Class NmrMolecule
- java.lang.Object
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- org.openscience.jmol.app.janocchio.NmrMolecule
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public class NmrMolecule extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description (package private) class
NmrMolecule.DihedralCouple
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Field Summary
Fields Modifier and Type Field Description private javajs.util.BS
bsMol
protected java.lang.String
CHequation
protected java.util.Vector<java.lang.Double>
couples
protected java.util.Vector<NmrMolecule.DihedralCouple>
couplesWhole
protected java.util.Vector<java.lang.Double>
distances
private java.lang.String[]
labelArray
(package private) NMR_JmolPanel
nmrPanel
protected NMRNoeMatrix
noeMatrix
(package private) NMRNoeMatrix.NOEParams
params
protected NMR_Viewer
viewer
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Constructor Summary
Constructors Constructor Description NmrMolecule(NMR_JmolPanel nmrPanel, javajs.util.BS bsMol, java.lang.String[] labelArray, boolean forNOE)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
addAtomstoMatrix()
Generate noeMatrix and map fields for DistanceJMolecule.void
addCouple(Atom[] atoms)
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()
java.util.Vector<java.lang.Double>
getCouples()
protected NmrMolecule.DihedralCouple
getDihedralCouple(Atom[] atoms)
java.util.Vector<java.lang.Double>
getDistances()
double
getJmolDistance(int a, int b)
Calc using Jmol atom indexdouble
getJmolNoe(int a, int b)
void
setCHequation(java.lang.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 Detail
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viewer
protected final NMR_Viewer viewer
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nmrPanel
final NMR_JmolPanel nmrPanel
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bsMol
private final javajs.util.BS bsMol
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labelArray
private final java.lang.String[] labelArray
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distances
protected final java.util.Vector<java.lang.Double> distances
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couples
protected final java.util.Vector<java.lang.Double> couples
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couplesWhole
protected final java.util.Vector<NmrMolecule.DihedralCouple> couplesWhole
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noeMatrix
protected NMRNoeMatrix noeMatrix
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CHequation
protected java.lang.String CHequation
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params
NMRNoeMatrix.NOEParams params
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Constructor Detail
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NmrMolecule
public NmrMolecule(NMR_JmolPanel nmrPanel, javajs.util.BS bsMol, java.lang.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 Detail
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getDihedralCouple
protected NmrMolecule.DihedralCouple getDihedralCouple(Atom[] atoms)
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addAtomstoMatrix
protected void addAtomstoMatrix()
Generate noeMatrix and map fields for DistanceJMolecule.
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getDistances
public java.util.Vector<java.lang.Double> getDistances()
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getCouples
public java.util.Vector<java.lang.Double> getCouples()
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calcNOEs
public void calcNOEs()
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addCouple
public void addCouple(Atom[] atoms)
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addJmolCouple
public void addJmolCouple(int a1, int a2, int a3, int a4)
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calcCouple
public double[] calcCouple(Atom[] atoms)
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calcJmolCouple
public double[] calcJmolCouple(int a1, int a2, int a3, int a4)
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setCorrelationTimeTauPS
public void setCorrelationTimeTauPS(double t)
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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)
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setNoesy
public void setNoesy(boolean b)
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setCHequation
public void setCHequation(java.lang.String eq)
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getJmolNoe
public double getJmolNoe(int a, int b)
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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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