Package ffx.potential.bonded
Class SturmMethod
java.lang.Object
ffx.potential.bonded.SturmMethod
SturmMethod class.
- Since:
- 1.0
- Author:
- Mallory R. Tollefson
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Constructor Summary
ConstructorDescriptionSturmMethod constructor with termination criteria for polynomial solver. -
Method Summary
Modifier and TypeMethodDescriptiondouble[][]
getr_o()
Used only in JUnit testing.int
solveSturm
(int order, double[] poly_coeffs, double[] roots) Solve using the Sturm method.writePDBBackbone
(double[][] r_n, double[][] r_a, double[][] r_c, int stt_res, int end_res, MolecularAssembly molAss, int counter, boolean writeFile) Write out loop coordinates and determine oxygen placement.
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Constructor Details
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SturmMethod
public SturmMethod()SturmMethod constructor with termination criteria for polynomial solver.
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Method Details
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getr_o
public double[][] getr_o()Used only in JUnit testing.- Returns:
- oxygen coordinates.
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solveSturm
public int solveSturm(int order, double[] poly_coeffs, double[] roots) Solve using the Sturm method.- Parameters:
order
- the order of the polynomial.poly_coeffs
- an array ofinvalid reference
double
roots
- an array ofinvalid reference
double
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writePDBBackbone
public File writePDBBackbone(double[][] r_n, double[][] r_a, double[][] r_c, int stt_res, int end_res, MolecularAssembly molAss, int counter, boolean writeFile) Write out loop coordinates and determine oxygen placement.- Parameters:
r_n
- an array ofinvalid reference
double
r_a
- an array ofinvalid reference
double
r_c
- an array ofinvalid reference
double
stt_res
- a int.end_res
- a int.molAss
- aMolecularAssembly
object.counter
- a int.writeFile
- a boolean.- Returns:
- the File.
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