Class SBMStructuralModelNodeResidue#
ClassList > SBMStructuralModelNodeResidue
#include <SBMStructuralModelNodeResidue.hpp>
Inherits the following classes: SBMStructuralModelNodeGroup
Public Types#
| Type | Name |
|---|---|
| enum | HydrophobicityScale |
| enum | ResidueType |
| enum | SecondaryStructureType |
| enum | SideChainCharge |
| enum | SideChainPolarity |
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 () |
|
| SBMStructuralModelNodeResidue (const std::string & n) |
|
| 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 leastchi1 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 () |
Public Functions inherited from SBMStructuralModelNodeGroup#
See SBMStructuralModelNodeGroup
| Type | Name |
|---|---|
| SBMStructuralModelNodeGroup () Builds a base model. |
|
| SBMStructuralModelNodeGroup (const std::string & n) |
|
| 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 an action on each node. |
| virtual void | forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) override Performs an action on each node. |
| 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 anodeType , a selection status and avisitPredicate , 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 aselectionPredicate and avisitPredicate , 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 avisitPredicate , 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 avisitPredicate , 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) |
| 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 () |
Public Functions inherited from 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=0, void(SBCReferenceTarget::*)(SBStructuralEvent *) nextFunctionPointer=0) |
| void | disconnectStructuralSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBStructuralEvent *) functionPointer, SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) |
| virtual void | forEachNodeDepthFirst (void(*)(SBDDataGraphNode *node) action) override Performs an action on each node. |
| virtual void | forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) override Performs an action on each node. |
| void | forEachStructuralNodeBreadthFirst (void(*)(SBMStructuralModelNode *node) action) |
| void | forEachStructuralNodeBreadthFirst (SBCClass * object, void(SBCClass::*)(SBMStructuralModelNode *node) action) |
| void | forEachStructuralNodeDepthFirst (void(*)(SBMStructuralModelNode *node) action) |
| void | forEachStructuralNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBMStructuralModelNode *node) action) |
| void | getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| void | getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| void | getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| virtual SBPointerList< SBMStructuralModelNode > const * | getChildren () const Returns the list of child nodes. |
| void | getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| void | getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| void | getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| void | getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| void | getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| void | getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer) |
| virtual bool | getLockedFlag () override const Returns the locked flag of the model. |
| virtual unsigned int | getMaximumTransparency () override const Returns the maximum transparency. |
| virtual unsigned int | getMinimumOpacity () override const Returns the minimum opacity. |
| SBMStructuralModel * | getModel () const |
| SBMStructuralModelNode * | getNextStructuralNode () const |
| 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 anodeType , a selection status and avisitPredicate , 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 aselectionPredicate and avisitPredicate , with or without dependencies. |
| virtual unsigned int | getOpacity () override const Returns the opacity. |
| SBMStructuralModelNode * | getPreviousStructuralNode () const |
| void | getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode * > & nodeVectorTopDown, std::vector< SBMStructuralModelNode * > & nodeVectorBottomUp, bool(*)(SBMStructuralModelNode *) selectionRule) |
| void | getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool(*)(SBMStructuralModelNode *) selectionRule) |
| void | getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool(*)(SBMStructuralModelNode *) selectionRule) |
| void | getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > & nodeIndexer, bool(*)(SBMStructuralModelNode *) selectionRule) |
| 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 type of the data graph node. |
| 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 avisitPredicate , 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 avisitPredicate , 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 |
| 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 () |
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 |
|---|---|
| SB_DECLARE_DATA (SBDDataGraphNode) |
|
| 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 avisitPredicate , 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 avisitPredicate , 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 an action on each node. |
| virtual void | forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) Performs an action on each node. |
| virtual unsigned int | getDefaultOpacity () const Returns the default opacity. |
| virtual 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. |
| virtual unsigned int | getMaximumOpacity () const Returns the maximum opacity. |
| virtual unsigned int | getMaximumTransparency () const Returns the maximum transparency. |
| virtual unsigned int | getMinimumOpacity () const Returns the minimum opacity. |
| virtual 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 anodeType , a selection status and avisitPredicate , 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 aselectionPredicate and avisitPredicate , 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. |
| virtual unsigned int | getOpacitySingleStep () const Returns the opacity single step. |
| virtual 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. |
| virtual unsigned int | getTransparencySingleStep () const Returns the transparency single step. |
| virtual 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 avisitPredicate , 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 avisitPredicate , 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. |
| virtual bool | hasOpacityRange () const Returns whether the node has the opacity range. |
| virtual 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 innode . |
| 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 thenodeIndexer . |
| 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 thenodePointerIndexer . |
| 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#
| Type | Name |
|---|---|
| SBCReferenceTarget () |
|
| unsigned int | getMemoryFootprint () const |
| void | printReferencesToOwners () const |
| virtual | ~SBCReferenceTarget () |
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 scalehydrophobicityScale . |
| 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#
| Type | Name |
|---|---|
| void | forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > & selection, void(*)(SBMStructuralModelNode *node) action) |
| void | forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > & selection, SBCClass * object, void(SBCClass::*)(SBMStructuralModelNode *node) action) |
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 indestinationNodeIndexer . |
| void | forEachNodeInSelection (SBNodeIndexer & nodeIndexer, void(*)(SBDDataGraphNode *node) action) Performs an action for each node in a selection. |
| void | forEachNodeInSelection (SBNodeIndexer & nodeIndexer, SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) Performs an action for each node in a selection. |
| 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#
| Type | Name |
|---|---|
| SBCReferenceTargetData * | dataPointer |
Protected Functions inherited from SBMStructuralModelNodeGroup#
See SBMStructuralModelNodeGroup
| Type | Name |
|---|---|
| SBMStructuralModelNodeGroup (SBMStructuralModelNodeGroupData * dataPointer) Builds a base object. |
Protected Functions inherited from 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 () |
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#
| Type | Name |
|---|---|
| SBCReferenceTarget (SBCReferenceTargetData * dataPointer) |
|
| void | removeAllReferenceOwners () |
Detailed Description#
This class describes a residue in a structural model.
Short name: SBResidue
Public Types Documentation#
enum HydrophobicityScale#
enum SBMStructuralModelNodeResidue::HydrophobicityScale {
KyteDoolittle1982 = 0,
SeredaEtAl1994 = 1,
MoneraEtAl1995 = 2,
WimleyWhite1996 = 3,
HessaEtAl2005 = 4,
ZhaoLondon2006 = 5,
MoonFleming2011 = 6
};
enum ResidueType#
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#
enum SBMStructuralModelNodeResidue::SecondaryStructureType {
Unstructured = 0,
Alpha = 1,
Beta = 2
};
enum SideChainCharge#
enum SBMStructuralModelNodeResidue::SideChainCharge {
UndefinedSideChainCharge = 0,
Negative = 1,
Neutral = 2,
Positive = 3
};
enum SideChainPolarity#
enum SBMStructuralModelNodeResidue::SideChainPolarity {
UndefinedSideChainPolarity = 0,
Nonpolar = 1,
Polar = 2,
AcidicPolar = 3,
BasicPolar = 4
};
Public Functions Documentation#
function SBMStructuralModelNodeResidue [1/2]#
function SBMStructuralModelNodeResidue [2/2]#
function SB_DECLARE_DATA#
function SB_NODE_GETTER_0 [1/13]#
SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
SBMStructuralModelNodeResidue::ResidueType,
GetResidueType
)
function SB_NODE_GETTER_0 [2/13]#
function SB_NODE_GETTER_0 [3/13]#
SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
SBMStructuralModelNodeResidue::SecondaryStructureType,
GetSecondaryStructureType
)
function SB_NODE_GETTER_0 [4/13]#
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]#
function SB_NODE_GETTER_0 [8/13]#
SBMStructuralModelNodeResidue::SB_NODE_GETTER_0 (
SBMStructuralModelNodeResidue::SideChainPolarity,
GetSideChainPolarity
)
function SB_NODE_GETTER_0 [9/13]#
function SB_NODE_GETTER_0 [10/13]#
function SB_NODE_GETTER_0 [11/13]#
function SB_NODE_GETTER_0 [12/13]#
function SB_NODE_GETTER_0 [13/13]#
function SB_NODE_PREDICATE_0 [1/10]#
function SB_NODE_PREDICATE_0 [2/10]#
function SB_NODE_PREDICATE_0 [3/10]#
function SB_NODE_PREDICATE_0 [4/10]#
function SB_NODE_PREDICATE_0 [5/10]#
function SB_NODE_PREDICATE_0 [6/10]#
function SB_NODE_PREDICATE_0 [7/10]#
function SB_NODE_PREDICATE_0 [8/10]#
function SB_NODE_PREDICATE_0 [9/10]#
function SB_NODE_PREDICATE_0 [10/10]#
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.
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.
Implements SBMStructuralModelNodeGroup::clone
function computeAminoAcidChi1Angle#
Computes the chi1 angle (in degrees) for the amino acid residue's side chain.
function computeAminoAcidChi2Angle#
Computes the chi2 angle (in degrees) for the amino acid residue's side chain.
function computeAminoAcidChi3Angle#
Computes the chi3 angle (in degrees) for the amino acid residue's side chain.
function computeAminoAcidChi4Angle#
Computes the chi4 angle (in degrees) for the amino acid residue's side chain.
function computeAminoAcidChi5Angle#
Computes the chi5 angle (in degrees) for the amino acid residue's side chain.
function computeAminoAcidPhiAngle#
Computes the phi dihedral angle (in degrees) for the amino acid's backbone.
function computeAminoAcidPsiAngle#
Computes the psi dihedral angle (in degrees) for the amino acid's backbone.
function computeNucleicAcidAlphaAngle#
Computes the alpha (O3'(i-1)-P-O5'-C5') dihedral angle (in degrees) for the nucleic acid's backbone.
function computeNucleicAcidBetaAngle#
Computes the beta (P-O5'-C5'-C4') dihedral angle (in degrees) for the nucleic acid's backbone.
function computeNucleicAcidChiAngle#
Computes the chi dihedral angle (in degrees) for the nucleic acid's backbone.
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.
function computeNucleicAcidEpsilonAngle#
Computes the epsilon (C4'-C3'-O3'-P(i+1)) dihedral angle (in degrees) for the nucleic acid's backbone.
function computeNucleicAcidGammaAngle#
Computes the gamma (O5'-C5'-C4'-C3') dihedral angle (in degrees) for the nucleic acid's backbone.
function computeNucleicAcidZetaAngle#
Computes the zeta (C3'-O3'-P(i+1)-O5'(i+1)) dihedral angle (in degrees) for the nucleic acid's backbone.
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.
function getAminoAcidOneLetterCode [1/2]#
Returns one letter code of the amino acid residue.
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.
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.
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.
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.
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.
function getHydrophobicityScaleCount#
Returns the number of hydrophobicity scales.
function getHydrophobicityScaleCurrentIndex#
Returns the current scale's index in the list of hydrophobicity scales.
function getHydrophobicityScaleItemText#
Returns the hydrophobicity scale index as a string.
function getHydrophobicityScaleString [1/2]#
Returns the current hydrophobicity scale as a string.
function getIsoelectricPointPH [1/2]#
Returns the pI value (the pH at the isoelectric point) for this residue.
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.
function getNextNucleicAcid#
Returns the next nucleic acid if any, else returns nullptr.
function getNextResidue#
Returns the next residue if any, else returns nullptr.
function getPreviousAminoAcid#
Returns the previous amino acid if any, else returns nullptr.
function getPreviousNucleicAcid#
Returns the previous nucleic acid if any, else returns nullptr.
function getPreviousResidue#
Returns the previous residue if any, else returns nullptr.
function getResidueType#
Returns the residue's type.
function getResidueTypeFullName [1/2]#
Returns the full name of the residue's type.
function getResidueTypeString [1/2]#
Returns the string representation of the residue's type.
function getSecondaryStructureType#
Returns the most probable secondary structure based on bonds parameters and residue geometry.
function getSecondaryStructureTypeString [1/2]#
Returns the secondary structure type as a string.
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.
function getSideChainCharge [1/2]#
Returns the residue's side chain charge.
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.
function getSideChainPolarity [1/2]#
Returns the residue's side chain polarity.
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.
function getType#
Returns the node type (returns SBNode::Residue )
Implements SBMStructuralModelNodeGroup::getType
function hasAminoAcidChi1Angle [1/2]#
Returns true if it is an amino acid and has chi1 angle.
function hasAminoAcidChi2Angle [1/2]#
Returns true if it is an amino acid and has chi2 angle.
function hasAminoAcidChi3Angle [1/2]#
Returns true if it is an amino acid and has chi3 angle.
function hasAminoAcidChi4Angle [1/2]#
Returns true if it is an amino acid and has chi4 angle.
function hasAminoAcidChi5Angle [1/2]#
Returns true if it is an amino acid and has chi5 angle.
function hasCompleteAminoAcidBackbone#
Returns true if and only if the residue has a complete amino-acid backbone.
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.
function hasHydrophobicity [1/2]#
Returns true if the residue's hydrophobicity is defined.
function hasSideChainCharge [1/2]#
Returns true if the residue's side chain charge is defined.
function hasSideChainPolarity [1/2]#
Returns true if the residue's side chain polarity is defined.
function hasStandardResidueName#
Returns true if and only if the residue name corresponds to one of the standard PDB residue names.
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.
See also: SBMStructuralModelNodeResidue::isStandardResidueName
function isAminoAcid [1/2]#
Returns true if and only if the residue is an amino acid.
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.
Returns true if and only if the residue type is a nucleic acid.
function isSerializable#
Returns true.
Implements SBMStructuralModelNodeGroup::isSerializable
function isTerminal#
Returns true if and only if the residue is terminal.
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.
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.
function setName#
Sets the name of the residue, and updates accordingly names for its backbone and side chain.
Implements SBMStructuralModelNodeGroup::setName
function setResidueType [1/2]#
Sets the residue's type to residueType .
function setResidueType [2/2]#
Sets the residue's type based on the string s .
function setSecondaryStructureType#
Sets the most probable secondary structure based on bonds parameters and residue geometry.
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#
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:
residueTypeThe 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:
residueTypeThe 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:
residueTypeThe 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
)
Returns the residue type based on the string s. The input string can be a 3-letter code for amino acids and 1 or 2 letter code for nucleic acids.
Returns:
Residue type (SBResidue::ResidueType) that corresponds to the given string if found, else SBResidue::ResidueType::Undefined.
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 .
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:
residueTypeThe 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:
residueTypeThe 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 type residueType is an amino acid and has chi1 angle.
function hasAminoAcidChi2Angle [2/2]#
Returns true if the residue type residueType is an amino acid and has chi2 angle.
function hasAminoAcidChi3Angle [2/2]#
Returns true if the residue type residueType is an amino acid and has chi3 angle.
function hasAminoAcidChi4Angle [2/2]#
Returns true if the residue type residueType is an amino acid and has chi4 angle.
function hasAminoAcidChi5Angle [2/2]#
Returns true if the residue type residueType is an amino acid and has chi5 angle.
function hasDissociationConstant [2/2]#
Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for the residue residueType .
static bool SBMStructuralModelNodeResidue::hasDissociationConstant (
const ResidueType residueType
)
function hasHydrophobicity [2/2]#
Returns true if for the residue type residueType the hydrophobicity is defined.
function hasSideChainCharge [2/2]#
Returns true if for the residue type residueType the side chain charge is defined.
function hasSideChainPolarity [2/2]#
Returns true if for the residue type residueType the side chain polarity is defined.
function isAminoAcid [2/2]#
Returns true if and only if the residue of residueType is an amino acid.
function isNucleicAcid [2/2]#
Returns true if and only if the residue of residueType is a nucleic acid.
function isStandardAminoAcidName#
Returns true if and only if the name name corresponds to one of the standard PDB amino acid residue names.
Returns true if and only if the name name corresponds to one of the standard PDB amino acid residue names (3 letter code).
See also: SBMStructuralModelNodeResidue::isStandardResidueName
function isStandardNucleicAcidName#
Returns true if and only if the name name corresponds to one of the standard PDB nucleic acid residue names.
Returns true if and only if the name name corresponds to one of the standard PDB nucleic acid residue names (1 or 2 letter code).
See also: SBMStructuralModelNodeResidue::isStandardResidueName
function isStandardResidueName#
Returns true if and only if the name name corresponds to one of the standard PDB amino or nucleic acid residue names.
Returns true if and only if the name name corresponds to one of the standard PDB residue names: 3 letter code for amino acids, and 1 or 2 letter code for nucleic acids.
See also: SBMStructuralModelNodeResidue::isStandardAminoAcidName, SBMStructuralModelNodeResidue::isStandardNucleicAcidName