OBResidue Class Reference
Residue information. More...
#include <openbabel/residue.h>

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 | 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 |
unsigned 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 |
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 |
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 | ( | void | ) |
Constructor.
~OBResidue | ( | void | ) | [virtual] |
Destructor.
Member Function Documentation
void AddAtom | ( | OBAtom * | atom | ) |
Add atom
to this residue. Updates the atom via OBAtom::SetResidue().
Referenced by OBMol::AddHydrogens(), OBResidue::InsertAtom(), and OBMol::operator=().
void InsertAtom | ( | OBAtom * | atom | ) |
Add atom
to this residue. Updates the atom via OBAtom::SetResidue().
void RemoveAtom | ( | OBAtom * | atom | ) |
Remove atom
from this residue and update the atom.
Referenced by OBAtom::~OBAtom().
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.
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 OBMol::operator=().
void SetNum | ( | const unsigned int | resnum | ) |
Set the residue number (in the sequence).
Referenced by OBMol::operator=().
void SetNum | ( | const std::string | resnum | ) |
void SetChain | ( | const char | chain | ) |
Set the chain ID for this residue.
Referenced by OBMol::operator=().
void SetChainNum | ( | const unsigned int | chainnum | ) |
Set the chain number for this residue.
Referenced by OBMol::operator=().
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().
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::AddHydrogens(), and OBMol::operator=().
void SetHetAtom | ( | OBAtom * | atom, | |
bool | hetatm | |||
) |
Referenced by OBMol::operator=().
void SetSerialNum | ( | OBAtom * | atom, | |
unsigned int | sernum | |||
) |
Set the atomic serial number for a given atom (see OBSerialNums).
Referenced by OBMol::operator=().
string GetName | ( | void | ) | const |
- Returns:
- The residue name
Referenced by OBResidueData::AssignBonds(), and OBMol::operator=().
unsigned int GetNum | ( | void | ) |
- Returns:
- The residue number (in the sequence)
std::string GetNumString | ( | void | ) |
Referenced by OBResidueData::AssignBonds(), and OBMol::operator=().
unsigned int GetNumAtoms | ( | void | ) | const |
- Returns:
- The number of atoms in this residue
char GetChain | ( | void | ) | const |
- Returns:
- The ID of the chain which includes this residue
Referenced by OBResidueData::AssignBonds(), and OBMol::operator=().
unsigned int GetChainNum | ( | void | ) | const |
- Returns:
- The number of the chain which includes this residue
Referenced by OBMol::operator=().
unsigned int GetIdx | ( | void | ) | const |
- Returns:
- The internal index of this residue in the parent OBMol
Referenced by OBMol::DeleteResidue().
unsigned int GetResKey | ( | void | ) | const |
- Returns:
- The residue key (i.e., an entry in the OBResidueIndex namespace)
vector< OBAtom * > GetAtoms | ( | void | ) | const |
- Returns:
- a vector of all atoms in this residue
vector< OBBond * > GetBonds | ( | bool | exterior = true |
) | const |
- Returns:
- all bonds in this residue.
exterior
includes bonds to atoms outside this residue (default is true)
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(), OBResidue::GetAtomProperty(), and OBMol::operator=().
unsigned int GetSerialNum | ( | OBAtom * | atom | ) | const |
- Returns:
- the serial number of the supplied atom (uses OBSerialNums)
Referenced by OBMol::operator=().
bool GetAminoAcidProperty | ( | int | property | ) | const |
- Returns:
- Whether this residue has the supplied amino acid property defined from the OBAminoAcidProperty namespace
bool GetAtomProperty | ( | OBAtom * | a, | |
int | property | |||
) | const |
- Returns:
- Whether atom
a
has the supplied residue atom property defined from the OBResidueAtomProperty namespace
bool GetResidueProperty | ( | int | property | ) | const |
- Returns:
- Whether this residue has the supplied property defined from the OBResidueProperty namespace
Referenced by OBResidue::GetAtomProperty().
bool IsHetAtom | ( | OBAtom * | atom | ) | const |
- Returns:
- If the given atom is a HETATM record
Referenced by OBResidue::GetAtomProperty(), and OBMol::operator=().
bool IsResidueType | ( | int | restype | ) | const |
- Returns:
- If this residue matches the supplied
restype
Set by SetResidueKeys()
OBAtomIterator BeginAtoms | ( | ) | [inline] |
- Returns:
- An iterator to the beginning of the atom list in this residue
OBAtomIterator EndAtoms | ( | ) | [inline] |
- Returns:
- An iterator to the end of the atom list in this residue
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=().
Increment the iterator i
- Returns:
- The next atom (or NULL if none exist)
Referenced by OBResidueAtomIter::operator++(), and OBMol::operator=().
virtual OBBase* DoTransformations | ( | const std::map< std::string, std::string > * | , | |
OBConversion * | ||||
) | [inline, virtual, inherited] |
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.
static const char* ClassDescription | ( | ) | [inline, static, inherited] |
- Returns:
- A list of descriptions of command-line options for DoTransformations()
Reimplemented in OBMol, and OBReaction.
T* CastAndClear | ( | bool | clear = true |
) | [inline, inherited] |
By default clears the object. Called from ReadMolecule of most format classes.
virtual const char* GetTitle | ( | bool | replaceNewlines = true |
) | const [inline, virtual, inherited] |
Base type does nothing Made virtual around r3535 to simplify code which passes around OBBase*.
Reimplemented in OBMol.
Referenced by OBMoleculeFormat::DoOutputOptions().
virtual void SetTitle | ( | const char * | ) | [inline, virtual, inherited] |
Reimplemented in OBMol.
Referenced by OBMoleculeFormat::DoOutputOptions().
bool HasData | ( | const std::string & | s | ) | [inherited] |
- Returns:
- whether the generic attribute/value pair exists
Referenced by OBMol::AddAtom(), OBDepict::DrawMolecule(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBBase::HasData(), OBDescriptor::MatchPairData(), OBMol::NewAtom(), OBMol::operator=(), OBMoleculeFormat::ReadChemObjectImpl(), and OBMol::SetEnergies().
bool HasData | ( | const char * | s | ) | [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.
Referenced by OBMol::AddAtom(), OBMol::BeginModify(), OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OBMol::EndModify(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::NewAtom(), OBMol::RenumberAtoms(), and OBForceField::Setup().
void DeleteData | ( | OBGenericData * | gd | ) | [inherited] |
Delete the given generic data from this object.
void DeleteData | ( | std::vector< OBGenericData * > & | vg | ) | [inherited] |
Delete all of the given generic data from this object.
bool DeleteData | ( | const std::string & | s | ) | [inherited] |
Deletes the generic data with the specified attribute, returning false if not found.
void SetData | ( | OBGenericData * | d | ) | [inline, inherited] |
Adds a data object; does nothing if d==NULL.
Referenced by OBMol::AddBond(), OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::DoTransformations(), OBAtom::Duplicate(), AliasData::Expand(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::operator=(), OBDescriptor::PredictAndSave(), OBMol::SetEnergies(), and OBMol::SetFormula().
void CloneData | ( | OBGenericData * | d | ) | [inherited] |
Adds a copy of a data object; does nothing if d == NULL
- Since:
- version 2.2
Referenced by OBMol::AddBond().
size_t 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
Referenced by OpenBabel::CalcSignedVolume(), OpenBabel::CorrectChirality(), OBDepict::DrawMolecule(), AliasData::Expand(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), OBMol::operator=(), and OBDescriptor::PredictAndSave().
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
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
std::vector<OBGenericData*>& GetData | ( | ) | [inline, inherited] |
- Returns:
- all data, suitable for iterating
Referenced by OBMol::BeginModify(), OBMol::DoTransformations(), OBBase::GetData(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBMol::SetEnergies(), and OBMol::SetFormula().
std::vector< OBGenericData * > GetData | ( | DataOrigin | source | ) | [inherited] |
- Returns:
- all data with a specific origin, suitable for iterating
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(), OBBuilder::CorrectStereoAtoms(), and OBBuilder::CorrectStereoBonds().
OBDataIterator BeginData | ( | ) | [inline, inherited] |
- Returns:
- An iterator pointing to the beginning of the data
Referenced by OBMol::AddAtom(), OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::NewAtom(), and OBMol::operator=().
OBDataIterator EndData | ( | ) | [inline, inherited] |
- Returns:
- An iterator pointing to the end of the data
Referenced by OBMol::AddAtom(), OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::NewAtom(), and OBMol::operator=().
Member Data Documentation
unsigned int _idx [protected] |
Residue index (i.e., internal index in an OBMol).
Referenced by OBResidue::Clear(), OBResidue::GetIdx(), OBResidue::OBResidue(), and OBResidue::SetIdx().
char _chain [protected] |
Chain ID.
Referenced by OBResidue::Clear(), OBResidue::GetChain(), OBResidue::GetChainNum(), OBResidue::OBResidue(), OBResidue::operator=(), OBResidue::SetChain(), and OBResidue::SetChainNum().
unsigned int _aakey [protected] |
Amino Acid key ID -- see SetResidueKeys().
Referenced by OBResidue::Clear(), OBResidue::GetAminoAcidProperty(), OBResidue::OBResidue(), OBResidue::operator=(), and OBResidue::SetName().
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().
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().
std::string _resname [protected] |
Residue text name.
Referenced by OBResidue::Clear(), OBResidue::GetName(), OBResidue::OBResidue(), OBResidue::operator=(), and OBResidue::SetName().
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().
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().
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().
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().
std::vector<OBGenericData*> _vdata [protected, inherited] |
Custom data.
Referenced by OBBase::Clear(), OBBase::CloneData(), OBBase::DeleteData(), OBAtom::Duplicate(), OBBase::GetAllData(), OBBase::GetData(), OBBase::HasData(), OBBond::OBBond(), OBMol::OBMol(), and OBResidue::OBResidue().
The documentation for this class was generated from the following files: