Package org.jmol.quantum
Class NMRNoeMatrix
java.lang.Object
org.jmol.quantum.NMRNoeMatrix
Class for calculating NOE intensities by full matrix relaxation approach.
create an instance of the class:
NoeMatrix n = new NoeMatrix();
Create the atom list:
n.makeAtomList(x);
where x is the number of atoms (methyls count as 1). add the atoms in turn with:
n.addAtom(x,y,z);
where x y and z are the atom coordinates, or:
n.addMethyl(x,y,z,x1,y1,z1,x2,y2,z2);
which does the same for a methyl. T
hen just call calcNOEs:
double[][] results = n.calcNOEs();
This will need to be in a try statement as this routine throws an exception if the atoms have not been set up properly.
- Author:
- YE91009
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Nested Class Summary
Nested Classes -
Method Summary
Modifier and TypeMethodDescriptionvoid
addAtom
(double x, double y, double z) add a proton to the atom listvoid
addEquiv
(double[] xa, double[] ya, double[] za) void
addMethyl
(double x, double y, double z, double x1, double y1, double z1, double x2, double y2, double z2) Add a methyl group to the atom listvoid
calcNOEs()
calculate the NOESY spectrum at a particular mixing time.static NMRNoeMatrix
createMatrix
(Viewer viewer, BS bsMol, String[] labelArray, NMRNoeMatrix.NOEParams params) double
getJmolDistance
(int a, int b) double
getJmolNoe
(int a, int b) void
initArrays
(int n) create an empty atom list for subsequent population with atomsstatic void
toString()
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Method Details
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createMatrix
public static NMRNoeMatrix createMatrix(Viewer viewer, BS bsMol, String[] labelArray, NMRNoeMatrix.NOEParams params) -
getParams
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calcNOEs
calculate the NOESY spectrum at a particular mixing time. Onc eyou have created and built the atom list, this is the only function you need to call. -
initArrays
public void initArrays(int n) create an empty atom list for subsequent population with atoms- Parameters:
n
- the number of atoms to be added
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addAtom
public void addAtom(double x, double y, double z) add a proton to the atom list- Parameters:
x
- the x position of the atom (in Angstroms)y
- the x position of the atom (in Angstroms)z
- the z position of the atom (in Angstroms)
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addMethyl
public void addMethyl(double x, double y, double z, double x1, double y1, double z1, double x2, double y2, double z2) Add a methyl group to the atom list- Parameters:
x
- the x position of atom 1 (in Angstroms)y
- the y position of atom 1 (in Angstroms)z
- the z position of atom 1 (in Angstroms)x1
- the x position of atom 2 (in Angstroms)y1
- the y position of atom 2 (in Angstroms)z1
- the z position of atom 2 (in Angstroms)x2
- the x position of atom 3 (in Angstroms)y2
- the y position of atom 3 (in Angstroms)z2
- the z position of atom 3 (in Angstroms)
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addEquiv
public void addEquiv(double[] xa, double[] ya, double[] za) -
toString
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toStringNormRow
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main
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getJmolDistance
public double getJmolDistance(int a, int b) -
getJmolNoe
public double getJmolNoe(int a, int b)
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