This class describes a bond in a structural model.
Public Member Functions | |
SB_NODE_GETTER_0 (, SBQuantity::dimensionless, GetOrder) | |
SB_NODE_GETTER_0 (, SBMStructuralModelNodeBond::BondType, GetBondType) | |
SB_NODE_GETTER_0 (, SBMStructuralModelNodeAtom *, GetLeftAtom) | |
SB_NODE_GETTER_0 (, SBMStructuralModelNodeAtom *, GetRightAtom) | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetLength) | |
SB_NODE_GETTER_0 (, SBPosition3, GetMidPoint) | |
SB_NODE_GETTER_0 (, std::string, GetStatusBit) | |
SB_NODE_GETTER_0 (, int, GetCustomType) | |
SB_NODE_PREDICATE_0 (, HasStatusBit) | |
SB_NODE_PREDICATE_0 (, HasCustomType) | |
SB_DECLARE_DATA (SBMStructuralModelNodeBond) | |
Public Member Functions inherited from SBMStructuralModelNode | |
SB_NODE_GETTER_0 (, bool, GetMobilityFlag) | |
SB_DECLARE_DATA (SBMStructuralModelNode) | |
virtual | ~SBMStructuralModelNode () |
virtual SBPointerList< SBMStructuralModelNode > const * | getChildren () const |
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 *)) |
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. | |
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 | canAddChildType (SBDDataGraphNode::Type nodeType) const |
Returns whether this node can add a node with type nodeType as a child. More... | |
virtual bool | canHaveDescendantType (SBDDataGraphNode::Type nodeType) const |
Returns whether this node can have a node with type nodeType as a descendant. 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. | |
virtual void | setName (const std::string &name) |
Sets the name of the node. More... | |
bool | isType (Type type) const |
Returns true when the type of the node corresponds to type . | |
bool | isModel () const |
Returns true when the node is a model. | |
bool | isStructuralNode () const |
Returns true when the node is a structural node. | |
bool | isStructuralModel () const |
Returns true when the node is a structural model. | |
bool | isVisualModel () const |
Returns true when the node is a visual model. | |
bool | isDynamicalModel () const |
Returns true when the node is a dynamical model. | |
bool | isInteractionModel () const |
Returns true when the node is a interaction model. | |
bool | isPropertyModel () const |
Returns true when the node is a property model. | |
bool | 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 | getNumberOfChains () |
Returns the number of chains. | |
virtual unsigned int | getNumberOfMolecules () |
Returns the number of molecules. | |
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 | getNumberOfAtoms () |
Returns the number of atoms. | |
virtual unsigned int | getNumberOfCarbons () |
Returns the number of carbons. | |
virtual unsigned int | getNumberOfHydrogens () |
Returns the number of hydrogens. | |
virtual unsigned int | getNumberOfNitrogens () |
Returns the number of nitrogens. | |
virtual unsigned int | getNumberOfOxygens () |
Returns the number of oxygens. | |
virtual unsigned int | getNumberOfSulfurs () |
Returns the number of sulfurs. | |
virtual unsigned int | getNumberOfOtherAtoms () |
Returns the number of other atoms. | |
virtual int | getSumOfFormalCharges () |
Returns the sum of formal charges. | |
virtual float | getSumOfPartialCharges () |
Returns the sum of partial charges. | |
virtual SBQuantity::mass | getMolecularWeight () |
Returns the molecular weight. | |
Public Member Functions inherited from SBCReferenceTarget | |
SBCReferenceTarget () | |
virtual | ~SBCReferenceTarget () |
unsigned int | getMemoryFootprint () const |
void | printReferencesToOwners () const |
Constructors and destructors | |
SBMStructuralModelNodeBond () | |
Constructs a bond. | |
SBMStructuralModelNodeBond (SBMStructuralModelNodeAtom *leftAtom, SBMStructuralModelNodeAtom *rightAtom, const SBQuantity::dimensionless &order=SBQuantity::dimensionless(1.0)) | |
Constructs a bond between atoms leftAtom and rightAtom and a specific bond order . | |
virtual | ~SBMStructuralModelNodeBond () |
Destructs the bond. | |
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 bond. | |
virtual void | unserialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) |
Unserializes the bond. | |
Topology | |
enum | BondType { Undefined, Single, Double, Triple, Amide, Aromatic, Dummy } |
The bond type. More... | |
SBQuantity::dimensionless const & | getOrder () const |
Returns the bond order. | |
void | setOrder (const SBQuantity::dimensionless &order) |
Sets the bond order to order . | |
SBQuantity::dimensionless const & | getMinimumOrder () const |
Returns the minimum bond order for the inspector. | |
SBQuantity::dimensionless const & | getMaximumOrder () const |
Returns the maximum bond order for the inspector. | |
SBQuantity::dimensionless const & | getOrderSingleStep () const |
Returns the bond order single step for the inspector. | |
std::string | getOrderSuffix () const |
Returns the bond order suffix for the inspector. | |
BondType | getBondType () const |
Returns the bond type. | |
void | setBondType (BondType bondType) |
Sets the bond type to bondType . | |
SBMStructuralModelNodeAtom * | getLeftAtom () const |
Returns a pointer to the left atom. | |
SBMStructuralModelNodeAtom * | getRightAtom () const |
Returns a pointer to the right atom. | |
SBMStructuralModelNodeAtom * | getOppositeAtom (const SBMStructuralModelNodeAtom *atom) const |
Returns the pointer to the atom opposite atom , when atom is either the left atom or the right atom of the bond. | |
SBQuantity::length | getLength () const |
Compute the length of the bond. | |
SBPosition3 | getMidPoint () const |
Compute the mid point of the bond. | |
const SBVector3 & | getDisplacement () const |
Returns the displacement used for display when multiple bond rendering is turned on. | |
bool | isLinking (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if either atom is in nodeIndexer , or descends from a node of nodeIndexer . | |
virtual SBMStructuralModelNodeBond * | clone () |
Returns a copy of the node and its descendants. | |
static std::string | getBondTypeString (BondType bondType) |
Returns the string corresponding to the bondType . | |
Identity | |
SBDDataGraphNode::Type | getType () const |
Returns the node type (SBNode::Bond) | |
Selection functions | |
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. More... | |
virtual void | getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
Returns some nodes. More... | |
Properties | |
bool | hasStatusBit () const |
Returns true when the bond's status bit is set. | |
std::string const & | getStatusBit () const |
Returns the bond's status bit. | |
void | setStatusBit (const std::string &statusBit) |
Sets the bond's status bit. | |
void | clearStatusBit () |
Clears the bond's status bit. | |
bool | hasCustomType () const |
Returns true when the bond's custom type is set. | |
int const & | getCustomType () const |
Returns the bond's custom type. | |
void | setCustomType (const int &water) |
Sets the bond's custom type. | |
void | clearCustomType () |
Clears the bond's custom type. | |
bool | isAmideBond () const |
Returns true if the bond is an amide bond, i.e. between a Nitrogen and a carbonyl Carbon: N-C=O. More... | |
bool | isPrimaryAmideBond () const |
Returns true if the bond is a primary amide bond, i.e. an amid bond where the Nitrogen atom has exactly one non-Hydrogen bond. More... | |
bool | isSecondaryAmideBond () const |
Returns true if the bond is a secondary amide bond, i.e. an amid bond where the Nitrogen atom has exactly two non-Hydrogen bonds. More... | |
bool | isTertiaryAmideBond () const |
Returns true if the bond is a tertiary amide bond, i.e. an amid bond where the Nitrogen atom has exactly three non-Hydrogen bonds. More... | |
bool | isCarbonylBond () const |
Returns true if the bond is a carbonyl bond (C=O) More... | |
bool | isEsterBond () const |
Returns true if the bond is an ester bond, i.e. between an Oxygen and a carbonyl Carbon: O-C=O. | |
Debugging | |
virtual void | print (unsigned int offset=0) const |
Prints debugging information. | |
|
virtual |
This function adds to nodeIndexer the bond itself (if the predicates are valid) and, if includeDependencies
is true, attempts to add the bonded atoms as well.
Reimplemented from SBMStructuralModelNode.
|
virtual |
This function adds to nodeIndexer the bond itself (if the predicates are valid) and, if includeDependencies
is true, attempts to add the bonded atoms as well.
Reimplemented from SBMStructuralModelNode.
bool SBMStructuralModelNodeBond::isAmideBond | ( | ) | const |
This function returns true if this bonds is an amide bond, i.e. a bond between a Nitrogen and a carbonyl Carbon. Amide has a general formula RC(=O)NR'R'', where R, R', and R'' represent organic groups or hydrogen atoms. This function checks for a single C-N bond in which Nitrogen has 3 bonds and Carbon has a carbonyl bond (C=O).
bool SBMStructuralModelNodeBond::isCarbonylBond | ( | ) | const |
This functions returns true if this bonds is a carbonyl bond - a double bond between carbon and oxygen.
bool SBMStructuralModelNodeBond::isPrimaryAmideBond | ( | ) | const |
This function returns true if this is an amide bond and Nitrogen participating in this bond has exactly one non hydrogen bond.
bool SBMStructuralModelNodeBond::isSecondaryAmideBond | ( | ) | const |
This function returns true if this is an amide bond and Nitrogen participating in this bond has exactly two non hydrogen bonds.
bool SBMStructuralModelNodeBond::isTertiaryAmideBond | ( | ) | const |
This function returns true if this is an amide bond and Nitrogen participating in this bond has exactly three non hydrogen bonds.