alias.h

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/**********************************************************************
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