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 BS |
getAtomSiteBS(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,
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,
BS bs) |
BS |
getUniqueTensorSet(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 JmolNMRInterface
public float getQuadrupolarConstant(Tensor efg)
JmolNMRInterface
getQuadrupolarConstant
in interface JmolNMRInterface
private javajs.util.Lst<Tensor> getInteractionTensorList(java.lang.String type, BS bsA)
type
- bsA
- private BS getAtomSiteBS(BS bsA)
bsA
- public BS getUniqueTensorSet(BS bsAtoms)
JmolNMRInterface
getUniqueTensorSet
in interface JmolNMRInterface
public float getIsoOrAnisoHz(boolean isIso, Atom a1, Atom a2, java.lang.String type, Tensor isc)
JmolNMRInterface
getIsoOrAnisoHz
in interface JmolNMRInterface
private java.lang.String getISCtype(Atom a1, java.lang.String type)
public float getDipolarConstantHz(Atom a1, Atom a2)
getDipolarConstantHz
in interface JmolNMRInterface
public float getDipolarCouplingHz(Atom a1, Atom a2, javajs.util.V3 vField)
getDipolarCouplingHz
in interface JmolNMRInterface
private double getIsotopeData(Atom a, int iType)
a
- iType
- private void getData()
public java.lang.Object getInfo(java.lang.String what)
getInfo
in interface JmolNMRInterface
what
- "C" or "14C" or "all"public float getChemicalShift(Atom atom)
JmolNMRInterface
getChemicalShift
in interface JmolNMRInterface
public float getMagneticShielding(Atom atom)
getMagneticShielding
in interface JmolNMRInterface
public boolean getState(javajs.util.SB sb)
getState
in interface JmolNMRInterface
public boolean setChemicalShiftReference(java.lang.String element, float value)
setChemicalShiftReference
in interface JmolNMRInterface
public javajs.util.Lst<java.lang.Object> getTensorInfo(java.lang.String tensorType, java.lang.String infoType, BS bs)
getTensorInfo
in interface JmolNMRInterface
public java.util.Map<java.lang.String,java.lang.Integer> getMinDistances(MeasurementData md)
getMinDistances
in interface JmolNMRInterface