This class describes a residue in a structural model.

Node property attributes
enum	ResidueType { Undefined , ALA , ARG , ASP , ASN , VAL , HIS , GLY , GLU , GLN , ILE , LEU , LYS , MET , PRO , SER , TYR , THR , TRP , PHE , CYS , ASX , GLX , XLE , XAA , SEC , PYL , A , C , G , U , I , DA , DC , DG , DT , DI }

enum	SecondaryStructureType { Unstructured , Alpha , Beta }

Hydrophobicity
enum class	HydrophobicityScale { KyteDoolittle1982 , SeredaEtAl1994 , MoneraEtAl1995 , WimleyWhite1996 , HessaEtAl2005 , ZhaoLondon2006 , MoonFleming2011 }

bool	hasHydrophobicity () const
	Returns true if the residue's hydrophobicity is defined.

double	getHydrophobicity () const
	Returns the residue's hydrophobicity in the current hydrophobicity scale.

double	getHydrophobicity (const HydrophobicityScale hydrophobicityScale) const
	Returns the residue's hydrophobicity in the given hydrophobicity scale `hydrophobicityScale`.

HydrophobicityScale	getHydrophobicityScale () const
	Returns the current scale of the residue's hydrophobicity.

void	setHydrophobicityScale (const HydrophobicityScale hydrophobicityScale)
	Sets the current hydrophobicity scale to `hydrophobicityScale`.

std::string	getHydrophobicityScaleString () const
	Returns the current hydrophobicity scale as a string.

int	getHydrophobicityScaleCount () const
	Returns the number of hydrophobicity scales.

int	getHydrophobicityScaleCurrentIndex () const
	Returns the current scale's index in the list of hydrophobicity scales.

void	setHydrophobicityScaleCurrentIndex (const int index)
	Sets the current hydrophobicity scale to the hydrophobicity scale from the list.

std::string	getHydrophobicityScaleItemText (const int index) const
	Returns the hydrophobicity scale `index` as a string.

static bool	hasHydrophobicity (const ResidueType residueType)
	Returns true if for the residue type `residueType` the hydrophobicity is defined.

static double	getHydrophobicity (const ResidueType residueType, const HydrophobicityScale hydrophobicityScale)
	Returns the hydrophobicity value for the residue `residueType` in the hydrophobicity scale `hydrophobicityScale`.

static std::string	getHydrophobicityScaleString (const HydrophobicityScale hydrophobicityScale)
	Returns the hydrophobicity scale `hydrophobicityScale` as a string.

Side chain properties
enum	SideChainCharge { UndefinedSideChainCharge , Negative , Neutral , Positive }

enum	SideChainPolarity { UndefinedSideChainPolarity , Nonpolar , Polar , AcidicPolar , BasicPolar }

bool	hasSideChainCharge () const
	Returns true if the residue's side chain charge is defined.

SideChainCharge	getSideChainCharge () const
	Returns the residue's side chain charge.

std::string	getSideChainChargeString () const
	Returns the residue's side chain charge as a string.

bool	hasSideChainPolarity () const
	Returns true if the residue's side chain polarity is defined.

SideChainPolarity	getSideChainPolarity () const
	Returns the residue's side chain polarity.

std::string	getSideChainPolarityString () const
	Returns the residue's side chain polarity as a string.

	SB_NODE_GETTER_0 (, SBMStructuralModelNodeResidue::ResidueType, GetResidueType)

	SB_NODE_GETTER_0 (, std::string, GetResidueTypeString)

	SB_NODE_GETTER_0 (, SBMStructuralModelNodeResidue::SecondaryStructureType, GetSecondaryStructureType)

	SB_NODE_GETTER_0 (, double, GetHydrophobicity)

	SB_NODE_GETTER_0 (, SBMStructuralModelNodeResidue::HydrophobicityScale, GetHydrophobicityScale)

	SB_NODE_GETTER_0 (, SBMStructuralModelNodeResidue::SideChainCharge, GetSideChainCharge)

	SB_NODE_GETTER_0 (, std::string, GetSideChainChargeString)

	SB_NODE_GETTER_0 (, SBMStructuralModelNodeResidue::SideChainPolarity, GetSideChainPolarity)

	SB_NODE_GETTER_0 (, std::string, GetSideChainPolarityString)

	SB_NODE_GETTER_0 (, double, GetDissociationConstant1)

	SB_NODE_GETTER_0 (, double, GetDissociationConstant2)

	SB_NODE_GETTER_0 (, double, GetIsoelectricPointPH)

	SB_NODE_GETTER_0 (, int, GetResidueSequenceNumber)

	SB_NODE_PREDICATE_0 (, IsAminoAcid)

	SB_NODE_PREDICATE_0 (, IsNucleicAcid)

	SB_NODE_PREDICATE_0 (, IsTerminal)

	SB_NODE_PREDICATE_0 (, HasStandardResidueName)

	SB_NODE_PREDICATE_0 (, HasCompleteAminoAcidBackbone)

	SB_NODE_PREDICATE_0 (, HasHydrophobicity)

	SB_NODE_PREDICATE_0 (, HasSideChainCharge)

	SB_NODE_PREDICATE_0 (, HasSideChainPolarity)

	SB_NODE_PREDICATE_0 (, HasDissociationConstant)

	SB_NODE_PREDICATE_0 (, HasResidueSequenceNumber)

	SB_DECLARE_DATA (SBMStructuralModelNodeResidue)

static bool	hasSideChainCharge (const ResidueType residueType)
	Returns true if for the residue type `residueType` the side chain charge is defined.

static SideChainCharge	getSideChainCharge (const ResidueType residueType)
	Returns the residue's side chain charge for the residue `residueType`.

static std::string	getSideChainChargeString (const SideChainCharge sideChainCharge)
	Returns a side chain charge `sideChainCharge` as a string.

static bool	hasSideChainPolarity (const ResidueType residueType)
	Returns true if for the residue type `residueType` the side chain polarity is defined.

static SideChainPolarity	getSideChainPolarity (const ResidueType residueType)
	Returns the residue's side chain polarity for the residue `residueType`.

static std::string	getSideChainPolarityString (const SideChainPolarity sideChainPolarity)
	Returns a side chain polarity `sideChainPolarity` as a string.

Constructors and destructors
	SBMStructuralModelNodeResidue ()

	SBMStructuralModelNodeResidue (const std::string &n)

virtual	~SBMStructuralModelNodeResidue ()

Serialization
virtual bool	isSerializable () const override
	Returns true.

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

Topology
virtual bool	canAddChild (const SBNode node, const SBNode nextNode=nullptr) const override
	Returns whether this node can add `node` as a child.

virtual bool	canAddChildType (SBNode::Type nodeType) const override
	Returns whether this node can add a node with type `nodeType` as a child.

virtual bool	canHaveDescendantType (SBNode::Type nodeType) const override
	Returns whether this node can have a node with type `nodeType` as a descendant.

virtual bool	addChild (SBNode node, SBNode nextNode=nullptr) override
	Adds a child to the node.

virtual bool	removeChild (SBNode *node) override
	Removes a child from the node.

SBMStructuralModelNodeResidue *	getNextResidue () const
	Returns the next residue if any, else returns nullptr.

SBMStructuralModelNodeResidue *	getPreviousResidue () const
	Returns the previous residue if any, else returns nullptr.

SBMStructuralModelNodeResidue *	getNextAminoAcid () const
	Returns the next amino acid if any, else returns nullptr.

SBMStructuralModelNodeResidue *	getPreviousAminoAcid () const
	Returns the previous amino acid if any, else returns nullptr.

SBMStructuralModelNodeResidue *	getNextNucleicAcid () const
	Returns the next nucleic acid if any, else returns nullptr.

SBMStructuralModelNodeResidue *	getPreviousNucleicAcid () const
	Returns the previous nucleic acid if any, else returns nullptr.

SBMStructuralModelNodeBackbone *	getBackbone () const
	Returns the residue's backbone if it has one, else returns nullptr.

SBMStructuralModelNodeSideChain *	getSideChain () const
	Returns the residue's side chain if it has one, else returns nullptr.

ResidueType	getResidueType () const
	Returns the residue's type.

void	setResidueType (ResidueType residueType)
	Sets the residue's type to `residueType`.

std::string	getResidueTypeString () const
	Returns the string representation of the residue's type.

void	setResidueType (const std::string &s)
	Sets the residue's type based on the string `s`.

std::string	getResidueTypeFullName () const
	Returns the full name of the residue's type.

bool	hasStandardResidueName () const
	Returns true if and only if the residue name corresponds to one of the standard PDB residue names.

bool	isAminoAcid () const
	Returns true if and only if the residue is an amino acid.

bool	isNucleicAcid () const
	Returns true if and only if the residue is a nucleic acid.

bool	isTerminal () const
	Returns true if and only if the residue is terminal.

bool	hasCompleteAminoAcidBackbone () const
	Returns true if and only if the residue has a complete amino-acid backbone.

virtual SBMStructuralModelNodeResidue *	clone () override
	Returns a copy of the node and its descendants.

static std::string	getResidueTypeString (ResidueType residueType)
	Returns the string representation of the residue type `residueType`.

static ResidueType	getResidueTypeFromString (const std::string &s)
	Returns the residue type based on the string `s`.

static std::string	getResidueTypeFullName (ResidueType residueType)
	Returns the full name of the residue type `residueType`.

static bool	isStandardResidueName (const std::string &name)
	Returns true if and only if the name `name` corresponds to one of the standard PDB amino or nucleic acid residue names.

static bool	isStandardAminoAcidName (const std::string &name)
	Returns true if and only if the name `name` corresponds to one of the standard PDB amino acid residue names.

static bool	isStandardNucleicAcidName (const std::string &name)
	Returns true if and only if the name `name` corresponds to one of the standard PDB nucleic acid residue names.

static bool	isAminoAcid (ResidueType residueType)
	Returns true if and only if the residue of `residueType` is an amino acid.

static bool	isNucleicAcid (ResidueType residueType)
	Returns true if and only if the residue of `residueType` is a nucleic acid.

Identity
virtual Type	getType () const override
	Returns the node type (returns SBNode::Residue)

virtual void	setName (const std::string &name) override
	Sets the name of the residue, and updates accordingly names for its backbone and side chain.

Covalent bonds
int	createCovalentBondsByResidueType ()
	Sets the order of covalent bonds for the atoms belonging to the residue according to the residue type, regardless of inter-atomic distances.

Hydrogens
int	addHydrogensByResidueType ()
	Adds hydrogen atoms to the residue based on its type.

Amino acid residue geometry
SBQuantity::dimensionless	computeAminoAcidPhiAngle ()
	Computes the phi dihedral angle (in degrees) for the amino acid's backbone.

SBQuantity::dimensionless	computeAminoAcidPsiAngle ()
	Computes the psi dihedral angle (in degrees) for the amino acid's backbone.

bool	hasAminoAcidChi1Angle () const
	Returns true if it is an amino acid and has chi1 angle.

bool	hasAminoAcidChi2Angle () const
	Returns true if it is an amino acid and has chi2 angle.

bool	hasAminoAcidChi3Angle () const
	Returns true if it is an amino acid and has chi3 angle.

bool	hasAminoAcidChi4Angle () const
	Returns true if it is an amino acid and has chi4 angle.

bool	hasAminoAcidChi5Angle () const
	Returns true if it is an amino acid and has chi5 angle.

SBQuantity::dimensionless	computeAminoAcidChi1Angle ()
	Computes the chi1 angle (in degrees) for the amino acid residue's side chain.

SBQuantity::dimensionless	computeAminoAcidChi2Angle ()
	Computes the chi2 angle (in degrees) for the amino acid residue's side chain.

SBQuantity::dimensionless	computeAminoAcidChi3Angle ()
	Computes the chi3 angle (in degrees) for the amino acid residue's side chain.

SBQuantity::dimensionless	computeAminoAcidChi4Angle ()
	Computes the chi4 angle (in degrees) for the amino acid residue's side chain.

SBQuantity::dimensionless	computeAminoAcidChi5Angle ()
	Computes the chi5 angle (in degrees) for the amino acid residue's side chain.

bool	orientAminoAcidSideChain (const SBQuantity::degree &chi1, const SBQuantity::degree &chi2=SBQuantity::degree(0.0), const SBQuantity::degree &chi3=SBQuantity::degree(0.0), const SBQuantity::degree &chi4=SBQuantity::degree(0.0), const SBQuantity::degree &chi5=SBQuantity::degree(0.0))
	Rotates the amino acid's side chain to orient it according to given dihedral angles `chi1`, `chi2`, `chi3`, `chi4`, `chi5`. Returns true if at least `chi1` rotation was performed.

static bool	hasAminoAcidChi1Angle (const ResidueType residueType)
	Returns true if the residue type `residueType` is an amino acid and has chi1 angle.

static bool	hasAminoAcidChi2Angle (const ResidueType residueType)
	Returns true if the residue type `residueType` is an amino acid and has chi2 angle.

static bool	hasAminoAcidChi3Angle (const ResidueType residueType)
	Returns true if the residue type `residueType` is an amino acid and has chi3 angle.

static bool	hasAminoAcidChi4Angle (const ResidueType residueType)
	Returns true if the residue type `residueType` is an amino acid and has chi4 angle.

static bool	hasAminoAcidChi5Angle (const ResidueType residueType)
	Returns true if the residue type `residueType` is an amino acid and has chi5 angle.

Nucleic acid residue geometry
SBQuantity::dimensionless	computeNucleicAcidAlphaAngle ()
	Computes the alpha (O3'(i-1)-P-O5'-C5') dihedral angle (in degrees) for the nucleic acid's backbone.

SBQuantity::dimensionless	computeNucleicAcidBetaAngle ()
	Computes the beta (P-O5'-C5'-C4') dihedral angle (in degrees) for the nucleic acid's backbone.

SBQuantity::dimensionless	computeNucleicAcidGammaAngle ()
	Computes the gamma (O5'-C5'-C4'-C3') dihedral angle (in degrees) for the nucleic acid's backbone.

SBQuantity::dimensionless	computeNucleicAcidDeltaAngle ()
	Computes the delta (C5'-C4'-C3'-O3') dihedral angle (in degrees) for the nucleic acid's backbone.

SBQuantity::dimensionless	computeNucleicAcidEpsilonAngle ()
	Computes the epsilon (C4'-C3'-O3'-P(i+1)) dihedral angle (in degrees) for the nucleic acid's backbone.

SBQuantity::dimensionless	computeNucleicAcidZetaAngle ()
	Computes the zeta (C3'-O3'-P(i+1)-O5'(i+1)) dihedral angle (in degrees) for the nucleic acid's backbone.

SBQuantity::dimensionless	computeNucleicAcidChiAngle ()
	Computes the chi dihedral angle (in degrees) for the nucleic acid's backbone.

Secondary structure
SecondaryStructureType	getSecondaryStructureType () const
	Returns the most probable secondary structure based on bonds parameters and residue geometry.

void	setSecondaryStructureType (SecondaryStructureType type)
	Sets the most probable secondary structure based on bonds parameters and residue geometry.

std::string	getSecondaryStructureTypeString () const
	Returns the secondary structure type as a string.

static std::string	getSecondaryStructureTypeString (SecondaryStructureType secondaryStructureType)
	Returns the secondary structure type `secondaryStructureType` as a string.

Amino acids information
std::string	getAminoAcidOneLetterCode () const
	Returns one letter code of the amino acid residue.

static std::string	getAminoAcidOneLetterCode (const ResidueType residueType)
	Returns one letter code of the amino acid residue `residueType`.

static ResidueType	getResidueTypeFromAminoAcidOneLetterCode (const std::string &s)
	Returns the amino acid residue type from the one letter code of the amino acid residue `s`.

Properties of common amino acid residues
bool	hasDissociationConstant () const
	Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for this residue.

double	getDissociationConstant1 () const
	Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for this residue.

double	getDissociationConstant2 () const
	Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for this residue.

double	getIsoelectricPointPH () const
	Returns the pI value (the pH at the isoelectric point) for this residue.

static bool	hasDissociationConstant (const ResidueType residueType)
	Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for the residue `residueType`.

static double	getDissociationConstant1 (const ResidueType residueType)
	Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for the residue `residueType`.

static double	getDissociationConstant2 (const ResidueType residueType)
	Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for the residue `residueType`.

static double	getIsoelectricPointPH (const ResidueType residueType)
	Returns the pI value (the pH at the isoelectric point) for the residue `residueType`.

Additional Inherited Members
Public Types inherited from SBDDataGraphNode
enum	Type { Undefined , StructuralModel , StructuralModelNode , StructuralModelConformation , Conformation , StructuralModelPath , Path , StructuralModelNodeGroup , StructuralGroup , StructuralModelNodeRoot , Root , StructuralModelNodeAtom , Atom , StructuralModelNodeBond , Bond , StructuralModelNodeHydrogenBond , HydrogenBond , StructuralModelNodeHydrogenBondGroup , HydrogenBondGroup , StructuralModelNodeResidue , Residue , StructuralModelNodeSegment , Segment , StructuralModelNodeChain , Chain , StructuralModelNodeMolecule , Molecule , StructuralModelNodeBackbone , Backbone , StructuralModelNodeSideChain , SideChain , VisualModel , VisualModelMesh , Mesh , DynamicalModel , DynamicalModelParticleSystem , ParticleSystem , DynamicalModelRigidBodySystem , RigidBodySystem , DynamicalModelArticulatedBodySystem , ArticulatedBodySystem , DynamicalModelNode , DynamicalNode , DynamicalModelNodeGroup , DynamicalGroup , DynamicalModelNodeRoot , DynamicalRoot , DynamicalModelNodeParticle , Particle , DynamicalModelNodeRigidBody , RigidBody , DynamicalModelNodeArticulatedBody , ArticulatedBody , InteractionModel , InteractionModelParticleSystem , InteractionModelRigidBodySystem , InteractionModelArticulatedBodySystem , PropertyModel , PropertyModelFunction , Simulator , SimulatorParticleSystem , SimulatorRigidBodySystem , SimulatorArticulatedBodySystem , StateUpdater , StateUpdaterParticleSystem , StateUpdaterRigidBodySystem , StateUpdaterArticulatedBodySystem , Animation , Camera , Document , DocumentManager , File , Folder , Label , Light , Note , Presentation , RenderPreset , DataGraphNodeGroup , NodeGroup , Controller , ControllerNode , Asset }
	The type of the data graph node. More...

enum class	RenderingPass { Setup , OpaqueGeometry , SelectableGeometry , ShadowingGeometry , TransparentGeometry , Interface , Text }
	The rendering pass. More...

Public Member Functions inherited from SBMStructuralModelNodeGroup
	SBMStructuralModelNodeGroup ()
	Builds a base model.

	SBMStructuralModelNodeGroup (const std::string &n)

virtual	~SBMStructuralModelNodeGroup ()

virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () const override
	Returns the list of child nodes.

bool	hasComment () const
	Returns true when the comment is set.

std::string const &	getComment () const
	Returns the comment.

void	setComment (const std::string &comment)
	Sets the comment.

void	clearComment ()
	Clears the comment.

bool	hasStatusBit () const
	Returns true when the status bit is set.

std::string const &	getStatusBit () const
	Returns the status bit.

void	setStatusBit (const std::string &statusBit)
	Sets the status bit.

void	clearStatusBit ()
	Clears the status bit.

bool	hasStructuralID () const
	Returns true when the structural group's id is set.

int const &	getStructuralID () const
	Returns the structural group's id.

void	setStructuralID (const int &groupID)
	Sets the structural group's id.

void	clearStructuralID ()
	Clears the structural group's id.

virtual void	onBaseEvent (SBEvent *event)

virtual void	getNodes (SBNodeIndexer &nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override
	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 override
	Collects nodes into `nodeIndexer`, based on a `selectionPredicate` and a `visitPredicate`, with or without dependencies.

virtual bool	hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override
	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) const override
	Checks for nodes based on a `selectionPredicate` and a `visitPredicate`, with or without dependencies.

bool	isWater ()
	Returns true if the structural group is a water molecule.

bool	isMonatomicIon ()
	Returns true if the structural group is a monatomic ion.

virtual void	forEachNodeDepthFirst (void(action)(SBDDataGraphNode node)) override
	Performs an action on each node.

virtual void	forEachNodeDepthFirst (SBCClass object, void(SBCClass::action)(SBDDataGraphNode *node)) override
	Performs an action on each node.

virtual unsigned int	getNumberOfChains () override
	Returns the number of chains.

virtual unsigned int	getNumberOfMolecules () override
	Returns the number of molecules.

virtual unsigned int	getNumberOfResidues () override
	Returns the number of residues.

virtual unsigned int	getNumberOfSegments () override
	Returns the number of segments.

virtual unsigned int	getNumberOfStructuralGroups () override
	Returns the number of structural groups.

virtual unsigned int	getNumberOfAtoms () override
	Returns the number of atoms.

virtual unsigned int	getNumberOfCarbons () override
	Returns the number of carbons.

virtual unsigned int	getNumberOfHydrogens () override
	Returns the number of hydrogens.

virtual unsigned int	getNumberOfNitrogens () override
	Returns the number of nitrogens.

virtual unsigned int	getNumberOfOxygens () override
	Returns the number of oxygens.

virtual unsigned int	getNumberOfSulfurs () override
	Returns the number of sulfurs.

virtual unsigned int	getNumberOfCoarseGrainedAtoms () override
	Returns the number of coarse-grained atoms.

virtual unsigned int	getNumberOfOtherAtoms () override
	Returns the number of other atoms.

virtual int	getSumOfFormalCharges () override
	Returns the sum of formal charges.

virtual float	getSumOfPartialCharges () override
	Returns the sum of partial charges.

virtual SBQuantity::mass	getMolecularWeight () override
	Returns the molecular weight.

virtual void	print (unsigned int offset=0) const override
	Prints debugging information.

	SB_NODE_GETTER_0 (, std::string, GetComment)

	SB_NODE_GETTER_0 (, std::string, GetStatusBit)

	SB_NODE_GETTER_0 (, int, GetStructuralID)

	SB_NODE_PREDICATE_0 (, HasComment)

	SB_NODE_PREDICATE_0 (, HasStatusBit)

	SB_NODE_PREDICATE_0 (, HasStructuralID)

	SB_DECLARE_DATA (SBMStructuralModelNodeGroup)

Public Member Functions inherited from SBMStructuralModelNode
virtual	~SBMStructuralModelNode ()

SBMStructuralModelNode *	getNextStructuralNode () const

SBMStructuralModelNode *	getPreviousStructuralNode () const

virtual bool	isLocked () const override
	Returns whether the node is locked (because of the model)

virtual bool	getLockedFlag () const override
	Returns the locked flag of the model.

SBMStructuralModel *	getModel () const

virtual unsigned int	getOpacity () const override
	Returns the opacity.

virtual unsigned int	getMinimumOpacity () const override
	Returns the minimum opacity.

virtual unsigned int	getTransparency () const override
	Returns the transparency.

virtual unsigned int	getMaximumTransparency () const override
	Returns the maximum transparency.

bool	getStructuralSignalFlag () const
	Returns true when the node can send structural signals.

void	setStructuralSignalFlag (bool structuralSignalFlag)
	Sets whether the node can send structural signals.

void	connectStructuralSignalToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBStructuralEvent ), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any, SBCReferenceTarget nextReferenceTarget=0, void(SBCReferenceTarget::nextFunctionPointer)(SBStructuralEvent )=0)

bool	structuralSignalIsConnectedToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBStructuralEvent *), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) const

void	disconnectStructuralSignalFromSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBStructuralEvent *), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any)

void	getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > &nodeIndexer, bool(selectionRule)(SBMStructuralModelNode ))

void	getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > &nodeIndexer, bool(selectionRule)(SBMStructuralModelNode ))

void	getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > &nodeIndexer)

void	getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > &nodeIndexer, bool(selectionRule)(SBMStructuralModelNode ))

void	getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode * > &nodeVectorTopDown, std::vector< SBMStructuralModelNode * > &nodeVectorBottomUp, bool(selectionRule)(SBMStructuralModelNode ))

void	forEachStructuralNodeBreadthFirst (void(action)(SBMStructuralModelNode node))

void	forEachStructuralNodeDepthFirst (void(action)(SBMStructuralModelNode node))

void	forEachStructuralNodeBreadthFirst (SBCClass object, void(SBCClass::action)(SBMStructuralModelNode *node))

void	forEachStructuralNodeDepthFirst (SBCClass object, void(SBCClass::action)(SBMStructuralModelNode *node))

	SB_DECLARE_DATA (SBMStructuralModelNode)

Public Member Functions inherited from SBMModelNode
	SB_DECLARE_DATA (SBMModelNode)

Public Member Functions inherited from SBDDataGraphNode
SBDDataGraphNode *	getParent () const
	Returns the parent of the node.

SBDDataGraphNode *	getThisNode () const
	Returns the pointer to this node.

SBDDataGraphNode *	getNextNode () const
	Returns the pointer to the next node in the children of the node's parent.

SBDDataGraphNode *	getPreviousNode () const
	Returns the pointer to the previous 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.

SBDDataGraphNode *	getPreviousNode (SBDDataGraphNode::Type nodeType) const
	Returns the pointer to the previous node with type `nodeType` in the children of the node's parent.

SBDDocument *	getDocument () const
	Returns the document the node belongs to.

virtual bool	canAddChild (const SBDDataGraphNode node, const SBDDataGraphNode nextNode=nullptr) const
	Returns whether this node can add `node` as a child.

virtual bool	addChild (SBDDataGraphNode node, SBDDataGraphNode nextNode=nullptr)
	Adds a child to the node.

virtual bool	removeChild (SBDDataGraphNode *node)
	Removes a child from the node.

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	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.

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	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`.

SBDDataGraphNode *	getRoot () const
	Returns the root of the hierarchy the node belongs to.

unsigned int	getNodeIndex () const
	Returns the node index (unique in the whole data graph, but non-persistent)

std::string	getTypeString (bool humanReadable=false) const
	Returns a string describing the type of the data graph node.

virtual std::string const &	getName () const
	Returns the name of the node.

bool	isType (Type type) const
	Returns true when the type of the node corresponds to `type`.

bool	isModel () const
	Returns true when the node is a model.

bool	isAtom () const
	Returns true when the node is an atom.

bool	isBond () const
	Returns true when the node is a bond.

bool	isStructuralNode () const
	Returns true when the node is a structural node.

bool	isStructuralModel () const
	Returns true when the node is a structural model.

bool	isVisualModel () const
	Returns true when the node is a visual model.

bool	isDynamicalModel () const
	Returns true when the node is a dynamical model.

bool	isInteractionModel () const
	Returns true when the node is a interaction model.

bool	isPropertyModel () const
	Returns true when the node is a property model.

bool	isMesh () const
	Returns true when the node is a mesh.

bool	isLight () const
	Returns true when the node is a light.

bool	isSimulator () const
	Returns true when the node is a simulator.

bool	isBallAndStick () const
	Returns true when the node is the default ball-and-stick visual model.

bool	isLicorice () const
	Returns true when the node is the default licorice visual model.

bool	isVanDerWaals () const
	Returns true when the node is the default van der Waals visual model.

bool	isCartoon () const
	Returns true when the node is the default cartoon visual model.

bool	isRibbon () const
	Returns true when the node is the default ribbon visual model.

bool	isTube () const
	Returns true when the node is the default tube visual model.

bool	isGaussianSurface () const
	Returns true when the node is the default Gaussian surface visual model.

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.

virtual void	setLockedFlag (bool flag)
	Sets the locked flag.

bool	isCreated () const
	Returns true if and only if the node is created.

void	create ()
	Creates the node.

bool	isErased () const
	Returns true if and only if the node is erased.

void	erase ()
	Erases the node.

virtual unsigned int	getFlags () const
	Returns the flags.

virtual unsigned int	getInheritedFlags () const
	Returns the inherited flags.

bool	isSelected () const
	Returns whether the node is selected.

bool	getSelected () const
	Returns whether the node is selected.

bool	getSelectionFlag () const
	Returns the selection flag.

void	setSelectionFlag (bool flag)
	Sets the selection flag.

bool	isVisible () const
	Returns whether the node is visible.

bool	getVisible () const
	Returns whether the node is visible.

bool	getVisibilityFlag () const
	Returns the visibility flag.

void	setVisibilityFlag (bool flag)
	Sets the visibility flag.

bool	isHighlighted () const
	Returns whether the node is highlighted.

bool	getHighlightingFlag () const
	Returns the highlighting flag.

void	setHighlightingFlag (bool flag)
	Sets the highlighting flag.

virtual void	display (RenderingPass renderingPass)
	Displays the node.

virtual void	display ()
	Displays the node (deprecated)

virtual void	displayForShadow ()
	Displays the node for shadowing purposes (deprecated)

virtual void	displayForSelection ()
	Displays the node for selection purposes (deprecated)

virtual void	setOpacity (unsigned int opacity)
	Sets the opacity.

virtual bool	hasOpacityRange () const
	Returns whether the node has the opacity range.

virtual unsigned int	getDefaultOpacity () const
	Returns the default opacity.

virtual unsigned int	getMaximumOpacity () const
	Returns the maximum opacity.

virtual unsigned int	getOpacitySingleStep () const
	Returns the opacity single step.

virtual std::string	getOpacitySuffix () const
	Returns the opacity suffix.

virtual void	setTransparency (unsigned int transparency)
	Sets the transparency.

virtual bool	hasTransparencyRange () const
	Returns whether the node has the transparency range.

virtual unsigned int	getDefaultTransparency () const
	Returns the default transparency.

virtual unsigned int	getMinimumTransparency () const
	Returns the minimum transparency.

virtual unsigned int	getTransparencySingleStep () const
	Returns the transparency single step.

virtual std::string	getTransparencySuffix () const
	Returns the transparency suffix.

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.

bool	canAddMaterial () const
	Returns whether can add a material to the node based on its type.

bool	addMaterial (SBDDataGraphNodeMaterial *material)
	Adds a material.

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.

bool	hasMaterial () const
	Returns whether the node has a material (by itself, or inherited)

bool	ownsMaterial () const
	Returns whether the node owns a material.

SBDDataGraphNodeMaterial *	getMaterial () const
	Returns the material.

SBDDataGraphNode *	getMaterialOwner () const
	Returns the node whose material is inherited.

void	connectBaseSignalToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent ), SBCReferenceTarget nextReferenceTarget=0, void(SBCReferenceTarget::nextFunctionPointer)(SBBaseEvent )=0)
	Connects the base signal to a slot.

bool	baseSignalIsConnectedToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent *)) const
	Returns true when the base signal is connected to a slot.

void	disconnectBaseSignalFromSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent *))
	Disconnects the base signal from 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.

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.

virtual unsigned int	getNumberOfStructuralModels ()
	Returns the number of structural models.

	SB_DECLARE_DATA (SBDDataGraphNode)

Public Member Functions inherited from SBCReferenceTarget
unsigned int	getMemoryFootprint () const

void	printReferencesToOwners () const

	SBCReferenceTarget ()

virtual	~SBCReferenceTarget ()

Static Public Member Functions inherited from SBMStructuralModelNode
static void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > &selection, void(action)(SBMStructuralModelNode node))

static void	forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > &selection, SBCClass object, void(SBCClass::action)(SBMStructuralModelNode *node))

Static Public Member Functions inherited from SBDDataGraphNode
static void	clone (const SBNodeIndexer &sourceNodeIndexer, SBNodeIndexer &destinationNodeIndexer)
	Clones the nodes in `sourceNodeIndexer` (treated as a whole) and places the clones in `destinationNodeIndexer`.

static SBDDataGraphNode *	getNode (unsigned int nodeIndex)
	Returns the unique node corresponding to the node index `nodeIndex`.

static std::string	getTypeString (Type type, bool humanReadable=false)
	Returns a string describing the type of the data graph node.

static bool	canAddMaterial (SBDDataGraphNode::Type nodeType)
	Returns whether can add a material to a node of type `nodeType`.

static void	forEachNodeInSelection (SBNodeIndexer &nodeIndexer, void(action)(SBDDataGraphNode node))
	Performs an action for each node in a selection.

static void	forEachNodeInSelection (SBNodeIndexer &nodeIndexer, SBCClass object, void(SBCClass::action)(SBDDataGraphNode *node))
	Performs an action for each node in a selection.

Protected Member Functions inherited from SBMStructuralModelNodeGroup
	SBMStructuralModelNodeGroup (SBMStructuralModelNodeGroupData *dataPointer)
	Builds a base object.

Protected Member Functions inherited from SBMStructuralModelNode
	SBMStructuralModelNode ()
	Builds a structural model node.

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

Protected Member Functions inherited from SBMModelNode
	SBMModelNode ()
	Builds a base object.

	SBMModelNode (SBMModelNodeData *dataPointer)
	Builds a base object.

virtual	~SBMModelNode ()

Protected Member Functions inherited from SBDDataGraphNode
	SBDDataGraphNode ()
	Builds a data graph node.

	SBDDataGraphNode (SBDDataGraphNodeData *dataPointer)
	Builds a data graph node.

virtual	~SBDDataGraphNode ()
	Destroys the node.

Protected Member Functions inherited from SBCReferenceTarget
void	removeAllReferenceOwners ()

	SBCReferenceTarget (SBCReferenceTargetData *dataPointer)

Protected Attributes inherited from SBCReferenceTarget
SBCReferenceTargetData *	dataPointer

Member Enumeration Documentation

◆ HydrophobicityScale

enum class SBMStructuralModelNodeResidue::HydrophobicityScale

strong

Enumerator
KyteDoolittle1982	A hydrophobicity scale of Kyte J, Doolittle RF, "A simple method for displaying the hydropathic character of a protein", J Mol Biol. 1982. DOI: https://doi.org/10.1016/0022-2836(82)90515-0.
SeredaEtAl1994	A hydrophobicity scale of Sereda TJ et al. 1994. DOI: https://doi.org/10.1016/0021-9673(94)00371-8.
MoneraEtAl1995	A hydrophobicity scale of Monera et al. 1995. DOI: https://doi.org/10.1002/psc.310010507.
WimleyWhite1996	A hydrophobicity scale of Wimley WC, White SH, "Experimentally determined hydrophobicity scale for proteins at membrane interfaces", Nat Struct Biol. 1996. DOI: https://doi.org/10.1038/nsb1096-842.
HessaEtAl2005	A hydrophobicity scale of Hessa T et al. "Recognition of transmembrane helices by the endoplasmic reticulum translocon". Nature. 2005. DOI: https://doi.org/10.1038/nature03216.
ZhaoLondon2006	A hydrophobicity scale of Zhao G, London E. "An amino acid “transmembrane tendency” scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity". Protein Sci. 2006. DOI: https://doi.org/10.1110/ps.062286306.
MoonFleming2011	A hydrophobicity scale of Moon CP, Fleming KG. "Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers". Proc Natl Acad Sci USA. 2011. DOI: https://doi.org/10.1073/pnas.1103979108.

◆ ResidueType

enum SBMStructuralModelNodeResidue::ResidueType

Enumerator
Undefined	Undefined residue type.
ALA	Alanine.
ARG	Arginine.
ASP	Aspartic acid.
ASN	Asparagine.
VAL	Valine.
HIS	Histidine.
GLY	Glycine.
GLU	Glutamic acid.
GLN	Glutamine.
ILE	Isoleucine.
LEU	Leucine.
LYS	Lysine.
MET	Methionine.
PRO	Proline.
SER	Serine.
TYR	Tyrosine.
THR	Threonine.
TRP	Tryptophan.
PHE	Phenylalanine.
CYS	Cysteine.
ASX	ASN or ASP (Asparagine or Aspartic acid)
GLX	GLN or GLU (Glutamine or Glutamic acid)
XLE	LEU or ILE (Leucine or Isoleucine)
XAA	Unknown residue type.
SEC	Selenocysteine.
PYL	Pyrrolysine.
A	Adenosine-5'-monophosphate.
C	Cytidine-5'-monophosphate.
G	Guanosine-5'-monophosphate.
U	Uridine-5'-monophosphate.
I	Inosinic acid.
DA	2'-deoxyadenosine-5'-monophosphate
DC	2'-deoxycytidine-5'-monophosphate
DG	2'-deoxyguanosine-5'-monophosphate
DT	Thymidine-5'-monophosphate.
DI	2'-deoxyinosine-5'-monophosphate

◆ SecondaryStructureType

enum SBMStructuralModelNodeResidue::SecondaryStructureType

Enumerator
Unstructured	Unstructured secondary structure element.
Alpha	Alpha helix secondary structure element.
Beta	Beta strand/sheet secondary structure element.

◆ SideChainCharge

enum SBMStructuralModelNodeResidue::SideChainCharge

Enumerator
UndefinedSideChainCharge	Undefined side chain charge.
Negative	Residue has a side chain with negative charge.
Neutral	Residue has a side chain with neutral charge.
Positive	Residue has a side chain with positive charge.

◆ SideChainPolarity

enum SBMStructuralModelNodeResidue::SideChainPolarity

Enumerator
UndefinedSideChainPolarity	Undefined side chain polarity.
Nonpolar	Residue has a nonpolar side chain.
Polar	Residue has a polar side chain.
AcidicPolar	Residue has a side chain with acidic polarity.
BasicPolar	Residue has a side chain with basic polarity.

Member Function Documentation

◆ addChild()

bool SBMStructuralModelNodeResidue::addChild	(	SBNode *	node,
		SBNode *	nextNode = `nullptr`
	)

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ canAddChild()

bool SBMStructuralModelNodeResidue::canAddChild	(	const SBNode *	node,
		const SBNode *	nextNode = `nullptr`
	)		const

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ canAddChildType()

bool SBMStructuralModelNodeResidue::canAddChildType ( SBNode::Type nodeType ) const

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ canHaveDescendantType()

bool SBMStructuralModelNodeResidue::canHaveDescendantType ( SBNode::Type nodeType ) const

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ clone()

SBMStructuralModelNodeResidue * SBMStructuralModelNodeResidue::clone ( )

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ computeNucleicAcidChiAngle()

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeNucleicAcidChiAngle ( )

Computes the chi dihedral angle (in degrees) for the nucleic acid's backbone: for pyrimidines(Y): O4'-C1'-N1-C2 for purines(R): O4'-C1'-N9-C4

◆ getAminoAcidOneLetterCode() [1/2]

std::string SBMStructuralModelNodeResidue::getAminoAcidOneLetterCode ( ) const

Returns the one letter code of the amino acid residue. For nucleic acids and a residue of an SBResidue::Undefined type it will return an empty string.

◆ getAminoAcidOneLetterCode() [2/2]

std::string SBMStructuralModelNodeResidue::getAminoAcidOneLetterCode ( const ResidueType residueType )

static

Returns the one letter code of the amino acid residue residueType. For nucleic acids and a residue of an SBResidue::Undefined type it will return an empty string.

◆ getDissociationConstant1() [1/2]

double SBMStructuralModelNodeResidue::getDissociationConstant1 ( ) const

SBMStructuralModelNodeResidue::getDissociationConstant1.

Returns: Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for this residue

Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

◆ getDissociationConstant1() [2/2]

double SBMStructuralModelNodeResidue::getDissociationConstant1 ( const ResidueType residueType )

static

SBMStructuralModelNodeResidue::getDissociationConstant1.

Parameters

residueType The type of the residue

Returns: Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for the residue residueType

Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

◆ getDissociationConstant2() [1/2]

double SBMStructuralModelNodeResidue::getDissociationConstant2 ( ) const

SBMStructuralModelNodeResidue::getDissociationConstant2.

Returns: Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for this residue

Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

◆ getDissociationConstant2() [2/2]

double SBMStructuralModelNodeResidue::getDissociationConstant2 ( const ResidueType residueType )

static

SBMStructuralModelNodeResidue::getDissociationConstant2.

Parameters

residueType The type of the residue

Returns: Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for the residue residueType

Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

◆ getIsoelectricPointPH() [1/2]

double SBMStructuralModelNodeResidue::getIsoelectricPointPH ( ) const

SBMStructuralModelNodeResidue::getIsoelectricPointPH.

Returns: Returns the pI value (the pH at the isoelectric point) for this residue

Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

◆ getIsoelectricPointPH() [2/2]

double SBMStructuralModelNodeResidue::getIsoelectricPointPH ( const ResidueType residueType )

static

SBMStructuralModelNodeResidue::getIsoelectricPointPH.

Parameters

residueType The type of the residue

Returns: Returns the pI value (the pH at the isoelectric point) for the residue residueType

Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

◆ getResidueTypeFromString()

SBMStructuralModelNodeResidue::ResidueType SBMStructuralModelNodeResidue::getResidueTypeFromString ( const std::string & s )

static

Returns the residue type based on the string s. The input string can be a 3-letter code for amino acids and 1 or 2 letter code for nucleic acids.

Returns: Residue type (SBResidue::ResidueType) that corresponds to the given string if found, else SBResidue::ResidueType::Undefined.

◆ getSecondaryStructureTypeString() [1/2]

std::string SBMStructuralModelNodeResidue::getSecondaryStructureTypeString ( ) const

Returns the secondary structure type as a string:

"Alpha" for alpha helix
"Beta" for beta strand/sheet
"Unstructured" for unstructured/loop

◆ getSecondaryStructureTypeString() [2/2]

std::string SBMStructuralModelNodeResidue::getSecondaryStructureTypeString ( SBMStructuralModelNodeResidue::SecondaryStructureType secondaryStructureType )

static

Returns the secondary structure type secondaryStructureType as a string:

"Alpha" for alpha helix
"Beta" for beta strand/sheet
"Unstructured" for unstructured/loop

◆ getSideChainCharge() [1/2]

SBMStructuralModelNodeResidue::SideChainCharge SBMStructuralModelNodeResidue::getSideChainCharge ( ) const

SBMStructuralModelNodeResidue::getSideChainCharge.

Returns: The charge of the residue's side chain at physiological pH 7.4

Reference: Cooper GM, Hausman RE (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 978-0-87893-214-6.

◆ getSideChainCharge() [2/2]

SBMStructuralModelNodeResidue::SideChainCharge SBMStructuralModelNodeResidue::getSideChainCharge ( const ResidueType residueType )

static

SBMStructuralModelNodeResidue::getSideChainCharge.

Parameters

residueType The type of the residue

Returns: The charge of the residue's residueType side chain at physiological pH 7.4

Reference: Cooper GM, Hausman RE (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 978-0-87893-214-6.

◆ getSideChainPolarity() [1/2]

SBMStructuralModelNodeResidue::SideChainPolarity SBMStructuralModelNodeResidue::getSideChainPolarity ( ) const

SBMStructuralModelNodeResidue::getSideChainPolarity.

Returns: The polarity of the residue's side chain

Reference: Cooper GM, Hausman RE (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 978-0-87893-214-6.

◆ getSideChainPolarity() [2/2]

SBMStructuralModelNodeResidue::SideChainPolarity SBMStructuralModelNodeResidue::getSideChainPolarity ( const ResidueType residueType )

static

SBMStructuralModelNodeResidue::getSideChainPolarity.

Parameters

residueType The type of the residue

Returns: The polarity of the residue's residueType side chain

Reference: Cooper GM, Hausman RE (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 978-0-87893-214-6.

◆ getType()

SBDDataGraphNode::Type SBMStructuralModelNodeResidue::getType ( ) const

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ hasCompleteAminoAcidBackbone()

bool SBMStructuralModelNodeResidue::hasCompleteAminoAcidBackbone ( ) const

Returns true if and only if the residue has a complete amino acid backbone, i.e. it has alpha-Carbon (CA), Carbon (C), Nitrogen (N), and Oxygen (O).

◆ hasStandardResidueName()

bool SBMStructuralModelNodeResidue::hasStandardResidueName ( ) const

Returns true if and only if the residue name corresponds to one of the standard PDB residue names. It takes the first letters preceeding any numeric or white space characters and it will check whether this name corresponds to standard PDB residue names. Examples:

for "HIS 1" it will get "HIS" and it will check whether it is a standard residue name;
for "CYS58" it will get "CYS" and it will check whether it is a standard residue name.

See also: SBMStructuralModelNodeResidue::isStandardResidueName

◆ isAminoAcid()

bool SBMStructuralModelNodeResidue::isAminoAcid ( ) const

Returns true if and only if the residue type is an amino acid.

◆ isNucleicAcid()

bool SBMStructuralModelNodeResidue::isNucleicAcid ( ) const

Returns true if and only if the residue type is a nucleic acid.

◆ isSerializable()

bool SBMStructuralModelNodeResidue::isSerializable ( ) const

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ isStandardAminoAcidName()

bool SBMStructuralModelNodeResidue::isStandardAminoAcidName ( const std::string & s )

static

Returns true if and only if the name name corresponds to one of the standard PDB amino acid residue names (3 letter code).

See also: SBMStructuralModelNodeResidue::isStandardResidueName

◆ isStandardNucleicAcidName()

bool SBMStructuralModelNodeResidue::isStandardNucleicAcidName ( const std::string & s )

static

Returns true if and only if the name name corresponds to one of the standard PDB nucleic acid residue names (1 or 2 letter code).

See also: SBMStructuralModelNodeResidue::isStandardResidueName

◆ isStandardResidueName()

bool SBMStructuralModelNodeResidue::isStandardResidueName ( const std::string & name )

static

Returns true if and only if the name name corresponds to one of the standard PDB residue names: 3 letter code for amino acids, and 1 or 2 letter code for nucleic acids.

See also: SBMStructuralModelNodeResidue::isStandardAminoAcidName, SBMStructuralModelNodeResidue::isStandardNucleicAcidName

◆ removeChild()

bool SBMStructuralModelNodeResidue::removeChild ( SBNode * node )

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ serialize()

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

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ setName()

void SBMStructuralModelNodeResidue::setName ( const std::string & name )

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

◆ unserialize()

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

overridevirtual

Reimplemented from SBMStructuralModelNodeGroup.

Node property attributes

Hydrophobicity

Side chain properties

Constructors and destructors

Serialization

Topology

Identity

Covalent bonds

Hydrogens

Amino acid residue geometry

Nucleic acid residue geometry

Secondary structure

Amino acids information

Properties of common amino acid residues

Additional Inherited Members

Member Enumeration Documentation

◆ HydrophobicityScale

◆ ResidueType

◆ SecondaryStructureType

◆ SideChainCharge

◆ SideChainPolarity

Member Function Documentation

◆ addChild()

◆ canAddChild()

◆ canAddChildType()

◆ canHaveDescendantType()

◆ clone()

◆ computeNucleicAcidChiAngle()

◆ getAminoAcidOneLetterCode() [1/2]

◆ getAminoAcidOneLetterCode() [2/2]

◆ getDissociationConstant1() [1/2]

◆ getDissociationConstant1() [2/2]

◆ getDissociationConstant2() [1/2]

◆ getDissociationConstant2() [2/2]

◆ getIsoelectricPointPH() [1/2]

◆ getIsoelectricPointPH() [2/2]

◆ getResidueTypeFromString()

◆ getSecondaryStructureTypeString() [1/2]

◆ getSecondaryStructureTypeString() [2/2]

◆ getSideChainCharge() [1/2]

◆ getSideChainCharge() [2/2]

◆ getSideChainPolarity() [1/2]

◆ getSideChainPolarity() [2/2]

◆ getType()

◆ hasCompleteAminoAcidBackbone()

◆ hasStandardResidueName()

◆ isAminoAcid()

◆ isNucleicAcid()

◆ isSerializable()

◆ isStandardAminoAcidName()

◆ isStandardNucleicAcidName()

◆ isStandardResidueName()

◆ removeChild()

◆ serialize()

◆ setName()

◆ unserialize()