This class describes an atom in a structural model.
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SBPointerList< SBBond > const * | getBondList () const |
| | Returns the bond list.
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SBBond * | getBondTo (SBMStructuralModelNodeAtom *atom) const |
| | Returns the bond to an atom (0 if no bond)
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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)
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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.
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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)
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void | getBondedAtoms (SBNodeIndexer &nodeIndexer) const |
| | Gets all bonded atoms.
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void | getBondedAtoms (SBNodeIndexer &nodeIndexer, const SBElement::Type element) const |
| | Gets all bonded atoms of type element.
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void | getBondedHeavyAtoms (SBNodeIndexer &nodeIndexer) const |
| | Gets all bonded heavy atoms (non-Hydrogens)
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unsigned int | getNumberOfBondedAtoms (const SBElement::Type element) const |
| | Returns the number of bonded atoms with element type element.
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unsigned int | getNumberOfBondedAtoms () const |
| | Returns the number of bonded atoms.
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unsigned int | getNumberOfBondedHeavyAtoms () const |
| | Returns the number of bonded heavy atoms.
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unsigned int | getNumberOfBondedCarbons () const |
| | Returns the number of bonded carbons.
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unsigned int | getNumberOfBondedHydrogens () const |
| | Returns the number of bonded hydrogens.
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unsigned int | getNumberOfBondedOxygens () const |
| | Returns the number of bonded oxygens.
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unsigned int | getNumberOfBondedNitrogens () const |
| | Returns the number of bonded nitrogens.
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unsigned int | getNumberOfBondedSulfurs () const |
| | Returns the number of bonded sulfurs.
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void | getHydrogens (SBNodeIndexer &nodeIndexer) const |
| | Gets all bonded hydrogens.
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| unsigned int | addHydrogens () |
| | Adds hydrogens and returns the number of added hydrogens.
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unsigned int | removeHydrogens () |
| | Removes the hydrogens bonded to the atom and returns the number of removed hydrogens.
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void | getNewBondDirections (SBVector< SBVector3 > &bondDirectionVector, unsigned int numberOfBonds, bool includeExistingHydrogens=false) |
| | Generates directions that numberOfBonds new neighboring bonds would have.
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| void | getConnectedComponent (SBNodeIndexer &nodeIndexer) const |
| | Gets all atoms in the connected component containing the atom.
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| bool | getConnectedComponent (SBNodeIndexer &nodeIndexer, unsigned int maximumNumberOfAtoms) const |
| | Gets atoms in the connected component containing the atom and stops once maximumNumberOfAtoms is reached, returns whether the whole connected component has no more than maximumNumberOfAtoms atoms.
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bool | isPlanar () const |
| | Returns true if the atom with atoms bonded to it are in the same plane.
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bool | isCarbon () const |
| | Returns true when the atom is a carbon atom.
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bool | isHydrogen () const |
| | Returns true when the atom is a hydrogen atom.
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bool | isNitrogen () const |
| | Returns true when the atom is a nitrogen atom.
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bool | isOxygen () const |
| | Returns true when the atom is an oxygen atom.
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bool | isSulfur () const |
| | Returns true when the atom is a sulfur atom.
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bool | isUnknown () const |
| | Returns true when the atom is an unknown atom.
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| bool | isCarboxylOxygen () const |
| | Returns true for an Oxygen atom in a carboxyl group (C(=O)OH)
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| bool | isThiocarboxylOxygen () const |
| | Returns true for an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH)
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| bool | isNitroOxygen () const |
| | Returns true for an Oxygen atom in a nitro group (-NO2)
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| bool | isSulfoneOxygen () const |
| | Returns true for an Oxygen atom in a sulfone (R1-SO2-R2)
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| bool | isHydrogenBondAcceptor () const |
| | Returns true if the atom is an H-Bond acceptor (N, O, S, F)
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| bool | isHydrogenBondDonor () const |
| | Returns true if the atom is an H-Bond donor (N, O, S, F)
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| bool | isDonorBorneHydrogen () const |
| | Returns true if the atom is a hydrogen connected to an H-Bond donor.
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| bool | isAttachedToHydrogenBondDonor () const |
| | Returns true if the atom is connected to an H-Bond donor.
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| virtual SBMStructuralModelNodeAtom * | clone () override |
| | Returns a copy of the node and its descendants.
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bool | hasName () const |
| | Returns true when the atom's name is set.
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| virtual std::string const & | getName () const override |
| | Returns the atom's full name (e.g. CA for an alpha carbon)
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| virtual void | setName (const std::string &name) override |
| | Sets the atom's full name.
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void | clearName () |
| | Clears the atom's full name.
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bool | hasAltLocation () const |
| | Returns true when the atom's alternate location is set.
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char const & | getAltLocation () const |
| | Returns the atom's alternate location.
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void | setAltLocation (const char &altLocation) |
| | Sets the atom's alternate location.
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void | clearAltLocation () |
| | Clears the atom's alternate location.
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bool | hasInsertionCode () const |
| | Returns true when the atom's insertion code is set.
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char const & | getInsertionCode () const |
| | Returns the atom's insertion code.
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void | setInsertionCode (const char &insertionCode) |
| | Sets the atom's insertion code.
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void | clearInsertionCode () |
| | Clears the atom's insertion code.
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bool | hasSerialNumber () const |
| | Returns true when the atom's serial number is set.
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int const & | getSerialNumber () const |
| | Returns the atom's serial number.
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void | setSerialNumber (const int &serialNumber) |
| | Sets the atom's serial number.
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void | clearSerialNumber () |
| | Clears the atom's serial number.
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bool | hasOccupancy () const |
| | Returns true when the atom's occupancy is set.
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SBQuantity::dimensionless const & | getOccupancy () const |
| | Returns the atom's occupancy.
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void | setOccupancy (const SBQuantity::dimensionless &occupancy) |
| | Sets the atom's occupancy.
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void | clearOccupancy () |
| | Clears the atom's occupancy.
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bool | hasRecordType () const |
| | Returns true when the atom's record type is set.
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char *const & | getRecordType () const |
| | Returns the atom's record type.
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unsigned int | getRecordTypeSize () const |
| | Returns the atom's record type size.
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void | setRecordType (char *const &recordType, int const &size) |
| | Sets the atom's record type.
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void | clearRecordType () |
| | Clears the atom's record type.
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bool | hasTemperatureFactor () const |
| | Returns true when the atom's temperature factor is set.
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double const & | getTemperatureFactor () const |
| | Returns the atom's temperature factor.
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void | setTemperatureFactor (const double &temperatureFactor) |
| | Sets the atom's temperature factor.
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void | clearTemperatureFactor () |
| | Clears the atom's temperature factor.
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bool | hasPartialCharge () const |
| | Returns true when the atom's partial charge is set.
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float const & | getPartialCharge () const |
| | Returns the atom's partial charge.
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void | setPartialCharge (const float &partialCharge) |
| | Sets the atom's partial charge.
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void | clearPartialCharge () |
| | Clears the atom's partial charge.
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bool | hasFormalCharge () const |
| | Returns true when the atom's formal charge is set.
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int const & | getFormalCharge () const |
| | Returns the atom's formal charge.
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void | setFormalCharge (const int &formalCharge) |
| | Sets the atom's formal charge.
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void | clearFormalCharge () |
| | Clears the atom's formal charge.
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bool | hasComment () const |
| | Returns true when the atom's comment is set.
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char *const & | getComment () const |
| | Returns the atom's comment.
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unsigned int | getCommentSize () const |
| | Returns the atom's comment size.
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void | setComment (char *const &comment, int const &size) |
| | Sets the atom's comment.
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void | clearComment () |
| | Clears the atom's comment.
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bool | hasAnisotropicTFactors () const |
| | Returns true when the atom's anisotropic temperature factors are set.
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std::vector< int > const & | getAnisotropicTFactors () const |
| | Returns the atom's anisotropic temperature factors.
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void | setAnisotropicTFactors (const std::vector< int > &ATF) |
| | Sets the atom's anisotropic temperature factors.
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void | clearAnisotropicTFactors () |
| | Clears the atom's anisotropic temperature factors.
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bool | hasSYBYLType () const |
| | Returns true when the SYBYL atom's type is set.
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char *const & | getSYBYLType () const |
| | Returns the SYBYL atom's type.
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unsigned int | getSYBYLTypeSize () const |
| | Returns the SYBYL atom's type size.
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void | setSYBYLType (char *const &SYBYLType, int const &size) |
| | Sets the SYBYL atom's type.
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void | clearSYBYLType () |
| | Clears the SYBYL atom's type.
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bool | hasStatusBit () const |
| | Returns true when the atom's status bit is set.
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char *const & | getStatusBit () const |
| | Returns the atom's status bit.
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unsigned int | getStatusBitSize () const |
| | Returns the atom's status bit size.
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void | setStatusBit (char *const &statusBit, int const &size) |
| | Sets the atom's status bit.
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void | clearStatusBit () |
| | Clears the atom's status bit.
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bool | hasHybridization () const |
| | Returns true when the atom's hybridization is set.
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Hybridization const & | getHybridization () const |
| | Returns the atom's hybridization.
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void | setHybridization (const Hybridization &hybridization) |
| | Sets the atom's hybridization.
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void | clearHybridization () |
| | Clears the atom's hybridization.
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std::string | getHybridizationString () const |
| | Returns the hybridization as a string.
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Hybridization | perceiveHybridization () |
| | Perceives, sets and returns the atom's hybridization.
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bool | hasGeometry () const |
| | Returns true when the atom's geometry is set.
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Geometry const & | getGeometry () const |
| | Returns the atom's geometry.
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void | setGeometry (const Geometry &geometry) |
| | Sets the atom's geometry.
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void | clearGeometry () |
| | Clears the atom's geometry.
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std::string | getGeometryString () const |
| | Returns the geometry as a string.
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bool | hasOxidationState () const |
| | Returns true when the atom's oxidation state is set.
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int const & | getOxidationState () const |
| | Returns the atom's oxidation state.
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void | setOxidationState (const int &oxidationState) |
| | Sets the atom's oxidation state.
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void | clearOxidationState () |
| | Clears the atom's oxidation state.
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bool | hasResonance () const |
| | Returns true when the atom's resonance is set.
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bool const & | getResonance () const |
| | Returns the atom's resonance (true if resonant, false else)
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void | setResonance (const bool &resonance) |
| | Sets the atom's resonance.
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void | clearResonance () |
| | Clears the atom's resonance.
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bool | hasAromaticity () const |
| | Returns true when the atom's aromaticity is set.
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bool const & | getAromaticity () const |
| | Returns the atom's aromaticity (true if aromatic, false else)
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void | setAromaticity (const bool &aromaticity) |
| | Sets the atom's aromaticity.
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void | clearAromaticity () |
| | Clears the atom's aromaticity.
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bool | hasWaterFlag () const |
| | Returns true when the atom's water flag is set.
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bool const & | getWaterFlag () const |
| | Returns the atom's water flag (true if the atom is a water atom, false else)
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void | setWaterFlag (const bool &water) |
| | Sets the atom's water flag.
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void | clearWaterFlag () |
| | Clears the atom's water flag.
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bool | hasCustomType () const |
| | Returns true when the atom's custom type is set.
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int const & | getCustomType () const |
| | Returns the atom's custom type.
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void | setCustomType (const int &water) |
| | Sets the atom's custom type.
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void | clearCustomType () |
| | Clears the atom's custom type.
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static std::string | getHybridizationString (Hybridization hybridization) |
| | Returns the hybridization as a string.
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static std::string | getGeometryString (Geometry geometry) |
| | Returns the geometry as a string.
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| virtual void | print (unsigned int offset=0) const override |
| | Prints debugging information.
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| SB_NODE_GETTER_0 (, SBQuantity::length, GetX) |
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| SB_NODE_GETTER_0 (, SBQuantity::length, GetY) |
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| SB_NODE_GETTER_0 (, SBQuantity::length, GetZ) |
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| SB_NODE_GETTER_0 (, SBPosition3, GetPosition) |
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| SB_NODE_GETTER_0 (, SBElement::Type, GetElementType) |
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| SB_NODE_GETTER_0 (, std::string, GetElementName) |
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| SB_NODE_GETTER_0 (, std::string, GetElementSymbol) |
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| SB_NODE_GETTER_0 (, std::string, GetPeriod) |
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| SB_NODE_GETTER_0 (, unsigned int, GetGroup) |
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| SB_NODE_GETTER_0 (, std::string, GetBlock) |
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| SB_NODE_GETTER_0 (, SBQuantity::mass, GetAtomicWeight) |
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| SB_NODE_GETTER_0 (, SBQuantity::length, GetCovalentRadius) |
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| SB_NODE_GETTER_0 (, SBQuantity::length, GetVanDerWaalsRadius) |
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| SB_NODE_GETTER_0 (, SBQuantity::dimensionless, GetElectronegativity) |
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| SB_NODE_GETTER_0 (, SBElement::MetalSubcategory, GetMetalSubcategory) |
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| SB_NODE_GETTER_0 (, std::string, GetName) |
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| SB_NODE_GETTER_0 (, char, GetAltLocation) |
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| SB_NODE_GETTER_0 (, std::string, GetChainName) |
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| SB_NODE_GETTER_0 (, char, GetInsertionCode) |
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| SB_NODE_GETTER_0 (, int, GetSerialNumber) |
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| SB_NODE_GETTER_0 (, SBQuantity::dimensionless, GetOccupancy) |
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| SB_NODE_GETTER_0 (, std::string, GetRecordType) |
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| SB_NODE_GETTER_0 (, unsigned int, GetRecordTypeSize) |
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| SB_NODE_GETTER_0 (, std::string, GetResidueName) |
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| SB_NODE_GETTER_0 (, std::string, GetResidueTypeString) |
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| SB_NODE_GETTER_0 (, int, GetResidueSequenceNumber) |
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| SB_NODE_GETTER_0 (, std::string, GetSegmentName) |
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| SB_NODE_GETTER_0 (, double, GetTemperatureFactor) |
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| SB_NODE_GETTER_0 (, float, GetPartialCharge) |
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| SB_NODE_GETTER_0 (, int, GetFormalCharge) |
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| SB_NODE_GETTER_0 (, std::string, GetComment) |
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| SB_NODE_GETTER_0 (, unsigned int, GetCommentSize) |
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| SB_NODE_GETTER_0 (, std::vector< int >, GetAnisotropicTFactors) |
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| SB_NODE_GETTER_0 (, std::string, GetSYBYLType) |
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| SB_NODE_GETTER_0 (, unsigned int, GetSYBYLTypeSize) |
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| SB_NODE_GETTER_0 (, std::string, GetStatusBit) |
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| SB_NODE_GETTER_0 (, unsigned int, GetStatusBitSize) |
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| SB_NODE_GETTER_0 (, std::string, GetMoleculeName) |
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| SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedAtoms) |
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| SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedCarbons) |
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| SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedHeavyAtoms) |
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| SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedHydrogens) |
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| SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedNitrogens) |
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| SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedOxygens) |
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| SB_NODE_GETTER_0 (, unsigned int, GetNumberOfBondedSulfurs) |
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| SB_NODE_GETTER_0 (, std::string, GetSubstructureName) |
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| SB_NODE_GETTER_0 (, int, GetSubstructureSequenceNumber) |
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| SB_NODE_GETTER_0 (, int, GetChainID) |
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| SB_NODE_GETTER_0 (, Hybridization, GetHybridization) |
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| SB_NODE_GETTER_0 (, Geometry, GetGeometry) |
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| SB_NODE_GETTER_0 (, int, GetOxidationState) |
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| SB_NODE_GETTER_0 (, bool, GetResonance) |
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| SB_NODE_GETTER_0 (, bool, GetAromaticity) |
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| SB_NODE_GETTER_0 (, bool, GetWaterFlag) |
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| SB_NODE_GETTER_0 (, int, GetCustomType) |
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| SB_NODE_GETTER_0 (, std::string, GetCoarseGrainedType) |
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| SB_NODE_GETTER_0 (, SBQuantity::length, GetCoarseGrainedRadius) |
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| SB_NODE_GETTER_0 (, SBQuantity::mass, GetCoarseGrainedMass) |
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| SB_NODE_GETTER_0 (, SBColor, GetCoarseGrainedColor) |
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| SB_NODE_GETTER_0 (, bool, GetFixedFlag) |
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| SB_NODE_PREDICATE_0 (, HasName) |
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| SB_NODE_PREDICATE_0 (, HasAltLocation) |
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| SB_NODE_PREDICATE_0 (, HasInsertionCode) |
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| SB_NODE_PREDICATE_0 (, HasSerialNumber) |
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| SB_NODE_PREDICATE_0 (, HasOccupancy) |
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| SB_NODE_PREDICATE_0 (, HasRecordType) |
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| SB_NODE_PREDICATE_0 (, HasResidueSequenceNumber) |
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| SB_NODE_PREDICATE_0 (, HasTemperatureFactor) |
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| SB_NODE_PREDICATE_0 (, HasPartialCharge) |
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| SB_NODE_PREDICATE_0 (, HasFormalCharge) |
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| SB_NODE_PREDICATE_0 (, HasComment) |
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| SB_NODE_PREDICATE_0 (, HasAnisotropicTFactors) |
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| SB_NODE_PREDICATE_0 (, HasSYBYLType) |
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| SB_NODE_PREDICATE_0 (, HasStatusBit) |
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| SB_NODE_PREDICATE_0 (, HasSubstructureSequenceNumber) |
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| SB_NODE_PREDICATE_0 (, HasChainID) |
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| SB_NODE_PREDICATE_0 (, HasHybridization) |
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| SB_NODE_PREDICATE_0 (, HasGeometry) |
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| SB_NODE_PREDICATE_0 (, HasOxidationState) |
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| SB_NODE_PREDICATE_0 (, HasResonance) |
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| SB_NODE_PREDICATE_0 (, HasAromaticity) |
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| SB_NODE_PREDICATE_0 (, HasWaterFlag) |
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| SB_NODE_PREDICATE_0 (, HasCustomType) |
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| SB_NODE_PREDICATE_0 (, IsInMolecule) |
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| SB_NODE_PREDICATE_0 (, IsInChain) |
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| SB_NODE_PREDICATE_0 (, IsInSegment) |
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| SB_NODE_PREDICATE_0 (, IsInResidue) |
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| SB_NODE_PREDICATE_0 (, IsInAminoAcid) |
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| SB_NODE_PREDICATE_0 (, IsInNucleicAcid) |
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| SB_NODE_PREDICATE_0 (, IsInBackbone) |
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| SB_NODE_PREDICATE_0 (, IsInSideChain) |
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| SB_NODE_PREDICATE_0 (, IsInSubstructure) |
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| SB_NODE_PREDICATE_0 (, IsPlanar) |
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| SB_NODE_PREDICATE_0 (, IsCarbon) |
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| SB_NODE_PREDICATE_0 (, IsHydrogen) |
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| SB_NODE_PREDICATE_0 (, IsNitrogen) |
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| SB_NODE_PREDICATE_0 (, IsOxygen) |
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| SB_NODE_PREDICATE_0 (, IsSulfur) |
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| SB_NODE_PREDICATE_0 (, IsUnknown) |
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| SB_NODE_PREDICATE_0 (, IsFromAminoAcidBackbone) |
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| SB_NODE_PREDICATE_0 (, IsFromNucleicAcidBackbone) |
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| SB_NODE_PREDICATE_0 (, HasAminoAcidBackboneAtomName) |
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| SB_NODE_PREDICATE_0 (, HasNucleicAcidBackboneAtomName) |
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| SB_NODE_PREDICATE_0 (, IsMetal) |
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| SB_NODE_PREDICATE_0 (, IsAlkaliMetal) |
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| SB_NODE_PREDICATE_0 (, IsAlkalineEarthMetal) |
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| SB_NODE_PREDICATE_0 (, IsLanthanide) |
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| SB_NODE_PREDICATE_0 (, IsActinide) |
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| SB_NODE_PREDICATE_0 (, IsTransitionMetal) |
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| SB_NODE_PREDICATE_0 (, IsPostTransitionMetal) |
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| SB_NODE_PREDICATE_0 (, IsMetalloid) |
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| SB_NODE_PREDICATE_0 (, IsNobleGas) |
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| SB_NODE_PREDICATE_0 (, IsReactiveNonmetal) |
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| SB_NODE_PREDICATE_0 (, IsDiatomicNonmetal) |
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| SB_NODE_PREDICATE_0 (, IsPolyatomicNonmetal) |
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| SB_NODE_PREDICATE_0 (, IsHalogen) |
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| SB_NODE_PREDICATE_0 (, IsCoarseGrained) |
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| SB_NODE_PREDICATE_0 (, IsHydrogenBondAcceptor) |
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| SB_NODE_PREDICATE_0 (, IsHydrogenBondDonor) |
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| SB_NODE_PREDICATE_0 (, IsDonorBorneHydrogen) |
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| SB_NODE_PREDICATE_0 (, IsAttachedToHydrogenBondDonor) |
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| SB_DECLARE_DATA (SBMStructuralModelNodeAtom) |
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virtual | ~SBMStructuralModelNode () |
| |
| virtual SBPointerList< SBMStructuralModelNode > const * | getChildren () const |
| | Returns the list of child nodes.
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SBMStructuralModelNode * | getNextStructuralNode () const |
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SBMStructuralModelNode * | getPreviousStructuralNode () const |
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| virtual bool | isLocked () const override |
| | Returns whether the node is locked (because of the model)
|
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| virtual bool | getLockedFlag () const override |
| | Returns the locked flag of the model.
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SBMStructuralModel * | getModel () const |
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| virtual unsigned int | getOpacity () const override |
| | Returns the opacity.
|
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| virtual unsigned int | getMinimumOpacity () const override |
| | Returns the minimum opacity.
|
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| virtual unsigned int | getTransparency () const override |
| | Returns the transparency.
|
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| virtual unsigned int | getMaximumTransparency () const override |
| | Returns the maximum transparency.
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bool | getStructuralSignalFlag () const |
| | Returns true when the node can send structural signals.
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void | setStructuralSignalFlag (bool structuralSignalFlag) |
| | Sets whether the node can send structural signals.
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void | connectStructuralSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any, SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBStructuralEvent *)=0) |
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bool | structuralSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) const |
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void | disconnectStructuralSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBStructuralEvent::Type eventType=SBStructuralEvent::Type::Any) |
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| virtual void | getNodes (SBNodeIndexer &nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override |
| | Collects nodes into nodeIndexer, based on a nodeType, a selection status and a visitPredicate, with or without dependencies.
|
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| virtual void | getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override |
| | Collects nodes into nodeIndexer, based on a selectionPredicate and a visitPredicate, with or without dependencies.
|
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| virtual bool | hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override |
| | Checks for nodes based on a nodeType, a selection status and a visitPredicate, with or without dependencies.
|
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| virtual bool | hasNode (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override |
| | Checks for nodes based on a selectionPredicate and a visitPredicate, with or without dependencies.
|
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void | getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode * > &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
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void | getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode * > &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
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void | getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > &nodeIndexer) |
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void | getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode * > &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
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void | getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode * > &nodeVectorTopDown, std::vector< SBMStructuralModelNode * > &nodeVectorBottomUp, bool(*selectionRule)(SBMStructuralModelNode *)) |
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| virtual void | forEachNodeDepthFirst (void(*action)(SBDDataGraphNode *node)) override |
| | Performs an action on each node.
|
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| virtual void | forEachNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node)) override |
| | Performs an action on each node.
|
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void | forEachStructuralNodeBreadthFirst (void(*action)(SBMStructuralModelNode *node)) |
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void | forEachStructuralNodeDepthFirst (void(*action)(SBMStructuralModelNode *node)) |
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void | forEachStructuralNodeBreadthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
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void | forEachStructuralNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
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| SB_DECLARE_DATA (SBMStructuralModelNode) |
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| SB_DECLARE_DATA (SBMModelNode) |
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| SBDDataGraphNode * | getParent () const |
| | Returns the parent of the node.
|
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| SBDDataGraphNode * | getThisNode () const |
| | Returns the pointer to this node.
|
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| SBDDataGraphNode * | getNextNode () const |
| | Returns the pointer to the next node in the children of the node's parent.
|
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| SBDDataGraphNode * | getPreviousNode () const |
| | Returns the pointer to the previous node in the children of the node's parent.
|
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| SBDDataGraphNode * | getNextNode (SBDDataGraphNode::Type nodeType) const |
| | Returns the pointer to the next node with type nodeType in the children of the node's parent.
|
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| SBDDataGraphNode * | getPreviousNode (SBDDataGraphNode::Type nodeType) const |
| | Returns the pointer to the previous node with type nodeType in the children of the node's parent.
|
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| SBDDocument * | getDocument () const |
| | Returns the document the node belongs to.
|
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| virtual bool | canAddChild (const SBDDataGraphNode *node, const SBDDataGraphNode *nextNode=nullptr) const |
| | Returns whether this node can add node as a child.
|
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| virtual bool | canAddChildType (SBDDataGraphNode::Type nodeType) const |
| | Returns whether this node can add a node with type nodeType as a child.
|
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| virtual bool | canHaveDescendantType (SBDDataGraphNode::Type nodeType) const |
| | Returns whether this node can have a node with type nodeType as a descendant.
|
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| virtual bool | addChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=nullptr) |
| | Adds a child to the node.
|
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| virtual bool | removeChild (SBDDataGraphNode *node) |
| | Removes a child from the node.
|
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| 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.
|
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| bool | descendsFrom (const SBDDataGraphNode *node) const |
| | Returns true if and only if this node is node, or descends from it.
|
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| 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.
|
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| 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.
|
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| bool | isIn (const SBDDataGraphNode *node) const |
| | Returns true if and only if this node is node, or descends from it, or belongs to a group stored in node.
|
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| 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.
|
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| 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.
|
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| bool | isOneOf (const SBNodeIndexer &nodeIndexer) const |
| | Returns true if and only if this node is one of the nodes of the nodeIndexer.
|
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| bool | isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
| | Returns true if and only if this node is one of the nodes of the nodePointerIndexer.
|
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| SBDDataGraphNode * | getRoot () const |
| | Returns the root of the hierarchy the node belongs to.
|
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| unsigned int | getNodeIndex () const |
| | Returns the node index (unique in the whole data graph, but non-persistent)
|
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| std::string | getTypeString (bool humanReadable=false) const |
| | Returns a string describing the type of the data graph node.
|
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bool | isType (Type type) const |
| | Returns true when the type of the node corresponds to type.
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bool | isModel () const |
| | Returns true when the node is a model.
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bool | isAtom () const |
| | Returns true when the node is an atom.
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bool | isBond () const |
| | Returns true when the node is a bond.
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bool | isStructuralNode () const |
| | Returns true when the node is a structural node.
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bool | isStructuralModel () const |
| | Returns true when the node is a structural model.
|
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bool | isVisualModel () const |
| | Returns true when the node is a visual model.
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bool | isDynamicalModel () const |
| | Returns true when the node is a dynamical model.
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bool | isInteractionModel () const |
| | Returns true when the node is a interaction model.
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bool | isPropertyModel () const |
| | Returns true when the node is a property model.
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bool | isMesh () const |
| | Returns true when the node is a mesh.
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bool | isLight () const |
| | Returns true when the node is a light.
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bool | isSimulator () const |
| | Returns true when the node is a simulator.
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bool | isBallAndStick () const |
| | Returns true when the node is the default ball-and-stick visual model.
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bool | isLicorice () const |
| | Returns true when the node is the default licorice visual model.
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bool | isVanDerWaals () const |
| | Returns true when the node is the default van der Waals visual model.
|
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bool | isCartoon () const |
| | Returns true when the node is the default cartoon visual model.
|
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bool | isRibbon () const |
| | Returns true when the node is the default ribbon visual model.
|
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bool | isTube () const |
| | Returns true when the node is the default tube visual model.
|
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bool | isGaussianSurface () const |
| | Returns true when the node is the default Gaussian surface visual model.
|
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bool | isSolventAccessibleSurface () const |
| | Returns true when the node is the default solvent accessible surface visual model.
|
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bool | isSolventExcludedSurface () const |
| | Returns true when the node is the default solvent excluded surface visual model.
|
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| virtual void | setLockedFlag (bool flag) |
| | Sets the locked flag.
|
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| bool | isCreated () const |
| | Returns true if and only if the node is created.
|
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| void | create () |
| | Creates the node.
|
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| bool | isErased () const |
| | Returns true if and only if the node is erased.
|
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| void | erase () |
| | Erases the node.
|
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| bool | isSelected () const |
| | Returns whether the node is selected.
|
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bool | getSelected () const |
| | Returns whether the node is selected.
|
| |
| bool | getSelectionFlag () const |
| | Returns the selection flag.
|
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| void | setSelectionFlag (bool flag) |
| | Sets the selection flag.
|
| |
| bool | isVisible () const |
| | Returns whether the node is visible.
|
| |
|
bool | getVisible () const |
| | Returns whether the node is visible.
|
| |
| bool | getVisibilityFlag () const |
| | Returns the visibility flag.
|
| |
| void | setVisibilityFlag (bool flag) |
| | Sets the visibility flag.
|
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| bool | isHighlighted () const |
| | Returns whether the node is highlighted.
|
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| bool | getHighlightingFlag () const |
| | Returns the highlighting flag.
|
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| void | setHighlightingFlag (bool flag) |
| | Sets the highlighting flag.
|
| |
| virtual void | display (RenderingPass renderingPass) |
| | Displays the node.
|
| |
| virtual void | display () |
| | Displays the node (deprecated)
|
| |
| virtual void | displayForShadow () |
| | Displays the node for shadowing purposes (deprecated)
|
| |
| virtual void | displayForSelection () |
| | Displays the node for selection purposes (deprecated)
|
| |
| virtual void | setOpacity (unsigned int opacity) |
| | Sets the opacity.
|
| |
|
virtual bool | hasOpacityRange () const |
| | Returns whether the node has the opacity range.
|
| |
|
virtual unsigned int | getDefaultOpacity () const |
| | Returns the default opacity.
|
| |
|
virtual unsigned int | getMaximumOpacity () const |
| | Returns the maximum opacity.
|
| |
|
virtual unsigned int | getOpacitySingleStep () const |
| | Returns the opacity single step.
|
| |
|
virtual std::string | getOpacitySuffix () const |
| | Returns the opacity suffix.
|
| |
| virtual void | setTransparency (unsigned int transparency) |
| | Sets the transparency.
|
| |
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virtual bool | hasTransparencyRange () const |
| | Returns whether the node has the transparency range.
|
| |
|
virtual unsigned int | getDefaultTransparency () const |
| | Returns the default transparency.
|
| |
|
virtual unsigned int | getMinimumTransparency () const |
| | Returns the minimum transparency.
|
| |
|
virtual unsigned int | getTransparencySingleStep () const |
| | Returns the transparency single step.
|
| |
|
virtual std::string | getTransparencySuffix () const |
| | Returns the transparency suffix.
|
| |
|
float | getInheritedOpacity () const |
| | Returns the cumulative opacity, when taking into account the ascendants.
|
| |
|
float | getInheritedTransparency () const |
| | Returns the cumulative transparency, when taking into account the ascendants.
|
| |
| bool | canAddMaterial () const |
| | Returns whether can add a material to the node based on its type.
|
| |
| bool | addMaterial (SBDDataGraphNodeMaterial *material) |
| | Adds a material.
|
| |
| bool | removeMaterial () |
| | Removes the material.
|
| |
| void | removeMaterialsFromDescendants () |
| | Removes materials from all nodes that descend from this node, but it does not remove the material from the node itself.
|
| |
| bool | hasMaterial () const |
| | Returns whether the node has a material (by itself, or inherited)
|
| |
| bool | ownsMaterial () const |
| | Returns whether the node owns a material.
|
| |
| SBDDataGraphNodeMaterial * | getMaterial () const |
| | Returns the material.
|
| |
| SBDDataGraphNode * | getMaterialOwner () const |
| | Returns the node whose material is inherited.
|
| |
| void | connectBaseSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBBaseEvent *)=0) |
| | Connects the base signal to a slot.
|
| |
|
bool | baseSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) const |
| | Returns true when the base signal is connected to a slot.
|
| |
|
void | disconnectBaseSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) |
| | Disconnects the base signal from a slot.
|
| |
| unsigned int | countNodes (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
| | Counts nodes based on a nodeType, a selection status and a visitPredicate, with or without dependencies.
|
| |
| unsigned int | countNodes (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
| | Counts nodes based on a selectionPredicate and a visitPredicate, with or without dependencies.
|
| |
| virtual 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.
|
| |
|
| SB_DECLARE_DATA (SBDDataGraphNode) |
| |
|
unsigned int | getMemoryFootprint () const |
| |
|
void | printReferencesToOwners () const |
| |
|
| SBCReferenceTarget () |
| |
|
virtual | ~SBCReferenceTarget () |
| |
|
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 void | clone (const SBNodeIndexer &sourceNodeIndexer, SBNodeIndexer &destinationNodeIndexer) |
| | Clones the nodes in sourceNodeIndexer (treated as a whole) and places the clones in destinationNodeIndexer.
|
| |
| static SBDDataGraphNode * | getNode (unsigned int nodeIndex) |
| | Returns the unique node corresponding to the node index nodeIndex.
|
| |
| static std::string | getTypeString (Type type, bool humanReadable=false) |
| | Returns a string describing the type of the data graph node.
|
| |
| static bool | canAddMaterial (SBDDataGraphNode::Type nodeType) |
| | Returns whether can add a material to a node of type nodeType.
|
| |
|
static void | forEachNodeInSelection (SBNodeIndexer &nodeIndexer, void(*action)(SBDDataGraphNode *node)) |
| | Performs an action for each node in a selection.
|
| |
|
static void | forEachNodeInSelection (SBNodeIndexer &nodeIndexer, SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node)) |
| | Performs an action for each node in a selection.
|
| |
|
| SBMStructuralModelNode () |
| | Builds a structural model node.
|
| |
|
| SBMStructuralModelNode (SBMStructuralModelNodeData *dataPointer) |
| | Builds a structural model node.
|
| |
|
| SBMModelNode () |
| | Builds a base object.
|
| |
|
| SBMModelNode (SBMModelNodeData *dataPointer) |
| | Builds a base object.
|
| |
|
virtual | ~SBMModelNode () |
| |
| | SBDDataGraphNode () |
| | Builds a data graph node.
|
| |
|
| SBDDataGraphNode (SBDDataGraphNodeData *dataPointer) |
| | Builds a data graph node.
|
| |
| virtual | ~SBDDataGraphNode () |
| | Destroys the node.
|
| |
|
void | removeAllReferenceOwners () |
| |
|
| SBCReferenceTarget (SBCReferenceTargetData *dataPointer) |
| |
|
SBCReferenceTargetData * | dataPointer |
| |
Public Member Functions inherited from SBMStructuralModelNode