RdcPanda
Class Residue

java.lang.Object
  extended by RdcPanda.Residue

public class Residue
extends java.lang.Object

A very simple Residue class with the Notation like Val1, Ala25. Written by Lincong Wang (2001-2005).


Nested Class Summary
static class Residue.caComparator
          The Class caComparator.
static class Residue.cbComparator
          The Class cbComparator.
 
Constructor Summary
Residue()
          Instantiates a new residue.
Residue(int no)
          A constructor designed specifically for the Comparator class used for the Sort and BinarySearch.
Residue(int no, java.lang.String type)
          Instantiates a new residue.
Residue(int no, java.lang.String type, java.util.Vector hcVec)
          Instantiates a new residue.
Residue(int no, java.lang.String type, java.util.Vector pkVec, java.util.Map nVec)
          Instantiates a new residue.
Residue(int no, java.lang.String type, java.util.Vector pkVec, java.util.Vector hcVec)
          Instantiates a new residue.
 
Method Summary
 java.util.Map fromCB(java.lang.String type)
          The atom identifiers are based on the IUPAC-IUB and X-plor For different nomenclature this functions should modified correspondingly input: residue type output: all atoms belong to one amino acid.
 java.util.Vector getHcchVec()
          Gets the hcch vec.
 java.util.Map getNoeMap()
          Gets the noe map.
 java.util.Vector getPeakVec()
          Gets the peak vec.
 int getResidueNo()
          Gets the residue no.
 java.lang.String getResidueType()
          Gets the residue type.
 java.util.Map nucluesByAA(java.lang.String type)
          The atom identifiers are based on the IUPAC-IUB and X-plor For different nomenclature this functions should modified correspondingly input: residue type output: all atoms belong to one amino acid.
 void setHcchVec(java.util.Vector vec)
          Sets the hcch vec.
 void setPeakVec(java.util.Vector vec)
          Sets the peak vec.
 void setResidueNo(int R)
          Sets the residue no.
 void setResidueType(java.lang.String R)
          Sets the residue type.
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Residue

public Residue()
Instantiates a new residue.


Residue

public Residue(int no)
A constructor designed specifically for the Comparator class used for the Sort and BinarySearch.

Parameters:
no - the no

Residue

public Residue(int no,
               java.lang.String type)
Instantiates a new residue.

Parameters:
no - the no
type - the type

Residue

public Residue(int no,
               java.lang.String type,
               java.util.Vector hcVec)
Instantiates a new residue.

Parameters:
no - the no
type - the type
hcVec - the hc vec

Residue

public Residue(int no,
               java.lang.String type,
               java.util.Vector pkVec,
               java.util.Vector hcVec)
Instantiates a new residue.

Parameters:
no - the no
type - the type
pkVec - the pk vec
hcVec - the hc vec

Residue

public Residue(int no,
               java.lang.String type,
               java.util.Vector pkVec,
               java.util.Map nVec)
Instantiates a new residue.

Parameters:
no - the no
type - the type
pkVec - the pk vec
nVec - the n vec
Method Detail

getResidueNo

public int getResidueNo()
Gets the residue no.

Returns:
the residue no

getResidueType

public java.lang.String getResidueType()
Gets the residue type.

Returns:
the residue type

getPeakVec

public java.util.Vector getPeakVec()
Gets the peak vec.

Returns:
the peak vec

getHcchVec

public java.util.Vector getHcchVec()
Gets the hcch vec.

Returns:
the hcch vec

getNoeMap

public java.util.Map getNoeMap()
Gets the noe map.

Returns:
the noe map

setResidueNo

public void setResidueNo(int R)
Sets the residue no.

Parameters:
R - the new residue no

setResidueType

public void setResidueType(java.lang.String R)
Sets the residue type.

Parameters:
R - the new residue type

setPeakVec

public void setPeakVec(java.util.Vector vec)
Sets the peak vec.

Parameters:
vec - the new peak vec

setHcchVec

public void setHcchVec(java.util.Vector vec)
Sets the hcch vec.

Parameters:
vec - the new hcch vec

nucluesByAA

public java.util.Map nucluesByAA(java.lang.String type)
The atom identifiers are based on the IUPAC-IUB and X-plor For different nomenclature this functions should modified correspondingly input: residue type output: all atoms belong to one amino acid.

Parameters:
type - the type
Returns:
the map

fromCB

public java.util.Map fromCB(java.lang.String type)
The atom identifiers are based on the IUPAC-IUB and X-plor For different nomenclature this functions should modified correspondingly input: residue type output: all atoms belong to one amino acid.

Parameters:
type - the type
Returns:
the map

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object