;}
  void SetAlias(const char* alias) {_alias = alias;}

  std::string GetAlias(bool rightAligned = false) const;

  std::string GetColor() const { return _color; }

  void SetColor(std::string color){ _color = color; }

  bool IsExpanded()const { return !_expandedatoms.empty(); }

  static void RevertToAliasForm(OBMol& mol);

  bool Expand(OBMol& mol, const unsigned int atomindex);

 #ifdef HAVE_SHARED_POINTER
  static bool AddAliases(OBMol* pmol);
 #endif

private:
  bool FormulaParse(OBMol& mol, const unsigned atomindex);

  void AddExpandedAtom(int id);

  void DeleteExpandedAtoms(OBMol& mol);

  struct AliasItem
  {
    std::string right_form;
    std::string smiles;
    std::string color;
  };
  typedef std::map<std::string, AliasItem> SuperAtomTable; //key=alias left-form

  static bool LoadFile(SuperAtomTable& table);
  static SuperAtomTable& table()
  {
    static SuperAtomTable t;
    if(t.empty())
      LoadFile(t);
    return t;
  }
  bool        FromNameLookup(OBMol& mol, const unsigned int atomindex);
#ifdef HAVE_SHARED_POINTER
  typedef std::vector< std::pair<std::string, obsharedptr<OBSmartsPattern> > > SmartsTable;
  static bool LoadFile(SmartsTable& smtable);
#endif
};
} //namespace

#endif // OB_ALIAS_H