Subsections

8.3 OEAtomBase

class OEAtomBase : public OESystem::OEBase

The OEAtomBase class is the abstract interface for representing atoms within OEChem. OEAtomBases are created by calling the OEMolBase::NewAtom method on the parent molecule.

8.3.1 GetAtomicNum

virtual unsigned int GetAtomicNum() const

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 OEAtomBase::NewAtom and may be changed using OEAtomBase::SetAtomicNum. The set of unsigned integer values for this property are defined by the OEElemNo namespace.

8.3.2 GetAtoms

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

Return an OEAtomBase iterator of the neighboring atoms of this atom. The returned iterator traverses only the explicit atoms that are bonded to the OEAtomBase. The number of neighbors in the iterator is identical to OEAtomBase::GetExplicitDegree.

8.3.3 GetBond

virtual OEBondBase *GetBond(const OEAtomBase *nbor) const

Return a pointer to the bond connecting the OEAtomBase to the atom specified in the method argument. If the OEAtomBase is not connected to the specified atom, a NULL pointer code(OEBondBase*)0 is returned.

8.3.4 GetBonds

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

Return an OEBondBase iterator of the bonds connected to an atom. The returned iterator traverses only the explicit bonds that are attached to the OEAtomBase. The number of bonds in the iterator is identical to OEAtomBase::GetExplicitDegree.

8.3.5 GetDegree

virtual unsigned int GetDegree() const

Return the total number of neighbor atoms bonded to an atom, or equivalently the total number of bonds connected to an atom. This value includes bonds to implicit hydrogen atoms. This value is identical to OEAtomBase::GetExplicitDegree() + OEAtomBase::GetImplicitHCount(), and is also identical to OEAtomBase::GetHvyDegree() + OEAtomBase::GetTotalHCount().

8.3.6 GetExplicitDegree

virtual unsigned int GetExplicitDegree() const

Return the number of explicit neighbor atoms bonded to an atom. This value does not include bonds to implicit hydrogen atoms.

8.3.7 GetExplicitHCount

virtual unsigned int GetExplicitHCount() const

Return the number of explicit hydrogen neighbors bonded to an atom.

8.3.8 GetExplicitValence

virtual unsigned int GetExplicitValence() const

Return the sum of the bond orders of explicit bonds connected to an atom.

8.3.9 GetFormalCharge

virtual int GetFormalCharge() const

Return the formal charge on an atom. The default value is zero. The ``formal charge'' property may be set using the OEAtomBase::SetFormalCharge method. Formal charges may also be set on a molecule using the OEAssignFormalCharges function that infers reasonable formal charges using the atomic number, and implicit hydrogen count for each atom.

8.3.10 GetHvyDegree

virtual unsigned int GetHvyDegree() const

Return the number of non-hydrogen neighbors of an atom.

8.3.11 GetHvyValence

virtual unsigned int GetHvyValence() const

Return the sum of bond orders of bonds to non-hydrogen atoms.

8.3.12 GetHyb

virtual unsigned int GetHyb() const

Return the ``hybridization'' of an atom. The set of unsigned integer values for this property are defined in the namespace OEHybridization. The default value is zero, OEHybridization::Unknown. The ``hybridization'' property may be set with the OEAtomBase::SetHyb method. Hybridizations may also be set on a molecule using the function OEAssignHybridization. The hybridization property of an atom is a stored, not a computed, property. To calculate a reasonable hybridization of an atom from connectivity, use the function OEGetHybridization.

8.3.13 GetIdx

virtual unsigned int GetIdx() const

Return the atom index of an atom. This value is assigned by OEChem when an atom is created. The atom index is unique for the atoms of a given molecule, and is stable (not reused) for the lifetime of that OEMolBase. These values may not be assigned sequentially, and may contain gaps. Atom indices are guaranteed to be less than OEMolBase::GetMaxAtomIdx. Atom indices are typically only used for efficiently storing data in arrays (or vectors) externally to the OEMolBase. They arrays can be conveniently indexed via OEAtomBase::GetIdx(). For iterating across the atoms of a molecule, use OEMolBase::GetAtoms() and for keeping track of a particular atom use an OEAtomBase*.

8.3.14 GetImplicitHCount

virtual unsigned int GetImplicitHCount() const

Return the number of implicit hydrogens attached to atom. The default value is zero. The ``implicit hydrogen count'' property may be set using the OEAtomBase::SetImplicitHCount method. Implicit hydrogen counts may also be set on a molecule using the function OEAssignImplicitHydrogens. The implicit hydrogen count property of an atom is a stored, not a computed, property. To calculate a reasonable implicit hydrogen count for an atom from connectivity, use the function OEDefaultImplicitHCount.

To convert explicit hydrogens to implicit hydrogens, use the OEChem function OESupressHydrogens, and to convert implicit hydrogens to explicit hydrogens, use the function OEAddExplicitHydrogens.

8.3.15 GetIntType

virtual int GetIntType() const

Return the integer atom type of an atom. The default value is zero. The ``integer atom type'' property may be set using the OEAtomBase::SetIntType method.

8.3.16 GetIsotope

virtual unsigned int GetIsotope() const

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.

8.3.17 GetMapIdx

virtual unsigned int GetMapIdx() const

Return the reaction atom map index of an atom. This integer value is used for tracking equivalent atom positions in a reaction molecule/transform. The default value is zero, meaning that the atom isn't mapped in the reaction. The ``reaction map index'' property may be set using the OEAtomBase::SetMapIdx method.

8.3.18 GetName

virtual const char *GetName() const

Return the atom name string of an atom. This property is typically used when reading or writing molecular file formats. For example in PDB files, the atom name `` CA '' is used to denote that the atom is a peptide alpha carbon. The default value is the empty string. The ``atom name'' property may be set using the OEAtomBase:SetName method.

8.3.19 GetParent

virtual OEMolBase *GetParent() const

Return the parent molecule of an atom. All OEAtomBases are created as a component of an OEMolBase, this method can be used to determine the molecule of which an atom is part. The ``parent molecule'' property of an atom cannot be assigned, as its determined at the point the atom is created.

8.3.20 GetPartialCharge

virtual double GetPartialCharge() const

Return the floating point partial charge on an atom. The default value is 0.0. The ``partial charge'' property on an atom may be set using the OEAtomBase::SetPartialCharge method. The partial charge property is a stored, not a calculated, property. The function OEClearPartialCharges may be used to reset the partial charges on a molecule to zero, and the function OEFormalPartialCharges may be used to set the partial charge on each atom equal to its formal charge.

8.3.21 GetRadius

virtual 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.

8.3.22 GetRxnRole

virtual unsigned int GetRxnRole() const

Return the reaction role of an atom in a reaction molecule/transform. The set of unsigned integer values for this property are defined in the namespace OERxnRole. The default value is zero, OERxnRole::None, which means that the atom does have a role, i.e. is part of a normal molecule. Other values include OERxnRole::Reactant, OERxnRole::Agent and OERxnRole::Product which correspond to reactant, agent and product atoms in a reaction or transform. The reaction role property may be set using the OEAtomBase::SetRxnRole method.

8.3.23 GetStereo

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

Return the chirality (or stereochemistry) annotation of the current atom. This method takes a STL vector of neighboring atoms, v, and a specific stereochemistry class, c, and returns whether that stereochemisty is specified at this atom, and if so, what that specified value is. The chiral annotation of an atom may be set using the OEAtomBase::SetStereo method. This function returns the value OEAtomStereo::Undefined if the stereo chemistry for the given stereochemistry class is unspecified, if the stereo chemistry class is invalid or if the vector of neighboring atoms is invalid.

In the current version of OEChem, the only class of stereochemistry supported for atoms is OEAtomStereo::Tetrahedral which corresponds to sp3 tetrahedral chirality. Valid return values for the OEAtomStereo::Tetrahedral stereochemistry class are OEAtomStereo::Left and OEAtomStereo::Right.

8.3.24 GetSymmetryClass

virtual unsigned int GetSymmetryClass()

Return the symmetry class of an atom. The default value is zero, indicating that symmetry classes haven't been assigned. The symmetry class property may be set using the OEAtomBase::SetSymmetryClass method. Symmetry classes of a molecule are usually set by calling the function OEPerceiveSymmetry.

8.3.25 GetTotalHCount

virtual unsigned int GetTotalHCount() const

Return the total number of hydrogen atoms attached to an atom. This value includes the implicit hydrogen atoms. This value is identical to OEAtomBase::GetExplicitHCount() + OEAtomBase::GetImplicitHCount().

8.3.26 GetType

virtual const char *GetType() const

Return the ``atom type name'' string of an atom. This value is typically used when reading and writing molecular formats. For example, in Sybyl mol2 file, the atom type name ``N.pl3'' means that the atom should be treated as a three-valent planar nitrogen. The default value is the empty string. The atom type name property may be set using the OEAtomBase::SetType method.

8.3.27 GetValence

virtual unsigned int GetValence() const

Return the sum of all bond orders to an atom. This value includes bonds to implicit hydrogen atoms. This value is equal to OEAtomBase::GetExplicitValence()+OEAtomBase::GetImplicitHCount().

8.3.28 HasStereoSpecified

virtual bool HasStereoSpecified(unsigned int c=OEAtomStereo::All) const

Determine whether the given atom has specified stereochemistry. The optional argument specifies the class of stereochemisty to check for. The default value, OEAtomStereo::All, checks whether any class of stereochemistry is specified for the current atom.

In the current version of OEChem, the only class of stereochemistry supported for atoms is OEAtomStereo::Tetrahedral which corresponds to sp3 tetrahedral chirality. If a chiral atom has unspecified stereochemistry, and this function returns false, the molecule is assumed to represent either a racemic mixture or an undetermined isomer of this compound. If this function returns true, this atom has an explicit stereochemistry which may be retrieved using the OEAtomBase::GetStereo method.

This method initially returns false for a newly created atom. The stereochemistry of an atom may be set by calling the OEAtomBase::SetStereo method with the appropriate stereochemistry class, c, and any value other than OEAtomStereo::Undefined. The atom stereochemistry may subsequently be cleared by calling the same method, with the appropriate stereochemistry class, but specifying the value OEAtomStereo::Undefined.

8.3.29 IsAromatic

virtual bool IsAromatic() const

Return the Boolean aromatic property of an atom. The default value is false. The aromatic property of an atom can be set using the OEAtomBase::SetAromatic method. The aromatic properties of atoms and bonds in a molecule are typically set by calling either the OEChem OEAssignAromaticFlags function, or possibly the OEClearAromaticFlags function.

8.3.30 IsCarbon

virtual bool IsCarbon() const

Determine whether an atom is a carbon atom. This method tests whether the atom's atomic number is 6, and is equivalent to OEAtomBase::GetAtomicNum() == OEElemNo::C.

8.3.31 IsChiral

virtual bool IsChiral() const

Determine whether the current atom is a stereogenic center. If this method returns true, the atom is a chiral center and the different left-handed and right-handed configurations about this atom represent two distinct isomers. If this function returns false, this atom is not a chiral stereocenter.

This method/value is independent of the current OEAtomBase::HasStereoSpecified setting which records whether a particular left-handed or right-handed configuration is specified at a particular atom.

8.3.32 IsConnected

virtual bool IsConnected(const OEAtomBase *nbor) const

Determine whether the atom is bonded to the given atom ``nbor''. To obtain the actual bond linking the atom to its neighbor use the OEAtomBase::GetBond method. This method is equivalent to OEAtomBase::GetBond() != (OEBondBase*)0.

8.3.33 IsHalogen

virtual bool IsHalogen() const

Determine whether an atom is a halogen atom. This method tests whether the atom is Fluorine, Chlorine, Bromine, Iodine or Astatine (atomic number 9, 17, 35, 53 or 85).

8.3.34 IsHydrogen

virtual bool IsHydrogen() const

Determine whether an atom is a hydrogen atom. This method tests whether the atom's atomic number is 1, and is equivalent to OEAtomBase::GetAtomicNum() == OEElemNo::H.

8.3.35 IsInRing

virtual bool IsInRing() const

Return the Boolean ``in ring'' property of an atom. The default value is false. The ``in ring'' property of an atom may be set using the OEAtomBase::SetInRing method. The ``in ring'' properties of atoms and bonds are typically set by calling OEChem's OEFindRingAtomsAndBonds function. This is a stored, not a computed, property.

To determine whether an atom is a member of a specific ring/cycle size, use the function OEAtomIsInRingSize().

8.3.36 IsMetal

virtual bool IsMetal() const

Determine whether an atom is a metal atom. This tests whether the atom is not H, He, B, C, N, O, F, Ne, Si, P, S, Cl, Ar, As, Se, Br, Kr, Te, I, Xe, At or Rn.

8.3.37 IsNitrogen

virtual bool IsNitrogen() const

Determine whether an atom is a nitrogen atom. This method tests whether the atom's atomic number is 7, and is equivalent to OEAtomBase::GetAtomicNum() == OEElemNo::N.

8.3.38 IsOxygen

virtual bool IsOxygen() const

Determine whether an atom is an oxygen atom. This method tests whether the atom's atomic number is 8, and is equivalent to OEAtomBase::GetAtomicNum() == OEElemNo::O.

8.3.39 IsPhosphorus

virtual bool IsPhosphorus() const

Determine whether an atom is a phosphorus atom. This method tests whether the atom's atomic number is 15, and is equivalent to OEAtomBase::GetAtomicNum() == OEElemNo::P.

8.3.40 IsPolar

virtual bool IsPolar() const

Determine whether an atom is neither a carbon nor hydrogen. The method tests whether the atom's atomic number is any value other the 1 or 6.

8.3.41 IsPolarHydrogen

virtual bool IsPolarHydrogen() const

Determine whether an atom is a hydrogen attached to a polar atom. If the atom's atomic number is not one, OEAtomBase::IsHydrogen() == false, then this method returns false. Otherwise, this method returns true if any of its neighbors return true for OEAtomBase::IsPolar().

8.3.42 IsSulfur

virtual bool IsSulfur() const

Determine whether an atom is a sulfur (sulphur) atom. This method tests whether the atom's atomic number is 16, and is equivalent to OEAtomBase::GetAtomicNum() == OEElemNo::S.

8.3.43 SetAromatic

virtual bool SetAromatic(bool arom)

Set the Boolean aromatic property of an atom. This value is false by default. The aromatic property of an atom may be retrieved using the OEAtomBase::IsAromatic method. This function is normally only used by the functions OEClearAromaticity and OEAssignAromaticityFlags.

8.3.44 SetAtomicNum

virtual bool SetAtomicNum(unsigned int atno)

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

8.3.45 SetFormalCharge

virtual bool SetFormalCharge(int charge)

Set the formal charge of an atom. The default value is zero. The formal charge property may be retrieved using the OEAtomBase::GetFormalCharge method.

8.3.46 SetHyb

virtual bool SetHyb(unsigned int hyb)

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::undefined. The hybridization property may be retrieved using the OEAtomBase::GetHybridization method.

8.3.47 SetImplicitHCount

virtual bool SetImplicitHCount(unsigned int imph)

Set the implicit hydrogen count of an atom. The default value is zero. The implicit hydrogen count property may be retrieved using the OEAtomBase::GetImplicitHCount method.

8.3.48 SetIntType

virtual bool SetIntType(int type)

Set the integer atom type property of an atom. The default value is zero. The integer atom type property may be retrieved using the OEAtomBase::GetIntType method.

8.3.49 SetInRing

virtual bool SetInRing(bool inring)

Set the Boolean ``in ring'' property of an atom. This property is usually set by the OEChem function OEFindRingAtomsAndBonds. The default value is false. The ``in ring'' property of an atom may be retrieved using the OEAtomBase::IsInRing method.

8.3.50 SetIsotope

virtual bool SetIsotope(unsigned int mass)

Set 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::GetIsotope method.

8.3.51 SetMapIdx

virtual bool SetMapIdx(unsigned int mapidx)

Set the reaction atom map index of an atom. This integer value is used for tracking equivalent atom positions in a reaction molecule/transform. The default value is zero, meaning that the atom isn't mapped in the reaction. The ``reaction map index'' property may be retrieved using the OEAtomBase::GetMapIdx method.

8.3.52 SetName

virtual bool SetName(const std::string &nam)
virtual bool SetName(const char *nam)

Set the atom name string of an atom. This property is typically used when reading or writing molecular file formats. For example in PDB files, the atom name `` CA '' is used to denote that the atom is a peptide alpha carbon. The default value is the empty string. The ``atom name'' property may be retrieved using the OEAtomBase:GetName method.

8.3.53 SetPartialCharge

virtual bool SetPartialCharge(double charge)

Set the partial charge property of an atom. The default value is 0.0. The partial charge property may be retrieved using the OEAtomBase::GetPartialCharge method.

8.3.54 SetRadius

virtual bool SetRadius(double radius)

Set the ``radius'' property of an atom. The default value is 0.0. 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.

8.3.55 SetRxnRole

virtual bool SetRxnRole(unsigned int role)

Set the reaction role of an atom in a reaction molecule/transform. The set of unsigned integer values for this property is defined by the OERxnRole namespace. The default value is zero, OERxnRole::None, which means that the atom does have a role, i.e. is part of a normal molecule. Other values include OERxnRole::Reactant, OERxnRole::Agent and OERxnRole::Product which correspond to reactant, agent and product atoms in a reaction or transform. The reaction role property may be retrieved using the OEAtomBase::SetRxnRole method.

8.3.56 SetStereo

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

Set the chirality (or stereochemistry) annotation of the current atom. This method takes a STL vector of neighboring atoms, v, and a specific stereochemisty class, c and the value for that chirality to be set to. This function returns true if the atom chirality was correctly set, and false if the stereochemistry class is invalid, the stereochemistry value is invalid for the stereochemistry class, or the vector of neighboring atoms is invalid. The chiral annotation of a atom may be retrieved using the OEAtomBase::GetStereo.

If set sucessfully, to a value other than OEAtomStereo::Undefined, future calls to OEAtomBase::HasStereoSpecified with the given stereochemistry class (or OEAtomStereo::All) will return true. If sucessfully set to the value OEAtomStereo::Undefined, future calls to OEAtomBase::HasStereoSpecified will return false.

In the current version of OEChem, the only class of stereochemistry supported for atoms is OEAtomStereo::Tetrahedral which corresponds to sp3 tetrahedral chirality. Valid values for the OEAtomStereo::Tetrahedral stereochemistry class are OEAtomStereo::Left and OEAtomStereo::Right.

8.3.57 SetSymmetryClass

virtual bool SetSymmetryClass(unsigned int symclass)

Set the symmetry class of an atom. This routine is normally only called by the OEChem function OEPerceiveSymmetry. The default value is zero, indicating that the symmetry class hasn't be perceived. The symmetry class of an atom may be retrieved by using the OEAtomBase::OEGetSymmetryClass function.

8.3.58 SetType

virtual bool SetType(const std::string &typ)
virtual bool SetType(const char *typ)

Set the ``atom type name'' string property of an atom. This value is typically used when reading and writing molecular formats. For example, in Sybyl mol2 file, the atom type name ``N.pl3'' means that the atom should be treated as a three-valent planar nitrogen. The default value is the empty string. The atom type name property may be retrieved using the OEAtomBase::GetType method.

				OEChem - API Manual

				OEChem - API Manual