SBMStructuralModelNodeMolecule Class Reference
This class describes a molecule in a structural model.
Constructors and destructors | |
| SBMStructuralModelNodeMolecule () | |
| Builds a base model. | |
| SBMStructuralModelNodeMolecule (const std::string &n) | |
| virtual | ~SBMStructuralModelNodeMolecule () |
| Deletes the model. | |
Topology | |
| 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 SBMStructuralModelNodeMolecule * | clone () |
| Returns a copy of the node and its descendants. | |
Identity | |
| virtual SBDDataGraphNode::Type | getType () const |
| Returns the type of the data graph node. | |
Additional Inherited Members | |
 Public Types inherited from SBDDataGraphNode | |
| enum | RenderingPass { RenderingPass::Setup, RenderingPass::OpaqueGeometry, RenderingPass::SelectableGeometry, RenderingPass::ShadowingGeometry, RenderingPass::TransparentGeometry, RenderingPass::Interface, RenderingPass::Text } |
| The rendering pass. More... | |
| enum | Type { Undefined, StructuralModel, StructuralModelNode, StructuralModelConformation, Conformation, StructuralModelPath, Path, StructuralModelNodeGroup, StructuralGroup, StructuralModelNodeRoot, Root, StructuralModelNodeParticle, StructuralParticle, StructuralModelNodeAtom, Atom, StructuralModelNodePseudoAtom, PseudoAtom, StructuralModelNodeBond, Bond, StructuralModelNodePseudoBond, PseudoBond, StructuralModelNodeHydrogenBond, HydrogenBond, StructuralModelNodeHydrogenBondGroup, HydrogenBondGroup, StructuralModelNodeResidue, Residue, StructuralModelNodeSegment, Segment, StructuralModelNodeProtein, Protein, 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, DynamicalParticle, DynamicalModelNodeRigidBody, RigidBody, DynamicalModelNodeArticulatedBody, ArticulatedBody, InteractionModel, InteractionModelParticleSystem, InteractionModelRigidBodySystem, InteractionModelArticulatedBodySystem, PropertyModel, PropertyModelFunction, Simulator, SimulatorParticleSystem, SimulatorRigidBodySystem, SimulatorArticulatedBodySystem, StateUpdater, StateUpdaterParticleSystem, StateUpdaterRigidBodySystem, StateUpdaterArticulatedBodySystem, DocumentManager, Document, Folder, Camera, Label, Note, Animation, Presentation, DataGraphNodeGroup, NodeGroup, Controller, ControllerNode, Asset } |
| The type of the data graph node. More... | |
| 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 () |
| 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. | |
| virtual bool | canAddChild (SBNode *node, SBNode *nextNode=0) const |
Returns whether this node can add node as a child. | |
| 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. | |
| 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 () const |
| Returns true if the structural group is a water molecule. More... | |
| SBQuantity::mass | getMolecularWeight () const |
| Returns the cumulative molecular weight of atoms in the structural group. 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. | |
| 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. | |
| 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... | |
| 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... | |
| Public Member Functions inherited from SBCReferenceTarget | |
| SBCReferenceTarget () | |
| virtual | ~SBCReferenceTarget () |
| unsigned int | getMemoryFootprint () const |
| void | printReferencesToOwners () const |
| 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. More... | |
| static SBDDataGraphNode * | getNode (unsigned int nodeIndex) |
Returns the unique node corresponding to the node index nodeIndex. More... | |
| static std::string | getTypeString (Type type, bool humanReadable=false) |
| Returns a string describing the type of the data graph node. More... | |
| 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 SBMStructuralModelNodeGroup | |
| SBMStructuralModelNodeGroup (SBMStructuralModelNodeGroupData *dataPointer) | |
| Builds a base object. | |
| 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. More... | |
| SBDDataGraphNode (SBDDataGraphNodeData *dataPointer) | |
| Builds a data graph node. | |
| virtual | ~SBDDataGraphNode () |
| Destroys the node. More... | |
| Protected Member Functions inherited from SBCReferenceTarget | |
| void | removeAllReferenceOwners () |
| SBCReferenceTarget (SBCReferenceTargetData *dataPointer) | |
| Protected Attributes inherited from SBCReferenceTarget | |
| SBCReferenceTargetData * | dataPointer |