src/openbabel/generic.hpp

/**********************************************************************
generic.h - Handle generic data classes. Custom data for atoms, bonds, etc.
 
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
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_GENERIC_H
#define OB_GENERIC_H

#include "babelconfig.hpp"

#include <string>
#include <vector>
#include <map>

namespace OpenBabel
{

class OBAtom;
class OBBond;
class OBRing;

OBAPI void Trim(std::string& txt);

//! \brief Classification of data stored via OBGenericData class and subclasses.
//!
//! OBGenericDataType can be used as a faster, direct access to a particular category
//! instead of the slower access via GetData(std::string), which must loop
//! through all data to find a match with the supplied key. It is implemented
//! as a set of unsigned integer constants for maximum flexibility and future
//! expansion.
//! 
//! CustomData0 through CustomData15 are data slots that are not used in 
//! OpenBabel directly and are meant for use in derivative programs.
//! Macro definitions can be used to define what each data slot is used in your code.
namespace OBGenericDataType
{
  //! Unknown data type (default)
  static const unsigned int UndefinedData =      0;

  //! Arbitrary key/value data, i.e., OBPairData
  static const unsigned int PairData      =      1;

  //! Energetics data (e.g., total energy, heat of formation, etc.)
  static const unsigned int EnergyData    =      2;

  //! Storing text comments (one per molecule, atom, bond, etc.) (for other data, e.g., author, keyword, ... use OBPairData)
  static const unsigned int CommentData   =      3;

  //! Arbitrary information about conformers, i.e., OBConformerData
  static const unsigned int ConformerData =      4;

  //! Bond data external to OpenBabel, i.e., OBExternalBond, OBExternalBondData
  static const unsigned int ExternalBondData =   5;

  //! Information for generating & manipulating rotamers, i.e. OBRotamerList
  static const unsigned int RotamerList =        6;

  //! Info. for storing bonds to atoms yet to be added, i.e. OBVirtualBond
  static const unsigned int VirtualBondData =    7;

  //! Information on rings in a molecule, i.e., OBRingData
  static const unsigned int RingData =           8;

  //! Information about torsion/dihedral angles, i.e., OBTorsionData and OBTorsion
  static const unsigned int TorsionData =        9;

  //! Bond angles in a molecule, i.e., OBAngle, OBAngleData
  static const unsigned int AngleData =         10;

  //! Residue serial numbers
  static const unsigned int SerialNums =        11;

  //! Crystallographic unit cell data, i.e., OBUnitCell
  static const unsigned int UnitCell =          12;

  //! Spin data, including NMR, atomic and molecular spin, etc.
  static const unsigned int SpinData =          13;

  //! Arbitrary partial and total charges, dipole moments, etc.
  static const unsigned int ChargeData =        14;

  //! Symmetry data -- point and space groups, transforms, etc. i.e., OBSymmetryData
  static const unsigned int SymmetryData =      15;

  //! Arbitrary chiral information (atom, bond, molecule, etc.) i.e., OBChiralData
  static const unsigned int ChiralData =        16;

  //! Atomic and molecular occupation data
  static const unsigned int OccupationData =    17;

  //! Density (cube) data and surfaces
  static const unsigned int DensityData =       18;

  //! Electronic levels, redox states, orbitals, etc.
  static const unsigned int ElectronicData =    19;

  //! Vibrational modes, frequencies, etc.
  static const unsigned int VibrationData =     20;

  //! Rotational energy information
  static const unsigned int RotationData =      21;

  //! Nuclear transitions (e.g., decay, fission, fusion)
  static const unsigned int NuclearData =       22;

  // space for up to 2^14 more entries...

  //! Custom (user-defined data)
  static const unsigned int CustomData0 = 16384;
  static const unsigned int CustomData1 = 16385;
  static const unsigned int CustomData2 = 16386;
  static const unsigned int CustomData3 = 16387;
  static const unsigned int CustomData4 = 16388;
  static const unsigned int CustomData5 = 16389;
  static const unsigned int CustomData6 = 16390;
  static const unsigned int CustomData7 = 16391;
  static const unsigned int CustomData8 = 16392;
  static const unsigned int CustomData9 = 16393;
  static const unsigned int CustomData10 = 16394;
  static const unsigned int CustomData11 = 16395;
  static const unsigned int CustomData12 = 16396;
  static const unsigned int CustomData13 = 16397;
  static const unsigned int CustomData14 = 16398;
  static const unsigned int CustomData15 = 16399;
} // end namespace

//! \brief Base class for generic data
// class introduction in generic.cpp
class OBAPI OBGenericData
{
protected:
    std::string     _attr; //!< attribute tag (e.g., "UnitCell", "Comment" or "Author")
    unsigned int            _type; //!< attribute type -- declared for each subclass
public:
    OBGenericData();
    OBGenericData(const OBGenericData&);
    virtual ~OBGenericData()    {}
    OBGenericData& operator=(const OBGenericData &src);

    void                      SetAttribute(const std::string &v)
    {        _attr = v;        }
    virtual const std::string &GetAttribute()  const
    {        return(_attr);    }
    unsigned int                GetDataType()    const
    {        return(_type);    }
};

//! Used to store a comment string (can be multiple lines long)
class OBAPI OBCommentData : public OBGenericData
{
protected:
    std::string _data;
public:
    OBCommentData();
    OBCommentData(const OBCommentData&);
    OBCommentData& operator=(const OBCommentData &src);

    void          SetData(const std::string &data)
    { _data = data; Trim(_data); }
    void          SetData(const char *d)
    {_data = d; Trim(_data);     }
    const std::string &GetData()              const
    {        return(_data);      }
};

//! \brief Used to store information on an external bond 
//! (e.g., SMILES fragments)
class OBAPI OBExternalBond
{
    int     _idx;
    OBAtom *_atom;
    OBBond *_bond;
public:
    OBExternalBond()    {}
    OBExternalBond(OBAtom *,OBBond *,int);
    OBExternalBond(const OBExternalBond &);
    ~OBExternalBond()   {}

    int     GetIdx()  const    {        return(_idx);    }
    OBAtom *GetAtom() const    {        return(_atom);   }
    OBBond *GetBond() const    {        return(_bond);   }
    void SetIdx(int idx)       {        _idx = idx;      }
    void SetAtom(OBAtom *atom) {        _atom = atom;    }
    void SetBond(OBBond *bond) {        _bond = bond;    }
};

//! \brief Used to store information on external bonds (e.g., in SMILES fragments)
class OBAPI OBExternalBondData : public OBGenericData
{
protected:
    std::vector<OBExternalBond> _vexbnd;
public:
    OBExternalBondData();
    void SetData(OBAtom*,OBBond*,int);
    std::vector<OBExternalBond> *GetData()
    {
        return(&_vexbnd);
    }
};

//! \brief Used to store arbitrary attribute/value relationships.
//!
//! Ideal for arbitrary text descriptors for molecules, atoms, bonds, residues,
//!  e.g. in QSAR.
class OBAPI OBPairData : public OBGenericData
{
protected:
    std::string _value;
public:
    OBPairData();
    void    SetValue(const char *v)
    {
        _value = v;
    }
    void    SetValue(const std::string &v)
    {
        _value = v;
    }
    std::string &GetValue()
    {
        return(_value);
    }
};

//! \brief Used to temporarily store bonds that reference
//! an atom that has not yet been added to a molecule
class OBAPI OBVirtualBond : public OBGenericData
{
protected:
    int _bgn;
    int _end;
    int _ord;
    int _stereo;
public:
    OBVirtualBond();
    OBVirtualBond(int,int,int,int stereo=0);
    int GetBgn()
    {
        return(_bgn);
    }
    int GetEnd()
    {
        return(_end);
    }
    int GetOrder()
    {
        return(_ord);
    }
    int GetStereo()
    {
        return(_stereo);
    }
};

//! Used to store the SSSR set (filled in by OBMol::GetSSSR())
class OBAPI OBRingData : public OBGenericData
{
protected:
    std::vector<OBRing*> _vr;
public:
    OBRingData();
    OBRingData(const OBRingData &);
    ~OBRingData();

    OBRingData &operator=(const OBRingData &);

    void SetData(std::vector<OBRing*> &vr)
    {
        _vr = vr;
    }
    void PushBack(OBRing *r)
    {
        _vr.push_back(r);
    }
    std::vector<OBRing*> &GetData()
    {
        return(_vr);
    }
};

//! \brief Used for storing information about periodic boundary conditions
//!   with conversion to/from translation vectors and
//!  (a, b, c, alpha, beta, gamma)
class OBAPI OBUnitCell: public OBGenericData
{
protected:
    double _a, _b, _c, _alpha, _beta, _gamma;
    vector3 _offset; //!< offset for origin
    vector3 _v1, _v2, _v3; //!< translation vectors
    std::string _spaceGroup;
public:
    OBUnitCell();
    OBUnitCell(const OBUnitCell &);
    ~OBUnitCell()    {}

    OBUnitCell &operator=(const OBUnitCell &);

    void SetData(const double a, const double b, const double c,
                 const double alpha, const double beta, const double gamma)
    {   _a = a; _b = b; _c = c;
        _alpha = alpha; _beta = beta; _gamma = gamma; }
    void SetData(const vector3 v1, const vector3 v2, const vector3 v3);
    void SetOffset(const vector3 v1) { _offset = v1; }
    //! Set the space group symbol for this unit cell.
    //! Does not create an OBSymmetryData entry or attempt to convert
    //!  between different symbol notations
    void SetSpaceGroup(const std::string sg) { _spaceGroup = sg; }

    double GetA()    { return(_a);    }
    double GetB()    { return(_b);    }
    double GetC()    { return(_c);    }
    double GetAlpha(){ return(_alpha);}
    double GetBeta() { return(_beta); }
    double GetGamma(){ return(_gamma);}
    vector3 GetOffset() { return(_offset); }
    const std::string GetSpaceGroup() { return(_spaceGroup); }

    //! \return v1, v2, v3 cell vectors
    std::vector<vector3> GetCellVectors();
    //! \return v1, v2, v3 cell vectors as a 3x3 matrix
    matrix3x3   GetCellMatrix();
    //! \return The orthogonalization matrix, used for converting from fractional to Cartesian coords.
    matrix3x3 GetOrthoMatrix();
    //! \return The fractionalization matrix, used for converting from Cartesian to fractional coords.
    matrix3x3 GetFractionalMatrix();
};

//! \brief Used to hold data on conformers or geometry optimization steps
class OBAPI OBConformerData: public OBGenericData
{
protected:
  //! Dimensionalities of conformers
  std::vector<unsigned short>              _vDimension;
  //! Relative energies of conformers (preferably in kJ/mol)
  std::vector<double>                      _vEnergies;
  //! Atomic forces for each conformer
  std::vector< std::vector< vector3 > >    _vForces;
  //! Atomic velocities for each conformer (e.g., trajectories)
  std::vector< std::vector< vector3 > >    _vVelocity;
  //! Atomic displacements for each conformer (e.g., RMS distances)
  std::vector< std::vector< vector3 > >    _vDisplace;
  //! Additional data (as strings)
  std::vector<std::string>                 _vData;
    
public:
    OBConformerData();
    OBConformerData(const OBConformerData &);
    ~OBConformerData()    {}

    OBConformerData &operator=(const OBConformerData &);

    void SetDimension(std::vector<unsigned short> vd) { _vDimension = vd; }
    void SetEnergies(std::vector<double> ve) { _vEnergies = ve; }
    void SetForces(std::vector< std::vector< vector3 > > vf) {_vForces = vf;}
    void SetVelocities(std::vector< std::vector< vector3 > > vv)
      { _vVelocity = vv; }
    void SetDisplacements(std::vector< std::vector< vector3 > > vd)
      { _vDisplace = vd; }
    void SetData(std::vector<std::string> vdat) { _vData = vdat; }

    std::vector<unsigned short> GetDimension() { return _vDimension; }
    std::vector<double>         GetEnergies()  { return _vEnergies; }
    std::vector< std::vector< vector3 > > GetForces() {return _vForces; }
    std::vector< std::vector< vector3 > > GetVelocities()
      {return _vVelocity;}
    std::vector< std::vector< vector3 > > GetDisplacements()
      {return _vDisplace;}
    std::vector<std::string>    GetData() { return _vData; }

};

//! \brief Used to hold the point-group and/or space-group symmetry
//! \todo Add support for translation between symbol notations.
//!        Add symmetry perception routines.
class OBAPI OBSymmetryData: public OBGenericData
{
protected:
    std::string _spaceGroup;
    std::string _pointGroup;
public:
    OBSymmetryData();
    OBSymmetryData(const OBSymmetryData &);
    ~OBSymmetryData()    {}

    OBSymmetryData &operator=(const OBSymmetryData &);

    void SetData(std::string pg, std::string sg = "")
      { _pointGroup = pg; _spaceGroup = sg; }
    void SetPointGroup(std::string pg) { _pointGroup = pg; }
    void SetSpaceGroup(std::string sg) { _spaceGroup = sg; }

    std::string GetPointGroup() { return _pointGroup; }
    std::string GetSpaceGroup() { return _spaceGroup; }
};

//! \brief Used to hold the torsion data for a single rotatable bond
//! and all four atoms around it
class OBAPI OBTorsion
{
    friend class OBMol;
    friend class OBTorsionData;

protected:
    std::pair<OBAtom*,OBAtom*> _bc;
    //! double is angle in rads
    std::vector<triple<OBAtom*,OBAtom*,double> > _ads;

    OBTorsion()
    {
        _bc.first=0;
        _bc.second=0;
    }
    ;  //protected for use only by friend classes
    OBTorsion(OBAtom *, OBAtom *, OBAtom *, OBAtom *);

    std::vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > GetTorsions();

public:
    OBTorsion(const OBTorsion &);
    ~OBTorsion()
    {}

    OBTorsion& operator=(const OBTorsion &);

    void Clear();
    bool Empty()
    {
        return(_bc.first == 0 && _bc.second == 0);
    }

    bool AddTorsion(OBAtom *a,OBAtom *b, OBAtom *c,OBAtom *d);
    bool AddTorsion(quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> &atoms);

    bool SetAngle(double radians, unsigned int index = 0);
    bool SetData(OBBond *bond);

    bool GetAngle(double &radians, unsigned int index =0);
    unsigned int GetBondIdx();
    unsigned int GetSize() const
    {
        return (unsigned int)_ads.size();
    }

    std::pair<OBAtom*,OBAtom*>                  GetBC()
    {
        return(_bc);
    }
    std::vector<triple<OBAtom*,OBAtom*,double> > GetADs()
    {
        return(_ads) ;
    }

    bool IsProtonRotor();
};

//! \brief Used to hold torsions as generic data for OBMol.
//! Filled by OBMol::FindTorsions()
class OBAPI OBTorsionData : public OBGenericData
{
    friend class OBMol;

protected:
    std::vector<OBTorsion> _torsions;

    OBTorsionData();
    OBTorsionData(const OBTorsionData &);

public:
    OBTorsionData &operator=(const OBTorsionData &);

    void Clear();

    std::vector<OBTorsion> GetData() const
    {
        return _torsions;
    }
    unsigned int      GetSize() const
    {
        return (unsigned int)_torsions.size();
    }

    void SetData(OBTorsion &torsion);

    bool FillTorsionArray(std::vector<std::vector<unsigned int> > &torsions);
};

//! Used to hold the 3 atoms in an angle and the angle itself
class OBAPI OBAngle
{
    friend class OBMol;
    friend class OBAngleData;

protected:

    //member data

    OBAtom                *_vertex;
    std::pair<OBAtom*,OBAtom*>  _termini;
    double                  _radians;

    //protected member functions

    OBAngle();  //protect constructor for use only by friend classes
    OBAngle(OBAtom *vertex,OBAtom *a,OBAtom *b);

    triple<OBAtom*,OBAtom*,OBAtom*> GetAtoms();
    void SortByIndex();

public:

    OBAngle(const OBAngle &);
    ~OBAngle()
    {
        _vertex = NULL;
    }

    OBAngle &operator = (const OBAngle &);
    bool     operator ==(const OBAngle &);

    void  Clear();

    double GetAngle() const
    {
        return(_radians);
    }

    void  SetAngle(double radians)
    {
        _radians = radians;
    }
    void  SetAtoms(OBAtom *vertex,OBAtom *a,OBAtom *b);
    void  SetAtoms(triple<OBAtom*,OBAtom*,OBAtom*> &atoms);

};


//! \brief Used to hold all angles in a molecule as generic data for OBMol
class OBAPI OBAngleData : public OBGenericData
{
    friend class OBMol;

protected:
    std::vector<OBAngle> _angles;

    OBAngleData();
    OBAngleData(const OBAngleData &);
    std::vector<OBAngle> GetData() const
    {
        return(_angles);
    }

public:
    OBAngleData &operator =(const OBAngleData &);

    void Clear();
    unsigned int FillAngleArray(int **angles, unsigned int &size);
    void         SetData(OBAngle &);
    unsigned int GetSize() const
    {
        return (unsigned int)_angles.size();
    }
};

enum atomreftype{output,input,calcvolume}; // sets which atom4ref is accessed

//! \brief Used to hold chiral inforamtion about the atom as OBGenericData
class OBAPI OBChiralData : public OBGenericData
{
    friend class OBMol;
    friend class OBAtom;

protected:
    std::vector<unsigned int> _atom4refs;
    int parity;
    std::vector<unsigned int> _atom4refo;
    std::vector<unsigned int> _atom4refc;

public:
    std::vector<unsigned int> GetAtom4Refs(atomreftype t) const;
    unsigned int GetAtomRef(int a,atomreftype t);

    OBChiralData();
    OBChiralData(const OBChiralData &src);
    OBChiralData &operator =(const OBChiralData &);
    ~OBChiralData(){}

    void Clear();
    bool SetAtom4Refs(std::vector<unsigned int> atom4refs, atomreftype t);
    int AddAtomRef(unsigned int atomref, atomreftype t);
    unsigned int GetSize(atomreftype t) const;
};

//! Defines a map between serial numbers (e.g., in a PDB file) and OBAtom objects
class OBSerialNums : public OBGenericData
{
protected:
    std::map<int, OBAtom*> _serialMap;

public:

    OBSerialNums()
    {
        _attr = "obSerialNums";
        _type = OBGenericDataType::SerialNums;
    }
    OBSerialNums(const OBSerialNums &cp) : OBGenericData(cp)
    {
        _serialMap = cp._serialMap;
    }

    std::map<int,OBAtom*> &GetData()    { return _serialMap;    }
    void SetData(std::map<int,OBAtom*> &sm) { _serialMap = sm;  }

};

//****************doxygen for inline functions***********
/*!
**\fn OBTorsionData::GetSize() const
**\brief Gets the number of torsion structs
**\return integer count of the number of torsions
*/

/*!
**\fn OBTorsionData::GetData() const
**\brief Gets a vector of the OBTorsions
**\return the vector of torsions
*/

/*!
**\fn OBAngleData::GetSize() const
**\brief Gets the number of angles 
**\return integer count of the number of angles
*/

/*!
**\fn OBAngleData::GetData() const
**\brief Gets the angle vector data
**\return pointer to vector<OBAngle>
*/

/*!
**\fn OBAngle::SetAngle(double angle)
**\brief Sets the OBAngle angle value
**\param angle in radians
*/

/*!
**\fn OBAngle::GetAngle() const
**\brief Gets the OBAngle angle value
**\return angle in radians
*/

/*!
**\fn OBTorsion::GetBondIdx()
**\brief Gets the bond index of the central bond
**\return int bond index
*/

/*!
**\fn OBTorsion::GetBC()
**\brief Gets the two central atoms of ABCD torsion
**\return pair<OBAtom*,OBAtom*>
*/

/*!
**\fn OBTorsion::GetADs()
**\brief Gets the vector of distal atoms of ABCD torsion
**\return vector of A,D atom pointers and a double
*/

} //end namespace OpenBabel

#endif // OB_GENERIC_H

//! \file generic.h
//! \brief Handle generic data classes. Custom data for atoms, bonds, etc.
Revision:	741
Committed:	Wed Nov 16 19:42:11 2005 UTC (19 years, 11 months ago) by tim
File size:	20041 byte(s)
Log Message:	adding openbabel
#	Content
1	/**********************************************************************
2	generic.h - Handle generic data classes. Custom data for atoms, bonds, etc.
3
4	Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
5	Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
6
7	This file is part of the Open Babel project.
8	For more information, see <http://openbabel.sourceforge.net/>
9
10	This program is free software; you can redistribute it and/or modify
11	it under the terms of the GNU General Public License as published by
12	the Free Software Foundation version 2 of the License.
13
14	This program is distributed in the hope that it will be useful,
15	but WITHOUT ANY WARRANTY; without even the implied warranty of
16	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17	GNU General Public License for more details.
18	***********************************************************************/
19
20	#ifndef OB_GENERIC_H
21	#define OB_GENERIC_H
22
23	#include "babelconfig.hpp"
24
25	#include <string>
26	#include <vector>
27	#include <map>
28
29	namespace OpenBabel
30	{
31
32	class OBAtom;
33	class OBBond;
34	class OBRing;
35
36	OBAPI void Trim(std::string& txt);
37
38	//! \brief Classification of data stored via OBGenericData class and subclasses.
39	//!
40	//! OBGenericDataType can be used as a faster, direct access to a particular category
41	//! instead of the slower access via GetData(std::string), which must loop
42	//! through all data to find a match with the supplied key. It is implemented
43	//! as a set of unsigned integer constants for maximum flexibility and future
44	//! expansion.
45	//!
46	//! CustomData0 through CustomData15 are data slots that are not used in
47	//! OpenBabel directly and are meant for use in derivative programs.
48	//! Macro definitions can be used to define what each data slot is used in your code.
49	namespace OBGenericDataType
50	{
51	//! Unknown data type (default)
52	static const unsigned int UndefinedData = 0;
53
54	//! Arbitrary key/value data, i.e., OBPairData
55	static const unsigned int PairData = 1;
56
57	//! Energetics data (e.g., total energy, heat of formation, etc.)
58	static const unsigned int EnergyData = 2;
59
60	//! Storing text comments (one per molecule, atom, bond, etc.) (for other data, e.g., author, keyword, ... use OBPairData)
61	static const unsigned int CommentData = 3;
62
63	//! Arbitrary information about conformers, i.e., OBConformerData
64	static const unsigned int ConformerData = 4;
65
66	//! Bond data external to OpenBabel, i.e., OBExternalBond, OBExternalBondData
67	static const unsigned int ExternalBondData = 5;
68
69	//! Information for generating & manipulating rotamers, i.e. OBRotamerList
70	static const unsigned int RotamerList = 6;
71
72	//! Info. for storing bonds to atoms yet to be added, i.e. OBVirtualBond
73	static const unsigned int VirtualBondData = 7;
74
75	//! Information on rings in a molecule, i.e., OBRingData
76	static const unsigned int RingData = 8;
77
78	//! Information about torsion/dihedral angles, i.e., OBTorsionData and OBTorsion
79	static const unsigned int TorsionData = 9;
80
81	//! Bond angles in a molecule, i.e., OBAngle, OBAngleData
82	static const unsigned int AngleData = 10;
83
84	//! Residue serial numbers
85	static const unsigned int SerialNums = 11;
86
87	//! Crystallographic unit cell data, i.e., OBUnitCell
88	static const unsigned int UnitCell = 12;
89
90	//! Spin data, including NMR, atomic and molecular spin, etc.
91	static const unsigned int SpinData = 13;
92
93	//! Arbitrary partial and total charges, dipole moments, etc.
94	static const unsigned int ChargeData = 14;
95
96	//! Symmetry data -- point and space groups, transforms, etc. i.e., OBSymmetryData
97	static const unsigned int SymmetryData = 15;
98
99	//! Arbitrary chiral information (atom, bond, molecule, etc.) i.e., OBChiralData
100	static const unsigned int ChiralData = 16;
101
102	//! Atomic and molecular occupation data
103	static const unsigned int OccupationData = 17;
104
105	//! Density (cube) data and surfaces
106	static const unsigned int DensityData = 18;
107
108	//! Electronic levels, redox states, orbitals, etc.
109	static const unsigned int ElectronicData = 19;
110
111	//! Vibrational modes, frequencies, etc.
112	static const unsigned int VibrationData = 20;
113
114	//! Rotational energy information
115	static const unsigned int RotationData = 21;
116
117	//! Nuclear transitions (e.g., decay, fission, fusion)
118	static const unsigned int NuclearData = 22;
119
120	// space for up to 2^14 more entries...
121
122	//! Custom (user-defined data)
123	static const unsigned int CustomData0 = 16384;
124	static const unsigned int CustomData1 = 16385;
125	static const unsigned int CustomData2 = 16386;
126	static const unsigned int CustomData3 = 16387;
127	static const unsigned int CustomData4 = 16388;
128	static const unsigned int CustomData5 = 16389;
129	static const unsigned int CustomData6 = 16390;
130	static const unsigned int CustomData7 = 16391;
131	static const unsigned int CustomData8 = 16392;
132	static const unsigned int CustomData9 = 16393;
133	static const unsigned int CustomData10 = 16394;
134	static const unsigned int CustomData11 = 16395;
135	static const unsigned int CustomData12 = 16396;
136	static const unsigned int CustomData13 = 16397;
137	static const unsigned int CustomData14 = 16398;
138	static const unsigned int CustomData15 = 16399;
139	} // end namespace
140
141	//! \brief Base class for generic data
142	// class introduction in generic.cpp
143	class OBAPI OBGenericData
144	{
145	protected:
146	std::string _attr; //!< attribute tag (e.g., "UnitCell", "Comment" or "Author")
147	unsigned int _type; //!< attribute type -- declared for each subclass
148	public:
149	OBGenericData();
150	OBGenericData(const OBGenericData&);
151	virtual ~OBGenericData() {}
152	OBGenericData& operator=(const OBGenericData &src);
153
154	void SetAttribute(const std::string &v)
155	{ _attr = v; }
156	virtual const std::string &GetAttribute() const
157	{ return(_attr); }
158	unsigned int GetDataType() const
159	{ return(_type); }
160	};
161
162	//! Used to store a comment string (can be multiple lines long)
163	class OBAPI OBCommentData : public OBGenericData
164	{
165	protected:
166	std::string _data;
167	public:
168	OBCommentData();
169	OBCommentData(const OBCommentData&);
170	OBCommentData& operator=(const OBCommentData &src);
171
172	void SetData(const std::string &data)
173	{ _data = data; Trim(_data); }
174	void SetData(const char *d)
175	{_data = d; Trim(_data); }
176	const std::string &GetData() const
177	{ return(_data); }
178	};
179
180	//! \brief Used to store information on an external bond
181	//! (e.g., SMILES fragments)
182	class OBAPI OBExternalBond
183	{
184	int _idx;
185	OBAtom *_atom;
186	OBBond *_bond;
187	public:
188	OBExternalBond() {}
189	OBExternalBond(OBAtom ,OBBond ,int);
190	OBExternalBond(const OBExternalBond &);
191	~OBExternalBond() {}
192
193	int GetIdx() const { return(_idx); }
194	OBAtom *GetAtom() const { return(_atom); }
195	OBBond *GetBond() const { return(_bond); }
196	void SetIdx(int idx) { _idx = idx; }
197	void SetAtom(OBAtom *atom) { _atom = atom; }
198	void SetBond(OBBond *bond) { _bond = bond; }
199	};
200
201	//! \brief Used to store information on external bonds (e.g., in SMILES fragments)
202	class OBAPI OBExternalBondData : public OBGenericData
203	{
204	protected:
205	std::vector<OBExternalBond> _vexbnd;
206	public:
207	OBExternalBondData();
208	void SetData(OBAtom,OBBond,int);
209	std::vector<OBExternalBond> *GetData()
210	{
211	return(&_vexbnd);
212	}
213	};
214
215	//! \brief Used to store arbitrary attribute/value relationships.
216	//!
217	//! Ideal for arbitrary text descriptors for molecules, atoms, bonds, residues,
218	//! e.g. in QSAR.
219	class OBAPI OBPairData : public OBGenericData
220	{
221	protected:
222	std::string _value;
223	public:
224	OBPairData();
225	void SetValue(const char *v)
226	{
227	_value = v;
228	}
229	void SetValue(const std::string &v)
230	{
231	_value = v;
232	}
233	std::string &GetValue()
234	{
235	return(_value);
236	}
237	};
238
239	//! \brief Used to temporarily store bonds that reference
240	//! an atom that has not yet been added to a molecule
241	class OBAPI OBVirtualBond : public OBGenericData
242	{
243	protected:
244	int _bgn;
245	int _end;
246	int _ord;
247	int _stereo;
248	public:
249	OBVirtualBond();
250	OBVirtualBond(int,int,int,int stereo=0);
251	int GetBgn()
252	{
253	return(_bgn);
254	}
255	int GetEnd()
256	{
257	return(_end);
258	}
259	int GetOrder()
260	{
261	return(_ord);
262	}
263	int GetStereo()
264	{
265	return(_stereo);
266	}
267	};
268
269	//! Used to store the SSSR set (filled in by OBMol::GetSSSR())
270	class OBAPI OBRingData : public OBGenericData
271	{
272	protected:
273	std::vector<OBRing*> _vr;
274	public:
275	OBRingData();
276	OBRingData(const OBRingData &);
277	~OBRingData();
278
279	OBRingData &operator=(const OBRingData &);
280
281	void SetData(std::vector<OBRing*> &vr)
282	{
283	_vr = vr;
284	}
285	void PushBack(OBRing *r)
286	{
287	_vr.push_back(r);
288	}
289	std::vector<OBRing*> &GetData()
290	{
291	return(_vr);
292	}
293	};
294
295	//! \brief Used for storing information about periodic boundary conditions
296	//! with conversion to/from translation vectors and
297	//! (a, b, c, alpha, beta, gamma)
298	class OBAPI OBUnitCell: public OBGenericData
299	{
300	protected:
301	double _a, _b, _c, _alpha, _beta, _gamma;
302	vector3 _offset; //!< offset for origin
303	vector3 _v1, _v2, _v3; //!< translation vectors
304	std::string _spaceGroup;
305	public:
306	OBUnitCell();
307	OBUnitCell(const OBUnitCell &);
308	~OBUnitCell() {}
309
310	OBUnitCell &operator=(const OBUnitCell &);
311
312	void SetData(const double a, const double b, const double c,
313	const double alpha, const double beta, const double gamma)
314	{ _a = a; _b = b; _c = c;
315	_alpha = alpha; _beta = beta; _gamma = gamma; }
316	void SetData(const vector3 v1, const vector3 v2, const vector3 v3);
317	void SetOffset(const vector3 v1) { _offset = v1; }
318	//! Set the space group symbol for this unit cell.
319	//! Does not create an OBSymmetryData entry or attempt to convert
320	//! between different symbol notations
321	void SetSpaceGroup(const std::string sg) { _spaceGroup = sg; }
322
323	double GetA() { return(_a); }
324	double GetB() { return(_b); }
325	double GetC() { return(_c); }
326	double GetAlpha(){ return(_alpha);}
327	double GetBeta() { return(_beta); }
328	double GetGamma(){ return(_gamma);}
329	vector3 GetOffset() { return(_offset); }
330	const std::string GetSpaceGroup() { return(_spaceGroup); }
331
332	//! \return v1, v2, v3 cell vectors
333	std::vector<vector3> GetCellVectors();
334	//! \return v1, v2, v3 cell vectors as a 3x3 matrix
335	matrix3x3 GetCellMatrix();
336	//! \return The orthogonalization matrix, used for converting from fractional to Cartesian coords.
337	matrix3x3 GetOrthoMatrix();
338	//! \return The fractionalization matrix, used for converting from Cartesian to fractional coords.
339	matrix3x3 GetFractionalMatrix();
340	};
341
342	//! \brief Used to hold data on conformers or geometry optimization steps
343	class OBAPI OBConformerData: public OBGenericData
344	{
345	protected:
346	//! Dimensionalities of conformers
347	std::vector<unsigned short> _vDimension;
348	//! Relative energies of conformers (preferably in kJ/mol)
349	std::vector<double> _vEnergies;
350	//! Atomic forces for each conformer
351	std::vector< std::vector< vector3 > > _vForces;
352	//! Atomic velocities for each conformer (e.g., trajectories)
353	std::vector< std::vector< vector3 > > _vVelocity;
354	//! Atomic displacements for each conformer (e.g., RMS distances)
355	std::vector< std::vector< vector3 > > _vDisplace;
356	//! Additional data (as strings)
357	std::vector<std::string> _vData;
358
359	public:
360	OBConformerData();
361	OBConformerData(const OBConformerData &);
362	~OBConformerData() {}
363
364	OBConformerData &operator=(const OBConformerData &);
365
366	void SetDimension(std::vector<unsigned short> vd) { _vDimension = vd; }
367	void SetEnergies(std::vector<double> ve) { _vEnergies = ve; }
368	void SetForces(std::vector< std::vector< vector3 > > vf) {_vForces = vf;}
369	void SetVelocities(std::vector< std::vector< vector3 > > vv)
370	{ _vVelocity = vv; }
371	void SetDisplacements(std::vector< std::vector< vector3 > > vd)
372	{ _vDisplace = vd; }
373	void SetData(std::vector<std::string> vdat) { _vData = vdat; }
374
375	std::vector<unsigned short> GetDimension() { return _vDimension; }
376	std::vector<double> GetEnergies() { return _vEnergies; }
377	std::vector< std::vector< vector3 > > GetForces() {return _vForces; }
378	std::vector< std::vector< vector3 > > GetVelocities()
379	{return _vVelocity;}
380	std::vector< std::vector< vector3 > > GetDisplacements()
381	{return _vDisplace;}
382	std::vector<std::string> GetData() { return _vData; }
383
384	};
385
386	//! \brief Used to hold the point-group and/or space-group symmetry
387	//! \todo Add support for translation between symbol notations.
388	//! Add symmetry perception routines.
389	class OBAPI OBSymmetryData: public OBGenericData
390	{
391	protected:
392	std::string _spaceGroup;
393	std::string _pointGroup;
394	public:
395	OBSymmetryData();
396	OBSymmetryData(const OBSymmetryData &);
397	~OBSymmetryData() {}
398
399	OBSymmetryData &operator=(const OBSymmetryData &);
400
401	void SetData(std::string pg, std::string sg = "")
402	{ _pointGroup = pg; _spaceGroup = sg; }
403	void SetPointGroup(std::string pg) { _pointGroup = pg; }
404	void SetSpaceGroup(std::string sg) { _spaceGroup = sg; }
405
406	std::string GetPointGroup() { return _pointGroup; }
407	std::string GetSpaceGroup() { return _spaceGroup; }
408	};
409
410	//! \brief Used to hold the torsion data for a single rotatable bond
411	//! and all four atoms around it
412	class OBAPI OBTorsion
413	{
414	friend class OBMol;
415	friend class OBTorsionData;
416
417	protected:
418	std::pair<OBAtom,OBAtom> _bc;
419	//! double is angle in rads
420	std::vector<triple<OBAtom,OBAtom,double> > _ads;
421
422	OBTorsion()
423	{
424	_bc.first=0;
425	_bc.second=0;
426	}
427	; //protected for use only by friend classes
428	OBTorsion(OBAtom , OBAtom , OBAtom , OBAtom );
429
430	std::vector<quad<OBAtom,OBAtom,OBAtom,OBAtom> > GetTorsions();
431
432	public:
433	OBTorsion(const OBTorsion &);
434	~OBTorsion()
435	{}
436
437	OBTorsion& operator=(const OBTorsion &);
438
439	void Clear();
440	bool Empty()
441	{
442	return(_bc.first == 0 && _bc.second == 0);
443	}
444
445	bool AddTorsion(OBAtom a,OBAtom b, OBAtom c,OBAtom d);
446	bool AddTorsion(quad<OBAtom,OBAtom,OBAtom,OBAtom> &atoms);
447
448	bool SetAngle(double radians, unsigned int index = 0);
449	bool SetData(OBBond *bond);
450
451	bool GetAngle(double &radians, unsigned int index =0);
452	unsigned int GetBondIdx();
453	unsigned int GetSize() const
454	{
455	return (unsigned int)_ads.size();
456	}
457
458	std::pair<OBAtom,OBAtom> GetBC()
459	{
460	return(_bc);
461	}
462	std::vector<triple<OBAtom,OBAtom,double> > GetADs()
463	{
464	return(_ads) ;
465	}
466
467	bool IsProtonRotor();
468	};
469
470	//! \brief Used to hold torsions as generic data for OBMol.
471	//! Filled by OBMol::FindTorsions()
472	class OBAPI OBTorsionData : public OBGenericData
473	{
474	friend class OBMol;
475
476	protected:
477	std::vector<OBTorsion> _torsions;
478
479	OBTorsionData();
480	OBTorsionData(const OBTorsionData &);
481
482	public:
483	OBTorsionData &operator=(const OBTorsionData &);
484
485	void Clear();
486
487	std::vector<OBTorsion> GetData() const
488	{
489	return _torsions;
490	}
491	unsigned int GetSize() const
492	{
493	return (unsigned int)_torsions.size();
494	}
495
496	void SetData(OBTorsion &torsion);
497
498	bool FillTorsionArray(std::vector<std::vector<unsigned int> > &torsions);
499	};
500
501	//! Used to hold the 3 atoms in an angle and the angle itself
502	class OBAPI OBAngle
503	{
504	friend class OBMol;
505	friend class OBAngleData;
506
507	protected:
508
509	//member data
510
511	OBAtom *_vertex;
512	std::pair<OBAtom,OBAtom> _termini;
513	double _radians;
514
515	//protected member functions
516
517	OBAngle(); //protect constructor for use only by friend classes
518	OBAngle(OBAtom vertex,OBAtom a,OBAtom *b);
519
520	triple<OBAtom,OBAtom,OBAtom*> GetAtoms();
521	void SortByIndex();
522
523	public:
524
525	OBAngle(const OBAngle &);
526	~OBAngle()
527	{
528	_vertex = NULL;
529	}
530
531	OBAngle &operator = (const OBAngle &);
532	bool operator ==(const OBAngle &);
533
534	void Clear();
535
536	double GetAngle() const
537	{
538	return(_radians);
539	}
540
541	void SetAngle(double radians)
542	{
543	_radians = radians;
544	}
545	void SetAtoms(OBAtom vertex,OBAtom a,OBAtom *b);
546	void SetAtoms(triple<OBAtom,OBAtom,OBAtom*> &atoms);
547
548	};
549
550
551	//! \brief Used to hold all angles in a molecule as generic data for OBMol
552	class OBAPI OBAngleData : public OBGenericData
553	{
554	friend class OBMol;
555
556	protected:
557	std::vector<OBAngle> _angles;
558
559	OBAngleData();
560	OBAngleData(const OBAngleData &);
561	std::vector<OBAngle> GetData() const
562	{
563	return(_angles);
564	}
565
566	public:
567	OBAngleData &operator =(const OBAngleData &);
568
569	void Clear();
570	unsigned int FillAngleArray(int **angles, unsigned int &size);
571	void SetData(OBAngle &);
572	unsigned int GetSize() const
573	{
574	return (unsigned int)_angles.size();
575	}
576	};
577
578	enum atomreftype{output,input,calcvolume}; // sets which atom4ref is accessed
579
580	//! \brief Used to hold chiral inforamtion about the atom as OBGenericData
581	class OBAPI OBChiralData : public OBGenericData
582	{
583	friend class OBMol;
584	friend class OBAtom;
585
586	protected:
587	std::vector<unsigned int> _atom4refs;
588	int parity;
589	std::vector<unsigned int> _atom4refo;
590	std::vector<unsigned int> _atom4refc;
591
592	public:
593	std::vector<unsigned int> GetAtom4Refs(atomreftype t) const;
594	unsigned int GetAtomRef(int a,atomreftype t);
595
596	OBChiralData();
597	OBChiralData(const OBChiralData &src);
598	OBChiralData &operator =(const OBChiralData &);
599	~OBChiralData(){}
600
601	void Clear();
602	bool SetAtom4Refs(std::vector<unsigned int> atom4refs, atomreftype t);
603	int AddAtomRef(unsigned int atomref, atomreftype t);
604	unsigned int GetSize(atomreftype t) const;
605	};
606
607	//! Defines a map between serial numbers (e.g., in a PDB file) and OBAtom objects
608	class OBSerialNums : public OBGenericData
609	{
610	protected:
611	std::map<int, OBAtom*> _serialMap;
612
613	public:
614
615	OBSerialNums()
616	{
617	_attr = "obSerialNums";
618	_type = OBGenericDataType::SerialNums;
619	}
620	OBSerialNums(const OBSerialNums &cp) : OBGenericData(cp)
621	{
622	_serialMap = cp._serialMap;
623	}
624
625	std::map<int,OBAtom*> &GetData() { return _serialMap; }
626	void SetData(std::map<int,OBAtom*> &sm) { _serialMap = sm; }
627
628	};
629
630	//**************doxygen for inline functions*********
631	/*!
632	**\fn OBTorsionData::GetSize() const
633	**\brief Gets the number of torsion structs
634	**\return integer count of the number of torsions
635	*/
636
637	/*!
638	**\fn OBTorsionData::GetData() const
639	**\brief Gets a vector of the OBTorsions
640	**\return the vector of torsions
641	*/
642
643	/*!
644	**\fn OBAngleData::GetSize() const
645	**\brief Gets the number of angles
646	**\return integer count of the number of angles
647	*/
648
649	/*!
650	**\fn OBAngleData::GetData() const
651	**\brief Gets the angle vector data
652	**\return pointer to vector<OBAngle>
653	*/
654
655	/*!
656	**\fn OBAngle::SetAngle(double angle)
657	**\brief Sets the OBAngle angle value
658	**\param angle in radians
659	*/
660
661	/*!
662	**\fn OBAngle::GetAngle() const
663	**\brief Gets the OBAngle angle value
664	**\return angle in radians
665	*/
666
667	/*!
668	**\fn OBTorsion::GetBondIdx()
669	**\brief Gets the bond index of the central bond
670	**\return int bond index
671	*/
672
673	/*!
674	**\fn OBTorsion::GetBC()
675	**\brief Gets the two central atoms of ABCD torsion
676	*\return pair<OBAtom,OBAtom*>
677	*/
678
679	/*!
680	**\fn OBTorsion::GetADs()
681	**\brief Gets the vector of distal atoms of ABCD torsion
682	**\return vector of A,D atom pointers and a double
683	*/
684
685	} //end namespace OpenBabel
686
687	#endif // OB_GENERIC_H
688
689	//! \file generic.h
690	//! \brief Handle generic data classes. Custom data for atoms, bonds, etc.