SBMStructuralModel Class Reference
This class describes a structural model.
Constructors and destructors | |
| SBMStructuralModel () | |
| Builds a base model. | |
| virtual | ~SBMStructuralModel () |
| Deletes the model. | |
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. | |
Rendering | |
| virtual void | display () |
| Displays the property model. | |
| virtual void | displayForShadow () |
| Displays the property model for shadow purposes. | |
| virtual void | displayForSelection () |
| Displays the property model for selection purposes. | |
| virtual void | expandBounds (SBIAPosition3 &bounds) const |
| Expands the bounds to make sure the visual model fits inside them. | |
| virtual void | collectAmbientOcclusion (const SBPosition3 &boxOrigin, const SBPosition3 &boxSize, unsigned int nCellsX, unsigned int nCellsY, unsigned int nCellsZ, float *ambientOcclusionData) |
| To collect ambient occlusion data. | |
Topology | |
| SBMStructuralModelNodeRoot * | getStructuralRoot () const |
| virtual SBMStructuralModel * | clone () |
| Returns a copy of the node and its descendants. | |
Identity | |
| virtual SBDDataGraphNode::Type | getType () const |
| Returns the type of the data graph node. | |
| virtual SBDDataGraphNode::Type | getModelType () const |
| Returns the model type. | |
Covalent bonds | |
| void | createCovalentBonds () |
| Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances. | |
| void | createCovalentBondsByResidueType () |
| Builds covalent bonds for the atoms belonging to the structural model according to the residue types, regardless of inter-atomic distances. | |
Secondary structure | |
| bool | computeSecondaryStructure (bool &updated, bool forceUpdate=false) |
| Computes the secondary structure for all residues in the structural model. More... | |
Messaging | |
| 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 *)) |
Selection functions | |
| virtual void | getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) |
| Returns some nodes. | |
Visitor functions | |
| 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. | |
Properties | |
| bool | hasTitleInformation () const |
| Returns true when the model's title information is set. | |
| std::string const & | getTitleInformation () const |
| Returns the model's title information. | |
| void | setTitleInformation (const std::string &info) |
| Sets the model's title information. | |
| void | clearTitleInformation () |
| Clears the model's title information. | |
| bool | hasPrimaryStructureInformation () const |
| Returns true when the model's primary structure information is set. | |
| std::string const & | getPrimaryStructureInformation () const |
| Returns the model's primary structure information. | |
| void | setPrimaryStructureInformation (const std::string &info) |
| Sets the model's primary structure information. | |
| void | clearPrimaryStructureInformation () |
| Clears the model's primary structure information. | |
| bool | hasHeterogenInformation () const |
| Returns true when the model's heterogen information is set. | |
| std::string const & | getHeterogenInformation () const |
| Returns the model's heterogen information. | |
| void | setHeterogenInformation (const std::string &info) |
| Sets the model's heterogen information. | |
| void | clearHeterogenInformation () |
| Clears the model's heterogen information. | |
| bool | hasSecondaryStructureInformation () const |
| Returns true when the model's secondary structure information is set. | |
| std::string const & | getSecondaryStructureInformation () const |
| Returns the model's secondary structure information. | |
| void | setSecondaryStructureInformation (const std::string &info) |
| Sets the model's secondary structure information. | |
| void | clearSecondaryStructureInformation () |
| Clears the model's secondary structure information. | |
| bool | hasConnectivityAnnotationInformation () const |
| Returns true when the model's connectivity annotation information is set. | |
| std::string const & | getConnectivityAnnotationInformation () const |
| Returns the model's connectivity annotation information. | |
| void | setConnectivityAnnotationInformation (const std::string &info) |
| Sets the model's connectivity annotation information. | |
| void | clearConnectivityAnnotationInformation () |
| Clears the model's connectivity annotation information. | |
| bool | hasMiscellaneousInformation () const |
| Returns true when the model's miscellaneous information is set. | |
| std::string const & | getMiscellaneousInformation () const |
| Returns the model's miscellaneous information. | |
| void | setMiscellaneousInformation (const std::string &info) |
| Sets the model's miscellaneous information. | |
| void | clearMiscellaneousInformation () |
| Clears the model's miscellaneous information. | |
| bool | hasCrystallographicAndTransformationInformation () const |
| Returns true when the model's crystallographic and transformation information is set. | |
| std::string const & | getCrystallographicAndTransformationInformation () const |
| Returns the model's crystallographic and transformation information. | |
| void | setCrystallographicAndTransformationInformation (const std::string &info) |
| Sets the model's crystallographic and transformation information. | |
| void | clearCrystallographicAndTransformationInformation () |
| Clears the model's crystallographic and transformation information. | |
Debugging | |
| virtual void | print (unsigned int offset=0) const |
| Prints debugging information. | |
Additional Inherited Members | |
 Public Types inherited from SBDDataGraphNode | |
| enum | Type { Undefined, StructuralModel, StructuralModelNode, StructuralModelConformation, Conformation, StructuralModelPath, Path, StructuralModelNodeGroup, StructuralGroup, StructuralModelNodeRoot, Root, StructuralModelNodeParticle, StructuralParticle, StructuralModelNodeAtom, Atom, StructuralModelNodePseudoAtom, PseudoAtom, StructuralModelNodeBond, Bond, StructuralModelNodeResidue, Residue, StructuralModelNodeSegment, Segment, StructuralModelNodeProtein, Protein, StructuralModelNodeChain, Chain, StructuralModelNodeMolecule, Molecule, StructuralModelNodeBackbone, Backbone, StructuralModelNodeSideChain, SideChain, VisualModel, 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, DocumentLayer, Layer, DocumentCamera, Camera, DocumentLabel, Label, DataGraphNodeGroup, NodeGroup, Controller, ControllerNode } |
| The type of the data graph node. More... | |
| Public Member Functions inherited from SBMModel | |
| virtual | ~SBMModel () |
| Delete the model. | |
| SBDDataGraphNode * | getParent () const |
| Returns the parent node. | |
| SBDDocumentLayer * | getLayer () const |
| Returns the owning document layer. | |
| SBMModel * | getNextModel () const |
| Returns the next model in the document layer. | |
| SBMModel * | getPreviousModel () const |
| Returns the previous model in the document layer. | |
| std::string const & | getName () const |
| Returns the name of the model. | |
| void | setName (const std::string &name) |
| Sets the name of the model. | |
| Public Member Functions inherited from SBDDataGraphNode | |
| SBDDataGraphNode * | getThisNode () const |
| Returns the pointer to this node. 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 | isIn (SBDDataGraphNode *node) const |
Returns true if and only if this node is node, or descends from it. 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. More... | |
| bool | isOneOf (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer. 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... | |
| 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 visible. | |
| 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... | |
| 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 (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) |
Collects nodes into nodeIndexer, based on a selectionPredicate and a visitPredicate, with our without dependencies. More... | |
| 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... | |
| Public Member Functions inherited from SBCReferenceTarget | |
| SBCReferenceTarget () | |
| virtual | ~SBCReferenceTarget () |
| unsigned int | getMemoryFootprint () const |
| void | printReferencesToOwners () const |
| Static Public Member Functions inherited from SBDDataGraphNode | |
| static SBDDataGraphNode * | getNode (unsigned int nodeIndex) |
Returns the unique node corresponding to the node index nodeIndex. More... | |
| static std::string | getTypeString (Type type) |
| 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 SBMModel | |
| SBMModel () | |
| Builds a model. | |
| SBMModel (SBMModelData *dataPointer) | |
| Builds a model. | |
| 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... | |
Member Function Documentation
◆ computeSecondaryStructure()
| bool SBMStructuralModel::computeSecondaryStructure | ( | bool & | secondaryStructureChanged, |
| bool | forceUpdate = false |
||
| ) |
This functions incrementally computes the secondary structure of the structural model, i.e. both the secondary structure types of residues and geometric descriptors. The function returns true if and only if everything went well. The boolean secondaryStructureChanged is modified by the function and is true if and only if the secondary structure was changed compared to the previous call. Since several objects may call this function, a SecondaryStructureChanged event is also sent when this is the case, so that all objects may be warned.