Class NmrMolecule
java.lang.Object
org.openscience.jmol.app.janocchio.NmrMolecule
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Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionprivate final javajs.util.BS
protected String
protected final Vector<NmrMolecule.DihedralCouple>
private final String[]
(package private) final NMR_JmolPanel
protected NMRNoeMatrix
(package private) NMRNoeMatrix.NOEParams
protected final NMR_Viewer
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Constructor Summary
ConstructorsConstructorDescriptionNmrMolecule
(NMR_JmolPanel nmrPanel, javajs.util.BS bsMol, String[] labelArray, boolean forNOE) -
Method Summary
Modifier and TypeMethodDescriptionprotected void
Generate noeMatrix and map fields for DistanceJMolecule.void
void
addJmolCouple
(int a1, int a2, int a3, int a4) void
addJmolDistance
(int a, int b) Add using Jmol atom indexdouble[]
calcCouple
(Atom[] atoms) double[]
calcJmolCouple
(int a1, int a2, int a3, int a4) void
calcNOEs()
protected NmrMolecule.DihedralCouple
getDihedralCouple
(Atom[] atoms) double
getJmolDistance
(int a, int b) Calc using Jmol atom indexdouble
getJmolNoe
(int a, int b) void
setCHequation
(String eq) void
setCorrelationTimeTauPS
(double t) void
setCutoffAng
(double c) sets the cutoff distance beyond which atom interactions are not consideredvoid
setMixingTimeSec
(double t) sets the mixing time for the NOE experimentvoid
setNMRfreqMHz
(double f) set the NMR frequency for the NOE simulationvoid
setNoesy
(boolean b) void
setRhoStar
(double c)
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Field Details
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viewer
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nmrPanel
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bsMol
private final javajs.util.BS bsMol -
labelArray
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distances
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couples
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couplesWhole
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noeMatrix
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CHequation
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params
NMRNoeMatrix.NOEParams params
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Constructor Details
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NmrMolecule
public NmrMolecule(NMR_JmolPanel nmrPanel, javajs.util.BS bsMol, String[] labelArray, boolean forNOE) - Parameters:
nmrPanel
-bsMol
-labelArray
- optional array of atom labels, one per atom in the current frameforNOE
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Method Details
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getDihedralCouple
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addAtomstoMatrix
protected void addAtomstoMatrix()Generate noeMatrix and map fields for DistanceJMolecule. -
getDistances
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getCouples
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calcNOEs
public void calcNOEs() -
addCouple
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addJmolCouple
public void addJmolCouple(int a1, int a2, int a3, int a4) -
calcCouple
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calcJmolCouple
public double[] calcJmolCouple(int a1, int a2, int a3, int a4) -
setCorrelationTimeTauPS
public void setCorrelationTimeTauPS(double t) -
setMixingTimeSec
public void setMixingTimeSec(double t) sets the mixing time for the NOE experiment- Parameters:
t
- the mixing time in seconds. Typically 0.5-1.5 seconds for small molecules
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setNMRfreqMHz
public void setNMRfreqMHz(double f) set the NMR frequency for the NOE simulation- Parameters:
f
- the frequency in MHz
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setCutoffAng
public void setCutoffAng(double c) sets the cutoff distance beyond which atom interactions are not considered- Parameters:
c
- the cutoff distance in Angstroms
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setRhoStar
public void setRhoStar(double c) -
setNoesy
public void setNoesy(boolean b) -
setCHequation
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getJmolNoe
public double getJmolNoe(int a, int b) -
addJmolDistance
public void addJmolDistance(int a, int b) Add using Jmol atom index- Parameters:
a
-b
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getJmolDistance
public double getJmolDistance(int a, int b) Calc using Jmol atom index- Parameters:
a
-b
-- Returns:
- NOE-based distance, averaged for equivalent H atoms
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