meshi.applications.corpus
Class CorrectRottenRamachandrans

java.lang.Object
  meshi.applications.corpus.CorrectRottenRamachandrans

public class CorrectRottenRamachandrans
extends java.lang.Object

Field Summary

private CommandList	commands
private Corpus	corpus
private EnergyCreator[]	creators
private double	CUTOFF_GLY
private double	CUTOFF_NON_GLY
private double	DIVERSITY_RMS_IN_LIB
private DunbrackLib	dunbrack
private double	FACTOR_LARGE_CONTIG_RMS_CUTOFF_IN_OVERLAP
private int	MAX_LIB_SIZE_FOR_EACH_ROTTEN
private double	RMS_CUTOFF_IN_OVERLAP

Constructor Summary

CorrectRottenRamachandrans(CommandList commands, Corpus corpus)

CorrectRottenRamachandrans(CommandList commands, Corpus corpus, DunbrackLib lib)
The Dunbrack lib is needed for Rot1 only.

Method Summary

private double	calcRMS(Protein prot, int start, int end, double[][] refCoors)
private void	correctFrag(Protein prot, java.util.Vector<java.lang.Integer> contig)
int[]	detectAndCorrectRottenResidues(Protein prot) This correct the rotten-ramach residues as mentioned on top.
int[]	detectRottenResidues(Protein prot) This method returns an array with the residue numbers of the rotten-ramach residues.
private double[][]	saveCaCbCoordinates(Protein prot, int resStart, int resEnd)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CUTOFF_NON_GLY

private final double CUTOFF_NON_GLY

See Also:

Constant Field Values

CUTOFF_GLY

private final double CUTOFF_GLY

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Constant Field Values

MAX_LIB_SIZE_FOR_EACH_ROTTEN

private final int MAX_LIB_SIZE_FOR_EACH_ROTTEN

See Also:

Constant Field Values

DIVERSITY_RMS_IN_LIB

private final double DIVERSITY_RMS_IN_LIB

See Also:

Constant Field Values

RMS_CUTOFF_IN_OVERLAP

private final double RMS_CUTOFF_IN_OVERLAP

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Constant Field Values

FACTOR_LARGE_CONTIG_RMS_CUTOFF_IN_OVERLAP

private final double FACTOR_LARGE_CONTIG_RMS_CUTOFF_IN_OVERLAP

See Also:

Constant Field Values

corpus

private Corpus corpus

creators

private EnergyCreator[] creators

dunbrack

private DunbrackLib dunbrack

commands

private CommandList commands

Constructor Detail

CorrectRottenRamachandrans

public CorrectRottenRamachandrans(CommandList commands,
                                  Corpus corpus)

CorrectRottenRamachandrans

public CorrectRottenRamachandrans(CommandList commands,
                                  Corpus corpus,
                                  DunbrackLib lib)

The Dunbrack lib is needed for Rot1 only.

Method Detail

detectRottenResidues

public int[] detectRottenResidues(Protein prot)

This method returns an array with the residue numbers of the rotten-ramach residues. NO changes to the coordinates are made.

detectAndCorrectRottenResidues

public int[] detectAndCorrectRottenResidues(Protein prot)

This correct the rotten-ramach residues as mentioned on top. It returns an array with the residue numbers of the rotten-ramach residues.

correctFrag

private void correctFrag(Protein prot,
                         java.util.Vector<java.lang.Integer> contig)

calcRMS

private double calcRMS(Protein prot,
                       int start,
                       int end,
                       double[][] refCoors)

saveCaCbCoordinates

private double[][] saveCaCbCoordinates(Protein prot,
                                       int resStart,
                                       int resEnd)