This class describes an atom in a structural model.
Public Member Functions | |
SB_NODE_GETTER_0 (, SBElement::Type, GetElementType) | |
SB_NODE_GETTER_0 (, std::string, GetElementName) | |
SB_NODE_GETTER_0 (, std::string, GetElementSymbol) | |
SB_NODE_GETTER_0 (, std::string, GetPeriod) | |
SB_NODE_GETTER_0 (, unsigned int, GetGroup) | |
SB_NODE_GETTER_0 (, std::string, GetBlock) | |
SB_NODE_GETTER_0 (, SBQuantity::mass, GetAtomicWeight) | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetCovalentRadius) | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetVanDerWaalsRadius) | |
SB_NODE_GETTER_0 (, SBQuantity::dimensionless, GetElectronegativity) | |
SB_NODE_GETTER_0 (, SBElement::MetalSubcategory, GetMetalSubcategory) | |
SB_NODE_GETTER_0 (, std::string, GetName) | |
SB_NODE_GETTER_0 (, char, GetAltLocation) | |
SB_NODE_GETTER_0 (, std::string, GetChainName) | |
SB_NODE_GETTER_0 (, char, GetInsertionCode) | |
SB_NODE_GETTER_0 (, int, GetSerialNumber) | |
SB_NODE_GETTER_0 (, SBQuantity::dimensionless, GetOccupancy) | |
SB_NODE_GETTER_0 (, std::string, GetRecordType) | |
SB_NODE_GETTER_0 (, unsigned int, GetRecordTypeSize) | |
SB_NODE_GETTER_0 (, std::string, GetResidueName) | |
SB_NODE_GETTER_0 (, std::string, GetResidueTypeString) | |
SB_NODE_GETTER_0 (, int, GetResidueSequenceNumber) | |
SB_NODE_GETTER_0 (, std::string, GetSegmentName) | |
SB_NODE_GETTER_0 (, double, GetTemperatureFactor) | |
SB_NODE_GETTER_0 (, float, GetPartialCharge) | |
SB_NODE_GETTER_0 (, int, GetFormalCharge) | |
SB_NODE_GETTER_0 (, std::string, GetComment) | |
SB_NODE_GETTER_0 (, unsigned int, GetCommentSize) | |
SB_NODE_GETTER_0 (, std::vector< int >, GetAnisotropicTFactors) | |
SB_NODE_GETTER_0 (, std::string, GetSYBYLType) | |
SB_NODE_GETTER_0 (, unsigned int, GetSYBYLTypeSize) | |
SB_NODE_GETTER_0 (, std::string, GetStatusBit) | |
SB_NODE_GETTER_0 (, unsigned int, GetStatusBitSize) | |
SB_NODE_GETTER_0 (, std::string, GetMoleculeName) | |
SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedAtoms) | |
SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedCarbons) | |
SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedHeavyAtoms) | |
SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedHydrogens) | |
SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedNitrogens) | |
SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedOxygens) | |
SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedSulfurs) | |
SB_NODE_GETTER_0 (, std::string, GetSubstructureName) | |
SB_NODE_GETTER_0 (, int, GetSubstructureSequenceNumber) | |
SB_NODE_GETTER_0 (, int, GetChainID) | |
SB_NODE_GETTER_0 (, Hybridization, GetHybridization) | |
SB_NODE_GETTER_0 (, Geometry, GetGeometry) | |
SB_NODE_GETTER_0 (, int, GetOxidationState) | |
SB_NODE_GETTER_0 (, bool, GetResonance) | |
SB_NODE_GETTER_0 (, bool, GetAromaticity) | |
SB_NODE_GETTER_0 (, bool, GetWaterFlag) | |
SB_NODE_GETTER_0 (, int, GetCustomType) | |
SB_NODE_PREDICATE_0 (, HasName) | |
SB_NODE_PREDICATE_0 (, HasAltLocation) | |
SB_NODE_PREDICATE_0 (, HasInsertionCode) | |
SB_NODE_PREDICATE_0 (, HasSerialNumber) | |
SB_NODE_PREDICATE_0 (, HasOccupancy) | |
SB_NODE_PREDICATE_0 (, HasRecordType) | |
SB_NODE_PREDICATE_0 (, HasResidueSequenceNumber) | |
SB_NODE_PREDICATE_0 (, HasTemperatureFactor) | |
SB_NODE_PREDICATE_0 (, HasPartialCharge) | |
SB_NODE_PREDICATE_0 (, HasFormalCharge) | |
SB_NODE_PREDICATE_0 (, HasComment) | |
SB_NODE_PREDICATE_0 (, HasAnisotropicTFactors) | |
SB_NODE_PREDICATE_0 (, HasSYBYLType) | |
SB_NODE_PREDICATE_0 (, HasStatusBit) | |
SB_NODE_PREDICATE_0 (, HasSubstructureSequenceNumber) | |
SB_NODE_PREDICATE_0 (, HasChainID) | |
SB_NODE_PREDICATE_0 (, HasHybridization) | |
SB_NODE_PREDICATE_0 (, HasGeometry) | |
SB_NODE_PREDICATE_0 (, HasOxidationState) | |
SB_NODE_PREDICATE_0 (, HasResonance) | |
SB_NODE_PREDICATE_0 (, HasAromaticity) | |
SB_NODE_PREDICATE_0 (, HasWaterFlag) | |
SB_NODE_PREDICATE_0 (, HasCustomType) | |
SB_NODE_PREDICATE_0 (, IsInMolecule) | |
SB_NODE_PREDICATE_0 (, IsInChain) | |
SB_NODE_PREDICATE_0 (, IsInSegment) | |
SB_NODE_PREDICATE_0 (, IsInResidue) | |
SB_NODE_PREDICATE_0 (, IsInAminoAcid) | |
SB_NODE_PREDICATE_0 (, IsInNucleicAcid) | |
SB_NODE_PREDICATE_0 (, IsInBackbone) | |
SB_NODE_PREDICATE_0 (, IsInSideChain) | |
SB_NODE_PREDICATE_0 (, IsInSubstructure) | |
SB_NODE_PREDICATE_0 (, IsPlanar) | |
SB_NODE_PREDICATE_0 (, IsFromAminoAcidBackbone) | |
SB_NODE_PREDICATE_0 (, IsFromNucleicAcidBackbone) | |
SB_NODE_PREDICATE_0 (, HasAminoAcidBackboneAtomName) | |
SB_NODE_PREDICATE_0 (, HasNucleicAcidBackboneAtomName) | |
SB_NODE_PREDICATE_0 (, IsMetal) | |
SB_NODE_PREDICATE_0 (, IsAlkaliMetal) | |
SB_NODE_PREDICATE_0 (, IsAlkalineEarthMetal) | |
SB_NODE_PREDICATE_0 (, IsLanthanide) | |
SB_NODE_PREDICATE_0 (, IsActinide) | |
SB_NODE_PREDICATE_0 (, IsTransitionMetal) | |
SB_NODE_PREDICATE_0 (, IsPosttransitionMetal) | |
SB_NODE_PREDICATE_0 (, IsMetalloid) | |
SB_NODE_PREDICATE_0 (, IsNobleGas) | |
SB_NODE_PREDICATE_0 (, IsReactiveNonmetal) | |
SB_NODE_PREDICATE_0 (, IsDiatomicNonmetal) | |
SB_NODE_PREDICATE_0 (, IsPolyatomicNonmetal) | |
SB_NODE_PREDICATE_0 (, IsHalogen) | |
SB_NODE_PREDICATE_0 (, IsHydrogenBondAcceptor) | |
SB_NODE_PREDICATE_0 (, IsHydrogenBondDonor) | |
SB_NODE_PREDICATE_0 (, IsAttachedToHydrogenBondDonor) | |
SB_DECLARE_DATA (SBMStructuralModelNodeAtom) | |
Public Member Functions inherited from SBMStructuralModelNodeParticle | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetX) | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetY) | |
SB_NODE_GETTER_0 (, SBQuantity::length, GetZ) | |
SB_NODE_GETTER_0 (, SBPosition3, GetPosition) | |
SB_DECLARE_DATA (SBMStructuralModelNodeParticle) | |
virtual | ~SBMStructuralModelNodeParticle () |
bool | isSerializable () const |
Returns true. | |
SBQuantity::length const & | getX () const |
Returns the x coordinate. | |
void | setX (const SBQuantity::length &x) |
Sets the x coordinate. | |
SBQuantity::length const & | getY () const |
Returns the y coordinate. | |
void | setY (const SBQuantity::length &y) |
Sets the y coordinate. | |
SBQuantity::length const & | getZ () const |
Returns the z coordinate. | |
void | setZ (const SBQuantity::length &z) |
Sets the z coordinate. | |
SBPosition3 const & | getPosition () const |
Returns the particle's position. | |
void | setPosition (SBPosition3 const &newPosition) |
Sets the particle's position. | |
void | setPosition (SBPosition3 const &newPosition, SBPosition3 const &oldPosition) |
Sets the particle's position. | |
void | setPositionOnTetrahedron (SBPosition3 const ¢er, SBPosition3 const &vertex1, SBPosition3 const &vertex2, SBPosition3 const &vertex3, SBQuantity::length const &distanceFromCenter) |
Sets the particle's position on a tetrahedron vertex based on the center position, the distance from the center distanceFromCenter , and positions of other 3 vertices vertex1 , vertex2 , and vertex3 . | |
Public Member Functions inherited from SBMStructuralModelNode | |
SB_NODE_GETTER_0 (, bool, GetMobilityFlag) | |
SB_DECLARE_DATA (SBMStructuralModelNode) | |
virtual | ~SBMStructuralModelNode () |
virtual SBPointerList< SBMStructuralModelNode > const * | getChildren () const |
SBMStructuralModelNode * | getNextStructuralNode () const |
SBMStructuralModelNode * | getPreviousStructuralNode () const |
virtual bool | isLocked () const |
Returns whether the node is locked (because of the model) | |
virtual bool | getLockedFlag () const |
Returns the locked flag of the model. | |
SBMStructuralModel * | getModel () const |
bool | getMobilityFlag () const |
Returns the mobility flag. | |
void | setMobilityFlag (bool flag) |
Sets the mobility flag to flag . | |
virtual unsigned int | getOpacity () const |
Returns the opacity. | |
virtual unsigned int | getMinimumOpacity () const |
Returns the minimum opacity. | |
virtual unsigned int | getTransparency () const |
Returns the transparency. | |
virtual unsigned int | getMaximumTransparency () const |
Returns the maximum transparency. | |
void | connectStructuralSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBStructuralEvent *)=0) |
bool | structuralSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *)) const |
void | disconnectStructuralSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *)) |
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. | |
void | getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
void | getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
void | getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
void | getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
void | getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode *> &nodeVectorTopDown, std::vector< SBMStructuralModelNode *> &nodeVectorBottomUp, bool(*selectionRule)(SBMStructuralModelNode *)) |
virtual void | forEachNodeDepthFirst (void(*action)(SBDDataGraphNode *node)) |
Performs an action on each node. | |
virtual void | forEachNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node)) |
Performs an action on each node. | |
void | forEachStructuralNodeBreadthFirst (void(*action)(SBMStructuralModelNode *node)) |
void | forEachStructuralNodeDepthFirst (void(*action)(SBMStructuralModelNode *node)) |
void | forEachStructuralNodeBreadthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
void | forEachStructuralNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
Public Member Functions inherited from SBMModelNode | |
SB_DECLARE_DATA (SBMModelNode) | |
Public Member Functions inherited from SBDDataGraphNode | |
SB_DECLARE_DATA (SBDDataGraphNode) | |
SBDDataGraphNode * | getParent () const |
Returns the parent of the node. More... | |
SBDDataGraphNode * | getThisNode () const |
Returns the pointer to this node. More... | |
SBDDataGraphNode * | getNextNode () const |
Returns the pointer to the next node in the children of the node's parent. More... | |
SBDDataGraphNode * | getPreviousNode () const |
Returns the pointer to the previous node in the children of the node's parent. More... | |
SBDDataGraphNode * | getNextNode (SBDDataGraphNode::Type nodeType) const |
Returns the pointer to the next node with type nodeType in the children of the node's parent. More... | |
SBDDataGraphNode * | getPreviousNode (SBDDataGraphNode::Type nodeType) const |
Returns the pointer to the previous node with type nodeType in the children of the node's parent. More... | |
SBDDocument * | getDocument () const |
Returns the document the node belongs to. More... | |
virtual bool | canAddChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) const |
Returns whether this node can add node as a child. More... | |
virtual bool | canAddChildType (SBDDataGraphNode::Type nodeType) const |
Returns whether this node can add a node with type nodeType as a child. More... | |
virtual bool | canHaveDescendantType (SBDDataGraphNode::Type nodeType) const |
Returns whether this node can have a node with type nodeType as a descendant. More... | |
virtual bool | addChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) |
Adds a child to the node. More... | |
virtual bool | removeChild (SBDDataGraphNode *node) |
Removes a child from the node. More... | |
bool | hasOneOf (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer , or is the ancestor of one of them. More... | |
bool | descendsFrom (SBDDataGraphNode *node) const |
Returns true if and only if this node is node , or descends from it. More... | |
bool | descendsFrom (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer , or descends from one of them. More... | |
bool | descendsFrom (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
Returns true if and only if this node is one of the nodes of the nodePointerIndexer , or descends from one of them. More... | |
bool | isIn (SBDDataGraphNode *node) const |
Returns true if and only if this node is node , or descends from it, or belongs to a group stored in node . More... | |
bool | isIn (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer , or descends from one of them, or belongs to a group stored in one of the nodes of the nodeIndexer . More... | |
bool | isIn (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
Returns true if and only if this node is one of the nodes of the nodePointerIndexer , or descends from one of them, or belongs to a group stored in of the nodes of the nodePointerIndexer . More... | |
bool | isOneOf (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer . More... | |
bool | isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
Returns true if and only if this node is one of the nodes of the nodePointerIndexer . More... | |
SBDDataGraphNode * | getRoot () const |
Returns the root of the hierarchy the node belongs to. More... | |
unsigned int | getNodeIndex () const |
Returns the node index (unique in the whole data graph, but non-persistent) More... | |
std::string | getTypeString (bool humanReadable=false) const |
Returns a string describing the type of the data graph node. More... | |
bool | isType (Type type) const |
Returns true when the type of the node corresponds to type . | |
bool | isModel () const |
Returns true when the node is a model. | |
bool | isStructuralNode () const |
Returns true when the node is a structural node. | |
bool | isStructuralModel () const |
Returns true when the node is a structural model. | |
bool | isVisualModel () const |
Returns true when the node is a visual model. | |
bool | isDynamicalModel () const |
Returns true when the node is a dynamical model. | |
bool | isInteractionModel () const |
Returns true when the node is a interaction model. | |
bool | isPropertyModel () const |
Returns true when the node is a property model. | |
bool | isMesh () const |
Returns true when the node is a mesh. | |
bool | isSimulator () const |
Returns true when the node is a simulator. | |
bool | isStructuralParticle () const |
Returns true when the node is a structural particle (an atom or a pseudo-atom) | |
virtual void | setLockedFlag (bool flag) |
Sets the locked flag. | |
bool | isCreated () const |
Returns true if and only if the node is created. More... | |
void | create () |
Creates the node. More... | |
bool | isErased () const |
Returns true if and only if the node is erased. More... | |
void | erase () |
Erases the node. More... | |
unsigned int | getFlags () const |
Returns the flags. More... | |
unsigned int | getInheritedFlags () const |
Returns the inherited flags. More... | |
bool | isSelected () const |
Returns whether the node is selected. More... | |
bool | getSelected () const |
Returns whether the node is selected. | |
bool | getSelectionFlag () const |
Returns the selection flag. More... | |
void | setSelectionFlag (bool flag) |
Sets the selection flag. More... | |
bool | isVisible () const |
Returns whether the node is visible. More... | |
bool | getVisible () const |
Returns whether the node is visible. | |
bool | getVisibilityFlag () const |
Returns the visibility flag. More... | |
void | setVisibilityFlag (bool flag) |
Sets the visibility flag. More... | |
bool | isHighlighted () const |
Returns whether the node is highlighted. More... | |
bool | getHighlightingFlag () const |
Returns the highlighting flag. More... | |
void | setHighlightingFlag (bool flag) |
Sets the highlighting flag. More... | |
virtual void | display (RenderingPass renderingPass) |
Displays the node. More... | |
virtual void | display () |
Displays the node (deprecated) More... | |
virtual void | displayForShadow () |
Displays the node for shadowing purposes (deprecated) More... | |
virtual void | displayForSelection () |
Displays the node for selection purposes (deprecated) More... | |
virtual void | setOpacity (unsigned int opacity) |
Sets the opacity. | |
virtual bool | hasOpacityRange () const |
Returns whether the node has the opacity range. | |
virtual unsigned int | getDefaultOpacity () const |
Returns the default opacity. | |
virtual unsigned int | getMaximumOpacity () const |
Returns the maximum opacity. | |
virtual unsigned int | getOpacitySingleStep () const |
Returns the opacity single step. | |
virtual std::string | getOpacitySuffix () const |
Returns the opacity suffix. | |
virtual void | setTransparency (unsigned int transparency) |
Sets the transparency. | |
virtual bool | hasTransparencyRange () const |
Returns whether the node has the transparency range. | |
virtual unsigned int | getDefaultTransparency () const |
Returns the default transparency. | |
virtual unsigned int | getMinimumTransparency () const |
Returns the minimum transparency. | |
virtual unsigned int | getTransparencySingleStep () const |
Returns the transparency single step. | |
virtual std::string | getTransparencySuffix () const |
Returns the transparency suffix. | |
float | getInheritedOpacity () const |
Returns the cumulative opacity, when taking into account the ascendants. | |
float | getInheritedTransparency () const |
Returns the cumulative transparency, when taking into account the ascendants. | |
bool | addMaterial (SBDDataGraphNodeMaterial *material) |
Adds a material. More... | |
bool | removeMaterial () |
Removes the material. More... | |
bool | hasMaterial () const |
Returns whether the node has a material (by itself, or inherited) | |
bool | ownsMaterial () const |
Returns whether the node owns a material. | |
SBDDataGraphNodeMaterial * | getMaterial () const |
Returns the material. More... | |
SBDDataGraphNode * | getMaterialOwner () const |
Returns the node whose material is inherited. More... | |
void | connectBaseSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBBaseEvent *)=0) |
Connects the base signal to a slot. More... | |
bool | baseSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) const |
Returns true when the base signal is connected to a slot. | |
void | disconnectBaseSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) |
Disconnects the base signal from a slot. | |
unsigned int | countNodes (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
Collects nodes into nodeIndexer , based on a nodeType , a selection status and a visitPredicate , with our without dependencies. More... | |
unsigned int | countNodes (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
Collects nodes into nodeIndexer , based on a selectionPredicate and a visitPredicate , with our without dependencies. More... | |
virtual unsigned int | getNumberOfChains () |
Returns the number of chains. | |
virtual unsigned int | getNumberOfMolecules () |
Returns the number of molecules. | |
virtual unsigned int | getNumberOfResidues () |
Returns the number of residues. | |
virtual unsigned int | getNumberOfSegments () |
Returns the number of segments. | |
virtual unsigned int | getNumberOfStructuralGroups () |
Returns the number of structural groups. | |
virtual unsigned int | getNumberOfStructuralModels () |
Returns the number of structural models. | |
Public Member Functions inherited from SBCReferenceTarget | |
SBCReferenceTarget () | |
virtual | ~SBCReferenceTarget () |
unsigned int | getMemoryFootprint () const |
void | printReferencesToOwners () const |
Constructors and destructors | |
SBMStructuralModelNodeAtom () | |
SBMStructuralModelNodeAtom (SBElement::Type element) | |
Constructs an atom (default position = (0,0,0)) | |
SBMStructuralModelNodeAtom (SBElement::Type element, const SBQuantity::length &x, const SBQuantity::length &y, const SBQuantity::length &z) | |
Constructs an atom at position = (x,y,z) | |
SBMStructuralModelNodeAtom (SBElement::Type element, SBPosition3 const &p) | |
Constructs an atom at position p. | |
SBMStructuralModelNodeAtom (SBElement::Type element, std::string &n, SBPosition3 const &p) | |
Constructs an atom with name n at position p. | |
virtual | ~SBMStructuralModelNodeAtom () |
Destructs the atom. | |
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 atom. | |
virtual void | unserialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) |
Unserializes the atom. | |
Topology | |
SBPointerList< SBBond > const * | getBondList () const |
Returns the bond list. | |
SBBond * | getBondTo (SBMStructuralModelNodeAtom *atom) const |
Returns the bond to an atom (0 if no bond) | |
unsigned int | getNumberOfBonds () const |
Returns the number of bonds without taking into account the bond order (NB: a double bond is considered as one bond) | |
SBQuantity::dimensionless | getCurrentValence () const |
Returns the current valence, i.e. the sum of the orders of the bonds connected to the atom, rounded to the closest integer. | |
SBQuantity::dimensionless | getExpectedValence () const |
Returns the expected valence of the atom based on its formal charge and its number of bonds (based on the MDL valence model) | |
void | getBondedAtoms (SBNodeIndexer &nodeIndexer) const |
Gets all bonded atoms. | |
void | getBondedAtoms (SBNodeIndexer &nodeIndexer, const SBElement::Type element) const |
Gets all bonded atoms of type element . | |
void | getBondedHeavyAtoms (SBNodeIndexer &nodeIndexer) const |
Gets all bonded heavy atoms (non-Hydrogens) | |
unsigned int | getNumberOfBondedAtoms (const SBElement::Type element) const |
Returns the number of bonded atoms with element type element . | |
unsigned int | getNumberOfBondedAtoms () const |
Returns the number of bonded atoms. | |
unsigned int | getNumberOfBondedHeavyAtoms () const |
Returns the number of bonded heavy atoms. | |
unsigned int | getNumberOfBondedCarbons () const |
Returns the number of bonded carbons. | |
unsigned int | getNumberOfBondedHydrogens () const |
Returns the number of bonded hydrogens. | |
unsigned int | getNumberOfBondedOxygens () const |
Returns the number of bonded oxygens. | |
unsigned int | getNumberOfBondedNitrogens () const |
Returns the number of bonded nitrogens. | |
unsigned int | getNumberOfBondedSulfurs () const |
Returns the number of bonded sulfurs. | |
void | getHydrogens (SBNodeIndexer &nodeIndexer) const |
Gets all bonded hydrogens. | |
unsigned int | addHydrogens () |
Adds hydrogens and returns the number of added hydrogens. More... | |
unsigned int | removeHydrogens () |
Removes the hydrogens bonded to the atom and returns the number of removed hydrogens. | |
void | getNewBondDirections (SBVector< SBVector3 > &bondDirectionVector, unsigned int numberOfBonds, bool includeExistingHydrogens=false) |
Generates directions that numberOfBonds new neighboring bonds would have. | |
void | getConnectedComponent (SBNodeIndexer &nodeIndexer) const |
Gets all atoms in the connected component containing the atom. | |
bool | isPlanar () const |
Returns true if the atom with atoms bonded to it are in the same plane. | |
bool | isCarboxylOxygen () const |
Returns true for an Oxygen atom in a carboxyl group (C(=O)OH) More... | |
bool | isThiocarboxylOxygen () const |
Returns true for an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH) More... | |
bool | isNitroOxygen () const |
Returns true for an Oxygen atom in a nitro group (-NO2) More... | |
bool | isSulfoneOxygen () const |
Returns true for an Oxygen atom in a sulfone (R1-SO2-R2) More... | |
bool | isHydrogenBondAcceptor () const |
Returns true if the atom is an H-Bond acceptor (N, O, S, F) More... | |
bool | isHydrogenBondDonor () const |
Returns true if the atom is an H-Bond donor (N, O, S, F) More... | |
bool | isDonorborneHydrogen () const |
Returns true if the atom is a hydrogen connected to an H-Bond donor. More... | |
bool | isAttachedToHydrogenBondDonor () const |
Returns true if the atom is connected to an H-Bond donor. More... | |
virtual SBMStructuralModelNodeAtom * | clone () |
Returns a copy of the node and its descendants. | |
Identity | |
virtual SBDDataGraphNode::Type | getType () const |
Returns the node type (returns SBNode::Atom) | |
virtual SBElement::Type | getElementType () const |
Returns the atom's element type. | |
virtual void | setElementType (SBElement::Type e) |
Sets the atom's element type. | |
virtual std::string | getElementName () const |
Returns the atom's element name. | |
virtual std::string | getElementSymbol () const |
Returns the atom's element symbol. | |
std::string | getPeriod () const |
Returns the atom's element period. | |
unsigned int | getGroup () const |
Returns the atom's element group. | |
std::string | getBlock () const |
Returns the atom's element block. | |
SBQuantity::mass | getAtomicWeight () const |
Returns the atom's element atomic weight. | |
SBQuantity::length | getCovalentRadius () const |
Returns the atom's element covalent radius. | |
SBQuantity::length | getVanDerWaalsRadius () const |
Returns the atom's element van der Waals radius. | |
SBQuantity::dimensionless | getElectronegativity () const |
Returns the atom's element electronegativity. | |
SBElement::MetalSubcategory | getMetalSubcategory () const |
Returns the atom's subcategory type in the metal–metalloid–nonmetal trend. | |
std::string | getMetalSubcategoryString () const |
Returns the string representation of the atom's subcategory type in the metal–metalloid–nonmetal trend. | |
bool | isMetal () const |
Returns true if the atom is metal. | |
bool | isAlkaliMetal () const |
Returns true if the atom is alkali metal. | |
bool | isAlkalineEarthMetal () const |
Returns true if the atom is alkaline earth metal. | |
bool | isLanthanide () const |
Returns true if the atom is lanthanide metal. | |
bool | isActinide () const |
Returns true if the atom is actinide metal. | |
bool | isTransitionMetal () const |
Returns true if the atom is transition metal. | |
bool | isPosttransitionMetal () const |
Returns true if the atom is posttransition metal. | |
bool | isMetalloid () const |
Returns true if the atom is metalloid. | |
bool | isNobleGas () const |
Returns true if the atom is noble gas. | |
bool | isReactiveNonmetal () const |
Returns true if the atom is reactive nonmetal. | |
bool | isDiatomicNonmetal () const |
Returns true if the atom is diatomic nonmetal. | |
bool | isPolyatomicNonmetal () const |
Returns true if the atom is polyatomic nonmetal. | |
bool | isHalogen () const |
Returns true if the atom is halogen. | |
Hierarchy | |
bool | isInMolecule () const |
Returns true when the atom is in a molecule. | |
SBMStructuralModelNodeMolecule * | getMolecule () const |
Returns a pointer to the molecule. | |
std::string | getMoleculeName () const |
Returns the atom's molecule name. | |
bool | isInChain () const |
Returns true when the atom is in a chain. | |
SBMStructuralModelNodeChain * | getChain () const |
Returns a pointer to the chain. | |
std::string | getChainName () const |
Returns the atom's chain name. | |
bool | hasChainID () const |
Returns true when the atom's chain ID is set. The chain ID is used to separate chains with the same name but divided into 2, e.g. with TER record. More... | |
int | getChainID () const |
Returns the atom's chain ID. More... | |
std::string | getChainIDString () const |
Returns the atom's chain ID string. More... | |
bool | isInSegment () const |
Returns true when the atom is in a segment. | |
SBMStructuralModelNodeSegment * | getSegment () const |
Returns a pointer to the segment. | |
std::string | getSegmentName () const |
Returns the atom's segment name. | |
bool | isInSubstructure () const |
Returns true when the atom is in a substructure. More... | |
SBMStructuralModelNodeGroup * | getSubstructure () const |
Returns a pointer to the substructure. More... | |
std::string | getSubstructureName () const |
Returns the atom's substructure name. More... | |
bool | hasSubstructureSequenceNumber () const |
Returns true when the atom's substructure sequence number is set. More... | |
int | getSubstructureSequenceNumber () const |
Returns the atom's substructure sequence number. More... | |
std::string | getSubstructureSequenceNumberString () const |
Returns the atom's substructure sequence number string. More... | |
bool | isInResidue () const |
Returns true when the atom is in a residue. | |
SBMStructuralModelNodeResidue * | getResidue () const |
Returns a pointer to the residue. | |
std::string | getResidueName () const |
Returns the atom's residue name. | |
std::string | getResidueTypeString () const |
Returns the atom's residue type string. More... | |
bool | hasResidueSequenceNumber () const |
Returns true when the atom's residue sequence number is set. More... | |
int | getResidueSequenceNumber () const |
Returns the atom's residue sequence number. More... | |
std::string | getResidueSequenceNumberString () const |
Returns the atom's residue sequence number string. More... | |
bool | isInAminoAcid () const |
Returns true when the atom is in an amino acid residue. More... | |
bool | isInNucleicAcid () const |
Returns true when the atom is in a nucleic acid residue. More... | |
bool | isInBackbone () const |
Returns true when the atom is in a backbone. More... | |
SBMStructuralModelNodeBackbone * | getBackbone () const |
Returns a pointer to the backbone. More... | |
bool | isInSideChain () const |
Returns true when the atom is in a side chain. More... | |
SBMStructuralModelNodeSideChain * | getSideChain () const |
Returns a pointer to the side chain. More... | |
bool | isFromAminoAcidBackbone () const |
Returns true when the atom is from an amino-acid backbone. More... | |
bool | isFromNucleicAcidBackbone () const |
Returns true when the atom is from a nucleic acid backbone. More... | |
bool | hasAminoAcidBackboneAtomName () const |
Returns true when the atom's name corresponds to one of the amino-acid backbone atoms. More... | |
bool | hasNucleicAcidBackboneAtomName () const |
Returns true when the atom's name corresponds to one of the nucleic acid backbone atoms. More... | |
Properties | |
bool | hasName () const |
Returns true when the atom's name is set. | |
virtual std::string const & | getName () const |
Returns the atom's full name (e.g. CA for an alpha carbon) | |
virtual void | setName (const std::string &name) |
Sets the atom's full name. | |
void | clearName () |
Clears the atom's full name. | |
bool | hasAltLocation () const |
Returns true when the atom's alternate location is set. | |
char const & | getAltLocation () const |
Returns the atom's alternate location. | |
void | setAltLocation (const char &altLocation) |
Sets the atom's alternate location. | |
void | clearAltLocation () |
Clears the atom's alternate location. | |
bool | hasInsertionCode () const |
Returns true when the atom's insertion code is set. | |
char const & | getInsertionCode () const |
Returns the atom's insertion code. | |
void | setInsertionCode (const char &insertionCode) |
Sets the atom's insertion code. | |
void | clearInsertionCode () |
Clears the atom's insertion code. | |
bool | hasSerialNumber () const |
Returns true when the atom's serial number is set. | |
int const & | getSerialNumber () const |
Returns the atom's serial number. | |
void | setSerialNumber (const int &serialNumber) |
Sets the atom's serial number. | |
void | clearSerialNumber () |
Clears the atom's serial number. | |
bool | hasOccupancy () const |
Returns true when the atom's occupancy is set. | |
SBQuantity::dimensionless const & | getOccupancy () const |
Returns the atom's occupancy. | |
void | setOccupancy (const SBQuantity::dimensionless &occupancy) |
Sets the atom's occupancy. | |
void | clearOccupancy () |
Clears the atom's occupancy. | |
bool | hasRecordType () const |
Returns true when the atom's record type is set. | |
char *const & | getRecordType () const |
Returns the atom's record type. | |
unsigned int | getRecordTypeSize () const |
Returns the atom's record type size. | |
void | setRecordType (char *const &recordType, int const &size) |
Sets the atom's record type. | |
void | clearRecordType () |
Clears the atom's record type. | |
bool | hasTemperatureFactor () const |
Returns true when the atom's temperature factor is set. | |
double const & | getTemperatureFactor () const |
Returns the atom's temperature factor. | |
void | setTemperatureFactor (const double &temperatureFactor) |
Sets the atom's temperature factor. | |
void | clearTemperatureFactor () |
Clears the atom's temperature factor. | |
bool | hasPartialCharge () const |
Returns true when the atom's partial charge is set. | |
float const & | getPartialCharge () const |
Returns the atom's partial charge. | |
void | setPartialCharge (const float &partialCharge) |
Sets the atom's partial charge. | |
void | clearPartialCharge () |
Clears the atom's partial charge. | |
bool | hasFormalCharge () const |
Returns true when the atom's formal charge is set. | |
int const & | getFormalCharge () const |
Returns the atom's formal charge. | |
void | setFormalCharge (const int &formalCharge) |
Sets the atom's formal charge. | |
void | clearFormalCharge () |
Clears the atom's formal charge. | |
bool | hasComment () const |
Returns true when the atom's comment is set. | |
char *const & | getComment () const |
Returns the atom's comment. | |
unsigned int | getCommentSize () const |
Returns the atom's comment size. | |
void | setComment (char *const &comment, int const &size) |
Sets the atom's comment. | |
void | clearComment () |
Clears the atom's comment. | |
bool | hasAnisotropicTFactors () const |
Returns true when the atom's anisotropic temperature factors are set. | |
std::vector< int > const & | getAnisotropicTFactors () const |
Returns the atom's anisotropic temperature factors. | |
void | setAnisotropicTFactors (const std::vector< int > &ATF) |
Sets the atom's anisotropic temperature factors. | |
void | clearAnisotropicTFactors () |
Clears the atom's anisotropic temperature factors. | |
bool | hasSYBYLType () const |
Returns true when the SYBYL atom's type is set. | |
char *const & | getSYBYLType () const |
Returns the SYBYL atom's type. | |
unsigned int | getSYBYLTypeSize () const |
Returns the SYBYL atom's type size. | |
void | setSYBYLType (char *const &SYBYLType, int const &size) |
Sets the SYBYL atom's type. | |
void | clearSYBYLType () |
Clears the SYBYL atom's type. | |
bool | hasStatusBit () const |
Returns true when the atom's status bit is set. | |
char *const & | getStatusBit () const |
Returns the atom's status bit. | |
unsigned int | getStatusBitSize () const |
Returns the atom's status bit size. | |
void | setStatusBit (char *const &statusBit, int const &size) |
Sets the atom's status bit. | |
void | clearStatusBit () |
Clears the atom's status bit. | |
bool | hasHybridization () const |
Returns true when the atom's hybridization is set. | |
Hybridization const & | getHybridization () const |
Returns the atom's hybridization. | |
void | setHybridization (const Hybridization &hybridization) |
Sets the atom's hybridization. | |
void | clearHybridization () |
Clears the atom's hybridization. | |
std::string | getHybridizationString () const |
Returns the hybridization as a string. | |
Hybridization | perceiveHybridization () |
Perceives, sets and returns the atom's hybridization. | |
bool | hasGeometry () const |
Returns true when the atom's geometry is set. | |
Geometry const & | getGeometry () const |
Returns the atom's geometry. | |
void | setGeometry (const Geometry &geometry) |
Sets the atom's geometry. | |
void | clearGeometry () |
Clears the atom's geometry. | |
std::string | getGeometryString () const |
Returns the geometry as a string. | |
bool | hasOxidationState () const |
Returns true when the atom's oxidation state is set. | |
int const & | getOxidationState () const |
Returns the atom's oxidation state. | |
void | setOxidationState (const int &oxidationState) |
Sets the atom's oxidation state. | |
void | clearOxidationState () |
Clears the atom's oxidation state. | |
bool | hasResonance () const |
Returns true when the atom's resonance is set. | |
bool const & | getResonance () const |
Returns the atom's resonance (true if resonant, false else) | |
void | setResonance (const bool &resonance) |
Sets the atom's resonance. | |
void | clearResonance () |
Clears the atom's resonance. | |
bool | hasAromaticity () const |
Returns true when the atom's aromaticity is set. | |
bool const & | getAromaticity () const |
Returns the atom's aromaticity (true if aromatic, false else) | |
void | setAromaticity (const bool &aromaticity) |
Sets the atom's aromaticity. | |
void | clearAromaticity () |
Clears the atom's aromaticity. | |
bool | hasWaterFlag () const |
Returns true when the atom's water flag is set. | |
bool const & | getWaterFlag () const |
Returns the atom's water flag (true if the atom is a water atom, false else) | |
void | setWaterFlag (const bool &water) |
Sets the atom's water flag. | |
void | clearWaterFlag () |
Clears the atom's water flag. | |
bool | hasCustomType () const |
Returns true when the atom's custom type is set. | |
int const & | getCustomType () const |
Returns the atom's custom type. | |
void | setCustomType (const int &water) |
Sets the atom's custom type. | |
void | clearCustomType () |
Clears the atom's custom type. | |
static std::string | getHybridizationString (Hybridization hybridization) |
Returns the hybridization as a string. | |
static std::string | getGeometryString (Geometry geometry) |
Returns the geometry as a string. | |
Information | |
virtual std::string | getHierarchyString (const std::string &separator=" / ", bool includeNodeType=false) const |
Returns a string with hierarchical information on the atom and its parents names. More... | |
Statistics | |
unsigned int | getNumberOfAtoms () |
Returns the number of atoms. | |
unsigned int | getNumberOfCarbons () |
Returns the number of carbons. | |
unsigned int | getNumberOfHydrogens () |
Returns the number of hydrogens. | |
unsigned int | getNumberOfNitrogens () |
Returns the number of nitrogens. | |
unsigned int | getNumberOfOxygens () |
Returns the number of oxygens. | |
unsigned int | getNumberOfSulfurs () |
Returns the number of sulfurs. | |
unsigned int | getNumberOfOtherAtoms () |
Returns the number of other atoms. | |
int | getSumOfFormalCharges () |
Returns the sum of formal charges. | |
float | getSumOfPartialCharges () |
Returns the sum of partial charges. | |
SBQuantity::mass | getMolecularWeight () |
Returns the molecular weight. | |
Debugging | |
virtual void | print (unsigned int offset=0) const |
Prints debugging information. | |
Additional Inherited Members | |
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 SBMStructuralModelNodeParticle | |
SBMStructuralModelNodeParticle (SBMStructuralModelNodeParticleData *dataPointer) | |
Builds a particle at position p. | |
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 |
|
strong |
|
strong |
unsigned int SBMStructuralModelNodeAtom::addHydrogens | ( | ) |
The number of expected hydrogens is the expected valence minus the number of bonds. The added hydrogens and bonds become children of the atom's parent if it has one.
If an atom has an alternate location or occupancy fields, the same values will be set for added hydrogens.
SBMStructuralModelNodeBackbone * SBMStructuralModelNodeAtom::getBackbone | ( | ) | const |
SBMStructuralModelNodeAtom::getBackbone.
int SBMStructuralModelNodeAtom::getChainID | ( | ) | const |
SBMStructuralModelNodeAtom::getChainID.
std::string SBMStructuralModelNodeAtom::getChainIDString | ( | ) | const |
SBMStructuralModelNodeAtom::getChainIDString.
|
virtual |
SBMStructuralModelNodeAtom::getHierarchyString This functions returns a string with information on the atom's hierarchy. If the atom has a name then this name is provided in the hierarchy information, else the atom's element symbol is used. If the atom has an alternate location then it is added after its name in square brackets. This information can be used for logging and debugging.
Reimplemented from SBDDataGraphNode.
int SBMStructuralModelNodeAtom::getResidueSequenceNumber | ( | ) | const |
SBMStructuralModelNodeAtom::getResidueSequenceNumber.
std::string SBMStructuralModelNodeAtom::getResidueSequenceNumberString | ( | ) | const |
SBMStructuralModelNodeAtom::getResidueSequenceNumberString.
std::string SBMStructuralModelNodeAtom::getResidueTypeString | ( | ) | const |
SBMStructuralModelNodeAtom::getResidueTypeString.
SBMStructuralModelNodeSideChain * SBMStructuralModelNodeAtom::getSideChain | ( | ) | const |
SBMStructuralModelNodeAtom::getSideChain.
SBMStructuralModelNodeGroup * SBMStructuralModelNodeAtom::getSubstructure | ( | ) | const |
SBMStructuralModelNodeAtom::getSubstructure.
std::string SBMStructuralModelNodeAtom::getSubstructureName | ( | ) | const |
SBMStructuralModelNodeAtom::getSubstructureName.
int SBMStructuralModelNodeAtom::getSubstructureSequenceNumber | ( | ) | const |
SBMStructuralModelNodeAtom::getSubstructureSequenceNumber.
std::string SBMStructuralModelNodeAtom::getSubstructureSequenceNumberString | ( | ) | const |
SBMStructuralModelNodeAtom::getSubstructureSequenceNumberString.
bool SBMStructuralModelNodeAtom::hasAminoAcidBackboneAtomName | ( | ) | const |
SBMStructuralModelNodeAtom::hasAminoAcidBackboneAtomName.
bool SBMStructuralModelNodeAtom::hasChainID | ( | ) | const |
SBMStructuralModelNodeAtom::hasChainID.
bool SBMStructuralModelNodeAtom::hasNucleicAcidBackboneAtomName | ( | ) | const |
SBMStructuralModelNodeAtom::hasNucleicAcidBackboneAtomName.
bool SBMStructuralModelNodeAtom::hasResidueSequenceNumber | ( | ) | const |
SBMStructuralModelNodeAtom::hasResidueSequenceNumber.
bool SBMStructuralModelNodeAtom::hasSubstructureSequenceNumber | ( | ) | const |
SBMStructuralModelNodeAtom::hasSubstructureSequenceNumber.
bool SBMStructuralModelNodeAtom::isAttachedToHydrogenBondDonor | ( | ) | const |
SBMStructuralModelNodeAtom::isAttachedToHydrogenBondDonor This function checks whether the atom is attached to a hydrogen bond donor.
bool SBMStructuralModelNodeAtom::isCarboxylOxygen | ( | ) | const |
SBMStructuralModelNodeAtom::isCarboxylOxygen Checks if the atom is an Oxygen atom in a carboxyl group (C(=O)OH): an Oxygen atom connected to a Carbon atom in a carboxyl group.
HO-C(=O)-R
bool SBMStructuralModelNodeAtom::isDonorborneHydrogen | ( | ) | const |
SBMStructuralModelNodeAtom::isDonorborneHydrogen This function checks whether the atom is a hydrogen atom attached to a hydrogen bond donor.
bool SBMStructuralModelNodeAtom::isFromAminoAcidBackbone | ( | ) | const |
SBMStructuralModelNodeAtom::isFromAminoAcidBackbone.
bool SBMStructuralModelNodeAtom::isFromNucleicAcidBackbone | ( | ) | const |
SBMStructuralModelNodeAtom::isFromNucleicAcidBackbone.
bool SBMStructuralModelNodeAtom::isHydrogenBondAcceptor | ( | ) | const |
SBMStructuralModelNodeAtom::isHydrogenBondAcceptor This function checks whether the atom is a hydrogen bond acceptor. Only the following atom types are considered to as possible acceptors: N, O, S, F.
bool SBMStructuralModelNodeAtom::isHydrogenBondDonor | ( | ) | const |
SBMStructuralModelNodeAtom::isHydrogenBondDonor This function checks whether the atom is a hydrogen bond donor: an electronegative atom (N, O, S, F) that has at least one hydrogen covalently bound to it.
bool SBMStructuralModelNodeAtom::isInAminoAcid | ( | ) | const |
SBMStructuralModelNodeAtom::isInAminoAcid This function checks whether the atom is in a residue which type corresponds to an amino acid.
bool SBMStructuralModelNodeAtom::isInBackbone | ( | ) | const |
SBMStructuralModelNodeAtom::isInBackbone This function checks whether the atom is in a backbone.
bool SBMStructuralModelNodeAtom::isInNucleicAcid | ( | ) | const |
SBMStructuralModelNodeAtom::isInNucleicAcid This function checks whether the atom is in a residue which type corresponds to a nucleic acid.
bool SBMStructuralModelNodeAtom::isInSideChain | ( | ) | const |
SBMStructuralModelNodeAtom::isInSideChain This function checks whether the atom is in a side chain.
bool SBMStructuralModelNodeAtom::isInSubstructure | ( | ) | const |
SBMStructuralModelNodeAtom::isInSubstructure This function checks whether the atom is in a substructure (a structural group).
bool SBMStructuralModelNodeAtom::isNitroOxygen | ( | ) | const |
SBMStructuralModelNodeAtom::isNitroOxygen Check if the atom is an Oxygen atom in a nitro (-NO2) group:
HO-N(OH)-R
bool SBMStructuralModelNodeAtom::isSulfoneOxygen | ( | ) | const |
SBMStructuralModelNodeAtom::isSulfoneOxygen Check if the atom is an Oxygen atom in a sulfone (R1-SO2-R2).
bool SBMStructuralModelNodeAtom::isThiocarboxylOxygen | ( | ) | const |
SBMStructuralModelNodeAtom::isThiocarboxylOxygen Checks if the atom is an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH): an Oxygen atom connected to a Carbon atom in a thiocarboxyl group.