public class NMRCalculation extends java.lang.Object implements JmolNMRInterface
| Modifier and Type | Field and Description |
|---|---|
private static double |
DIPOLAR_FACTOR |
private static double |
e_charge |
private static double |
h_bar_planck |
private static double |
h_planck |
private java.util.Map<java.lang.String,double[]> |
isotopeData
isotopeData keyed by nnnSym, for example: 1H, 19F, etc.; and also by
element name itself: H, F, etc., for default
|
private static double |
J_FACTOR |
private static int |
MAGNETOGYRIC_RATIO |
private static double |
Q_FACTOR |
private static int |
QUADRUPOLE_MOMENT |
private static java.lang.String |
resource
NOTE! Do not change this txt file! Instead, edit
trunk/Jmol/_documents/nmr_data.xls and then clip its contents to
org/jmol/quantum/nmr_data.txt.
|
private java.util.Map<java.lang.String,java.lang.Float> |
shiftRefsPPM |
private Viewer |
vwr |
| Constructor and Description |
|---|
NMRCalculation() |
| Modifier and Type | Method and Description |
|---|---|
private javajs.util.BS |
getAtomSiteBS(javajs.util.BS bsA)
Interaction tensors are not repeated for every possible combination.
|
float |
getChemicalShift(Atom atom)
If shift reference has not been set, it defaults to 0 and just
displays the negative of magnetic shielding
|
private void |
getData()
Creates the data set necessary for doing NMR calculations.
|
float |
getDipolarConstantHz(Atom a1,
Atom a2) |
float |
getDipolarCouplingHz(Atom a1,
Atom a2,
javajs.util.V3 vField) |
java.lang.Object |
getInfo(java.lang.String what) |
private javajs.util.Lst<Tensor> |
getInteractionTensorList(java.lang.String type,
javajs.util.BS bsA)
Returns a list of tensors that are of the specified type and have both
atomIndex1 and atomIndex2 in bsA.
|
private java.lang.String |
getISCtype(Atom a1,
java.lang.String type) |
float |
getIsoOrAnisoHz(boolean isIso,
Atom a1,
Atom a2,
java.lang.String type,
Tensor isc)
If t is null, then a1, a2, and type are used to find the appropriate
tensor.
|
private double |
getIsotopeData(Atom a,
int iType)
Get magnetogyricRatio (gamma/10^7 rad s^-1 T^-1) and quadrupoleMoment
(Q/10^-2 fm^2) for a given isotope or for the default isotope of an
element.
|
float |
getJCouplingHz(Atom a1,
Atom a2,
java.lang.String type,
Tensor isc) |
float |
getMagneticShielding(Atom atom) |
java.util.Map<java.lang.String,java.lang.Integer> |
getMinDistances(MeasurementData md) |
float |
getQuadrupolarConstant(Tensor efg)
Quadrupolar constant, directly proportional to Vzz and dependent on the
quadrupolar moment of the isotope considered
|
boolean |
getState(javajs.util.SB sb) |
javajs.util.Lst<java.lang.Object> |
getTensorInfo(java.lang.String tensorType,
java.lang.String infoType,
javajs.util.BS bs) |
javajs.util.BS |
getUniqueTensorSet(javajs.util.BS bsAtoms)
An attempt to find unique atoms using tensors.
|
boolean |
setChemicalShiftReference(java.lang.String element,
float value) |
JmolNMRInterface |
setViewer(Viewer vwr) |
private static final int MAGNETOGYRIC_RATIO
private static final int QUADRUPOLE_MOMENT
private static final double e_charge
private static final double h_planck
private static final double h_bar_planck
private static final double DIPOLAR_FACTOR
private static final double J_FACTOR
private static final double Q_FACTOR
private Viewer vwr
private java.util.Map<java.lang.String,double[]> isotopeData
private static final java.lang.String resource
private java.util.Map<java.lang.String,java.lang.Float> shiftRefsPPM
public JmolNMRInterface setViewer(Viewer vwr)
setViewer in interface JmolNMRInterfacepublic float getQuadrupolarConstant(Tensor efg)
JmolNMRInterfacegetQuadrupolarConstant in interface JmolNMRInterfaceprivate javajs.util.Lst<Tensor> getInteractionTensorList(java.lang.String type, javajs.util.BS bsA)
type - bsA - private javajs.util.BS getAtomSiteBS(javajs.util.BS bsA)
bsA - public javajs.util.BS getUniqueTensorSet(javajs.util.BS bsAtoms)
JmolNMRInterfacegetUniqueTensorSet in interface JmolNMRInterfacepublic float getIsoOrAnisoHz(boolean isIso,
Atom a1,
Atom a2,
java.lang.String type,
Tensor isc)
JmolNMRInterfacegetIsoOrAnisoHz in interface JmolNMRInterfaceprivate java.lang.String getISCtype(Atom a1, java.lang.String type)
public float getDipolarConstantHz(Atom a1, Atom a2)
getDipolarConstantHz in interface JmolNMRInterfacepublic float getDipolarCouplingHz(Atom a1, Atom a2, javajs.util.V3 vField)
getDipolarCouplingHz in interface JmolNMRInterfaceprivate double getIsotopeData(Atom a, int iType)
a - iType - private void getData()
public java.lang.Object getInfo(java.lang.String what)
getInfo in interface JmolNMRInterfacewhat - "C" or "14C" or "all"public float getChemicalShift(Atom atom)
JmolNMRInterfacegetChemicalShift in interface JmolNMRInterfacepublic float getMagneticShielding(Atom atom)
getMagneticShielding in interface JmolNMRInterfacepublic boolean getState(javajs.util.SB sb)
getState in interface JmolNMRInterfacepublic boolean setChemicalShiftReference(java.lang.String element,
float value)
setChemicalShiftReference in interface JmolNMRInterfacepublic javajs.util.Lst<java.lang.Object> getTensorInfo(java.lang.String tensorType,
java.lang.String infoType,
javajs.util.BS bs)
getTensorInfo in interface JmolNMRInterfacepublic java.util.Map<java.lang.String,java.lang.Integer> getMinDistances(MeasurementData md)
getMinDistances in interface JmolNMRInterface