OEAtomBase

class OEAtomBase : public OESystem::OEBase

This class represents OEAtomBase.

The following methods are publicly inherited from OEBase:

The following classes derive from this class:

OEQAtomBase

operator=¶

OEAtomBase &operator=(const OEAtomBase &a)

AddBond¶

bool AddBond(const OEBondBase *)=0

Clear¶

void Clear()=0

GetAtomicNum¶

unsigned int GetAtomicNum() const =0

Return the atomic number of the atom. A value of zero is returned for wildcard atoms, such as MDL super atoms. An atomic number is specified as the argument to OEMolBase.NewAtom and may be changed using OEAtomBase.SetAtomicNum. The set of unsigned integer values for this property are defined by the OEElemNo namespace.

GetAtoms¶

OESystem::OEIterBase<OEAtomBase> *GetAtoms() const =0
OESystem::OEIterBase<OEAtomBase> *
  GetAtoms(const OESystem::OEUnaryPredicate<OEChem::OEAtomBase> &) const =0

GetBond¶

OEBondBase *GetBond(const OEAtomBase *) const

GetBonds¶

OESystem::OEIterBase<OEBondBase> *GetBonds() const =0
OESystem::OEIterBase<OEBondBase> *
  GetBonds(const OESystem::OEUnaryPredicate<OEChem::OEBondBase> &) const =0

GetDegree¶

unsigned int GetDegree() const

GetExplicitDegree¶

unsigned int GetExplicitDegree() const =0

GetExplicitHCount¶

unsigned int GetExplicitHCount() const

GetExplicitValence¶

unsigned int GetExplicitValence() const

GetFormalCharge¶

int GetFormalCharge() const =0

GetHvyDegree¶

unsigned int GetHvyDegree() const

GetHvyValence¶

unsigned int GetHvyValence() const

GetHyb¶

unsigned int GetHyb() const =0

Return the “hybridization” property of an atom. The set of unsigned integer values for this property are defined in the OEHybridization namespace. The default value is zero, (OEHybridization_Unknown). The “hybridization” property can be set with the OEAtomBase.SetHyb method.

GetIdx¶

unsigned int GetIdx() const =0

GetImplicitHCount¶

unsigned int GetImplicitHCount() const =0

GetIntType¶

int GetIntType() const =0

GetIsotope¶

unsigned int GetIsotope() const =0

Return the isotopic mass of an atom. The default value is zero, meaning that the atom isn’t a specific single isotope, but a composition of isotopes in their naturally occurring abundances. A non-zero value indicates that the atom is a specific isotope. The “isotopic mass” property may be set using the OEAtomBase.SetIsotope method.

GetMapIdx¶

unsigned int GetMapIdx() const =0

GetName¶

const char *GetName() const =0

GetParent¶

OEMolBase *GetParent() const =0

GetPartialCharge¶

double GetPartialCharge() const =0

GetRadius¶

double GetRadius() const

Return the floating point radius assigned to an atom. The default value is 0.0. The “radius” property on an atom may be set using the OEAtomBase.SetRadius method. The radius property is typically used to hold a Van der Waal’s or ionic radius for a given atom when passing an OEMolBase to an algorithm requiring some form of radii, such as a surface area calculation.

GetRxnRole¶

unsigned int GetRxnRole() const

GetStereo¶

unsigned int GetStereo(const std::vector<OEAtomBase *> &, unsigned int) const

GetSymmetryClass¶

unsigned int GetSymmetryClass() const =0

GetTotalHCount¶

unsigned int GetTotalHCount() const

GetType¶

const char *GetType() const =0

GetValence¶

unsigned int GetValence() const

HasStereoSpecified¶

bool HasStereoSpecified(unsigned int v=OEAtomStereo::All) const

IsAromatic¶

bool IsAromatic() const =0

IsCarbon¶

bool IsCarbon() const

IsChiral¶

bool IsChiral() const

IsConnected¶

bool IsConnected(const OEAtomBase *) const

IsDataType¶

bool IsDataType(const void *) const

IsDeleted¶

bool IsDeleted() const =0

IsHalogen¶

bool IsHalogen() const

IsHydrogen¶

bool IsHydrogen() const

IsInRing¶

bool IsInRing() const =0

IsMetal¶

bool IsMetal() const

IsNitrogen¶

bool IsNitrogen() const

IsOxygen¶

bool IsOxygen() const

IsPhosphorus¶

bool IsPhosphorus() const

IsPolar¶

bool IsPolar() const

IsPolarHydrogen¶

bool IsPolarHydrogen() const

IsSulfur¶

bool IsSulfur() const

OrderBonds¶

bool OrderBonds(const std::vector<OEBondBase *> &)=0

RemoveBond¶

bool RemoveBond(OEBondBase *)=0

SetAromatic¶

bool SetAromatic(bool)=0

SetAtomicNum¶

bool SetAtomicNum(unsigned int)=0

Set the atomic number of an atom. The set of unsigned integer values for this property is specified by the OEElemNo. The default value is specified when an atom is created with OEMolBase.NewAtom method. The atomic number property of an atom can be retrieved using the OEAtomBase.GetAtomicNum method.

SetChiral¶

bool SetChiral(bool)

SetFormalCharge¶

bool SetFormalCharge(int)=0

SetHyb¶

bool SetHyb(unsigned int)=0

Set the hybridization of an atom. The set of unsigned integer values for this property is specified by the OEHybridization namespace. The default value is zero (OEHybridization_Unknown). The “hybridization” property may be retrieved using the OEAtomBase.GetHyb method.

SetIdx¶

bool SetIdx(unsigned int)=0

SetImplicitHCount¶

bool SetImplicitHCount(unsigned int)=0

SetInRing¶

bool SetInRing(bool)

SetIntType¶

bool SetIntType(int)=0

SetIsotope¶

bool SetIsotope(unsigned int)=0

Set the isotopic mass of an atom (i.e. number of protons and neutrons). The default value is zero, meaning that the atom isn’t a specific single isotope, but a composition of isotopes in their naturally occurring abundances. A non-zero value indicates that the atom is a specific isotope. The “isotopic mass” property can be retrieved using the OEAtomBase.GetIsotope method.

SetMapIdx¶

bool SetMapIdx(unsigned int)=0

SetName¶

bool SetName(const char *)=0
bool SetName(const std::string &)=0

SetPartialCharge¶

bool SetPartialCharge(float)=0
bool SetPartialCharge(double)=0

SetRadius¶

bool SetRadius(double)

Set the “radius” property of an atom. The assigned radius may be retrieved using the OEAtomBase.GetRadius method. The radius property is typically used to hold a Van der Waal’s or ionic radius for a given atom when passing an OEMolBase to an algorithm requiring some form of radii, such as a surface area calculation.

SetRxnRole¶

bool SetRxnRole(unsigned int)

SetStereo¶

bool SetStereo(const std::vector<OEAtomBase *> &, unsigned int, unsigned int)

SetSymmetryClass¶

bool SetSymmetryClass(unsigned int)=0

SetType¶

bool SetType(const char *)=0
bool SetType(const std::string &)=0

Sweep¶

bool Sweep()=0

`operator=`	`GetData`	`IsDataType`
`operator+=`	`GetDataIter`	`SetBaseData`
`AddBaseData`	`GetDataType`	`SetBoolData`
`AddData`	`GetDoubleData`	`SetData`
`Clear`	`GetFloatData`	`SetDoubleData`
`CreateCopy`	`GetIntData`	`SetFloatData`
`DeleteData`	`GetStringData`	`SetIntData`
`GetBoolData`	`HasData`	`SetStringData`

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