RdcPanda
Class H1CS

java.lang.Object
  extended by RdcPanda.H1CS

public class H1CS
extends java.lang.Object

This class provides data structures that involve chemical shifts. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).


Nested Class Summary
static class H1CS.csComparator
          The Class csComparator.
static class H1CS.resNoComparator
          The Class resNoComparator.
 
Field Summary
 int protonID
          The proton id.
 int resonID
          The reson id.
 
Constructor Summary
H1CS()
          Instantiates a new h1 cs.
H1CS(int no)
          Instantiates a new h1 cs.
H1CS(int no, java.lang.String resid, java.lang.String atomid)
          Instantiates a new h1 cs.
H1CS(int no, java.lang.String resid, java.lang.String atomid, double cs)
          Instantiates a new h1 cs.
H1CS(int no, java.lang.String resid, java.lang.String atomid, double csL, double csU)
          Instantiates a new h1 cs.
H1CS(int no, java.lang.String resid, java.lang.String atomid, double csL, double csU, double cs_ave, double cs_sigma)
          Instantiates a new h1 cs.
H1CS(int no, java.lang.String resid, java.lang.String atomid, double cs, int proton_id, int reson_id)
          Instantiates a new h1 cs.
 
Method Summary
 double BMRBSatisticsScore(java.util.Vector vecSrcAsg, java.util.Vector vecBMRB)
          compute the fitness score compared to BMRB statistical information.
 boolean checkCSBMRBOrder(java.util.Vector vecOneResidue)
          written by LW.
 void CompareSCAsgsWRefAsgs(java.util.Vector vecSrcAsg, java.util.Vector vecRefAsg, java.util.Vector vecBBAsg)
          compute the statistical information of the sidechain assignment, compared with the reference assignment list.
 void CompareSCAsgsWRefAsgsOld(java.util.Vector vecSrcAsg, java.util.Vector vecRefAsg)
          This is an old function.
 java.util.Vector CSNameConvertFromBMRBNewToPDBNew(java.util.Vector vecAsg)
          Convert naming scheme From BMRBNew To PDBNew, including pseudo protons of methyl groups.
 java.util.Vector CSNameConvertFromPDBNewToBMRBNew(java.util.Vector vecAsg)
          Convert naming scheme From PDBNew To BMRBNew, including pseudo protons of methyl groups.
 java.util.Vector DeleteRepeatAsg(java.util.Vector vecAsg)
          delete repeated resonance assignments.
 java.util.Vector GenerateStereoAsg(java.util.Vector vecSrcAsg)
          generate all stereospecific assignments Note: there might exist two frequencies assigning to the same proton.
 java.lang.String getAtomName()
          Gets the atom name.
 double getCSAverage()
          Gets the cS average.
 double getCSLower()
          Gets the cS lower.
 double getCSSigma()
          Gets the cS sigma.
 double getCSUpper()
          Gets the cS upper.
 double getH1CS()
          Gets the h1 cs.
 int getResidueNo()
          Gets the residue no.
 java.lang.String getResidueType()
          Gets the residue type.
 java.util.Vector h1CSReader_BMRB(java.lang.String filename)
          Another method for reading chemical shifts, in BMRB format.
 java.util.Vector h1CSReader(java.lang.String filename, java.util.Vector vecSeq)
          Read resonance list The required file format is:.
static void main(java.lang.String[] argv)
          The main method for testing.
static void main0(java.lang.String[] argv)
          Main0 for testing.
static void main2(java.lang.String[] argv)
          Main2 for testing.
 void PrintAllAssignment(java.util.Vector vecH1CS)
          print all resonance assignments.
 void PrintAllAssignmentCyana(java.util.Vector vecH1CS)
          print all resonance assignments in CYANA format.
 void PrintAllAssignmentToFileBMRB(java.util.Vector vecH1CS, java.io.PrintWriter out)
          print all resonance assignments to file, in BMRB format.
 void PrintAllAssignmentToFileCyana(java.util.Vector vecH1CS, java.io.PrintWriter out)
          print all resonance assignments to file, in CYANA format.
 java.util.Vector ReadBMRBSatistics(java.lang.String filename)
          read BMRB statistical information.
 void setAtomName(java.lang.String R)
          Sets the atom name.
 void setCS(double cs)
          Sets the cS.
 void setResidueNo(int R)
          Sets the residue no.
 void setResidueType(java.lang.String R)
          Sets the residue type.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

protonID

public int protonID
The proton id.


resonID

public int resonID
The reson id.

Constructor Detail

H1CS

public H1CS()
Instantiates a new h1 cs.


H1CS

public H1CS(int no)
Instantiates a new h1 cs.

Parameters:
no - the no

H1CS

public H1CS(int no,
            java.lang.String resid,
            java.lang.String atomid)
Instantiates a new h1 cs.

Parameters:
no - the no
resid - the resid
atomid - the atomid

H1CS

public H1CS(int no,
            java.lang.String resid,
            java.lang.String atomid,
            double cs,
            int proton_id,
            int reson_id)
Instantiates a new h1 cs.

Parameters:
no - the no
resid - the resid
atomid - the atomid
cs - the cs
proton_id - the proton_id
reson_id - the reson_id

H1CS

public H1CS(int no,
            java.lang.String resid,
            java.lang.String atomid,
            double cs)
Instantiates a new h1 cs.

Parameters:
no - the no
resid - the resid
atomid - the atomid
cs - the cs

H1CS

public H1CS(int no,
            java.lang.String resid,
            java.lang.String atomid,
            double csL,
            double csU)
Instantiates a new h1 cs.

Parameters:
no - the no
resid - the resid
atomid - the atomid
csL - the cs l
csU - the cs u

H1CS

public H1CS(int no,
            java.lang.String resid,
            java.lang.String atomid,
            double csL,
            double csU,
            double cs_ave,
            double cs_sigma)
Instantiates a new h1 cs.

Parameters:
no - the no
resid - the resid
atomid - the atomid
csL - the cs l
csU - the cs u
cs_ave - the cs_ave
cs_sigma - the cs_sigma
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

getAtomName

public java.lang.String getAtomName()
Gets the atom name.

Returns:
the atom name

getH1CS

public double getH1CS()
Gets the h1 cs.

Returns:
the h1 cs

getCSLower

public double getCSLower()
Gets the cS lower.

Returns:
the cS lower

getCSAverage

public double getCSAverage()
Gets the cS average.

Returns:
the cS average

getCSSigma

public double getCSSigma()
Gets the cS sigma.

Returns:
the cS sigma

getCSUpper

public double getCSUpper()
Gets the cS upper.

Returns:
the cS upper

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

setAtomName

public void setAtomName(java.lang.String R)
Sets the atom name.

Parameters:
R - the new atom name

setCS

public void setCS(double cs)
Sets the cS.

Parameters:
cs - the new cS

PrintAllAssignmentToFileCyana

public void PrintAllAssignmentToFileCyana(java.util.Vector vecH1CS,
                                          java.io.PrintWriter out)
print all resonance assignments to file, in CYANA format.

Parameters:
vecH1CS - resonance assignment list
out - the out

PrintAllAssignmentCyana

public void PrintAllAssignmentCyana(java.util.Vector vecH1CS)
print all resonance assignments in CYANA format.

Parameters:
vecH1CS - resonance assignment list

PrintAllAssignmentToFileBMRB

public void PrintAllAssignmentToFileBMRB(java.util.Vector vecH1CS,
                                         java.io.PrintWriter out)
print all resonance assignments to file, in BMRB format.

Parameters:
vecH1CS - resonance assignment list
out - the out

PrintAllAssignment

public void PrintAllAssignment(java.util.Vector vecH1CS)
print all resonance assignments.

Parameters:
vecH1CS - resonance assignment list

h1CSReader

public java.util.Vector h1CSReader(java.lang.String filename,
                                   java.util.Vector vecSeq)
Read resonance list The required file format is:.

Parameters:
filename - the name of the file
vecSeq - backbone structure to update the residue name
Returns:
a vector of resonance list

DeleteRepeatAsg

public java.util.Vector DeleteRepeatAsg(java.util.Vector vecAsg)
delete repeated resonance assignments.

Parameters:
vecAsg - original assignment list
Returns:
new assignment list

GenerateStereoAsg

public java.util.Vector GenerateStereoAsg(java.util.Vector vecSrcAsg)
generate all stereospecific assignments Note: there might exist two frequencies assigning to the same proton.

Parameters:
vecSrcAsg - original assignment list
Returns:
new assignment list with additional stereospecific assignments

CompareSCAsgsWRefAsgs

public void CompareSCAsgsWRefAsgs(java.util.Vector vecSrcAsg,
                                  java.util.Vector vecRefAsg,
                                  java.util.Vector vecBBAsg)
compute the statistical information of the sidechain assignment, compared with the reference assignment list.

Parameters:
vecSrcAsg - original assignment list
vecRefAsg - reference assignment list
vecBBAsg - the vec bb asg

checkCSBMRBOrder

public boolean checkCSBMRBOrder(java.util.Vector vecOneResidue)
written by LW. check the order of chemical shifts for protons in one residue

Parameters:
vecOneResidue - the vec one residue
Returns:
true, if check csbmrb order

CompareSCAsgsWRefAsgsOld

public void CompareSCAsgsWRefAsgsOld(java.util.Vector vecSrcAsg,
                                     java.util.Vector vecRefAsg)
This is an old function. compute the statistical information of the sidechain assignment

Parameters:
vecSrcAsg - original assignment list
vecRefAsg - reference assignment list

h1CSReader_BMRB

public java.util.Vector h1CSReader_BMRB(java.lang.String filename)
Another method for reading chemical shifts, in BMRB format.

Parameters:
filename - the name of the file
Returns:
a vector of h1cs object

BMRBSatisticsScore

public double BMRBSatisticsScore(java.util.Vector vecSrcAsg,
                                 java.util.Vector vecBMRB)
compute the fitness score compared to BMRB statistical information.

Parameters:
vecSrcAsg - the vec src asg
vecBMRB - the vec bmrb
Returns:
matching score

ReadBMRBSatistics

public java.util.Vector ReadBMRBSatistics(java.lang.String filename)
read BMRB statistical information. The required file format is:

Parameters:
filename - the name of the file
Returns:
a vector of H1CS object

CSNameConvertFromBMRBNewToPDBNew

public java.util.Vector CSNameConvertFromBMRBNewToPDBNew(java.util.Vector vecAsg)
Convert naming scheme From BMRBNew To PDBNew, including pseudo protons of methyl groups.

Parameters:
vecAsg - the vec asg
Returns:
the vector

CSNameConvertFromPDBNewToBMRBNew

public java.util.Vector CSNameConvertFromPDBNewToBMRBNew(java.util.Vector vecAsg)
Convert naming scheme From PDBNew To BMRBNew, including pseudo protons of methyl groups.

Parameters:
vecAsg - the vec asg
Returns:
the vector

main0

public static void main0(java.lang.String[] argv)
Main0 for testing.

Parameters:
argv - the argv

main

public static void main(java.lang.String[] argv)
The main method for testing.

Parameters:
argv - the arguments

main2

public static void main2(java.lang.String[] argv)
Main2 for testing.

Parameters:
argv - the argv