#include <openbabel/residue.h>

Inheritance diagram for OBResidue:

Public Member Functions
	OBResidue (void)

	OBResidue (const OBResidue &)

virtual	~OBResidue (void)

OBResidue &	operator= (const OBResidue &)

void	AddAtom (OBAtom *atom)

void	InsertAtom (OBAtom *atom)

void	RemoveAtom (OBAtom *atom)

bool	Clear ()

void	SetName (const std::string &resname)

void	SetNum (const unsigned int resnum)

void	SetNum (const std::string resnum)

void	SetChain (const char chain)

void	SetChainNum (const unsigned int chainnum)

void	SetIdx (const unsigned int idx)

void	SetInsertionCode (const char insertioncode)

void	SetAtomID (OBAtom *atom, const std::string &id)

void	SetHetAtom (OBAtom *atom, bool hetatm)

void	SetSerialNum (OBAtom *atom, unsigned int sernum)

std::string	GetName (void) const

int	GetNum (void)

std::string	GetNumString (void)

unsigned int	GetNumAtoms () const

char	GetChain (void) const

unsigned int	GetChainNum (void) const

unsigned int	GetIdx (void) const

unsigned int	GetResKey (void) const

std::vector< OBAtom * >	GetAtoms (void) const

std::vector< OBBond * >	GetBonds (bool exterior=true) const

std::string	GetAtomID (OBAtom *atom) const

unsigned	GetSerialNum (OBAtom *atom) const

char	GetInsertionCode (void) const

bool	GetAminoAcidProperty (int) const

bool	GetAtomProperty (OBAtom *a, int) const

bool	GetResidueProperty (int) const

bool	IsHetAtom (OBAtom *atom) const

bool	IsResidueType (int) const

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

template<class T >
T *	CastAndClear (bool clear=true)

virtual const char *	GetTitle (bool replaceNewlines=true) const

virtual void	SetTitle (const char *)

Iterator methods
OBAtomIterator	BeginAtoms ()

OBAtomIterator	EndAtoms ()

OBAtom *	BeginAtom (std::vector< OBAtom *>::iterator &i)

OBAtom *	NextAtom (std::vector< OBAtom *>::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 *> &)

bool	DeleteData (const std::string &s)

void	SetData (OBGenericData *d)

void	CloneData (OBGenericData *d)

size_t	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)

std::vector< OBGenericData * >	GetAllData (const unsigned int type)

OBDataIterator	BeginData ()

OBDataIterator	EndData ()

Static Public Member Functions
static const char *	ClassDescription ()

Protected Attributes
unsigned int	_idx

char	_chain

unsigned int	_aakey

unsigned int	_reskey

std::string	_resnum

std::string	_resname

char	_insertioncode

std::vector< bool >	_hetatm

std::vector< std::string >	_atomid

std::vector< OBAtom * >	_atoms

std::vector< unsigned int >	_sernum

std::vector< OBGenericData * >	_vdata

Detailed Description

Residue information.

The residue information is drawn from PDB or MOL2 files (or similar), which track biomolecule information, and are stored in the OBResidue class. OBResidues are stored inside the OBAtom class and OBMol classes. The residue information for an atom can be requested in the following way:

OBAtom *atom;
OBResidue *r;
atom = mol.GetAtom(1);
r = atom->GetResidue();

The residue information for a molecule can be manipulated too:

cout << "This molecule has " << mol.NumResidues() << " residues." << endl;
OBResidue *r;
r = mol.GetResidue(1);

Constructor & Destructor Documentation

◆ OBResidue() [1/2]

OBResidue ( void )

Constructor.

◆ OBResidue() [2/2]

OBResidue ( const OBResidue & src )

Copy constructor.

◆ ~OBResidue()

~OBResidue ( void )

virtual

Destructor.

Member Function Documentation

◆ operator=()

OBResidue & operator= ( const OBResidue & src )

◆ AddAtom()

void AddAtom ( OBAtom * atom )

Add atom to this residue. Updates the atom via OBAtom::SetResidue()

Referenced by OBMol::AddNewHydrogens(), OBMol::CopySubstructure(), OBResidue::InsertAtom(), OBMol::operator=(), and OBChainsParser::~OBChainsParser().

◆ InsertAtom()

void InsertAtom ( OBAtom * atom )

Add atom to this residue. Updates the atom via OBAtom::SetResidue()

◆ RemoveAtom()

void RemoveAtom ( OBAtom * atom )

Remove atom from this residue and update the atom.

◆ Clear()

bool Clear ( void )

virtual

Clear any and all data associated with this residue. Updates all atoms included in the residue, as well as calling OBBase::Clear() for any generic data.

Returns: Whether the call was successful.

Reimplemented from OBBase.

◆ SetName()

void SetName ( const std::string & resname )

Set the name of this residue (e.g., "ALA"). Use 3-char PDB standard names. http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_79.html MODRES records for modified residues: http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_36.html.

Referenced by OBChainsParser::~OBChainsParser().

◆ SetNum() [1/2]

void SetNum ( const unsigned int resnum )

Set the residue number (in the sequence)

Referenced by OBChainsParser::~OBChainsParser().

◆ SetNum() [2/2]

void SetNum ( const std::string resnum )

◆ SetChain()

void SetChain ( const char chain )

Set the chain ID for this residue.

Referenced by OBChainsParser::~OBChainsParser().

◆ SetChainNum()

void SetChainNum ( const unsigned int chainnum )

Set the chain number for this residue.

◆ SetIdx()

void SetIdx ( const unsigned int idx )

Set the internal index of this residue in the parent OBMol. Intended mostly for internal use

Referenced by OBMol::AddResidue(), and OBMol::NewResidue().

◆ SetInsertionCode()

void SetInsertionCode ( const char insertioncode )

Set PDB insertion code information for this residue. This allows consecutive residues to have the same number. Some communities that work in a well-conserved structural world use this, e.g. for immunoglobulins.

◆ SetAtomID()

void SetAtomID	(	OBAtom *	atom,
		const std::string &	id
	)

Set the character code ID for an ATOM record for the supplied atom This does nothing if the supplied atom is not found in the residue

Referenced by OBMol::AddNewHydrogens(), OBMol::CopySubstructure(), OBMol::operator=(), and OBChainsParser::~OBChainsParser().

◆ SetHetAtom()

void SetHetAtom	(	OBAtom *	atom,
		bool	hetatm
	)

Referenced by OBMol::AddNewHydrogens(), OBMol::CopySubstructure(), OBMol::operator=(), and OBChainsParser::~OBChainsParser().

◆ SetSerialNum()

void SetSerialNum	(	OBAtom *	atom,
		unsigned int	sernum
	)

Set the atomic serial number for a given atom (see OBSerialNums)

Referenced by OBMol::CopySubstructure(), OBMol::operator=(), and OBChainsParser::~OBChainsParser().

◆ GetName()

string GetName ( void ) const

Returns: The residue name

Referenced by OBResidueData::AssignBonds().

◆ GetNum()

int GetNum ( void )

Returns: The residue number (in the sequence)

◆ GetNumString()

std::string GetNumString ( void )

Referenced by OBResidueData::AssignBonds().

◆ GetNumAtoms()

unsigned int GetNumAtoms ( void ) const

Returns: The number of atoms in this residue

◆ GetChain()

char GetChain ( void ) const

Returns: The ID of the chain which includes this residue

Referenced by OBResidueData::AssignBonds().

◆ GetChainNum()

unsigned int GetChainNum ( void ) const

Returns: The number of the chain which includes this residue

◆ GetIdx()

unsigned int GetIdx ( void ) const

Returns: The internal index of this residue in the parent OBMol

Referenced by OBMol::DeleteResidue().

◆ GetResKey()

unsigned int GetResKey ( void ) const

Returns: The residue key (i.e., an entry in the OBResidueIndex namespace)

◆ GetAtoms()

vector< OBAtom * > GetAtoms ( void ) const

Returns: a vector of all atoms in this residue

◆ GetBonds()

vector< OBBond * > GetBonds ( bool exterior = true ) const

Returns: all bonds in this residue. exterior includes bonds to atoms outside this residue (default is true)

◆ GetAtomID()

string GetAtomID ( OBAtom * atom ) const

Returns: the atom ID (character code) for the supplied atom or "" if the atom is not found in this residue

Referenced by OBResidueData::AssignBonds(), OBMol::CopySubstructure(), OBResidue::GetAtomProperty(), and OBMol::operator=().

◆ GetSerialNum()

unsigned int GetSerialNum ( OBAtom * atom ) const

Returns: the serial number of the supplied atom (uses OBSerialNums)

Referenced by OBMol::CopySubstructure(), and OBMol::operator=().

◆ GetInsertionCode()

char GetInsertionCode ( void ) const

Returns: The Insertion Code (i.e., an extra position motivated by a multiple sequence alignment against a template with defined numbers)

◆ GetAminoAcidProperty()

bool GetAminoAcidProperty ( int property ) const

Returns: Whether this residue has the supplied amino acid property defined from the OBAminoAcidProperty namespace

◆ GetAtomProperty()

bool GetAtomProperty	(	OBAtom *	a,
		int	property
	)		const

Returns: Whether atom a has the supplied residue atom property defined from the OBResidueAtomProperty namespace

◆ GetResidueProperty()

bool GetResidueProperty ( int property ) const

Returns: Whether this residue has the supplied property defined from the OBResidueProperty namespace

Referenced by OBResidue::GetAtomProperty().

◆ IsHetAtom()

bool IsHetAtom ( OBAtom * atom ) const

Returns: If the given atom is a HETATM record

Referenced by OBMol::AddNewHydrogens(), OBMol::CopySubstructure(), OBResidue::GetAtomProperty(), OBAtom::IsHetAtom(), and OBMol::operator=().

◆ IsResidueType()

bool IsResidueType ( int restype ) const

Returns: If this residue matches the supplied restype Set by SetResidueKeys()

◆ BeginAtoms()

OBAtomIterator BeginAtoms ( )

inline

Returns: An iterator to the beginning of the atom list in this residue

◆ EndAtoms()

OBAtomIterator EndAtoms ( )

inline

Returns: An iterator to the end of the atom list in this residue

◆ BeginAtom()

OBAtom * BeginAtom ( std::vector< OBAtom *>::iterator & i )

Set the iterator i to the beginning of the atom list in this residue

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

Referenced by OBMol::operator=().

◆ NextAtom()

OBAtom * NextAtom ( std::vector< OBAtom *>::iterator & i )

Increment the iterator i

Returns: The next atom (or NULL if none exist)

Referenced by OBResidueAtomIter::operator++(), and OBMol::operator=().

◆ DoTransformations()

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

inlinevirtualinherited

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() Base type does nothing

Reimplemented in OBMol.

◆ ClassDescription()

static const char* ClassDescription ( )

inlinestaticinherited

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

◆ CastAndClear()

T* CastAndClear ( bool clear = true )

inlineinherited

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

◆ GetTitle()

virtual const char* GetTitle ( bool replaceNewlines = true ) const

inlinevirtualinherited

Base type does nothing Made virtual around r3535 to simplify code which passes around OBBase*.

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ SetTitle()

virtual void SetTitle ( const char * )

inlinevirtualinherited

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ HasData() [1/3]

bool HasData ( const std::string & s )

inherited

Returns: whether the generic attribute/value pair exists

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBDescriptor::MatchPairData(), OBMoleculeFormat::ReadChemObjectImpl(), and OBMol::SetEnergies().

◆ HasData() [2/3]

bool HasData ( const char * s )

inherited

Returns: whether the generic attribute/value pair exists

◆ HasData() [3/3]

bool HasData ( const unsigned int type )

inherited

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

◆ DeleteData() [1/4]

void DeleteData ( unsigned int type )

inherited

Delete any data matching the given OBGenericDataType.

Referenced by OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OpenBabel::DeleteStereoOnAtom(), and OBMol::RenumberAtoms().

◆ DeleteData() [2/4]

void DeleteData ( OBGenericData * gd )

inherited

Delete the given generic data from this object.

◆ DeleteData() [3/4]

void DeleteData ( std::vector< OBGenericData *> & vg )

inherited

Delete all of the given generic data from this object.

◆ DeleteData() [4/4]

bool DeleteData ( const std::string & s )

inherited

Deletes the generic data with the specified attribute, returning false if not found.

◆ SetData()

void SetData ( OBGenericData * d )

inlineinherited

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

Referenced by OBGastChrg::AssignPartialCharges(), OBMol::CopySubstructure(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBMoleculeFormat::MakeCombinedMolecule(), OBDescriptor::PredictAndSave(), AliasData::RevertToAliasForm(), and OBMol::SetEnergies().

◆ CloneData()

void CloneData ( OBGenericData * d )

inherited

Adds a copy of a data object; does nothing if d == NULL

Since: version 2.2

Referenced by AliasData::Expand().

◆ DataSize()

size_t DataSize ( ) const

inlineinherited

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

◆ GetData() [1/5]

OBGenericData * GetData ( const unsigned int type )

inherited

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

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OpenBabel::extract_thermochemistry(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OpenBabel::IsSuppressibleHydrogen(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), and OBDescriptor::PredictAndSave().

◆ GetData() [2/5]

OBGenericData * GetData ( const std::string & s )

inherited

Returns: any data matching the given attribute name or NULL if nothing matches; the value given an attribute name

◆ GetData() [3/5]

OBGenericData * GetData ( const char * s )

inherited

Returns: any data matching the given attribute name or NULL if nothing matches; the value given an attribute name

◆ GetData() [4/5]

std::vector<OBGenericData*>& GetData ( )

inlineinherited

Returns: all data, suitable for iterating

Referenced by OBMol::GetEnergies(), OBMol::GetEnergy(), and OBMol::SetEnergies().

◆ GetData() [5/5]

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

inherited

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

◆ GetAllData()

std::vector< OBGenericData * > GetAllData ( const unsigned int type )

inherited

Returns: the all matching data for a given type from OBGenericDataType or an empty vector if nothing matches

Since: version 2.2

Referenced by OpenBabel::CanonicalLabels(), OBMol::CopySubstructure(), OBBuilder::CorrectStereoAtoms(), OBBuilder::CorrectStereoBonds(), OpenBabel::DeleteStereoOnAtom(), and OBMol::operator+=().

◆ BeginData()

OBDataIterator BeginData ( )

inlineinherited

Returns: An iterator pointing to the beginning of the data

Referenced by OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

◆ EndData()

OBDataIterator EndData ( )

inlineinherited

Returns: An iterator pointing to the end of the data

Referenced by OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

Member Data Documentation

◆ _idx

unsigned int _idx

protected

Residue index (i.e., internal index in an OBMol)

Referenced by OBResidue::Clear(), OBResidue::GetIdx(), and OBResidue::SetIdx().

◆ _chain

char _chain

protected

Chain ID.

Referenced by OBResidue::Clear(), OBResidue::GetChain(), OBResidue::GetChainNum(), OBResidue::OBResidue(), OBResidue::operator=(), OBResidue::SetChain(), and OBResidue::SetChainNum().

◆ _aakey

unsigned int _aakey

protected

Amino Acid key ID – see SetResidueKeys()

Referenced by OBResidue::Clear(), OBResidue::GetAminoAcidProperty(), OBResidue::OBResidue(), OBResidue::operator=(), and OBResidue::SetName().

◆ _reskey

unsigned int _reskey

protected

Residue key ID – see SetResidueKeys()

Referenced by OBResidue::Clear(), OBResidue::GetResidueProperty(), OBResidue::GetResKey(), OBResidue::IsResidueType(), OBResidue::OBResidue(), OBResidue::operator=(), and OBResidue::SetName().

◆ _resnum

std::string _resnum

protected

Residue number (i.e., in file) 23, 1B, etc.

Referenced by OBResidue::Clear(), OBResidue::GetNum(), OBResidue::GetNumString(), OBResidue::OBResidue(), OBResidue::operator=(), and OBResidue::SetNum().

◆ _resname

std::string _resname

protected

Residue text name.

Referenced by OBResidue::Clear(), OBResidue::GetName(), OBResidue::OBResidue(), OBResidue::operator=(), and OBResidue::SetName().

◆ _insertioncode

char _insertioncode

protected

PBB insertion code.

Referenced by OBResidue::Clear(), OBResidue::GetInsertionCode(), OBResidue::OBResidue(), and OBResidue::operator=().

◆ _hetatm

std::vector<bool> _hetatm

protected

Is a given atom a HETAM.

Referenced by OBResidue::AddAtom(), OBResidue::Clear(), OBResidue::IsHetAtom(), OBResidue::OBResidue(), OBResidue::operator=(), OBResidue::RemoveAtom(), and OBResidue::SetHetAtom().

◆ _atomid

std::vector<std::string> _atomid

protected

Residue atom text IDs.

Referenced by OBResidue::AddAtom(), OBResidue::Clear(), OBResidue::GetAtomID(), OBResidue::OBResidue(), OBResidue::operator=(), OBResidue::RemoveAtom(), and OBResidue::SetAtomID().

◆ _atoms

std::vector<OBAtom*> _atoms

protected

List of OBAtom in this residue.

Referenced by OBResidue::AddAtom(), OBResidue::BeginAtom(), OBResidue::Clear(), OBResidue::GetAtomID(), OBResidue::GetAtoms(), OBResidue::GetBonds(), OBResidue::GetNumAtoms(), OBResidue::GetSerialNum(), OBResidue::IsHetAtom(), OBResidue::NextAtom(), OBResidue::RemoveAtom(), OBResidue::SetAtomID(), OBResidue::SetHetAtom(), OBResidue::SetSerialNum(), and OBResidue::~OBResidue().

◆ _sernum

std::vector<unsigned int> _sernum

protected

List of serial numbers.

Referenced by OBResidue::AddAtom(), OBResidue::Clear(), OBResidue::GetSerialNum(), OBResidue::OBResidue(), OBResidue::operator=(), OBResidue::RemoveAtom(), and OBResidue::SetSerialNum().

◆ _vdata

std::vector<OBGenericData*> _vdata

protectedinherited

Custom data.

Referenced by OBMol::OBMol().

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OBResidue() [1/2]

◆ OBResidue() [2/2]

◆ ~OBResidue()

Member Function Documentation

◆ operator=()

◆ AddAtom()

◆ InsertAtom()

◆ RemoveAtom()

◆ Clear()

◆ SetName()

◆ SetNum() [1/2]

◆ SetNum() [2/2]

◆ SetChain()

◆ SetChainNum()

◆ SetIdx()

◆ SetInsertionCode()

◆ SetAtomID()

◆ SetHetAtom()

◆ SetSerialNum()

◆ GetName()

◆ GetNum()

◆ GetNumString()

◆ GetNumAtoms()

◆ GetChain()

◆ GetChainNum()

◆ GetIdx()

◆ GetResKey()

◆ GetAtoms()

◆ GetBonds()

◆ GetAtomID()

◆ GetSerialNum()

◆ GetInsertionCode()

◆ GetAminoAcidProperty()

◆ GetAtomProperty()

◆ GetResidueProperty()

◆ IsHetAtom()

◆ IsResidueType()

◆ BeginAtoms()

◆ EndAtoms()

◆ BeginAtom()

◆ NextAtom()

◆ DoTransformations()

◆ ClassDescription()

◆ CastAndClear()

◆ GetTitle()

◆ SetTitle()

◆ HasData() [1/3]

◆ HasData() [2/3]

◆ HasData() [3/3]

◆ DeleteData() [1/4]

◆ DeleteData() [2/4]

◆ DeleteData() [3/4]

◆ DeleteData() [4/4]

◆ SetData()

◆ CloneData()

◆ DataSize()

◆ GetData() [1/5]

◆ GetData() [2/5]

◆ GetData() [3/5]

◆ GetData() [4/5]

◆ GetData() [5/5]

◆ GetAllData()

◆ BeginData()

◆ EndData()

Member Data Documentation

◆ _idx

◆ _chain

◆ _aakey

◆ _reskey

◆ _resnum

◆ _resname

◆ _insertioncode

◆ _hetatm

◆ _atomid

◆ _atoms