Open Babel: OBMol Class Reference

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.

      #include <iostream.h>

      #include <openbabel/mol.h>
      #include <openbabel/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

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

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

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

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<OBAtom*> and vector<OBBond*> 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 <openbabel/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 )
      ...

      #include <openbabel/obiter.h>
      #include <openbabel/mol.h>

      OBMol mol;
      double exactMass = 0.0;
      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, copies atoms,bonds and OBGenericData.

~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, copies atoms,bonds and OBGenericData.

OBMol & operator+= ( const OBMol & mol )

Copies atoms and bonds but not OBGenericData.

void ReserveAtoms ( int natoms ) [inline]

Reserve a minimum number of atoms for internal storage This improves performance since the internal atom vector does not grow.

OBAtom * CreateAtom ( void ) [virtual]

Create a new OBAtom pointer. Does no bookkeeping

Deprecated:: Use NewAtom instead, which ensures internal connections

OBBond * CreateBond ( void ) [virtual]

Create a new OBBond pointer. Does no bookkeeping

Deprecated:: Use NewBond instead, which ensures internal connections

OBResidue * CreateResidue ( void ) [virtual]

Create a new OBResidue pointer. Does no bookkeeping

Deprecated:: Use NewResidue instead, which ensures internal connections

void DestroyAtom ( OBAtom * ) [virtual]

Free an OBAtom pointer if defined. Does no bookkeeping

See also:: DeleteAtom which ensures internal connections

void DestroyBond ( OBBond * ) [virtual]

Free an OBBond pointer if defined. Does no bookkeeping

See also:: DeleteBond which ensures internal connections

void DestroyResidue ( OBResidue * ) [virtual]

Free an OBResidue pointer if defined. Does no bookkeeping

See also:: DeleteResidue which ensures internal connections

bool AddAtom ( OBAtom & )

Add an atom to a molecule.

Add the specified atom to this molecule

Returns:: Whether the method was successful

bool InsertAtom ( OBAtom & )

Add a new atom to this molecule (like AddAtom) Calls BeginModify() before insertion and EndModify() after insertion

bool AddBond	(	int	beginIdx,
		int	endIdx,
		int	order,
		int	flags = `0`,
		int	insertpos = `-1`
	)

Add a new bond to the molecule with the specified parameters

Parameters:

	beginIdx	the atom index of the "start" atom
	endIdx	the atom index of the "end" atom
	order	the bond order (see OBBond::GetBO())
	flags	any bond flags such as stereochemistry (default = none)
	insertpos	the position index to insert the bond (default = none)

Returns:: Whether the new bond creation was successful

bool AddBond ( OBBond & )

Add the specified residue to this molecule and update connections

Returns:: Whether the method was successful

bool AddResidue ( OBResidue & )

Add the specified residue to this molecule and update connections

Returns:: Whether the method was successful

OBAtom * NewAtom ( ) [virtual]

Instantiate a New Atom and add it to the molecule.

Create a new OBAtom in this molecule and ensure connections. (e.g. OBAtom::GetParent()

OBBond * NewBond ( ) [virtual]

Instantiate a New Bond and add it to the molecule.

Create a new OBBond in this molecule and ensure connections. (e.g. OBBond::GetParent()

OBResidue * NewResidue ( ) [virtual]

Create a new OBResidue in this molecule and ensure connections.

bool DeleteAtom ( OBAtom * )

Deletes an atom from this molecule and all appropriate bonds. Updates the molecule and atom and bond indexes accordingly.

Warning:: Does not update any residues which may contain this atom

Returns:: Whether deletion was successful

bool DeleteBond ( OBBond * )

Deletes an bond from this molecule and updates accordingly

Returns:: Whether deletion was successful

bool DeleteResidue ( OBResidue * )

Deletes a residue from this molecule and updates accordingly.

Returns:: Whether deletion was successful

void BeginModify ( void ) [virtual]

Call when making many modifications -- clears conformer/rotomer data. The method "turns off" perception routines, improving performance. Changes in molecular structure will be re-considered after modifications.

void EndModify ( bool nukePerceivedData = true ) [virtual]

Call when done with modificaions -- re-perceive data as needed. This method "turns on" perception routines and re-evaluates molecular structure.

int GetMod ( ) [inline]

Returns:: The number of nested BeginModify() calls. Used internally.

void IncrementMod ( ) [inline]

Increase the number of nested BeginModify calls. Dangerous! Instead, properly use BeginModify as needed.

void DecrementMod ( ) [inline]

Decrease the number of nested BeginModify calls. Dangerous! Instead, properly use EndModify as needed.

int GetFlags ( ) [inline]

Returns:: the entire set of flags. (Internal use, mainly.)

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:: the atom at index idx or NULL if it does not exist.

Warning:: Atom indexing will change. Use iterator methods instead.

OBAtom * GetFirstAtom ( )

Returns:: the first atom in this molecule, or NULL if none exist.

Deprecated:: Will be removed in favor of more standard iterator methods

OBBond * GetBond ( int idx )

Returns:: the bond at index idx or NULL if it does not exist.

Warning:: Bond indexing may change. Use iterator methods instead.

OBBond * GetBond	(	int	a,
		int	b
	)

Returns:: the bond connecting the atom indexed by a and b or NULL if none exists.

Warning:: Atom indexing will change. Use atom objects and iterators instead.

OBBond * GetBond	(	OBAtom *	bgn,
		OBAtom *	end
	)

Returns:: the bond between the atoms bgn and end or NULL if none exists

OBResidue * GetResidue ( int )

Returns:: the residue indexed by idx, or NULL if none exists

Warning:: Residue indexing may change. Use iterator methods instead.

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 *	a,
		OBAtom *	b,
		OBAtom *	c,
		OBAtom *	d
	)

Returns:: the dihedral angle between the four atoms a, b, c, and d)

double GetAngle	(	OBAtom *	a,
		OBAtom *	b,
		OBAtom *	c
	)

Returns:: the angle between the three atoms a, b and c (where a-> b (vertex) -> c )

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.

string GetSpacedFormula	(	int	ones = `0`,
		const char *	sp = `" "`
	)

Returns:: the stochoimetric formula in spaced format e.g. C 4 H 6 O 1

Stochoimetric formula in spaced format e.g. C 4 H 6 O 1 No pair data is stored. Normally use without parameters: GetSpacedFormula()

Since:: version 2.1

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]

Returns:: the set of all atomic coordinates. See OBAtom::GetCoordPtr for more

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 )

Set the title of this molecule to title.

void SetTitle ( std::string & title )

Set the title of this molecule to 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 )

Set the total charge of this molecule to charge.

void SetTotalSpinMultiplicity ( unsigned int spin )

Set the total spin multiplicity of this molecule to spin (i.e., 0 = singlet (default), 1 = doublet, 2 = triplet, etc.)

void SetInternalCoord ( std::vector< OBInternalCoord * > int_coord ) [inline]

Set the internal coordinates to int_coord (Does not call InternalToCartesian to update the 3D cartesian coordinates)

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]

Mark that hybridization of all atoms has been assigned.

void SetImplicitValencePerceived ( ) [inline]

Mark that the implicit hydrogen valence of all atoms has been assigned.

void SetKekulePerceived ( ) [inline]

Mark that Kekule forms have been assigned by Kekulize().

void SetClosureBondsPerceived ( ) [inline]

Mark that ring closure bonds have been assigned by graph traversal.

void SetHydrogensAdded ( ) [inline]

Mark that explicit hydrogen atoms have been added.

void SetCorrectedForPH ( ) [inline]

void SetAromaticCorrected ( ) [inline]

void SetSpinMultiplicityAssigned ( ) [inline]

void SetFlags ( int flags ) [inline]

void UnsetAromaticPerceived ( ) [inline]

void UnsetPartialChargesPerceived ( ) [inline]

void UnsetImplicitValencePerceived ( ) [inline]

void UnsetHydrogensAdded ( ) [inline]

void UnsetFlag ( int flag ) [inline]

OBBase * DoTransformations ( const std::map< std::string, std::string > * ) [virtual]

Perform a set of transformations specified by the user

Typically these are program options to filter or modify an object For example, see OBMol::DoTransformations() and OBMol::ClassDescription()

Reimplemented from OBBase.

const char * ClassDescription ( ) [static]

Returns:: A list of descriptions of command-line options for DoTransformations()

Reimplemented from OBBase.

bool Clear ( ) [virtual]

Clear all information from a molecule.

Reimplemented from OBBase.

void RenumberAtoms ( std::vector< OBAtom * > & 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] )

Rotate all conformers using the supplied matrix u (a 3x3 array of double).

void Rotate ( const double m[9] )

Rotate all conformers using the supplied matrix m (a linear 3x3 row-major array of double).

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

Rotate a specific conformer nconf using the supplied rotation matrix m.

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 DeleteHydrogens ( )

Delete all hydrogens from the molecule

Returns:: Success

bool DeleteHydrogens ( OBAtom * )

Delete all hydrogens from the supplied atom

Returns:: Success

bool DeleteNonPolarHydrogens ( )

Delete all hydrogen atoms connected to a non-polar atom

See also:: OBAtom::IsNonPolarHydrogen

bool DeleteHydrogen ( OBAtom * )

Delete the supplied atom if it is a hydrogen (Helper function for DeleteHydrogens)

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

Add hydrogens to the entire molecule to fill out implicit valence spots

Parameters:

	polaronly	Whether to add hydrogens only to polar atoms (i.e., not to C atoms)
	correctForPH	Whether to call CorrectForPH() first

Returns:: Whether any hydrogens were added

bool AddHydrogens ( OBAtom * )

Add hydrogens only to the supplied atom to fill out implicit valence.

bool AddPolarHydrogens ( )

Add only polar hydrogens (i.e., attached to polar atoms, not C).

bool StripSalts ( )

Deletes all atoms except for the largest contiguous fragment.

vector< OBMol > Separate ( int StartIndex = 1 )

Copies each disconnected fragment as a separate OBMol.

bool ConvertDativeBonds ( )

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

bool CorrectForPH ( )

Correct for pH by applying the OBPhModel transformations.

bool AssignSpinMultiplicity ( )

set spin multiplicity for H-deficient atoms

vector3 Center ( int nconf )

Returns:: the center of the supplied conformer nconf

See also:: Center() to actually center all conformers at the origin

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 ( )

Find all ring atoms and bonds. Does not need to call FindSSSR().

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 & frag )

Find the largest fragment in OBMol (which may include multiple non-connected fragments)

Parameters:

frag

Return (by reference) a bit vector indicating the atoms in the largest fragment

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 FindAngles ( )

Fills out an OBAngleData with angles from the molecule.

void FindTorsions ( )

Fills out an OBTorsionData with angles from the molecule.

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]

Has aromatic perception been performed?

bool HasSSSRPerceived ( ) [inline]

Has the smallest set of smallest rings (FindSSSR) been performed?

bool HasRingAtomsAndBondsPerceived ( ) [inline]

Have ring atoms and bonds been assigned?

bool HasAtomTypesPerceived ( ) [inline]

Have atom types been assigned by OBAtomTyper?

bool HasChiralityPerceived ( ) [inline]

Has atom chirality been assigned?

bool HasPartialChargesPerceived ( ) [inline]

Have atomic Gasteiger partial charges been assigned by OBGastChrg?

bool HasHybridizationPerceived ( ) [inline]

Has atomic hybridization been assigned by OBAtomTyper?

bool HasImplicitValencePerceived ( ) [inline]

Has implicit hydrogen valence been assigned by OBAtomTyper?

bool HasKekulePerceived ( ) [inline]

Has aromaticity and Kekule forms been assigned by Kekulize?

bool HasClosureBondsPerceived ( ) [inline]

Have ring "closure" bonds been assigned? (e.g., OBBond::IsClosure()).

bool HasChainsPerceived ( ) [inline]

Have biomolecule chains and residues been assigned by OBChainsParser?

bool HasHydrogensAdded ( ) [inline]

Have hydrogens been added to the molecule?

bool HasAromaticCorrected ( ) [inline]

Have aromatic nitrogens been "corrected?" (deprecated).

bool IsCorrectedForPH ( ) [inline]

Has the molecule been corrected for pH by CorrectForPH?

bool HasSpinMultiplicityAssigned ( ) [inline]

Has total spin multiplicity been assigned?

bool IsChiral ( )

Is this molecule chiral?

bool Empty ( ) [inline]

Are there any atoms in this molecule?

int NumConformers ( ) [inline]

Returns:: the number of conformers in this molecule

void SetConformers ( std::vector< double * > & v )

Set the entire set of conformers for this molecule to v.

void AddConformer ( double * f ) [inline]

Add a new set of coordinates f as a new conformer.

void SetConformer ( int i )

Set the molecule's current conformer to i Does nothing if i is less than 0 or i is larger than NumConformers()

void CopyConformer	(	double *	c,
		int	nconf
	)

Copy the conformer nconf into the array c

Warning:: Does no checking to see if c is large enough

void DeleteConformer ( int nconf )

Delete the conformer nconf.

double* GetConformer ( int i ) [inline]

Returns:: the coordinates to conformer i

double* BeginConformer ( std::vector< double * >::iterator & i ) [inline]

Set the iterator to the beginning of the conformer list

Returns:: the array of coordinates for the first conformer

double* NextConformer ( std::vector< double * >::iterator & i ) [inline]

Advance the iterator to the next confomer, if possible

Returns:: The array of coordinates for the next conformer, or NULL if none exist

std::vector<double*>& GetConformers ( ) [inline]

Returns:: the entire set of conformers for this molecule as a vector of floating point arrays

OBAtomIterator BeginAtoms ( ) [inline]

Returns:: An atom iterator pointing to the beginning of the atom list

OBAtomIterator EndAtoms ( ) [inline]

Returns:: An atom iterator pointing to the end of the atom list

OBBondIterator BeginBonds ( ) [inline]

Returns:: A bond iterator pointing to the beginning of the bond list

OBBondIterator EndBonds ( ) [inline]

Returns:: A bond iterator pointing to the end of the bond list

OBResidueIterator BeginResidues ( ) [inline]

Returns:: A residue iterator pointing to the beginning of the residue list

OBResidueIterator EndResidues ( ) [inline]

Returns:: A residue iterator pointing to the end of the residue list

OBAtom * BeginAtom ( OBAtomIterator & i )

Set the iterator i to the beginning of the atom list

Returns:: the first atom (or NULL if none exist)

OBAtom * NextAtom ( OBAtomIterator & i )

Advance the iterator i to the next atom in the molecule

Returns:: the next atom (if any, or NULL if none exist)

OBBond * BeginBond ( OBBondIterator & i )

Set the iterator i to the beginning of the bond list

Returns:: the first bond (or NULL if none exist)

OBBond * NextBond ( OBBondIterator & i )

Advance the iterator i to the next bond in the molecule

Returns:: the next bond (if any, or NULL if none exist)

OBResidue* BeginResidue ( OBResidueIterator & i ) [inline]

Set the iterator i to the beginning of the resdiue list

Returns:: the first residue (or NULL if none exist)

OBResidue* NextResidue ( OBResidueIterator & i ) [inline]

Advance the iterator i to the next residue in the molecule

Returns:: the next residue (if any, or NULL if not possible)

OBInternalCoord* BeginInternalCoord ( std::vector< OBInternalCoord * >::iterator & i ) [inline]

Set the iterator to the beginning of the internal coordinate list

Returns:: the first internal coordinate record, or NULL if none exist

See also:: SetInternalCoord

OBInternalCoord* NextInternalCoord ( std::vector< OBInternalCoord * >::iterator & i ) [inline]

Advance the iterator to the next internal coordinate record

Returns:: the next first internal coordinate record, or NULL if none exist

See also:: SetInternalCoord

T* CastAndClear ( bool clear = true ) [inline, inherited]

By default clears the object. Called from ReadMolecule of most format classes.

bool HasData ( const std::string & ) [inherited]

Returns:: whether the generic attribute/value pair exists

bool HasData ( const char * ) [inherited]

Returns:: whether the generic attribute/value pair exists

bool HasData ( const unsigned int type ) [inherited]

Returns:: whether the generic attribute/value pair exists, for a given OBGenericDataType

void DeleteData ( unsigned int type ) [inherited]

Delete any data matching the given OBGenericDataType.

void DeleteData ( OBGenericData * ) [inherited]

Delete the given generic data from this object.

void DeleteData ( std::vector< OBGenericData * > & ) [inherited]

Delete all of the given generic data from this object.

void SetData ( OBGenericData * d ) [inline, inherited]

Adds a data object; does nothing if d==NULL.

unsigned int DataSize ( ) const [inline, inherited]

Returns:: the number of OBGenericData items attached to this molecule.

OBGenericData * GetData ( const unsigned int type ) [inherited]

Returns:: the first matching data for a given type from OBGenericDataType or NULL if nothing matches

OBGenericData * GetData ( const std::string & ) [inherited]

Returns:: the value given an attribute name

OBGenericData * GetData ( const char * ) [inherited]

Returns:: the value given an attribute name

std::vector<OBGenericData*>& GetData ( ) [inline, inherited]

Returns:: all data, suitable for iterating

std::vector< OBGenericData * > GetData ( DataOrigin source ) [inherited]

Returns:: all data with a specific origin, suitable for iterating

OBDataIterator BeginData ( ) [inline, inherited]

Returns:: An iterator pointing to the beginning of the data

OBDataIterator EndData ( ) [inline, inherited]

Returns:: An iterator pointing to the end of the data

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.

std::vector<OBAtom*> _vatom [protected]

vector of atoms

std::vector<OBBond*> _vbond [protected]

vector of bonds

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 int _natoms [protected]

Number of atoms.

unsigned int _nbonds [protected]

Number of bonds.

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

Residue information (if applicable).

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

Internal Coordinates (if applicable).

unsigned short int _mod [protected]

Number of nested calls to BeginModify().

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

Custom data.

OBMol Class Reference

Molecule modification methods

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation


Molecule modification methods
virtual OBBase *	DoTransformations (const std::map< std::string, std::string > *pOptions)
bool	Clear ()
void	RenumberAtoms (std::vector< OBAtom * > &)
void	ToInertialFrame (int conf, double *rmat)
void	ToInertialFrame ()
void	Translate (const vector3 &v)
void	Translate (const vector3 &v, int conf)
void	Rotate (const double u[3][3])
void	Rotate (const double m[9])
void	Rotate (const double m[9], int nconf)
void	Center ()
bool	Kekulize ()
bool	PerceiveKekuleBonds ()
void	NewPerceiveKekuleBonds ()
bool	DeleteHydrogens ()
bool	DeleteHydrogens (OBAtom *)
bool	DeleteNonPolarHydrogens ()
bool	DeleteHydrogen (OBAtom *)
bool	AddHydrogens (bool polaronly=false, bool correctForPH=true)
bool	AddHydrogens (OBAtom *)
bool	AddPolarHydrogens ()
bool	StripSalts ()
std::vector< OBMol >	Separate (int StartIndex=1)
bool	ConvertDativeBonds ()
bool	CorrectForPH ()
bool	AssignSpinMultiplicity ()
vector3	Center (int nconf)
void	SetTorsion (OBAtom , OBAtom , OBAtom , OBAtom , double)
static const char *	ClassDescription ()
Public Member Functions
template<class T>
T *	CastAndClear (bool clear=true)
Initialization and data (re)size methods
	OBMol ()
	OBMol (const OBMol &)
virtual	~OBMol ()
OBMol &	operator= (const OBMol &mol)
OBMol &	operator+= (const OBMol &mol)
void	ReserveAtoms (int natoms)
virtual OBAtom *	CreateAtom (void)
virtual OBBond *	CreateBond (void)
virtual OBResidue *	CreateResidue (void)
virtual void	DestroyAtom (OBAtom *)
virtual void	DestroyBond (OBBond *)
virtual void	DestroyResidue (OBResidue *)
bool	AddAtom (OBAtom &)
bool	InsertAtom (OBAtom &)
bool	AddBond (int beginIdx, int endIdx, int order, int flags=0, int insertpos=-1)
bool	AddBond (OBBond &)
bool	AddResidue (OBResidue &)
virtual OBAtom *	NewAtom ()
virtual OBBond *	NewBond ()
virtual OBResidue *	NewResidue ()
bool	DeleteAtom (OBAtom *)
bool	DeleteBond (OBBond *)
bool	DeleteResidue (OBResidue *)
Molecule modification methods
virtual void	BeginModify (void)
virtual void	EndModify (bool nukePerceivedData=true)
int	GetMod ()
void	IncrementMod ()
void	DecrementMod ()
Data retrieval methods
int	GetFlags ()
const char *	GetTitle () const
unsigned int	NumAtoms () const
unsigned int	NumBonds () const
unsigned int	NumHvyAtoms ()
unsigned int	NumResidues () const
unsigned int	NumRotors ()
OBAtom *	GetAtom (int idx)
OBAtom *	GetFirstAtom ()
OBBond *	GetBond (int idx)
OBBond *	GetBond (int a, int b)
OBBond *	GetBond (OBAtom bgn, OBAtom end)
OBResidue *	GetResidue (int)
std::vector< OBInternalCoord * >	GetInternalCoord ()
double	GetTorsion (int, int, int, int)
double	GetTorsion (OBAtom a, OBAtom b, OBAtom c, OBAtom d)
double	GetAngle (OBAtom a, OBAtom b, OBAtom *c)
std::string	GetFormula ()
std::string	GetSpacedFormula (int ones=0, const char *sp=" ")
double	GetEnergy () const
double	GetMolWt ()
double	GetExactMass ()
int	GetTotalCharge ()
unsigned int	GetTotalSpinMultiplicity ()
unsigned short int	GetDimension () const
double *	GetCoordinates ()
std::vector< OBRing * > &	GetSSSR ()
bool	AutomaticFormalCharge ()
bool	AutomaticPartialCharge ()
Data modification methods
void	SetTitle (const char *title)
void	SetTitle (std::string &title)
void	SetFormula (std::string molFormula)
void	SetEnergy (double energy)
void	SetDimension (unsigned short int d)
void	SetTotalCharge (int charge)
void	SetTotalSpinMultiplicity (unsigned int spin)
void	SetInternalCoord (std::vector< OBInternalCoord * > int_coord)
void	SetAutomaticFormalCharge (bool val)
void	SetAutomaticPartialCharge (bool val)
void	SetAromaticPerceived ()
void	SetSSSRPerceived ()
void	SetRingAtomsAndBondsPerceived ()
void	SetAtomTypesPerceived ()
void	SetChainsPerceived ()
void	SetChiralityPerceived ()
void	SetPartialChargesPerceived ()
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	UnsetHydrogensAdded ()
void	UnsetFlag (int flag)
Molecule utilities and perception methods
void	FindSSSR ()
void	FindRingAtomsAndBonds ()
void	FindChiralCenters ()
void	FindChildren (std::vector< int > &children, int bgnIdx, int endIdx)
void	FindChildren (std::vector< OBAtom * > &children, OBAtom bgn, OBAtom end)
void	FindLargestFragment (OBBitVec &frag)
void	ContigFragList (std::vector< std::vector< int > > &)
void	Align (OBAtom , OBAtom , vector3 &, vector3 &)
void	ConnectTheDots ()
void	PerceiveBondOrders ()
void	FindAngles ()
void	FindTorsions ()
bool	GetGTDVector (std::vector< int > &)
void	GetGIVector (std::vector< unsigned int > &)
void	GetGIDVector (std::vector< unsigned int > &)
Methods to check for existence of properties
bool	Has2D ()
bool	Has3D ()
bool	HasNonZeroCoords ()
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 ()
bool	Empty ()
Multiple conformer member functions
int	NumConformers ()
void	SetConformers (std::vector< double * > &v)
void	AddConformer (double *f)
void	SetConformer (int i)
void	CopyConformer (double *c, int nconf)
void	DeleteConformer (int nconf)
double *	GetConformer (int i)
double *	BeginConformer (std::vector< double * >::iterator &i)
double *	NextConformer (std::vector< double * >::iterator &i)
std::vector< double * > &	GetConformers ()
Iterator methods
OBAtomIterator	BeginAtoms ()
OBAtomIterator	EndAtoms ()
OBBondIterator	BeginBonds ()
OBBondIterator	EndBonds ()
OBResidueIterator	BeginResidues ()
OBResidueIterator	EndResidues ()
OBAtom *	BeginAtom (OBAtomIterator &i)
OBAtom *	NextAtom (OBAtomIterator &i)
OBBond *	BeginBond (OBBondIterator &i)
OBBond *	NextBond (OBBondIterator &i)
OBResidue *	BeginResidue (OBResidueIterator &i)
OBResidue *	NextResidue (OBResidueIterator &i)
OBInternalCoord *	BeginInternalCoord (std::vector< OBInternalCoord * >::iterator &i)
OBInternalCoord *	NextInternalCoord (std::vector< OBInternalCoord * >::iterator &i)
Generic data handling methods (via OBGenericData)
bool	HasData (const std::string &)
bool	HasData (const char *)
bool	HasData (const unsigned int type)
void	DeleteData (unsigned int type)
void	DeleteData (OBGenericData *)
void	DeleteData (std::vector< OBGenericData * > &)
void	SetData (OBGenericData *d)
unsigned int	DataSize () const
OBGenericData *	GetData (const unsigned int type)
OBGenericData *	GetData (const std::string &)
OBGenericData *	GetData (const char *)
std::vector< OBGenericData * > &	GetData ()
std::vector< OBGenericData * >	GetData (DataOrigin source)
OBDataIterator	BeginData ()
OBDataIterator	EndData ()
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)
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)
int	getorden (OBAtom *atom)
void	expandcycle (OBAtom *atom, OBBitVec &avisit)
Protected Attributes
int	_flags
bool	_autoPartialCharge
bool	_autoFormalCharge
std::string	_title
std::vector< OBAtom * >	_vatom
std::vector< OBBond * >	_vbond
unsigned short int	_dimension
double	_energy
int	_totalCharge
unsigned int	_totalSpin
double *	_c
std::vector< double * >	_vconf
unsigned int	_natoms
unsigned int	_nbonds
std::vector< OBResidue * >	_residue
std::vector< OBInternalCoord * >	_internals
unsigned short int	_mod
std::vector< OBGenericData * >	_vdata