This class describes a bond in a structural model.
Constructors and destructors | |
SBMStructuralModelNodeHydrogenBond () | |
Constructs a H-bond. | |
SBMStructuralModelNodeHydrogenBond (SBMStructuralModelNodeAtom *acceptor, SBMStructuralModelNodeAtom *donor, SBMStructuralModelNodeAtom *hydrogen=nullptr) | |
Constructs a H-bond. | |
virtual | ~SBMStructuralModelNodeHydrogenBond () |
Destructs the H-bond. | |
Serialization | |
virtual bool | isSerializable () const override |
Returns false. | |
virtual void | serialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) const override |
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)) override |
Unserializes the bond. | |
Selection | |
void | setSelectionFlag (bool flag) |
Sets the selection flag and selects corresponding atoms. | |
Topology | |
SBMStructuralModelNodeAtom * | getAcceptor () const |
Returns a pointer to the acceptor atom. | |
SBMStructuralModelNodeAtom * | getDonor () const |
Returns a pointer to the donor atom. | |
SBMStructuralModelNodeAtom * | getHydrogen () const |
Returns a pointer to the hydrogen atom. | |
SBQuantity::length | getDonorAcceptorDistance () const |
Returns the donor-acceptor distance. | |
SBQuantity::length | getHydrogenAcceptorDistance () const |
Returns the hydrogen-acceptor distance. | |
SBQuantity::length | getDonorHydrogenDistance () const |
Returns the donor-hydrogen distance. | |
SBQuantity::degree | getAngle () const |
Returns the donor-hydrogen-acceptor angle. | |
bool | isLinking (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if donor and acceptor atoms are in nodeIndexer , or descends from a node of nodeIndexer . | |
virtual SBMStructuralModelNodeHydrogenBond * | clone () override |
Returns a copy of the node and its descendants. | |
static SBQuantity::degree | getAngle (SBMStructuralModelNodeAtom *donor, SBMStructuralModelNodeAtom *hydrogen, SBMStructuralModelNodeAtom *acceptor) |
Returns the donor-hydrogen-acceptor angle. | |
Identity | |
SBDDataGraphNode::Type | getType () const override |
Returns the node type (SBNode::HydrogenBond) | |
Selection functions | |
virtual void | getNodes (SBNodeIndexer &nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override |
Collects nodes into nodeIndexer , based on a nodeType , a selection status and a visitPredicate , with or without dependencies. | |
virtual void | getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override |
Collects nodes into nodeIndexer , based on a selectionPredicate and a visitPredicate , with or without dependencies. | |
virtual bool | hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override |
Checks for nodes based on a nodeType , a selection status and a visitPredicate , with or without dependencies. | |
virtual bool | hasNode (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override |
Checks for nodes based on a selectionPredicate and a visitPredicate , with or without dependencies. | |
Debugging | |
virtual void | print (unsigned int offset=0) const override |
Prints debugging information. | |
SB_NODE_GETTER_0 (, SBMStructuralModelNodeAtom *, GetAcceptor) | |
SB_NODE_GETTER_0 (, SBMStructuralModelNodeAtom *, GetDonor) | |
SB_NODE_GETTER_0 (, SBMStructuralModelNodeAtom *, GetHydrogen) | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetDonorAcceptorDistance) | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetHydrogenAcceptorDistance) | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetDonorHydrogenDistance) | |
SB_NODE_GETTER_0 (, SBQuantity::degree, GetAngle) | |
SB_DECLARE_DATA (SBMStructuralModelNodeHydrogenBond) | |
Additional Inherited Members | |
Public Types inherited from SBMStructuralModelNodeBond | |
enum | BondType { Undefined , Single , Double , Triple , Amide , Aromatic , Dummy } |
The bond type. More... | |
Public Types inherited from SBDDataGraphNode | |
enum | Type { Undefined , StructuralModel , StructuralModelNode , StructuralModelConformation , Conformation , StructuralModelPath , Path , StructuralModelNodeGroup , StructuralGroup , StructuralModelNodeRoot , Root , StructuralModelNodeAtom , Atom , StructuralModelNodeBond , Bond , StructuralModelNodeHydrogenBond , HydrogenBond , StructuralModelNodeHydrogenBondGroup , HydrogenBondGroup , StructuralModelNodeResidue , Residue , StructuralModelNodeSegment , Segment , StructuralModelNodeChain , Chain , StructuralModelNodeMolecule , Molecule , StructuralModelNodeBackbone , Backbone , StructuralModelNodeSideChain , SideChain , VisualModel , VisualModelMesh , Mesh , DynamicalModel , DynamicalModelParticleSystem , ParticleSystem , DynamicalModelRigidBodySystem , RigidBodySystem , DynamicalModelArticulatedBodySystem , ArticulatedBodySystem , DynamicalModelNode , DynamicalNode , DynamicalModelNodeGroup , DynamicalGroup , DynamicalModelNodeRoot , DynamicalRoot , DynamicalModelNodeParticle , Particle , DynamicalModelNodeRigidBody , RigidBody , DynamicalModelNodeArticulatedBody , ArticulatedBody , InteractionModel , InteractionModelParticleSystem , InteractionModelRigidBodySystem , InteractionModelArticulatedBodySystem , PropertyModel , PropertyModelFunction , Simulator , SimulatorParticleSystem , SimulatorRigidBodySystem , SimulatorArticulatedBodySystem , StateUpdater , StateUpdaterParticleSystem , StateUpdaterRigidBodySystem , StateUpdaterArticulatedBodySystem , Animation , Camera , Document , DocumentManager , File , Folder , Label , Light , Note , Presentation , RenderPreset , DataGraphNodeGroup , NodeGroup , Controller , ControllerNode , Asset } |
The type of the data graph node. More... | |
enum class | RenderingPass { Setup , OpaqueGeometry , SelectableGeometry , ShadowingGeometry , TransparentGeometry , Interface , Text } |
The rendering pass. More... | |
Public Member Functions inherited from SBMStructuralModelNodeBond | |
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 (SBMElement::Type elementType) const |
Returns true if and only if at least one of the atoms that the bond links is of element type elementType . | |
bool | isLinking (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if either atom is in nodeIndexer , or descends from a node of nodeIndexer . | |
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. | |
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. | |
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. | |
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. | |
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. | |
bool | isCarbonylBond () const |
Returns true if the bond is a carbonyl bond (C=O) | |
bool | isEsterBond () const |
Returns true if the bond is an ester bond, i.e. between an Oxygen and a carbonyl Carbon: O-C=O. | |
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_NODE_PREDICATE_1 (, IsLinkingElementType, SBMElement::Type) | |
SB_DECLARE_DATA (SBMStructuralModelNodeBond) | |
Public Member Functions inherited from SBMStructuralModelNode | |
virtual | ~SBMStructuralModelNode () |
virtual SBPointerList< SBMStructuralModelNode > const * | getChildren () const |
Returns the list of child nodes. | |
SBMStructuralModelNode * | getNextStructuralNode () const |
SBMStructuralModelNode * | getPreviousStructuralNode () const |
virtual bool | isLocked () const override |
Returns whether the node is locked (because of the model) | |
virtual bool | getLockedFlag () const override |
Returns the locked flag of the model. | |
SBMStructuralModel * | getModel () const |
virtual unsigned int | getOpacity () const override |
Returns the opacity. | |
virtual unsigned int | getMinimumOpacity () const override |
Returns the minimum opacity. | |
virtual unsigned int | getTransparency () const override |
Returns the transparency. | |
virtual unsigned int | getMaximumTransparency () const override |
Returns the maximum transparency. | |
bool | getStructuralSignalFlag () const |
Returns true when the node can send structural signals. | |
void | setStructuralSignalFlag (bool structuralSignalFlag) |
Sets whether the node can send structural signals. | |
void | connectStructuralSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any, SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBStructuralEvent *)=0) |
bool | structuralSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) const |
void | disconnectStructuralSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) |
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)) override |
Performs an action on each node. | |
virtual void | forEachNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node)) override |
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)) |
SB_DECLARE_DATA (SBMStructuralModelNode) | |
Public Member Functions inherited from SBMModelNode | |
SB_DECLARE_DATA (SBMModelNode) | |
Public Member Functions inherited from SBDDataGraphNode | |
SBDDataGraphNode * | getParent () const |
Returns the parent of the node. | |
SBDDataGraphNode * | getThisNode () const |
Returns the pointer to this node. | |
SBDDataGraphNode * | getNextNode () const |
Returns the pointer to the next node in the children of the node's parent. | |
SBDDataGraphNode * | getPreviousNode () const |
Returns the pointer to the previous 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. | |
SBDDataGraphNode * | getPreviousNode (SBDDataGraphNode::Type nodeType) const |
Returns the pointer to the previous node with type nodeType in the children of the node's parent. | |
SBDDocument * | getDocument () const |
Returns the document the node belongs to. | |
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. | |
virtual bool | canHaveDescendantType (SBDDataGraphNode::Type nodeType) const |
Returns whether this node can have a node with type nodeType as a descendant. | |
virtual bool | addChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=nullptr) |
Adds a child to the node. | |
virtual bool | removeChild (SBDDataGraphNode *node) |
Removes a child from the node. | |
bool | hasOneOf (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer , or is the ancestor of one of them, or is a group that stores one of them. | |
bool | 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. | |
bool | isIn (const SBDDataGraphNode *node) const |
Returns true if and only if this node is node , or descends from it, or belongs to a group stored in node . | |
bool | isIn (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer , or descends from one of them, or belongs to a group stored in one of the nodes of the nodeIndexer . | |
bool | isIn (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
Returns true if and only if this node is one of the nodes of the nodePointerIndexer , or descends from one of them, or belongs to a group stored in of the nodes of the nodePointerIndexer . | |
bool | 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 . | |
SBDDataGraphNode * | getRoot () const |
Returns the root of the hierarchy the node belongs to. | |
unsigned int | getNodeIndex () const |
Returns the node index (unique in the whole data graph, but non-persistent) | |
std::string | getTypeString (bool humanReadable=false) const |
Returns a string describing the type of the data graph node. | |
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. | |
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 | isAtom () const |
Returns true when the node is an atom. | |
bool | isBond () const |
Returns true when the node is a bond. | |
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 | isLight () const |
Returns true when the node is a light. | |
bool | isSimulator () const |
Returns true when the node is a simulator. | |
bool | isBallAndStick () const |
Returns true when the node is the default ball-and-stick visual model. | |
bool | isLicorice () const |
Returns true when the node is the default licorice visual model. | |
bool | isVanDerWaals () const |
Returns true when the node is the default van der Waals visual model. | |
bool | isCartoon () const |
Returns true when the node is the default cartoon visual model. | |
bool | isRibbon () const |
Returns true when the node is the default ribbon visual model. | |
bool | isTube () const |
Returns true when the node is the default tube visual model. | |
bool | isGaussianSurface () const |
Returns true when the node is the default Gaussian surface visual model. | |
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. | |
virtual void | setLockedFlag (bool flag) |
Sets the locked flag. | |
bool | isCreated () const |
Returns true if and only if the node is created. | |
void | create () |
Creates the node. | |
bool | isErased () const |
Returns true if and only if the node is erased. | |
void | erase () |
Erases the node. | |
virtual unsigned int | getFlags () const |
Returns the flags. | |
virtual unsigned int | getInheritedFlags () const |
Returns the inherited flags. | |
bool | isSelected () const |
Returns whether the node is selected. | |
bool | getSelected () const |
Returns whether the node is selected. | |
bool | getSelectionFlag () const |
Returns the selection flag. | |
void | setSelectionFlag (bool flag) |
Sets the selection flag. | |
bool | isVisible () const |
Returns whether the node is visible. | |
bool | getVisible () const |
Returns whether the node is visible. | |
bool | getVisibilityFlag () const |
Returns the visibility flag. | |
void | setVisibilityFlag (bool flag) |
Sets the visibility flag. | |
bool | isHighlighted () const |
Returns whether the node is highlighted. | |
bool | getHighlightingFlag () const |
Returns the highlighting flag. | |
void | setHighlightingFlag (bool flag) |
Sets the highlighting flag. | |
virtual void | display (RenderingPass renderingPass) |
Displays the node. | |
virtual void | display () |
Displays the node (deprecated) | |
virtual void | displayForShadow () |
Displays the node for shadowing purposes (deprecated) | |
virtual void | displayForSelection () |
Displays the node for selection purposes (deprecated) | |
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 | canAddMaterial () const |
Returns whether can add a material to the node based on its type. | |
bool | addMaterial (SBDDataGraphNodeMaterial *material) |
Adds a material. | |
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. | |
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. | |
SBDDataGraphNode * | getMaterialOwner () const |
Returns the node whose material is inherited. | |
void | connectBaseSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBBaseEvent *)=0) |
Connects the base signal to a slot. | |
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 |
Counts nodes based on a nodeType , a selection status and a visitPredicate , with or without dependencies. | |
unsigned int | countNodes (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
Counts nodes based on a selectionPredicate and a visitPredicate , with or without dependencies. | |
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. | |
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 | getNumberOfCoarseGrainedAtoms () |
Returns the number of coarse-grained atoms. | |
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. | |
SB_DECLARE_DATA (SBDDataGraphNode) | |
Public Member Functions inherited from SBCReferenceTarget | |
unsigned int | getMemoryFootprint () const |
void | printReferencesToOwners () const |
SBCReferenceTarget () | |
virtual | ~SBCReferenceTarget () |
Static Public Member Functions inherited from SBMStructuralModelNodeBond | |
static std::string | getBondTypeString (BondType bondType) |
Returns the string corresponding to the bondType . | |
Static Public Member Functions inherited from SBMStructuralModelNode | |
static void | forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > &selection, void(*action)(SBMStructuralModelNode *node)) |
static void | forEachStructuralNodeInSelection (std::vector< SBMStructuralModelNode * > &selection, SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
Static Public Member Functions inherited from SBDDataGraphNode | |
static void | clone (const SBNodeIndexer &sourceNodeIndexer, SBNodeIndexer &destinationNodeIndexer) |
Clones the nodes in sourceNodeIndexer (treated as a whole) and places the clones in destinationNodeIndexer . | |
static SBDDataGraphNode * | getNode (unsigned int nodeIndex) |
Returns the unique node corresponding to the node index nodeIndex . | |
static std::string | getTypeString (Type type, bool humanReadable=false) |
Returns a string describing the type of the data graph node. | |
static bool | canAddMaterial (SBDDataGraphNode::Type nodeType) |
Returns whether can add a material to a node of type nodeType . | |
static void | forEachNodeInSelection (SBNodeIndexer &nodeIndexer, void(*action)(SBDDataGraphNode *node)) |
Performs an action for each node in a selection. | |
static void | forEachNodeInSelection (SBNodeIndexer &nodeIndexer, SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node)) |
Performs an action for each node in a selection. | |
Protected Member Functions inherited from SBMStructuralModelNodeBond | |
SBMStructuralModelNodeBond (SBMStructuralModelNodeBondData *dataPointer) | |
Builds a bond. | |
Protected Member Functions inherited from SBMStructuralModelNode | |
SBMStructuralModelNode () | |
Builds a structural model node. | |
SBMStructuralModelNode (SBMStructuralModelNodeData *dataPointer) | |
Builds a structural model node. | |
Protected Member Functions inherited from SBMModelNode | |
SBMModelNode () | |
Builds a base object. | |
SBMModelNode (SBMModelNodeData *dataPointer) | |
Builds a base object. | |
virtual | ~SBMModelNode () |
Protected Member Functions inherited from SBDDataGraphNode | |
SBDDataGraphNode () | |
Builds a data graph node. | |
SBDDataGraphNode (SBDDataGraphNodeData *dataPointer) | |
Builds a data graph node. | |
virtual | ~SBDDataGraphNode () |
Destroys the node. | |
Protected Member Functions inherited from SBCReferenceTarget | |
void | removeAllReferenceOwners () |
SBCReferenceTarget (SBCReferenceTargetData *dataPointer) | |
Protected Attributes inherited from SBCReferenceTarget | |
SBCReferenceTargetData * | dataPointer |
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overridevirtual |
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
This function adds to nodeIndexer
the hydrogen bond itself (if the predicates are valid) and, if includeDependencies
is true, attempts to add the bonded atoms as well.
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
This function adds to nodeIndexer
the hydrogen bond itself (if the predicates are valid) and, if includeDependencies
is true, attempts to add the bonded atoms as well.
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
This function checks the bond itself (if the predicates are valid) and, if includeDependencies
is true, checks the bonded atoms as well.
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
This function checks the bond itself (if the predicates are valid) and, if includeDependencies
is true, checks the bonded atoms as well.
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
Reimplemented from SBMStructuralModelNodeBond.
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overridevirtual |
Reimplemented from SBMStructuralModelNodeBond.