RdcPanda
Class BackNoe

java.lang.Object
  extended by RdcPanda.BackNoe

public class BackNoe
extends java.lang.Object

This class provides functions that involves back-computed NOEs. Written by Jianyang (Michael) Zeng (2005-2009).


Constructor Summary
BackNoe()
          Instantiates a new back noe.
BackNoe(double csh1, double csheavy, double csh2)
          Instantiates a new back noe.
BackNoe(double csh1, double csheavy, double csh2, double dist, double inten, int no1, int no2, java.lang.String res1, java.lang.String res2, java.lang.String h1, java.lang.String heavy, java.lang.String h2)
          Instantiates a new back noe.
 
Method Summary
 void addCaNoe(HcchTocsy ca_noe)
          Adds the ca noe.
 void addHnNoe(HnNoe hn_noe)
          Adds the hn noe.
 java.util.Vector DeleteRepeat(java.util.Vector vecBackNoe)
          delete repeated back-computed NOEs.
 java.util.Vector getCaNoeVector()
          Gets the ca noe vector.
 double getCSH1()
          Gets the cS h1.
 double getCSH2()
          Gets the cS h2.
 double getCSHeavy()
          Gets the cS heavy.
 double getDistance()
          Gets the distance.
 java.lang.String getFirstResName()
          Gets the first res name.
 int getFirstResNo()
          Gets the first res no.
 java.lang.String getH1Name()
          Gets the h1 name.
 java.lang.String getH2Name()
          Gets the h2 name.
 java.lang.String getHeavyName()
          Gets the heavy name.
 java.util.Vector getHnNoeVector()
          Gets the hn noe vector.
 double getIntensity()
          Gets the intensity.
 boolean getIsMissing()
          Gets the checks if is missing.
 double getMissingPenalty()
          Gets the missing penalty.
 double getMissingProb()
          Gets the missing prob.
 double getRmsd()
          Gets the rmsd.
 double getRmsdH1()
          Gets the rmsd h1.
 double getRmsdH2()
          Gets the rmsd h2.
 double getRmsdHeavy()
          Gets the rmsd heavy.
 java.lang.String getSecondResName()
          Gets the second res name.
 int getSecondResNo()
          Gets the second res no.
 void setIsMissing(boolean bool)
          Sets the checks if is missing.
 void setMissingPenalty(double distThresh, double penalty4SmallDist, double penalty4LargeDist)
          Sets the missing penalty.
 void setMissingProb(double pr)
          Sets the missing prob.
 void setRmsd(double dst)
          Sets the rmsd.
 void setRmsdAll(double csh1, double csheavy, double csh2)
          Sets the rmsd all.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BackNoe

public BackNoe()
Instantiates a new back noe.


BackNoe

public BackNoe(double csh1,
               double csheavy,
               double csh2)
Instantiates a new back noe.

Parameters:
csh1 - the csh1
csheavy - the csheavy
csh2 - the csh2

BackNoe

public BackNoe(double csh1,
               double csheavy,
               double csh2,
               double dist,
               double inten,
               int no1,
               int no2,
               java.lang.String res1,
               java.lang.String res2,
               java.lang.String h1,
               java.lang.String heavy,
               java.lang.String h2)
Instantiates a new back noe.

Parameters:
csh1 - the csh1
csheavy - the csheavy
csh2 - the csh2
dist - the dist
inten - the inten
no1 - the no1
no2 - the no2
res1 - the res1
res2 - the res2
h1 - the h1
heavy - the heavy
h2 - the h2
Method Detail

setMissingPenalty

public void setMissingPenalty(double distThresh,
                              double penalty4SmallDist,
                              double penalty4LargeDist)
Sets the missing penalty.

Parameters:
distThresh - the dist thresh
penalty4SmallDist - the penalty4 small dist
penalty4LargeDist - the penalty4 large dist

setMissingProb

public void setMissingProb(double pr)
Sets the missing prob.

Parameters:
pr - the new missing prob

addHnNoe

public void addHnNoe(HnNoe hn_noe)
Adds the hn noe.

Parameters:
hn_noe - the hn_noe

addCaNoe

public void addCaNoe(HcchTocsy ca_noe)
Adds the ca noe.

Parameters:
ca_noe - the ca_noe

setRmsd

public void setRmsd(double dst)
Sets the rmsd.

Parameters:
dst - the new rmsd

setIsMissing

public void setIsMissing(boolean bool)
Sets the checks if is missing.

Parameters:
bool - the new checks if is missing

setRmsdAll

public void setRmsdAll(double csh1,
                       double csheavy,
                       double csh2)
Sets the rmsd all.

Parameters:
csh1 - the csh1
csheavy - the csheavy
csh2 - the csh2

getRmsdH1

public double getRmsdH1()
Gets the rmsd h1.

Returns:
the rmsd h1

getRmsdHeavy

public double getRmsdHeavy()
Gets the rmsd heavy.

Returns:
the rmsd heavy

getRmsdH2

public double getRmsdH2()
Gets the rmsd h2.

Returns:
the rmsd h2

getRmsd

public double getRmsd()
Gets the rmsd.

Returns:
the rmsd

getMissingPenalty

public double getMissingPenalty()
Gets the missing penalty.

Returns:
the missing penalty

getDistance

public double getDistance()
Gets the distance.

Returns:
the distance

getIntensity

public double getIntensity()
Gets the intensity.

Returns:
the intensity

getH1Name

public java.lang.String getH1Name()
Gets the h1 name.

Returns:
the h1 name

getHeavyName

public java.lang.String getHeavyName()
Gets the heavy name.

Returns:
the heavy name

getH2Name

public java.lang.String getH2Name()
Gets the h2 name.

Returns:
the h2 name

getFirstResName

public java.lang.String getFirstResName()
Gets the first res name.

Returns:
the first res name

getSecondResName

public java.lang.String getSecondResName()
Gets the second res name.

Returns:
the second res name

getCSH1

public double getCSH1()
Gets the cS h1.

Returns:
the cS h1

getCSHeavy

public double getCSHeavy()
Gets the cS heavy.

Returns:
the cS heavy

getCSH2

public double getCSH2()
Gets the cS h2.

Returns:
the cS h2

getIsMissing

public boolean getIsMissing()
Gets the checks if is missing.

Returns:
the checks if is missing

getFirstResNo

public int getFirstResNo()
Gets the first res no.

Returns:
the first res no

getMissingProb

public double getMissingProb()
Gets the missing prob.

Returns:
the missing prob

getSecondResNo

public int getSecondResNo()
Gets the second res no.

Returns:
the second res no

getHnNoeVector

public java.util.Vector getHnNoeVector()
Gets the hn noe vector.

Returns:
the hn noe vector

getCaNoeVector

public java.util.Vector getCaNoeVector()
Gets the ca noe vector.

Returns:
the ca noe vector

DeleteRepeat

public java.util.Vector DeleteRepeat(java.util.Vector vecBackNoe)
delete repeated back-computed NOEs.

Parameters:
vecBackNoe - original back-computed NOEs
Returns:
new back-computed NOEs