This class describes a residue in a structural model.

Constructors and destructors
	SBMStructuralModelNodeResidue ()

	SBMStructuralModelNodeResidue (const std::string &n)

virtual	~SBMStructuralModelNodeResidue ()

Serialization
bool	isSerializable () 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)) 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))
	Unserializes the node.

Node property attributes
enum	ResidueType

enum	SecondaryStructureType

Topology
virtual Type	getType () const
	Returns the type of the data graph node. More...

virtual bool	canAddChild (SBNode node, SBNode nextNode=0) const
	Returns whether this node can add `node` as a child.

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

virtual bool	addChild (SBNode node, SBNode nextNode=0)
	Adds a child to the node.

virtual bool	removeChild (SBNode *node)
	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

void	setResidueType (ResidueType residueType)

std::string	getResidueTypeString () const

void	setResidueType (const std::string &residueType)

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 ()
	Returns a copy of the node and its descendants.

static std::string	getResidueTypeString (ResidueType residueType)

Identity
void	setName (const std::string &name)
	Sets the name of the residue, and updates accordingle 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.

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.

Hydrophobicity
enum	HydrophobicityScale { HydrophobicityScale::KyteDoolittle1982, HydrophobicityScale::SeredaEtAl1994, HydrophobicityScale::MoneraEtAl1995, HydrophobicityScale::WimleyWhite1996, HydrophobicityScale::HessaEtAl2005, HydrophobicityScale::ZhaoLondon2006, HydrophobicityScale::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 `hydrophobicityScale` 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.

Properties of common amino acids
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. More...

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. More...

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

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`. More...

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`. More...

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

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. More...

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. More...

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

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`. More...

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`. More...

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

Additional Inherited Members
Public Types inherited from SBDDataGraphNode
enum	RenderingPass { RenderingPass::OpaqueGeometry, RenderingPass::SelectableGeometry, RenderingPass::ShadowingGeometry, RenderingPass::TransparentGeometry, RenderingPass::Interface, RenderingPass::Text }
	The rendering pass. More...

enum	Type { Undefined, StructuralModel, StructuralModelNode, StructuralModelConformation, Conformation, StructuralModelPath, Path, StructuralModelNodeGroup, StructuralGroup, StructuralModelNodeRoot, Root, StructuralModelNodeParticle, StructuralParticle, StructuralModelNodeAtom, Atom, StructuralModelNodePseudoAtom, PseudoAtom, StructuralModelNodeBond, Bond, StructuralModelNodeResidue, Residue, StructuralModelNodeSegment, Segment, StructuralModelNodeProtein, Protein, StructuralModelNodeChain, Chain, StructuralModelNodeMolecule, Molecule, StructuralModelNodeBackbone, Backbone, StructuralModelNodeSideChain, SideChain, VisualModel, DynamicalModel, DynamicalModelParticleSystem, ParticleSystem, DynamicalModelRigidBodySystem, RigidBodySystem, DynamicalModelArticulatedBodySystem, ArticulatedBodySystem, DynamicalModelNode, DynamicalNode, DynamicalModelNodeGroup, DynamicalGroup, DynamicalModelNodeRoot, DynamicalRoot, DynamicalModelNodeParticle, DynamicalParticle, DynamicalModelNodeRigidBody, RigidBody, DynamicalModelNodeArticulatedBody, ArticulatedBody, InteractionModel, InteractionModelParticleSystem, InteractionModelRigidBodySystem, InteractionModelArticulatedBodySystem, PropertyModel, PropertyModelFunction, Simulator, SimulatorParticleSystem, SimulatorRigidBodySystem, SimulatorArticulatedBodySystem, StateUpdater, StateUpdaterParticleSystem, StateUpdaterRigidBodySystem, StateUpdaterArticulatedBodySystem, DocumentManager, Document, Folder, Camera, Label, DataGraphNodeGroup, NodeGroup, Controller, ControllerNode, Asset }
	The type of the data graph node. 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

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

void	setName (const std::string &name)
	Sets the name of the group.

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, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false)
	Returns some nodes.

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

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

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

Public Member Functions inherited from SBMStructuralModelNode
virtual	~SBMStructuralModelNode ()

SBMStructuralModelNode *	getNextStructuralNode () const

SBMStructuralModelNode *	getPreviousStructuralNode () const

SBMStructuralModel *	getModel () const

bool	getMobilityFlag () const
	Returns the mobility flag.

void	setMobilityFlag (bool flag)
	Sets the mobility flag to `flag`.

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

bool	structuralSignalIsConnectedToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBStructuralEvent *)) const

void	disconnectStructuralSignalFromSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBStructuralEvent *))

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))

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

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

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

SBDDataGraphNode *	getPreviousNode () const
	Returns the pointer to the previous node in the children of the node's parent. More...

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

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

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

virtual bool	canAddChild (SBDDataGraphNode node, SBDDataGraphNode nextNode=0) const
	Returns whether this node can add `node` as a child. More...

virtual bool	addChild (SBDDataGraphNode node, SBDDataGraphNode nextNode=0)
	Adds a child to the node. More...

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

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. More...

bool	isIn (SBDDataGraphNode *node) const
	Returns true if and only if this node is `node`, or descends from it. More...

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. More...

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. More...

bool	isOneOf (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodeIndexer`. More...

bool	isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodePointerIndexer`. More...

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

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

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

bool	isStructuralParticle () const
	Returns true when the node is a structural particle (an atom or a pseudo-atom)

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

void	create ()
	Creates the node. More...

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

void	erase ()
	Erases the node. More...

unsigned int	getFlags () const
	Returns the flags. More...

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

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

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

bool	getSelectionFlag () const
	Returns the selection flag. More...

void	setSelectionFlag (bool flag)
	Sets the selection flag. More...

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

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

bool	getVisibilityFlag () const
	Returns the visibility flag. More...

void	setVisibilityFlag (bool flag)
	Sets the visibility flag. More...

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

bool	getHighlightingFlag () const
	Returns the highlighting flag. More...

void	setHighlightingFlag (bool flag)
	Sets the highlighting flag. More...

virtual void	display (RenderingPass renderingPass)
	Displays the node. More...

virtual void	display ()
	Displays the node (deprecated) More...

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

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

bool	addMaterial (SBDDataGraphNodeMaterial *material)
	Adds a material. More...

bool	removeMaterial ()
	Removes the material. More...

SBDDataGraphNodeMaterial *	getMaterial () const
	Returns the material. More...

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

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

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 (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false)
	Collects nodes into `nodeIndexer`, based on a `selectionPredicate` and a `visitPredicate`, with our without dependencies. More...

Public Member Functions inherited from SBCReferenceTarget
	SBCReferenceTarget ()

virtual	~SBCReferenceTarget ()

unsigned int	getMemoryFootprint () const

void	printReferencesToOwners () const

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`. More...

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

static std::string	getTypeString (Type type)
	Returns a string describing the type of the data graph node. More...

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. More...

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

virtual	~SBDDataGraphNode ()
	Destroys the node. More...

Member Enumeration Documentation

◆ HydrophobicityScale

enum 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.

◆ 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 with.
AcidicPolar	Residue has a side chain with acidic polarity.
BasicPolar	Residue has a side chain with basic polarity.

Member Function Documentation

◆ 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.

◆ 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

virtual

Each node in the data graph has a type, which can be used, for example, to rapidly search the data graph:

// Find all atoms
SBNodeIndexer nodeIndexer;
SAMSON::getActiveDocument()->getNodes(nodeIndexer, SBNode::IsType(SBNode::Atom));

Reimplemented from SBMStructuralModelNodeGroup.

Constructors and destructors

Serialization

Node property attributes

Topology

Identity

Covalent bonds

Structure

Hydrophobicity

Properties of common amino acids

Side chain properties

Additional Inherited Members

Member Enumeration Documentation

◆ HydrophobicityScale

◆ SideChainCharge

◆ SideChainPolarity

Member Function Documentation

◆ getDissociationConstant1() [1/2]

◆ getDissociationConstant1() [2/2]

◆ getDissociationConstant2() [1/2]

◆ getDissociationConstant2() [2/2]

◆ getIsoelectricPointPH() [1/2]

◆ getIsoelectricPointPH() [2/2]

◆ getSideChainCharge() [1/2]

◆ getSideChainCharge() [2/2]

◆ getSideChainPolarity() [1/2]

◆ getSideChainPolarity() [2/2]

◆ getType()