Package org.jmol.quantum
Class NMRCalculation
java.lang.Object
org.jmol.quantum.NMRCalculation
- All Implemented Interfaces:
JmolNMRInterface
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic double[]
calc2or3JorNOE
(Viewer viewer, Atom[] atoms, String CHEquation, int mode) Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;static double
static double
calcJKarplus
(double theta) static double[]
static int
getCalcType
(Atom[] atoms, String[] elementsToFill, int mode) float
getChemicalShift
(Atom atom) If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shieldingfloat
getDipolarConstantHz
(Atom a1, Atom a2) float
getDipolarCouplingHz
(Atom a1, Atom a2, V3 vField) float
getIsoOrAnisoHz
(boolean isIso, Atom a1, Atom a2, String units, Tensor isc) If t is null, then a1, a2, and type are used to find the appropriate tensor.float
getJCouplingHz
(Atom a1, Atom a2, String type, Tensor isc) float
getMagneticShielding
(Atom atom) double[]
getNOEorJHH
(Atom[] atoms, int mode) float
Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope consideredboolean
getTensorInfo
(String tensorType, String infoType, BS bs) getUniqueTensorSet
(BS bsAtoms) An attempt to find unique atoms using tensors.boolean
setChemicalShiftReference
(String element, float value)
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Field Details
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MODE_CALC_INVALID
public static final int MODE_CALC_INVALID- See Also:
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MODE_CALC_2JHH
public static final int MODE_CALC_2JHH- See Also:
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MODE_CALC_3JHH
public static final int MODE_CALC_3JHH- See Also:
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MODE_CALC_JHH
public static final int MODE_CALC_JHH- See Also:
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MODE_CALC_3JCH
public static final int MODE_CALC_3JCH- See Also:
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MODE_CALC_J
public static final int MODE_CALC_J- See Also:
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MODE_CALC_NOE
public static final int MODE_CALC_NOE- See Also:
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MODE_CALC_ALL
public static final int MODE_CALC_ALL- See Also:
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JCH3_NONE
- See Also:
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JCH3_WASYLISHEN_SCHAEFER
- See Also:
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JCH3_TVAROSKA_TARAVEL
- See Also:
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JCH3_AYDIN_GUETHER
- See Also:
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Constructor Details
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NMRCalculation
public NMRCalculation()
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Method Details
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setViewer
- Specified by:
setViewer
in interfaceJmolNMRInterface
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getQuadrupolarConstant
Description copied from interface:JmolNMRInterface
Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope considered- Specified by:
getQuadrupolarConstant
in interfaceJmolNMRInterface
- Returns:
- float value
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getUniqueTensorSet
Description copied from interface:JmolNMRInterface
An attempt to find unique atoms using tensors.- Specified by:
getUniqueTensorSet
in interfaceJmolNMRInterface
- Returns:
- bitset of atoms
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getJCouplingHz
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getIsoOrAnisoHz
Description copied from interface:JmolNMRInterface
If t is null, then a1, a2, and type are used to find the appropriate tensor.- Specified by:
getIsoOrAnisoHz
in interfaceJmolNMRInterface
- Returns:
- 0 if not found
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getDipolarConstantHz
- Specified by:
getDipolarConstantHz
in interfaceJmolNMRInterface
- Returns:
- desired constant
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getDipolarCouplingHz
- Specified by:
getDipolarCouplingHz
in interfaceJmolNMRInterface
- Returns:
- projected value
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getInfo
- Specified by:
getInfo
in interfaceJmolNMRInterface
- Parameters:
what
- "C" or "14C" or "all"- Returns:
- list of double[isotopeNumber,g,Q] if no isotope number is given, or a single double[] if it does.
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getChemicalShift
Description copied from interface:JmolNMRInterface
If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shielding- Specified by:
getChemicalShift
in interfaceJmolNMRInterface
- Returns:
- value
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getMagneticShielding
- Specified by:
getMagneticShielding
in interfaceJmolNMRInterface
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getState
- Specified by:
getState
in interfaceJmolNMRInterface
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setChemicalShiftReference
- Specified by:
setChemicalShiftReference
in interfaceJmolNMRInterface
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getTensorInfo
- Specified by:
getTensorInfo
in interfaceJmolNMRInterface
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getMinDistances
- Specified by:
getMinDistances
in interfaceJmolNMRInterface
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calcJKarplus
public static double calcJKarplus(double theta) -
calc3JCH
- Parameters:
CHequation
- 'was' Simple equation for 3JCH, from Wasylishen and Schaefer Can J Chem (1973) 51 961 used in Kozerski et al. J Chem Soc Perkin 2, (1997) 1811 'tva' Tvaroska and Taravel Adv. Carbohydrate Chem. Biochem. (1995) 51, 15-61 'ayd' Aydin and Guether Mag. Res. Chem. (1990) 28, 448-457theta
- dihedralis23Double
-- Returns:
- 3JCH prediction
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calcNOE
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calc2or3JorNOE
Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;- Parameters:
viewer
-atoms
- required Atom[4]; can be just two atoms, then in atom[0] and atom[4]CHEquation
- 'none' or 'was' or 'tva' or 'ayd'mode
-- Returns:
- [theta, jvalue, atom2.i, atom3.i] for 3JHH; [theta, jvalue, center.i] for 2JHH; [distance, noe] for NOE
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getCalcType
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getNOEorJHH
- Specified by:
getNOEorJHH
in interfaceJmolNMRInterface
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