Class SBMStructuralModelNodeAtom#

ClassList > SBMStructuralModelNodeAtom

This class describes an atom in a structural model. More...

#include <SBMStructuralModelNodeAtom.hpp>

Inherits the following classes: SBMStructuralModelNode

Classes#

Type	Name
class	IsBeyond
class	IsWithin

Public Types#

Type	Name
enum	Geometry The available atom geometry types.
enum	Hybridization The available atom hybridization types.

Public Types inherited from SBDDataGraphNode#

See SBDDataGraphNode

Type	Name
enum	RenderingPass The rendering pass.
enum	Type The type of the data graph node.

Public Functions#

Type	Name
	SBMStructuralModelNodeAtom () Default constructor.
	SBMStructuralModelNodeAtom (SBElement::Type element) Constructs an atom (default position = (0,0,0))
	SBMStructuralModelNodeAtom (SBElement::Type element, const SBQuantity::length & x, const SBQuantity::length & y, const SBQuantity::length & z) Constructs an atom at position = (x,y,z)
	SBMStructuralModelNodeAtom (SBElement::Type element, const SBPosition3 & position) Constructs an atom at position `position` .
	SBMStructuralModelNodeAtom (SBPosition3 const & position, const std::string & coarseGrainedType, const SBQuantity::length & coarseGrainedRadius, const SBQuantity::mass & coarseGrainedMass, const SBColor & coarseGrainedColor) Constructs a coarse-grained atom.
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::length, GetX)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::length, GetY)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::length, GetZ)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBPosition3, GetPosition)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBElement::Type, GetElementType)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetElementName)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetElementSymbol)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetPeriod)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetGroup)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetBlock)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::mass, GetAtomicWeight)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::length, GetCovalentRadius)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::length, GetVanDerWaalsRadius)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::dimensionless, GetElectronegativity)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBElement::MetalSubcategory, GetMetalSubcategory)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetName)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, char, GetAltLocation)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetChainName)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, char, GetInsertionCode)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, int, GetSerialNumber)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::dimensionless, GetOccupancy)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetRecordType)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetRecordTypeSize)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetResidueName)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetResidueTypeString)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, int, GetResidueSequenceNumber)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetSegmentName)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, double, GetTemperatureFactor)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, float, GetPartialCharge)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, int, GetFormalCharge)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetComment)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetCommentSize)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::vector< int >, GetAnisotropicTFactors)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetSYBYLType)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetSYBYLTypeSize)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetStatusBit)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetStatusBitSize)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetMoleculeName)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetNumberOfBondedAtoms)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetNumberOfBondedCarbons)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetNumberOfBondedHeavyAtoms)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetNumberOfBondedHydrogens)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetNumberOfBondedNitrogens)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetNumberOfBondedOxygens)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, unsigned int, GetNumberOfBondedSulfurs)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetSubstructureName)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, int, GetSubstructureSequenceNumber)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, int, GetChainID)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, Hybridization, GetHybridization)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, Geometry, GetGeometry)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, int, GetOxidationState)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, bool, GetResonance)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, bool, GetAromaticity)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, bool, GetWaterFlag)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, int, GetCustomType)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, std::string, GetCoarseGrainedType)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::length, GetCoarseGrainedRadius)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBQuantity::mass, GetCoarseGrainedMass)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, SBColor, GetCoarseGrainedColor)
	SB_NODE_GETTER_0 (SB_SBMSTRUCTURALMODEL_EXPORT, bool, GetFixedFlag)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasName)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasAltLocation)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasInsertionCode)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasSerialNumber)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasOccupancy)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasRecordType)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasResidueSequenceNumber)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasTemperatureFactor)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasPartialCharge)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasFormalCharge)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasComment)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasAnisotropicTFactors)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasSYBYLType)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasStatusBit)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasSubstructureSequenceNumber)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasChainID)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasHybridization)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasGeometry)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasOxidationState)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasResonance)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasAromaticity)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasWaterFlag)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasCustomType)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInMolecule)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInChain)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInSegment)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInResidue)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInAminoAcid)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInNucleicAcid)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInBackbone)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInSideChain)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsInSubstructure)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsPlanar)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsCarbon)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsHydrogen)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsNitrogen)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsOxygen)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsSulfur)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsUnknown)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsFromAminoAcidBackbone)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsFromNucleicAcidBackbone)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasAminoAcidBackboneAtomName)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, HasNucleicAcidBackboneAtomName)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsMetal)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsAlkaliMetal)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsAlkalineEarthMetal)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsLanthanide)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsActinide)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsTransitionMetal)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsPostTransitionMetal)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsMetalloid)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsNobleGas)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsReactiveNonmetal)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsDiatomicNonmetal)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsPolyatomicNonmetal)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsHalogen)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsCoarseGrained)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsHydrogenBondAcceptor)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsHydrogenBondDonor)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsDonorBorneHydrogen)
	SB_NODE_PREDICATE_0 (SB_SBMSTRUCTURALMODEL_EXPORT, IsAttachedToHydrogenBondDonor)
unsigned int	addHydrogens () Adds hydrogens and returns the number of added hydrogens.
void	clearAltLocation () Clears the atom's alternate location.
void	clearAnisotropicTFactors () Clears the atom's anisotropic temperature factors.
void	clearAromaticity () Clears the atom's aromaticity.
void	clearComment () Clears the atom's comment.
void	clearCustomType () Clears the atom's custom type.
void	clearFormalCharge () Clears the atom's formal charge.
void	clearGeometry () Clears the atom's geometry.
void	clearHybridization () Clears the atom's hybridization.
void	clearInsertionCode () Clears the atom's insertion code.
void	clearName () Clears the atom's full name.
void	clearOccupancy () Clears the atom's occupancy.
void	clearOxidationState () Clears the atom's oxidation state.
void	clearPartialCharge () Clears the atom's partial charge.
void	clearRecordType () Clears the atom's record type.
void	clearResonance () Clears the atom's resonance.
void	clearSYBYLType () Clears the SYBYL atom's type.
void	clearSerialNumber () Clears the atom's serial number.
void	clearStatusBit () Clears the atom's status bit.
void	clearTemperatureFactor () Clears the atom's temperature factor.
void	clearWaterFlag () Clears the atom's water flag.
virtual SBMStructuralModelNodeAtom *	clone () override Returns a copy of the node and its descendants.
char const &	getAltLocation () const Returns the atom's alternate location.
std::vector< int > const &	getAnisotropicTFactors () const Returns the atom's anisotropic temperature factors.
bool const &	getAromaticity () const Returns the atom's aromaticity (true if aromatic, false else)
SBQuantity::mass	getAtomicWeight () const Returns the atom's element atomic weight (regular or coarse grained)
SBMStructuralModelNodeBackbone *	getBackbone () const Returns a pointer to the backbone.
std::string	getBlock () const Returns the atom's element block.
SBPointerList< SBBond > const *	getBondList () const Returns the bond list.
SBBond *	getBondTo (const SBMStructuralModelNodeAtom * atom) const Returns the bond to an atom (0 if no bond)
void	getBondedAtoms (SBNodeIndexer & nodeIndexer) const Gets all bonded atoms.
void	getBondedAtoms (SBNodeIndexer & nodeIndexer, const SBElement::Type element) const Gets all bonded atoms of type `element` .
void	getBondedHeavyAtoms (SBNodeIndexer & nodeIndexer) const Gets all bonded heavy atoms (non-Hydrogens)
SBMStructuralModelNodeChain *	getChain () const Returns a pointer to the chain.
int	getChainID () const Returns the atom's chain ID.
std::string	getChainIDString () const Returns the atom's chain ID string.
std::string	getChainName () const Returns the atom's chain name.
SBColor const &	getCoarseGrainedColor () const Returns the coarse-grained atom's color.
SBQuantity::mass const &	getCoarseGrainedMass () const Returns the coarse-grained atom's mass.
SBQuantity::length const &	getCoarseGrainedRadius () const Returns the coarse-grained atom's radius.
std::string const &	getCoarseGrainedType () const Returns the coarse-grained atom's type.
const float *	getColor () const Returns the atom's element color pointer (CPK or coarse grained)
char *const &	getComment () const Returns the atom's comment.
unsigned int	getCommentSize () const Returns the atom's comment size.
void	getConnectedComponent (SBNodeIndexer & nodeIndexer) const Gets all atoms in the connected component containing the atom.
bool	getConnectedComponent (SBNodeIndexer & nodeIndexer, unsigned int maximumNumberOfAtoms) const Gets atoms in the connected component containing the atom and stops once `maximumNumberOfAtoms` is reached, returns whether the whole connected component has no more than`maximumNumberOfAtoms` atoms.
SBQuantity::length	getCovalentRadius () const Returns the atom's element covalent radius (regular or coarse grained)
SBQuantity::dimensionless	getCurrentValence () const Returns the current valence, i.e. the sum of the orders of the bonds connected to the atom, rounded to the closest integer.
int const &	getCustomType () const Returns the atom's custom type.
SBQuantity::dimensionless	getElectronegativity () const Returns the atom's element electronegativity.
virtual std::string	getElementName () const Returns the atom's element name.
virtual std::string	getElementSymbol () const Returns the atom's element symbol.
virtual SBElement::Type	getElementType () const Returns the atom's element type.
SBQuantity::dimensionless	getExpectedValence () const Returns the expected valence of the atom based on its formal charge and its number of bonds (based on the MDL valence model)
bool	getFixedFlag () const Returns the fixed flag.
virtual unsigned int	getFlags () override const Returns the flags.
int const &	getFormalCharge () const Returns the atom's formal charge.
Geometry const &	getGeometry () const Returns the atom's geometry.
std::string	getGeometryString () const Returns the geometry as a string.
unsigned int	getGroup () const Returns the atom's element group.
virtual std::string	getHierarchyString (const std::string & separator=" / ", bool includeNodeType=false) override const Returns a string with hierarchical information on the atom and its parents names.
Hybridization const &	getHybridization () const Returns the atom's hybridization.
std::string	getHybridizationString () const Returns the hybridization as a string.
void	getHydrogens (SBNodeIndexer & nodeIndexer) const Gets all bonded hydrogens.
virtual unsigned int	getInheritedFlags () override const Returns the inherited flags.
char const &	getInsertionCode () const Returns the atom's insertion code.
SBQuantity::length	getMaximumBondLength () const Computes the maximum bond length for atom's bonds.
SBElement::MetalSubcategory	getMetalSubcategory () const Returns the atom's subcategory type in the metal-metalloid-nonmetal trend.
std::string	getMetalSubcategoryString () const Returns the string representation of the atom's subcategory type in the metal-metalloid-nonmetal trend.
SBQuantity::length	getMinimumBondLength () const Computes the minimum bond length for atom's bonds.
bool	getMobilityFlag () const Returns the mobility flag. Please note that the following method has been marked as deprecated and will be removed in future versions of the software. We recommend that you update your code to use the recommended alternative method instead, which is getFixedFlag() __
virtual SBQuantity::mass	getMolecularWeight () override Returns the molecular weight.
SBMStructuralModelNodeMolecule *	getMolecule () const Returns a pointer to the molecule.
std::string	getMoleculeName () const Returns the atom's molecule name.
virtual std::string const &	getName () override const Returns the atom's full name (e.g. CA for an alpha carbon)
void	getNewBondDirections (SBVector< SBVector3 > & bondDirectionVector, unsigned int numberOfBonds, bool includeExistingHydrogens=false) Generates directions that `numberOfBonds` new neighboring bonds would have.
virtual unsigned int	getNumberOfAtoms () override Returns the number of atoms.
unsigned int	getNumberOfBondedAtoms (const SBElement::Type element) const Returns the number of bonded atoms with element type `element` .
unsigned int	getNumberOfBondedAtoms () const Returns the number of bonded atoms.
unsigned int	getNumberOfBondedCarbons () const Returns the number of bonded carbons.
unsigned int	getNumberOfBondedHeavyAtoms () const Returns the number of bonded heavy atoms.
unsigned int	getNumberOfBondedHydrogens () const Returns the number of bonded hydrogens.
unsigned int	getNumberOfBondedNitrogens () const Returns the number of bonded nitrogens.
unsigned int	getNumberOfBondedOxygens () const Returns the number of bonded oxygens.
unsigned int	getNumberOfBondedSulfurs () const Returns the number of bonded sulfurs.
unsigned int	getNumberOfBonds () const Returns the number of bonds without taking into account the bond order (NB: a double bond is considered as one bond)
virtual unsigned int	getNumberOfCarbons () override Returns the number of carbons.
virtual unsigned int	getNumberOfCoarseGrainedAtoms () override Returns the number of coarse-grained atoms.
virtual unsigned int	getNumberOfHydrogens () override Returns the number of hydrogens.
virtual unsigned int	getNumberOfNitrogens () override Returns the number of nitrogens.
virtual unsigned int	getNumberOfOtherAtoms () override Returns the number of other atoms.
virtual unsigned int	getNumberOfOxygens () override Returns the number of oxygens.
virtual unsigned int	getNumberOfSulfurs () override Returns the number of sulfurs.
SBQuantity::dimensionless const &	getOccupancy () const Returns the atom's occupancy.
int const &	getOxidationState () const Returns the atom's oxidation state.
float const &	getPartialCharge () const Returns the atom's partial charge.
std::string	getPeriod () const Returns the atom's element period.
SBPosition3 const &	getPosition () const Returns the atom's position.
char *const &	getRecordType () const Returns the atom's record type.
unsigned int	getRecordTypeSize () const Returns the atom's record type size.
SBMStructuralModelNodeResidue *	getResidue () const Returns a pointer to the residue.
std::string	getResidueName () const Returns the atom's residue name.
int	getResidueSequenceNumber () const Returns the atom's residue sequence number.
std::string	getResidueSequenceNumberString () const Returns the atom's residue sequence number string.
std::string	getResidueTypeString () const Returns the atom's residue type string.
bool const &	getResonance () const Returns the atom's resonance (true if resonant, false else)
char *const &	getSYBYLType () const Returns the SYBYL atom's type.
unsigned int	getSYBYLTypeSize () const Returns the SYBYL atom's type size.
SBMStructuralModelNodeSegment *	getSegment () const Returns a pointer to the segment.
std::string	getSegmentName () const Returns the atom's segment name.
int const &	getSerialNumber () const Returns the atom's serial number.
SBMStructuralModelNodeSideChain *	getSideChain () const Returns a pointer to the side chain.
char *const &	getStatusBit () const Returns the atom's status bit.
unsigned int	getStatusBitSize () const Returns the atom's status bit size.
SBMStructuralModelNodeGroup *	getSubstructure () const Returns a pointer to the substructure.
std::string	getSubstructureName () const Returns the atom's substructure name.
int	getSubstructureSequenceNumber () const Returns the atom's substructure sequence number.
std::string	getSubstructureSequenceNumberString () const Returns the atom's substructure sequence number string.
virtual int	getSumOfFormalCharges () override Returns the sum of formal charges.
virtual float	getSumOfPartialCharges () override Returns the sum of partial charges.
double const &	getTemperatureFactor () const Returns the atom's temperature factor.
virtual SBDDataGraphNode::Type	getType () override const Returns the node type (returns SBNode::Atom )
SBQuantity::length	getVanDerWaalsRadius () const Returns the atom's element van der Waals radius (regular or coarse grained)
bool const &	getWaterFlag () const Returns the atom's water flag (true if the atom is a water atom, false else)
SBQuantity::length const &	getX () const Returns the x coordinate.
SBQuantity::length const &	getY () const Returns the y coordinate.
SBQuantity::length const &	getZ () const Returns the z coordinate.
bool	hasAltLocation () const Returns `true` when the atom's alternate location is set.
bool	hasAminoAcidBackboneAtomName () const Returns `true` when the atom's name corresponds to one of the amino-acid backbone atoms.
bool	hasAnisotropicTFactors () const Returns `true` when the atom's anisotropic temperature factors are set.
bool	hasAromaticity () const Returns `true` when the atom's aromaticity is set.
bool	hasChainID () const Returns `true` when the atom's chain ID is set. The chain ID is used to separate chains with the same name but divided into 2, e.g. with TER record.
bool	hasComment () const Returns `true` when the atom's comment is set.
bool	hasCustomType () const Returns `true` when the atom's custom type is set.
bool	hasFormalCharge () const Returns `true` when the atom's formal charge is set.
bool	hasGeometry () const Returns `true` when the atom's geometry is set.
bool	hasHybridization () const Returns `true` when the atom's hybridization is set.
bool	hasInsertionCode () const Returns `true` when the atom's insertion code is set.
bool	hasName () const Returns `true` when the atom's name is set.
bool	hasNucleicAcidBackboneAtomName () const Returns `true` when the atom's name corresponds to one of the nucleic acid backbone atoms.
bool	hasOccupancy () const Returns `true` when the atom's occupancy is set.
bool	hasOxidationState () const Returns `true` when the atom's oxidation state is set.
bool	hasPartialCharge () const Returns `true` when the atom's partial charge is set.
bool	hasRecordType () const Returns `true` when the atom's record type is set.
bool	hasResidueSequenceNumber () const Returns `true` when the atom's residue sequence number is set.
bool	hasResonance () const Returns `true` when the atom's resonance is set.
bool	hasSYBYLType () const Returns `true` when the SYBYL atom's type is set.
bool	hasSerialNumber () const Returns `true` when the atom's serial number is set.
bool	hasStatusBit () const Returns `true` when the atom's status bit is set.
bool	hasSubstructureSequenceNumber () const Returns `true` when the atom's substructure sequence number is set.
bool	hasTemperatureFactor () const Returns `true` when the atom's temperature factor is set.
bool	hasWaterFlag () const Returns `true` when the atom's water flag is set.
bool	isActinide () const Returns `true` if the atom is actinide metal.
bool	isAlkaliMetal () const Returns `true` if the atom is alkali metal.
bool	isAlkalineEarthMetal () const Returns `true` if the atom is alkaline earth metal.
bool	isAttachedToHydrogenBondDonor () const Returns `true` if the atom is connected to an H-Bond donor.
bool	isCarbon () const Returns `true` when the atom is a carbon atom.
bool	isCarboxylOxygen () const Returns `true` for an Oxygen atom in a carboxyl group (C(=O)OH)
bool	isCoarseGrained () const Returns `true` if the atom is coarse grained.
bool	isDiatomicNonmetal () const Returns `true` if the atom is diatomic nonmetal.
bool	isDonorBorneHydrogen () const Returns `true` if the atom is a hydrogen connected to an H-Bond donor.
bool	isFixed () const Returns whether the node is fixed (opposite of mobile)
bool	isFromAminoAcidBackbone () const Returns `true` when the atom is from an amino-acid backbone.
bool	isFromNucleicAcidBackbone () const Returns `true` when the atom is from a nucleic acid backbone.
bool	isHalogen () const Returns `true` if the atom is halogen.
bool	isHydrogen () const Returns `true` when the atom is a hydrogen atom.
bool	isHydrogenBondAcceptor () const Returns `true` if the atom is an H-Bond acceptor (N, O, S, F)
bool	isHydrogenBondDonor () const Returns `true` if the atom is an H-Bond donor (N, O, S, F)
bool	isInAminoAcid () const Returns `true` when the atom is in an amino acid residue.
bool	isInBackbone () const Returns `true` when the atom is in a backbone.
bool	isInChain () const Returns `true` when the atom is in a chain.
bool	isInMolecule () const Returns `true` when the atom is in a molecule.
bool	isInNucleicAcid () const Returns `true` when the atom is in a nucleic acid residue.
bool	isInResidue () const Returns `true` when the atom is in a residue.
bool	isInSegment () const Returns `true` when the atom is in a segment.
bool	isInSideChain () const Returns `true` when the atom is in a side chain.
bool	isInSubstructure () const Returns `true` when the atom is in a substructure.
bool	isLanthanide () const Returns `true` if the atom is lanthanide metal.
bool	isMetal () const Returns `true` if the atom is metal.
bool	isMetalloid () const Returns `true` if the atom is metalloid.
bool	isMobile () const Returns whether the node is mobile. Please note that the following method has been marked as deprecated and will be removed in future versions of the software. We recommend that you update your code to use the recommended alternative method instead, which is isFixed() __
bool	isNitroOxygen () const Returns `true` for an Oxygen atom in a nitro group (-NO2)
bool	isNitrogen () const Returns `true` when the atom is a nitrogen atom.
bool	isNobleGas () const Returns `true` if the atom is noble gas.
bool	isOxygen () const Returns `true` when the atom is an oxygen atom.
bool	isPlanar () const Returns `true` if the atom with atoms bonded to it are in the same plane.
bool	isPolyatomicNonmetal () const Returns `true` if the atom is polyatomic nonmetal.
bool	isPostTransitionMetal () const Returns `true` if the atom is post-transition metal.
bool	isReactiveNonmetal () const Returns `true` if the atom is reactive nonmetal.
virtual bool	isSerializable () override const Returns `true` __
bool	isSulfoneOxygen () const Returns `true` for an Oxygen atom in a sulfone (R1-SO2-R2)
bool	isSulfur () const Returns `true` when the atom is a sulfur atom.
bool	isThiocarboxylOxygen () const Returns `true` for an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH)
bool	isTransitionMetal () const Returns `true` if the atom is transition metal.
bool	isUnknown () const Returns `true` when the atom is an unknown atom.
Hybridization	perceiveHybridization () Perceives, sets and returns the atom's hybridization.
virtual void	print (unsigned int offset=0) override const Prints debugging information.
unsigned int	removeHydrogens () Removes the hydrogens bonded to the atom and returns the number of removed hydrogens.
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the atom.
void	setAltLocation (const char & altLocation) Sets the atom's alternate location.
void	setAnisotropicTFactors (const std::vector< int > & ATF) Sets the atom's anisotropic temperature factors.
void	setAromaticity (const bool & aromaticity) Sets the atom's aromaticity.
void	setCoarseGrainedColor (const SBColor & coarseGrainedColor) Sets the coarse-grained atom's color.
void	setCoarseGrainedMass (const SBQuantity::mass & coarseGrainedMass) Sets the coarse-grained atom's mass.
void	setCoarseGrainedRadius (const SBQuantity::length & coarseGrainedRadius) Sets the coarse-grained atom's radius.
void	setCoarseGrainedType (const std::string & coarseGrainedType) Sets the coarse-grained atom's type.
void	setComment (char const & comment, int const & size) Sets the atom's comment.*
void	setCustomType (const int & water) Sets the atom's custom type.
virtual void	setElementType (SBElement::Type e) Sets the atom's element type.
void	setFixedFlag (bool flag) Sets the fixed flag to `flag` .
void	setFixedFlag (bool newflag, bool oldFlag) Sets the fixed flag to `flag` .
void	setFormalCharge (const int & formalCharge) Sets the atom's formal charge.
void	setGeometry (const Geometry & geometry) Sets the atom's geometry.
void	setHybridization (const Hybridization & hybridization) Sets the atom's hybridization.
void	setInsertionCode (const char & insertionCode) Sets the atom's insertion code.
void	setMobilityFlag (bool flag) Sets the mobility flag to `flag` . Please note that the following method has been marked as deprecated and will be removed in future versions of the software. We recommend that you update your code to use the recommended alternative method instead, which issetFixedFlag(bool flag) __
virtual void	setName (const std::string & name) override Sets the atom's full name.
void	setOccupancy (const SBQuantity::dimensionless & occupancy) Sets the atom's occupancy.
void	setOxidationState (const int & oxidationState) Sets the atom's oxidation state.
void	setPartialCharge (const float & partialCharge) Sets the atom's partial charge.
void	setPosition (SBPosition3 const & newPosition) Sets the atom's position if the atom is not fixed.
void	setPosition (SBPosition3 const & newPosition, SBPosition3 const & oldPosition) Sets the atom's position.
void	setPosition (SBPosition3 const & newPosition, bool ignoreFixed) Sets the atom's position.
void	setPosition (SBPosition3 const & newPosition, SBPosition3 const & oldPosition, bool ignoreFixed) Sets the atom's position.
void	setPositionOnTetrahedron (SBPosition3 const & center, SBPosition3 const & vertex1, SBPosition3 const & vertex2, SBPosition3 const & vertex3, SBQuantity::length const & distanceFromCenter) Sets the atom's position on a tetrahedron vertex based on the `center` position, the distance from the center`distanceFromCenter` , and positions of other 3 vertices`vertex1` ,`vertex2` , and`vertex3` .
void	setRecordType (char const & recordType, int const & size) Sets the atom's record type.*
void	setResonance (const bool & resonance) Sets the atom's resonance.
void	setSYBYLType (char const & SYBYLType, int const & size) Sets the SYBYL atom's type.*
void	setSerialNumber (const int & serialNumber) Sets the atom's serial number.
void	setStatusBit (char const & statusBit, int const & size) Sets the atom's status bit.*
void	setTemperatureFactor (const double & temperatureFactor) Sets the atom's temperature factor.
void	setWaterFlag (const bool & water) Sets the atom's water flag.
void	setX (const SBQuantity::length & x) Sets the x coordinate.
void	setY (const SBQuantity::length & y) Sets the y coordinate.
void	setZ (const SBQuantity::length & z) Sets the z coordinate.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override Unserializes the atom.
virtual	~SBMStructuralModelNodeAtom () Destructs the atom.

Public Functions inherited from SBMStructuralModelNode#

See SBMStructuralModelNode

Type	Name
virtual SBMStructuralModelNode *	clone () override Returns a copy of the node and its descendants.
void	connectStructuralSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBStructuralEvent* ) functionPointer, SBStructuralEvent::Type* eventType=SBStructuralEvent::Type::Any, SBCReferenceTarget * nextReferenceTarget=nullptr, void(SBCReferenceTarget::)(SBStructuralEvent* ) nextFunctionPointer=nullptr) Connects the structural signal to a slot.*
void	disconnectStructuralSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBStructuralEvent* ) functionPointer, SBStructuralEvent::Type* eventType=SBStructuralEvent::Type::Any) Disconnects the structural signal from a slot.
virtual void	forEachNodeDepthFirst (void()(SBDDataGraphNode* node) action) override Performs the* `action` on this node.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) override Performs the* `object` 's`action` on this node.
void	forEachStructuralNodeBreadthFirst (void()(SBMStructuralModelNode* node) action) Performs the* `action` on this node and all its structural node children in the breadth-first way.
void	forEachStructuralNodeBreadthFirst (SBCClass * object, void(SBCClass::)(SBMStructuralModelNode* node) action) Performs the* `object` 's`action` on this node and all its structural node children in the breadth-first way.
void	forEachStructuralNodeDepthFirst (void()(SBMStructuralModelNode* node) action) Performs the* `action` on this node and all its structural node children in the depth-first way.
void	forEachStructuralNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBMStructuralModelNode* node) action) Performs the* `object` 's`action` on this node and all its structural node children in the depth-first way.
void	getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with all structural nodes (the node itself and all its structural node children), breadth-first, bottom-up.
void	getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with all structural nodes (the node itself and all its structural node children), breadth-first, top-down.
void	getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with all structural nodes (the node itself and all its structural node children), depth-first.
virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () const Returns the list of child nodes.
void	getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with internal structural nodes (the node's structural node children), breadth-first, bottom-up.
void	getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with internal structural nodes (the node's structural node children), breadth-first, top-down.
void	getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with internal structural nodes (the node's structural node children), depth-first.
void	getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with leaf structural nodes (i.e., only with the nodes that have no shildren), breadth-first, bottom-up.
void	getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with leaf structural nodes (i.e., only with the nodes that have no shildren), breadth-first, top-down.
void	getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) Populates `nodeIndexer` with leaf structural nodes (i.e., only with the nodes that have no shildren), depth-first.
virtual bool	getLockedFlag () override const Returns the locked flag of the model.
SBMStructuralModel *	getModel () const Returns a pointer to the structural model this structural node belongs to.
SBMStructuralModelNode *	getNextStructuralNode () const Returns the next structural node in the node's parent.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into `nodeIndexer` , based on a`nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into `nodeIndexer` , based on a`selectionPredicate` and a`visitPredicate` , with or without dependencies.
virtual unsigned int	getOpacity () override const Returns the opacity.
SBMStructuralModelNode *	getPreviousStructuralNode () const Returns the previous structural node in the node's parent.
void	getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode * > & nodeVectorTopDown, std::vector< SBMStructuralModelNode * > & nodeVectorBottomUp, bool()(SBMStructuralModelNode* ) selectionRule) Selects some structural nodes, breadth-first, both top-down and bottom-up.*
void	getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool()(SBMStructuralModelNode* ) selectionRule) Populates* `nodeIndexer` with some structural nodes based on the`selectionRule` , breadth-first, bottom-up.
void	getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool()(SBMStructuralModelNode* ) selectionRule) Populates* `nodeIndexer` with some structural nodes based on the`selectionRule` , breadth-first, top-down.
void	getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool()(SBMStructuralModelNode* ) selectionRule) Populates* `nodeIndexer` with some structural nodes based on the`selectionRule` , depth-first.
bool	getStructuralSignalFlag () const Returns `true` when the node can send structural signals.
virtual unsigned int	getTransparency () override const Returns the transparency.
virtual SBDDataGraphNode::Type	getType () override const Returns the node type.
virtual bool	hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a `nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
virtual bool	hasNode (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a `selectionPredicate` and a`visitPredicate` , with or without dependencies.
virtual bool	isLocked () override const Returns whether the node is locked (because of the model)
virtual bool	isSerializable () override const Returns `true` __
virtual void	print (unsigned int offset=0) override const Prints debugging information.
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the node.
void	setStructuralSignalFlag (bool structuralSignalFlag) Sets whether the node can send structural signals.
bool	structuralSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBStructuralEvent* ) functionPointer, SBStructuralEvent::Type* eventType=SBStructuralEvent::Type::Any) const Returns `true` if and only if the structural signal is connected to a given slot.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override Unserializes the node.
virtual	~SBMStructuralModelNode () Destructor.

Public Functions inherited from SBMModelNode#

See SBMModelNode

Type	Name
virtual SBMModelNode *	clone () override Returns a copy of the node and its descendants.
virtual SBDDataGraphNode::Type	getType () override const Returns the type of the data graph node.
virtual bool	isSerializable () override const Returns `true` __
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the node.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override Unserializes the node.

Public Functions inherited from SBDDataGraphNode#

See SBDDataGraphNode

Type	Name
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBCClassProxy *, GetProxy)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, This)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetParent)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetThis)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetNextNode)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetPreviousNode)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDocument *, GetDocument)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode *, GetRoot)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, unsigned int, GetNodeIndex)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBDDataGraphNode::Type, GetType)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetSelectionFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetLockedFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetVisibilityFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, bool, GetHighlightingFlag)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, unsigned int, GetFlags)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetName)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetClass)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, std::string, GetElement)
	SB_NODE_GETTER_0 (SB_SBDDATAGRAPH_EXPORT, SBCContainerUUID, GetElementUUID)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, All)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, None)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsAtom)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsBond)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsStructuralNode)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsStructuralModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVisualModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsMesh)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLight)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsInteractionModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsDynamicalModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsPropertyModel)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSimulator)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsBallAndStick)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLicorice)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVanDerWaals)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsCartoon)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsRibbon)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsTube)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsGaussianSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSolventAccessibleSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSolventExcludedSurface)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, HasMaterial)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, OwnsMaterial)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsLocked)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSerializable)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsCreated)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsErased)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsSelected)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsVisible)
	SB_NODE_PREDICATE_0 (SB_SBDDATAGRAPH_EXPORT, IsHighlighted)
	SB_NODE_PREDICATE_1 (SB_SBDDATAGRAPH_EXPORT, IsType, SBDDataGraphNode::Type)
	SB_NODE_PREDICATE_1 (SB_SBDDATAGRAPH_EXPORT, HasOneOf, SBNodeIndexer)
virtual bool	addChild (SBDDataGraphNode * node, SBDDataGraphNode * nextNode=nullptr) Adds a child to the node.
bool	addMaterial (SBDDataGraphNodeMaterial * material) Adds a material.
bool	baseSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBBaseEvent* ) functionPointer) const Returns* `true` when the base signal is connected to a slot.
virtual bool	canAddChild (const SBDDataGraphNode * node, const SBDDataGraphNode * nextNode=nullptr) const Returns whether this node can add `node` as a child.
virtual bool	canAddChildType (SBDDataGraphNode::Type nodeType) const Returns whether this node can add a node with type `nodeType` as a child.
bool	canAddMaterial () const Returns whether can add a material to the node based on its type.
virtual bool	canHaveDescendantType (SBDDataGraphNode::Type nodeType) const Returns whether this node can have a node with type `nodeType` as a descendant.
virtual SBDDataGraphNode *	clone () Returns a copy of the node and its descendants.
void	connectBaseSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBBaseEvent* ) functionPointer, SBCReferenceTarget* * nextReferenceTarget=0, void(SBCReferenceTarget::)(SBBaseEvent* ) nextFunctionPointer=0) Connects the base signal to a slot.*
unsigned int	countNodes (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Counts nodes based on a `nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
unsigned int	countNodes (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Counts nodes based on a `selectionPredicate` and a`visitPredicate` , with or without dependencies.
void	create () Creates the node.
bool	descendsFrom (const SBDDataGraphNode * node) const Returns `true` if and only if this node is`node` , or descends from it.
bool	descendsFrom (const SBNodeIndexer & nodeIndexer) const Returns `true` if and only if this node is one of the nodes of the`nodeIndexer` , or descends from one of them.
bool	descendsFrom (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns `true` if and only if this node is one of the nodes of the`nodePointerIndexer` , or descends from one of them.
void	disconnectBaseSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::)(SBBaseEvent* ) functionPointer) Disconnects the base signal from a slot.*
virtual void	display (RenderingPass renderingPass) Displays the node.
virtual void	display () Displays the node (deprecated)
virtual void	displayForSelection () Displays the node for selection purposes (deprecated)
virtual void	displayForShadow () Displays the node for shadowing purposes (deprecated)
void	erase () Erases the node.
virtual void	forEachNodeDepthFirst (void()(SBDDataGraphNode* node) action) Performs the* `action` on this node.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) Performs the* `objects` 's`action` on this node.
unsigned int	getDefaultOpacity () const Returns the default opacity.
unsigned int	getDefaultTransparency () const Returns the default transparency.
SBDDocument *	getDocument () const Returns the document the node belongs to.
virtual unsigned int	getFlags () const Returns the flags.
virtual std::string	getHierarchyString (const std::string & separator=" / ", bool includeNodeType=false) const Returns a string with hierarchical information on the node and its parents names.
bool	getHighlightingFlag () const Returns the highlighting flag.
virtual unsigned int	getInheritedFlags () const Returns the inherited flags.
float	getInheritedOpacity () const Returns the cumulative opacity, when taking into account the ascendants.
float	getInheritedTransparency () const Returns the cumulative transparency, when taking into account the ascendants.
virtual bool	getLockedFlag () const Returns the locked flag.
SBDDataGraphNodeMaterial *	getMaterial () const Returns the material.
SBDDataGraphNode *	getMaterialOwner () const Returns the node whose material is inherited.
unsigned int	getMaximumOpacity () const Returns the maximum opacity.
unsigned int	getMaximumTransparency () const Returns the maximum transparency.
unsigned int	getMinimumOpacity () const Returns the minimum opacity.
unsigned int	getMinimumTransparency () const Returns the minimum transparency.
virtual SBQuantity::mass	getMolecularWeight () Returns the molecular weight.
virtual std::string const &	getName () const Returns the name of the node.
SBDDataGraphNode *	getNextNode () const Returns the pointer to the next node in the children of the node's parent.
SBDDataGraphNode *	getNextNode (SBDDataGraphNode::Type nodeType) const Returns the pointer to the next node with type `nodeType` in the children of the node's parent.
unsigned int	getNodeIndex () const Returns the node index (unique in the whole data graph, but non-persistent)
SBUUID	getNodeUUID () const Returns the node UUID.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Collects nodes into `nodeIndexer` , based on a`nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
virtual void	getNodes (SBNodeIndexer & nodeIndexer, const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Collects nodes into `nodeIndexer` , based on a`selectionPredicate` and a`visitPredicate` , with or without dependencies.
virtual unsigned int	getNumberOfAtoms () Returns the number of atoms.
virtual unsigned int	getNumberOfCarbons () Returns the number of carbons.
virtual unsigned int	getNumberOfChains () Returns the number of chains.
virtual unsigned int	getNumberOfCoarseGrainedAtoms () Returns the number of coarse-grained atoms.
virtual unsigned int	getNumberOfHydrogens () Returns the number of hydrogens.
virtual unsigned int	getNumberOfMolecules () Returns the number of molecules.
virtual unsigned int	getNumberOfNitrogens () Returns the number of nitrogens.
virtual unsigned int	getNumberOfOtherAtoms () Returns the number of other atoms.
virtual unsigned int	getNumberOfOxygens () Returns the number of oxygens.
virtual unsigned int	getNumberOfResidues () Returns the number of residues.
virtual unsigned int	getNumberOfSegments () Returns the number of segments.
virtual unsigned int	getNumberOfStructuralGroups () Returns the number of structural groups.
virtual unsigned int	getNumberOfStructuralModels () Returns the number of structural models.
virtual unsigned int	getNumberOfSulfurs () Returns the number of sulfurs.
virtual unsigned int	getOpacity () const Returns the opacity.
unsigned int	getOpacitySingleStep () const Returns the opacity single step.
std::string	getOpacitySuffix () const Returns the opacity suffix.
SBDDataGraphNode *	getParent () const Returns the parent of the node.
SBDDataGraphNode *	getPreviousNode () const Returns the pointer to the previous node in the children of the node's parent.
SBDDataGraphNode *	getPreviousNode (SBDDataGraphNode::Type nodeType) const Returns the pointer to the previous node with type `nodeType` in the children of the node's parent.
SBDDataGraphNode *	getRoot () const Returns the root of the hierarchy the node belongs to.
bool	getSelected () const Returns whether the node is selected.
bool	getSelectionFlag () const Returns the selection flag.
virtual int	getSumOfFormalCharges () Returns the sum of formal charges.
virtual float	getSumOfPartialCharges () Returns the sum of partial charges.
SBDDataGraphNode *	getThisNode () const Returns the pointer to this node.
virtual unsigned int	getTransparency () const Returns the transparency.
unsigned int	getTransparencySingleStep () const Returns the transparency single step.
std::string	getTransparencySuffix () const Returns the transparency suffix.
virtual Type	getType () const Returns the type of the data graph node.
std::string	getTypeString (bool humanReadable=false) const Returns a string describing the type of the data graph node.
bool	getVisibilityFlag () const Returns the visibility flag.
bool	getVisible () const Returns whether the node is visible.
bool	hasMaterial () const Returns whether the node has a material (by itself, or inherited)
virtual bool	hasNode (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Returns whether the node has nodes based on a `nodeType` , a selection status and a`visitPredicate` , with or without dependencies.
virtual bool	hasNode (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Returns whether the node has nodes based on a `selectionPredicate` and a`visitPredicate` , with or without dependencies.
bool	hasOneOf (const SBNodeIndexer & nodeIndexer) const Returns `true` if and only if this node is one of the nodes of the`nodeIndexer` , or is the ancestor of one of them, or is a group that stores one of them.
bool	hasOpacityRange () const Returns whether the node has the opacity range.
bool	hasTransparencyRange () const Returns whether the node has the transparency range.
bool	isAtom () const Returns `true` when the node is an atom.
bool	isBallAndStick () const Returns `true` when the node is the default ball-and-stick visual model.
bool	isBond () const Returns `true` when the node is a bond.
bool	isCartoon () const Returns `true` when the node is the default cartoon visual model.
bool	isCreated () const Returns `true` if and only if the node is created.
bool	isDynamicalModel () const Returns `true` when the node is a dynamical model.
bool	isErased () const Returns `true` if and only if the node is erased.
bool	isGaussianSurface () const Returns `true` when the node is the default Gaussian surface visual model.
bool	isHighlighted () const Returns whether the node is highlighted.
bool	isIn (const SBDDataGraphNode * node) const Returns `true` if and only if this node is`node` , or descends from it, or belongs to a group stored in`node` .
bool	isIn (const SBNodeIndexer & nodeIndexer) const Returns `true` if and only if this node is one of the nodes of the`nodeIndexer` , or descends from one of them, or belongs to a group stored in one of the nodes of the`nodeIndexer` .
bool	isIn (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns `true` if and only if this node is one of the nodes of the`nodePointerIndexer` , or descends from one of them, or belongs to a group stored in of the nodes of the`nodePointerIndexer` .
bool	isInteractionModel () const Returns `true` when the node is a interaction model.
bool	isLicorice () const Returns `true` when the node is the default licorice visual model.
bool	isLight () const Returns `true` when the node is a light.
virtual bool	isLocked () const Returns whether the node is locked.
bool	isMesh () const Returns `true` when the node is a mesh.
bool	isModel () const Returns `true` when the node is a model.
bool	isOneOf (const SBNodeIndexer & nodeIndexer) const Returns `true` if and only if this node is one of the nodes of the`nodeIndexer` .
bool	isOneOf (SBPointerIndexer< SBDDataGraphNode > * nodePointerIndexer) const Returns `true` if and only if this node is one of the nodes of the`nodePointerIndexer` .
bool	isPropertyModel () const Returns `true` when the node is a property model.
bool	isRibbon () const Returns `true` when the node is the default ribbon visual model.
bool	isSelected () const Returns whether the node is selected.
virtual bool	isSerializable () const Returns `true` when the class is serializable.
bool	isSimulator () const Returns `true` when the node is a simulator.
bool	isSolventAccessibleSurface () const Returns `true` when the node is the default solvent accessible surface visual model.
bool	isSolventExcludedSurface () const Returns `true` when the node is the default solvent excluded surface visual model.
bool	isStructuralModel () const Returns `true` when the node is a structural model.
bool	isStructuralNode () const Returns `true` when the node is a structural node.
bool	isTube () const Returns `true` when the node is the default tube visual model.
bool	isType (Type type) const Returns `true` when the type of the node corresponds to`type` .
bool	isVanDerWaals () const Returns `true` when the node is the default van der Waals visual model.
bool	isVisible () const Returns whether the node is visible.
bool	isVisualModel () const Returns `true` when the node is a visual model.
bool	ownsMaterial () const Returns whether the node owns a material.
virtual void	print (unsigned int offset=0) const Prints some debugging information.
virtual bool	removeChild (SBDDataGraphNode * node) Removes a child from the node.
bool	removeMaterial () Removes the material.
void	removeMaterialsFromDescendants () Removes materials from all nodes that descend from this node, but it does not remove the material from the node itself.
virtual void	serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) const Serializes the node.
void	setHighlightingFlag (bool flag) Sets the highlighting flag.
virtual void	setLockedFlag (bool flag) Sets the locked flag.
virtual void	setName (const std::string & name) Sets the name of the node.
virtual void	setOpacity (unsigned int opacity) Sets the opacity.
void	setSelectionFlag (bool flag) Sets the selection flag.
virtual void	setTransparency (unsigned int transparency) Sets the transparency.
void	setVisibilityFlag (bool flag) Sets the visibility flag.
virtual void	unserialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) Unserializes the node.

Public Functions inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
	SBCReferenceTarget () Builds the reference target.
unsigned int	getMemoryFootprint () const Returns the memory footprint.
void	printReferencesToOwners () const Prints the references to the owners of this reference target.
virtual	~SBCReferenceTarget () Destructor.

Public Static Functions#

Type	Name
std::string	getGeometryString (Geometry geometry) Returns the `geometry` as a string.
std::string	getHybridizationString (Hybridization hybridization) Returns the `hybridization` as a string.
void	setPosition (SBAttributeChangeVector< SBMStructuralModelNodeAtom , SBPosition3 > positionChangeVector, bool reverse=false) Sets the position of a vector of atoms.
void	setPosition (const SBVector< SBMStructuralModelNodeAtom * > & atomVector, const SBVector< SBPosition3 > & newPositionVector) Sets the position of a vector of atoms.

Public Static Functions inherited from SBMStructuralModelNode#

See SBMStructuralModelNode

Type	Name
void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > & selection, void()(SBMStructuralModelNode* node) action) Performs the* `action` on nodes in the`selection` __
void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > & selection, SBCClass * object, void(SBCClass::)(SBMStructuralModelNode* node) action) Performs the* `object` 's`action` on nodes in the`selection` __

Public Static Functions inherited from SBDDataGraphNode#

See SBDDataGraphNode

Type	Name
bool	canAddMaterial (SBDDataGraphNode::Type nodeType) Returns whether can add a material to a node of type `nodeType` .
void	clone (const SBNodeIndexer & sourceNodeIndexer, SBNodeIndexer & destinationNodeIndexer) Clones the nodes in `sourceNodeIndexer` (treated as a whole) and places the clones in`destinationNodeIndexer` .
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, void()(SBDDataGraphNode* node) action) Performs the* `action` for each node in`nodeIndexer` __
void	forEachNodeInSelection (SBNodeIndexer & nodeIndexer, SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) Performs the* `objects` 's`action` for each node in`nodeIndexer` __
SBDDataGraphNode *	getNode (unsigned int nodeIndex) Returns the unique node corresponding to the node index `nodeIndex` .
std::string	getTypeString (Type type, bool humanReadable=false) Returns a string describing the type of the data graph node.

Protected Attributes inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
SBCReferenceTargetData *	dataPointer A pointer to the private data.

Protected Functions inherited from SBMStructuralModelNode#

See SBMStructuralModelNode

Type	Name
	SBMStructuralModelNode () Builds a structural model node.
	SBMStructuralModelNode (SBMStructuralModelNodeData * dataPointer) Builds a structural model node.

Protected Functions inherited from SBMModelNode#

See SBMModelNode

Type	Name
	SBMModelNode () Builds a base object.
	SBMModelNode (SBMModelNodeData * dataPointer) Builds a base object.
virtual	~SBMModelNode () Destructor.

Protected Functions inherited from SBDDataGraphNode#

See SBDDataGraphNode

Type	Name
	SBDDataGraphNode () Builds a data graph node.
	SBDDataGraphNode (SBDDataGraphNodeData * dataPointer) Builds a data graph node.
virtual	~SBDDataGraphNode () Destroys the node.

Protected Functions inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
	SBCReferenceTarget (SBCReferenceTargetData * dataPointer) Protected constructor.
void	removeAllReferenceOwners () Stops all the reference owners from referencing this reference target.

Detailed Description#

Short name: SBAtom

Public Types Documentation#

enum Geometry#

The available atom geometry types.

href="#__codelineno-0-1">enum SBMStructuralModelNodeAtom::Geometry { Undefined = 0, Linear = 21, Bent = 22, TrigonalPlanar = 31, TrigonalPyramidal = 32, TShaped = 33, Tetrahedral = 41, SquarePlanar = 42, Seesaw = 43, TrigonalBipyramidal = 51, SquarePyramidal = 52, PentagonalPlanar = 53, Octahedral = 61, TrigonalPrismatic = 62, PentagonalPyramidal = 63, PentagonalBipyramidal = 71, CappedOctahedral = 72, CappedTrigonalPrismatic = 73, SquareAntiprismatic = 81, Dodecahedral = 82, BicappedTrigonalPrismatic = 83, TricappedTrigonalPrismatic = 91, CappedSquareAntiprismatic = 92 };

enum Hybridization#

The available atom hybridization types.

enum SBMStructuralModelNodeAtom::Hybridization {
    NoHybridization = 0,
    SP = 1,
    SP2 = 2,
    SP3 = 3,
    SP3D = 4,
    SP3D2 = 5,
    Unknown = 6
};

Public Functions Documentation#

function SBMStructuralModelNodeAtom [1/5]#

Default constructor.

SBMStructuralModelNodeAtom::SBMStructuralModelNodeAtom ()

Constructs an atom node with default values.

function SBMStructuralModelNodeAtom [2/5]#

Constructs an atom (default position = (0,0,0))

SBMStructuralModelNodeAtom::SBMStructuralModelNodeAtom (
    SBElement::Type element
)

Constructor with element type.

Constructs an atom node with the specified element type and default position (0,0,0).

Parameters:

e The element type of the atom.

function SBMStructuralModelNodeAtom [3/5]#

Constructs an atom at position = (x,y,z)

SBMStructuralModelNodeAtom::SBMStructuralModelNodeAtom (
    SBElement::Type element,
    const SBQuantity::length & x,
    const SBQuantity::length & y,
    const SBQuantity::length & z
)

Constructor with element type and coordinates.

Constructs an atom node with the specified element type and position given by coordinates.

Parameters:

e The element type of the atom.
x The x-coordinate of the atom's position.
y The y-coordinate of the atom's position.
z The z-coordinate of the atom's position.

function SBMStructuralModelNodeAtom [4/5]#

Constructs an atom at position position .

SBMStructuralModelNodeAtom::SBMStructuralModelNodeAtom (
    SBElement::Type element,
    const SBPosition3 & position
)

Constructor with element type and position vector.

Constructs an atom node with the specified element type and position.

Parameters:

e The element type of the atom.
p The position of the atom.

function SBMStructuralModelNodeAtom [5/5]#

Constructs a coarse-grained atom.

SBMStructuralModelNodeAtom::SBMStructuralModelNodeAtom (
    SBPosition3 const & position,
    const std::string & coarseGrainedType,
    const SBQuantity::length & coarseGrainedRadius,
    const SBQuantity::mass & coarseGrainedMass,
    const SBColor & coarseGrainedColor
)

Constructor for a coarse-grained atom.

Constructs a coarse-grained atom with the given position, type, radius, mass, and color.

Parameters:

position The position of the coarse-grained atom.
coarseGrainedType The type identifier for the coarse-grained atom.
coarseGrainedRadius The radius of the coarse-grained atom.
coarseGrainedMass The mass of the coarse-grained atom.
coarseGrainedColor The color of the coarse-grained atom.

function SB_NODE_GETTER_0 [1/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::length,
    GetX
)

function SB_NODE_GETTER_0 [2/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::length,
    GetY
)

function SB_NODE_GETTER_0 [3/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::length,
    GetZ
)

function SB_NODE_GETTER_0 [4/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBPosition3,
    GetPosition
)

function SB_NODE_GETTER_0 [5/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBElement::Type,
    GetElementType
)

function SB_NODE_GETTER_0 [6/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetElementName
)

function SB_NODE_GETTER_0 [7/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetElementSymbol
)

function SB_NODE_GETTER_0 [8/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetPeriod
)

function SB_NODE_GETTER_0 [9/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetGroup
)

function SB_NODE_GETTER_0 [10/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetBlock
)

function SB_NODE_GETTER_0 [11/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::mass,
    GetAtomicWeight
)

function SB_NODE_GETTER_0 [12/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::length,
    GetCovalentRadius
)

function SB_NODE_GETTER_0 [13/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::length,
    GetVanDerWaalsRadius
)

function SB_NODE_GETTER_0 [14/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::dimensionless,
    GetElectronegativity
)

function SB_NODE_GETTER_0 [15/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBElement::MetalSubcategory,
    GetMetalSubcategory
)

function SB_NODE_GETTER_0 [16/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetName
)

function SB_NODE_GETTER_0 [17/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    char,
    GetAltLocation
)

function SB_NODE_GETTER_0 [18/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetChainName
)

function SB_NODE_GETTER_0 [19/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    char,
    GetInsertionCode
)

function SB_NODE_GETTER_0 [20/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    int,
    GetSerialNumber
)

function SB_NODE_GETTER_0 [21/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::dimensionless,
    GetOccupancy
)

function SB_NODE_GETTER_0 [22/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetRecordType
)

function SB_NODE_GETTER_0 [23/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetRecordTypeSize
)

function SB_NODE_GETTER_0 [24/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetResidueName
)

function SB_NODE_GETTER_0 [25/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetResidueTypeString
)

function SB_NODE_GETTER_0 [26/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    int,
    GetResidueSequenceNumber
)

function SB_NODE_GETTER_0 [27/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetSegmentName
)

function SB_NODE_GETTER_0 [28/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    double,
    GetTemperatureFactor
)

function SB_NODE_GETTER_0 [29/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    float,
    GetPartialCharge
)

function SB_NODE_GETTER_0 [30/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    int,
    GetFormalCharge
)

function SB_NODE_GETTER_0 [31/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetComment
)

function SB_NODE_GETTER_0 [32/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetCommentSize
)

function SB_NODE_GETTER_0 [33/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::vector< int >,
    GetAnisotropicTFactors
)

function SB_NODE_GETTER_0 [34/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetSYBYLType
)

function SB_NODE_GETTER_0 [35/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetSYBYLTypeSize
)

function SB_NODE_GETTER_0 [36/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetStatusBit
)

function SB_NODE_GETTER_0 [37/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetStatusBitSize
)

function SB_NODE_GETTER_0 [38/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetMoleculeName
)

function SB_NODE_GETTER_0 [39/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetNumberOfBondedAtoms
)

function SB_NODE_GETTER_0 [40/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetNumberOfBondedCarbons
)

function SB_NODE_GETTER_0 [41/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetNumberOfBondedHeavyAtoms
)

function SB_NODE_GETTER_0 [42/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetNumberOfBondedHydrogens
)

function SB_NODE_GETTER_0 [43/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetNumberOfBondedNitrogens
)

function SB_NODE_GETTER_0 [44/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetNumberOfBondedOxygens
)

function SB_NODE_GETTER_0 [45/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    unsigned int,
    GetNumberOfBondedSulfurs
)

function SB_NODE_GETTER_0 [46/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetSubstructureName
)

function SB_NODE_GETTER_0 [47/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    int,
    GetSubstructureSequenceNumber
)

function SB_NODE_GETTER_0 [48/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    int,
    GetChainID
)

function SB_NODE_GETTER_0 [49/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    Hybridization,
    GetHybridization
)

function SB_NODE_GETTER_0 [50/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    Geometry,
    GetGeometry
)

function SB_NODE_GETTER_0 [51/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    int,
    GetOxidationState
)

function SB_NODE_GETTER_0 [52/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    bool,
    GetResonance
)

function SB_NODE_GETTER_0 [53/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    bool,
    GetAromaticity
)

function SB_NODE_GETTER_0 [54/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    bool,
    GetWaterFlag
)

function SB_NODE_GETTER_0 [55/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    int,
    GetCustomType
)

function SB_NODE_GETTER_0 [56/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    std::string,
    GetCoarseGrainedType
)

function SB_NODE_GETTER_0 [57/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::length,
    GetCoarseGrainedRadius
)

function SB_NODE_GETTER_0 [58/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBQuantity::mass,
    GetCoarseGrainedMass
)

function SB_NODE_GETTER_0 [59/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    SBColor,
    GetCoarseGrainedColor
)

function SB_NODE_GETTER_0 [60/60]#

SBMStructuralModelNodeAtom::SB_NODE_GETTER_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    bool,
    GetFixedFlag
)

function SB_NODE_PREDICATE_0 [1/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasName
)

function SB_NODE_PREDICATE_0 [2/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasAltLocation
)

function SB_NODE_PREDICATE_0 [3/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasInsertionCode
)

function SB_NODE_PREDICATE_0 [4/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasSerialNumber
)

function SB_NODE_PREDICATE_0 [5/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasOccupancy
)

function SB_NODE_PREDICATE_0 [6/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasRecordType
)

function SB_NODE_PREDICATE_0 [7/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasResidueSequenceNumber
)

function SB_NODE_PREDICATE_0 [8/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasTemperatureFactor
)

function SB_NODE_PREDICATE_0 [9/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasPartialCharge
)

function SB_NODE_PREDICATE_0 [10/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasFormalCharge
)

function SB_NODE_PREDICATE_0 [11/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasComment
)

function SB_NODE_PREDICATE_0 [12/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasAnisotropicTFactors
)

function SB_NODE_PREDICATE_0 [13/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasSYBYLType
)

function SB_NODE_PREDICATE_0 [14/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasStatusBit
)

function SB_NODE_PREDICATE_0 [15/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasSubstructureSequenceNumber
)

function SB_NODE_PREDICATE_0 [16/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasChainID
)

function SB_NODE_PREDICATE_0 [17/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasHybridization
)

function SB_NODE_PREDICATE_0 [18/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasGeometry
)

function SB_NODE_PREDICATE_0 [19/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasOxidationState
)

function SB_NODE_PREDICATE_0 [20/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasResonance
)

function SB_NODE_PREDICATE_0 [21/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasAromaticity
)

function SB_NODE_PREDICATE_0 [22/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasWaterFlag
)

function SB_NODE_PREDICATE_0 [23/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasCustomType
)

function SB_NODE_PREDICATE_0 [24/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInMolecule
)

function SB_NODE_PREDICATE_0 [25/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInChain
)

function SB_NODE_PREDICATE_0 [26/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInSegment
)

function SB_NODE_PREDICATE_0 [27/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInResidue
)

function SB_NODE_PREDICATE_0 [28/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInAminoAcid
)

function SB_NODE_PREDICATE_0 [29/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInNucleicAcid
)

function SB_NODE_PREDICATE_0 [30/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInBackbone
)

function SB_NODE_PREDICATE_0 [31/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInSideChain
)

function SB_NODE_PREDICATE_0 [32/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsInSubstructure
)

function SB_NODE_PREDICATE_0 [33/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsPlanar
)

function SB_NODE_PREDICATE_0 [34/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsCarbon
)

function SB_NODE_PREDICATE_0 [35/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsHydrogen
)

function SB_NODE_PREDICATE_0 [36/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsNitrogen
)

function SB_NODE_PREDICATE_0 [37/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsOxygen
)

function SB_NODE_PREDICATE_0 [38/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsSulfur
)

function SB_NODE_PREDICATE_0 [39/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsUnknown
)

function SB_NODE_PREDICATE_0 [40/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsFromAminoAcidBackbone
)

function SB_NODE_PREDICATE_0 [41/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsFromNucleicAcidBackbone
)

function SB_NODE_PREDICATE_0 [42/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasAminoAcidBackboneAtomName
)

function SB_NODE_PREDICATE_0 [43/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    HasNucleicAcidBackboneAtomName
)

function SB_NODE_PREDICATE_0 [44/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsMetal
)

function SB_NODE_PREDICATE_0 [45/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsAlkaliMetal
)

function SB_NODE_PREDICATE_0 [46/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsAlkalineEarthMetal
)

function SB_NODE_PREDICATE_0 [47/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsLanthanide
)

function SB_NODE_PREDICATE_0 [48/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsActinide
)

function SB_NODE_PREDICATE_0 [49/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsTransitionMetal
)

function SB_NODE_PREDICATE_0 [50/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsPostTransitionMetal
)

function SB_NODE_PREDICATE_0 [51/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsMetalloid
)

function SB_NODE_PREDICATE_0 [52/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsNobleGas
)

function SB_NODE_PREDICATE_0 [53/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsReactiveNonmetal
)

function SB_NODE_PREDICATE_0 [54/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsDiatomicNonmetal
)

function SB_NODE_PREDICATE_0 [55/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsPolyatomicNonmetal
)

function SB_NODE_PREDICATE_0 [56/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsHalogen
)

function SB_NODE_PREDICATE_0 [57/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsCoarseGrained
)

function SB_NODE_PREDICATE_0 [58/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsHydrogenBondAcceptor
)

function SB_NODE_PREDICATE_0 [59/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsHydrogenBondDonor
)

function SB_NODE_PREDICATE_0 [60/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsDonorBorneHydrogen
)

function SB_NODE_PREDICATE_0 [61/61]#

SBMStructuralModelNodeAtom::SB_NODE_PREDICATE_0 (
    SB_SBMSTRUCTURALMODEL_EXPORT,
    IsAttachedToHydrogenBondDonor
)

function addHydrogens#

Adds hydrogens and returns the number of added hydrogens.

unsigned int SBMStructuralModelNodeAtom::addHydrogens ()

Adds hydrogen atoms to satisfy the expected valence of this atom.

The number of expected hydrogens is the expected valence (see getExpectedValence) minus the current number of bonds (see getCurrentValence). The added hydrogen atoms and the corresponding bonds become children of the atom's parent, if the atom has a parent. If the atom has an alternate location, occupancy, or insertion code, those fields are copied to the newly added hydrogens.

Returns:

The number of hydrogen atoms added.

function clearAltLocation#

Clears the atom's alternate location.

void SBMStructuralModelNodeAtom::clearAltLocation ()

function clearAnisotropicTFactors#

Clears the atom's anisotropic temperature factors.

void SBMStructuralModelNodeAtom::clearAnisotropicTFactors ()

function clearAromaticity#

Clears the atom's aromaticity.

void SBMStructuralModelNodeAtom::clearAromaticity ()

function clearComment#

Clears the atom's comment.

void SBMStructuralModelNodeAtom::clearComment ()

function clearCustomType#

Clears the atom's custom type.

void SBMStructuralModelNodeAtom::clearCustomType ()

function clearFormalCharge#

Clears the atom's formal charge.

void SBMStructuralModelNodeAtom::clearFormalCharge ()

function clearGeometry#

Clears the atom's geometry.

void SBMStructuralModelNodeAtom::clearGeometry ()

function clearHybridization#

Clears the atom's hybridization.

void SBMStructuralModelNodeAtom::clearHybridization ()

function clearInsertionCode#

Clears the atom's insertion code.

void SBMStructuralModelNodeAtom::clearInsertionCode ()

function clearName#

Clears the atom's full name.

void SBMStructuralModelNodeAtom::clearName ()

function clearOccupancy#

Clears the atom's occupancy.

void SBMStructuralModelNodeAtom::clearOccupancy ()

function clearOxidationState#

Clears the atom's oxidation state.

void SBMStructuralModelNodeAtom::clearOxidationState ()

function clearPartialCharge#

Clears the atom's partial charge.

void SBMStructuralModelNodeAtom::clearPartialCharge ()

function clearRecordType#

Clears the atom's record type.

void SBMStructuralModelNodeAtom::clearRecordType ()

function clearResonance#

Clears the atom's resonance.

void SBMStructuralModelNodeAtom::clearResonance ()

function clearSYBYLType#

Clears the SYBYL atom's type.

void SBMStructuralModelNodeAtom::clearSYBYLType ()

function clearSerialNumber#

Clears the atom's serial number.

void SBMStructuralModelNodeAtom::clearSerialNumber ()

function clearStatusBit#

Clears the atom's status bit.

void SBMStructuralModelNodeAtom::clearStatusBit ()

function clearTemperatureFactor#

Clears the atom's temperature factor.

void SBMStructuralModelNodeAtom::clearTemperatureFactor ()

function clearWaterFlag#

Clears the atom's water flag.

void SBMStructuralModelNodeAtom::clearWaterFlag ()

function clone#

Returns a copy of the node and its descendants.

virtual SBMStructuralModelNodeAtom * SBMStructuralModelNodeAtom::clone () override

Creates a deep copy of this atom node and its descendants.

The method returns a new atom object that is a clone of the current instance.

Returns:

A pointer to the cloned SBMStructuralModelNodeAtom.

Implements SBMStructuralModelNode::clone

function getAltLocation#

Returns the atom's alternate location.

char const & SBMStructuralModelNodeAtom::getAltLocation () const

function getAnisotropicTFactors#

Returns the atom's anisotropic temperature factors.

std::vector< int > const & SBMStructuralModelNodeAtom::getAnisotropicTFactors () const

function getAromaticity#

Returns the atom's aromaticity (true if aromatic, false else)

bool const & SBMStructuralModelNodeAtom::getAromaticity () const

function getAtomicWeight#

Returns the atom's element atomic weight (regular or coarse grained)

SBQuantity::mass SBMStructuralModelNodeAtom::getAtomicWeight () const

Returns the atomic weight of the atom.

If the atom is coarse-grained then returns its coarse-grained mass.

Returns:

The atomic weight as an SBQuantity::mass.

function getBackbone#

Returns a pointer to the backbone.

SBMStructuralModelNodeBackbone * SBMStructuralModelNodeAtom::getBackbone () const

SBMStructuralModelNodeAtom::getBackbone.

Returns:

If the atom is in a backbone it returns the backbone pointer, else NULL.

function getBlock#

Returns the atom's element block.

std::string SBMStructuralModelNodeAtom::getBlock () const

Returns the block of the element.

Returns:

The block as a std::string.

function getBondList#

Returns the bond list.

SBPointerList< SBBond > const * SBMStructuralModelNodeAtom::getBondList () const

Returns a pointer to the list of bonds associated with the atom.

Returns:

Pointer to a constant SBPointerList of SBBond objects, or nullptr if none.

function getBondTo#

Returns the bond to an atom (0 if no bond)

SBBond * SBMStructuralModelNodeAtom::getBondTo (
    const SBMStructuralModelNodeAtom * atom
) const

Returns the bond connecting this atom to the specified atom, if such a bond exists.

Parameters:

atom Pointer to the other atom.

Returns:

Pointer to the SBBond object connecting the two atoms, or nullptr if no bond exists.

function getBondedAtoms [1/2]#

Gets all bonded atoms.

void SBMStructuralModelNodeAtom::getBondedAtoms (
    SBNodeIndexer & nodeIndexer
) const

Populates the provided node indexer with all atoms bonded to this atom.

Parameters:

nodeIndexer Reference to an SBNodeIndexer that will receive the bonded atoms.

function getBondedAtoms [2/2]#

Gets all bonded atoms of type element .

void SBMStructuralModelNodeAtom::getBondedAtoms (
    SBNodeIndexer & nodeIndexer,
    const SBElement::Type element
) const

Populates the provided node indexer with bonded atoms of a specific element type.

Parameters:

nodeIndexer Reference to an SBNodeIndexer that will receive the bonded atoms.
element The element type to filter bonded atoms.

function getBondedHeavyAtoms#

Gets all bonded heavy atoms (non-Hydrogens)

void SBMStructuralModelNodeAtom::getBondedHeavyAtoms (
    SBNodeIndexer & nodeIndexer
) const

Populates the provided node indexer with all heavy (non-hydrogen) atoms bonded to this atom.

Parameters:

nodeIndexer Reference to an SBNodeIndexer that will receive the bonded heavy atoms.

function getChain#

Returns a pointer to the chain.

SBMStructuralModelNodeChain * SBMStructuralModelNodeAtom::getChain () const

function getChainID#

Returns the atom's chain ID.

int SBMStructuralModelNodeAtom::getChainID () const

SBMStructuralModelNodeAtom::getChainID.

Returns:

If the atom is in a chain and this chain has an id (a structural id) it returns the chain's id, else it returns -1.

See also: hasChainID

function getChainIDString#

Returns the atom's chain ID string.

std::string SBMStructuralModelNodeAtom::getChainIDString () const

SBMStructuralModelNodeAtom::getChainIDString.

Returns:

If the atom is in a chain and this chain has an id (a structural id) it returns the chain's id as a string, else it returns "Undefined".

See also: hasChainID, getChainID

function getChainName#

Returns the atom's chain name.

std::string SBMStructuralModelNodeAtom::getChainName () const

function getCoarseGrainedColor#

Returns the coarse-grained atom's color.

SBColor const & SBMStructuralModelNodeAtom::getCoarseGrainedColor () const

Retrieves the coarse-grained color of the atom.

Returns:

A constant reference to the atom's coarse-grained color.

function getCoarseGrainedMass#

Returns the coarse-grained atom's mass.

SBQuantity::mass const & SBMStructuralModelNodeAtom::getCoarseGrainedMass () const

Retrieves the coarse-grained mass of the atom.

Returns:

A constant reference to the atom's coarse-grained mass.

function getCoarseGrainedRadius#

Returns the coarse-grained atom's radius.

SBQuantity::length const & SBMStructuralModelNodeAtom::getCoarseGrainedRadius () const

Returns the coarse-grained radius of the atom.

Returns:

The coarse-grained radius as an SBQuantity::length reference.

function getCoarseGrainedType#

Returns the coarse-grained atom's type.

std::string const & SBMStructuralModelNodeAtom::getCoarseGrainedType () const

Returns the coarse-grained type string of the atom.

Returns:

The coarse-grained type as a const reference to std::string.

function getColor#

Returns the atom's element color pointer (CPK or coarse grained)

const float * SBMStructuralModelNodeAtom::getColor () const

Returns a pointer to the color data of the atom.

Returns:

Pointer to the color data (RGB), or a default color if unavailable.

function getComment#

Returns the atom's comment.

char *const & SBMStructuralModelNodeAtom::getComment () const

function getCommentSize#

Returns the atom's comment size.

unsigned int SBMStructuralModelNodeAtom::getCommentSize () const

function getConnectedComponent [1/2]#

Gets all atoms in the connected component containing the atom.

void SBMStructuralModelNodeAtom::getConnectedComponent (
    SBNodeIndexer & nodeIndexer
) const

Adds all atoms from the connected component containing this atom to the provided indexer.

The method traverses the entire set of atoms that are reachable via bonds from this atom and appends each atom to nodeIndexer.

Parameters:

nodeIndexer The indexer that will receive the atoms of the connected component.

function getConnectedComponent [2/2]#

Gets atoms in the connected component containing the atom and stops once maximumNumberOfAtoms is reached, returns whether the whole connected component has no more thanmaximumNumberOfAtoms atoms.

bool SBMStructuralModelNodeAtom::getConnectedComponent (
    SBNodeIndexer & nodeIndexer,
    unsigned int maximumNumberOfAtoms
) const

Adds atoms from the connected component containing this atom to the provided indexer, up to a limit.

The method traverses the connected component and appends each visited atom to nodeIndexer until either the entire component has been visited or maximumNumberOfAtoms atoms have been added.

Parameters:

nodeIndexer The indexer that will receive the atoms of the connected component.
maximumNumberOfAtoms The maximum number of atoms to traverse; traversal stops when this limit is reached.

Returns:

true if the entire connected component was traversed (i.e., the number of atoms does not exceed maximumNumberOfAtoms); otherwise false.

function getCovalentRadius#

Returns the atom's element covalent radius (regular or coarse grained)

SBQuantity::length SBMStructuralModelNodeAtom::getCovalentRadius () const

Returns the covalent radius of the atom.

If the atom is coarse-grained then returns its coarse-grained radius.

Returns:

The covalent radius as an SBQuantity::length.

function getCurrentValence#

Returns the current valence, i.e. the sum of the orders of the bonds connected to the atom, rounded to the closest integer.

SBQuantity::dimensionless SBMStructuralModelNodeAtom::getCurrentValence () const

Returns the current valence of the atom.

Returns:

The current valence as a dimensionless quantity.

function getCustomType#

Returns the atom's custom type.

int const & SBMStructuralModelNodeAtom::getCustomType () const

function getElectronegativity#

Returns the atom's element electronegativity.

SBQuantity::dimensionless SBMStructuralModelNodeAtom::getElectronegativity () const

Returns the electronegativity of the atom.

Returns:

The electronegativity as an SBQuantity::dimensionless.

function getElementName#

Returns the atom's element name.

virtual std::string SBMStructuralModelNodeAtom::getElementName () const

Returns the name of the chemical element of this atom.

Returns:

The element name as a string.

function getElementSymbol#

Returns the atom's element symbol.

virtual std::string SBMStructuralModelNodeAtom::getElementSymbol () const

Returns the element symbol of the atom.

Returns:

The element symbol as a std::string.

function getElementType#

Returns the atom's element type.

virtual SBElement::Type SBMStructuralModelNodeAtom::getElementType () const

Returns the chemical element type of this atom.

Returns:

The element type enumeration value.

function getExpectedValence#

Returns the expected valence of the atom based on its formal charge and its number of bonds (based on the MDL valence model)

SBQuantity::dimensionless SBMStructuralModelNodeAtom::getExpectedValence () const

Returns the expected valence of the atom according to the MDL valence model.

Returns:

The expected valence as a dimensionless quantity.

function getFixedFlag#

Returns the fixed flag.

bool SBMStructuralModelNodeAtom::getFixedFlag () const

Returns the fixed flag of the atom.

Returns:

true if the atom is fixed, false otherwise.

function getFlags#

Returns the flags.

virtual unsigned int SBMStructuralModelNodeAtom::getFlags () override const

Returns the flags of the atom.

Returns:

The current flags as an unsigned int.

Implements SBDDataGraphNode::getFlags

function getFormalCharge#

Returns the atom's formal charge.

int const & SBMStructuralModelNodeAtom::getFormalCharge () const

function getGeometry#

Returns the atom's geometry.

Geometry const & SBMStructuralModelNodeAtom::getGeometry () const

function getGeometryString [1/2]#

Returns the geometry as a string.

std::string SBMStructuralModelNodeAtom::getGeometryString () const

Returns a string describing the atom's geometry.

Returns:

The geometry as a human-readable string, or "Undefined" if not set.

function getGroup#

Returns the atom's element group.

unsigned int SBMStructuralModelNodeAtom::getGroup () const

Returns the group number of the element.

Returns:

The group number.

function getHierarchyString#

Returns a string with hierarchical information on the atom and its parents names.

virtual std::string SBMStructuralModelNodeAtom::getHierarchyString (
    const std::string & separator=" / ",
    bool includeNodeType=false
) override const

SBMStructuralModelNodeAtom::getHierarchyString This function returns a string with information on the atom's hierarchy.

If the atom has a name then this name is provided in the hierarchy information, else the atom's element symbol is used. If the atom has an alternate location then it is added after its name in square brackets. This information can be used for logging and debugging.

Parameters:

separator The string used to separate hierarchy levels.
includeNodeType If true, the node type is included in the hierarchy string.

Returns:

A string with information on the atom's hierarchy.

Implements SBDDataGraphNode::getHierarchyString

function getHybridization#

Returns the atom's hybridization.

Hybridization const & SBMStructuralModelNodeAtom::getHybridization () const

function getHybridizationString [1/2]#

Returns the hybridization as a string.

std::string SBMStructuralModelNodeAtom::getHybridizationString () const

Returns a string representation of the atom's hybridization.

Returns:

The hybridization as a human-readable string, or "Unknown" if not set.

function getHydrogens#

Gets all bonded hydrogens.

void SBMStructuralModelNodeAtom::getHydrogens (
    SBNodeIndexer & nodeIndexer
) const

Retrieves all hydrogen atoms bonded to this atom.

The method adds each bonded hydrogen atom to the provided nodeIndexer.

Parameters:

nodeIndexer The indexer to which bonded hydrogen atoms will be added.

function getInheritedFlags#

Returns the inherited flags.

virtual unsigned int SBMStructuralModelNodeAtom::getInheritedFlags () override const

Returns an unsigned int that contains the inherited flags of the node.

the first bit is true if the node is selected
the second bit is true if the node is highlighted
the third bit is true if the node is fixed

Returns:

the flags

See also: isSelected, isHighlighted

Implements SBDDataGraphNode::getInheritedFlags

function getInsertionCode#

Returns the atom's insertion code.

char const & SBMStructuralModelNodeAtom::getInsertionCode () const

function getMaximumBondLength#

Computes the maximum bond length for atom's bonds.

SBQuantity::length SBMStructuralModelNodeAtom::getMaximumBondLength () const

Computes the longest bond length among all bonds of this atom.

If the atom has at least one bond, the method returns the maximum bond length; otherwise it returns a length of zero.

Returns:

The maximum bond length, or zero if the atom has no bonds.

function getMetalSubcategory#

Returns the atom's subcategory type in the metal-metalloid-nonmetal trend.

SBElement::MetalSubcategory SBMStructuralModelNodeAtom::getMetalSubcategory () const

Returns the metal subcategory of the atom.

Returns:

The metal subcategory as SBElement::MetalSubcategory.

function getMetalSubcategoryString#

Returns the string representation of the atom's subcategory type in the metal-metalloid-nonmetal trend.

std::string SBMStructuralModelNodeAtom::getMetalSubcategoryString () const

Returns a string describing the metal subcategory.

Returns:

The subcategory description as a std::string.

function getMinimumBondLength#

Computes the minimum bond length for atom's bonds.

SBQuantity::length SBMStructuralModelNodeAtom::getMinimumBondLength () const

Computes the shortest bond length among all bonds of this atom.

If the atom has at least one bond, the method returns the minimum bond length; otherwise it returns a length of zero.

Returns:

The minimum bond length, or zero if the atom has no bonds.

function getMobilityFlag#

Returns the mobility flag. Please note that the following method has been marked as deprecated and will be removed in future versions of the software. We recommend that you update your code to use the recommended alternative method instead, which is getFixedFlag() __

bool SBMStructuralModelNodeAtom::getMobilityFlag () const

Returns the mobility flag of the atom.

Returns:

true if the atom is mobile, false otherwise.

function getMolecularWeight#

Returns the molecular weight.

virtual SBQuantity::mass SBMStructuralModelNodeAtom::getMolecularWeight () override

Returns the atomic weight of this atom.

Returns:

The atomic weight.

Implements SBDDataGraphNode::getMolecularWeight

function getMolecule#

Returns a pointer to the molecule.

SBMStructuralModelNodeMolecule * SBMStructuralModelNodeAtom::getMolecule () const

function getMoleculeName#

Returns the atom's molecule name.

std::string SBMStructuralModelNodeAtom::getMoleculeName () const

function getName#

Returns the atom's full name (e.g. CA for an alpha carbon)

virtual std::string const & SBMStructuralModelNodeAtom::getName () override const

Implements SBDDataGraphNode::getName

function getNewBondDirections#

Generates directions that numberOfBonds new neighboring bonds would have.

void SBMStructuralModelNodeAtom::getNewBondDirections (
    SBVector< SBVector3 > & bondDirectionVector,
    unsigned int numberOfBonds,
    bool includeExistingHydrogens=false
)

Generates directions for new bonds attached to this atom.

The method computes numberOfBonds new bond direction vectors and appends them to bondDirectionVector. Existing hydrogen bonds can be optionally excluded from the current bond list.

Parameters:

bondDirectionVector Vector that will receive the generated bond direction vectors.
numberOfBonds The number of new bond directions to generate.
includeExistingHydrogens If true, existing hydrogen bonds are considered when determining new directions; otherwise they are ignored.

function getNumberOfAtoms#

Returns the number of atoms.

virtual unsigned int SBMStructuralModelNodeAtom::getNumberOfAtoms () override

Returns the number of atoms represented by this node (always 1 for an atom node).

Returns:

The number of atoms.

Implements SBDDataGraphNode::getNumberOfAtoms

function getNumberOfBondedAtoms [1/2]#

Returns the number of bonded atoms with element type element .

unsigned int SBMStructuralModelNodeAtom::getNumberOfBondedAtoms (
    const SBElement::Type element
) const

Returns the number of bonded atoms of the specified element type.

Parameters:

element The element type to count.

Returns:

The number of bonded atoms of the given element.

function getNumberOfBondedAtoms [2/2]#

Returns the number of bonded atoms.

unsigned int SBMStructuralModelNodeAtom::getNumberOfBondedAtoms () const

Returns the total number of atoms bonded to this atom.

Returns:

The total count of bonded atoms.

function getNumberOfBondedCarbons#

Returns the number of bonded carbons.

unsigned int SBMStructuralModelNodeAtom::getNumberOfBondedCarbons () const

Returns the number of bonded carbon atoms.

Returns:

The number of bonded carbons.

function getNumberOfBondedHeavyAtoms#

Returns the number of bonded heavy atoms.

unsigned int SBMStructuralModelNodeAtom::getNumberOfBondedHeavyAtoms () const

Returns the number of bonded heavy atoms (non-hydrogen) attached to this atom.

Returns:

The count of bonded heavy atoms.

function getNumberOfBondedHydrogens#

Returns the number of bonded hydrogens.

unsigned int SBMStructuralModelNodeAtom::getNumberOfBondedHydrogens () const

Returns the number of bonded hydrogen atoms.

Returns:

The number of bonded hydrogens.

function getNumberOfBondedNitrogens#

Returns the number of bonded nitrogens.

unsigned int SBMStructuralModelNodeAtom::getNumberOfBondedNitrogens () const

Returns the number of bonded nitrogen atoms.

Returns:

The number of bonded nitrogens.

function getNumberOfBondedOxygens#

Returns the number of bonded oxygens.

unsigned int SBMStructuralModelNodeAtom::getNumberOfBondedOxygens () const

Returns the number of bonded oxygen atoms.

Returns:

The number of bonded oxygens.

function getNumberOfBondedSulfurs#

Returns the number of bonded sulfurs.

unsigned int SBMStructuralModelNodeAtom::getNumberOfBondedSulfurs () const

Returns the number of bonded sulfur atoms.

Returns:

The number of bonded sulfurs.

function getNumberOfBonds#

Returns the number of bonds without taking into account the bond order (NB: a double bond is considered as one bond)

unsigned int SBMStructuralModelNodeAtom::getNumberOfBonds () const

Returns the number of bonds associated with the atom.

Returns:

The number of bonds as an unsigned integer.

function getNumberOfCarbons#

Returns the number of carbons.

virtual unsigned int SBMStructuralModelNodeAtom::getNumberOfCarbons () override

Returns the number of carbon atoms associated with this node.

Returns:

Number of carbon atoms.

Implements SBDDataGraphNode::getNumberOfCarbons

function getNumberOfCoarseGrainedAtoms#

Returns the number of coarse-grained atoms.

virtual unsigned int SBMStructuralModelNodeAtom::getNumberOfCoarseGrainedAtoms () override

Returns the number of coarse-grained atoms associated with this node.

Returns:

Number of coarse-grained atoms.

Implements SBDDataGraphNode::getNumberOfCoarseGrainedAtoms

function getNumberOfHydrogens#

Returns the number of hydrogens.

virtual unsigned int SBMStructuralModelNodeAtom::getNumberOfHydrogens () override

Returns the number of hydrogen atoms associated with this node.

Returns:

Number of hydrogen atoms.

Implements SBDDataGraphNode::getNumberOfHydrogens

function getNumberOfNitrogens#

Returns the number of nitrogens.

virtual unsigned int SBMStructuralModelNodeAtom::getNumberOfNitrogens () override

Returns the number of nitrogen atoms associated with this node.

Returns:

Number of nitrogen atoms.

Implements SBDDataGraphNode::getNumberOfNitrogens

function getNumberOfOtherAtoms#

Returns the number of other atoms.

virtual unsigned int SBMStructuralModelNodeAtom::getNumberOfOtherAtoms () override

Returns the number of other (non-standard) atoms associated with this node.

Returns:

Number of other atoms.

Implements SBDDataGraphNode::getNumberOfOtherAtoms

function getNumberOfOxygens#

Returns the number of oxygens.

virtual unsigned int SBMStructuralModelNodeAtom::getNumberOfOxygens () override

Returns the number of oxygen atoms associated with this node.

Returns:

Number of oxygen atoms.

Implements SBDDataGraphNode::getNumberOfOxygens

function getNumberOfSulfurs#

Returns the number of sulfurs.

virtual unsigned int SBMStructuralModelNodeAtom::getNumberOfSulfurs () override

Returns the number of sulfur atoms associated with this node.

Returns:

Number of sulfur atoms.

Implements SBDDataGraphNode::getNumberOfSulfurs

function getOccupancy#

Returns the atom's occupancy.

SBQuantity::dimensionless const & SBMStructuralModelNodeAtom::getOccupancy () const

function getOxidationState#

Returns the atom's oxidation state.

int const & SBMStructuralModelNodeAtom::getOxidationState () const

function getPartialCharge#

Returns the atom's partial charge.

float const & SBMStructuralModelNodeAtom::getPartialCharge () const

function getPeriod#

Returns the atom's element period.

std::string SBMStructuralModelNodeAtom::getPeriod () const

Returns the period of the element.

Returns:

The period as a std::string.

function getPosition#

Returns the atom's position.

SBPosition3 const & SBMStructuralModelNodeAtom::getPosition () const

Retrieves the atom's 3D position.

Returns:

Constant reference to the atom's position vector.

function getRecordType#

Returns the atom's record type.

char *const & SBMStructuralModelNodeAtom::getRecordType () const

function getRecordTypeSize#

Returns the atom's record type size.

unsigned int SBMStructuralModelNodeAtom::getRecordTypeSize () const

function getResidue#

Returns a pointer to the residue.

SBMStructuralModelNodeResidue * SBMStructuralModelNodeAtom::getResidue () const

function getResidueName#

Returns the atom's residue name.

std::string SBMStructuralModelNodeAtom::getResidueName () const

function getResidueSequenceNumber#

Returns the atom's residue sequence number.

int SBMStructuralModelNodeAtom::getResidueSequenceNumber () const

SBMStructuralModelNodeAtom::getResidueSequenceNumber.

Returns:

If the atom is in a residue and this residue has a sequence number (a structural id) it returns the residue's sequence number, else it returns -1.

function getResidueSequenceNumberString#

Returns the atom's residue sequence number string.

std::string SBMStructuralModelNodeAtom::getResidueSequenceNumberString () const

SBMStructuralModelNodeAtom::getResidueSequenceNumberString.

Returns:

If the atom is in a residue and this residue has a sequence number (a structural id) it returns the residue's sequence number as a string, else it returns "Undefined".

function getResidueTypeString#

Returns the atom's residue type string.

std::string SBMStructuralModelNodeAtom::getResidueTypeString () const

SBMStructuralModelNodeAtom::getResidueTypeString.

Returns:

If the atom is in a residue it returns the residue's type as a string, else it returns "Undefined".

See also: isInResidue

function getResonance#

Returns the atom's resonance (true if resonant, false else)

bool const & SBMStructuralModelNodeAtom::getResonance () const

function getSYBYLType#

Returns the SYBYL atom's type.

char *const & SBMStructuralModelNodeAtom::getSYBYLType () const

function getSYBYLTypeSize#

Returns the SYBYL atom's type size.

unsigned int SBMStructuralModelNodeAtom::getSYBYLTypeSize () const

function getSegment#

Returns a pointer to the segment.

SBMStructuralModelNodeSegment * SBMStructuralModelNodeAtom::getSegment () const

function getSegmentName#

Returns the atom's segment name.

std::string SBMStructuralModelNodeAtom::getSegmentName () const

function getSerialNumber#

Returns the atom's serial number.

int const & SBMStructuralModelNodeAtom::getSerialNumber () const

function getSideChain#

Returns a pointer to the side chain.

SBMStructuralModelNodeSideChain * SBMStructuralModelNodeAtom::getSideChain () const

SBMStructuralModelNodeAtom::getSideChain.

Returns:

If the atom is in a side chain it returns the side chain pointer, else NULL.

function getStatusBit#

Returns the atom's status bit.

char *const & SBMStructuralModelNodeAtom::getStatusBit () const

function getStatusBitSize#

Returns the atom's status bit size.

unsigned int SBMStructuralModelNodeAtom::getStatusBitSize () const

function getSubstructure#

Returns a pointer to the substructure.

SBMStructuralModelNodeGroup * SBMStructuralModelNodeAtom::getSubstructure () const

SBMStructuralModelNodeAtom::getSubstructure.

Returns:

If the atom is in a structural group it returns the structural group pointer, else NULL.

See also: isInSubstructure, isInResidue

function getSubstructureName#

Returns the atom's substructure name.

std::string SBMStructuralModelNodeAtom::getSubstructureName () const

SBMStructuralModelNodeAtom::getSubstructureName.

Returns:

If the atom is in a substructure (a structural group) it returns the substructure's name, else an empty string.

function getSubstructureSequenceNumber#

Returns the atom's substructure sequence number.

int SBMStructuralModelNodeAtom::getSubstructureSequenceNumber () const

SBMStructuralModelNodeAtom::getSubstructureSequenceNumber.

Returns:

If the atom is in a substructure (a structural group) and this substructure has a sequence number (a structural id) it returns the substructure's sequence number, else it returns -1.

function getSubstructureSequenceNumberString#

Returns the atom's substructure sequence number string.

std::string SBMStructuralModelNodeAtom::getSubstructureSequenceNumberString () const

SBMStructuralModelNodeAtom::getSubstructureSequenceNumberString.

Returns:

If the atom is in a substructure (a structural group) and this substructure has a sequence number (a structural id) it returns the substructure's sequence number as a string, else it returns "Undefined".

function getSumOfFormalCharges#

Returns the sum of formal charges.

virtual int SBMStructuralModelNodeAtom::getSumOfFormalCharges () override

Returns the formal charge of this atom.

Returns:

The atom's formal charge.

Implements SBDDataGraphNode::getSumOfFormalCharges

function getSumOfPartialCharges#

Returns the sum of partial charges.

virtual float SBMStructuralModelNodeAtom::getSumOfPartialCharges () override

Returns the partial charge of this atom.

Returns:

The atom's partial charge.

Implements SBDDataGraphNode::getSumOfPartialCharges

function getTemperatureFactor#

Returns the atom's temperature factor.

double const & SBMStructuralModelNodeAtom::getTemperatureFactor () const

function getType#

Returns the node type (returns SBNode::Atom )

virtual SBDDataGraphNode::Type SBMStructuralModelNodeAtom::getType () override const

Returns the node type identifier for this atom.

Returns:

The type enum value representing a structural model atom node.

Implements SBMStructuralModelNode::getType

function getVanDerWaalsRadius#

Returns the atom's element van der Waals radius (regular or coarse grained)

SBQuantity::length SBMStructuralModelNodeAtom::getVanDerWaalsRadius () const

Returns the van der Waals radius of the atom.

If the atom is coarse-grained then returns its coarse-grained radius.

Returns:

The van der Waals radius as an SBQuantity::length.

function getWaterFlag#

Returns the atom's water flag (true if the atom is a water atom, false else)

bool const & SBMStructuralModelNodeAtom::getWaterFlag () const

function getX#

Returns the x coordinate.

SBQuantity::length const & SBMStructuralModelNodeAtom::getX () const

Returns the x coordinate of the atom.

Returns:

The x coordinate as a const reference to SBQuantity::length.

function getY#

Returns the y coordinate.

SBQuantity::length const & SBMStructuralModelNodeAtom::getY () const

Returns the y coordinate of the atom.

Returns:

The y coordinate as a const reference to SBQuantity::length.

function getZ#

Returns the z coordinate.

SBQuantity::length const & SBMStructuralModelNodeAtom::getZ () const

Returns the z coordinate of the atom.

Returns:

The z coordinate as a const reference to SBQuantity::length.

function hasAltLocation#

Returns true when the atom's alternate location is set.

bool SBMStructuralModelNodeAtom::hasAltLocation () const

function hasAminoAcidBackboneAtomName#

Returns true when the atom's name corresponds to one of the amino-acid backbone atoms.

bool SBMStructuralModelNodeAtom::hasAminoAcidBackboneAtomName () const

SBMStructuralModelNodeAtom::hasAminoAcidBackboneAtomName.

Returns:

true if the atom's name corresponds to one of the amino-acid backbone atoms.

See also: isFromAminoAcidBackbone

function hasAnisotropicTFactors#

Returns true when the atom's anisotropic temperature factors are set.

bool SBMStructuralModelNodeAtom::hasAnisotropicTFactors () const

function hasAromaticity#

Returns true when the atom's aromaticity is set.

bool SBMStructuralModelNodeAtom::hasAromaticity () const

function hasChainID#

Returns true when the atom's chain ID is set. The chain ID is used to separate chains with the same name but divided into 2, e.g. with TER record.

bool SBMStructuralModelNodeAtom::hasChainID () const

SBMStructuralModelNodeAtom::hasChainID.

Returns:

true if the atom is in a chain and this chain has an id (a structural id).

See also: getChainID

function hasComment#

Returns true when the atom's comment is set.

bool SBMStructuralModelNodeAtom::hasComment () const

function hasCustomType#

Returns true when the atom's custom type is set.

bool SBMStructuralModelNodeAtom::hasCustomType () const

function hasFormalCharge#

Returns true when the atom's formal charge is set.

bool SBMStructuralModelNodeAtom::hasFormalCharge () const

function hasGeometry#

Returns true when the atom's geometry is set.

bool SBMStructuralModelNodeAtom::hasGeometry () const

function hasHybridization#

Returns true when the atom's hybridization is set.

bool SBMStructuralModelNodeAtom::hasHybridization () const

function hasInsertionCode#

Returns true when the atom's insertion code is set.

bool SBMStructuralModelNodeAtom::hasInsertionCode () const

function hasName#

Returns true when the atom's name is set.

bool SBMStructuralModelNodeAtom::hasName () const

function hasNucleicAcidBackboneAtomName#

Returns true when the atom's name corresponds to one of the nucleic acid backbone atoms.

bool SBMStructuralModelNodeAtom::hasNucleicAcidBackboneAtomName () const

SBMStructuralModelNodeAtom::hasNucleicAcidBackboneAtomName.

Returns:

true if the atom's name corresponds to one of nucleic acid backbone atoms.

See also: isFromNucleicAcidBackbone

function hasOccupancy#

Returns true when the atom's occupancy is set.

bool SBMStructuralModelNodeAtom::hasOccupancy () const

function hasOxidationState#

Returns true when the atom's oxidation state is set.

bool SBMStructuralModelNodeAtom::hasOxidationState () const

function hasPartialCharge#

Returns true when the atom's partial charge is set.

bool SBMStructuralModelNodeAtom::hasPartialCharge () const

function hasRecordType#

Returns true when the atom's record type is set.

bool SBMStructuralModelNodeAtom::hasRecordType () const

function hasResidueSequenceNumber#

Returns true when the atom's residue sequence number is set.

bool SBMStructuralModelNodeAtom::hasResidueSequenceNumber () const

SBMStructuralModelNodeAtom::hasResidueSequenceNumber.

Returns:

true if the atom is in a residue and this residue has a sequence number (a structural id).

function hasResonance#

Returns true when the atom's resonance is set.

bool SBMStructuralModelNodeAtom::hasResonance () const

function hasSYBYLType#

Returns true when the SYBYL atom's type is set.

bool SBMStructuralModelNodeAtom::hasSYBYLType () const

function hasSerialNumber#

Returns true when the atom's serial number is set.

bool SBMStructuralModelNodeAtom::hasSerialNumber () const

function hasStatusBit#

Returns true when the atom's status bit is set.

bool SBMStructuralModelNodeAtom::hasStatusBit () const

function hasSubstructureSequenceNumber#

Returns true when the atom's substructure sequence number is set.

bool SBMStructuralModelNodeAtom::hasSubstructureSequenceNumber () const

SBMStructuralModelNodeAtom::hasSubstructureSequenceNumber.

Returns:

true if the atom is in a substructure (a structural group) and this substructure has a sequence number (a structural id).

function hasTemperatureFactor#

Returns true when the atom's temperature factor is set.

bool SBMStructuralModelNodeAtom::hasTemperatureFactor () const

function hasWaterFlag#

Returns true when the atom's water flag is set.

bool SBMStructuralModelNodeAtom::hasWaterFlag () const

function isActinide#

Returns true if the atom is actinide metal.

bool SBMStructuralModelNodeAtom::isActinide () const

Returns true if the atom is an actinide.

Returns:

true if the atom is an actinide, false otherwise.

function isAlkaliMetal#

Returns true if the atom is alkali metal.

bool SBMStructuralModelNodeAtom::isAlkaliMetal () const

Returns true if the atom is an alkali metal.

Returns:

true if the atom is an alkali metal, false otherwise.

function isAlkalineEarthMetal#

Returns true if the atom is alkaline earth metal.

bool SBMStructuralModelNodeAtom::isAlkalineEarthMetal () const

Returns true if the atom is an alkaline earth metal.

Returns:

true if the atom is an alkaline earth metal, false otherwise.

function isAttachedToHydrogenBondDonor#

Returns true if the atom is connected to an H-Bond donor.

bool SBMStructuralModelNodeAtom::isAttachedToHydrogenBondDonor () const

SBMStructuralModelNodeAtom::isAttachedToHydrogenBondDonor This function checks whether the atom is attached to a hydrogen bond donor.

Returns:

true if the atom is attached to a hydrogen bond donor.

function isCarbon#

Returns true when the atom is a carbon atom.

bool SBMStructuralModelNodeAtom::isCarbon () const

Returns true if the atom's element is carbon.

Returns:

true if the atom is a carbon atom, false otherwise.

function isCarboxylOxygen#

Returns true for an Oxygen atom in a carboxyl group (C(=O)OH)

bool SBMStructuralModelNodeAtom::isCarboxylOxygen () const

SBMStructuralModelNodeAtom::isCarboxylOxygen Checks if the atom is an Oxygen atom in a carboxyl group (C(=O)OH): an Oxygen atom connected to a Carbon atom in a carboxyl group.

HO-C(=O)-R

Returns:

true if the atom is an Oxygen in a carboxyl group

function isCoarseGrained#

Returns true if the atom is coarse grained.

bool SBMStructuralModelNodeAtom::isCoarseGrained () const

Returns true if the atom is coarse-grained.

Returns:

true if the atom is coarse-grained, false otherwise.

function isDiatomicNonmetal#

Returns true if the atom is diatomic nonmetal.

bool SBMStructuralModelNodeAtom::isDiatomicNonmetal () const

Returns true if the atom is a diatomic non-metal.

Returns:

true if the atom is a diatomic non-metal, false otherwise.

function isDonorBorneHydrogen#

Returns true if the atom is a hydrogen connected to an H-Bond donor.

bool SBMStructuralModelNodeAtom::isDonorBorneHydrogen () const

SBMStructuralModelNodeAtom::isDonorBorneHydrogen This function checks whether the atom is a hydrogen atom attached to a hydrogen bond donor.

Returns:

true if the atom is a hydrogen attached to a hydrogen bond donor.

function isFixed#

Returns whether the node is fixed (opposite of mobile)

bool SBMStructuralModelNodeAtom::isFixed () const

Returns whether the atom is fixed.

Returns:

true if the atom is fixed, false otherwise.

See also: getMobilityFlag

function isFromAminoAcidBackbone#

Returns true when the atom is from an amino-acid backbone.

bool SBMStructuralModelNodeAtom::isFromAminoAcidBackbone () const

SBMStructuralModelNodeAtom::isFromAminoAcidBackbone.

Returns:

true if the atom is from an amino-acid backbone: the atom is in a backbone and its name corresponds to one of the amino-acid backbone atoms.

See also: hasAminoAcidBackboneAtomName

function isFromNucleicAcidBackbone#

Returns true when the atom is from a nucleic acid backbone.

bool SBMStructuralModelNodeAtom::isFromNucleicAcidBackbone () const

SBMStructuralModelNodeAtom::isFromNucleicAcidBackbone.

Returns:

true if the atom is from a nucleic acid backbone: the atom is in a backbone and its name corresponds to one of the nucleic acid backbone atoms.

function isHalogen#

Returns true if the atom is halogen.

bool SBMStructuralModelNodeAtom::isHalogen () const

Returns true if the atom is a halogen.

Returns:

true if the atom is a halogen, false otherwise.

function isHydrogen#

Returns true when the atom is a hydrogen atom.

bool SBMStructuralModelNodeAtom::isHydrogen () const

Returns true if the atom's element is hydrogen.

Returns:

true if the atom is a hydrogen atom, false otherwise.

function isHydrogenBondAcceptor#

Returns true if the atom is an H-Bond acceptor (N, O, S, F)

bool SBMStructuralModelNodeAtom::isHydrogenBondAcceptor () const

SBMStructuralModelNodeAtom::isHydrogenBondAcceptor This function checks whether the atom is a hydrogen bond acceptor.

Only the following atom types are considered to as possible acceptors: N, O, S, F

Returns:

true if the atom is a hydrogen bond acceptor.

function isHydrogenBondDonor#

Returns true if the atom is an H-Bond donor (N, O, S, F)

bool SBMStructuralModelNodeAtom::isHydrogenBondDonor () const

SBMStructuralModelNodeAtom::isHydrogenBondDonor This function checks whether the atom is a hydrogen bond donor: an electronegative atom (N, O, S, F) that has at least one hydrogen covalently bound to it.

Returns:

true if the atom is a hydrogen bond donor.

function isInAminoAcid#

Returns true when the atom is in an amino acid residue.

bool SBMStructuralModelNodeAtom::isInAminoAcid () const

SBMStructuralModelNodeAtom::isInAminoAcid This function checks whether the atom is in a residue which type corresponds to an amino acid.

Returns:

true if the atom is in an amino acid residue.

See also: isInResidue, isInNucleicAcid

function isInBackbone#

Returns true when the atom is in a backbone.

bool SBMStructuralModelNodeAtom::isInBackbone () const

SBMStructuralModelNodeAtom::isInBackbone This function checks whether the atom is in a backbone.

Returns:

true if the atom is in a backbone.

function isInChain#

Returns true when the atom is in a chain.

bool SBMStructuralModelNodeAtom::isInChain () const

function isInMolecule#

Returns true when the atom is in a molecule.

bool SBMStructuralModelNodeAtom::isInMolecule () const

function isInNucleicAcid#

Returns true when the atom is in a nucleic acid residue.

bool SBMStructuralModelNodeAtom::isInNucleicAcid () const

SBMStructuralModelNodeAtom::isInNucleicAcid This function checks whether the atom is in a residue which type corresponds to a nucleic acid.

Returns:

true if the atom is in a nucleic acid residue.

See also: isInResidue, isInAminoAcid

function isInResidue#

Returns true when the atom is in a residue.

bool SBMStructuralModelNodeAtom::isInResidue () const

function isInSegment#

Returns true when the atom is in a segment.

bool SBMStructuralModelNodeAtom::isInSegment () const

function isInSideChain#

Returns true when the atom is in a side chain.

bool SBMStructuralModelNodeAtom::isInSideChain () const

SBMStructuralModelNodeAtom::isInSideChain This function checks whether the atom is in a side chain.

Returns:

true if the atom is in a side chain.

function isInSubstructure#

Returns true when the atom is in a substructure.

bool SBMStructuralModelNodeAtom::isInSubstructure () const

SBMStructuralModelNodeAtom::isInSubstructure This function checks whether the atom is in a substructure (a structural group).

Returns:

true if the atom is in a structural group.

See also: getSubstructure, isInResidue

function isLanthanide#

Returns true if the atom is lanthanide metal.

bool SBMStructuralModelNodeAtom::isLanthanide () const

Returns true if the atom is a lanthanide.

Returns:

true if the atom is a lanthanide, false otherwise.

function isMetal#

Returns true if the atom is metal.

bool SBMStructuralModelNodeAtom::isMetal () const

Returns true if the atom is a metal.

Returns:

true if the atom is a metal, false otherwise.

function isMetalloid#

Returns true if the atom is metalloid.

bool SBMStructuralModelNodeAtom::isMetalloid () const

Returns true if the atom is a metalloid.

Returns:

true if the atom is a metalloid, false otherwise.

function isMobile#

Returns whether the node is mobile. Please note that the following method has been marked as deprecated and will be removed in future versions of the software. We recommend that you update your code to use the recommended alternative method instead, which is isFixed() __

bool SBMStructuralModelNodeAtom::isMobile () const

Returns whether the atom is mobile.

Returns:

true if the atom is mobile, false otherwise.

function isNitroOxygen#

Returns true for an Oxygen atom in a nitro group (-NO2)

bool SBMStructuralModelNodeAtom::isNitroOxygen () const

SBMStructuralModelNodeAtom::isNitroOxygen Check if the atom is an Oxygen atom in a nitro (-NO2) group:

HO-N(OH)-R

Returns:

true if the atom is an Oxygen in a nitro group

function isNitrogen#

Returns true when the atom is a nitrogen atom.

bool SBMStructuralModelNodeAtom::isNitrogen () const

Returns true if the atom's element is nitrogen.

Returns:

true if the atom is a nitrogen atom, false otherwise.

function isNobleGas#

Returns true if the atom is noble gas.

bool SBMStructuralModelNodeAtom::isNobleGas () const

Returns true if the atom is a noble gas.

Returns:

true if the atom is a noble gas, false otherwise.

function isOxygen#

Returns true when the atom is an oxygen atom.

bool SBMStructuralModelNodeAtom::isOxygen () const

Returns true if the atom's element is oxygen.

Returns:

true if the atom is an oxygen atom, false otherwise.

function isPlanar#

Returns true if the atom with atoms bonded to it are in the same plane.

bool SBMStructuralModelNodeAtom::isPlanar () const

Determines whether the atom and its bonded atoms lie in a single plane.

Returns:

true if the atom and its bonded atoms are planar; otherwise false.

function isPolyatomicNonmetal#

Returns true if the atom is polyatomic nonmetal.

bool SBMStructuralModelNodeAtom::isPolyatomicNonmetal () const

Returns true if the atom is a polyatomic non-metal.

Returns:

true if the atom is a polyatomic non-metal, false otherwise.

function isPostTransitionMetal#

Returns true if the atom is post-transition metal.

bool SBMStructuralModelNodeAtom::isPostTransitionMetal () const

Returns true if the atom is a post-transition metal.

Returns:

true if the atom is a post-transition metal, false otherwise.

function isReactiveNonmetal#

Returns true if the atom is reactive nonmetal.

bool SBMStructuralModelNodeAtom::isReactiveNonmetal () const

Returns true if the atom is a reactive non-metal.

Returns:

true if the atom is a reactive non-metal, false otherwise.

function isSerializable#

Returns true __

virtual bool SBMStructuralModelNodeAtom::isSerializable () override const

Indicates whether the atom node can be serialized.

Always returns true for atom nodes.

Returns:

true.

Implements SBMStructuralModelNode::isSerializable

function isSulfoneOxygen#

Returns true for an Oxygen atom in a sulfone (R1-SO2-R2)

bool SBMStructuralModelNodeAtom::isSulfoneOxygen () const

SBMStructuralModelNodeAtom::isSulfoneOxygen Check if the atom is an Oxygen atom in a sulfone (R1-SO2-R2).

Returns:

true if the atom is an Oxygen in a sulfone

function isSulfur#

Returns true when the atom is a sulfur atom.

bool SBMStructuralModelNodeAtom::isSulfur () const

Returns true if the atom's element is sulfur.

Returns:

true if the atom is a sulfur atom, false otherwise.

function isThiocarboxylOxygen#

Returns true for an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH)

bool SBMStructuralModelNodeAtom::isThiocarboxylOxygen () const

SBMStructuralModelNodeAtom::isThiocarboxylOxygen Checks if the atom is an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH): an Oxygen atom connected to a Carbon atom in a thiocarboxyl group.

Returns:

true if the atom is an Oxygen in a thiocarboxyl group

function isTransitionMetal#

Returns true if the atom is transition metal.

bool SBMStructuralModelNodeAtom::isTransitionMetal () const

Returns true if the atom is a transition metal.

Returns:

true if the atom is a transition metal, false otherwise.

function isUnknown#

Returns true when the atom is an unknown atom.

bool SBMStructuralModelNodeAtom::isUnknown () const

Returns true if the atom's element is unknown.

Returns:

true if the atom type is unknown, false otherwise.

function perceiveHybridization#

Perceives, sets and returns the atom's hybridization.

Hybridization SBMStructuralModelNodeAtom::perceiveHybridization ()

Determines the atom's hybridization based on its bonding pattern and updates it.

Returns:

The perceived hybridization type.

function print#

Prints debugging information.

virtual void SBMStructuralModelNodeAtom::print (
    unsigned int offset=0
) override const

Prints debugging information for the atom to standard output.

Parameters:

offset Number of tab characters to prepend to each printed line.

Implements SBMStructuralModelNode::print

function removeHydrogens#

Removes the hydrogens bonded to the atom and returns the number of removed hydrogens.

unsigned int SBMStructuralModelNodeAtom::removeHydrogens ()

Removes all hydrogen atoms bonded to this atom.

The method erases each bonded hydrogen atom and its associated bond from the model.

Returns:

The number of hydrogen atoms removed.

function serialize#

Serializes the atom.

virtual void SBMStructuralModelNodeAtom::serialize (
    SBCSerializer * serializer,
    const SBNodeIndexer & nodeIndexer,
    const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER,
    const SBVersionNumber & classVersionNumber=SBVersionNumber (1, 0, 0)
) override const

Serializes the atom node to a serializer.

Writes the atom's data, including position, element type, and optional properties, to the provided serializer.

Parameters:

serializer The serializer used to write the atom's data.
nodeIndexer Indexer used to map node references during serialization.
sdkVersionNumber The SDK version number for compatibility handling (default: SB_SDK_VERSION_NUMBER).
classVersionNumber The class version number for compatibility handling (default: SBVersionNumber(1, 0, 0)).

Implements SBMStructuralModelNode::serialize

function setAltLocation#

Sets the atom's alternate location.

void SBMStructuralModelNodeAtom::setAltLocation (
    const char & altLocation
)

function setAnisotropicTFactors#

Sets the atom's anisotropic temperature factors.

void SBMStructuralModelNodeAtom::setAnisotropicTFactors (
    const std::vector< int > & ATF
)

function setAromaticity#

Sets the atom's aromaticity.

void SBMStructuralModelNodeAtom::setAromaticity (
    const bool & aromaticity
)

function setCoarseGrainedColor#

Sets the coarse-grained atom's color.

void SBMStructuralModelNodeAtom::setCoarseGrainedColor (
    const SBColor & coarseGrainedColor
)

Sets the coarse-grained color of the atom.

Parameters:

coarseGrainedColor The new color to assign to the atom.

function setCoarseGrainedMass#

Sets the coarse-grained atom's mass.

void SBMStructuralModelNodeAtom::setCoarseGrainedMass (
    const SBQuantity::mass & coarseGrainedMass
)

Sets the coarse-grained mass of the atom.

Parameters:

coarseGrainedMass The new mass to assign to the atom.

function setCoarseGrainedRadius#

Sets the coarse-grained atom's radius.

void SBMStructuralModelNodeAtom::setCoarseGrainedRadius (
    const SBQuantity::length & coarseGrainedRadius
)

Sets the coarse-grained radius of the atom.

Parameters:

coarseGrainedRadius The new radius to assign to the atom.

function setCoarseGrainedType#

Sets the coarse-grained atom's type.

void SBMStructuralModelNodeAtom::setCoarseGrainedType (
    const std::string & coarseGrainedType
)

Sets the coarse-grained type of the atom.

Parameters:

coarseGrainedType The new coarse-grained type string.

function setComment#

Sets the atom's comment.

void SBMStructuralModelNodeAtom::setComment (
    char *const & comment,
    int const & size
)

function setCustomType#

Sets the atom's custom type.

void SBMStructuralModelNodeAtom::setCustomType (
    const int & water
)

function setElementType#

Sets the atom's element type.

virtual void SBMStructuralModelNodeAtom::setElementType (
    SBElement::Type e
)

Sets the element type of the atom.

Parameters:

e The element type to assign to the atom.

function setFixedFlag [1/2]#

Sets the fixed flag to flag .

void SBMStructuralModelNodeAtom::setFixedFlag (
    bool flag
)

Sets the fixed flag of the atom.

Parameters:

flag The new fixed flag value.

function setFixedFlag [2/2]#

Sets the fixed flag to flag .

void SBMStructuralModelNodeAtom::setFixedFlag (
    bool newflag,
    bool oldFlag
)

Sets the fixed flag of the atom with undo support.

Parameters:

newFlag The new fixed flag value.
oldFlag The previous fixed flag value.

function setFormalCharge#

Sets the atom's formal charge.

void SBMStructuralModelNodeAtom::setFormalCharge (
    const int & formalCharge
)

function setGeometry#

Sets the atom's geometry.

void SBMStructuralModelNodeAtom::setGeometry (
    const Geometry & geometry
)

function setHybridization#

Sets the atom's hybridization.

void SBMStructuralModelNodeAtom::setHybridization (
    const Hybridization & hybridization
)

function setInsertionCode#

Sets the atom's insertion code.

void SBMStructuralModelNodeAtom::setInsertionCode (
    const char & insertionCode
)

function setMobilityFlag#

Sets the mobility flag to flag . Please note that the following method has been marked as deprecated and will be removed in future versions of the software. We recommend that you update your code to use the recommended alternative method instead, which issetFixedFlag(bool flag) __

void SBMStructuralModelNodeAtom::setMobilityFlag (
    bool flag
)

Sets the mobility flag of the atom.

Parameters:

flag The new mobility flag value (true for mobile, false for fixed).

function setName#

Sets the atom's full name.

virtual void SBMStructuralModelNodeAtom::setName (
    const std::string & name
) override

Implements SBDDataGraphNode::setName

function setOccupancy#

Sets the atom's occupancy.

void SBMStructuralModelNodeAtom::setOccupancy (
    const SBQuantity::dimensionless & occupancy
)

function setOxidationState#

Sets the atom's oxidation state.

void SBMStructuralModelNodeAtom::setOxidationState (
    const int & oxidationState
)

function setPartialCharge#

Sets the atom's partial charge.

void SBMStructuralModelNodeAtom::setPartialCharge (
    const float & partialCharge
)

function setPosition [1/6]#

Sets the atom's position if the atom is not fixed.

void SBMStructuralModelNodeAtom::setPosition (
    SBPosition3 const & newPosition
)

Sets the atom's position to a new location.

Parameters:

newPosition The new 3D position for the atom.

function setPosition [2/6]#

Sets the atom's position.

void SBMStructuralModelNodeAtom::setPosition (
    SBPosition3 const & newPosition,
    SBPosition3 const & oldPosition
)

Sets the atom's position and records the old position for undo support.

Parameters:

newPosition The new 3D position for the atom.
oldPosition The previous 3D position of the atom.

function setPosition [3/6]#

Sets the atom's position.

void SBMStructuralModelNodeAtom::setPosition (
    SBPosition3 const & newPosition,
    bool ignoreFixed
)

Sets the atom's position, optionally ignoring the fixed flag.

Parameters:

newPosition The new 3D position for the atom.
ignoreFixed If true, the atom's fixed status is ignored when setting the position.

function setPosition [4/6]#

Sets the atom's position.

void SBMStructuralModelNodeAtom::setPosition (
    SBPosition3 const & newPosition,
    SBPosition3 const & oldPosition,
    bool ignoreFixed
)

Sets the atom's position, records the old position, and optionally ignores the fixed flag.

This method checks if the node is locked or fixed (unless ignoreFixed is true), creates an undo command for the position change, temporarily disables the fixed flag, updates the atom's position, emits a structural event, and restores the original fixed flag.

Parameters:

newPosition The new 3D position for the atom.
oldPosition The previous 3D position of the atom.
ignoreFixed If true, the atom's fixed status is ignored when setting the position.

function setPositionOnTetrahedron#

Sets the atom's position on a tetrahedron vertex based on the center position, the distance from the centerdistanceFromCenter , and positions of other 3 verticesvertex1 ,vertex2 , andvertex3 .

void SBMStructuralModelNodeAtom::setPositionOnTetrahedron (
    SBPosition3 const & center,
    SBPosition3 const & vertex1,
    SBPosition3 const & vertex2,
    SBPosition3 const & vertex3,
    SBQuantity::length const & distanceFromCenter
)

Sets the atom's position on a tetrahedron defined by three vertices and a center point.

Parameters:

center Center position of the tetrahedron.
vertex1 Position of the first vertex.
vertex2 Position of the second vertex.
vertex3 Position of the third vertex.
distanceFromCenter Distance from the center to the vertex where the atom will be placed.

function setRecordType#

Sets the atom's record type.

void SBMStructuralModelNodeAtom::setRecordType (
    char *const & recordType,
    int const & size
)

function setResonance#

Sets the atom's resonance.

void SBMStructuralModelNodeAtom::setResonance (
    const bool & resonance
)

function setSYBYLType#

Sets the SYBYL atom's type.

void SBMStructuralModelNodeAtom::setSYBYLType (
    char *const & SYBYLType,
    int const & size
)

function setSerialNumber#

Sets the atom's serial number.

void SBMStructuralModelNodeAtom::setSerialNumber (
    const int & serialNumber
)

function setStatusBit#

Sets the atom's status bit.

void SBMStructuralModelNodeAtom::setStatusBit (
    char *const & statusBit,
    int const & size
)

function setTemperatureFactor#

Sets the atom's temperature factor.

void SBMStructuralModelNodeAtom::setTemperatureFactor (
    const double & temperatureFactor
)

function setWaterFlag#

Sets the atom's water flag.

void SBMStructuralModelNodeAtom::setWaterFlag (
    const bool & water
)

function setX#

Sets the x coordinate.

void SBMStructuralModelNodeAtom::setX (
    const SBQuantity::length & x
)

Sets the x coordinate of the atom.

Parameters:

x The new x coordinate value.

function setY#

Sets the y coordinate.

void SBMStructuralModelNodeAtom::setY (
    const SBQuantity::length & y
)

Sets the y coordinate of the atom.

Parameters:

y The new y coordinate value.

function setZ#

Sets the z coordinate.

void SBMStructuralModelNodeAtom::setZ (
    const SBQuantity::length & z
)

Sets the z coordinate of the atom.

Parameters:

z The new z coordinate value.

function unserialize#

Unserializes the atom.

virtual void SBMStructuralModelNodeAtom::unserialize (
    SBCSerializer * serializer,
    const SBNodeIndexer & nodeIndexer,
    const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER,
    const SBVersionNumber & classVersionNumber=SBVersionNumber (1, 0, 0)
) override

Deserializes the atom from a serializer.

This method reads the atom's serialized data, restoring its position, element type, and all optional properties while handling backward compatibility with older SDK versions.

Parameters:

serializer Pointer to the serializer used for reading the atom's data.
nodeIndexer Indexer that provides context for node identifiers during deserialization.
sdkVersionNumber Version number of the SDK used when the data was serialized.
classVersionNumber Version number of the class used when the data was serialized.

Implements SBMStructuralModelNode::unserialize

function ~SBMStructuralModelNodeAtom#

Destructs the atom.

virtual SBMStructuralModelNodeAtom::~SBMStructuralModelNodeAtom ()

Destructor.

Destroys the atom node and releases associated resources.

Public Static Functions Documentation#

function getGeometryString [2/2]#

Returns the geometry as a string.

static std::string SBMStructuralModelNodeAtom::getGeometryString (
    Geometry geometry
)

Converts a Geometry enumeration value to its string representation.

Parameters:

geometry The geometry value to convert.

Returns:

The corresponding string, or "Undefined" for unrecognized values.

function getHybridizationString [2/2]#

Returns the hybridization as a string.

static std::string SBMStructuralModelNodeAtom::getHybridizationString (
    Hybridization hybridization
)

Converts a Hybridization enumeration value to its string representation.

Parameters:

hybridization The hybridization value to convert.

Returns:

The corresponding string, or "Unknown" for unrecognized values.

function setPosition [5/6]#

Sets the position of a vector of atoms.

static void SBMStructuralModelNodeAtom::setPosition (
    SBAttributeChangeVector< SBMStructuralModelNodeAtom *, SBPosition3 > * positionChangeVector,
    bool reverse=false
)

function setPosition [6/6]#

Sets the position of a vector of atoms.

static void SBMStructuralModelNodeAtom::setPosition (
    const SBVector< SBMStructuralModelNodeAtom * > & atomVector,
    const SBVector< SBPosition3 > & newPositionVector
)