Class SBMStructuralModel#
ClassList > SBMStructuralModel
#include <SBMStructuralModel.hpp>
Inherits the following classes: SBMModel
Public Types inherited from SBDDataGraphNode#
See SBDDataGraphNode
| Type | Name |
|---|---|
| enum | RenderingPass The rendering pass. |
| enum | Type The type of the data graph node. |
Public Functions#
| Type | Name |
|---|---|
| SBMStructuralModel () Builds a base model. |
|
| SB_DECLARE_DATA (SBMStructuralModel) |
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| SB_NODE_GETTER_0 (std::string, GetTitleInformation) |
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| SB_NODE_GETTER_0 (std::string, GetPrimaryStructureInformation) |
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| SB_NODE_GETTER_0 (std::string, GetHeterogenInformation) |
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| SB_NODE_GETTER_0 (std::string, GetSecondaryStructureInformation) |
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| SB_NODE_GETTER_0 (std::string, GetConnectivityAnnotationInformation) |
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| SB_NODE_GETTER_0 (std::string, GetMiscellaneousInformation) |
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| SB_NODE_GETTER_0 (std::string, GetCrystallographicAndTransformationInformation) |
|
| SB_NODE_PREDICATE_0 (HasTitleInformation) |
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| SB_NODE_PREDICATE_0 (HasPrimaryStructureInformation) |
|
| SB_NODE_PREDICATE_0 (HasHeterogenInformation) |
|
| SB_NODE_PREDICATE_0 (HasSecondaryStructureInformation) |
|
| SB_NODE_PREDICATE_0 (HasConnectivityAnnotationInformation) |
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| SB_NODE_PREDICATE_0 (HasMiscellaneousInformation) |
|
| SB_NODE_PREDICATE_0 (HasCrystallographicAndTransformationInformation) |
|
| virtual bool | addChild (SBNode * node, SBNode * nextNode=nullptr) override Adds a child to the node. |
| virtual bool | canAddChild (const SBNode * node, const SBNode * nextNode=nullptr) override const Returns whether this node can add node as a child. |
| virtual bool | canAddChildType (SBNode::Type nodeType) override const Returns whether this node can add a node with type nodeType as a child. |
| virtual bool | canHaveDescendantType (SBNode::Type nodeType) override const Returns whether this node can have a node with type nodeType as a descendant. |
| void | centerTransform () Centers the pivot of the transform on the center of mass of the atoms contained in the structural model. |
| void | clearConnectivityAnnotationInformation () Clears the model's connectivity annotation information. |
| void | clearCrystallographicAndTransformationInformation () Clears the model's crystallographic and transformation information. |
| void | clearHeterogenInformation () Clears the model's heterogen information. |
| void | clearMiscellaneousInformation () Clears the model's miscellaneous information. |
| void | clearPrimaryStructureInformation () Clears the model's primary structure information. |
| void | clearSecondaryStructureInformation () Clears the model's secondary structure information. |
| void | clearTitleInformation () Clears the model's title information. |
| virtual SBMStructuralModel * | clone () override Returns a copy of the node and its descendants. |
| 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. |
| bool | computeSecondaryStructure (bool & updated, bool forceUpdate=false) Computes the secondary structure for all residues in the structural model. |
| void | connectStructuralSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBStructuralEvent *) functionPointer, SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any, SBCReferenceTarget * nextReferenceTarget=0, void(SBCReferenceTarget::*)(SBStructuralEvent *) nextFunctionPointer=0) |
| void | createCovalentBonds () Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances. |
| void | createCovalentBonds (SBQuantity::length additionalMargin) Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances with the additional margin additionalMargin . |
| int | createCovalentBondsByResidueType () Builds covalent bonds for the atoms belonging to the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types. |
| void | disconnectStructuralSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBStructuralEvent *) functionPointer, SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) |
| virtual void | expandBounds (SBIAPosition3 & bounds) const Expands the bounds to make sure the visual model fits inside them. |
| virtual void | forEachNodeDepthFirst (void(*)(SBDDataGraphNode *node) action) override Performs an action on each node. |
| virtual void | forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) override Performs an action on each node. |
| virtual SBPointerList< SBMStructuralModelNode > const * | getChildren () const This function is a convenience function equivalent to getStructuralRoot() ->getChildren __ |
| std::string const & | getConnectivityAnnotationInformation () const Returns the model's connectivity annotation information. |
| std::string const & | getCrystallographicAndTransformationInformation () const Returns the model's crystallographic and transformation information. |
| std::string const & | getHeterogenInformation () const Returns the model's heterogen information. |
| virtual bool | getLockedFlag () override const Returns the locked flag. |
| std::string const & | getMiscellaneousInformation () const Returns the model's miscellaneous information. |
| virtual SBDDataGraphNode::Type | getModelType () override const Returns the model type. |
| virtual SBQuantity::mass | getMolecularWeight () override Returns the molecular weight. |
| virtual void | getNodes (SBNodeIndexer & nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into nodeIndexer , based on anodeType , a selection status and avisitPredicate , with or without dependencies. |
| virtual void | getNodes (SBNodeIndexer & nodeIndexer, const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Collects nodes into nodeIndexer , based on aselectionPredicate and avisitPredicate , with or without dependencies. |
| virtual unsigned int | getNumberOfAtoms () override Returns the number of atoms. |
| virtual unsigned int | getNumberOfCarbons () override Returns the number of carbons. |
| virtual unsigned int | getNumberOfChains () override Returns the number of chains. |
| virtual unsigned int | getNumberOfCoarseGrainedAtoms () override Returns the number of coarse-grained atoms. |
| virtual unsigned int | getNumberOfHydrogens () override Returns the number of hydrogens. |
| virtual unsigned int | getNumberOfMolecules () override Returns the number of molecules. |
| virtual unsigned int | getNumberOfNitrogens () override Returns the number of nitrogens. |
| virtual unsigned int | getNumberOfOtherAtoms () override Returns the number of other atoms. |
| virtual unsigned int | getNumberOfOxygens () override Returns the number of oxygens. |
| virtual unsigned int | getNumberOfResidues () override Returns the number of residues. |
| virtual unsigned int | getNumberOfSegments () override Returns the number of segments. |
| virtual unsigned int | getNumberOfStructuralGroups () override Returns the number of structural groups. |
| virtual unsigned int | getNumberOfStructuralModels () override Returns the number of structural models. |
| virtual unsigned int | getNumberOfSulfurs () override Returns the number of sulfurs. |
| SBMatrix33 const & | getOrientation () const Returns the orientation of the structural model. |
| SBPosition3 const & | getPosition () const Returns the position of the structural model. |
| std::string const & | getPrimaryStructureInformation () const Returns the model's primary structure information. |
| std::string const & | getSecondaryStructureInformation () const Returns the model's secondary structure information. |
| SBMStructuralModelNodeRoot * | getStructuralRoot () const |
| bool | getStructuralSignalFlag () const Returns true when the model can send structural signals. |
| virtual int | getSumOfFormalCharges () override Returns the sum of formal charges. |
| virtual float | getSumOfPartialCharges () override Returns the sum of partial charges. |
| std::string const & | getTitleInformation () const Returns the model's title information. |
| SBSpatialTransform const & | getTransform () const Returns the spatial transform of the structural model. |
| virtual SBDDataGraphNode::Type | getType () override const Returns the type of the data graph node. |
| void | getWater (SBNodeIndexer & resultNodeIndexer) const Finds water nodes in the structural model. |
| bool | hasConnectivityAnnotationInformation () const Returns true when the model's connectivity annotation information is set. |
| bool | hasCrystallographicAndTransformationInformation () const Returns true when the model's crystallographic and transformation information is set. |
| bool | hasHeterogenInformation () const Returns true when the model's heterogen information is set. |
| bool | hasMiscellaneousInformation () const Returns true when the model's miscellaneous information is set. |
| virtual bool | hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a nodeType , a selection status and avisitPredicate , with or without dependencies. |
| virtual bool | hasNode (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) override const Checks for nodes based on a selectionPredicate and avisitPredicate , with or without dependencies. |
| bool | hasPrimaryStructureInformation () const Returns true when the model's primary structure information is set. |
| bool | hasSecondaryStructureInformation () const Returns true when the model's secondary structure information is set. |
| bool | hasTitleInformation () const Returns true when the model's title information is set. |
| virtual bool | isLocked () override const Returns whether the model is locked. |
| virtual bool | isSerializable () override const Returns true. |
| bool | populateChainIDs (bool forceRenumbering=false) Populates the chain IDs for all chains in the structural model. |
| virtual void | print (unsigned int offset=0) override const Prints debugging information. |
| virtual bool | removeChild (SBNode * node) override Removes a child from the node. |
| void | rotate (const SBVector3 & axis, const SBQuantity::dimensionless & angle) Rotates the structural model. |
| virtual void | serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the node. |
| void | setConnectivityAnnotationInformation (const std::string & info) Sets the model's connectivity annotation information. |
| void | setCrystallographicAndTransformationInformation (const std::string & info) Sets the model's crystallographic and transformation information. |
| void | setHeterogenInformation (const std::string & info) Sets the model's heterogen information. |
| virtual void | setLockedFlag (bool flag) override Sets the locked flag. |
| void | setMiscellaneousInformation (const std::string & info) Sets the model's miscellaneous information. |
| void | setOrientation (const SBMatrix33 & orientation) Sets the orientation of the structural model. |
| void | setOrientation (const SBMatrix33 & orientation, bool transformParticles) Sets the orientation of the structural model. |
| void | setOrientation (SBMatrix33 const & newOrientation, SBMatrix33 const & oldOrientation, bool transformParticles=true) Sets the newOrientation and theoldOrientation of the structural model. |
| void | setPosition (const SBPosition3 & position) Sets the position of the structural model. |
| void | setPosition (const SBPosition3 & position, bool transformParticles) Sets the position of the structural model. |
| void | setPosition (SBPosition3 const & newPosition, SBPosition3 const & oldPosition, bool transformParticles=true) Sets the newPosition and theoldPosition of the structural model. |
| void | setPrimaryStructureInformation (const std::string & info) Sets the model's primary structure information. |
| void | setSecondaryStructureInformation (const std::string & info) Sets the model's secondary structure information. |
| void | setStructuralSignalFlag (bool structuralSignalFlag) Sets whether the model can send structural signals. |
| void | setTitleInformation (const std::string & info) Sets the model's title information. |
| void | setTransform (const SBSpatialTransform & transform) Sets the spatial transform of the structural model. |
| void | setTransform (const SBSpatialTransform & transform, bool transformParticles) Sets the spatial transform of the structural model. |
| void | setTransform (SBSpatialTransform const & newTransform, SBSpatialTransform const & oldTransform, bool transformParticles=true) Sets the newTransform and theoldTransform of the structural model. |
| bool | structuralSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBStructuralEvent *) functionPointer, SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) const |
| void | transform (const SBSpatialTransform & transform) Applies a spatial transform to the structural model. |
| void | translate (const SBLength3 & translation) Translates the structural model. |
| 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 node. |
| virtual | ~SBMStructuralModel () Deletes the model. |
Public Functions inherited from SBMModel#
See SBMModel
| Type | Name |
|---|---|
| SB_DECLARE_DATA (SBMModel) |
|
| SB_NODE_GETTER_0 (SBDDataGraphNode::Type, GetModelType) |
|
| SB_NODE_PREDICATE_1 (IsModelType, SBDDataGraphNode::Type) |
|
| virtual SBMModel * | clone () override Returns a copy of the node and its descendants. |
| virtual unsigned int | getMaximumTransparency () override const Returns the maximum transparency. |
| virtual unsigned int | getMinimumOpacity () override const Returns the minimum opacity. |
| virtual SBDDataGraphNode::Type | getModelType () const Returns the model type. |
| SBMModel * | getNextModel () const Returns the next model in the parent. |
| virtual unsigned int | getOpacity () override const Returns the opacity. |
| SBMModel * | getPreviousModel () const Returns the previous model in the parent. |
| bool | getShadowingFlag () const Returns whether the model casts shadows. |
| virtual unsigned int | getTransparency () override const Returns the transparency. |
| virtual SBDDataGraphNode::Type | getType () override const Returns the type of the data graph node. |
| virtual bool | isSerializable () override const Returns true. |
| virtual void | print (unsigned int offset=0) override const Prints debugging information. |
| virtual void | serialize (SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber & classVersionNumber=SBVersionNumber(1, 0, 0)) override const Serializes the node. |
| virtual void | setOpacity (unsigned int opacity) override Sets the opacity. |
| void | setShadowingFlag (bool shadowingFlag) Sets whether the model casts shadows. |
| virtual void | setTransparency (unsigned int transparency) override Sets the transparency. |
| 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 node. |
| virtual | ~SBMModel () Delete the model. |
Public Functions inherited from SBDDataGraphNode#
See SBDDataGraphNode
| Type | Name |
|---|---|
| SB_DECLARE_DATA (SBDDataGraphNode) |
|
| virtual bool | addChild (SBDDataGraphNode * node, SBDDataGraphNode * nextNode=nullptr) Adds a child to the node. |
| bool | addMaterial (SBDDataGraphNodeMaterial * material) Adds a material. |
| bool | baseSignalIsConnectedToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBBaseEvent *) functionPointer) const Returns true when the base signal is connected to a slot. |
| 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. |
| bool | canAddMaterial () const Returns whether can add a material to the node based on its type. |
| virtual bool | canHaveDescendantType (SBDDataGraphNode::Type nodeType) const Returns whether this node can have a node with type nodeType as a descendant. |
| virtual SBDDataGraphNode * | clone () Returns a copy of the node and its descendants. |
| void | connectBaseSignalToSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBBaseEvent *) functionPointer, SBCReferenceTarget * nextReferenceTarget=0, void(SBCReferenceTarget::*)(SBBaseEvent *) nextFunctionPointer=0) Connects the base signal to 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 avisitPredicate , 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 avisitPredicate , with or without dependencies. |
| void | create () Creates the node. |
| 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. |
| void | disconnectBaseSignalFromSlot (SBCReferenceTarget * referenceTarget, void(SBCReferenceTarget::*)(SBBaseEvent *) functionPointer) Disconnects the base signal from a slot. |
| virtual void | display (RenderingPass renderingPass) Displays the node. |
| virtual void | display () Displays the node (deprecated) |
| virtual void | displayForSelection () Displays the node for selection purposes (deprecated) |
| virtual void | displayForShadow () Displays the node for shadowing purposes (deprecated) |
| void | erase () Erases the node. |
| virtual void | forEachNodeDepthFirst (void(*)(SBDDataGraphNode *node) action) Performs an action on each node. |
| virtual void | forEachNodeDepthFirst (SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) Performs an action on each node. |
| virtual unsigned int | getDefaultOpacity () const Returns the default opacity. |
| virtual unsigned int | getDefaultTransparency () const Returns the default transparency. |
| SBDDocument * | getDocument () const Returns the document the node belongs to. |
| virtual unsigned int | getFlags () const Returns the flags. |
| 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. |
| bool | getHighlightingFlag () const Returns the highlighting flag. |
| virtual unsigned int | getInheritedFlags () const Returns the inherited flags. |
| 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. |
| virtual bool | getLockedFlag () const Returns the locked flag. |
| SBDDataGraphNodeMaterial * | getMaterial () const Returns the material. |
| SBDDataGraphNode * | getMaterialOwner () const Returns the node whose material is inherited. |
| virtual unsigned int | getMaximumOpacity () const Returns the maximum opacity. |
| virtual unsigned int | getMaximumTransparency () const Returns the maximum transparency. |
| virtual unsigned int | getMinimumOpacity () const Returns the minimum opacity. |
| virtual unsigned int | getMinimumTransparency () const Returns the minimum transparency. |
| virtual SBQuantity::mass | getMolecularWeight () Returns the molecular weight. |
| virtual std::string const & | getName () const Returns the name of the node. |
| SBDDataGraphNode * | getNextNode () const Returns the pointer to the next 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. |
| unsigned int | getNodeIndex () const Returns the node index (unique in the whole data graph, but non-persistent) |
| SBUUID | getNodeUUID () const Returns the node UUID. |
| virtual void | getNodes (SBNodeIndexer & nodeIndexer, SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Collects nodes into nodeIndexer , based on anodeType , a selection status and avisitPredicate , with or without dependencies. |
| virtual void | getNodes (SBNodeIndexer & nodeIndexer, const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Collects nodes into nodeIndexer , based on aselectionPredicate and avisitPredicate , with or without dependencies. |
| virtual unsigned int | getNumberOfAtoms () Returns the number of atoms. |
| virtual unsigned int | getNumberOfCarbons () Returns the number of carbons. |
| virtual unsigned int | getNumberOfChains () Returns the number of chains. |
| virtual unsigned int | getNumberOfCoarseGrainedAtoms () Returns the number of coarse-grained atoms. |
| virtual unsigned int | getNumberOfHydrogens () Returns the number of hydrogens. |
| virtual unsigned int | getNumberOfMolecules () Returns the number of molecules. |
| virtual unsigned int | getNumberOfNitrogens () Returns the number of nitrogens. |
| virtual unsigned int | getNumberOfOtherAtoms () Returns the number of other atoms. |
| virtual unsigned int | getNumberOfOxygens () Returns the number of oxygens. |
| 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 | getNumberOfSulfurs () Returns the number of sulfurs. |
| virtual unsigned int | getOpacity () const Returns the opacity. |
| virtual unsigned int | getOpacitySingleStep () const Returns the opacity single step. |
| virtual std::string | getOpacitySuffix () const Returns the opacity suffix. |
| SBDDataGraphNode * | getParent () const Returns the parent of the node. |
| SBDDataGraphNode * | getPreviousNode () const Returns the pointer to the previous node 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. |
| SBDDataGraphNode * | getRoot () const Returns the root of the hierarchy the node belongs to. |
| bool | getSelected () const Returns whether the node is selected. |
| bool | getSelectionFlag () const Returns the selection flag. |
| virtual int | getSumOfFormalCharges () Returns the sum of formal charges. |
| virtual float | getSumOfPartialCharges () Returns the sum of partial charges. |
| SBDDataGraphNode * | getThisNode () const Returns the pointer to this node. |
| virtual unsigned int | getTransparency () const Returns the transparency. |
| virtual unsigned int | getTransparencySingleStep () const Returns the transparency single step. |
| virtual std::string | getTransparencySuffix () const Returns the transparency suffix. |
| virtual Type | getType () const Returns the type of the data graph node. |
| std::string | getTypeString (bool humanReadable=false) const Returns a string describing the type of the data graph node. |
| bool | getVisibilityFlag () const Returns the visibility flag. |
| bool | getVisible () const Returns whether the node is visible. |
| bool | hasMaterial () const Returns whether the node has a material (by itself, or inherited) |
| virtual bool | hasNode (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Returns whether the node has nodes based on a nodeType , a selection status and avisitPredicate , with or without dependencies. |
| virtual bool | hasNode (const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate & visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const Returns whether the node has nodes based on a selectionPredicate and avisitPredicate , with or without dependencies. |
| 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. |
| virtual bool | hasOpacityRange () const Returns whether the node has the opacity range. |
| virtual bool | hasTransparencyRange () const Returns whether the node has the transparency range. |
| bool | isAtom () const Returns true when the node is an atom. |
| bool | isBallAndStick () const Returns true when the node is the default ball-and-stick visual model. |
| bool | isBond () const Returns true when the node is a bond. |
| bool | isCartoon () const Returns true when the node is the default cartoon visual model. |
| bool | isCreated () const Returns true if and only if the node is created. |
| bool | isDynamicalModel () const Returns true when the node is a dynamical model. |
| bool | isErased () const Returns true if and only if the node is erased. |
| bool | isGaussianSurface () const Returns true when the node is the default Gaussian surface visual model. |
| bool | isHighlighted () const Returns whether the node is highlighted. |
| 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 innode . |
| 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 thenodeIndexer . |
| 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 thenodePointerIndexer . |
| bool | isInteractionModel () const Returns true when the node is a interaction model. |
| bool | isLicorice () const Returns true when the node is the default licorice visual model. |
| bool | isLight () const Returns true when the node is a light. |
| virtual bool | isLocked () const Returns whether the node is locked. |
| bool | isMesh () const Returns true when the node is a mesh. |
| bool | isModel () const Returns true when the node is a model. |
| 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 . |
| bool | isPropertyModel () const Returns true when the node is a property model. |
| bool | isRibbon () const Returns true when the node is the default ribbon visual model. |
| bool | isSelected () const Returns whether the node is selected. |
| virtual bool | isSerializable () const Returns true when the class is serializable. |
| bool | isSimulator () const Returns true when the node is a simulator. |
| 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. |
| bool | isStructuralModel () const Returns true when the node is a structural model. |
| bool | isStructuralNode () const Returns true when the node is a structural node. |
| bool | isTube () const Returns true when the node is the default tube visual model. |
| bool | isType (Type type) const Returns true when the type of the node corresponds to type . |
| bool | isVanDerWaals () const Returns true when the node is the default van der Waals visual model. |
| bool | isVisible () const Returns whether the node is visible. |
| bool | isVisualModel () const Returns true when the node is a visual model. |
| bool | ownsMaterial () const Returns whether the node owns a material. |
| virtual void | print (unsigned int offset=0) const Prints some debugging information. |
| virtual bool | removeChild (SBDDataGraphNode * node) Removes a child from the node. |
| 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. |
| 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. |
| void | setHighlightingFlag (bool flag) Sets the highlighting flag. |
| virtual void | setLockedFlag (bool flag) Sets the locked flag. |
| virtual void | setName (const std::string & name) Sets the name of the node. |
| virtual void | setOpacity (unsigned int opacity) Sets the opacity. |
| void | setSelectionFlag (bool flag) Sets the selection flag. |
| virtual void | setTransparency (unsigned int transparency) Sets the transparency. |
| void | setVisibilityFlag (bool flag) Sets the visibility flag. |
| 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. |
Public Functions inherited from SBCReferenceTarget#
| Type | Name |
|---|---|
| SBCReferenceTarget () |
|
| unsigned int | getMemoryFootprint () const |
| void | printReferencesToOwners () const |
| virtual | ~SBCReferenceTarget () |
Public Static Functions#
| Type | Name |
|---|---|
| bool | bondExists (SBMStructuralModelNodeAtom * atom1, SBMStructuralModelNodeAtom * atom2) Checks whether the bond between atoms atom1 andatom2 exists. |
| bool | cloneStructuralNodes (SBNodeIndexer & structuralModelIndexer, const SBNodeIndexer & structuralNodeIndexer) Adds in structuralModelIndexer the structural models resulting from cloning the structural nodes instructuralNodeIndexer . |
| SBSpatialDomain | computeDomain (const SBNodeIndexer & nodeIndexer) Computes the domain containing the atoms and bond atoms in the node indexer. |
| bool | createBond (SBMStructuralModelNodeAtom * atom1, SBMStructuralModelNodeAtom * atom2, double bondOrder=1.0, SBBond::BondType bondType=SBBond::BondType::Undefined) Creates a bond between atom1 andatom2 if there is none; sets the bond order tobondOrder and the bond type tobondType . |
| int | createCovalentBondsByResidueType (const SBNodeIndexer & nodeIndexer) Builds covalent bonds for the atoms belonging to the given residues of the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types. |
| bool | extractStructuralNodes (SBNodeIndexer & structuralModelIndexer, const SBNodeIndexer & structuralNodeIndexer) Adds in structuralModelIndexer the structural models resulting from extracting the structural nodes instructuralNodeIndexer . |
| SBMStructuralModelNodeAtom * | findAtom (const SBNodeIndexer & nodeIndexer, SBElement::Type type, const std::string & name) Returns, if found, an atom from a node indexer nodeIndexer with the typetype and namename ; else returns 0. |
| SBMStructuralModelNodeAtom * | findAtom (const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer, SBElement::Type type, const std::string & name) Returns, if found, an atom from an atom node indexer atomIndexer with the typetype and namename ; else returns 0. |
| SBMStructuralModelNodeAtom * | findAtom (const SBNodeIndexer & nodeIndexer, SBElement::Type type, const std::string & name, char altLoc) Returns, if found, an atom from a node indexer nodeIndexer with the typetype , namename , and an alternate locationaltLoc (if the atom has an alternate location); else returns 0. |
| SBMStructuralModelNodeAtom * | findAtom (const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer, SBElement::Type type, const std::string & name, char altLoc) Returns, if found, an atom from an atom node indexer atomIndexer with the typetype , namename , and an alternate locationaltLoc (if the atom has an alternate location); else returns 0. |
| std::set< char > | getAltLocations (const SBNodeIndexer & nodeIndexer) Returns a set of all alternate locations for atoms that belong to nodes present in nodeIndexer . |
| std::set< char > | getAltLocations (const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer) Returns a set of all alternate locations of atoms present in the atomIndexer . |
| double | getAsphericity (const SBNodeIndexer & nodeIndexer) Returns the asphericity parameter of the system of atoms (based on their positions and masses) in nodeIndexer . The asphericity parameter changes in the [0, 1] interval: 0 - a sphere, 1 - a rod. |
| SBPosition3 | getCenterOfFormalCharge (const SBNodeIndexer & nodeIndexer) Returns the center of formal charge of atoms in nodeIndexer . |
| SBPosition3 | getCenterOfMass (const SBNodeIndexer & nodeIndexer) Returns the center of mass of atoms in nodeIndexer . |
| SBPosition3 | getCenterOfPartialCharge (const SBNodeIndexer & nodeIndexer) Returns the center of partial charge of atoms in nodeIndexer . |
| SBPosition3 | getCentroid (const SBNodeIndexer & nodeIndexer) Returns the centroid (the geometric center) of atoms in nodeIndexer . |
| SBQuantity::length | getDipoleMomentAtCenterOfCharge (const SBNodeIndexer & nodeIndexer) Returns the dipole moment of atoms in nodeIndexer at their center of charge (based on partial charge) |
| SBQuantity::length | getDipoleMomentAtCenterOfMass (const SBNodeIndexer & nodeIndexer) Returns the dipole moment of atoms in nodeIndexer at their center of mass. |
| SBPosition3 | getDipoleVectorAtCenterOfCharge (const SBNodeIndexer & nodeIndexer) Returns the dipole vector of atoms in nodeIndexer at their center of charge (based on partial charge) |
| SBPosition3 | getDipoleVectorAtCenterOfMass (const SBNodeIndexer & nodeIndexer) Returns the dipole vector of atoms in nodeIndexer at their center of mass. |
| SBInertiaTensor33 | getInertiaTensor (const SBNodeIndexer & nodeIndexer) Returns the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer . |
| SBQuantity::mass | getMolecularWeight (const SBNodeIndexer & nodeIndexer) Returns the cumulative molecular weight of nodes in nodeIndexer . |
| SBMatrix33 | getPrincipalAxes (const SBNodeIndexer & nodeIndexer) Returns the principal axes of the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer . |
| SBQuantity::length | getRadiusOfGyration (const SBNodeIndexer & nodeIndexer) Returns the radius of gyration of the system of atoms (based on their positions and masses) in nodeIndexer . |
| double | getShapeParameter (const SBNodeIndexer & nodeIndexer) Returns the shape parameter of the system of atoms (based on their positions and masses) in nodeIndexer . The shape parameter, S, changes in the [-0.25, 2] interval, where 0 corresponds to a sphere, negative values correspond to oblate ellipsoid, positive values correspond to prolate ellipsoid. |
| SBQuantity::squareLength | getSolventAccessibleSurfaceArea (const SBNodeIndexer & nodeIndexer, const SBQuantity::length & probeRadius, const unsigned int numberOfPointsOnSphere) Returns the solvent-accessible surface area (SASA) of the system of atoms in nodeIndexer with the probe radiusprobeRadius , and the number of points on a spherenumberOfPointsOnSphere . |
| SBDTypeSpatialTransform | getSpatialTransform (const SBNodeIndexer & nodeIndexer) Returns the spatial transform based on the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer . |
| int | getSumOfFormalCharges (const SBNodeIndexer & nodeIndexer) Returns the sum of formal charges of nodes in nodeIndexer . |
| float | getSumOfPartialCharges (const SBNodeIndexer & nodeIndexer) Returns the sum of partial charges of nodes in nodeIndexer . |
| void | getWater (SBNodeIndexer & resultNodeIndexer, const SBNodeIndexer & nodeIndexer) Finds water nodes in the nodeIndexer . |
| bool | isPlanar (const SBNodeIndexer & nodeIndexer) Returns true if all atoms in nodeIndexer are in the same plane. |
| void | replaceAtom (SBMStructuralModelNodeAtom * oldAtom, SBMStructuralModelNodeAtom * newAtom, bool preserveOldAtomPosition=false) Replaces atom oldAtom with atomnewAtom . All bonds from the old atom are transferred to the new atom. |
| void | replaceBond (SBMStructuralModelNodeBond * oldBond, SBMStructuralModelNodeBond * newBond, bool flipBond=false, bool preserveOldBondPosition=false) Replaces bond oldBond with bondnewBond . All neighboring bonds from the old bond are transferred to the new bond. |
Public Static Functions inherited from SBDDataGraphNode#
See SBDDataGraphNode
| Type | Name |
|---|---|
| bool | canAddMaterial (SBDDataGraphNode::Type nodeType) Returns whether can add a material to a node of type nodeType . |
| void | clone (const SBNodeIndexer & sourceNodeIndexer, SBNodeIndexer & destinationNodeIndexer) Clones the nodes in sourceNodeIndexer (treated as a whole) and places the clones indestinationNodeIndexer . |
| void | forEachNodeInSelection (SBNodeIndexer & nodeIndexer, void(*)(SBDDataGraphNode *node) action) Performs an action for each node in a selection. |
| void | forEachNodeInSelection (SBNodeIndexer & nodeIndexer, SBCClass * object, void(SBCClass::*)(SBDDataGraphNode *node) action) Performs an action for each node in a selection. |
| SBDDataGraphNode * | getNode (unsigned int nodeIndex) Returns the unique node corresponding to the node index nodeIndex . |
| std::string | getTypeString (Type type, bool humanReadable=false) Returns a string describing the type of the data graph node. |
Protected Attributes inherited from SBCReferenceTarget#
| Type | Name |
|---|---|
| SBCReferenceTargetData * | dataPointer |
Protected Functions inherited from SBMModel#
See SBMModel
| Type | Name |
|---|---|
| SBMModel () Builds a model. |
|
| SBMModel (SBMModelData * dataPointer) Builds a model. |
Protected Functions inherited from SBDDataGraphNode#
See SBDDataGraphNode
| Type | Name |
|---|---|
| SBDDataGraphNode () Builds a data graph node. |
|
| SBDDataGraphNode (SBDDataGraphNodeData * dataPointer) Builds a data graph node. |
|
| virtual | ~SBDDataGraphNode () Destroys the node. |
Protected Functions inherited from SBCReferenceTarget#
| Type | Name |
|---|---|
| SBCReferenceTarget (SBCReferenceTargetData * dataPointer) |
|
| void | removeAllReferenceOwners () |
Detailed Description#
This class describes a structural model.
Short name: SBStructuralModel
Public Functions Documentation#
function SBMStructuralModel#
Builds a base model.
function SB_DECLARE_DATA#
function SB_NODE_GETTER_0 [1/7]#
function SB_NODE_GETTER_0 [2/7]#
function SB_NODE_GETTER_0 [3/7]#
function SB_NODE_GETTER_0 [4/7]#
function SB_NODE_GETTER_0 [5/7]#
function SB_NODE_GETTER_0 [6/7]#
function SB_NODE_GETTER_0 [7/7]#
SBMStructuralModel::SB_NODE_GETTER_0 (
std::string,
GetCrystallographicAndTransformationInformation
)
function SB_NODE_PREDICATE_0 [1/7]#
function SB_NODE_PREDICATE_0 [2/7]#
function SB_NODE_PREDICATE_0 [3/7]#
function SB_NODE_PREDICATE_0 [4/7]#
function SB_NODE_PREDICATE_0 [5/7]#
function SB_NODE_PREDICATE_0 [6/7]#
function SB_NODE_PREDICATE_0 [7/7]#
function addChild#
Adds a child to the node.
This function is a convenience function equivalent to getStructuralRoot() ->addChild(node, nextNode)
function canAddChild#
Returns whether this node can add node as a child.
virtual bool SBMStructuralModel::canAddChild (
const SBNode * node,
const SBNode * nextNode=nullptr
) override const
This function is a convenience function equivalent to getStructuralRoot() ->canAddChild(node, nextNode)
function canAddChildType#
Returns whether this node can add a node with type nodeType as a child.
This function is a convenience function equivalent to getStructuralRoot() ->canAddChildType(nodeType)
Implements SBDDataGraphNode::canAddChildType
function canHaveDescendantType#
Returns whether this node can have a node with type nodeType as a descendant.
This function is a convenience function equivalent to getStructuralRoot() ->canHaveDescendantType(nodeType)
Implements SBDDataGraphNode::canHaveDescendantType
function centerTransform#
Centers the pivot of the transform on the center of mass of the atoms contained in the structural model.
Centers the pivot of the transform on the center of mass of the atoms contained in the structural model. This changes the transform only, and does not move atoms belonging to the structural model.
function clearConnectivityAnnotationInformation#
Clears the model's connectivity annotation information.
function clearCrystallographicAndTransformationInformation#
Clears the model's crystallographic and transformation information.
function clearHeterogenInformation#
Clears the model's heterogen information.
function clearMiscellaneousInformation#
Clears the model's miscellaneous information.
function clearPrimaryStructureInformation#
Clears the model's primary structure information.
function clearSecondaryStructureInformation#
Clears the model's secondary structure information.
function clearTitleInformation#
Clears the model's title information.
function clone#
Returns a copy of the node and its descendants.
Implements SBMModel::clone
function collectAmbientOcclusion#
To collect ambient occlusion data.
virtual void SBMStructuralModel::collectAmbientOcclusion (
const SBPosition3 & boxOrigin,
const SBPosition3 & boxSize,
unsigned int nCellsX,
unsigned int nCellsY,
unsigned int nCellsZ,
float * ambientOcclusionData
)
function computeSecondaryStructure#
Computes the secondary structure for all residues in the structural model.
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.
function connectStructuralSignalToSlot#
void SBMStructuralModel::connectStructuralSignalToSlot (
SBCReferenceTarget * referenceTarget,
void(SBCReferenceTarget::*)( SBStructuralEvent *) functionPointer,
SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any,
SBCReferenceTarget * nextReferenceTarget=0,
void(SBCReferenceTarget::*)( SBStructuralEvent *) nextFunctionPointer=0
)
function createCovalentBonds [1/2]#
Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances.
function createCovalentBonds [2/2]#
Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances with the additional margin additionalMargin .
function createCovalentBondsByResidueType [1/2]#
Builds covalent bonds for the atoms belonging to the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types.
function disconnectStructuralSignalFromSlot#
void SBMStructuralModel::disconnectStructuralSignalFromSlot (
SBCReferenceTarget * referenceTarget,
void(SBCReferenceTarget::*)( SBStructuralEvent *) functionPointer,
SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any
)
function expandBounds#
Expands the bounds to make sure the visual model fits inside them.
function forEachNodeDepthFirst [1/2]#
Performs an action on each node.
virtual void SBMStructuralModel::forEachNodeDepthFirst (
void(*)( SBDDataGraphNode *node) action
) override
Implements SBDDataGraphNode::forEachNodeDepthFirst
function forEachNodeDepthFirst [2/2]#
Performs an action on each node.
virtual void SBMStructuralModel::forEachNodeDepthFirst (
SBCClass * object,
void(SBCClass::*)( SBDDataGraphNode *node) action
) override
Implements SBDDataGraphNode::forEachNodeDepthFirst
function getChildren#
This function is a convenience function equivalent to getStructuralRoot() ->getChildren __
function getConnectivityAnnotationInformation#
Returns the model's connectivity annotation information.
function getCrystallographicAndTransformationInformation#
Returns the model's crystallographic and transformation information.
function getHeterogenInformation#
Returns the model's heterogen information.
function getLockedFlag#
Returns the locked flag.
This function returns the locked flag of the structural model. When the structural model is locked, its geometry (the atoms positions), topology (the bonds) and identities (node names and indices) cannot be edited by the user. However, other properties can still be edited. For example, secondary structure information can still be computed, and materials and color schemes can still be applied.
Note that some properties that cannot be edited by users can still be edited by developers.
See also: isLocked, setLockedFlag
Implements SBDDataGraphNode::getLockedFlag
function getMiscellaneousInformation#
Returns the model's miscellaneous information.
function getModelType#
Returns the model type.
Implements SBMModel::getModelType
function getMolecularWeight [2/2]#
Returns the molecular weight.
This function returns the cumulative molecular weight of atoms in the structural model.
If the structural model doesn't contain any atoms then the function returns zero.
Implements SBDDataGraphNode::getMolecularWeight
function getNodes [1/2]#
Collects nodes into nodeIndexer , based on anodeType , a selection status and avisitPredicate , with or without dependencies.
virtual void SBMStructuralModel::getNodes (
SBNodeIndexer & nodeIndexer,
SBNode::Type nodeType,
bool selectedNodesOnly=false,
const SBNodePredicate & visitPredicate=SBDDataGraphNode::All (),
bool includeDependencies=false
) override const
Implements SBDDataGraphNode::getNodes
function getNodes [2/2]#
Collects nodes into nodeIndexer , based on aselectionPredicate and avisitPredicate , with or without dependencies.
virtual void SBMStructuralModel::getNodes (
SBNodeIndexer & nodeIndexer,
const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All (),
const SBNodePredicate & visitPredicate=SBDDataGraphNode::All (),
bool includeDependencies=false
) override const
Implements SBDDataGraphNode::getNodes
function getNumberOfAtoms#
Returns the number of atoms.
Implements SBDDataGraphNode::getNumberOfAtoms
function getNumberOfCarbons#
Returns the number of carbons.
Implements SBDDataGraphNode::getNumberOfCarbons
function getNumberOfChains#
Returns the number of chains.
Implements SBDDataGraphNode::getNumberOfChains
function getNumberOfCoarseGrainedAtoms#
Returns the number of coarse-grained atoms.
Implements SBDDataGraphNode::getNumberOfCoarseGrainedAtoms
function getNumberOfHydrogens#
Returns the number of hydrogens.
Implements SBDDataGraphNode::getNumberOfHydrogens
function getNumberOfMolecules#
Returns the number of molecules.
Implements SBDDataGraphNode::getNumberOfMolecules
function getNumberOfNitrogens#
Returns the number of nitrogens.
Implements SBDDataGraphNode::getNumberOfNitrogens
function getNumberOfOtherAtoms#
Returns the number of other atoms.
Implements SBDDataGraphNode::getNumberOfOtherAtoms
function getNumberOfOxygens#
Returns the number of oxygens.
Implements SBDDataGraphNode::getNumberOfOxygens
function getNumberOfResidues#
Returns the number of residues.
Implements SBDDataGraphNode::getNumberOfResidues
function getNumberOfSegments#
Returns the number of segments.
Implements SBDDataGraphNode::getNumberOfSegments
function getNumberOfStructuralGroups#
Returns the number of structural groups.
Implements SBDDataGraphNode::getNumberOfStructuralGroups
function getNumberOfStructuralModels#
Returns the number of structural models.
Implements SBDDataGraphNode::getNumberOfStructuralModels
function getNumberOfSulfurs#
Returns the number of sulfurs.
Implements SBDDataGraphNode::getNumberOfSulfurs
function getOrientation#
Returns the orientation of the structural model.
function getPosition#
Returns the position of the structural model.
function getPrimaryStructureInformation#
Returns the model's primary structure information.
function getSecondaryStructureInformation#
Returns the model's secondary structure information.
function getStructuralRoot#
This function returns a pointer to the structural root of the structural model. This root is a structural node, and can be used as a convenience root for e.g. recursive algorithms that operate on structural nodes (such algorithms could not work on the structural model itself, since the SBMStructuralModel class does not derive from SBMStructuralModelNode).
function getStructuralSignalFlag#
Returns true when the model can send structural signals.
function getSumOfFormalCharges [2/2]#
Returns the sum of formal charges.
Implements SBDDataGraphNode::getSumOfFormalCharges
function getSumOfPartialCharges [2/2]#
Returns the sum of partial charges.
Implements SBDDataGraphNode::getSumOfPartialCharges
function getTitleInformation#
Returns the model's title information.
function getTransform#
Returns the spatial transform of the structural model.
function getType#
Returns the type of the data graph node.
Implements SBMModel::getType
function getWater [1/2]#
Finds water nodes in the structural model.
This function finds water nodes in the structural model and adds them to resultNodeIndexer.
function hasConnectivityAnnotationInformation#
Returns true when the model's connectivity annotation information is set.
function hasCrystallographicAndTransformationInformation#
Returns true when the model's crystallographic and transformation information is set.
function hasHeterogenInformation#
Returns true when the model's heterogen information is set.
function hasMiscellaneousInformation#
Returns true when the model's miscellaneous information is set.
function hasNode [1/2]#
Checks for nodes based on a nodeType , a selection status and avisitPredicate , with or without dependencies.
virtual bool SBMStructuralModel::hasNode (
SBNode::Type nodeType,
bool selectedNodesOnly=false,
const SBNodePredicate & visitPredicate=SBDDataGraphNode::All (),
bool includeDependencies=false
) override const
Implements SBDDataGraphNode::hasNode
function hasNode [2/2]#
Checks for nodes based on a selectionPredicate and avisitPredicate , with or without dependencies.
virtual bool SBMStructuralModel::hasNode (
const SBNodePredicate & selectionPredicate=SBDDataGraphNode::All (),
const SBNodePredicate & visitPredicate=SBDDataGraphNode::All (),
bool includeDependencies=false
) override const
Implements SBDDataGraphNode::hasNode
function hasPrimaryStructureInformation#
Returns true when the model's primary structure information is set.
function hasSecondaryStructureInformation#
Returns true when the model's secondary structure information is set.
function hasTitleInformation#
Returns true when the model's title information is set.
function isLocked#
Returns whether the model is locked.
This function is equivalent to getLockedFlag
See also: getLockedFlag, setLockedFlag
Implements SBDDataGraphNode::isLocked
function isSerializable#
Returns true.
Implements SBMModel::isSerializable
function populateChainIDs#
Populates the chain IDs for all chains in the structural model.
This function populates the chain IDs for all chains in the structural model.
The numbering of chain IDs for the chains with missing IDs will start from the maximum chain ID present in the structural model, for example, if there are chains with IDs 0, 1, 4 then the numbering of other chains with missing IDs will commence from 5.
If some chains have the same IDs then the repetitions will be renumbered, for example, chain IDs 0, 2, 2 will become 0, 2, 3.
If forceRenumbering is set to true then it renumbers chains IDs starting from 0 iff at least on of the chains has a missing ID or has the same ID as another chain in the structural model.
function print#
Prints debugging information.
Implements SBMModel::print
function removeChild#
Removes a child from the node.
This function is a convenience function equivalent to getStructuralRoot() ->removeChild(node)
function rotate#
Rotates the structural model.
function serialize#
Serializes the node.
virtual void SBMStructuralModel::serialize (
SBCSerializer * serializer,
const SBNodeIndexer & nodeIndexer,
const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER,
const SBVersionNumber & classVersionNumber=SBVersionNumber (1, 0, 0)
) override const
Implements SBMModel::serialize
function setConnectivityAnnotationInformation#
Sets the model's connectivity annotation information.
function setCrystallographicAndTransformationInformation#
Sets the model's crystallographic and transformation information.
void SBMStructuralModel::setCrystallographicAndTransformationInformation (
const std::string & info
)
function setHeterogenInformation#
Sets the model's heterogen information.
function setLockedFlag#
Sets the locked flag.
This function sets the locked flag of the structural model.
This function is undoable.
See also: isLocked, getLockedFlag
Implements SBDDataGraphNode::setLockedFlag
function setMiscellaneousInformation#
Sets the model's miscellaneous information.
function setOrientation [1/3]#
Sets the orientation of the structural model.
function setOrientation [2/3]#
Sets the orientation of the structural model.
function setOrientation [3/3]#
Sets the newOrientation and theoldOrientation of the structural model.
void SBMStructuralModel::setOrientation (
SBMatrix33 const & newOrientation,
SBMatrix33 const & oldOrientation,
bool transformParticles=true
)
function setPosition [1/3]#
Sets the position of the structural model.
function setPosition [2/3]#
Sets the position of the structural model.
function setPosition [3/3]#
Sets the newPosition and theoldPosition of the structural model.
void SBMStructuralModel::setPosition (
SBPosition3 const & newPosition,
SBPosition3 const & oldPosition,
bool transformParticles=true
)
function setPrimaryStructureInformation#
Sets the model's primary structure information.
function setSecondaryStructureInformation#
Sets the model's secondary structure information.
function setStructuralSignalFlag#
Sets whether the model can send structural signals.
function setTitleInformation#
Sets the model's title information.
function setTransform [1/3]#
Sets the spatial transform of the structural model.
function setTransform [2/3]#
Sets the spatial transform of the structural model.
void SBMStructuralModel::setTransform (
const SBSpatialTransform & transform,
bool transformParticles
)
function setTransform [3/3]#
Sets the newTransform and theoldTransform of the structural model.
void SBMStructuralModel::setTransform (
SBSpatialTransform const & newTransform,
SBSpatialTransform const & oldTransform,
bool transformParticles=true
)
function structuralSignalIsConnectedToSlot#
bool SBMStructuralModel::structuralSignalIsConnectedToSlot (
SBCReferenceTarget * referenceTarget,
void(SBCReferenceTarget::*)( SBStructuralEvent *) functionPointer,
SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any
) const
function transform#
Applies a spatial transform to the structural model.
function translate#
Translates the structural model.
function unserialize#
Unserializes the node.
virtual void SBMStructuralModel::unserialize (
SBCSerializer * serializer,
const SBNodeIndexer & nodeIndexer,
const SBVersionNumber & sdkVersionNumber=SB_SDK_VERSION_NUMBER,
const SBVersionNumber & classVersionNumber=SBVersionNumber (1, 0, 0)
) override
Implements SBMModel::unserialize
function ~SBMStructuralModel#
Deletes the model.
Public Static Functions Documentation#
function bondExists#
Checks whether the bond between atoms atom1 andatom2 exists.
static bool SBMStructuralModel::bondExists (
SBMStructuralModelNodeAtom * atom1,
SBMStructuralModelNodeAtom * atom2
)
This function checks whether the bond between atoms atom1 and atom2 exists: it returns true if the bond exists and false otherwise.
function cloneStructuralNodes#
Adds in structuralModelIndexer the structural models resulting from cloning the structural nodes instructuralNodeIndexer .
static bool SBMStructuralModel::cloneStructuralNodes (
SBNodeIndexer & structuralModelIndexer,
const SBNodeIndexer & structuralNodeIndexer
)
function computeDomain#
Computes the domain containing the atoms and bond atoms in the node indexer.
function createBond#
Creates a bond between atom1 andatom2 if there is none; sets the bond order tobondOrder and the bond type tobondType .
static bool SBMStructuralModel::createBond (
SBMStructuralModelNodeAtom * atom1,
SBMStructuralModelNodeAtom * atom2,
double bondOrder=1.0,
SBBond::BondType bondType=SBBond::BondType::Undefined
)
function createCovalentBondsByResidueType [2/2]#
Builds covalent bonds for the atoms belonging to the given residues of the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types.
static int SBMStructuralModel::createCovalentBondsByResidueType (
const SBNodeIndexer & nodeIndexer
)
function extractStructuralNodes#
Adds in structuralModelIndexer the structural models resulting from extracting the structural nodes instructuralNodeIndexer .
static bool SBMStructuralModel::extractStructuralNodes (
SBNodeIndexer & structuralModelIndexer,
const SBNodeIndexer & structuralNodeIndexer
)
function findAtom [1/4]#
Returns, if found, an atom from a node indexer nodeIndexer with the typetype and namename ; else returns 0.
static SBMStructuralModelNodeAtom * SBMStructuralModel::findAtom (
const SBNodeIndexer & nodeIndexer,
SBElement::Type type,
const std::string & name
)
function findAtom [2/4]#
Returns, if found, an atom from an atom node indexer atomIndexer with the typetype and namename ; else returns 0.
static SBMStructuralModelNodeAtom * SBMStructuralModel::findAtom (
const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer,
SBElement::Type type,
const std::string & name
)
function findAtom [3/4]#
Returns, if found, an atom from a node indexer nodeIndexer with the typetype , namename , and an alternate locationaltLoc (if the atom has an alternate location); else returns 0.
static SBMStructuralModelNodeAtom * SBMStructuralModel::findAtom (
const SBNodeIndexer & nodeIndexer,
SBElement::Type type,
const std::string & name,
char altLoc
)
function findAtom [4/4]#
Returns, if found, an atom from an atom node indexer atomIndexer with the typetype , namename , and an alternate locationaltLoc (if the atom has an alternate location); else returns 0.
static SBMStructuralModelNodeAtom * SBMStructuralModel::findAtom (
const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer,
SBElement::Type type,
const std::string & name,
char altLoc
)
function getAltLocations [1/2]#
Returns a set of all alternate locations for atoms that belong to nodes present in nodeIndexer .
function getAltLocations [2/2]#
Returns a set of all alternate locations of atoms present in the atomIndexer .
static std::set< char > SBMStructuralModel::getAltLocations (
const SBIndexer< SBMStructuralModelNodeAtom * > & atomIndexer
)
function getAsphericity#
Returns the asphericity parameter of the system of atoms (based on their positions and masses) in nodeIndexer . The asphericity parameter changes in the [0, 1] interval: 0 - a sphere, 1 - a rod.
This function returns the asphericity parameter of the system of atoms (based on their positions and masses) in nodeIndexer.
The asphericity parameter changes in the [0, 1] range, where 0 corresponds to a sphere and 1 corresponds to a rod.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.
function getCenterOfFormalCharge#
Returns the center of formal charge of atoms in nodeIndexer .
static SBPosition3 SBMStructuralModel::getCenterOfFormalCharge (
const SBNodeIndexer & nodeIndexer
)
This function returns the center of formal charge of atoms from nodeIndexer
The center of formal charge is computed as follows:
R = sum(q_i * r_i, i=1..N) / Q
where N is the number of atoms, q_i is the i-th atom's formal charge, r_i is the i-th atom's position, and Q is the total formal charge of all of the N atoms.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).
function getCenterOfMass#
Returns the center of mass of atoms in nodeIndexer .
This function returns the center of mass of atoms from nodeIndexer
The center of mass is computed as follows:
R = sum(m_i * r_i, i=1..N) / M
where N is the number of atoms, m_i is the i-th atom's mass, r_i is the i-th atom's position, and M is the total mass of all of the N atoms.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).
function getCenterOfPartialCharge#
Returns the center of partial charge of atoms in nodeIndexer .
static SBPosition3 SBMStructuralModel::getCenterOfPartialCharge (
const SBNodeIndexer & nodeIndexer
)
This function returns the center of partial charge of atoms from nodeIndexer
The center of partial charge is computed as follows:
R = sum(q_i * r_i, i=1..N) / Q
where N is the number of atoms, q_iis thei-th atom's partial charge,r_iis thei-th atom's position, andQis the total partial charge of all of theN` atoms.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).
function getCentroid#
Returns the centroid (the geometric center) of atoms in nodeIndexer .
This function returns the centroid (the geometric center) of atoms from nodeIndexer
If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).
function getDipoleMomentAtCenterOfCharge#
Returns the dipole moment of atoms in nodeIndexer at their center of charge (based on partial charge)
static SBQuantity::length SBMStructuralModel::getDipoleMomentAtCenterOfCharge (
const SBNodeIndexer & nodeIndexer
)
This function returns the dipole moment of atoms from nodeIndexer at their center of charge.
The dipole moment at center of charge is computed as follows:
m = norm(mu)
where mu is the dipole vector of atoms from nodeIndexer at their center of partial charge.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).
function getDipoleMomentAtCenterOfMass#
Returns the dipole moment of atoms in nodeIndexer at their center of mass.
static SBQuantity::length SBMStructuralModel::getDipoleMomentAtCenterOfMass (
const SBNodeIndexer & nodeIndexer
)
This function returns the dipole moment of atoms from nodeIndexer at their center of mass. The dipole moment at center of mass is computed as follows:
m = norm(mu)
where mu is the dipole vector of atoms from nodeIndexer at their center of mass.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).
function getDipoleVectorAtCenterOfCharge#
Returns the dipole vector of atoms in nodeIndexer at their center of charge (based on partial charge)
static SBPosition3 SBMStructuralModel::getDipoleVectorAtCenterOfCharge (
const SBNodeIndexer & nodeIndexer
)
This function returns the dipole vector of atoms from nodeIndexer at their center of partial charge.
The dipole vector at center of charge is computed as follows:
mu = sum(q_i * (r_i - r_coc), i=1..N)
where N is the number of atoms, q_i is the i-th atom's partial charge, r_i is the i-th atom's position, and r_coc is the center of partial charge of these atoms.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).
function getDipoleVectorAtCenterOfMass#
Returns the dipole vector of atoms in nodeIndexer at their center of mass.
static SBPosition3 SBMStructuralModel::getDipoleVectorAtCenterOfMass (
const SBNodeIndexer & nodeIndexer
)
This function returns the dipole vector of atoms from nodeIndexer at their center of mass.
The dipole vector at center of mass is computed as follows:
mu = sum(q_i * (r_i - r_com), i=1..N)
where N is the number of atoms, q_i is the i-th atom's partial charge, r_i is the i-th atom's position, and `r_com is the center of mass of these atoms.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns the center of coordinates (SBPosition3::zero).
function getInertiaTensor#
Returns the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer .
This function returns the moment of inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer relative to their center of mass.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns a zero tensor.
function getMolecularWeight [1/2]#
Returns the cumulative molecular weight of nodes in nodeIndexer .
static SBQuantity::mass SBMStructuralModel::getMolecularWeight (
const SBNodeIndexer & nodeIndexer
)
This function returns the cumulative molecular weight of nodes in nodeIndexer.
function getPrincipalAxes#
Returns the principal axes of the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer .
Returns the principal axes of the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer.
The eigen vectors are sorted by their eigen value in the descending order, i.e. the first one corresponds to the first principal axes. In other words: the first axis corresponds to the longest domain dimension, while the third axis corresponds to the smallest domain dimension.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns a zero matrix.
function getRadiusOfGyration#
Returns the radius of gyration of the system of atoms (based on their positions and masses) in nodeIndexer .
static SBQuantity::length SBMStructuralModel::getRadiusOfGyration (
const SBNodeIndexer & nodeIndexer
)
This function returns the radius of gyration of the system of atoms (based on their positions and masses) from nodeIndexer.
The radius of gyration is computed as follows:
Rg = sqrt(sum(m_i * (r_i - r_c)^2, i=1..N) / M)
where N is the number of atoms, m_i is the mass of i-th atom, r_i is the i-th atom's position, r_c is the center of mass of all N atoms, M is the total mass of all of the N atoms.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.
function getShapeParameter#
Returns the shape parameter of the system of atoms (based on their positions and masses) in nodeIndexer . The shape parameter, S, changes in the [-0.25, 2] interval, where 0 corresponds to a sphere, negative values correspond to oblate ellipsoid, positive values correspond to prolate ellipsoid.
This function returns the shape parameter of the system of atoms (based on their positions and masses) in nodeIndexer. The shape parameter, S, changes in the [-0.25, 2] range, where 0 corresponds to a sphere, negative values correspond to oblate ellipsoid, positive values correspond to prolate ellipsoid.
It is computed as follows:
S = prod((lambda_i - lambda_mean), i=1..3) / (lambda_mean^3)
where lambda_i is the i-th eigen value of the inertia tensor, lambda_mean is the mean of eigen values and is equal to sum(lambda_i, i=1..3).
If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.
function getSolventAccessibleSurfaceArea#
Returns the solvent-accessible surface area (SASA) of the system of atoms in nodeIndexer with the probe radiusprobeRadius , and the number of points on a spherenumberOfPointsOnSphere .
static SBQuantity::squareLength SBMStructuralModel::getSolventAccessibleSurfaceArea (
const SBNodeIndexer & nodeIndexer,
const SBQuantity::length & probeRadius,
const unsigned int numberOfPointsOnSphere
)
This function returns the solvent-accessible surface area (SASA) of the system of atoms in nodeIndexer with the probe radius probeRadius, and the number of points on a sphere numberOfPointsOnSphere.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns zero.
function getSpatialTransform#
Returns the spatial transform based on the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer .
static SBDTypeSpatialTransform SBMStructuralModel::getSpatialTransform (
const SBNodeIndexer & nodeIndexer
)
Returns the spatial transform based on the inertia tensor of the system of atoms (based on their positions and masses) in nodeIndexer.
The eigen vectors are sorted by their eigen value in the descending order, i.e. the first one corresponds to the first principal axes. In other words: the first axis corresponds to the longest domain dimension, while the third axis corresponds to the smallest domain dimension.
If the nodeIndexer doesn't contain any atoms or their parents then the function returns a zero transform.
function getSumOfFormalCharges [1/2]#
Returns the sum of formal charges of nodes in nodeIndexer .
This function returns the sum of formal charges of nodes in nodeIndexer.
function getSumOfPartialCharges [1/2]#
Returns the sum of partial charges of nodes in nodeIndexer .
This function returns the sum of partial charges of nodes in nodeIndexer.
function getWater [2/2]#
Finds water nodes in the nodeIndexer .
static void SBMStructuralModel::getWater (
SBNodeIndexer & resultNodeIndexer,
const SBNodeIndexer & nodeIndexer
)
This function finds water nodes in the nodeIndexer and adds them to resultNodeIndexer
The resulting water nodes might include water structural groups and water atoms.
function isPlanar#
Returns true if all atoms in nodeIndexer are in the same plane.
This function returns true if all atoms in nodeIndexer are in the same plane Note that for 3 atoms and less it will always return true
function replaceAtom#
Replaces atom oldAtom with atomnewAtom . All bonds from the old atom are transferred to the new atom.
static void SBMStructuralModel::replaceAtom (
SBMStructuralModelNodeAtom * oldAtom,
SBMStructuralModelNodeAtom * newAtom,
bool preserveOldAtomPosition=false
)
function replaceBond#
Replaces bond oldBond with bondnewBond . All neighboring bonds from the old bond are transferred to the new bond.
static void SBMStructuralModel::replaceBond (
SBMStructuralModelNodeBond * oldBond,
SBMStructuralModelNodeBond * newBond,
bool flipBond=false,
bool preserveOldBondPosition=false
)