|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectRdcPanda.Peak
public class Peak
This class is modified from LW's original one, and some functions might be redundant with other classes. This class hasn't been completely cleaned. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).
Nested Class Summary | |
---|---|
static class |
Peak.csComparator
The Class csComparator. |
Constructor Summary | |
---|---|
Peak()
Instantiates a new peak. |
|
Peak(double csV)
A constructor designed specifically for the Comparator class used for the Sort and BinarySearch. |
|
Peak(java.lang.String type,
double no)
Instantiates a new peak. |
|
Peak(java.lang.String type,
double no,
boolean isAsg)
Instantiates a new peak. |
|
Peak(java.lang.String type,
double no,
double inten)
Instantiates a new peak. |
|
Peak(java.lang.String type,
double no,
double inten,
boolean isAsg)
Instantiates a new peak. |
Method Summary | |
---|---|
java.util.Vector |
allNoes(java.util.Vector pdbVec,
java.util.Vector asgVec,
double[] coordA,
double noeLimit,
double methylCorrection)
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the. |
java.util.Vector |
allProtonSorted_old(java.util.Vector asgVec)
A method to extract all the protons and convert the Assign object to Peak object Please note that the returned Peak has special identification for the nucleus element. |
java.util.Vector |
allProtonSorted(java.util.Vector asgVec)
A method to extract all the protons and convert the Assign object to Peak object Please note that the returned Peak has special identification for the nucleus element. |
java.util.Vector |
BackCSGenerate(java.util.Vector allCSVec,
int resNo1,
java.lang.String resName1,
java.lang.String atomName1,
int resNo2,
java.lang.String resName2,
java.lang.String atomName2,
java.lang.String heavyName2,
double csSigma)
A function to generate and check back NOE chemical shifts. |
void |
BackNOEGenerate(java.util.Vector h1Vec,
java.util.Vector asgVec,
java.util.Vector pdbVecXray,
java.util.Vector allCSVec,
java.util.Vector allHnVec,
java.util.Vector allHaVec)
generate the back noes from assignment based on x-ray structure. |
boolean |
CheckBackNOE(java.util.Vector hnNoeVec,
java.util.Vector haNoeVec,
java.util.Vector csAllAsg,
int resNo1,
java.lang.String resName1,
java.lang.String atomName1,
int resNo2,
java.lang.String resName2,
java.lang.String atomName2,
double chkErr)
check whether there exists a back Noe from H2 to H1. |
java.util.Vector |
CheckLongRangNOE(java.util.Vector vecNoe,
int Threshold)
for long-range noes, check whether number of neighboring noes is larger than some bound. |
boolean |
checkNoe_old(java.util.Vector pdbVec,
java.util.Vector asgVec,
int no,
java.lang.String nucleus,
int no2,
java.lang.String nucleus2,
double noeLimit,
double methylCorrection,
double[] noe)
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the. |
boolean |
checkNoe(java.util.Vector pdbVec,
int no,
java.lang.String nucleus,
int no2,
java.lang.String nucleus2,
double noeLimit,
double methylCorrection,
double[] noe)
Refined function: for the general case. |
boolean |
checkNoe2(java.util.Vector pdbVec,
int no,
java.lang.String nucleus,
int no2,
java.lang.String nucleus2,
double noeLimit,
double methylCorrection,
double[] noe)
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the. |
boolean |
checkNoeNew(java.util.Vector pdbVec,
int no,
java.lang.String nucleus,
int no2,
java.lang.String nucleus2,
double noeLimit,
double methylCorrection,
double[] noe)
better version of "checkNoe" Refined function: for the general case. |
boolean |
checkNoeNew2(java.util.Vector pdbVec,
int no,
java.lang.String nucleus,
int no2,
java.lang.String nucleus2,
double noeLimit,
double methylCorrection,
double[] noe)
similar to checkNoeNew, with additional0.5 A |
java.util.Vector |
CheckNoeSym(java.util.Vector vecNoe)
refine NOEs and only keep those NOE with symmetry property, for C13 NOESY and sidechain N15 NOESY. |
boolean |
checkSymmetry(java.util.Vector scNoe,
double csBbH,
double csScH,
double winErr)
check whether there exists a symmetric Noe from side-chains to other protons. |
double |
getCS()
Gets the cS. |
double |
getCSFromList(java.util.Vector vecAsg,
int resNo,
java.lang.String atom)
Gets the cS from list. |
java.lang.String |
GetHeavyAtomFromProton(java.lang.String resName,
java.lang.String protonName)
Gets the heavy atom from proton. |
boolean |
getIsAssg()
Gets the checks if is assg. |
java.lang.String |
getNucleus()
Gets the nucleus. |
void |
intensityVsDistance(java.util.Vector h1Vec,
java.util.Vector asgVec,
java.util.Vector pdbVec)
A temporary method to relate NOE intensity with distance,. |
double[] |
internuclearVec(double[] n1,
double[] n2)
Compute the internuclear vector between two atoms. |
boolean |
isCharged(java.lang.String resName)
check whether a residue is a charged amino acid. |
boolean |
isHydrophobic(java.lang.String resName)
check whether a residue is a hydrophobic amino acid. |
double |
length(double[] v1)
Length. |
void |
noeAssign1st(java.util.Vector h1Vec,
java.util.Vector asgVec)
This is an earlier version of NOE assignment method, not filtered by Structure. |
void |
noeAssign2nd(java.util.Vector h1Vec,
java.util.Vector asgVec,
java.util.Vector pdbVec,
java.util.Vector pdbVecXray,
java.util.Vector hnNoeVec,
java.util.Vector cNoeVec)
an NOE assignment method, filtered by Structure. |
void |
noeAssign2ndLW(java.util.Vector h1Vec,
java.util.Vector asgVec,
java.util.Vector pdbVec,
java.util.Vector pdbVecXray)
Lw's original + rotamer library an NOE assignment method, filtered by Structure. |
void |
noeAssign3rd(java.util.Vector h1Vec,
java.util.Vector asgVec,
java.util.Vector pdbVec,
java.util.Vector pdbVecXray,
java.util.Vector hnNoeVec,
java.util.Vector cNoeVec)
an NOE assignment method, filtered by Structure. |
void |
noeAssign3rdLW(java.util.Vector h1Vec,
java.util.Vector asgVec,
java.util.Vector pdbVec,
java.util.Vector pdbVecXray,
java.util.Vector hnNoeVec,
java.util.Vector cNoeVec)
Lincong's original + rotamer library an NOE assignment method, filtered by Structure. |
Matrix |
noeAssignMat(java.util.Vector h1Vec,
java.util.Vector asgVec)
Compute the possbile NOE assignment matrix, an idea not further pursued. |
void |
noeBackCompute(java.util.Vector pdbVec,
java.util.Vector asgVec)
A method for back-computing NOEs, in the current implementation only compute the NOEs from amide protons ("H" in the Pdb file). |
double[] |
noeLimit(double dis)
Noe limit. |
boolean |
noeSearch(java.util.Vector h1Vec,
java.util.Vector asgVec,
int no1,
java.lang.String nucleus1,
int no2,
java.lang.String nucleus2,
double[] noe)
return NOEs between the two nuclei specified in the input if exists. |
java.util.Vector |
rangeSearch(java.util.Vector sortedH1Vec,
double csValue,
double h1Err)
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err]. |
java.util.Vector |
rangeSearchScNoeCS1(java.util.Vector sortedH1Vec,
double csValue,
double h1Err)
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err]. |
java.util.Vector |
rangeSearchScNoeCS2(java.util.Vector sortedH1Vec,
double csValue,
double h1Err)
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err]. |
java.util.Vector |
ringResonanceAsg(double csValue,
double hErr)
ringResonaceAsg: search all the protons with in the range [CS-Err, CS + Err] and assign the H resonance. |
java.util.Vector |
scNoeGenerate(java.util.Vector h1CSVec,
int resNo1,
java.lang.String nucleus1,
double csH1Err,
java.util.Vector pdbVecXray)
A function to generate NOEs from side-chains to HN or HA, //no longer used. |
void |
setCS(double R)
Sets the cS. |
void |
setNucleus(java.lang.String R)
Sets the nucleus. |
java.util.Vector |
SimulatedCaNoe(java.util.Vector pdbVecXray,
java.util.Vector asgVec,
double distBound)
generate the simulated ca noes from x-ray structure. |
java.lang.String |
toString()
|
java.util.Vector |
ubqNoeGenerate(java.util.Vector h1CSVec,
double csH1Err,
java.util.Vector pdbVecXray)
A function to generate ubq NOEs from side-chains to HN or HA,. |
java.lang.String |
xplorNoeStatement_old(int no1,
java.lang.String nucleus1,
int no2,
java.lang.String resid,
java.lang.String nucleus2,
double dis,
double[] disUp)
Xplor noe statement_old. |
java.lang.String |
xplorNoeStatement(int no1,
java.lang.String nucleus1,
int no2,
java.lang.String nucleus2,
double dis)
Xplor noe statement. |
java.lang.String |
xplorNoeStatement(int no1,
java.lang.String resid1,
java.lang.String nucleus1,
int no2,
java.lang.String resid,
java.lang.String nucleus2,
double dis,
double[] disUp)
Xplor noe statement. |
java.lang.String |
xplorNoeStatementNew(int no1,
java.lang.String resid1,
java.lang.String nucleus1,
int no2,
java.lang.String resid,
java.lang.String nucleus2,
double dis)
Xplor noe statement new. |
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public Peak()
public Peak(double csV)
csV
- the cs vpublic Peak(java.lang.String type, double no)
type
- the typeno
- the nopublic Peak(java.lang.String type, double no, boolean isAsg)
type
- the typeno
- the noisAsg
- the is asgpublic Peak(java.lang.String type, double no, double inten)
type
- the typeno
- the nointen
- the intenpublic Peak(java.lang.String type, double no, double inten, boolean isAsg)
type
- the typeno
- the nointen
- the intenisAsg
- the is asgMethod Detail |
---|
public double getCS()
public boolean getIsAssg()
public java.lang.String getNucleus()
public void setCS(double R)
R
- the new cSpublic void setNucleus(java.lang.String R)
R
- the new nucleuspublic java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String GetHeavyAtomFromProton(java.lang.String resName, java.lang.String protonName)
resName
- the res nameprotonName
- the proton name
public java.lang.String xplorNoeStatement(int no1, java.lang.String nucleus1, int no2, java.lang.String nucleus2, double dis)
no1
- the no1nucleus1
- the nucleus1no2
- the no2nucleus2
- the nucleus2dis
- the dis
public double[] noeLimit(double dis)
dis
- the dis
public java.lang.String xplorNoeStatementNew(int no1, java.lang.String resid1, java.lang.String nucleus1, int no2, java.lang.String resid, java.lang.String nucleus2, double dis)
no1
- the no1resid1
- the resid1nucleus1
- the nucleus1no2
- the no2resid
- the residnucleus2
- the nucleus2dis
- the dis
public java.lang.String xplorNoeStatement(int no1, java.lang.String resid1, java.lang.String nucleus1, int no2, java.lang.String resid, java.lang.String nucleus2, double dis, double[] disUp)
no1
- the no1resid1
- the resid1nucleus1
- the nucleus1no2
- the no2resid
- the residnucleus2
- the nucleus2dis
- the disdisUp
- the dis up
public java.lang.String xplorNoeStatement_old(int no1, java.lang.String nucleus1, int no2, java.lang.String resid, java.lang.String nucleus2, double dis, double[] disUp)
no1
- the no1nucleus1
- the nucleus1no2
- the no2resid
- the residnucleus2
- the nucleus2dis
- the disdisUp
- the dis up
public double length(double[] v1)
v1
- the v1
public double[] internuclearVec(double[] n1, double[] n2)
n1
- the coordinate for atom 1n2
- the coordinate for atom 2
public java.util.Vector allProtonSorted_old(java.util.Vector asgVec)
asgVec
- the asg vec
public java.util.Vector allProtonSorted(java.util.Vector asgVec)
asgVec
- the asg vec
public java.util.Vector ringResonanceAsg(double csValue, double hErr)
csValue
- the middle value of cs valuehErr
- error range for the csValue
public java.util.Vector scNoeGenerate(java.util.Vector h1CSVec, int resNo1, java.lang.String nucleus1, double csH1Err, java.util.Vector pdbVecXray)
csH1Err
- the cs h1 errpdbVecXray
- the x-ray Pdb fileh1CSVec
- the h1 cs vecresNo1
- the res no1nucleus1
- the nucleus1
public java.util.Vector BackCSGenerate(java.util.Vector allCSVec, int resNo1, java.lang.String resName1, java.lang.String atomName1, int resNo2, java.lang.String resName2, java.lang.String atomName2, java.lang.String heavyName2, double csSigma)
allCSVec
- the all cs vecresNo1
- the res no1resName1
- the res name1atomName1
- the atom name1resNo2
- the res no2resName2
- the res name2atomName2
- the atom name2heavyName2
- the heavy name2csSigma
- the cs sigma
public java.util.Vector ubqNoeGenerate(java.util.Vector h1CSVec, double csH1Err, java.util.Vector pdbVecXray)
csH1Err
- the cs h1 errpdbVecXray
- the x-ray Pdb fileh1CSVec
- the h1 cs vec
public java.util.Vector rangeSearch(java.util.Vector sortedH1Vec, double csValue, double h1Err)
sortedH1Vec
- is a sorted resonance assignment vector with
monotone increasing sequence number.csValue
- the middle value of cs valueh1Err
- error range for the csValue
public java.util.Vector rangeSearchScNoeCS1(java.util.Vector sortedH1Vec, double csValue, double h1Err)
sortedH1Vec
- is a sorted resonance assignment vector with
monotone increasing sequence number.csValue
- the middle value of cs valueh1Err
- error range for the csValue
public java.util.Vector rangeSearchScNoeCS2(java.util.Vector sortedH1Vec, double csValue, double h1Err)
sortedH1Vec
- is a sorted resonance assignment vector with
monotone increasing sequence number.csValue
- the middle value of cs valueh1Err
- error range for the csValue
public void noeAssign1st(java.util.Vector h1Vec, java.util.Vector asgVec)
h1Vec
- a sorted array of all protonsasgVec
- an array of Assign object for all the residuespublic java.util.Vector SimulatedCaNoe(java.util.Vector pdbVecXray, java.util.Vector asgVec, double distBound)
asgVec
- an array of Assign object for all the residuespdbVecXray
- the Xray structure of ubiquitindistBound
- the dist bound
public void BackNOEGenerate(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVecXray, java.util.Vector allCSVec, java.util.Vector allHnVec, java.util.Vector allHaVec)
h1Vec
- a sorted array of all protonsasgVec
- an array of Assign object for all the residuesallCSVec
- an array saving all chemical shiftspdbVecXray
- the Xray structure of ubiquitinallHnVec
- returning parameter, saving all Hn NOEs inlucding previous and backNOEsallHaVec
- returning parameter, saving all Ha NOEs inlucding previous and backNOEspublic void noeAssign2ndLW(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec, java.util.Vector pdbVecXray)
h1Vec
- a sorted array of all protonsasgVec
- an array of Assign object for all the residuespdbVec
- the backbone structure used to filter the assignmentpdbVecXray
- the Xray structure of ubiquitinpublic void noeAssign2nd(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec, java.util.Vector pdbVecXray, java.util.Vector hnNoeVec, java.util.Vector cNoeVec)
h1Vec
- a sorted array of all protonsasgVec
- an array of Assign object for all the residuespdbVec
- the backbone structure used to filter the assignmentpdbVecXray
- the Xray structure of ubiquitinhnNoeVec
- the hn noe veccNoeVec
- the c noe vecpublic void noeAssign3rdLW(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec, java.util.Vector pdbVecXray, java.util.Vector hnNoeVec, java.util.Vector cNoeVec)
h1Vec
- a sorted array of all protonsasgVec
- an array of Assign object for all the residuespdbVec
- the backbone structure used to filter the assignmentpdbVecXray
- the Xray structure of ubiquitinhnNoeVec
- the hn noe veccNoeVec
- the c noe vecpublic void noeAssign3rd(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec, java.util.Vector pdbVecXray, java.util.Vector hnNoeVec, java.util.Vector cNoeVec)
h1Vec
- a sorted array of all protonsasgVec
- an array of Assign object for all the residuespdbVec
- the backbone structure used to filter the assignmentpdbVecXray
- the Xray structure of ubiquitinhnNoeVec
- the hn noe veccNoeVec
- the c noe vecpublic boolean checkSymmetry(java.util.Vector scNoe, double csBbH, double csScH, double winErr)
scNoe
- the sc noecsBbH
- the cs bb hcsScH
- the cs sc hwinErr
- the win err
public boolean CheckBackNOE(java.util.Vector hnNoeVec, java.util.Vector haNoeVec, java.util.Vector csAllAsg, int resNo1, java.lang.String resName1, java.lang.String atomName1, int resNo2, java.lang.String resName2, java.lang.String atomName2, double chkErr)
hnNoeVec
- the hn noe vechaNoeVec
- the ha noe veccsAllAsg
- the cs all asgresNo1
- the res no1resName1
- the res name1atomName1
- the atom name1resNo2
- the res no2resName2
- the res name2atomName2
- the atom name2chkErr
- the chk err
public boolean isHydrophobic(java.lang.String resName)
resName
- the res name
public boolean isCharged(java.lang.String resName)
resName
- the res name
public boolean checkNoe(java.util.Vector pdbVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
pdbVec
- the pdb coordinatesno
- the first reside no.no2
- the second residue nonoeLimit
- the upper limit for NOEsmethylCorrection
- the methyl correctionnucleus
- the nucleusnucleus2
- the nucleus2noe
- the noe
public boolean checkNoeNew(java.util.Vector pdbVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
pdbVec
- the pdb coordinatesno
- the first reside no.no2
- the second residue nonoeLimit
- the upper limit for NOEsmethylCorrection
- the methyl correctionnucleus
- the nucleusnucleus2
- the nucleus2noe
- the noe
public boolean checkNoeNew2(java.util.Vector pdbVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
pdbVec
- the pdb coordinatesno
- the first reside no.no2
- the second residue nonoeLimit
- the upper limit for NOEsmethylCorrection
- the methyl correctionnucleus
- the nucleusnucleus2
- the nucleus2noe
- the noe
public double getCSFromList(java.util.Vector vecAsg, int resNo, java.lang.String atom)
vecAsg
- the vec asgresNo
- the res noatom
- the atom
public java.util.Vector CheckLongRangNOE(java.util.Vector vecNoe, int Threshold)
vecNoe
- previous noe assignmentThreshold
- threshold number of neighboring noes
public java.util.Vector CheckNoeSym(java.util.Vector vecNoe)
vecNoe
- original NOE assignments.
public boolean checkNoe_old(java.util.Vector pdbVec, java.util.Vector asgVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
asgVec
- the sorted resonance assignmentpdbVec
- the pdb coordinatesno
- the reside no.noeLimit
- the limitation set for NOEsnucleus
- the nucleusno2
- the no2nucleus2
- the nucleus2methylCorrection
- the methyl correctionnoe
- the noe
public boolean checkNoe2(java.util.Vector pdbVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
pdbVec
- the pdb coordinatesno
- the reside no.noeLimit
- the limitation set for NOEsnucleus
- the nucleusno2
- the no2nucleus2
- the nucleus2methylCorrection
- the methyl correctionnoe
- the noe
public java.util.Vector allNoes(java.util.Vector pdbVec, java.util.Vector asgVec, double[] coordA, double noeLimit, double methylCorrection)
asgVec
- the sorted resonance assignmentpdbVec
- the pdb coordinatescoordA
- the position (coordinate) of nucluesnoeLimit
- the limitation set for NOEsmethylCorrection
- the methyl correction
public void noeBackCompute(java.util.Vector pdbVec, java.util.Vector asgVec)
pdbVec
- the Pdb structure.asgVec
- the assignment table.public boolean noeSearch(java.util.Vector h1Vec, java.util.Vector asgVec, int no1, java.lang.String nucleus1, int no2, java.lang.String nucleus2, double[] noe)
h1Vec
- the sorted all proton CSsasgVec
- resonance assignment table and the NOE peak listno1
- the first residuenucleus1
- the nuclues of residue no1, assume to be HN.no2
- the second residuenucleus2
- the nuclues of residue no2noe
- for returning the find NOE intensity if exist
public void intensityVsDistance(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec)
h1Vec
- a sorted all H1 cs arrayasgVec
- an assign Vector with assignment tablem and both HN and HA NOEs peak listpdbVec
- the Pdb filepublic Matrix noeAssignMat(java.util.Vector h1Vec, java.util.Vector asgVec)
h1Vec
- the h1 vecasgVec
- the asg vec
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |