OBMol Class Reference

Molecule Class. More...

#include <mol.h>

Inheritance diagram for OBMol:

[legend]List of all members.

Initialization and data (re)size methods
	OBMol ()
	Constructor.
	OBMol (const OBMol &)
virtual	~OBMol ()
	Destructor.
OBMol &	operator= (const OBMol &mol)
	Assignment.
OBMol &	operator+= (const OBMol &mol)
void	ReserveAtoms (int natoms)
virtual OBAtom *	CreateAtom (void)
virtual OBBond *	CreateBond (void)
virtual void	DestroyAtom (OBNodeBase *)
virtual void	DestroyBond (OBEdgeBase *)
bool	AddAtom (OBAtom &)
	Add an atom to a molecule.
bool	AddBond (int, int, int, int flags=0, int insertpos=-1)
bool	AddBond (OBBond &)
bool	AddResidue (OBResidue &)
bool	InsertAtom (OBAtom &)
bool	DeleteAtom (OBAtom *)
bool	DeleteBond (OBBond *)
bool	DeleteResidue (OBResidue *)
OBAtom *	NewAtom ()
	Get a new atom to add to a molecule.
OBResidue *	NewResidue ()
Molecule modification methods
virtual OBBase *	DoTransformations (const std::map< std::string, std::string > *pOptions)
bool	Clear ()
	Clear all information from a molecule.
void	RenumberAtoms (std::vector< OBNodeBase * > &)
	Renumber the atoms of this molecule according to the order in the supplied vector.
void	ToInertialFrame (int conf, double *rmat)
	Translate one conformer and rotate by a rotation matrix (which is returned) to the inertial frame-of-reference.
void	ToInertialFrame ()
	Translate all conformers to the inertial frame-of-reference.
void	Translate (const vector3 &v)
	Translates all conformers in the molecule by the supplied vector.
void	Translate (const vector3 &v, int conf)
	Translates one conformer in the molecule by the supplied vector.
void	Rotate (const double u[3][3])
void	Rotate (const double m[9])
void	Rotate (const double m[9], int nconf)
void	Center ()
	Translate to the center of all coordinates (for this conformer).
bool	Kekulize ()
	Transform to standard Kekule bond structure (presumably from an aromatic form).
bool	PerceiveKekuleBonds ()
void	NewPerceiveKekuleBonds ()
	Kekulize aromatic rings without using implicit valence.
bool	DeleteHydrogen (OBAtom *)
bool	DeleteHydrogens ()
bool	DeleteHydrogens (OBAtom *)
bool	DeleteNonPolarHydrogens ()
bool	AddHydrogens (bool polaronly=false, bool correctForPH=true)
bool	AddHydrogens (OBAtom *)
bool	AddPolarHydrogens ()
bool	StripSalts ()
	Deletes all atoms except for the largest contiguous fragment.
bool	ConvertDativeBonds ()
	Converts for instance [N+]([O-])=O to N(=O)=O.
bool	CorrectForPH ()
bool	AssignSpinMultiplicity ()
	set spin multiplicity for H-deficient atoms
vector3	Center (int nconf)
void	SetTorsion (OBAtom *, OBAtom *, OBAtom *, OBAtom *, double)
	Set the torsion defined by these atoms, rotating bonded neighbors.
static const char *	ClassDescription ()
Public Member Functions
unsigned int	NumNodes ()
unsigned int	NumEdges ()
void	ResetVisitFlags ()
bool	SetVisitLock (bool)
bool	GetVisitLock ()
OBNodeBase *	Begin (std::vector< OBNodeBase * >::iterator &)
OBEdgeBase *	Begin (std::vector< OBEdgeBase * >::iterator &)
OBNodeBase *	Next (std::vector< OBNodeBase * >::iterator &)
OBEdgeBase *	Next (std::vector< OBEdgeBase * >::iterator &)
Molecule modification methods
virtual void	BeginModify (void)
	Call when making many modifications -- clears conformer/rotomer data.
virtual void	EndModify (bool nukePerceivedData=true)
	Call when done with modificaions -- re-perceive data as needed.
int	GetMod ()
void	IncrementMod ()
void	DecrementMod ()
Generic data handling methods (via OBGenericData)
bool	HasData (std::string &)
	Returns: whether the generic attribute/value pair exists
bool	HasData (const char *)
	Returns: whether the generic attribute/value pair exists
bool	HasData (unsigned int type)
	Returns: whether the generic attribute/value pair exists
void	DeleteData (unsigned int type)
void	DeleteData (OBGenericData *)
void	DeleteData (std::vector< OBGenericData * > &)
void	SetData (OBGenericData *d)
unsigned int	DataSize ()
	Returns: the number of OBGenericData items attached to this molecule.
OBGenericData *	GetData (unsigned int type)
OBGenericData *	GetData (std::string &)
	Returns the value given an attribute name.
OBGenericData *	GetData (const char *)
	Returns the value given an attribute name.
std::vector< OBGenericData * > &	GetData ()
std::vector< OBGenericData * >::iterator	BeginData ()
std::vector< OBGenericData * >::iterator	EndData ()
Data retrieval methods
int	GetFlags ()
const char *	GetTitle () const
	Returns: the title of this molecule (often the filename)
unsigned int	NumAtoms () const
	Returns: the number of atoms (i.e. OBAtom children)
unsigned int	NumBonds () const
	Returns: the number of bonds (i.e. OBBond children)
unsigned int	NumHvyAtoms ()
	Returns: the number of non-hydrogen atoms
unsigned int	NumResidues () const
	Returns: the number of residues (i.e. OBResidue substituents)
unsigned int	NumRotors ()
	Returns: the number of rotatble bonds. See OBBond::IsRotor() for details
OBAtom *	GetAtom (int)
OBAtom *	GetFirstAtom ()
OBBond *	GetBond (int)
OBBond *	GetBond (int, int)
OBBond *	GetBond (OBAtom *, OBAtom *)
OBResidue *	GetResidue (int)
std::vector< OBInternalCoord * >	GetInternalCoord ()
double	GetTorsion (int, int, int, int)
	Returns: the dihedral angle between the four atoms supplied a1-a2-a3-a4)
double	GetTorsion (OBAtom *, OBAtom *, OBAtom *, OBAtom *)
	Returns: the dihedral angle between the four atoms supplied a1-a2-a3-a4)
std::string	GetFormula ()
	Returns: the stochoimetric formula (e.g., C4H6O)
double	GetEnergy () const
	Returns: the heat of formation for this molecule (in kcal/mol)
double	GetMolWt ()
	Returns: the standard molar mass given by IUPAC atomic masses (amu)
double	GetExactMass ()
	Returns: the mass given by isotopes (or most abundant isotope, if not specified)
int	GetTotalCharge ()
	Returns: the total charge on this molecule (i.e., 0 = neutral, +1, -1...)
unsigned int	GetTotalSpinMultiplicity ()
	Returns: the total spin on this molecule (i.e., 1 = singlet, 2 = doublet...)
unsigned short int	GetDimension () const
	Returns: the dimensionality of coordinates (i.e., 0 = unknown or no coord, 2=2D, 3=3D)
double *	GetCoordinates ()
std::vector< OBRing * > &	GetSSSR ()
	Implements blue-obelisk:findSmallestSetOfSmallestRings.
bool	AutomaticFormalCharge ()
	Get the current flag for whether formal charges are set with pH correction.
bool	AutomaticPartialCharge ()
	Get the current flag for whether partial charges are auto-determined.
Data modification methods
void	SetTitle (const char *title)
void	SetTitle (std::string &title)
void	SetFormula (std::string molFormula)
	Set the stochiometric formula for this molecule.
void	SetEnergy (double energy)
	Set the heat of formation for this molecule (in kcal/mol).
void	SetDimension (unsigned short int d)
	Set the dimension of this molecule (i.e., 0, 1 , 2, 3).
void	SetTotalCharge (int charge)
void	SetTotalSpinMultiplicity (unsigned int spin)
void	SetInternalCoord (std::vector< OBInternalCoord * > int_coord)
void	SetAutomaticFormalCharge (bool val)
	Set the flag for determining automatic formal charges with pH (default=true).
void	SetAutomaticPartialCharge (bool val)
	Set the flag for determining partial charges automatically (default=true).
void	SetAromaticPerceived ()
	Mark that aromaticity has been perceived for this molecule (see OBAromaticTyper).
void	SetSSSRPerceived ()
	Mark that Smallest Set of Smallest Rings has been run (see OBRing class).
void	SetRingAtomsAndBondsPerceived ()
	Mark that rings have been perceived (see OBRing class for details).
void	SetAtomTypesPerceived ()
	Mark that atom types have been perceived (see OBAtomTyper for details).
void	SetChainsPerceived ()
	Mark that chains and residues have been perceived (see OBChainsParser).
void	SetChiralityPerceived ()
	Mark that chirality has been perceived.
void	SetPartialChargesPerceived ()
	Mark that partial charges have been assigned.
void	SetHybridizationPerceived ()
void	SetImplicitValencePerceived ()
void	SetKekulePerceived ()
void	SetClosureBondsPerceived ()
void	SetHydrogensAdded ()
void	SetCorrectedForPH ()
void	SetAromaticCorrected ()
void	SetSpinMultiplicityAssigned ()
void	SetFlags (int flags)
void	UnsetAromaticPerceived ()
void	UnsetPartialChargesPerceived ()
void	UnsetImplicitValencePerceived ()
void	UnsetFlag (int flag)
Molecule utilities and perception methods
void	FindSSSR ()
	Find Smallest Set of Smallest Rings (see OBRing class for more details).
void	FindRingAtomsAndBonds ()
void	FindChiralCenters ()
	Sets atom->IsChiral() to true for chiral atoms.
void	FindChildren (std::vector< int > &, int, int)
void	FindChildren (std::vector< OBAtom * > &, OBAtom *, OBAtom *)
void	FindLargestFragment (OBBitVec &)
void	ContigFragList (std::vector< std::vector< int > > &)
void	Align (OBAtom *, OBAtom *, vector3 &, vector3 &)
	Aligns atom a on p1 and atom b along p1->p2 vector.
void	ConnectTheDots ()
	Adds single bonds based on atom proximity.
void	PerceiveBondOrders ()
	Attempts to perceive multiple bonds based on geometries.
void	FindTorsions ()
	Fills the OBGeneric OBTorsionData with torsions from the mol.
bool	GetGTDVector (std::vector< int > &)
	Calculates the graph theoretical distance of each atom. Vector is indexed from zero.
void	GetGIVector (std::vector< unsigned int > &)
	Calculates a set of graph invariant indexes using the graph theoretical distance, number of connected heavy atoms, aromatic boolean, ring boolean, atomic number, and summation of bond orders connected to the atom. Vector is indexed from zero.
void	GetGIDVector (std::vector< unsigned int > &)
	Calculates a set of symmetry identifiers for a molecule. Atoms with the same symmetry ID are symmetrically equivalent. Vector is indexed from zero.
Methods to check for existence of properties
bool	Has2D ()
	Are there non-zero coordinates in two dimensions (i.e. X and Y)?
bool	Has3D ()
	Are there non-zero coordinates in all three dimensions (i.e. X, Y, Z)?
bool	HasNonZeroCoords ()
	Are there any non-zero coordinates?
bool	HasAromaticPerceived ()
bool	HasSSSRPerceived ()
bool	HasRingAtomsAndBondsPerceived ()
bool	HasAtomTypesPerceived ()
bool	HasChiralityPerceived ()
bool	HasPartialChargesPerceived ()
bool	HasHybridizationPerceived ()
bool	HasImplicitValencePerceived ()
bool	HasKekulePerceived ()
bool	HasClosureBondsPerceived ()
bool	HasChainsPerceived ()
bool	HasHydrogensAdded ()
bool	HasAromaticCorrected ()
bool	IsCorrectedForPH ()
bool	HasSpinMultiplicityAssigned ()
bool	IsChiral ()
	Is this molecule chiral?
bool	Empty ()
	Are there any atoms in this molecule?
Multiple conformer member functions
int	NumConformers ()
void	SetConformers (std::vector< double * > &v)
void	AddConformer (double *f)
void	SetConformer (int i)
void	CopyConformer (double *, int)
void	DeleteConformer (int)
double *	GetConformer (int i)
double *	BeginConformer (std::vector< double * >::iterator &i)
double *	NextConformer (std::vector< double * >::iterator &i)
std::vector< double * > &	GetConformers ()
Iterator methods
OBAtom *	BeginAtom (std::vector< OBNodeBase * >::iterator &i)
OBAtom *	NextAtom (std::vector< OBNodeBase * >::iterator &i)
OBBond *	BeginBond (std::vector< OBEdgeBase * >::iterator &i)
OBBond *	NextBond (std::vector< OBEdgeBase * >::iterator &i)
OBResidue *	BeginResidue (std::vector< OBResidue * >::iterator &i)
OBResidue *	NextResidue (std::vector< OBResidue * >::iterator &i)
OBInternalCoord *	BeginInternalCoord (std::vector< OBInternalCoord * >::iterator &i)
OBInternalCoord *	NextInternalCoord (std::vector< OBInternalCoord * >::iterator &i)
Protected Member Functions
bool	HasFlag (int flag)
void	SetFlag (int flag)
Internal Kekulization routines -- see kekulize.cpp and NewPerceiveKekuleBonds()
void	start_kekulize (std::vector< OBAtom * > &cycle, std::vector< int > &electron)
	Start kekulizing one or a fused set of aromatic ring(s).
int	expand_kekulize (OBAtom *atom1, OBAtom *atom2, std::vector< int > &currentState, std::vector< int > &initState, std::vector< int > &bcurrentState, std::vector< int > &binitState, std::vector< bool > &mark)
	recursively assign single and double bonds according to the electronical state of the atoms of the current bond
int	getorden (OBAtom *atom)
	Give the priority to give two electrons instead of 1.
void	expandcycle (OBAtom *atom, OBBitVec &avisit)
	Recursively find the aromatic atoms with an aromatic bond to the current atom.
Protected Attributes
int	_flags
	bitfield of flags
bool	_autoPartialCharge
	Assign partial charges automatically.
bool	_autoFormalCharge
	Assign formal charges automatically.
std::string	_title
	Molecule title.
unsigned short int	_dimension
	Dimensionality of coordinates.
double	_energy
	Molecular heat of formation (if applicable).
int	_totalCharge
	Total charge on the molecule.
unsigned int	_totalSpin
	Total spin on the molecule (if not specified, assumes lowest possible spin).
double *	_c
	coordinate array
std::vector< double * >	_vconf
	vector of conformers
unsigned short int	_natoms
	Number of atoms.
unsigned short int	_nbonds
	Number of bonds.
std::vector< OBResidue * >	_residue
	Residue information (if applicable).
std::vector< OBInternalCoord * >	_internals
	Internal Coordinates (if applicable).
std::vector< OBGenericData * >	_vdata
	Custom data -- see OBGenericData class for more.
unsigned short int	_mod
	Number of nested calls to BeginModify().
bool	_vlock
std::vector< OBNodeBase * >	_vatom
std::vector< OBEdgeBase * >	_vbond

---

Detailed Description

Molecule Class.

The most important class in Open Babel is OBMol, or the molecule class. The OBMol class is designed to store all the basic information associated with a molecule, to make manipulations on the connection table of a molecule facile, and to provide member functions which automatically perceive information about a molecule. A guided tour of the OBMol class is a good place to start.

An OBMol class can be declared:

      OBMol mol;

For example:

      #include <iostream.h>
      #include "mol.h"
      #include "obconversion.h"
      int main(int argc,char **argv)
      {
      OBConversion conv(&cin,&cout);
      if(conv.SetInAndOutFormats("SDF","MOL2"))
      { 
      OBMol mol;
      if(conv.Read(&mol))
      ...manipulate molecule 
                
      conv->Write(&mol);
      }
      return(1);
      }

will read in a molecule in SD file format from stdin (or the C++ equivalent cin) and write a MOL2 format file out to standard out. Additionally, The input and output formats can be altered using the OBConversion class

Once a molecule has been read into an OBMol (or created via other methods) the atoms and bonds can be accessed by the following methods:

      OBAtom *atom;
      atom = mol.GetAtom(5); //random access of an atom

or

      OBBond *bond;
      bond = mol.GetBond(14); //random access of a bond

or

      FOR_ATOMS_IN_MOL(atom, mol) // iterator access (see OBMolAtomIter)

or

      FOR_BONDS_IN_MOL(bond, mol) // iterator access (see OBMolBondIter)

It is important to note that atom arrays currently begin at 1 and bond arrays begin at 0. Requesting atom 0 (

      OBAtom *atom = mol.GetAtom(0); 

will result in an error, but

      OBBond *bond = mol.GetBond(0);

is perfectly valid. Note that this is expected to change in the near future to simplify coding and improve efficiency.

The ambiguity of numbering issues and off-by-one errors led to the use of iterators in Open Babel. An iterator is essentially just a pointer, but when used in conjunction with Standard Template Library (STL) vectors it provides an unambiguous way to loop over arrays. OBMols store their atom and bond information in STL vectors. Since vectors are template based, a vector of any user defined type can be declared. OBMols declare vector<OBNodeBase*> and vector<OBEdgeBase*> to store atom and bond information. Iterators are then a natural way to loop over the vectors of atoms and bonds.

A variety of predefined iterators have been created to simplify common looping requests (e.g., looping over all atoms in a molecule, bonds to a given atom, etc.)

      #include "obiter.h"
      ...
      #define FOR_ATOMS_OF_MOL(a,m)     for( OBMolAtomIter     a(m); a; a++ )
      #define FOR_BONDS_OF_MOL(b,m)     for( OBMolBondIter     b(m); b; b++ )
      #define FOR_NBORS_OF_ATOM(a,p)    for( OBAtomAtomIter    a(p); a; a++ )
      #define FOR_BONDS_OF_ATOM(b,p)    for( OBAtomBondIter    b(p); b; b++ )
      #define FOR_RESIDUES_OF_MOL(r,m)  for( OBResidueIter     r(m); r; r++ )
      #define FOR_ATOMS_OF_RESIDUE(a,r) for( OBResidueAtomIter a(r); a; a++ )
      ...

These convenience functions can be used like so:

      #include "obiter.h"
      #include "mol.h"

      OBMol mol;
      double exactMass = 0.0f;
      FOR_ATOMS_OF_MOL(a, mol)
      {
      exactMass +=  a->GetExactMass();
      }

Note that with these convenience macros, the iterator "a" (or whichever name you pick) is declared for you -- you do not need to do it beforehand.

---

Constructor & Destructor Documentation

OBMol

(

)

Constructor.

OBMol

(

const OBMol &

)

Copy constructor

Warning:

Currently does not copy all associated OBGenericData This requires a (minor) API change, and will thus only be fixed in 2.1 or later releases.

~OBMol

(

)

[virtual]

Destructor.

---

Member Function Documentation

bool HasFlag

(

int

flag

)

[inline, protected]

void SetFlag

(

int

flag

)

[inline, protected]

void start_kekulize	(	std::vector< OBAtom * > &	cycle,
		std::vector< int > &	electron
	)			[protected]

Start kekulizing one or a fused set of aromatic ring(s).

The initial electronic state indicates if an atoms must make a double bond or not Kekulizing is attempted recursively for all the atoms bonded to the first atom of the cycle.

int expand_kekulize	(	OBAtom *	atom1,
		OBAtom *	atom2,
		std::vector< int > &	currentState,
		std::vector< int > &	initState,
		std::vector< int > &	bcurrentState,
		std::vector< int > &	binitState,
		std::vector< bool > &	mark
	)			[protected]

recursively assign single and double bonds according to the electronical state of the atoms of the current bond

int getorden

(

OBAtom *

atom

)

[protected]

Give the priority to give two electrons instead of 1.

void expandcycle	(	OBAtom *	atom,
		OBBitVec &	avisit
	)			[protected]

Recursively find the aromatic atoms with an aromatic bond to the current atom.

OBMol & operator=

(

const OBMol &

mol

)

Assignment.

OBMol & operator+=

(

const OBMol &

mol

)

void ReserveAtoms

(

int

natoms

)

[inline]

OBAtom * CreateAtom

(

void

)

[virtual]

OBBond * CreateBond

(

void

)

[virtual]

void DestroyAtom

(

OBNodeBase *

)

[virtual]

void DestroyBond

(

OBEdgeBase *

)

[virtual]

bool AddAtom

(

OBAtom &

atom

)

Add an atom to a molecule.

Also checks bond_queue for any bonds that should be made to the new atom

bool AddBond	(	int	,
		int	,
		int	,
		int	flags = 0,
		int	insertpos = -1
	)

bool AddBond

(

OBBond &

)

bool AddResidue

(

OBResidue &

)

bool InsertAtom

(

OBAtom &

)

bool DeleteAtom

(

OBAtom *

)

bool DeleteBond

(

OBBond *

)

bool DeleteResidue

(

OBResidue *

)

OBAtom * NewAtom

(

)

Get a new atom to add to a molecule.

Also checks bond_queue for any bonds that should be made to the new atom

OBResidue * NewResidue

(

)

void BeginModify

(

void

)

[virtual]

Call when making many modifications -- clears conformer/rotomer data.

void EndModify

(

bool

nukePerceivedData = true

)

[virtual]

Call when done with modificaions -- re-perceive data as needed.

int GetMod

(

)

[inline]

void IncrementMod

(

)

[inline]

void DecrementMod

(

)

[inline]

bool HasData

(

std::string &

)

Returns:

whether the generic attribute/value pair exists

bool HasData

(

const char *

)

Returns:

whether the generic attribute/value pair exists

bool HasData

(

unsigned int

type

)

Returns:

whether the generic attribute/value pair exists

void DeleteData

(

unsigned int

type

)

void DeleteData

(

OBGenericData *

)

void DeleteData

(

std::vector< OBGenericData * > &

)

void SetData

(

OBGenericData *

d

)

[inline]

unsigned int DataSize

(

)

[inline]

Returns:

the number of OBGenericData items attached to this molecule.

OBGenericData * GetData

(

unsigned int

type

)

OBGenericData * GetData

(

std::string &

)

Returns the value given an attribute name.

OBGenericData * GetData

(

const char *

)

Returns the value given an attribute name.

std::vector<OBGenericData*>& GetData

(

)

[inline]

std::vector<OBGenericData*>::iterator BeginData

(

)

[inline]

std::vector<OBGenericData*>::iterator EndData

(

)

[inline]

int GetFlags

(

)

[inline]

const char* GetTitle

(

)

const [inline]

Returns:

the title of this molecule (often the filename)

unsigned int NumAtoms

(

)

const [inline]

Returns:

the number of atoms (i.e. OBAtom children)

unsigned int NumBonds

(

)

const [inline]

Returns:

the number of bonds (i.e. OBBond children)

unsigned int NumHvyAtoms

(

)

Returns:

the number of non-hydrogen atoms

unsigned int NumResidues

(

)

const [inline]

Returns:

the number of residues (i.e. OBResidue substituents)

unsigned int NumRotors

(

)

Returns:

the number of rotatble bonds. See OBBond::IsRotor() for details

OBAtom * GetAtom

(

int

idx

)

Returns a pointer to the atom after a safety check 0 < idx <= NumAtoms

OBAtom * GetFirstAtom

(

)

OBBond * GetBond

(

int

idx

)

Returns a pointer to the bond after a safety check 0 <= idx < NumBonds

OBBond * GetBond	(	int	,
		int
	)

OBBond * GetBond	(	OBAtom *	,
		OBAtom *
	)

OBResidue * GetResidue

(

int

)

std::vector< OBInternalCoord * > GetInternalCoord

(

)

double GetTorsion	(	int	,
		int	,
		int	,
		int
	)

Returns:

the dihedral angle between the four atoms supplied a1-a2-a3-a4)

double GetTorsion	(	OBAtom *	,
		OBAtom *	,
		OBAtom *	,
		OBAtom *
	)

Returns:

the dihedral angle between the four atoms supplied a1-a2-a3-a4)

string GetFormula

(

)

Returns:

the stochoimetric formula (e.g., C4H6O)

Stochoimetric formula (e.g., C4H6O). This is either set by OBMol::SetFormula() or generated on-the-fly using the "Hill order" -- i.e., C first if present, then H if present all other elements in alphabetical order.

double GetEnergy

(

)

const [inline]

Returns:

the heat of formation for this molecule (in kcal/mol)

double GetMolWt

(

)

Returns:

the standard molar mass given by IUPAC atomic masses (amu)

double GetExactMass

(

)

Returns:

the mass given by isotopes (or most abundant isotope, if not specified)

int GetTotalCharge

(

)

Returns:

the total charge on this molecule (i.e., 0 = neutral, +1, -1...)

Returns the total molecular charge -- if it has not previously been set it is calculated from the atomic formal charge information. (This may or may not be correct!) If you set atomic charges with OBAtom::SetFormalCharge() you really should set the molecular charge with OBMol::SetTotalCharge()

unsigned int GetTotalSpinMultiplicity

(

)

Returns:

the total spin on this molecule (i.e., 1 = singlet, 2 = doublet...)

Returns the total spin multiplicity -- if it has not previously been set it is calculated from the atomic spin multiplicity information assuming the high-spin case (i.e. it simply sums the atomic spins, making no attempt to pair spins). However, if you set atomic spins with OBAtom::SetSpinMultiplicity() you really should set the molecular spin with OBMol::SetTotalSpinMultiplicity()

unsigned short int GetDimension

(

)

const [inline]

Returns:

the dimensionality of coordinates (i.e., 0 = unknown or no coord, 2=2D, 3=3D)

double* GetCoordinates

(

)

[inline]

vector< OBRing * > & GetSSSR

(

)

Implements blue-obelisk:findSmallestSetOfSmallestRings.

bool AutomaticFormalCharge

(

)

[inline]

Get the current flag for whether formal charges are set with pH correction.

bool AutomaticPartialCharge

(

)

[inline]

Get the current flag for whether partial charges are auto-determined.

void SetTitle

(

const char *

title

)

void SetTitle

(

std::string &

title

)

void SetFormula

(

std::string

molFormula

)

Set the stochiometric formula for this molecule.

void SetEnergy

(

double

energy

)

[inline]

Set the heat of formation for this molecule (in kcal/mol).

void SetDimension

(

unsigned short int

d

)

[inline]

Set the dimension of this molecule (i.e., 0, 1 , 2, 3).

void SetTotalCharge

(

int

charge

)

void SetTotalSpinMultiplicity

(

unsigned int

spin

)

void SetInternalCoord

(

std::vector< OBInternalCoord * >

int_coord

)

[inline]

void SetAutomaticFormalCharge

(

bool

val

)

[inline]

Set the flag for determining automatic formal charges with pH (default=true).

void SetAutomaticPartialCharge

(

bool

val

)

[inline]

Set the flag for determining partial charges automatically (default=true).

void SetAromaticPerceived

(

)

[inline]

Mark that aromaticity has been perceived for this molecule (see OBAromaticTyper).

void SetSSSRPerceived

(

)

[inline]

Mark that Smallest Set of Smallest Rings has been run (see OBRing class).

void SetRingAtomsAndBondsPerceived

(

)

[inline]

Mark that rings have been perceived (see OBRing class for details).

void SetAtomTypesPerceived

(

)

[inline]

Mark that atom types have been perceived (see OBAtomTyper for details).

void SetChainsPerceived

(

)

[inline]

Mark that chains and residues have been perceived (see OBChainsParser).

void SetChiralityPerceived

(

)

[inline]

Mark that chirality has been perceived.

void SetPartialChargesPerceived

(

)

[inline]

Mark that partial charges have been assigned.

void SetHybridizationPerceived

(

)

[inline]

void SetImplicitValencePerceived

(

)

[inline]

void SetKekulePerceived

(

)

[inline]

void SetClosureBondsPerceived

(

)

[inline]

void SetHydrogensAdded

(

)

[inline]

void SetCorrectedForPH

(

)

[inline]

void SetAromaticCorrected

(

)

[inline]

void SetSpinMultiplicityAssigned

(

)

[inline]

void SetFlags

(

int

flags

)

[inline]

void UnsetAromaticPerceived

(

)

[inline]

void UnsetPartialChargesPerceived

(

)

[inline]

void UnsetImplicitValencePerceived

(

)

[inline]

void UnsetFlag

(

int

flag

)

[inline]

OBBase * DoTransformations

(

const std::map< std::string, std::string > *

pOptions

)

[virtual]

Reimplemented from OBBase.

const char * ClassDescription

(

)

[static]

Reimplemented from OBBase.

bool Clear

(

)

Clear all information from a molecule.

void RenumberAtoms

(

std::vector< OBNodeBase * > &

v

)

Renumber the atoms of this molecule according to the order in the supplied vector.

Renumber the atoms in this molecule according to the order in the supplied vector. This will return without action if the supplied vector is empty or does not have the same number of atoms as the molecule.

void ToInertialFrame	(	int	conf,
		double *	rmat
	)

Translate one conformer and rotate by a rotation matrix (which is returned) to the inertial frame-of-reference.

void ToInertialFrame

(

)

Translate all conformers to the inertial frame-of-reference.

void Translate

(

const vector3 &

v

)

Translates all conformers in the molecule by the supplied vector.

this method adds the vector v to all atom positions in all conformers

void Translate	(	const vector3 &	v,
		int	nconf
	)

Translates one conformer in the molecule by the supplied vector.

this method adds the vector v to all atom positions in the conformer nconf. If nconf == OB_CURRENT_CONFORMER, then the atom positions in the current conformer are translated.

void Rotate

(

const double

u[3][3]

)

void Rotate

(

const double

m[9]

)

void Rotate	(	const double	m[9],
		int	nconf
	)

void Center

(

)

Translate to the center of all coordinates (for this conformer).

bool Kekulize

(

)

Transform to standard Kekule bond structure (presumably from an aromatic form).

bool PerceiveKekuleBonds

(

)

void NewPerceiveKekuleBonds

(

)

Kekulize aromatic rings without using implicit valence.

This new perceive kekule bonds function has been especifically designed to handle molecule files without explicit hydrogens such as pdb or xyz. The function does not rely on GetImplicitValence function The function looks for groups of aromatic cycle For each group it tries to guess the number of electrons given by each atom in order to satisfy the huckel (4n+2) rule If the huckel rule cannot be satisfied the algorithm try with its best alternative guess Then it recursively walk on the atoms of the cycle and assign single and double bonds

bool DeleteHydrogen

(

OBAtom *

)

bool DeleteHydrogens

(

)

bool DeleteHydrogens

(

OBAtom *

)

bool DeleteNonPolarHydrogens

(

)

bool AddHydrogens	(	bool	polaronly = false,
		bool	correctForPH = true
	)

bool AddHydrogens

(

OBAtom *

)

bool AddPolarHydrogens

(

)

bool StripSalts

(

)

Deletes all atoms except for the largest contiguous fragment.

bool ConvertDativeBonds

(

)

Converts for instance [N+]([O-])=O to N(=O)=O.

bool CorrectForPH

(

)

bool AssignSpinMultiplicity

(

)

set spin multiplicity for H-deficient atoms

vector3 Center

(

int

nconf

)

void SetTorsion	(	OBAtom *	,
		OBAtom *	,
		OBAtom *	,
		OBAtom *	,
		double
	)

Set the torsion defined by these atoms, rotating bonded neighbors.

void FindSSSR

(

)

Find Smallest Set of Smallest Rings (see OBRing class for more details).

void FindRingAtomsAndBonds

(

)

void FindChiralCenters

(

)

Sets atom->IsChiral() to true for chiral atoms.

void FindChildren	(	std::vector< int > &	children,
		int	first,
		int	second
	)

locates all atoms for which there exists a path to 'second' without going through 'first' children must not include 'second'

void FindChildren	(	std::vector< OBAtom * > &	children,
		OBAtom *	bgn,
		OBAtom *	end
	)

locates all atoms for which there exists a path to 'end' without going through 'bgn' children must not include 'end'

void FindLargestFragment

(

OBBitVec &

)

void ContigFragList

(

std::vector< std::vector< int > > &

)

Sort a list of contig fragments by size from largest to smallest Each vector<int> contains the atom numbers of a contig fragment

void Align	(	OBAtom *	,
		OBAtom *	,
		vector3 &	,
		vector3 &
	)

Aligns atom a on p1 and atom b along p1->p2 vector.

void ConnectTheDots

(

void

)

Adds single bonds based on atom proximity.

This method adds single bonds between all atoms closer than their combined atomic covalent radii, then "cleans up" making sure bonded atoms are not closer than 0.4A and the atom does not exceed its valence. It implements blue-obelisk:rebondFrom3DCoordinates.

void PerceiveBondOrders

(

)

Attempts to perceive multiple bonds based on geometries.

This method uses bond angles and geometries from current connectivity to guess atom types and then filling empty valences with multiple bonds. It currently has a pass to detect some frequent functional groups. It still needs a pass to detect aromatic rings to "clean up."

void FindTorsions

(

)

Fills the OBGeneric OBTorsionData with torsions from the mol.

bool GetGTDVector

(

std::vector< int > &

)

Calculates the graph theoretical distance of each atom. Vector is indexed from zero.

void GetGIVector

(

std::vector< unsigned int > &

)

Calculates a set of graph invariant indexes using the graph theoretical distance, number of connected heavy atoms, aromatic boolean, ring boolean, atomic number, and summation of bond orders connected to the atom. Vector is indexed from zero.

void GetGIDVector

(

std::vector< unsigned int > &

)

Calculates a set of symmetry identifiers for a molecule. Atoms with the same symmetry ID are symmetrically equivalent. Vector is indexed from zero.

bool Has2D

(

)

Are there non-zero coordinates in two dimensions (i.e. X and Y)?

bool Has3D

(

)

Are there non-zero coordinates in all three dimensions (i.e. X, Y, Z)?

bool HasNonZeroCoords

(

)

Are there any non-zero coordinates?

bool HasAromaticPerceived

(

)

[inline]

bool HasSSSRPerceived

(

)

[inline]

bool HasRingAtomsAndBondsPerceived

(

)

[inline]

bool HasAtomTypesPerceived

(

)

[inline]

bool HasChiralityPerceived

(

)

[inline]

bool HasPartialChargesPerceived

(

)

[inline]

bool HasHybridizationPerceived

(

)

[inline]

bool HasImplicitValencePerceived

(

)

[inline]

bool HasKekulePerceived

(

)

[inline]

bool HasClosureBondsPerceived

(

)

[inline]

bool HasChainsPerceived

(

)

[inline]

bool HasHydrogensAdded

(

)

[inline]

bool HasAromaticCorrected

(

)

[inline]

bool IsCorrectedForPH

(

)

[inline]

bool HasSpinMultiplicityAssigned

(

)

[inline]

bool IsChiral

(

)

Is this molecule chiral?

bool Empty

(

)

[inline]

Are there any atoms in this molecule?

int NumConformers

(

)

[inline]

void SetConformers

(

std::vector< double * > &

v

)

void AddConformer

(

double *

f

)

[inline]

void SetConformer

(

int

i

)

[inline]

void CopyConformer	(	double *	,
		int
	)

void DeleteConformer

(

int

)

double* GetConformer

(

int

i

)

[inline]

double* BeginConformer

(

std::vector< double * >::iterator &

i

)

[inline]

double* NextConformer

(

std::vector< double * >::iterator &

i

)

[inline]

std::vector<double*>& GetConformers

(

)

[inline]

OBAtom * BeginAtom

(

std::vector< OBNodeBase * >::iterator &

i

)

Deprecated:

Use FOR_ATOMS_OF_MOL and OBMolAtomIter instead

OBAtom * NextAtom

(

std::vector< OBNodeBase * >::iterator &

i

)

Deprecated:

Use FOR_ATOMS_OF_MOL and OBMolAtomIter instead

OBBond * BeginBond

(

std::vector< OBEdgeBase * >::iterator &

i

)

Deprecated:

Use FOR_BONDS_OF_MOL and OBMolBondIter instead

OBBond * NextBond

(

std::vector< OBEdgeBase * >::iterator &

i

)

Deprecated:

Use FOR_BONDS_OF_MOL and OBMolBondIter instead

OBResidue* BeginResidue

(

std::vector< OBResidue * >::iterator &

i

)

[inline]

Deprecated:

Use FOR_RESIDUES_OF_MOL and OBResidueIter instead

OBResidue* NextResidue

(

std::vector< OBResidue * >::iterator &

i

)

[inline]

Deprecated:

Use FOR_RESIDUES_OF_MOL and OBResidueIter instead

OBInternalCoord* BeginInternalCoord

(

std::vector< OBInternalCoord * >::iterator &

i

)

[inline]

OBInternalCoord* NextInternalCoord

(

std::vector< OBInternalCoord * >::iterator &

i

)

[inline]

unsigned int NumNodes

(

)

[inline, inherited]

unsigned int NumEdges

(

)

[inline, inherited]

void ResetVisitFlags

(

)

[inherited]

bool SetVisitLock

(

bool

)

[inherited]

bool GetVisitLock

(

)

[inline, inherited]

OBNodeBase * Begin

(

std::vector< OBNodeBase * >::iterator &

)

[inherited]

OBEdgeBase * Begin

(

std::vector< OBEdgeBase * >::iterator &

)

[inherited]

OBNodeBase * Next

(

std::vector< OBNodeBase * >::iterator &

)

[inherited]

OBEdgeBase * Next

(

std::vector< OBEdgeBase * >::iterator &

)

[inherited]

---

Member Data Documentation

int _flags [protected]

bitfield of flags

bool _autoPartialCharge [protected]

Assign partial charges automatically.

bool _autoFormalCharge [protected]

Assign formal charges automatically.

std::string _title [protected]

Molecule title.

unsigned short int _dimension [protected]

Dimensionality of coordinates.

double _energy [protected]

Molecular heat of formation (if applicable).

int _totalCharge [protected]

Total charge on the molecule.

unsigned int _totalSpin [protected]

Total spin on the molecule (if not specified, assumes lowest possible spin).

double* _c [protected]

coordinate array

std::vector<double*> _vconf [protected]

vector of conformers

unsigned short int _natoms [protected]

Number of atoms.

unsigned short int _nbonds [protected]

Number of bonds.

std::vector<OBResidue*> _residue [protected]

Residue information (if applicable).

std::vector<OBInternalCoord*> _internals [protected]

Internal Coordinates (if applicable).

std::vector<OBGenericData*> _vdata [protected]

Custom data -- see OBGenericData class for more.

unsigned short int _mod [protected]

Number of nested calls to BeginModify().

bool _vlock [protected, inherited]

std::vector<OBNodeBase*> _vatom [protected, inherited]

std::vector<OBEdgeBase*> _vbond [protected, inherited]

---

The documentation for this class was generated from the following files:

• mol.h
• chiral.cpp
• kekulize.cpp
• mol.cpp
• ring.cpp
• transform.cpp

---

This file is part of the documentation for Open Babel, version 2.0.2.

Documentation copyright © 1998-2005, the Open Babel Developers.
Open Babel is hosted by:
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