A QObject derived molecule object with signals/slots.
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| Molecule (QObject *parent_=nullptr) |
| ~Molecule () override |
| Molecule (const Molecule &other) |
| Molecule (const Core::Molecule &other) |
Molecule & | operator= (const Molecule &other) |
Molecule & | operator= (const Core::Molecule &other) |
AtomType | addAtom (unsigned char atomicNumber) override |
virtual AtomType | addAtom (unsigned char atomicNumber, Index uniqueId) |
AtomType | addAtom (unsigned char number, Vector3 position3d, Index uniqueId=MaxIndex) |
bool | removeAtom (Index index) override |
| Remove the specified atom from the molecule.
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bool | removeAtom (const AtomType &atom) override |
| Remove the specified atom from the molecule.
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AtomType | atomByUniqueId (Index uniqueId) |
| Get the atom referenced by the uniqueId , the isValid method should be queried to ensure the id still referenced a valid atom.
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Core::Array< Index > & | atomUniqueIds () |
BondType | addBond (const AtomType &a, const AtomType &b, unsigned char bondOrder=1) override |
| Add a bond between the specified atoms.
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BondType | addBond (Index atomId1, Index atomId2, unsigned char bondOrder=1) override |
| Add a bond between the specified atoms.
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void | addBonds (const Core::Array< std::pair< Index, Index > > &bonds, const Core::Array< unsigned char > &orders) |
virtual BondType | addBond (const AtomType &a, const AtomType &b, unsigned char bondOrder, Index uniqueId) |
| Add a bond between the specified atoms.
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virtual BondType | addBond (Index atomId1, Index atomId2, unsigned char bondOrder, Index uniqueId) |
| Add a bond between the specified atoms.
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bool | removeBond (Index index) override |
| Remove the specified bond.
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bool | removeBond (const BondType &bond) override |
| Remove the specified bond.
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BondType | bondByUniqueId (Index uniqueId) |
| Get the bond referenced by the uniqueId , the isValid method should be queried to ensure the id still referenced a valid bond.
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Core::Array< Index > & | bondUniqueIds () |
Index | findAtomUniqueId (Index index) const |
Index | findBondUniqueId (Index index) const |
RWMolecule * | undoMolecule () |
void | swapBond (Index a, Index b) |
void | swapAtom (Index a, Index b) |
Index | atomUniqueId (const AtomType &atom) const |
| Get the unique ID of the atom, this will uniquely reference the atom as long as it exists.
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Index | atomUniqueId (Index atom) const |
| Get the unique ID of the atom, this will uniquely reference the atom as long as it exists.
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bool | removeBond (const AtomType &atom1, const AtomType &atom2) override |
| Remove the specified bond.
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bool | removeBond (Index atom1, Index atom2) override |
| Remove the specified bond.
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Index | bondUniqueId (const BondType &bond) const |
| Get the unique ID of the bond, this will uniquely reference the bond as long as it exists.
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Index | bondUniqueId (Index bond) const |
| Get the unique ID of the bond, this will uniquely reference the bond as long as it exists.
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| Molecule () |
| Molecule (const Molecule &other) |
| Molecule (Molecule &&other) noexcept |
Molecule & | operator= (const Molecule &other) |
Molecule & | operator= (Molecule &&other) noexcept |
void | readProperties (const Molecule &other) |
void | setData (const std::string &name, const Variant &value) |
Variant | data (const std::string &name) const |
bool | hasData (const std::string &name) const |
void | setDataMap (const VariantMap &map) |
const VariantMap & | dataMap () const |
VariantMap & | dataMap () |
MatrixX | spectra (const std::string &name) const |
void | setSpectra (const std::string &name, const MatrixX &value) |
std::set< std::string > | spectraTypes () const |
void | setPartialCharges (const std::string &type, const MatrixX &value) |
MatrixX | partialCharges (const std::string &type) const |
std::set< std::string > | partialChargeTypes () const |
Array< AtomHybridization > & | hybridizations () |
const Array< AtomHybridization > & | hybridizations () const |
AtomHybridization | hybridization (Index atomId) const |
bool | setHybridizations (const Core::Array< AtomHybridization > &hybs) |
bool | setHybridization (Index atomId, AtomHybridization hybridization) |
Array< signed char > & | formalCharges () |
const Array< signed char > & | formalCharges () const |
signed char | totalCharge () const |
char | totalSpinMultiplicity () const |
signed char | formalCharge (Index atomId) const |
bool | setFormalCharges (const Core::Array< signed char > &charges) |
bool | setFormalCharge (Index atomId, signed char charge) |
Array< Vector3ub > & | colors () |
const Array< Vector3ub > & | colors () const |
Vector3ub | color (Index atomId) const |
bool | setColors (const Core::Array< Vector3ub > &colors) |
bool | setColor (Index atomId, Vector3ub color) |
bool | setLayer (Index atomId, size_t layer) |
size_t | layer (Index atomId) const |
const Array< Vector2 > & | atomPositions2d () const |
Array< Vector2 > & | atomPositions2d () |
Vector2 | atomPosition2d (Index atomId) const |
bool | setAtomPositions2d (const Core::Array< Vector2 > &pos) |
bool | setAtomPosition2d (Index atomId, const Vector2 &pos) |
const Array< Vector3 > & | atomPositions3d () const |
Array< Vector3 > & | atomPositions3d () |
Vector3 | atomPosition3d (Index atomId) const |
bool | setAtomPositions3d (const Core::Array< Vector3 > &pos) |
bool | setAtomPosition3d (Index atomId, const Vector3 &pos) |
std::string | atomLabel (Index atomId) const |
bool | setAtomLabel (Index atomId, const std::string &label) |
const Core::Array< std::string > | atomLabels () const |
bool | setAtomLabels (const Core::Array< std::string > &label) |
void | setAtomSelected (Index atomId, bool selected) |
bool | atomSelected (Index atomId) const |
bool | isSelectionEmpty () const |
const ElementMask | elements () const |
AtomType | addAtom (unsigned char atomicNumber, Vector3 position3d) |
virtual void | clearAtoms () |
AtomType | atom (Index index) const |
virtual void | clearBonds () |
BondType | bond (Index index) const |
BondType | bond (const AtomType &a, const AtomType &b) const |
BondType | bond (Index atomId1, Index atomId2) const |
std::string | bondLabel (Index bondIndex) const |
bool | setBondLabel (Index bondIndex, const std::string &label) |
const Core::Array< std::string > | bondLabels () const |
bool | setBondLabels (const Core::Array< std::string > &label) |
Mesh * | addMesh () |
| Add a mesh to the molecule.
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Mesh * | mesh (Index index) |
const Mesh * | mesh (Index index) const |
Index | meshCount () const |
void | clearMeshes () |
Cube * | addCube () |
| Add a cube to the molecule.
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Cube * | cube (Index index) |
const Cube * | cube (Index index) const |
Index | cubeCount () const |
void | clearCubes () |
std::vector< Cube * > | cubes () |
| Get the cubes vector set (if present) for the molecule.
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const std::vector< Cube * > | cubes () const |
std::string | formula (const std::string &delimiter="", int showCountsOver=1) const |
double | mass () const |
Vector3 | centerOfGeometry () const |
Vector3 | centerOfMass () const |
double | radius () const |
std::pair< Vector3, Vector3 > | bestFitPlane () const |
void | setBasisSet (BasisSet *basis) |
BasisSet * | basisSet () |
const BasisSet * | basisSet () const |
Array< double > | vibrationFrequencies () const |
void | setVibrationFrequencies (const Array< double > &freq) |
Array< double > | vibrationIRIntensities () const |
void | setVibrationIRIntensities (const Array< double > &intensities) |
Array< double > | vibrationRamanIntensities () const |
void | setVibrationRamanIntensities (const Array< double > &intensities) |
Array< Vector3 > | vibrationLx (int mode) const |
void | setVibrationLx (const Array< Array< Vector3 > > &lx) |
void | perceiveBondsSimple (const double tolerance=0.45, const double minDistance=0.32) |
void | perceiveBondsFromResidueData () |
void | perceiveBondOrders () |
void | perceiveSubstitutedCations () |
int | coordinate3dCount () |
bool | setCoordinate3d (int coord) |
Array< Vector3 > | coordinate3d (int index) const |
bool | setCoordinate3d (const Array< Vector3 > &coords, int index) |
void | clearCoordinate3d () |
bool | setTimeStep (double timestep, int index) |
double | timeStep (int index, bool &status) |
const Array< Vector3 > & | forceVectors () const |
Array< Vector3 > & | forceVectors () |
Vector3 | forceVector (Index atomId) const |
bool | setForceVectors (const Core::Array< Vector3 > &forces) |
bool | setForceVector (Index atomId, const Vector3 &force) |
Residue & | addResidue (std::string &name, Index &number, char &id) |
void | addResidue (Residue &residue) |
Residue & | residue (Index index) |
Array< Residue > & | residues () |
const Array< Residue > & | residues () const |
Index | residueCount () const |
Index | atomCount () const |
Index | atomCount (unsigned char atomicNumber) const |
| Get the number of atoms in the molecule that match atomicNumber.
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Index | bondCount () const |
std::pair< Index, Index > | bondPair (Index bondId) const |
bool | setBondPairs (const Array< std::pair< Index, Index > > &pairs) |
const Array< std::pair< Index, Index > > & | bondPairs () const |
const Array< unsigned char > & | bondOrders () const |
const Graph & | graph () const |
const Array< unsigned char > & | atomicNumbers () const |
unsigned char | atomicNumber (Index atomId) const |
bool | setBondOrders (const Array< unsigned char > &orders) |
bool | setBondOrder (Index bondId, unsigned char order) |
bool | hasCustomElements () const |
bool | setBondPair (Index bondId, const std::pair< Index, Index > &pair) |
unsigned char | bondOrder (Index bondId) const |
bool | setAtomicNumbers (const Core::Array< unsigned char > &nums) |
bool | setAtomicNumber (Index atomId, unsigned char atomicNumber) |
void | setFrozenAtom (Index atomId, bool frozen) |
bool | frozenAtom (Index atomId) const |
void | setFrozenAtomAxis (Index atomId, int axis, bool frozen) |
Eigen::VectorXd | frozenAtomMask () const |
std::map< unsigned char, size_t > | composition () const |
Array< std::pair< Index, Index > > | getAtomBonds (Index index) const |
Array< unsigned char > | getAtomOrders (Index index) const |
bool | removeBonds (Index atom) |
void | addBonds (const Array< std::pair< Index, Index > > &bonds, const Array< unsigned char > &orders) |
void | swapBond (Index a, Index b) |
void | swapAtom (Index a, Index b) |
std::list< Index > | getAtomsAtLayer (size_t layer) |
Layer & | layer () |
const Layer & | layer () const |
void | boundingBox (Vector3 &boxMin, Vector3 &boxMax, const double radius=1.0) const |
const CustomElementMap & | customElementMap () const |
void | setCustomElementMap (const CustomElementMap &map) |
Array< BondType > | bonds (const AtomType &a) |
| Get all bonds to a .
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Array< BondType > | bonds (Index a) |
| Get all bonds to a .
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Array< const BondType * > | bonds (Index a) const |
| Get all bonds to a .
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void | setUnitCell (UnitCell *uc) |
UnitCell * | unitCell () |
const UnitCell * | unitCell () const |
void | setHallNumber (unsigned short hallNumber) |
unsigned short | hallNumber () const |