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java.lang.ObjectRdcPanda.H1CS
public class H1CS
This class provides data structures that involve chemical shifts. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).
Nested Class Summary | |
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static class |
H1CS.csComparator
The Class csComparator. |
static class |
H1CS.resNoComparator
The Class resNoComparator. |
Field Summary | |
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int |
protonID
The proton id. |
int |
resonID
The reson id. |
Constructor Summary | |
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H1CS()
Instantiates a new h1 cs. |
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H1CS(int no)
Instantiates a new h1 cs. |
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H1CS(int no,
java.lang.String resid,
java.lang.String atomid)
Instantiates a new h1 cs. |
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H1CS(int no,
java.lang.String resid,
java.lang.String atomid,
double cs)
Instantiates a new h1 cs. |
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H1CS(int no,
java.lang.String resid,
java.lang.String atomid,
double csL,
double csU)
Instantiates a new h1 cs. |
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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. |
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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 | |
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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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public int protonID
public int resonID
Constructor Detail |
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public H1CS()
public H1CS(int no)
no
- the nopublic H1CS(int no, java.lang.String resid, java.lang.String atomid)
no
- the noresid
- the residatomid
- the atomidpublic H1CS(int no, java.lang.String resid, java.lang.String atomid, double cs, int proton_id, int reson_id)
no
- the noresid
- the residatomid
- the atomidcs
- the csproton_id
- the proton_idreson_id
- the reson_idpublic H1CS(int no, java.lang.String resid, java.lang.String atomid, double cs)
no
- the noresid
- the residatomid
- the atomidcs
- the cspublic H1CS(int no, java.lang.String resid, java.lang.String atomid, double csL, double csU)
no
- the noresid
- the residatomid
- the atomidcsL
- the cs lcsU
- the cs upublic H1CS(int no, java.lang.String resid, java.lang.String atomid, double csL, double csU, double cs_ave, double cs_sigma)
no
- the noresid
- the residatomid
- the atomidcsL
- the cs lcsU
- the cs ucs_ave
- the cs_avecs_sigma
- the cs_sigmaMethod Detail |
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public int getResidueNo()
public java.lang.String getResidueType()
public java.lang.String getAtomName()
public double getH1CS()
public double getCSLower()
public double getCSAverage()
public double getCSSigma()
public double getCSUpper()
public void setResidueNo(int R)
R
- the new residue nopublic void setResidueType(java.lang.String R)
R
- the new residue typepublic void setAtomName(java.lang.String R)
R
- the new atom namepublic void setCS(double cs)
cs
- the new cSpublic void PrintAllAssignmentToFileCyana(java.util.Vector vecH1CS, java.io.PrintWriter out)
vecH1CS
- resonance assignment listout
- the outpublic void PrintAllAssignmentCyana(java.util.Vector vecH1CS)
vecH1CS
- resonance assignment listpublic void PrintAllAssignmentToFileBMRB(java.util.Vector vecH1CS, java.io.PrintWriter out)
vecH1CS
- resonance assignment listout
- the outpublic void PrintAllAssignment(java.util.Vector vecH1CS)
vecH1CS
- resonance assignment listpublic java.util.Vector h1CSReader(java.lang.String filename, java.util.Vector vecSeq)
filename
- the name of the filevecSeq
- backbone structure to update the residue name
public java.util.Vector DeleteRepeatAsg(java.util.Vector vecAsg)
vecAsg
- original assignment list
public java.util.Vector GenerateStereoAsg(java.util.Vector vecSrcAsg)
vecSrcAsg
- original assignment list
public void CompareSCAsgsWRefAsgs(java.util.Vector vecSrcAsg, java.util.Vector vecRefAsg, java.util.Vector vecBBAsg)
vecSrcAsg
- original assignment listvecRefAsg
- reference assignment listvecBBAsg
- the vec bb asgpublic boolean checkCSBMRBOrder(java.util.Vector vecOneResidue)
vecOneResidue
- the vec one residue
public void CompareSCAsgsWRefAsgsOld(java.util.Vector vecSrcAsg, java.util.Vector vecRefAsg)
vecSrcAsg
- original assignment listvecRefAsg
- reference assignment listpublic java.util.Vector h1CSReader_BMRB(java.lang.String filename)
filename
- the name of the file
public double BMRBSatisticsScore(java.util.Vector vecSrcAsg, java.util.Vector vecBMRB)
vecSrcAsg
- the vec src asgvecBMRB
- the vec bmrb
public java.util.Vector ReadBMRBSatistics(java.lang.String filename)
filename
- the name of the file
public java.util.Vector CSNameConvertFromBMRBNewToPDBNew(java.util.Vector vecAsg)
vecAsg
- the vec asg
public java.util.Vector CSNameConvertFromPDBNewToBMRBNew(java.util.Vector vecAsg)
vecAsg
- the vec asg
public static void main0(java.lang.String[] argv)
argv
- the argvpublic static void main(java.lang.String[] argv)
argv
- the argumentspublic static void main2(java.lang.String[] argv)
argv
- the argv
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