Class SBMStructuralModelNodeResidue#

ClassList > SBMStructuralModelNodeResidue

This class describes a residue in a structural model. More...

#include "SBMStructuralModelNodeResidue.hpp"

Inherits the following classes: SBMStructuralModelNodeGroup

Public Types#

Type	Name
enum	HydrophobicityScale The available hydrophobicity scale types.
enum	ResidueType The available residue types.
enum	SecondaryStructureType The available secondary structure types.
enum	SideChainCharge The available side chain charge types.
enum	SideChainPolarity The available side chain polarity 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
	SBMStructuralModelNodeResidue () Builds a residue.
	SBMStructuralModelNodeResidue (const std::string & n) Builds a residue with the given name.
	SB_DECLARE_DATA (SBMStructuralModelNodeResidue)
	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)
virtual bool	addChild (SBNode * node, SBNode * nextNode=nullptr) override Adds a child to the node.
int	addHydrogensByResidueType () Adds hydrogen atoms to the residue based on its type.
virtual bool	canAddChild (const SBNode * node, const SBNode * nextNode=nullptr) override const Returns whether this node can add `node` as a child.
virtual bool	canAddChildType (SBNode::Type nodeType) override const Returns whether this node can add a node with type `nodeType` as a child.
virtual bool	canHaveDescendantType (SBNode::Type nodeType) override const Returns whether this node can have a node with type `nodeType` as a descendant.
virtual SBMStructuralModelNodeResidue *	clone () override Returns a copy of the node and its descendants.
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.
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.
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	computeNucleicAcidChiAngle () Computes the chi 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	computeNucleicAcidGammaAngle () Computes the gamma (O5'-C5'-C4'-C3') 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.
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.
std::string	getAminoAcidOneLetterCode () const Returns one letter code of the amino acid residue.
SBMStructuralModelNodeBackbone *	getBackbone () const Returns the residue's backbone if it has one, else returns nullptr.
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	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.
int	getHydrophobicityScaleCount () const Returns the number of hydrophobicity scales.
int	getHydrophobicityScaleCurrentIndex () const Returns the current scale's index in the list of hydrophobicity scales.
std::string	getHydrophobicityScaleItemText (const int index) const Returns the hydrophobicity scale `index` as a string.
std::string	getHydrophobicityScaleString () const Returns the current hydrophobicity scale as a string.
double	getIsoelectricPointPH () const Returns the pI value (the pH at the isoelectric point) for this residue.
SBMStructuralModelNodeResidue *	getNextAminoAcid () const Returns the next amino acid if any, else returns nullptr.
SBMStructuralModelNodeResidue *	getNextNucleicAcid () const Returns the next nucleic acid if any, else returns nullptr.
SBMStructuralModelNodeResidue *	getNextResidue () const Returns the next residue if any, else returns nullptr.
SBMStructuralModelNodeResidue *	getPreviousAminoAcid () const Returns the previous amino acid if any, else returns nullptr.
SBMStructuralModelNodeResidue *	getPreviousNucleicAcid () const Returns the previous nucleic acid if any, else returns nullptr.
SBMStructuralModelNodeResidue *	getPreviousResidue () const Returns the previous residue if any, else returns nullptr.
ResidueType	getResidueType () const Returns the residue's type.
std::string	getResidueTypeFullName () const Returns the full name of the residue's type.
std::string	getResidueTypeString () const Returns the string representation of the residue's type.
SecondaryStructureType	getSecondaryStructureType () const Returns the most probable secondary structure based on bonds parameters and residue geometry.
std::string	getSecondaryStructureTypeString () const Returns the secondary structure type as a string.
SBMStructuralModelNodeSideChain *	getSideChain () const Returns the residue's side chain if it has one, else returns nullptr.
SideChainCharge	getSideChainCharge () const Returns the residue's side chain charge.
std::string	getSideChainChargeString () const Returns the residue's side chain charge as a string.
SideChainPolarity	getSideChainPolarity () const Returns the residue's side chain polarity.
std::string	getSideChainPolarityString () const Returns the residue's side chain polarity as a string.
virtual Type	getType () override const Returns the node type (returns SBNode::Residue )
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.
bool	hasCompleteAminoAcidBackbone () const Returns `true` if and only if the residue has a complete amino-acid backbone.
bool	hasDissociationConstant () const Returns `true` if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for this residue.
bool	hasHydrophobicity () const Returns `true` if the residue's hydrophobicity is defined.
bool	hasSideChainCharge () const Returns `true` if the residue's side chain charge is defined.
bool	hasSideChainPolarity () const Returns `true` if the residue's side chain polarity is defined.
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.
virtual bool	isSerializable () override const Returns `true` __
bool	isTerminal () const Returns `true` if and only if the residue is terminal.
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.
virtual bool	removeChild (SBNode * node) override Removes a child from the node.
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	setHydrophobicityScale (const HydrophobicityScale hydrophobicityScale) Sets the current hydrophobicity scale to `hydrophobicityScale` .
void	setHydrophobicityScaleCurrentIndex (const int index) Sets the current hydrophobicity scale to the hydrophobicity scale from the list.
virtual void	setName (const std::string & name) override Sets the name of the residue, and updates accordingly names for its backbone and side chain.
void	setResidueType (ResidueType residueType) Sets the residue's type to `residueType` .
void	setResidueType (const std::string & s) Sets the residue's type based on the string `s` .
void	setSecondaryStructureType (SecondaryStructureType type) Sets the most probable secondary structure based on bonds parameters and residue geometry.
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	~SBMStructuralModelNodeResidue () Destructor.

Public Functions inherited from SBMStructuralModelNodeGroup#

See SBMStructuralModelNodeGroup

Type	Name
	SBMStructuralModelNodeGroup () Builds a structural group.
	SBMStructuralModelNodeGroup (const std::string & n) Builds a structural group with the given name.
	SB_DECLARE_DATA (SBMStructuralModelNodeGroup)
	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)
virtual bool	addChild (SBNode * node, SBNode * nextNode=nullptr) override Adds a child to the node.
virtual bool	canAddChild (const SBNode * node, const SBNode * nextNode=nullptr) override const Returns whether this node can add `node` as a child.
virtual bool	canAddChildType (SBNode::Type nodeType) override const Returns whether this node can add a node with type `nodeType` as a child.
virtual bool	canHaveDescendantType (SBNode::Type nodeType) override const Returns whether this node can have a node with type `nodeType` as a descendant.
void	clearComment () Clears the comment.
void	clearStatusBit () Clears the status bit.
void	clearStructuralID () Clears the structural group's id.
virtual SBMStructuralModelNodeGroup *	clone () override Returns a copy of the node and its descendants.
virtual void	forEachNodeDepthFirst (void()(SBDDataGraphNode* node) action) override Performs the* `action` on this node and then its children in the depth-first way.
virtual void	forEachNodeDepthFirst (SBCClass * object, void(SBCClass::)(SBDDataGraphNode* node) action) override Performs the* `object` 's`action` on this node and then its children in the depth-first way.
virtual SBPointerList< SBMStructuralModelNode > const *	getChildren () override const Returns the list of child nodes.
std::string const &	getComment () const Returns the comment.
virtual SBQuantity::mass	getMolecularWeight () override Returns the molecular weight.
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	getNumberOfAtoms () override Returns the number of atoms.
virtual unsigned int	getNumberOfCarbons () override Returns the number of carbons.
virtual unsigned int	getNumberOfChains () override Returns the number of chains.
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	getNumberOfMolecules () override Returns the number of molecules.
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	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	getNumberOfSulfurs () override Returns the number of sulfurs.
std::string const &	getStatusBit () const Returns the status bit.
int const &	getStructuralID () const Returns the structural group's id.
virtual int	getSumOfFormalCharges () override Returns the sum of formal charges.
virtual float	getSumOfPartialCharges () override Returns the sum of partial charges.
virtual SBDDataGraphNode::Type	getType () override const Returns the node type ( SBNode::StructuralGroup )
bool	hasComment () const Returns `true` when the comment is set.
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.
bool	hasStatusBit () const Returns `true` when the status bit is set.
bool	hasStructuralID () const Returns `true` when the structural group's id is set.
bool	isMonatomicIon () Returns `true` if the structural group is a monatomic ion.
virtual bool	isSerializable () override const Returns `true` __
bool	isWater () Returns `true` if the structural group is a water molecule.
virtual void	onBaseEvent (SBEvent * event) Handles base events.
virtual void	print (unsigned int offset=0) override const Prints debugging information.
virtual bool	removeChild (SBNode * node) override Removes a child from the node.
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	setComment (const std::string & comment) Sets the comment.
virtual void	setName (const std::string & name) override Sets the name of the structural group.
void	setStatusBit (const std::string & statusBit) Sets the status bit.
void	setStructuralID (const int & groupID) Sets the structural group's id.
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	~SBMStructuralModelNodeGroup () Destructor.

Public Functions inherited from SBMStructuralModelNode#

See SBMStructuralModelNode

Type	Name
	SB_DECLARE_DATA (SBMStructuralModelNode)
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
	SB_DECLARE_DATA (SBMModelNode)
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
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.
SBDDataGraphNodeData *	getDataPointer ()
const SBDDataGraphNodeData *	getDataPointer () const
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	getAminoAcidOneLetterCode (const ResidueType residueType) Returns one letter code of the amino acid residue `residueType` .
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` .
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` .
double	getHydrophobicity (const ResidueType residueType, const HydrophobicityScale hydrophobicityScale) Returns the hydrophobicity value for the residue `residueType` in the hydrophobicity scale`hydrophobicityScale` .
std::string	getHydrophobicityScaleString (const HydrophobicityScale hydrophobicityScale) Returns the hydrophobicity scale `hydrophobicityScale` as a string.
double	getIsoelectricPointPH (const ResidueType residueType) Returns the pI value (the pH at the isoelectric point) for the residue `residueType` .
ResidueType	getResidueTypeFromAminoAcidOneLetterCode (const std::string & s) Returns the amino acid residue type from the one letter code of the amino acid residue `s` .
ResidueType	getResidueTypeFromString (const std::string & s) Returns the residue type based on the string `s` .
std::string	getResidueTypeFullName (ResidueType residueType) Returns the full name of the residue type `residueType` .
std::string	getResidueTypeString (ResidueType residueType) Returns the string representation of the residue type `residueType` .
std::string	getSecondaryStructureTypeString (SecondaryStructureType secondaryStructureType) Returns the secondary structure type `secondaryStructureType` as a string.
SideChainCharge	getSideChainCharge (const ResidueType residueType) Returns the residue's side chain charge for the residue `residueType` .
std::string	getSideChainChargeString (const SideChainCharge sideChainCharge) Returns a side chain charge `sideChainCharge` as a string.
SideChainPolarity	getSideChainPolarity (const ResidueType residueType) Returns the residue's side chain polarity for the residue `residueType` .
std::string	getSideChainPolarityString (const SideChainPolarity sideChainPolarity) Returns a side chain polarity `sideChainPolarity` as a string.
bool	hasAminoAcidChi1Angle (const ResidueType residueType) Returns `true` if the residue type`residueType` is an amino acid and has chi1 angle.
bool	hasAminoAcidChi2Angle (const ResidueType residueType) Returns `true` if the residue type`residueType` is an amino acid and has chi2 angle.
bool	hasAminoAcidChi3Angle (const ResidueType residueType) Returns `true` if the residue type`residueType` is an amino acid and has chi3 angle.
bool	hasAminoAcidChi4Angle (const ResidueType residueType) Returns `true` if the residue type`residueType` is an amino acid and has chi4 angle.
bool	hasAminoAcidChi5Angle (const ResidueType residueType) Returns `true` if the residue type`residueType` is an amino acid and has chi5 angle.
bool	hasDissociationConstant (const ResidueType residueType) Returns `true` if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for the residue`residueType` .
bool	hasHydrophobicity (const ResidueType residueType) Returns `true` if for the residue type`residueType` the hydrophobicity is defined.
bool	hasSideChainCharge (const ResidueType residueType) Returns `true` if for the residue type`residueType` the side chain charge is defined.
bool	hasSideChainPolarity (const ResidueType residueType) Returns `true` if for the residue type`residueType` the side chain polarity is defined.
bool	isAminoAcid (ResidueType residueType) Returns `true` if and only if the residue of`residueType` is an amino acid.
bool	isNucleicAcid (ResidueType residueType) Returns `true` if and only if the residue of`residueType` is a nucleic acid.
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.
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.
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.

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 SBMStructuralModelNodeGroup#

See SBMStructuralModelNodeGroup

Type	Name
	SBMStructuralModelNodeGroup (SBMStructuralModelNodeGroupData * dataPointer) Builds a base object.

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: SBResidue

Public Types Documentation#

enum HydrophobicityScale#

The available hydrophobicity scale types.

enum SBMStructuralModelNodeResidue::HydrophobicityScale {
    KyteDoolittle1982 = 0,
    SeredaEtAl1994 = 1,
    MoneraEtAl1995 = 2,
    WimleyWhite1996 = 3,
    HessaEtAl2005 = 4,
    ZhaoLondon2006 = 5,
    MoonFleming2011 = 6
};

enum ResidueType#

The available residue types.

href="#__codelineno-1-1">enum SBMStructuralModelNodeResidue::ResidueType { Undefined = 0, ALA = 1, ARG = 2, ASP = 3, ASN = 4, VAL = 5, HIS = 6, GLY = 7, GLU = 8, GLN = 9, ILE = 10, LEU = 11, LYS = 12, MET = 13, PRO = 14, SER = 15, TYR = 16, THR = 17, TRP = 18, PHE = 19, CYS = 20, ASX = 21, GLX = 22, XLE = 23, XAA = 24, SEC = 25, PYL = 26, A = 27, C = 28, G = 29, U = 30, I = 31, DA = 32, DC = 33, DG = 34, DT = 35, DI = 36 };

enum SecondaryStructureType#

The available secondary structure types.

enum SBMStructuralModelNodeResidue::SecondaryStructureType {
    Unstructured = 0,
    Alpha = 1,
    Beta = 2
};

enum SideChainCharge#

The available side chain charge types.

enum SBMStructuralModelNodeResidue::SideChainCharge {
    UndefinedSideChainCharge = 0,
    Negative = 1,
    Neutral = 2,
    Positive = 3
};

enum SideChainPolarity#

The available side chain polarity types.

enum SBMStructuralModelNodeResidue::SideChainPolarity {
    UndefinedSideChainPolarity = 0,
    Nonpolar = 1,
    Polar = 2,
    AcidicPolar = 3,
    BasicPolar = 4
};

Public Functions Documentation#

function SBMStructuralModelNodeResidue [1/2]#

Builds a residue.

SBMStructuralModelNodeResidue::SBMStructuralModelNodeResidue ()

function SBMStructuralModelNodeResidue [2/2]#

Builds a residue with the given name.

SBMStructuralModelNodeResidue::SBMStructuralModelNodeResidue (
    const std::string & n
)

function SB_DECLARE_DATA#

SBMStructuralModelNodeResidue::SB_DECLARE_DATA (
    SBMStructuralModelNodeResidue
)

function SB_NODE_GETTER_0 [1/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    SBMStructuralModelNodeResidue::ResidueType,
    GetResidueType
)

function SB_NODE_GETTER_0 [2/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    std::string,
    GetResidueTypeString
)

function SB_NODE_GETTER_0 [3/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    SBMStructuralModelNodeResidue::SecondaryStructureType,
    GetSecondaryStructureType
)

function SB_NODE_GETTER_0 [4/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    double,
    GetHydrophobicity
)

function SB_NODE_GETTER_0 [5/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    SBMStructuralModelNodeResidue::HydrophobicityScale,
    GetHydrophobicityScale
)

function SB_NODE_GETTER_0 [6/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    SBMStructuralModelNodeResidue::SideChainCharge,
    GetSideChainCharge
)

function SB_NODE_GETTER_0 [7/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    std::string,
    GetSideChainChargeString
)

function SB_NODE_GETTER_0 [8/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    SBMStructuralModelNodeResidue::SideChainPolarity,
    GetSideChainPolarity
)

function SB_NODE_GETTER_0 [9/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    std::string,
    GetSideChainPolarityString
)

function SB_NODE_GETTER_0 [10/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    double,
    GetDissociationConstant1
)

function SB_NODE_GETTER_0 [11/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    double,
    GetDissociationConstant2
)

function SB_NODE_GETTER_0 [12/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    double,
    GetIsoelectricPointPH
)

function SB_NODE_GETTER_0 [13/13]#

SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
    int,
    GetResidueSequenceNumber
)

function SB_NODE_PREDICATE_0 [1/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    IsAminoAcid
)

function SB_NODE_PREDICATE_0 [2/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    IsNucleicAcid
)

function SB_NODE_PREDICATE_0 [3/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    IsTerminal
)

function SB_NODE_PREDICATE_0 [4/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    HasStandardResidueName
)

function SB_NODE_PREDICATE_0 [5/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    HasCompleteAminoAcidBackbone
)

function SB_NODE_PREDICATE_0 [6/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    HasHydrophobicity
)

function SB_NODE_PREDICATE_0 [7/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    HasSideChainCharge
)

function SB_NODE_PREDICATE_0 [8/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    HasSideChainPolarity
)

function SB_NODE_PREDICATE_0 [9/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    HasDissociationConstant
)

function SB_NODE_PREDICATE_0 [10/10]#

SBMStructuralModelNodeResidue::SB_NODE_PREDICATE_0 (
    HasResidueSequenceNumber
)

function addChild#

Adds a child to the node.

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

Implements SBMStructuralModelNodeGroup::addChild

function addHydrogensByResidueType#

Adds hydrogen atoms to the residue based on its type.

int SBMStructuralModelNodeResidue::addHydrogensByResidueType ()

function canAddChild#

Returns whether this node can add node as a child.

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

Implements SBMStructuralModelNodeGroup::canAddChild

function canAddChildType#

Returns whether this node can add a node with type nodeType as a child.

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

Implements SBMStructuralModelNodeGroup::canAddChildType

function canHaveDescendantType#

Returns whether this node can have a node with type nodeType as a descendant.

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

Implements SBMStructuralModelNodeGroup::canHaveDescendantType

function clone#

Returns a copy of the node and its descendants.

virtual SBMStructuralModelNodeResidue * SBMStructuralModelNodeResidue::clone () override

Implements SBMStructuralModelNodeGroup::clone

function computeAminoAcidChi1Angle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeAminoAcidChi1Angle ()

function computeAminoAcidChi2Angle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeAminoAcidChi2Angle ()

function computeAminoAcidChi3Angle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeAminoAcidChi3Angle ()

function computeAminoAcidChi4Angle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeAminoAcidChi4Angle ()

function computeAminoAcidChi5Angle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeAminoAcidChi5Angle ()

function computeAminoAcidPhiAngle#

Computes the phi dihedral angle (in degrees) for the amino acid's backbone.

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeAminoAcidPhiAngle ()

function computeAminoAcidPsiAngle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeAminoAcidPsiAngle ()

function computeNucleicAcidAlphaAngle#

Computes the alpha (O3'(i-1)-P-O5'-C5') dihedral angle (in degrees) for the nucleic acid's backbone.

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeNucleicAcidAlphaAngle ()

function computeNucleicAcidBetaAngle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeNucleicAcidBetaAngle ()

function computeNucleicAcidChiAngle#

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

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.

function computeNucleicAcidDeltaAngle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeNucleicAcidDeltaAngle ()

function computeNucleicAcidEpsilonAngle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeNucleicAcidEpsilonAngle ()

function computeNucleicAcidGammaAngle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeNucleicAcidGammaAngle ()

function computeNucleicAcidZetaAngle#

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

SBQuantity::dimensionless SBMStructuralModelNodeResidue::computeNucleicAcidZetaAngle ()

function createCovalentBondsByResidueType#

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

int SBMStructuralModelNodeResidue::createCovalentBondsByResidueType ()

function getAminoAcidOneLetterCode [1/2]#

Returns one letter code of the amino acid residue.

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.

function getBackbone#

Returns the residue's backbone if it has one, else returns nullptr.

SBMStructuralModelNodeBackbone * SBMStructuralModelNodeResidue::getBackbone () const

function getDissociationConstant1 [1/2]#

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

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.

function getDissociationConstant2 [1/2]#

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

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.

function getHydrophobicity [1/3]#

Returns the residue's hydrophobicity in the current hydrophobicity scale.

double SBMStructuralModelNodeResidue::getHydrophobicity () const

function getHydrophobicity [2/3]#

Returns the residue's hydrophobicity in the given hydrophobicity scale hydrophobicityScale .

double SBMStructuralModelNodeResidue::getHydrophobicity (
    const HydrophobicityScale hydrophobicityScale
) const

function getHydrophobicityScale#

Returns the current scale of the residue's hydrophobicity.

HydrophobicityScale SBMStructuralModelNodeResidue::getHydrophobicityScale () const

function getHydrophobicityScaleCount#

Returns the number of hydrophobicity scales.

int SBMStructuralModelNodeResidue::getHydrophobicityScaleCount () const

function getHydrophobicityScaleCurrentIndex#

Returns the current scale's index in the list of hydrophobicity scales.

int SBMStructuralModelNodeResidue::getHydrophobicityScaleCurrentIndex () const

function getHydrophobicityScaleItemText#

Returns the hydrophobicity scale index as a string.

std::string SBMStructuralModelNodeResidue::getHydrophobicityScaleItemText (
    const int index
) const

function getHydrophobicityScaleString [1/2]#

Returns the current hydrophobicity scale as a string.

std::string SBMStructuralModelNodeResidue::getHydrophobicityScaleString () const

function getIsoelectricPointPH [1/2]#

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

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.

function getNextAminoAcid#

Returns the next amino acid if any, else returns nullptr.

SBMStructuralModelNodeResidue * SBMStructuralModelNodeResidue::getNextAminoAcid () const

function getNextNucleicAcid#

Returns the next nucleic acid if any, else returns nullptr.

SBMStructuralModelNodeResidue * SBMStructuralModelNodeResidue::getNextNucleicAcid () const

function getNextResidue#

Returns the next residue if any, else returns nullptr.

SBMStructuralModelNodeResidue * SBMStructuralModelNodeResidue::getNextResidue () const

function getPreviousAminoAcid#

Returns the previous amino acid if any, else returns nullptr.

SBMStructuralModelNodeResidue * SBMStructuralModelNodeResidue::getPreviousAminoAcid () const

function getPreviousNucleicAcid#

Returns the previous nucleic acid if any, else returns nullptr.

SBMStructuralModelNodeResidue * SBMStructuralModelNodeResidue::getPreviousNucleicAcid () const

function getPreviousResidue#

Returns the previous residue if any, else returns nullptr.

SBMStructuralModelNodeResidue * SBMStructuralModelNodeResidue::getPreviousResidue () const

function getResidueType#

Returns the residue's type.

ResidueType SBMStructuralModelNodeResidue::getResidueType () const

function getResidueTypeFullName [1/2]#

Returns the full name of the residue's type.

std::string SBMStructuralModelNodeResidue::getResidueTypeFullName () const

function getResidueTypeString [1/2]#

Returns the string representation of the residue's type.

std::string SBMStructuralModelNodeResidue::getResidueTypeString () const

function getSecondaryStructureType#

Returns the most probable secondary structure based on bonds parameters and residue geometry.

SecondaryStructureType SBMStructuralModelNodeResidue::getSecondaryStructureType () const

function getSecondaryStructureTypeString [1/2]#

Returns the secondary structure type as a string.

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

function getSideChain#

Returns the residue's side chain if it has one, else returns nullptr.

SBMStructuralModelNodeSideChain * SBMStructuralModelNodeResidue::getSideChain () const

function getSideChainCharge [1/2]#

Returns the residue's side chain charge.

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.

function getSideChainChargeString [1/2]#

Returns the residue's side chain charge as a string.

std::string SBMStructuralModelNodeResidue::getSideChainChargeString () const

function getSideChainPolarity [1/2]#

Returns the residue's side chain polarity.

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.

function getSideChainPolarityString [1/2]#

Returns the residue's side chain polarity as a string.

std::string SBMStructuralModelNodeResidue::getSideChainPolarityString () const

function getType#

Returns the node type (returns SBNode::Residue )

virtual Type SBMStructuralModelNodeResidue::getType () override const

Implements SBMStructuralModelNodeGroup::getType

function hasAminoAcidChi1Angle [1/2]#

Returns true if it is an amino acid and has chi1 angle.

bool SBMStructuralModelNodeResidue::hasAminoAcidChi1Angle () const

function hasAminoAcidChi2Angle [1/2]#

Returns true if it is an amino acid and has chi2 angle.

bool SBMStructuralModelNodeResidue::hasAminoAcidChi2Angle () const

function hasAminoAcidChi3Angle [1/2]#

Returns true if it is an amino acid and has chi3 angle.

bool SBMStructuralModelNodeResidue::hasAminoAcidChi3Angle () const

function hasAminoAcidChi4Angle [1/2]#

Returns true if it is an amino acid and has chi4 angle.

bool SBMStructuralModelNodeResidue::hasAminoAcidChi4Angle () const

function hasAminoAcidChi5Angle [1/2]#

Returns true if it is an amino acid and has chi5 angle.

bool SBMStructuralModelNodeResidue::hasAminoAcidChi5Angle () const

function hasCompleteAminoAcidBackbone#

Returns true if and only if the residue has a complete amino-acid backbone.

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).

function hasDissociationConstant [1/2]#

Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for this residue.

bool SBMStructuralModelNodeResidue::hasDissociationConstant () const

function hasHydrophobicity [1/2]#

Returns true if the residue's hydrophobicity is defined.

bool SBMStructuralModelNodeResidue::hasHydrophobicity () const

function hasSideChainCharge [1/2]#

Returns true if the residue's side chain charge is defined.

bool SBMStructuralModelNodeResidue::hasSideChainCharge () const

function hasSideChainPolarity [1/2]#

Returns true if the residue's side chain polarity is defined.

bool SBMStructuralModelNodeResidue::hasSideChainPolarity () const

function hasStandardResidueName#

Returns true if and only if the residue name corresponds to one of the standard PDB residue names.

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 preceding 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.

function isAminoAcid [1/2]#

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

bool SBMStructuralModelNodeResidue::isAminoAcid () const

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

function isNucleicAcid [1/2]#

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

bool SBMStructuralModelNodeResidue::isNucleicAcid () const

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

function isSerializable#

Returns true __

virtual bool SBMStructuralModelNodeResidue::isSerializable () override const

Implements SBMStructuralModelNodeGroup::isSerializable

function isTerminal#

Returns true if and only if the residue is terminal.

bool SBMStructuralModelNodeResidue::isTerminal () const

function orientAminoAcidSideChain#

Rotates the amino acid's side chain to orient it according to given dihedral angles chi1 ,chi2 ,chi3 ,chi4 ,chi5 . Returns true if at leastchi1 rotation was performed.

bool SBMStructuralModelNodeResidue::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)
)

function removeChild#

Removes a child from the node.

virtual bool SBMStructuralModelNodeResidue::removeChild (
    SBNode * node
) override

Implements SBMStructuralModelNodeGroup::removeChild

function serialize#

Serializes the node.

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

Implements SBMStructuralModelNodeGroup::serialize

function setHydrophobicityScale#

Sets the current hydrophobicity scale to hydrophobicityScale .

void SBMStructuralModelNodeResidue::setHydrophobicityScale (
    const HydrophobicityScale hydrophobicityScale
)

function setHydrophobicityScaleCurrentIndex#

Sets the current hydrophobicity scale to the hydrophobicity scale from the list.

void SBMStructuralModelNodeResidue::setHydrophobicityScaleCurrentIndex (
    const int index
)

function setName#

Sets the name of the residue, and updates accordingly names for its backbone and side chain.

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

Implements SBMStructuralModelNodeGroup::setName

function setResidueType [1/2]#

Sets the residue's type to residueType .

void SBMStructuralModelNodeResidue::setResidueType (
    ResidueType residueType
)

function setResidueType [2/2]#

Sets the residue's type based on the string s .

void SBMStructuralModelNodeResidue::setResidueType (
    const std::string & s
)

function setSecondaryStructureType#

Sets the most probable secondary structure based on bonds parameters and residue geometry.

void SBMStructuralModelNodeResidue::setSecondaryStructureType (
    SecondaryStructureType type
)

function unserialize#

Unserializes the node.

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

Implements SBMStructuralModelNodeGroup::unserialize

function ~SBMStructuralModelNodeResidue#

Destructor.

virtual SBMStructuralModelNodeResidue::~SBMStructuralModelNodeResidue ()

Public Static Functions Documentation#

function getAminoAcidOneLetterCode [2/2]#

Returns one letter code of the amino acid residue residueType .

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

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.

function getDissociationConstant1 [2/2]#

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 SBMStructuralModelNodeResidue::getDissociationConstant1 (
    const ResidueType residueType
)

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.

function getDissociationConstant2 [2/2]#

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 SBMStructuralModelNodeResidue::getDissociationConstant2 (
    const ResidueType residueType
)

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.

function getHydrophobicity [3/3]#

Returns the hydrophobicity value for the residue residueType in the hydrophobicity scalehydrophobicityScale .

static double SBMStructuralModelNodeResidue::getHydrophobicity (
    const ResidueType residueType,
    const HydrophobicityScale hydrophobicityScale
)

function getHydrophobicityScaleString [2/2]#

Returns the hydrophobicity scale hydrophobicityScale as a string.

static std::string SBMStructuralModelNodeResidue::getHydrophobicityScaleString (
    const HydrophobicityScale hydrophobicityScale
)

function getIsoelectricPointPH [2/2]#

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

static double SBMStructuralModelNodeResidue::getIsoelectricPointPH (
    const ResidueType residueType
)

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.

function getResidueTypeFromAminoAcidOneLetterCode#

Returns the amino acid residue type from the one letter code of the amino acid residue s .

static ResidueType SBMStructuralModelNodeResidue::getResidueTypeFromAminoAcidOneLetterCode (
    const std::string & s
)

function getResidueTypeFromString#

Returns the residue type based on the string s .

static ResidueType SBMStructuralModelNodeResidue::getResidueTypeFromString (
    const std::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.

function getResidueTypeFullName [2/2]#

Returns the full name of the residue type residueType .

static std::string SBMStructuralModelNodeResidue::getResidueTypeFullName (
    ResidueType residueType
)

function getResidueTypeString [2/2]#

Returns the string representation of the residue type residueType .

static std::string SBMStructuralModelNodeResidue::getResidueTypeString (
    ResidueType residueType
)

function getSecondaryStructureTypeString [2/2]#

Returns the secondary structure type secondaryStructureType as a string.

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

Returns the secondary structure type secondaryStructureType as a string:

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

function getSideChainCharge [2/2]#

Returns the residue's side chain charge for the residue residueType .

static SideChainCharge SBMStructuralModelNodeResidue::getSideChainCharge (
    const ResidueType residueType
)

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.

function getSideChainChargeString [2/2]#

Returns a side chain charge sideChainCharge as a string.

static std::string SBMStructuralModelNodeResidue::getSideChainChargeString (
    const SideChainCharge sideChainCharge
)

function getSideChainPolarity [2/2]#

Returns the residue's side chain polarity for the residue residueType .

static SideChainPolarity SBMStructuralModelNodeResidue::getSideChainPolarity (
    const ResidueType residueType
)

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.

function getSideChainPolarityString [2/2]#

Returns a side chain polarity sideChainPolarity as a string.

static std::string SBMStructuralModelNodeResidue::getSideChainPolarityString (
    const SideChainPolarity sideChainPolarity
)

function hasAminoAcidChi1Angle [2/2]#

Returns true if the residue typeresidueType is an amino acid and has chi1 angle.

static bool SBMStructuralModelNodeResidue::hasAminoAcidChi1Angle (
    const ResidueType residueType
)

function hasAminoAcidChi2Angle [2/2]#

Returns true if the residue typeresidueType is an amino acid and has chi2 angle.

static bool SBMStructuralModelNodeResidue::hasAminoAcidChi2Angle (
    const ResidueType residueType
)

function hasAminoAcidChi3Angle [2/2]#

Returns true if the residue typeresidueType is an amino acid and has chi3 angle.

static bool SBMStructuralModelNodeResidue::hasAminoAcidChi3Angle (
    const ResidueType residueType
)

function hasAminoAcidChi4Angle [2/2]#

Returns true if the residue typeresidueType is an amino acid and has chi4 angle.

static bool SBMStructuralModelNodeResidue::hasAminoAcidChi4Angle (
    const ResidueType residueType
)

function hasAminoAcidChi5Angle [2/2]#

Returns true if the residue typeresidueType is an amino acid and has chi5 angle.

static bool SBMStructuralModelNodeResidue::hasAminoAcidChi5Angle (
    const ResidueType residueType
)

function hasDissociationConstant [2/2]#

Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for the residueresidueType .

static bool SBMStructuralModelNodeResidue::hasDissociationConstant (
    const ResidueType residueType
)

function hasHydrophobicity [2/2]#

Returns true if for the residue typeresidueType the hydrophobicity is defined.

static bool SBMStructuralModelNodeResidue::hasHydrophobicity (
    const ResidueType residueType
)

function hasSideChainCharge [2/2]#

Returns true if for the residue typeresidueType the side chain charge is defined.

static bool SBMStructuralModelNodeResidue::hasSideChainCharge (
    const ResidueType residueType
)

function hasSideChainPolarity [2/2]#

Returns true if for the residue typeresidueType the side chain polarity is defined.

static bool SBMStructuralModelNodeResidue::hasSideChainPolarity (
    const ResidueType residueType
)

function isAminoAcid [2/2]#

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

static bool SBMStructuralModelNodeResidue::isAminoAcid (
    ResidueType residueType
)

function isNucleicAcid [2/2]#

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

static bool SBMStructuralModelNodeResidue::isNucleicAcid (
    ResidueType residueType
)

function isStandardAminoAcidName#

Returns true if and only if the namename corresponds to one of the standard PDB amino acid residue names.

static bool SBMStructuralModelNodeResidue::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 (3 letter code).

function isStandardNucleicAcidName#

Returns true if and only if the namename corresponds to one of the standard PDB nucleic acid residue names.

static bool SBMStructuralModelNodeResidue::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 (1 or 2 letter code).

function isStandardResidueName#

Returns true if and only if the namename corresponds to one of the standard PDB amino or nucleic acid residue names.

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

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.