This class describes a residue in a structural model.
Public Member Functions | |
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 (, HasCompleteAminoAcidBackbone) | |
SB_NODE_PREDICATE_0 (, HasHydrophobicity) | |
SB_NODE_PREDICATE_0 (, HasSideChainCharge) | |
SB_NODE_PREDICATE_0 (, HasSideChainPolarity) | |
SB_NODE_PREDICATE_0 (, HasDissociationConstant) | |
SB_NODE_PREDICATE_0 (, HasResidueSequenceNumber) | |
SB_DECLARE_DATA (SBMStructuralModelNodeResidue) | |
Public Member Functions inherited from 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) | |
SB_DECLARE_DATA (SBMStructuralModelNodeGroup) | |
SBMStructuralModelNodeGroup () | |
Builds a base model. | |
SBMStructuralModelNodeGroup (const std::string &n) | |
virtual | ~SBMStructuralModelNodeGroup () |
virtual SBPointerList< SBMStructuralModelNode > const * | getChildren () const |
bool | hasComment () const |
Returns true when the comment is set. | |
std::string const & | getComment () const |
Returns the comment. | |
void | setComment (const std::string &comment) |
Sets the comment. | |
void | clearComment () |
Clears the comment. | |
bool | hasStatusBit () const |
Returns true when the status bit is set. | |
std::string const & | getStatusBit () const |
Returns the status bit. | |
void | setStatusBit (const std::string &statusBit) |
Sets the status bit. | |
void | clearStatusBit () |
Clears the status bit. | |
bool | hasStructuralID () const |
Returns true when the structural group's id is set. | |
int const & | getStructuralID () const |
Returns the structural group's id. | |
void | setStructuralID (const int &groupID) |
Sets the structural group's id. | |
void | clearStructuralID () |
Clears the structural group's id. | |
virtual void | onBaseEvent (SBEvent *event) |
virtual void | getNodes (SBNodeIndexer &nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
Collects nodes into nodeIndexer , based on a nodeType , a selection status and a visitPredicate , with our without dependencies. | |
virtual void | getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
Returns some nodes. | |
bool | isWater () |
Returns true if the structural group is a water molecule. More... | |
virtual void | forEachNodeDepthFirst (void(*action)(SBDDataGraphNode *node)) |
Performs an action on each node. | |
virtual void | forEachNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node)) |
Performs an action on each node. | |
unsigned int | getNumberOfChains () |
Returns the number of chains. | |
unsigned int | getNumberOfMolecules () |
Returns the number of molecules. | |
unsigned int | getNumberOfResidues () |
Returns the number of residues. | |
unsigned int | getNumberOfSegments () |
Returns the number of segments. | |
unsigned int | getNumberOfStructuralGroups () |
Returns the number of structural groups. | |
unsigned int | getNumberOfAtoms () |
Returns the number of atoms. | |
unsigned int | getNumberOfCarbons () |
Returns the number of carbons. | |
unsigned int | getNumberOfHydrogens () |
Returns the number of hydrogens. | |
unsigned int | getNumberOfNitrogens () |
Returns the number of nitrogens. | |
unsigned int | getNumberOfOxygens () |
Returns the number of oxygens. | |
unsigned int | getNumberOfSulfurs () |
Returns the number of sulfurs. | |
unsigned int | getNumberOfOtherAtoms () |
Returns the number of other atoms. | |
int | getSumOfFormalCharges () |
Returns the sum of formal charges. | |
float | getSumOfPartialCharges () |
Returns the sum of partial charges. | |
SBQuantity::mass | getMolecularWeight () |
Returns the molecular weight. More... | |
virtual void | print (unsigned int offset=0) const |
Prints debugging information. | |
Public Member Functions inherited from SBMStructuralModelNode | |
SB_NODE_GETTER_0 (, bool, GetMobilityFlag) | |
SB_DECLARE_DATA (SBMStructuralModelNode) | |
virtual | ~SBMStructuralModelNode () |
SBMStructuralModelNode * | getNextStructuralNode () const |
SBMStructuralModelNode * | getPreviousStructuralNode () const |
virtual bool | isLocked () const |
Returns whether the node is locked (because of the model) | |
virtual bool | getLockedFlag () const |
Returns the locked flag of the model. | |
SBMStructuralModel * | getModel () const |
bool | getMobilityFlag () const |
Returns the mobility flag. | |
void | setMobilityFlag (bool flag) |
Sets the mobility flag to flag . | |
virtual unsigned int | getOpacity () const |
Returns the opacity. | |
virtual unsigned int | getMinimumOpacity () const |
Returns the minimum opacity. | |
virtual unsigned int | getTransparency () const |
Returns the transparency. | |
virtual unsigned int | getMaximumTransparency () const |
Returns the maximum transparency. | |
void | connectStructuralSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBStructuralEvent *)=0) |
bool | structuralSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *)) const |
void | disconnectStructuralSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *)) |
void | getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
void | getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
void | getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
void | getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode *> &nodeVectorTopDown, std::vector< SBMStructuralModelNode *> &nodeVectorBottomUp, bool(*selectionRule)(SBMStructuralModelNode *)) |
void | forEachStructuralNodeBreadthFirst (void(*action)(SBMStructuralModelNode *node)) |
void | forEachStructuralNodeDepthFirst (void(*action)(SBMStructuralModelNode *node)) |
void | forEachStructuralNodeBreadthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
void | forEachStructuralNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
Public Member Functions inherited from SBMModelNode | |
SB_DECLARE_DATA (SBMModelNode) | |
Public Member Functions inherited from SBDDataGraphNode | |
SB_DECLARE_DATA (SBDDataGraphNode) | |
SBDDataGraphNode * | getParent () const |
Returns the parent of the node. More... | |
SBDDataGraphNode * | getThisNode () const |
Returns the pointer to this node. More... | |
SBDDataGraphNode * | getNextNode () const |
Returns the pointer to the next node in the children of the node's parent. More... | |
SBDDataGraphNode * | getPreviousNode () const |
Returns the pointer to the previous node in the children of the node's parent. More... | |
SBDDataGraphNode * | getNextNode (SBDDataGraphNode::Type nodeType) const |
Returns the pointer to the next node with type nodeType in the children of the node's parent. More... | |
SBDDataGraphNode * | getPreviousNode (SBDDataGraphNode::Type nodeType) const |
Returns the pointer to the previous node with type nodeType in the children of the node's parent. More... | |
SBDDocument * | getDocument () const |
Returns the document the node belongs to. More... | |
virtual bool | canAddChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) const |
Returns whether this node can add node as a child. More... | |
virtual bool | addChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) |
Adds a child to the node. More... | |
virtual bool | removeChild (SBDDataGraphNode *node) |
Removes a child from the node. More... | |
bool | hasOneOf (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer , or is the ancestor of one of them. More... | |
bool | descendsFrom (SBDDataGraphNode *node) const |
Returns true if and only if this node is node , or descends from it. More... | |
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. More... | |
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. More... | |
bool | isIn (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 . More... | |
bool | isIn (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer , or descends from one of them, or belongs to a group stored in one of the nodes of the nodeIndexer . More... | |
bool | isIn (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
Returns true if and only if this node is one of the nodes of the nodePointerIndexer , or descends from one of them, or belongs to a group stored in of the nodes of the nodePointerIndexer . More... | |
bool | isOneOf (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer . More... | |
bool | isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
Returns true if and only if this node is one of the nodes of the nodePointerIndexer . More... | |
SBDDataGraphNode * | getRoot () const |
Returns the root of the hierarchy the node belongs to. More... | |
unsigned int | getNodeIndex () const |
Returns the node index (unique in the whole data graph, but non-persistent) More... | |
std::string | getTypeString (bool humanReadable=false) const |
Returns a string describing the type of the data graph node. More... | |
virtual std::string const & | getName () const |
Returns the name of the node. | |
bool | isType (Type type) const |
Returns true when the type of the node corresponds to type . | |
bool | isModel () const |
Returns true when the node is a model. | |
bool | isStructuralNode () const |
Returns true when the node is a structural node. | |
bool | isStructuralModel () const |
Returns true when the node is a structural model. | |
bool | isVisualModel () const |
Returns true when the node is a visual model. | |
bool | isDynamicalModel () const |
Returns true when the node is a dynamical model. | |
bool | isInteractionModel () const |
Returns true when the node is a interaction model. | |
bool | isPropertyModel () const |
Returns true when the node is a property model. | |
bool | isMesh () const |
Returns true when the node is a mesh. | |
bool | isSimulator () const |
Returns true when the node is a simulator. | |
bool | isStructuralParticle () const |
Returns true when the node is a structural particle (an atom or a pseudo-atom) | |
virtual void | setLockedFlag (bool flag) |
Sets the locked flag. | |
bool | isCreated () const |
Returns true if and only if the node is created. More... | |
void | create () |
Creates the node. More... | |
bool | isErased () const |
Returns true if and only if the node is erased. More... | |
void | erase () |
Erases the node. More... | |
unsigned int | getFlags () const |
Returns the flags. More... | |
unsigned int | getInheritedFlags () const |
Returns the inherited flags. More... | |
bool | isSelected () const |
Returns whether the node is selected. More... | |
bool | getSelected () const |
Returns whether the node is selected. | |
bool | getSelectionFlag () const |
Returns the selection flag. More... | |
void | setSelectionFlag (bool flag) |
Sets the selection flag. More... | |
bool | isVisible () const |
Returns whether the node is visible. More... | |
bool | getVisible () const |
Returns whether the node is visible. | |
bool | getVisibilityFlag () const |
Returns the visibility flag. More... | |
void | setVisibilityFlag (bool flag) |
Sets the visibility flag. More... | |
bool | isHighlighted () const |
Returns whether the node is highlighted. More... | |
bool | getHighlightingFlag () const |
Returns the highlighting flag. More... | |
void | setHighlightingFlag (bool flag) |
Sets the highlighting flag. More... | |
virtual void | display (RenderingPass renderingPass) |
Displays the node. More... | |
virtual void | display () |
Displays the node (deprecated) More... | |
virtual void | displayForShadow () |
Displays the node for shadowing purposes (deprecated) More... | |
virtual void | displayForSelection () |
Displays the node for selection purposes (deprecated) More... | |
virtual void | setOpacity (unsigned int opacity) |
Sets the opacity. | |
virtual bool | hasOpacityRange () const |
Returns whether the node has the opacity range. | |
virtual unsigned int | getDefaultOpacity () const |
Returns the default opacity. | |
virtual unsigned int | getMaximumOpacity () const |
Returns the maximum opacity. | |
virtual unsigned int | getOpacitySingleStep () const |
Returns the opacity single step. | |
virtual std::string | getOpacitySuffix () const |
Returns the opacity suffix. | |
virtual void | setTransparency (unsigned int transparency) |
Sets the transparency. | |
virtual bool | hasTransparencyRange () const |
Returns whether the node has the transparency range. | |
virtual unsigned int | getDefaultTransparency () const |
Returns the default transparency. | |
virtual unsigned int | getMinimumTransparency () const |
Returns the minimum transparency. | |
virtual unsigned int | getTransparencySingleStep () const |
Returns the transparency single step. | |
virtual std::string | getTransparencySuffix () const |
Returns the transparency suffix. | |
float | getInheritedOpacity () const |
Returns the cumulative opacity, when taking into account the ascendants. | |
float | getInheritedTransparency () const |
Returns the cumulative transparency, when taking into account the ascendants. | |
bool | addMaterial (SBDDataGraphNodeMaterial *material) |
Adds a material. More... | |
bool | removeMaterial () |
Removes the material. More... | |
bool | hasMaterial () const |
Returns whether the node has a material (by itself, or inherited) | |
bool | ownsMaterial () const |
Returns whether the node owns a material. | |
SBDDataGraphNodeMaterial * | getMaterial () const |
Returns the material. More... | |
SBDDataGraphNode * | getMaterialOwner () const |
Returns the node whose material is inherited. More... | |
void | connectBaseSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBBaseEvent *)=0) |
Connects the base signal to a slot. More... | |
bool | baseSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) const |
Returns true when the base signal is connected to a slot. | |
void | disconnectBaseSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) |
Disconnects the base signal from a slot. | |
unsigned int | countNodes (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 our without dependencies. More... | |
unsigned int | countNodes (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 our without dependencies. More... | |
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. More... | |
virtual unsigned int | getNumberOfStructuralModels () |
Returns the number of structural models. | |
Public Member Functions inherited from SBCReferenceTarget | |
SBCReferenceTarget () | |
virtual | ~SBCReferenceTarget () |
unsigned int | getMemoryFootprint () const |
void | printReferencesToOwners () const |
Constructors and destructors | |
SBMStructuralModelNodeResidue () | |
SBMStructuralModelNodeResidue (const std::string &n) | |
virtual | ~SBMStructuralModelNodeResidue () |
Serialization | |
bool | isSerializable () const |
Returns true. | |
virtual void | serialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) const |
Serializes the node. | |
virtual void | unserialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) |
Unserializes the node. | |
Node property attributes | |
enum | ResidueType { Undefined, ALA, ARG, ASP, ASN, VAL, HIS, GLY, GLU, GLN, ILE, LEU, LYS, MET, PRO, SER, TYR, THR, TRP, PHE, CYS, ASX, GLX, XLE, XAA, SEC, PYL, A, C, G, U, I, DA, DC, DG, DT, DI } |
enum | SecondaryStructureType { Unstructured, Alpha, Beta } |
Topology | |
virtual bool | canAddChild (SBNode *node, SBNode *nextNode=0) const |
Returns whether this node can add node as a child. | |
virtual bool | canAddChildType (SBNode::Type nodeType) const |
Returns whether this node can add a node with type nodeType as a child. | |
virtual bool | canHaveDescendantType (SBNode::Type nodeType) const |
Returns whether this node can have a node with type nodeType as a descendant. | |
virtual bool | addChild (SBNode *node, SBNode *nextNode=0) |
Adds a child to the node. | |
virtual bool | removeChild (SBNode *node) |
Removes a child from the node. | |
SBMStructuralModelNodeResidue * | getNextResidue () const |
Returns the next residue if any, else returns nullptr. | |
SBMStructuralModelNodeResidue * | getPreviousResidue () const |
Returns the previous residue if any, else returns nullptr. | |
SBMStructuralModelNodeResidue * | getNextAminoAcid () const |
Returns the next amino acid if any, else returns nullptr. | |
SBMStructuralModelNodeResidue * | getPreviousAminoAcid () const |
Returns the previous amino acid if any, else returns nullptr. | |
SBMStructuralModelNodeResidue * | getNextNucleicAcid () const |
Returns the next nucleic acid if any, else returns nullptr. | |
SBMStructuralModelNodeResidue * | getPreviousNucleicAcid () const |
Returns the previous nucleic acid if any, else returns nullptr. | |
SBMStructuralModelNodeBackbone * | getBackbone () const |
Returns the residue's backbone if it has one, else returns nullptr. | |
SBMStructuralModelNodeSideChain * | getSideChain () const |
Returns the residue's side-chain if it has one, else returns nullptr. | |
ResidueType | getResidueType () const |
Returns the residue's type. | |
void | setResidueType (ResidueType residueType) |
Sets the residue's type to residueType . | |
std::string | getResidueTypeString () const |
Returns the string representation of the residue's type. | |
void | setResidueType (const std::string &s) |
Sets the residue's type based on the string s . | |
std::string | getResidueTypeFullName () const |
Returns the full name of the residue's type. | |
bool | isAminoAcid () const |
Returns true if and only if the residue is an amino acid. | |
bool | isNucleicAcid () const |
Returns true if and only if the residue is a nucleic acid. | |
bool | isTerminal () const |
Returns true if and only if the residue is terminal. | |
bool | hasCompleteAminoAcidBackbone () const |
Returns true if and only if the residue has a complete amino-acid backbone. | |
virtual SBMStructuralModelNodeResidue * | clone () |
Returns a copy of the node and its descendants. | |
static std::string | getResidueTypeString (ResidueType residueType) |
Returns the string representation of the residue type residueType . | |
static ResidueType | getResidueTypeFromString (const std::string &s) |
Returns the residue type based on the string s . | |
static std::string | getResidueTypeFullName (ResidueType residueType) |
Returns the full name of the residue type residueType . | |
static bool | isAminoAcid (ResidueType residueType) |
Returns true if and only if the residue of residueType is an amino acid. | |
static bool | isNucleicAcid (ResidueType residueType) |
Returns true if and only if the residue of residueType is a nucleic acid. | |
Identity | |
virtual Type | getType () const |
Returns the type of the data graph node. | |
virtual void | setName (const std::string &name) |
Sets the name of the residue, and updates accordingle names for its backbone and side chain. | |
Covalent bonds | |
int | createCovalentBondsByResidueType () |
Sets the order of covalent bonds for the atoms belonging to the residue according to the residue type, regardless of inter-atomic distances. | |
Hydrogens | |
int | addHydrogensByResidueType () |
Adds hydrogen atoms to the residue based on its type. | |
Amino acid residue geometry | |
SBQuantity::dimensionless | computeAminoAcidPhiAngle () |
Computes the phi dihedral angle (in degrees) for the amino acid's backbone. | |
SBQuantity::dimensionless | computeAminoAcidPsiAngle () |
Computes the psi dihedral angle (in degrees) for the amino acid's backbone. | |
bool | hasAminoAcidChi1Angle () const |
Returns true if it is an amino acid and has chi1 angle. | |
bool | hasAminoAcidChi2Angle () const |
Returns true if it is an amino acid and has chi2 angle. | |
bool | hasAminoAcidChi3Angle () const |
Returns true if it is an amino acid and has chi3 angle. | |
bool | hasAminoAcidChi4Angle () const |
Returns true if it is an amino acid and has chi4 angle. | |
bool | hasAminoAcidChi5Angle () const |
Returns true if it is an amino acid and has chi5 angle. | |
SBQuantity::dimensionless | computeAminoAcidChi1Angle () |
Computes the chi1 angle (in degrees) for the amino acid residue's side chain. | |
SBQuantity::dimensionless | computeAminoAcidChi2Angle () |
Computes the chi2 angle (in degrees) for the amino acid residue's side chain. | |
SBQuantity::dimensionless | computeAminoAcidChi3Angle () |
Computes the chi3 angle (in degrees) for the amino acid residue's side chain. | |
SBQuantity::dimensionless | computeAminoAcidChi4Angle () |
Computes the chi4 angle (in degrees) for the amino acid residue's side chain. | |
SBQuantity::dimensionless | computeAminoAcidChi5Angle () |
Computes the chi5 angle (in degrees) for the amino acid residue's side chain. | |
bool | orientAminoAcidSideChain (const SBQuantity::degree &chi1, const SBQuantity::degree &chi2=SBQuantity::degree(0.0), const SBQuantity::degree &chi3=SBQuantity::degree(0.0), const SBQuantity::degree &chi4=SBQuantity::degree(0.0), const SBQuantity::degree &chi5=SBQuantity::degree(0.0)) |
Rotates the amino acid's side chain to orient it according to given digedral angles chi1 , chi2 , chi3 , chi4 , chi5 . Returns true if at least chi1 rotation was performed. | |
static bool | hasAminoAcidChi1Angle (const ResidueType residueType) |
Returns true if the residue type residueType is an amino acid and has chi1 angle. | |
static bool | hasAminoAcidChi2Angle (const ResidueType residueType) |
Returns true if the residue type residueType is an amino acid and has chi2 angle. | |
static bool | hasAminoAcidChi3Angle (const ResidueType residueType) |
Returns true if the residue type residueType is an amino acid and has chi3 angle. | |
static bool | hasAminoAcidChi4Angle (const ResidueType residueType) |
Returns true if the residue type residueType is an amino acid and has chi4 angle. | |
static bool | hasAminoAcidChi5Angle (const ResidueType residueType) |
Returns true if the residue type residueType is an amino acid and has chi5 angle. | |
Nucleic acid residue geometry | |
SBQuantity::dimensionless | computeNucleicAcidAlphaAngle () |
Computes the alpha (O3'(i-1)-P-O5'-C5') dihedral angle (in degrees) for the nucleic acid's backbone. | |
SBQuantity::dimensionless | computeNucleicAcidBetaAngle () |
Computes the beta (P-O5'-C5'-C4') dihedral angle (in degrees) for the nucleic acid's backbone. | |
SBQuantity::dimensionless | computeNucleicAcidGammaAngle () |
Computes the gamma (O5'-C5'-C4'-C3') dihedral angle (in degrees) for the nucleic acid's backbone. | |
SBQuantity::dimensionless | computeNucleicAcidDeltaAngle () |
Computes the delta (C5'-C4'-C3'-O3') dihedral angle (in degrees) for the nucleic acid's backbone. | |
SBQuantity::dimensionless | computeNucleicAcidEpsilonAngle () |
Computes the epsilon (C4'-C3'-O3'-P(i+1)) dihedral angle (in degrees) for the nucleic acid's backbone. | |
SBQuantity::dimensionless | computeNucleicAcidZetaAngle () |
Computes the zeta (C3'-O3'-P(i+1)-O5'(i+1)) dihedral angle (in degrees) for the nucleic acid's backbone. | |
SBQuantity::dimensionless | computeNucleicAcidChiAngle () |
Computes the chi dihedral angle (in degrees) for the nucleic acid's backbone. More... | |
Secondary structure | |
SecondaryStructureType | getSecondaryStructureType () const |
Returns the most probable secondary structure based on bonds parameters and residue geometry. | |
void | setSecondaryStructureType (SecondaryStructureType type) |
Sets the most probable secondary structure based on bonds parameters and residue geometry. | |
std::string | getSecondaryStructureTypeString () const |
Returns the secondary structure type as a string. | |
static std::string | getSecondaryStructureTypeString (SecondaryStructureType secondaryStructureType) |
Returns the secondary structure type secondaryStructureType as a string. | |
Hydrophobicity | |
enum | HydrophobicityScale { HydrophobicityScale::KyteDoolittle1982, HydrophobicityScale::SeredaEtAl1994, HydrophobicityScale::MoneraEtAl1995, HydrophobicityScale::WimleyWhite1996, HydrophobicityScale::HessaEtAl2005, HydrophobicityScale::ZhaoLondon2006, HydrophobicityScale::MoonFleming2011 } |
bool | hasHydrophobicity () const |
Returns true if the residue's hydrophobicity is defined. | |
double | getHydrophobicity () const |
Returns the residue's hydrophobicity in the current hydrophobicity scale. | |
double | getHydrophobicity (const HydrophobicityScale hydrophobicityScale) const |
Returns the residue's hydrophobicity in the given hydrophobicity scale hydrophobicityScale . | |
HydrophobicityScale | getHydrophobicityScale () const |
Returns the current scale of the residue's hydrophobicity. | |
void | setHydrophobicityScale (const HydrophobicityScale hydrophobicityScale) |
Sets the current hydrophobicity scale to hydrophobicityScale . | |
std::string | getHydrophobicityScaleString () const |
Returns the current hydrophobicity scale as a string. | |
int | getHydrophobicityScaleCount () const |
Returns the number of hydrophobicity scales. | |
int | getHydrophobicityScaleCurrentIndex () const |
Returns the current scale's index in the list of hydrophobicity scales. | |
void | setHydrophobicityScaleCurrentIndex (const int index) |
Sets the current hydrophobicity scale to the hydrophobicity scale from the list. | |
std::string | getHydrophobicityScaleItemText (const int index) const |
Returns the hydrophobicity scale index as a string. | |
static bool | hasHydrophobicity (const ResidueType residueType) |
Returns true if for the residue type residueType the hydrophobicity is defined. | |
static double | getHydrophobicity (const ResidueType residueType, const HydrophobicityScale hydrophobicityScale) |
Returns the hydrophobicity value for the residue residueType in the hydrophobicity scale hydrophobicityScale . | |
static std::string | getHydrophobicityScaleString (const HydrophobicityScale hydrophobicityScale) |
Returns the hydrophobicity scale hydrophobicityScale as a string. | |
Amino acids information | |
std::string | getAminoAcidOneLetterCode () const |
Returns one letter code of the amino acid residue. | |
static std::string | getAminoAcidOneLetterCode (const ResidueType residueType) |
Returns one letter code of the amino acid residue residueType . | |
Properties of common amino acid residues | |
bool | hasDissociationConstant () const |
Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for this residue. | |
double | getDissociationConstant1 () const |
Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for this residue. More... | |
double | getDissociationConstant2 () const |
Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for this residue. More... | |
double | getIsoelectricPointPH () const |
Returns the pI value (the pH at the isoelectric point) for this residue. More... | |
static bool | hasDissociationConstant (const ResidueType residueType) |
Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for the residue residueType . | |
static double | getDissociationConstant1 (const ResidueType residueType) |
Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for the residue residueType . More... | |
static double | getDissociationConstant2 (const ResidueType residueType) |
Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for the residue residueType . More... | |
static double | getIsoelectricPointPH (const ResidueType residueType) |
Returns the pI value (the pH at the isoelectric point) for the residue residueType . More... | |
Side chain properties | |
enum | SideChainCharge { UndefinedSideChainCharge, Negative, Neutral, Positive } |
enum | SideChainPolarity { UndefinedSideChainPolarity, Nonpolar, Polar, AcidicPolar, BasicPolar } |
bool | hasSideChainCharge () const |
Returns true if the residue's side chain charge is defined. | |
SideChainCharge | getSideChainCharge () const |
Returns the residue's side chain charge. More... | |
std::string | getSideChainChargeString () const |
Returns the residue's side chain charge as a string. | |
bool | hasSideChainPolarity () const |
Returns true if the residue's side chain polarity is defined. | |
SideChainPolarity | getSideChainPolarity () const |
Returns the residue's side chain polarity. More... | |
std::string | getSideChainPolarityString () const |
Returns the residue's side chain polarity as a string. | |
static bool | hasSideChainCharge (const ResidueType residueType) |
Returns true if for the residue type residueType the side chain charge is defined. | |
static SideChainCharge | getSideChainCharge (const ResidueType residueType) |
Returns the residue's side chain charge for the residue residueType . More... | |
static std::string | getSideChainChargeString (const SideChainCharge sideChainCharge) |
Returns a side chain charge sideChainCharge as a string. | |
static bool | hasSideChainPolarity (const ResidueType residueType) |
Returns true if for the residue type residueType the side chain polarity is defined. | |
static SideChainPolarity | getSideChainPolarity (const ResidueType residueType) |
Returns the residue's side chain polarity for the residue residueType . More... | |
static std::string | getSideChainPolarityString (const SideChainPolarity sideChainPolarity) |
Returns a side chain polarity sideChainPolarity as a string. | |
Enumerator | |
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KyteDoolittle1982 | A hydrophobicity scale of Kyte J, Doolittle RF, "A simple method for displaying the hydropathic character of a protein", J Mol Biol. 1982. DOI: https://doi.org/10.1016/0022-2836(82)90515-0. |
SeredaEtAl1994 | A hydrophobicity scale of Sereda TJ et al. 1994. DOI: https://doi.org/10.1016/0021-9673(94)00371-8. |
MoneraEtAl1995 | A hydrophobicity scale of Monera et al. 1995. DOI: https://doi.org/10.1002/psc.310010507. |
WimleyWhite1996 | A hydrophobicity scale of Wimley WC, White SH, "Experimentally determined hydrophobicity scale for proteins at membrane interfaces", Nat Struct Biol. 1996. DOI: https://doi.org/10.1038/nsb1096-842. |
HessaEtAl2005 | A hydrophobicity scale of Hessa T et al. "Recognition of transmembrane helices by the endoplasmic reticulum translocon". Nature. 2005. DOI: https://doi.org/10.1038/nature03216. |
ZhaoLondon2006 | A hydrophobicity scale of Zhao G, London E. "An amino acid “transmembrane tendency” scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity". Protein Sci. 2006. DOI: https://doi.org/10.1110/ps.062286306. |
MoonFleming2011 | A hydrophobicity scale of Moon CP, Fleming KG. "Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers". Proc Natl Acad Sci USA. 2011. DOI: https://doi.org/10.1073/pnas.1103979108. |
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
double SBMStructuralModelNodeResidue::getDissociationConstant1 | ( | ) | const |
SBMStructuralModelNodeResidue::getDissociationConstant1.
Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.
|
static |
SBMStructuralModelNodeResidue::getDissociationConstant1.
residueType | The type of the residue |
residueType
Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.
double SBMStructuralModelNodeResidue::getDissociationConstant2 | ( | ) | const |
SBMStructuralModelNodeResidue::getDissociationConstant2.
Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.
|
static |
SBMStructuralModelNodeResidue::getDissociationConstant2.
residueType | The type of the residue |
residueType
Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.
double SBMStructuralModelNodeResidue::getIsoelectricPointPH | ( | ) | const |
SBMStructuralModelNodeResidue::getIsoelectricPointPH.
Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.
|
static |
SBMStructuralModelNodeResidue::getIsoelectricPointPH.
residueType | The type of the residue |
residueType
Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.
SBMStructuralModelNodeResidue::SideChainCharge SBMStructuralModelNodeResidue::getSideChainCharge | ( | ) | const |
SBMStructuralModelNodeResidue::getSideChainCharge.
Reference: Cooper GM, Hausman RE (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 978-0-87893-214-6.
|
static |
SBMStructuralModelNodeResidue::getSideChainCharge.
residueType | The type of the residue |
residueType
side chain at physiological pH 7.4Reference: Cooper GM, Hausman RE (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 978-0-87893-214-6.
SBMStructuralModelNodeResidue::SideChainPolarity SBMStructuralModelNodeResidue::getSideChainPolarity | ( | ) | const |
SBMStructuralModelNodeResidue::getSideChainPolarity.
Reference: Cooper GM, Hausman RE (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 978-0-87893-214-6.
|
static |
SBMStructuralModelNodeResidue::getSideChainPolarity.
residueType | The type of the residue |
residueType
side chainReference: Cooper GM, Hausman RE (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 978-0-87893-214-6.