OBAtom Class Reference
Atom class. More...
#include <openbabel/atom.h>

Public Member Functions | |
OBAtom () | |
virtual | ~OBAtom () |
OBAtom & | operator= (OBAtom &) |
void | Duplicate (OBAtom *) |
bool | Clear () |
double | GetDistance (int index) |
double | GetDistance (OBAtom *) |
double | GetAngle (int b, int c) |
double | GetAngle (OBAtom *b, OBAtom *c) |
virtual OBBase * | DoTransformations (const std::map< std::string, std::string > *) |
template<class T> | |
T * | CastAndClear (bool clear=true) |
Methods to set atomic information | |
void | SetIdx (int idx) |
void | SetHyb (int hyb) |
void | SetAtomicNum (int atomicnum) |
void | SetIsotope (unsigned int iso) |
void | SetImplicitValence (int val) |
void | IncrementImplicitValence () |
void | DecrementImplicitValence () |
void | SetFormalCharge (int fcharge) |
void | SetSpinMultiplicity (short spin) |
void | SetType (const char *type) |
void | SetType (const std::string &type) |
void | SetPartialCharge (double pcharge) |
void | SetVector (const vector3 &v) |
void | SetVector (const double x, const double y, const double z) |
void | SetCoordPtr (double **c) |
void | SetVector () |
void | SetResidue (OBResidue *res) |
void | SetParent (OBMol *ptr) |
void | SetAromatic () |
void | UnsetAromatic () |
void | SetClockwiseStereo () |
void | SetAntiClockwiseStereo () |
void | SetPositiveStereo () |
void | SetNegativeStereo () |
void | UnsetStereo () |
void | SetInRing () |
void | SetChiral () |
void | ClearCoordPtr () |
Methods to retrieve atomic information | |
int | GetFormalCharge () const |
unsigned int | GetAtomicNum () const |
unsigned short int | GetIsotope () const |
int | GetSpinMultiplicity () const |
double | GetAtomicMass () const |
double | GetExactMass () const |
unsigned int | GetIdx () const |
unsigned int | GetCoordinateIdx () const |
unsigned int | GetCIdx () const |
unsigned int | GetValence () const |
unsigned int | GetHyb () const |
unsigned int | GetImplicitValence () const |
unsigned int | GetHvyValence () const |
unsigned int | GetHeteroValence () const |
char * | GetType () |
double | GetX () const |
double | GetY () const |
double | GetZ () const |
double | x () const |
double | y () const |
double | z () const |
double * | GetCoordinate () |
vector3 & | GetVector () |
const vector3 & | GetVector () const |
double | GetPartialCharge () |
OBResidue * | GetResidue () |
OBResidue * | GetResidue (bool perception) |
OBMol * | GetParent () |
bool | GetNewBondVector (vector3 &v, double length) |
OBBond * | GetBond (OBAtom *) |
OBAtom * | GetNextAtom () |
Iterator methods | |
OBBondIterator | BeginBonds () |
OBBondIterator | EndBonds () |
OBBond * | BeginBond (OBBondIterator &i) |
OBBond * | NextBond (OBBondIterator &i) |
OBAtom * | BeginNbrAtom (OBBondIterator &i) |
OBAtom * | NextNbrAtom (OBBondIterator &i) |
Addition of residue/bond info. for an atom | |
void | NewResidue () |
void | AddResidue (OBResidue *res) |
void | DeleteResidue () |
void | AddBond (OBBond *bond) |
void | InsertBond (OBBondIterator &i, OBBond *bond) |
bool | DeleteBond (OBBond *bond) |
void | ClearBond () |
Builder utilities | |
bool | HtoMethyl () |
bool | SetHybAndGeom (int) |
void | ForceNoH () |
bool | HasNoHForced () |
void | ForceImplH () |
bool | HasImplHForced () |
Property information | |
unsigned int | CountFreeOxygens () const |
unsigned int | ImplicitHydrogenCount () const |
unsigned int | ExplicitHydrogenCount (bool ExcludeIsotopes=false) const |
unsigned int | MemberOfRingCount () const |
unsigned int | MemberOfRingSize () const |
unsigned int | CountRingBonds () const |
double | SmallestBondAngle () |
double | AverageBondAngle () |
unsigned int | BOSum () const |
unsigned int | KBOSum () const |
bool | HasResidue () |
bool | IsHydrogen () |
bool | IsCarbon () |
bool | IsNitrogen () |
bool | IsOxygen () |
bool | IsSulfur () |
bool | IsPhosphorus () |
bool | IsAromatic () const |
bool | IsInRing () const |
bool | IsInRingSize (int) const |
bool | IsHeteroatom () |
bool | IsNotCorH () |
bool | IsConnected (OBAtom *) |
bool | IsOneThree (OBAtom *) |
bool | IsOneFour (OBAtom *) |
bool | IsCarboxylOxygen () |
bool | IsPhosphateOxygen () |
bool | IsSulfateOxygen () |
bool | IsNitroOxygen () |
bool | IsAmideNitrogen () |
bool | IsPolarHydrogen () |
bool | IsNonPolarHydrogen () |
bool | IsAromaticNOxide () |
bool | IsChiral () |
bool | IsAxial () |
bool | IsClockwise () |
bool | IsAntiClockwise () |
bool | IsPositiveStereo () |
bool | IsNegativeStereo () |
bool | HasChiralitySpecified () |
bool | HasChiralVolume () |
bool | IsHbondAcceptor () |
bool | IsHbondDonor () |
bool | IsHbondDonorH () |
bool | HasAlphaBetaUnsat (bool includePandS=true) |
bool | HasBondOfOrder (unsigned int bo) |
int | CountBondsOfOrder (unsigned int bo) |
bool | HasNonSingleBond () |
bool | HasSingleBond () |
bool | HasDoubleBond () |
bool | HasAromaticBond () |
bool | MatchesSMARTS (const char *) |
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) |
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) |
std::vector< OBGenericData * > | GetAllData (const unsigned int type) |
OBDataIterator | BeginData () |
OBDataIterator | EndData () |
Static Public Member Functions | |
static const char * | ClassDescription () |
Public Attributes | |
bool | Visit |
Protected Member Functions | |
int | GetFlag () const |
void | SetFlag (int flag) |
bool | HasFlag (int flag) |
Protected Attributes | |
char | _ele |
char | _impval |
char | _type [6] |
short | _fcharge |
unsigned short | _isotope |
short | _spinmultiplicity |
unsigned int | _idx |
OBMol * | _parent |
std::vector< OBBond * > | _vbond |
unsigned int | _cidx |
unsigned short | _hyb |
unsigned short | _flags |
double | _pcharge |
double ** | _c |
vector3 | _v |
OBResidue * | _residue |
std::vector< OBGenericData * > | _vdata |
Detailed Description
Atom class.To understand the OBAtom class it is important to state a key decision on which the design was based. The OBAtom class not only holds data, but facilitates extraction of data perceived from both the atom and the molecule. This prevents the OBMol class from becoming overly large and complicated.
A number of data extraction methods perform what is called `Lazy Evaluation,' which is essentially on-the-fly evaluation. For example, when an atom is queried as to whether it is cyclic or what it's hybridization state is the information is perceived automatically. The perception of a particular trait is actually performed on the entire molecule the first time it is requested of an atom or bond, and stored for subsequent requests for the same trait of additional atoms or bonds.The OBAtom class is similar to OBMol and the whole of Open Babel in that data access and modification is done through Get and Set methods.
The following code demonstrates how to print out the atom numbers, element numbers, and coordinates of a molecule:
OBMol mol; FOR_ATOMS_OF_MOL(atom, mol) { cout << atom->GetIdx() << ` `; cout << atom->GetAtomicNum() << ` `; cout << atom->GetVector() << endl; }
OBMol mol; OBAtom *atom; atom = mol.GetAtom(1); FOR_NBORS_OF_ATOM(nbr, atom) { cout << "atom #" << atom->GetIdx() << " is attached to atom #" << nbr->GetIdx() << endl; }
should produce an output like
atom #1 is attached to atom #2
Constructor & Destructor Documentation
OBAtom | ( | ) |
Constructor.
~OBAtom | ( | ) | [virtual] |
Destructor.
Member Function Documentation
int GetFlag | ( | ) | const [inline, protected] |
void SetFlag | ( | int | flag | ) | [inline, protected] |
Sets the bitwise flag
.
bool HasFlag | ( | int | flag | ) | [inline, protected] |
- Returns:
- True of the atom has the
flag
Referenced by OBAtom::IsAromatic(), OBAtom::IsChiral(), OBAtom::IsInRing(), and OBAtom::IsInRingSize().
void Duplicate | ( | OBAtom * | src | ) |
Duplicate another atom. Copies all information with the exception of index
- Since:
- version 2.2
Referenced by OBUnitCell::FillUnitCell(), and OBAtom::operator=().
bool Clear | ( | void | ) | [virtual] |
Clear all data. Calls OBBase::Clear() to handle any generic data.
- Returns:
- True if successful.
Reimplemented from OBBase.
Referenced by OBAtom::OBAtom().
void SetIdx | ( | int | idx | ) | [inline] |
Set atom index (i.e., in an OBMol).
Referenced by OBMol::AddAtom(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBMol::EndModify(), and OBMol::NewAtom().
void SetHyb | ( | int | hyb | ) | [inline] |
Set atom hybridization (i.e., 1 = sp, 2 = sp2, 3 = sp3 ...).
Referenced by OBResidueData::AssignBonds(), OBAtomTyper::AssignHyb(), OBAtom::HtoMethyl(), OBMol::PerceiveBondOrders(), and OBAtom::SetHybAndGeom().
void SetAtomicNum | ( | int | atomicnum | ) | [inline] |
Set atomic number.
Referenced by OBMol::AddHydrogens(), OBChemTsfm::Apply(), AliasData::Expand(), OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().
void SetIsotope | ( | unsigned int | iso | ) |
Set isotope number (actual atomic weight is tabulated automatically, 0 = most abundant).
Referenced by AliasData::Expand().
void SetImplicitValence | ( | int | val | ) | [inline] |
void IncrementImplicitValence | ( | ) | [inline] |
void DecrementImplicitValence | ( | ) | [inline] |
void SetFormalCharge | ( | int | fcharge | ) | [inline] |
Set the formal charge of the atom to fcharge
.
Referenced by OBChemTsfm::Apply(), OBResidueData::AssignBonds(), OBMol::ConvertDativeBonds(), AliasData::Expand(), OpenBabel::ExpandKekule(), and OBMol::NewPerceiveKekuleBonds().
void SetSpinMultiplicity | ( | short | spin | ) | [inline] |
void SetType | ( | const char * | type | ) |
Set the atomic type symbol (see OBTypeTable and OBAtomTyper for more).
Referenced by OBMol::AddHydrogens(), OBResidueData::AssignBonds(), OBAtomTyper::AssignTypes(), OBForceField::GetGrid(), OBAtom::HtoMethyl(), OBAtom::SetHybAndGeom(), and OBAtom::SetIsotope().
void SetType | ( | const std::string & | type | ) |
Set the atomic type symbol (see OBTypeTable and OBAtomTyper for more).
void SetPartialCharge | ( | double | pcharge | ) | [inline] |
Set the partial charge to pcharge
.
Referenced by OBGastChrg::AssignPartialCharges(), OBPhModel::AssignSeedPartialCharge(), OBForceField::GetGrid(), and OBAtom::GetPartialCharge().
void SetVector | ( | const vector3 & | v | ) |
Set the coordinate vector for this atom to v
as a vector3.
Referenced by OBMol::Align(), OpenBabel::ApplyRotMatToBond(), OBMol::BeginModify(), OBBuilder::Build(), OpenBabel::CalcSignedVolume(), OBMol::Center(), OBBuilder::Connect(), OBUnitCell::FillUnitCell(), OBForceField::GetCoordinates(), OBAtom::GetNewBondVector(), OBAtom::HtoMethyl(), OpenBabel::InternalToCartesian(), OBForceField::LineSearch(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OBForceField::SetConformers(), OBForceField::SetCoordinates(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateLineSearch(), and OBForceField::ValidateSteepestDescent().
void SetVector | ( | const double | x, | |
const double | y, | |||
const double | z | |||
) |
Set the coordinate vector for this atom based on x
y
& z
.
void SetCoordPtr | ( | double ** | c | ) | [inline] |
Set the position of this atom from a pointer-driven array of coordinates.
Referenced by OBMol::AddHydrogens(), OBMol::ConnectTheDots(), OBMol::EndModify(), and OBMol::SetCoordinates().
void SetVector | ( | ) |
Set the position of this atom based on the internal pointer array (i.e. from SetCoordPtr() ).
void SetResidue | ( | OBResidue * | res | ) | [inline] |
Attach an OBResidue res
as containing this atom.
Referenced by OBResidue::AddAtom(), OBMol::AddHydrogens(), and OBResidue::RemoveAtom().
void SetParent | ( | OBMol * | ptr | ) | [inline] |
Attach an OBMol ptr
as the parent container for this atom.
Referenced by OBMol::AddAtom(), and OBMol::NewAtom().
void SetAromatic | ( | ) | [inline] |
Mark atom as being aromatic.
Referenced by OBMol::AddBond(), OBAromaticTyper::CheckAromaticity(), OBBond::SetBondOrder(), and OBAromaticTyper::TraverseCycle().
void UnsetAromatic | ( | ) | [inline] |
void SetClockwiseStereo | ( | ) | [inline] |
Mark atom as having SMILES clockwise stereochemistry (i.e., "@@").
Referenced by OpenBabel::CorrectChirality().
void SetAntiClockwiseStereo | ( | ) | [inline] |
Mark atom as having SMILES anticlockwise stereochemistry (i.e., "@").
Referenced by OpenBabel::CorrectChirality().
void SetPositiveStereo | ( | ) | [inline] |
Mark an atom as having + chiral volume.
void SetNegativeStereo | ( | ) | [inline] |
Mark an atom as having - chiral volume.
void UnsetStereo | ( | ) | [inline] |
void SetInRing | ( | ) | [inline] |
Mark an atom as belonging to at least one ring.
void SetChiral | ( | ) | [inline] |
Mark an atom as being chiral with unknown stereochemistry.
Referenced by OBMol::FindChiralCenters().
void ClearCoordPtr | ( | ) | [inline] |
Clear the internal coordinate pointer.
Referenced by OBMol::BeginModify(), and OBMol::ConnectTheDots().
int GetFormalCharge | ( | ) | const [inline] |
- Returns:
- the formal charge for this atom
Referenced by OBMol::ConvertDativeBonds(), OBAtom::Duplicate(), OpenBabel::EvalAtomExpr(), AliasData::Expand(), OpenBabel::ExpandKekule(), OpenBabel::GetGIVector(), OBMol::getorden(), OBMol::GetTotalCharge(), OBMol::NewPerceiveKekuleBonds(), and OBMol::PerceiveKekuleBonds().
unsigned int GetAtomicNum | ( | ) | const [inline] |
- Returns:
- the atomic number for this atom
Referenced by OBMol::AddHydrogens(), OBAromaticTyper::AssignAromaticFlags(), OpenBabel::CalculateSymmetry(), OBMol::ConnectTheDots(), OpenBabel::construct_g_matrix(), OBAtom::Duplicate(), OpenBabel::EvalAtomExpr(), OBBond::GetEquibLength(), OBMol::GetGIVector(), OpenBabel::GetGIVector(), OpenBabel::GetHvyBondSum(), OBMol::getorden(), OBAtom::GetType(), OBAtom::HtoMethyl(), OpenBabel::InternalToCartesian(), OBBond::IsAmide(), OBAtom::IsAmideNitrogen(), OBBond::IsCarbonyl(), OBBond::IsEster(), OBAtom::IsHeteroatom(), OBAtom::IsNonPolarHydrogen(), OBAtom::IsNotCorH(), OBAtom::IsPolarHydrogen(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), OBMol::PerceiveBondOrders(), OBMol::PerceiveKekuleBonds(), and OBAtom::SetHybAndGeom().
unsigned short int GetIsotope | ( | ) | const [inline] |
- Returns:
- the isotope for this atom, if specified, or 0 for unspecified
Referenced by OBAtom::Duplicate(), OpenBabel::EvalAtomExpr(), and OBAtom::ExplicitHydrogenCount().
int GetSpinMultiplicity | ( | ) | const [inline] |
- Returns:
- the atomic spin, e.g., 0 (default) for normal atoms - note that this value is a convention, 2 for radical 1 or 3 for carbene
Referenced by OBMol::AddHydrogens(), OBAtom::Duplicate(), OBMol::GetTotalSpinMultiplicity(), and OBAtom::ImplicitHydrogenCount().
double GetAtomicMass | ( | ) | const |
- Returns:
- the atomic mass of this atom given by standard IUPAC average molar mass
Referenced by OBMol::GetMolWt(), and OBMol::ToInertialFrame().
double GetExactMass | ( | ) | const |
- Returns:
- the atomic mass of given by the isotope (default of 0 gives the most abundant isotope)
Referenced by OBMol::GetExactMass().
unsigned int GetIdx | ( | ) | const [inline] |
- Returns:
- the internal atom index (e.g., inside an OBMol)
Referenced by OBMol::AddAtom(), OBMol::AddHydrogens(), OBMol::Align(), OpenBabel::ApplyRotMatToBond(), OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBGastChrg::AssignPartialCharges(), OpenBabel::BreakChiralTies(), OBBuilder::Build(), OpenBabel::BuildOBRTreeVector(), OpenBabel::CalcSignedVolume(), OpenBabel::CalculateSymmetry(), OpenBabel::CartesianToInternal(), OBAromaticTyper::CheckAromaticity(), OBMol::ConnectTheDots(), OBMol::ContigFragList(), OBBuilder::CorrectStereoAtoms(), OpenBabel::CreateNewClassVector(), OBMolAtomBFSIter::CurrentDepth(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OpenBabel::EvalAtomExpr(), OBAromaticTyper::ExcludeSmallRing(), OBMol::expand_kekulize(), OBMol::expandcycle(), OpenBabel::ExpandKekule(), OpenBabel::FastSingleMatch(), OBMol::FindChildren(), OBMol::FindChiralCenters(), OpenBabel::FindConjugatedEZBonds(), OBMol::FindLargestFragment(), OpenBabel::FixCisTransBonds(), OBRTree::GetAtomIdx(), OpenBabel::GetDFFVector(), OBBuilder::GetFragment(), OpenBabel::GetGIVector(), OBForceField::GetGradient(), OBForceField::GetGrid(), OBMol::GetGTDVector(), OpenBabel::GetGTDVector(), OpenBabel::GetHvyBondSum(), OpenBabel::GetHvyValence(), OBAtom::GetNextAtom(), OBRotorRules::GetRotorIncrements(), OpenBabel::GetValence(), OBAtom::HtoMethyl(), OBGrid::Init(), OpenBabel::InternalToCartesian(), OBBond::IsClosure(), OBRotorList::IsFixedBond(), OBAtom::IsInRingSize(), OBForceField::IsInSameRing(), OBRing::IsMember(), OpenBabel::KekulePropagate(), OBSSMatch::Match(), OBAtom::MatchesSMARTS(), OBAtom::MemberOfRingCount(), OBAtom::MemberOfRingSize(), OBMol::NewAtom(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBMolPairIter::OBMolPairIter(), OBMolPairIter::operator++(), OBMolAtomBFSIter::operator++(), OBMolAtomDFSIter::operator++(), OBMol::operator=(), OBAtom::operator=(), OBMol::PerceiveKekuleBonds(), OBAromaticTyper::PropagatePotentialAromatic(), OBMol::RenumberAtoms(), OBAromaticTyper::SelectRootAtoms(), OBRotorList::SetEvalAtoms(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBMol::SetTorsion(), OBProxGrid::Setup(), OpenBabel::SetupAtomMatchTable(), OBMol::start_kekulize(), and OBAromaticTyper::TraverseCycle().
unsigned int GetCoordinateIdx | ( | ) | const [inline] |
- Returns:
- the index into a pointer-driven array as used by GetCoordPtr() or SetCoordPtr()
unsigned int GetCIdx | ( | ) | const [inline] |
- Deprecated:
- Use GetCoordinateIdx() instead
Referenced by OBMol::DeleteHydrogen(), OpenBabel::SetRotorToAngle(), and OBMol::SetTorsion().
unsigned int GetValence | ( | ) | const [inline] |
- Returns:
- The current number of explicit connections
Referenced by OBMol::AddBond(), OBMol::AddHydrogens(), OBResidueData::AssignBonds(), OBAtomTyper::AssignImplicitValence(), OBMol::ConnectTheDots(), OpenBabel::construct_c_matrix(), OpenBabel::construct_g_matrix(), OpenBabel::EvalAtomExpr(), OBBuilder::GetNewBondVector(), OBAtom::GetNewBondVector(), OBMol::getorden(), OBRing::GetRootAtom(), OBAtom::ImplicitHydrogenCount(), OBBond::IsDoubleBondGeometry(), OBAtom::IsHbondAcceptor(), OBMol::PerceiveBondOrders(), and OBAtom::SetHybAndGeom().
unsigned int GetHyb | ( | ) | const |
- Returns:
- The hybridization of this atom (i.e. 1 for sp, 2 for sp2, 3 for sp3)
Referenced by OBMol::AddHydrogens(), OBAromaticTyper::AssignAromaticFlags(), OpenBabel::construct_g_matrix(), OBAtom::Duplicate(), OpenBabel::EvalAtomExpr(), OBMol::FindChiralCenters(), OBBond::GetEquibLength(), OBBuilder::GetNewBondVector(), OBAtom::GetNewBondVector(), OBRotorRules::GetRotorIncrements(), OBAtom::HtoMethyl(), OBAtom::IsAxial(), OBBond::IsDoubleBondGeometry(), OBAtom::IsHbondAcceptor(), OBBond::IsRotor(), OBMol::PerceiveBondOrders(), and OBAtom::SetHybAndGeom().
unsigned int GetImplicitValence | ( | ) | const |
- Returns:
- The implicit valence of this atom type (i.e. maximum number of connections expected)
Referenced by OBMol::AddHydrogens(), OBAromaticTyper::AssignAromaticFlags(), OBAtomTyper::AssignImplicitValence(), OBMol::AssignSpinMultiplicity(), OpenBabel::EvalAtomExpr(), OpenBabel::ExpandKekule(), OpenBabel::GetCurrentValence(), OBMol::GetGIVector(), OpenBabel::GetHvyBondSum(), OBAtom::KBOSum(), and OpenBabel::ValenceSum().
unsigned int GetHvyValence | ( | ) | const |
- Returns:
- The number of non-hydrogens connected to this atom
Referenced by OBMol::AssignSpinMultiplicity(), OpenBabel::CalcSignedVolume(), OBAtom::CountFreeOxygens(), OpenBabel::ExpandKekule(), OBMol::FindChiralCenters(), OBMol::GetGIVector(), OBAtom::IsCarboxylOxygen(), OBMol::IsChiral(), OBAtom::IsNitroOxygen(), OBAtom::IsPhosphateOxygen(), OBBond::IsPrimaryAmide(), OBBond::IsRotor(), OBBond::IsSecondaryAmide(), OBAtom::IsSulfateOxygen(), and OBAtom::SetHybAndGeom().
unsigned int GetHeteroValence | ( | ) | const |
- Returns:
- The number of heteroatoms connected to an atom
char * GetType | ( | ) |
- Returns:
- the atomic type (e.g., for molecular mechanics)
Referenced by OBAtomTyper::AssignTypes(), and OBAtom::Duplicate().
double GetX | ( | ) | const [inline] |
double GetY | ( | ) | const [inline] |
double GetZ | ( | ) | const [inline] |
double x | ( | ) | const [inline] |
- Returns:
- the x coordinate
Referenced by OBMol::Center(), OBMol::Has2D(), OBMol::Has3D(), OBMol::ToInertialFrame(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateLineSearch(), and OBForceField::ValidateSteepestDescent().
double y | ( | ) | const [inline] |
- Returns:
- the y coordinate
Referenced by OBMol::Center(), OBMol::Has2D(), OBMol::Has3D(), OBMol::ToInertialFrame(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateLineSearch(), and OBForceField::ValidateSteepestDescent().
double z | ( | ) | const [inline] |
- Returns:
- the z coordinate
Referenced by OBMol::Center(), OBMol::Has3D(), OBMol::ToInertialFrame(), and OBForceField::ValidateConjugateGradients().
double* GetCoordinate | ( | ) | [inline] |
- Returns:
- the coordinates as a double* or NULL if none.
Referenced by OBForceField::GetGrid(), and OBForceField::UpdatePairsSimple().
vector3 & GetVector | ( | ) |
- Returns:
- the coordinates as a vector3 object
Referenced by OBMol::Align(), OpenBabel::ApplyRotMatToBond(), OBAtom::AverageBondAngle(), OpenBabel::CalcSignedVolume(), OpenBabel::CartesianToInternal(), OBMol::Center(), OBBuilder::Connect(), OBMol::ConnectTheDots(), OBAtom::Duplicate(), OBMol::EndModify(), OBAtom::GetAngle(), OBAtom::GetDistance(), OBBuilder::GetNewBondVector(), OBAtom::GetNewBondVector(), OBMol::GetTorsion(), OBMol::HasNonZeroCoords(), OBBond::IsDoubleBondGeometry(), OBForceField::LineSearch(), OpenBabel::match(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBAtom::SmallestBondAngle(), OBBuilder::Swap(), and OBForceField::ValidateLineSearch().
double GetPartialCharge | ( | ) |
- Returns:
- the partial charge of this atom, calculating a Gasteiger charge if needed
Referenced by OBGastChrg::AssignPartialCharges(), and OBAtom::Duplicate().
OBResidue * GetResidue | ( | ) |
- Returns:
- the residue which contains this atom, or NULL if none exists
Referenced by OBMol::AddHydrogens(), OBResidueData::AssignBonds(), and OBResidue::GetBonds().
OBResidue * GetResidue | ( | bool | perception | ) |
- Parameters:
-
perception implies whether chain perception should occur
- Returns:
- the residue which contains this atom, or NULL if none exists
OBMol* GetParent | ( | ) | [inline] |
- Returns:
- the molecule which contains this atom, or NULL if none exists
Referenced by OpenBabel::BuildOBRTreeVector(), OpenBabel::EvalAtomExpr(), OBAtom::GetAngle(), OBAtom::GetDistance(), OBAtom::GetHyb(), OBAtom::GetImplicitValence(), OBAtom::GetNextAtom(), OBAtom::GetPartialCharge(), OBAtom::GetResidue(), OBAtom::GetType(), OBAtom::HtoMethyl(), OBAtom::ImplicitHydrogenCount(), OBAtom::IsAromatic(), OBAtom::IsAxial(), OBAtom::IsChiral(), OBAtom::IsInRing(), OBAtom::IsInRingSize(), OBAtom::MatchesSMARTS(), OBAtom::MemberOfRingCount(), OBAtom::MemberOfRingSize(), OBAtom::SetHybAndGeom(), and OBBond::SetLength().
bool GetNewBondVector | ( | vector3 & | v, | |
double | length | |||
) |
Create a vector for a new bond from this atom, with length given by the supplied parameter
- Returns:
- success or failure
Referenced by OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().
- Returns:
- the OBBond object between this atom and that supplied, or NULL if the two atoms are not bonded
Referenced by OBBondTyper::AssignFunctionalGroupBonds(), OBBuilder::Build(), OpenBabel::CorrectBadResonanceForm(), OBBuilder::CorrectStereoBonds(), OBMol::expand_kekulize(), and OBMol::PerceiveBondOrders().
OBAtom * GetNextAtom | ( | ) |
- Returns:
- a pointer to the "next" atom (by atom index) in the parent OBMol, or NULL if no such atom exists.
- Deprecated:
- Use any of the other iterator methods. This method will be removed in the future.
OBBondIterator BeginBonds | ( | ) | [inline] |
- Returns:
- An iterator to the beginning of the bonds to this atom
Referenced by OBResidueData::AssignBonds().
OBBondIterator EndBonds | ( | ) | [inline] |
- Returns:
- An iterator to the end of the bonds to this atom
OBBond * BeginBond | ( | OBBondIterator & | i | ) |
Set the iterator i
to the beginning of the bonds
- Returns:
- The first bond to this atom (or NULL if none exist)
Referenced by OBAtom::BOSum(), OpenBabel::CalcSignedVolume(), OBMol::ConnectTheDots(), OBMol::ContigFragList(), OBMol::ConvertDativeBonds(), OBAtom::CountBondsOfOrder(), OBAtom::CountFreeOxygens(), OBAtom::CountRingBonds(), OpenBabel::ExpandKekule(), OBMol::FindLargestFragment(), OpenBabel::FindRings(), OBAtom::GetBond(), OBResidue::GetBonds(), OpenBabel::GetCurrentValence(), OpenBabel::GetDFFVector(), OBMol::GetGTDVector(), OpenBabel::GetGTDVector(), OBAtom::GetHeteroValence(), OpenBabel::GetHvyBondSum(), OpenBabel::GetHvyValence(), OBAtom::GetHvyValence(), OpenBabel::GetValence(), OBAtom::HasBondOfOrder(), OBAtom::HasNonSingleBond(), OBBond::IsAmide(), OBAtom::IsAmideNitrogen(), OBAtom::IsCarboxylOxygen(), OBAtom::IsConnected(), OBBond::IsEster(), OBAtom::IsHbondDonorH(), OBAtom::IsNitroOxygen(), OBAtom::IsNonPolarHydrogen(), OBAtom::IsOneFour(), OBAtom::IsOneThree(), OBAtom::IsPhosphateOxygen(), OBAtom::IsPolarHydrogen(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), OBAtom::IsSulfateOxygen(), OBAtom::KBOSum(), OpenBabel::KekulePropagate(), OBMol::NewPerceiveKekuleBonds(), OBAtomBondIter::OBAtomBondIter(), and OpenBabel::ValenceSum().
OBBond * NextBond | ( | OBBondIterator & | i | ) |
Increment the iterator i
- Returns:
- The next bond to this atom (or NULL if none exist)
Referenced by OpenBabel::CalcSignedVolume(), OBMol::ConnectTheDots(), OBMol::ContigFragList(), OBMol::ConvertDativeBonds(), OBAtom::CountBondsOfOrder(), OpenBabel::ExpandKekule(), OBMol::FindLargestFragment(), OpenBabel::FindRings(), OBAtom::GetBond(), OBResidue::GetBonds(), OpenBabel::GetCurrentValence(), OpenBabel::GetDFFVector(), OBMol::GetGTDVector(), OpenBabel::GetGTDVector(), OpenBabel::GetHvyBondSum(), OpenBabel::GetHvyValence(), OpenBabel::GetValence(), OBAtom::HasBondOfOrder(), OBAtom::HasNonSingleBond(), OBBond::IsAmide(), OBAtom::IsAmideNitrogen(), OBAtom::IsCarboxylOxygen(), OBAtom::IsConnected(), OBBond::IsEster(), OBAtom::IsHbondDonorH(), OBAtom::IsNitroOxygen(), OBAtom::IsNonPolarHydrogen(), OBAtom::IsOneFour(), OBAtom::IsOneThree(), OBAtom::IsPhosphateOxygen(), OBAtom::IsPolarHydrogen(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), OBAtom::IsSulfateOxygen(), OpenBabel::KekulePropagate(), OBMol::NewPerceiveKekuleBonds(), OBAtomBondIter::operator++(), and OpenBabel::ValenceSum().
OBAtom * BeginNbrAtom | ( | OBBondIterator & | i | ) |
Set the iterator i
to the beginning of the bonds
- Returns:
- The first neighboring atom (or NULL if none exist)
Referenced by OBMol::AddBond(), OBAtomTyper::AssignTypes(), OBAtom::AverageBondAngle(), OpenBabel::BuildOBRTreeVector(), OpenBabel::CalcSignedVolume(), OBAromaticTyper::CheckAromaticity(), OpenBabel::CreateNewClassVector(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBMol::DeleteHydrogens(), OBAromaticTyper::ExcludeSmallRing(), OBMol::expand_kekulize(), OBMol::expandcycle(), OpenBabel::ExpandKekule(), OBAtom::ExplicitHydrogenCount(), OpenBabel::FastSingleMatch(), OBMol::FindChildren(), OBMol::FindChiralCenters(), OBMol::FindTorsions(), OBMol::GetBond(), OBAtom::GetNewBondVector(), OBRotorRules::GetRotorIncrements(), OBAtom::HasAlphaBetaUnsat(), OBAtom::HtoMethyl(), OBAtom::IsAromaticNOxide(), OBAtom::IsAxial(), OBBond::IsClosure(), OBBond::IsDoubleBondGeometry(), OBRotorList::IsFixedBond(), OBAtom::IsHbondDonor(), OpenBabel::KekulePropagate(), OBSSMatch::Match(), OBAtomAtomIter::OBAtomAtomIter(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBMolAtomBFSIter::operator++(), OBMolAtomDFSIter::operator++(), OBMol::PerceiveBondOrders(), OBMol::PerceiveKekuleBonds(), OBAromaticTyper::PropagatePotentialAromatic(), OBAromaticTyper::SelectRootAtoms(), OBRotorList::SetEvalAtoms(), OBAtom::SetHybAndGeom(), OBAtom::SmallestBondAngle(), OBMol::start_kekulize(), and OBAromaticTyper::TraverseCycle().
OBAtom * NextNbrAtom | ( | OBBondIterator & | i | ) |
Increment the iterator i
- Returns:
- The next neighboring atom (or NULL if none exist)
Referenced by OBAtomTyper::AssignTypes(), OBAtom::AverageBondAngle(), OpenBabel::BuildOBRTreeVector(), OpenBabel::CalcSignedVolume(), OBAromaticTyper::CheckAromaticity(), OpenBabel::CreateNewClassVector(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBMol::DeleteHydrogens(), OBAromaticTyper::ExcludeSmallRing(), OBMol::expand_kekulize(), OBMol::expandcycle(), OpenBabel::ExpandKekule(), OBAtom::ExplicitHydrogenCount(), OpenBabel::FastSingleMatch(), OBMol::FindChildren(), OBMol::FindChiralCenters(), OBMol::FindTorsions(), OBMol::GetBond(), OBAtom::GetNewBondVector(), OBRotorRules::GetRotorIncrements(), OBAtom::HasAlphaBetaUnsat(), OBAtom::IsAromaticNOxide(), OBAtom::IsAxial(), OBBond::IsClosure(), OBRotorList::IsFixedBond(), OBAtom::IsHbondDonor(), OpenBabel::KekulePropagate(), OBSSMatch::Match(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBAtomAtomIter::operator++(), OBMolAtomBFSIter::operator++(), OBMolAtomDFSIter::operator++(), OBMol::PerceiveBondOrders(), OBMol::PerceiveKekuleBonds(), OBAromaticTyper::PropagatePotentialAromatic(), OBAromaticTyper::SelectRootAtoms(), OBRotorList::SetEvalAtoms(), OBAtom::SetHybAndGeom(), OBAtom::SmallestBondAngle(), OBMol::start_kekulize(), and OBAromaticTyper::TraverseCycle().
double GetDistance | ( | int | index | ) |
- Returns:
- the distance to the atom defined by OBMol::GetAtom()
Referenced by OBBondTyper::AssignFunctionalGroupBonds().
double GetAngle | ( | int | b, | |
int | c | |||
) |
- Returns:
- the angle defined by this atom -> b (vertex) -> c
void NewResidue | ( | ) | [inline] |
If no residue has been set for this atom, create a new one.
void AddResidue | ( | OBResidue * | res | ) | [inline] |
Add (set) the residue for this atom.
void DeleteResidue | ( | ) | [inline] |
Delete any residue associated with this atom.
void AddBond | ( | OBBond * | bond | ) | [inline] |
Add a bond to the internal list. Does not update the bond.
Referenced by OBMol::AddBond(), and OBBuilder::Connect().
void InsertBond | ( | OBBondIterator & | i, | |
OBBond * | bond | |||
) | [inline] |
Insert bond
into the internal list at the position from i
Does not modify the bond.
Referenced by OBMol::AddBond().
bool DeleteBond | ( | OBBond * | bond | ) |
Find bond
and remove it from the internal list. Does not update the bond.
void ClearBond | ( | ) | [inline] |
Clear all bonding information in this atom (does not delete them).
bool HtoMethyl | ( | ) |
If this is a hydrogen atom, transform into a methyl group.
- Returns:
- success or failure
bool SetHybAndGeom | ( | int | hyb | ) |
Change the hybridization of this atom and modify the geometry accordingly
- Returns:
- success or failure
void ForceNoH | ( | ) | [inline] |
Mark that atom has no hydrogens attached.
bool HasNoHForced | ( | ) | [inline] |
- Returns:
- if atom has been marked as having no hydrogens attached
Referenced by OBMol::AssignSpinMultiplicity().
void ForceImplH | ( | ) | [inline] |
Mark that atom is not hydrogen deficient (For SMILES input)
- Since:
- version 2.2
bool HasImplHForced | ( | ) | [inline] |
- Returns:
- if atom has been marked as having no hydrogens attached
- Since:
- version 2.2
Referenced by OBMol::AssignSpinMultiplicity().
unsigned int CountFreeOxygens | ( | ) | const |
- Returns:
- The number of oxygen atoms connected that only have one heavy valence
Referenced by OBAtom::IsCarboxylOxygen(), OBAtom::IsNitroOxygen(), OBAtom::IsPhosphateOxygen(), and OBAtom::IsSulfateOxygen().
unsigned int ImplicitHydrogenCount | ( | ) | const |
- Returns:
- The number of hydrogens needed to fill the implicit valence of this atom
Referenced by OpenBabel::EvalAtomExpr(), OBMol::GetExactMass(), and OBMol::GetMolWt().
unsigned int ExplicitHydrogenCount | ( | bool | ExcludeIsotopes = false |
) | const |
- Returns:
- The number of hydrogens explicitly bound to this atom, optionally excluding D,T and isotope explicitly set to 1
Referenced by OBMol::AssignSpinMultiplicity(), and OpenBabel::EvalAtomExpr().
unsigned int MemberOfRingCount | ( | ) | const |
unsigned int MemberOfRingSize | ( | ) | const |
- Returns:
- The size of the smallest ring that contains this atom (0 if not in a ring)
Referenced by OBAtom::SetHybAndGeom().
unsigned int CountRingBonds | ( | ) | const |
- Returns:
- The number of explicit ring connections to this atom
Referenced by OpenBabel::EvalAtomExpr().
double SmallestBondAngle | ( | ) |
double AverageBondAngle | ( | ) |
- Returns:
- The average angle of bonds to this atom
Referenced by OBBondTyper::AssignFunctionalGroupBonds(), and OBMol::PerceiveBondOrders().
unsigned int BOSum | ( | ) | const |
- Returns:
- The sum of the bond orders of the bonds to the atom (i.e. double bond = 2...)
Referenced by OBMol::ConnectTheDots(), OBRing::GetRootAtom(), and OBMol::PerceiveBondOrders().
unsigned int KBOSum | ( | ) | const |
- Returns:
- The sum of the bond orders of bonds to the atom, considering only KDouble, KTriple bonds
- Deprecated:
- Use BOSum() instead
Referenced by OpenBabel::EvalAtomExpr().
bool HasResidue | ( | ) | [inline] |
bool IsHydrogen | ( | ) | [inline] |
- Returns:
- Is the atom hydrogen?
Referenced by OBMol::AddHydrogens(), OBResidueData::AssignBonds(), OBGastChrg::AssignPartialCharges(), OBMol::AssignSpinMultiplicity(), OBMol::ConnectTheDots(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBMol::DeleteHydrogens(), OBAtom::ExplicitHydrogenCount(), OBMol::FindTorsions(), OBMol::GetExactMass(), OpenBabel::GetHvyBondSum(), OpenBabel::GetHvyValence(), OBAtom::GetHvyValence(), OBMol::GetMolWt(), OBRotorRules::GetRotorIncrements(), OBAtom::HtoMethyl(), OBAtom::IsHbondDonor(), OBAtom::IsHbondDonorH(), OBAtom::IsNonPolarHydrogen(), OBAtom::IsPolarHydrogen(), OBMol::NumHvyAtoms(), OBAromaticTyper::SelectRootAtoms(), and OBAtom::SetHybAndGeom().
bool IsCarbon | ( | ) | [inline] |
- Returns:
- Is the atom carbon?
Referenced by OBMol::getorden(), OBAtom::IsCarboxylOxygen(), OBMol::IsChiral(), and OBMol::PerceiveKekuleBonds().
bool IsNitrogen | ( | ) | [inline] |
- Returns:
- Is the atom nitrogen?
Referenced by OBMol::AddHydrogens(), OpenBabel::ExpandKekule(), OBMol::getorden(), OBRing::GetRootAtom(), OBAtom::IsAmideNitrogen(), OBAtom::IsAromaticNOxide(), OBMol::IsChiral(), OBAtom::IsNitroOxygen(), OBMol::NewPerceiveKekuleBonds(), and OBMol::PerceiveKekuleBonds().
bool IsOxygen | ( | ) | [inline] |
- Returns:
- Is the atom oxygen?
Referenced by OBMol::AddHydrogens(), OBResidueData::AssignBonds(), OBBondTyper::AssignFunctionalGroupBonds(), OBAtom::CountFreeOxygens(), OpenBabel::ExpandKekule(), OBAtom::GetNewBondVector(), OBMol::getorden(), OBRing::GetRootAtom(), OBAtom::IsAromaticNOxide(), OBAtom::IsCarboxylOxygen(), OBAtom::IsNitroOxygen(), OBAtom::IsPhosphateOxygen(), OBAtom::IsSulfateOxygen(), OBMol::NewPerceiveKekuleBonds(), and OBMol::PerceiveKekuleBonds().
bool IsSulfur | ( | ) | [inline] |
- Returns:
- Is the atom sulfur?
Referenced by OBMol::AddHydrogens(), OpenBabel::ExpandKekule(), OBMol::getorden(), OBRing::GetRootAtom(), OBAtom::HasAlphaBetaUnsat(), OBAtom::IsSulfateOxygen(), OBMol::PerceiveKekuleBonds(), and OBMol::start_kekulize().
bool IsPhosphorus | ( | ) | [inline] |
- Returns:
- Is the atom phosphorus?
Referenced by OBMol::AddHydrogens(), OBAtom::HasAlphaBetaUnsat(), and OBAtom::IsPhosphateOxygen().
bool IsAromatic | ( | ) | const |
- Returns:
- Is the atom aromatic?
Referenced by OpenBabel::EvalAtomExpr(), OBMol::GetGIVector(), OpenBabel::GetGIVector(), OpenBabel::GetHvyBondSum(), OBAtom::IsAromaticNOxide(), and OpenBabel::KekulePropagate().
bool IsInRing | ( | ) | const |
- Returns:
- Is the atom in a ring?
Referenced by OpenBabel::EvalAtomExpr(), OBAromaticTyper::ExcludeSmallRing(), OBMol::GetGIVector(), OBAtom::IsAxial(), OBAtom::MemberOfRingCount(), OBAtom::MemberOfRingSize(), OBMol::PerceiveBondOrders(), OBAromaticTyper::SelectRootAtoms(), and OBAtom::SetHybAndGeom().
bool IsInRingSize | ( | int | size | ) | const |
- Returns:
- Is the atom in a ring of a given size?
Referenced by OpenBabel::EvalAtomExpr(), and OBMol::getorden().
bool IsHeteroatom | ( | ) |
- Returns:
- Is this atom an element in the 15th or 16th main groups (i.e., N, O, P, S ...) ?
Referenced by OBAtom::GetHeteroValence().
bool IsNotCorH | ( | ) |
- Returns:
- Is this atom any element except carbon or hydrogen?
bool IsConnected | ( | OBAtom * | a1 | ) |
- Returns:
- Is this atom directly connected to the supplied OBAtom?
Referenced by OBMol::ConnectTheDots(), OpenBabel::construct_g_matrix(), OBAromaticTyper::ExcludeSmallRing(), OBAtom::IsOneFour(), OBMolPairIter::OBMolPairIter(), and OBMolPairIter::operator++().
bool IsOneThree | ( | OBAtom * | a1 | ) |
- Returns:
- Is this atom related to the supplied OBAtom in a 1,3 bonding pattern?
Referenced by OBMolPairIter::OBMolPairIter(), and OBMolPairIter::operator++().
bool IsOneFour | ( | OBAtom * | a1 | ) |
- Returns:
- Is this atom related to the supplied OBAtom in a 1,4 bonding pattern?
bool IsCarboxylOxygen | ( | ) |
- Returns:
- Is this atom an oxygen in a carboxyl (-CO2 or CO2H) group?
bool IsPhosphateOxygen | ( | ) |
- Returns:
- Is this atom an oxygen in a phosphate (R-PO3) group?
bool IsSulfateOxygen | ( | ) |
- Returns:
- Is this atom an oxygen in a sulfate (-SO3) group?
bool IsNitroOxygen | ( | ) |
- Returns:
- Is this atom an oxygen in a nitro (-NO2) group?
bool IsAmideNitrogen | ( | ) |
Returns true if nitrogen is part of an amide.
- Returns:
- Is this atom a nitrogen in an amide (-C(=O)NR2) group?
Referenced by OBMol::getorden().
bool IsPolarHydrogen | ( | ) |
- Returns:
- Is this atom a hydrogen connected to a polar atom (i.e., N, O, P, S)
bool IsNonPolarHydrogen | ( | ) |
- Returns:
- Is this atom a hydrogen connected to a non-polar atom (i.e., C)
Referenced by OBMol::DeleteNonPolarHydrogens().
bool IsAromaticNOxide | ( | ) |
- Returns:
- Is this atom an aromatic nitrogen with at least one double bond to an oxygen atom
bool IsChiral | ( | ) |
- Returns:
- Is this atom chiral?
Referenced by OpenBabel::EvalAtomExpr(), OBMol::FindChiralCenters(), and OBMol::IsChiral().
bool IsAxial | ( | ) |
- Returns:
- Is this atom an axial atom in a ring
bool IsClockwise | ( | ) | [inline] |
- Returns:
- Does this atom have SMILES-specified clockwise "@@" stereochemistry?
Referenced by OpenBabel::CorrectChirality(), and OpenBabel::EvalAtomExpr().
bool IsAntiClockwise | ( | ) | [inline] |
- Returns:
- Does this atom have SMILES-specified anticlockwise "@" stereochemistry?
Referenced by OpenBabel::CorrectChirality(), and OpenBabel::EvalAtomExpr().
bool IsPositiveStereo | ( | ) | [inline] |
- Returns:
- Does this atom have a positive chiral volume?
bool IsNegativeStereo | ( | ) | [inline] |
- Returns:
- Does this atom have a negative chiral volume?
bool HasChiralitySpecified | ( | ) | [inline] |
- Returns:
- Does this atom have SMILES-specified stereochemistry?
Referenced by OpenBabel::CorrectChirality(), and OpenBabel::EvalAtomExpr().
bool HasChiralVolume | ( | ) | [inline] |
- Returns:
- Does this atom have a specified chiral volume?
bool IsHbondAcceptor | ( | ) |
- Returns:
- Is this atom a hydrogen-bond acceptor (receptor)?
bool IsHbondDonor | ( | ) |
bool IsHbondDonorH | ( | ) |
- Returns:
- Is this a hydrogen atom attached to a hydrogen-bond donor?
bool HasAlphaBetaUnsat | ( | bool | includePandS = true |
) |
- Returns:
- Whether a neighboring atom (alpha) has an unsaturated bond to a third atom (beta).
- Parameters:
-
includePandS Whether to include phosphorus and sulfur neighbors in this determination (or to exclude them)
'*'
\
a=b
Referenced by OBAtom::GetNewBondVector().
bool HasBondOfOrder | ( | unsigned int | bo | ) |
- Returns:
- Whether this atom is connected to any bond with order ==
bo
Referenced by OBMol::PerceiveBondOrders().
int CountBondsOfOrder | ( | unsigned int | bo | ) |
- Returns:
- The count of bonds connected to this atom with order ==
bo
bool HasNonSingleBond | ( | ) |
- Returns:
- Whether this atom is connected to any bond with order >1
Referenced by OBMol::PerceiveBondOrders().
bool HasSingleBond | ( | ) | [inline] |
- Returns:
- Does this atom have a single bond
bool HasDoubleBond | ( | ) | [inline] |
- Returns:
- Does this atom have a double bond
Referenced by OBBondTyper::AssignFunctionalGroupBonds(), and OpenBabel::FindConjugatedEZBonds().
bool HasAromaticBond | ( | ) | [inline] |
bool MatchesSMARTS | ( | const char * | pattern | ) |
- Returns:
- Whether this atom matches the first atom in a given SMARTS pattern
virtual OBBase* DoTransformations | ( | const std::map< std::string, std::string > * | ) | [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()
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.
bool HasData | ( | const std::string & | s | ) | [inherited] |
- Returns:
- whether the generic attribute/value pair exists
Referenced by OBMol::AddAtom(), OBMol::FindAngles(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetSSSR(), OBBase::HasData(), OBDescriptor::MatchPairData(), OBMol::NewAtom(), OBMol::operator=(), 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(), OBBuilder::CorrectStereoBonds(), OBDescriptor::DeleteProperties(), OBMol::FindSSSR(), OBMol::NewAtom(), 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(), OBMol::FindAngles(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetNextFragment(), 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
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
Referenced by OpenBabel::CalcSignedVolume(), OpenBabel::CorrectChirality(), OBDescriptor::FilterCompare(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetNextFragment(), 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(), OBMol::FindSSSR(), OBBase::GetData(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), 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
OBDataIterator BeginData | ( | ) | [inline, inherited] |
- Returns:
- An iterator pointing to the beginning of the data
Referenced by OBMol::AddAtom(), 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(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::NewAtom(), and OBMol::operator=().
Member Data Documentation
char _ele [protected] |
atomic number (type char to minimize space -- allows for 0..255 elements)
Referenced by OBAtom::Clear(), OBAtom::Duplicate(), OBAtom::GetAtomicMass(), OBAtom::GetExactMass(), OBAtom::GetType(), OBAtom::IsHbondAcceptor(), OBAtom::IsHbondDonor(), OBAtom::SetIsotope(), and OBAtom::SetType().
char _impval [protected] |
implicit valence
Referenced by OBAtom::Clear(), OBAtom::GetImplicitValence(), and OBAtom::ImplicitHydrogenCount().
char _type[6] [protected] |
atomic type
Referenced by OBAtom::Clear(), OBAtom::Duplicate(), OBAtom::GetType(), and OBAtom::SetType().
short _fcharge [protected] |
unsigned short _isotope [protected] |
isotope (0 = most abundant)
Referenced by OBAtom::Clear(), OBAtom::Duplicate(), OBAtom::GetAtomicMass(), OBAtom::GetExactMass(), OBAtom::GetType(), OBAtom::SetIsotope(), and OBAtom::SetType().
short _spinmultiplicity [protected] |
atomic spin, e.g., 2 for radical 1 or 3 for carbene
Referenced by OBAtom::Clear(), and OBAtom::Duplicate().
unsigned int _idx [protected] |
bonds to this atom -- assumed to be one of the endpoints
Referenced by OBAtom::BeginBond(), OBAtom::BeginNbrAtom(), OBAtom::Clear(), OBAtom::DeleteBond(), OBAtom::NextBond(), and OBAtom::NextNbrAtom().
unsigned int _cidx [protected] |
index into coordinate array
Referenced by OBAtom::Clear(), OBAtom::GetVector(), and OBAtom::SetVector().
unsigned short _hyb [protected] |
unsigned short _flags [protected] |
double _pcharge [protected] |
double** _c [protected] |
coordinate array in double*
Referenced by OpenBabel::CartesianToInternal(), OBAtom::Clear(), OBAtom::GetVector(), and OBAtom::SetVector().
parent residue (if applicable)
Referenced by OBAtom::Clear(), OBAtom::Duplicate(), OBAtom::GetResidue(), and OBAtom::~OBAtom().
bool Visit |
Used internally by graph traversal algorithms.
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: