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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectRdcPanda.Pdb
public class Pdb
This class provides data structures and functions for processing and generating PDB files and extracting backbone angles etc. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).
Nested Class Summary | |
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static class |
Pdb.PdbComparator
The Class PdbComparator. |
Constructor Summary | |
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Pdb()
Instantiates a new pdb. |
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Pdb(int No)
Instantiates a new pdb. |
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Pdb(int No,
java.lang.String res,
java.util.Vector aa)
Instantiates a new pdb. |
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Pdb(int No,
java.lang.String res,
java.util.Vector aa,
double ra)
Instantiates a new pdb. |
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Pdb(Pdb pp)
Instantiates a new pdb. |
Method Summary | |
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java.util.Vector |
AlaninizeStructure(java.util.Vector vecPdb,
boolean[] resIndex,
java.lang.String rotSrc)
replace all non-NOE residues in pdb with alaline. |
java.util.Vector |
AlaninizeStructureResName(java.util.Vector vecPdb,
java.lang.String rotSrc)
replace all non-NOE residues in pdb with alaline, according to the residue names. |
java.util.Vector |
AllRotamersStructure(java.util.Vector pdbBBVec,
java.lang.String rotSrc)
put all rotamers at each redidue. |
java.util.Vector |
AssembleTwoSSEs(java.util.Vector vecSSEPdb1,
java.util.Vector vecSSEPdb2,
int brkResNo,
java.util.Vector<Dipolar> rdcVecNh,
java.util.Vector<Dipolar> rdcVecCh,
double Syy,
double Szz)
assemble two sses with some phi psi deviations in the break point, the assembled structure has minimum rdc rmsd and vdw energy. |
java.util.Vector |
CombinRotBB(java.util.Vector rotamVec,
java.util.Vector pdbVecN,
int resNo)
plug rotamer into backbone. |
java.util.Vector |
compDistPatternForRotam_old(java.util.Vector rotamVec,
int resNo,
java.util.Vector pdbVec,
double DistBound)
Compute all distance patterns for a rotamer, distances are from each proton in the rotamer to backbone protons including HA,HN, HB. |
java.util.Vector |
compDistPatternForRotam(java.util.Vector rotamVec,
int resNo,
java.util.Vector pdbVec,
double DistBound)
Compute all distance patterns for a rotamer, distances are from each proton in the rotamer to backbone protons including HA,HN, HB. |
java.util.Vector |
compDistPatternForSSEPacking(java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double DistBound)
Compute all distance patterns for two secondary structure elements, whose coordinates are fixed. |
java.util.Vector |
compDistPatternFromPairRotams(int resNoA,
int resNoB,
Pdb pdbA,
Pdb pdbB,
double DistBound)
Compute all distance patterns for a pair of rotamers, distances are from each proton in the rotamer to backbone protons including HA,HN, HB rotamers are in the same coordinate system,includes both from A->B and from B->A. |
double |
compOverAllRmsdBetweenRotXray(java.util.Vector pdbBBVec,
java.util.Vector asgVec,
java.lang.String rotSrc,
java.util.Vector hnNoeVec,
java.util.Vector cNoeVec,
java.util.Vector pdbVecXray,
double distBound,
int pickNum)
Compute a structure, given the backbone and rotamers at all residue positions. |
double |
compResRmsd(Pdb pdb1,
Pdb pdb2)
Compute rmsd between two rotamers only for non-proton atoms, assume they are in the same coordinate system. |
double |
compResRmsdPairWise(Pdb pdb1,
Pdb pdb2)
Compute rmsd between two rotamers (for all atoms), assume they are in the same coordinate system. |
double |
compRmsdBetwTwoPdbs(java.util.Vector vecPdb1,
java.util.Vector vecPdb2,
boolean isHeavy)
Compute rmsd between two pdb structures with the same length and in the same coordinate system. |
boolean |
compRmsdRotXrayBB(java.util.Vector vecPdbXray,
java.util.Vector vecRotam,
int resNo,
double[] rmsd,
boolean isHeavy)
Compute rmsd between a rotamer and corresponding side-chain in x-ray structure. |
double |
dihedralAngle(double[] n2CO1,
double[] n2CA,
double[] ca2CO)
Method for computing dihedral angles between two planes defined by three vectors. |
double[] |
dirCos(double[] vec)
cal the directioal cosines of the vector vec. |
void |
doCalNOEScores(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
* compute the NOE satisfaction scores for all structure in an ensemble. |
void |
doReadPdbFragments(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
HANA algorithm for the NOE assignment and output the NOE table. |
java.util.Vector |
extractBackbone(java.util.Vector pdbVec)
Extract backbone atoms from a PDB file. |
java.util.Vector |
extractFragment(java.util.Vector pdbVec,
int residueFirst,
int residueLast)
Extract backbone atoms from a PDB file. |
java.util.Vector |
extractFragment(java.util.Vector pdbVec,
int residueFirst,
int residueLast,
double[] firstCoords,
double[] lastCoords)
Extract backbone atoms from a PDB file. |
java.util.Vector |
getAtomVec()
Gets the atom vec. |
java.lang.String |
getResidue()
Gets the residue. |
int |
getResidueNo()
Gets the residue no. |
double |
getRotamerRatio()
Gets the rotamer ratio. |
void |
h1Distance(java.lang.String pdbLists,
java.lang.String aaType,
java.lang.String nucType)
A method to compute all the angles from ultrahigh resolution PDBs. |
double |
interAngle(double[] v1,
double[] v2)
calculate the angles between two vectors v1 and v2 The returned angle is the [0,Pi] region. |
double[] |
internuclearVec(double[] n1,
double[] n2)
Compute the internuclear vector between two atoms. |
boolean |
isInAtomVec(java.util.Vector vecAtom,
java.lang.String atomName)
Checks if is in atom vec. |
boolean |
isInPdbClusters(java.util.Vector vecEnsemblePdb,
java.util.Vector vecPdb,
double rmsThreshold)
tell whether a structure is within the clusters of previous ensemble. |
boolean |
isInPointClusters(java.util.Vector vecPoints,
Cartesian cc,
double rmsThreshold)
tell whether a point is within the clusters of previous ensemble. |
double |
length(double[] v1)
Length. |
java.util.Vector |
LoopComputFromNOEPatterns(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector seqVec,
java.util.Vector vecPdbBbSSE,
java.util.Vector asgVec,
java.lang.String rotSrc,
java.util.Vector NoesyVec,
double distBound,
int firstResNo,
int secondResNo)
Compute a structure, given the backbone and rotamers at all residue positions. |
static void |
main(java.lang.String[] argv)
The main method. |
static void |
main0(java.lang.String[] argv)
Main0. |
static void |
main00(java.lang.String[] argv)
Main00. |
static void |
main1(java.lang.String[] argv)
Main1. |
boolean |
measureDis(java.util.Vector pdbVec,
int noA,
java.lang.String residueA,
java.lang.String nucleusA,
int noB,
java.lang.String residueB,
java.lang.String nucleusB,
double[] distance)
Compute the NOE distance between two nuclei (A, B) in a structure specified by pdbVec There are two numbers: 15 Degree and 45 Degree for correct the most possible orientation changing. |
boolean |
measureDisFromRotam(java.util.Vector pdbVec,
java.util.Vector rotamVecA,
java.util.Vector rotamVecB,
int noA,
java.lang.String residueA,
java.lang.String nucleusA,
int noB,
java.lang.String residueB,
java.lang.String nucleusB,
double[] distance)
Compute the NOE distance between two nuclei (A, B) in a structure specified by pdbVec There are two numbers: 15 Degree and 45 Degree for correct the most possible orientation changing. |
boolean |
measureDisXray(java.util.Vector pdbVec,
int noA,
java.lang.String residueA,
java.lang.String nucleusA,
int noB,
java.lang.String residueB,
java.lang.String nucleusB,
double[] distance)
Compute the NOE distance between two nuclei (A, B) in a structure specified by pdbVec. |
boolean |
measurePackDisAllRotamers(java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
int noA,
java.lang.String nucleusA,
int noB,
java.lang.String nucleusB,
double lower,
double upper,
double[] disRMS,
double[] distance)
measure the packing distances between two sses all rotamers are put into the sse backbones The number themselves are set rather arbitrariry. |
java.util.Vector |
nameConvert(java.util.Vector pdbVec)
Lincong's original function: Convert the old PDB namaclature to new one bugs fixed... |
java.util.Vector |
nameConvert22(java.util.Vector pdbVec)
Convert the old PDB namaclature to new one. |
java.util.Vector |
nameConvert2PDBNew(java.util.Vector pdbVec)
Convert the old PDB namaclature to new one zeng changed the code,. |
java.util.Vector |
nameConvert4SmallRotLibCS(java.util.Vector pdbVec)
Convert the old PDB namaclature to new one zeng changed the code, such that all methel group protons become one proxy proton. |
java.util.Vector |
nameConvert4SmallRotLibStr(java.util.Vector pdbVec)
Convert the old PDB namaclature to new one for computing the structure rmsd. |
java.util.Vector |
nameConvertCS(java.util.Vector pdbVec)
Convert the old PDB namaclature to new one zeng changed the code, such that all methel group protons become one proxy proton. |
java.util.Vector |
nameConvertOrder(java.util.Vector pdbVec)
In this function, only the order of atom name is changed, and H-> HN eg 2HB=>HB2, 3HB=>HB3. |
java.util.Vector |
nameConvertStr(java.util.Vector pdbVec)
Convert the old PDB namaclature to new one zeng changed the code, such that all methel group protons become one proxy proton. |
java.lang.String |
NameFromBMRBToPDB(java.lang.String resName,
java.lang.String atomName)
Convert the BMRB-NEW namaclature to PDB-NEW namaclature return new atom name. |
java.lang.String |
NameFromPdbToBMRB(java.lang.String resid,
java.lang.String atomNameInput)
Convert the PDB-NEW namaclature to BMRB-NEW namaclature: e.g. |
java.lang.String |
NameFromPDBToPDB(java.lang.String resName,
java.lang.String atomName)
Convert the PDB-NEW namaclature to PDB-NEW namaclature change the methel groups return new atom name. |
java.util.Vector |
newPdb(java.util.Vector pdbVec,
Matrix R)
compute new PDB coordinates after the rotation by matrix R. |
java.util.Vector |
newPdbByTranslation(java.util.Vector pdbVec,
double[] vT)
compute new PDB coordinates after the translation. |
java.util.Vector |
OutputBackbone(java.util.Vector vecPdb)
output the backbone of a pdb structure. |
java.util.Vector |
OutputBackboneNoCB(java.util.Vector vecPdb)
output the backbone of a pdb structure. |
double |
PhiPsiCalPDB(double[] n2CO1,
double[] n2CA,
double[] ca2CO)
Compute Phi and Psi directly from three backbone vectors (not NH vector). |
java.util.Vector |
PhiPsiTotalPdb(java.util.Vector pdbVec)
Compute all the backbone Phi and Psi angles from PDB from the backbone backbone bond vectors between heavy atoms. |
void |
print(java.util.Vector pdbVec)
A method for printing the coordinates in PDB format the magic Number comes from PDB file format. |
void |
printArray(double[] n1)
Prints the array. |
void |
printToFile(java.util.Vector pdbVec,
java.lang.String fileName,
java.io.PrintWriter out)
A method for printing the coordinates in PDB format the magic Number comes from PDB file format. |
java.util.Vector |
radiiFromCb(java.util.Vector pdbVec,
java.lang.String residue,
java.lang.String hAtom)
We can also derived the minimum and maximam using analytic expression but using rotamer as appeared in PDB may have certain advantage. |
java.util.Vector |
radiiFromNH(java.util.Vector pdbVec,
java.lang.String residue,
java.lang.String hAtom)
Compute the distance from the nucleu NH to other nucleu. |
java.util.Vector |
readPdb(java.lang.String pdbFile)
Reading PDB file in PDB Format!!! the magic number for substring is based on format for pdb file. |
java.util.Vector |
readPdbAndNoeHarmFromEnsemble(java.lang.String pdbFile)
Reading PDB file and other parameters in PDB Format from ensemble!!!. |
java.util.Vector |
readPdbAndNoeRmsdFromEnsemble(java.lang.String pdbFile)
Reading PDB file and other parameters in PDB Format from ensemble!!!. |
java.util.Vector |
readPdbAndParametersFromEnsemble(java.lang.String pdbFile)
Reading PDB file and other parameters in PDB Format from ensemble!!!. |
java.util.Vector |
readPdbAndParaXplor(java.lang.String pdbFile,
double[] vdwSc,
double[] noeSc)
Read pdb and para xplor. |
void |
readPdbEnergy(java.lang.String pdbFile,
double[] scEnerg,
int rowPos,
int colPos)
Read pdb energy. |
java.util.Vector |
readPdbFromEnsemble(java.lang.String pdbFile)
Reading PDB file in PDB Format from ensemble!!! the magic number for substring is based on format for pdb file. |
java.util.Vector |
readRotamerPdb(java.lang.String pdbFile)
Reading Rotamer file in PDB Format!!!. |
java.util.Vector |
RefineRotamerSelection(java.util.Vector vecGrowPdb,
java.util.Vector vecRot4AllResidues,
int[] rotID)
refine the rotamer selection until no steric clash happens. |
java.util.Vector |
RefineRotamerSelectionRandom(java.util.Vector vecGrowPdb,
java.util.Vector vecRot4AllResidues,
int[] rotID)
refine the rotamer selection until no steric clash happens, using Gaussian random sampling at each rotamer position. |
boolean |
RefineRotamerSelectionRecur(java.util.Vector vecGrowPdb,
java.util.Vector vecRot4AllResidues,
int resInd,
java.util.Vector vecSavePdb,
boolean[] resNoeIndex)
refine the rotamer selection until no steric clash happens, by enumerating all possible rotamers in the order of NOE matching scores. |
java.util.Vector |
RefineRotamerSelectionSearch(java.util.Vector vecGrowPdb,
int resNo,
java.lang.String rotSrc,
int depth)
wait... |
java.lang.String |
residueNameFromSeq(java.util.Vector seqVec,
int resNo)
get the residue name from protein sequence. |
java.util.Vector |
residueNameUpdate_from_structure(java.util.Vector pdbVec1,
java.util.Vector pdbVec2)
A temporary method for converting the residue name in the RDC-derived PDB file, which are "ALA", to real Residue name, also to build the conformation of proline and glycine residue. |
java.util.Vector |
residueNameUpdate(java.util.Vector seqVec,
java.util.Vector pdbVec2)
work for bb only? A temporary method for converting the residue name in the RDC-derived PDB file, which are "ALA", to real Residue name, also to build the conformation of proline and glycine residue. |
java.util.Vector |
residueNameUpdateNoStr(java.util.Vector seqVec,
java.util.Vector pdbVec2)
change residue name according to sequnce, without changing structure. |
java.util.Vector |
RotamSelectAndStructure(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector pdbBBVec,
java.util.Vector asgVec,
java.lang.String rotSrc,
java.util.Vector NoesyVec,
double distBound,
int pickNum,
double constant)
Compute a structure, given the backbone and rotamers at all residue positions. |
java.util.Vector |
RotamSelectAndStructureNoClash(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector pdbBBVec,
java.util.Vector asgVec,
java.lang.String rotSrc,
java.util.Vector NoesyVec,
double distBound,
int pickNum,
boolean[] resIndex)
Rotam select and structure no clash. |
void |
setAtomVec(java.util.Vector aVec)
Sets the atom vec. |
void |
setResidue(java.lang.String res)
Sets the residue. |
void |
setResidueNo(int no)
Sets the residue no. |
void |
setRotamerRatio(double ra)
Sets the rotamer ratio. |
java.util.Vector |
sixAngles(java.util.Vector pdbVec)
pdbVec is a Vector of Pdb Objects e.g. |
void |
statsOfSixAngles(java.lang.String pdbLists)
A method to compute all the angles from ultrahigh resolution PDBs. |
java.lang.String |
toString()
|
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Pdb()
public Pdb(int No)
No
- the nopublic Pdb(int No, java.lang.String res, java.util.Vector aa)
No
- the nores
- the resaa
- the aapublic Pdb(int No, java.lang.String res, java.util.Vector aa, double ra)
No
- the nores
- the resaa
- the aara
- the rapublic Pdb(Pdb pp)
pp
- the ppMethod Detail |
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public int getResidueNo()
public java.util.Vector getAtomVec()
public java.lang.String getResidue()
public double getRotamerRatio()
public void setResidueNo(int no)
no
- the new residue nopublic void setResidue(java.lang.String res)
res
- the new residuepublic void setAtomVec(java.util.Vector aVec)
aVec
- the new atom vecpublic void setRotamerRatio(double ra)
ra
- the new rotamer ratiopublic java.lang.String toString()
toString
in class java.lang.Object
public void printArray(double[] n1)
n1
- the n1public double length(double[] v1)
v1
- the v1
public double[] dirCos(double[] vec)
vec
- the vec
public double interAngle(double[] v1, double[] v2)
v1
- the v1v2
- the v2
public double[] internuclearVec(double[] n1, double[] n2)
n1
- the coordinate for atom 1n2
- the coordinate for atom 2
public java.util.Vector readRotamerPdb(java.lang.String pdbFile)
pdbFile
- the pdb file
public java.util.Vector readPdb(java.lang.String pdbFile)
pdbFile
- the pdb file
public void doCalNOEScores(java.lang.String src, java.lang.String strOut, java.lang.String strInput) throws JampackException
src
- location of the input filestrOut
- location of the output filestrInput
- input file name
JampackException
- the jampack exceptionpublic static void main1(java.lang.String[] argv)
argv
- the argvpublic static void main00(java.lang.String[] argv)
argv
- the argvpublic static void main(java.lang.String[] argv)
argv
- the argumentspublic java.util.Vector readPdbAndNoeRmsdFromEnsemble(java.lang.String pdbFile)
pdbFile
- the pdb file
public java.util.Vector readPdbAndNoeHarmFromEnsemble(java.lang.String pdbFile)
pdbFile
- the pdb file
public java.util.Vector readPdbAndParaXplor(java.lang.String pdbFile, double[] vdwSc, double[] noeSc)
pdbFile
- the pdb filevdwSc
- the vdw scnoeSc
- the noe sc
public void readPdbEnergy(java.lang.String pdbFile, double[] scEnerg, int rowPos, int colPos)
pdbFile
- the pdb filescEnerg
- the sc energrowPos
- the row poscolPos
- the col pospublic java.util.Vector readPdbAndParametersFromEnsemble(java.lang.String pdbFile)
pdbFile
- the pdb file
public java.util.Vector readPdbFromEnsemble(java.lang.String pdbFile)
pdbFile
- the pdb file
public java.util.Vector newPdb(java.util.Vector pdbVec, Matrix R)
pdbVec
- original PDB coordinatesR
- the rotation matrix
public java.util.Vector newPdbByTranslation(java.util.Vector pdbVec, double[] vT)
pdbVec
- original PDB coordinatesvT
- the center in which the PDB is being tranlated to
public double dihedralAngle(double[] n2CO1, double[] n2CA, double[] ca2CO)
n2CO1
- the N(i)->CO(i-1) vectorn2CA
- the N(i)->CA(i) vectorca2CO
- the CA(i)->CO(i) vector
public double PhiPsiCalPDB(double[] n2CO1, double[] n2CA, double[] ca2CO)
n2CO1
- N->CO vectorn2CA
- N->CA vectorca2CO
- CA->CO vector
public java.util.Vector PhiPsiTotalPdb(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector extractBackbone(java.util.Vector pdbVec)
pdbVec
- the original Pdb vector
public java.util.Vector extractFragment(java.util.Vector pdbVec, int residueFirst, int residueLast, double[] firstCoords, double[] lastCoords)
pdbVec
- the original Pdb vectorresidueFirst
- the residue firstresidueLast
- the residue lastfirstCoords
- the first coordslastCoords
- the last coords
public java.util.Vector extractFragment(java.util.Vector pdbVec, int residueFirst, int residueLast)
pdbVec
- the original Pdb vectorresidueFirst
- the residue firstresidueLast
- the residue last
public java.util.Vector nameConvert2PDBNew(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector nameConvert4SmallRotLibCS(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector nameConvert4SmallRotLibStr(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector nameConvertCS(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector nameConvertStr(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector nameConvertOrder(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector nameConvert(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.lang.String NameFromPdbToBMRB(java.lang.String resid, java.lang.String atomNameInput)
resid
- the residatomNameInput
- the atom name input
public java.lang.String NameFromBMRBToPDB(java.lang.String resName, java.lang.String atomName)
resName
- the res nameatomName
- the atom name
public java.lang.String NameFromPDBToPDB(java.lang.String resName, java.lang.String atomName)
resName
- the res nameatomName
- the atom name
public java.util.Vector nameConvert22(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector residueNameUpdate_from_structure(java.util.Vector pdbVec1, java.util.Vector pdbVec2)
pdbVec1
- a pdb object with correct residue name,
which can be replaced with a protein sequence filepdbVec2
- a pdb object with all the residue name as "ALA"
public java.lang.String residueNameFromSeq(java.util.Vector seqVec, int resNo)
seqVec
- vector of residues, namely protein sequenceresNo
- residue no
public java.util.Vector residueNameUpdate(java.util.Vector seqVec, java.util.Vector pdbVec2)
seqVec
- vector of residues, namely protein sequencepdbVec2
- a pdb object with all the residue name as "ALA"
public java.util.Vector residueNameUpdateNoStr(java.util.Vector seqVec, java.util.Vector pdbVec2)
seqVec
- vector of residues, namely protein sequencepdbVec2
- a pdb object with all the residue name as "ALA"
public boolean isInPdbClusters(java.util.Vector vecEnsemblePdb, java.util.Vector vecPdb, double rmsThreshold)
vecEnsemblePdb
- ensemble of structures tovecPdb
- the pdb structurermsThreshold
- rmsd thresold to one structure in the ensemble
public boolean isInPointClusters(java.util.Vector vecPoints, Cartesian cc, double rmsThreshold)
vecPoints
- ensemble of point tocc
- the obj pointrmsThreshold
- rmsd thresold to one structure in the ensemble
public void doReadPdbFragments(java.lang.String src, java.lang.String strOut, java.lang.String strInput) throws JampackException
src
- location of the input filestrOut
- location of the output filestrInput
- input file name
JampackException
- the jampack exceptionpublic double compRmsdBetwTwoPdbs(java.util.Vector vecPdb1, java.util.Vector vecPdb2, boolean isHeavy)
vecPdb1
- the first structurevecPdb2
- the second structureisHeavy
- whether compute rmsd between heavy atoms or all atoms
public boolean compRmsdRotXrayBB(java.util.Vector vecPdbXray, java.util.Vector vecRotam, int resNo, double[] rmsd, boolean isHeavy)
vecPdbXray
- xray backbone structure, each proton uses specific name, eg hg21...vecRotam
- rotamer vector that keeps the same naming scheme as xray backboneisHeavy
- whether compute rmsd between heavy atoms or all atomsresNo
- the res normsd
- the rmsd
public double compResRmsd(Pdb pdb1, Pdb pdb2)
pdb1
- rotmaer 1pdb2
- rotmaer 2
public double compResRmsdPairWise(Pdb pdb1, Pdb pdb2)
pdb1
- rotmaer 1pdb2
- rotmaer 2
public java.util.Vector compDistPatternForSSEPacking(java.util.Vector pdbVecA, java.util.Vector pdbVecB, double DistBound)
pdbVecA
- the first ssepdbVecB
- the secondary sseDistBound
- the bound to compute noe distance beween two protons
public java.util.Vector compDistPatternFromPairRotams(int resNoA, int resNoB, Pdb pdbA, Pdb pdbB, double DistBound)
DistBound
- the bound to compute noe distance beween two protonsresNoA
- the res no aresNoB
- the res no bpdbA
- the pdb apdbB
- the pdb b
public java.util.Vector compDistPatternForRotam(java.util.Vector rotamVec, int resNo, java.util.Vector pdbVec, double DistBound)
rotamVec
- the rotamer vector in pdb format, note: only *one* rotamerresNo
- residue No of the rotamerpdbVec
- the pdb vector of the whole protein backboneDistBound
- the bound to compute noe distance beween two protons
public java.util.Vector compDistPatternForRotam_old(java.util.Vector rotamVec, int resNo, java.util.Vector pdbVec, double DistBound)
rotamVec
- the rotamer vector in pdb format, note: only *one* rotamerresNo
- residue No of the rotamerpdbVec
- the pdb vector of the whole protein backboneDistBound
- the bound to compute noe distance beween two protons
public boolean measureDisXray(java.util.Vector pdbVec, int noA, java.lang.String residueA, java.lang.String nucleusA, int noB, java.lang.String residueB, java.lang.String nucleusB, double[] distance)
pdbVec
- the PDB structurenoA
- the residue NO of nucleus AresidueA
- the residue type of nucleus AnucleusA
- the name of the nucleus of nucleus AnoB
- the residue NO of nucleus AresidueB
- the residue type of nucleus AnucleusB
- the name of the nucleus of nucleus Adistance
- save the back-computed NOE distance
public boolean measurePackDisAllRotamers(java.util.Vector pdbVecA, java.util.Vector pdbVecB, int noA, java.lang.String nucleusA, int noB, java.lang.String nucleusB, double lower, double upper, double[] disRMS, double[] distance)
noA
- the residue NO of nucleus AnucleusA
- the name of the nucleus of residue AnoB
- the residue NO of nucleus AnucleusB
- the name of the nucleus of residue Blower
- lower bound of NOE constraintupper
- upper bound of NOE constraintdistance
- save distance deviationpdbVecA
- the pdb vec apdbVecB
- the pdb vec bdisRMS
- the dis rms
public boolean measureDis(java.util.Vector pdbVec, int noA, java.lang.String residueA, java.lang.String nucleusA, int noB, java.lang.String residueB, java.lang.String nucleusB, double[] distance)
pdbVec
- the PDB structurenoA
- the residue NO of nucleus AresidueA
- the residue type of nucleus AnucleusA
- the name of the nucleus of residue AnoB
- the residue NO of nucleus AresidueB
- the residue type of nucleus BnucleusB
- the name of the nucleus of residue Bdistance
- save the back-computed NOE distance
public double compOverAllRmsdBetweenRotXray(java.util.Vector pdbBBVec, java.util.Vector asgVec, java.lang.String rotSrc, java.util.Vector hnNoeVec, java.util.Vector cNoeVec, java.util.Vector pdbVecXray, double distBound, int pickNum)
pdbBBVec
- the PDB backbone structureasgVec
- resonace listrotSrc
- the path of rotmaer libraryhnNoeVec
- hn Noe vectorcNoeVec
- ha noe vectorpdbVecXray
- x-ray structure, including both backbone and side-chainsdistBound
- the distance bound for back computing distance pattern for each rotamerpickNum
- the best number of rotamers picked for computation
public boolean isInAtomVec(java.util.Vector vecAtom, java.lang.String atomName)
vecAtom
- the vec atomatomName
- the atom name
public java.util.Vector OutputBackbone(java.util.Vector vecPdb)
vecPdb
- pdb structure, new naming scheme, eg HB2,HB3...
public java.util.Vector OutputBackboneNoCB(java.util.Vector vecPdb)
vecPdb
- pdb structure, new naming scheme, eg HB2,HB3...
public java.util.Vector CombinRotBB(java.util.Vector rotamVec, java.util.Vector pdbVecN, int resNo)
rotamVec
- the rotamer vector in pdb format, note: only *one* rotamerresNo
- residue No of the rotamerpdbVecN
- the pdb vec n
public java.util.Vector AllRotamersStructure(java.util.Vector pdbBBVec, java.lang.String rotSrc)
pdbBBVec
- the PDB backbone structurerotSrc
- the path of rotmaer library
public java.util.Vector RotamSelectAndStructure(double csErrH, double csErrN, double csErrCA, java.util.Vector pdbBBVec, java.util.Vector asgVec, java.lang.String rotSrc, java.util.Vector NoesyVec, double distBound, int pickNum, double constant)
csErrH
- csErrN csErrCA error window size at each dimensionpdbBBVec
- the PDB backbone structureasgVec
- resonace listrotSrc
- the path of rotmaer libraryNoesyVec
- Noe vector including both ha and hn noesdistBound
- the distance bound for back computing distance pattern for each rotamerpickNum
- the best number of rotamers picked for computationcsErrN
- the cs err ncsErrCA
- the cs err caconstant
- the constant
public java.util.Vector AlaninizeStructure(java.util.Vector vecPdb, boolean[] resIndex, java.lang.String rotSrc) throws JampackException
vecPdb
- original (bb) pdb structrueresIndex
- whether the residue index is non-ala, the value is true if yes,
otherwise falserotSrc
- the rot src
JampackException
- the jampack exceptionpublic java.util.Vector AlaninizeStructureResName(java.util.Vector vecPdb, java.lang.String rotSrc) throws JampackException
vecPdb
- original (bb) pdb structruerotSrc
- the rot src
JampackException
- the jampack exceptionpublic java.util.Vector RotamSelectAndStructureNoClash(double csErrH, double csErrN, double csErrCA, java.util.Vector pdbBBVec, java.util.Vector asgVec, java.lang.String rotSrc, java.util.Vector NoesyVec, double distBound, int pickNum, boolean[] resIndex) throws JampackException
csErrH
- csErrN csErrCA error window size at each dimensionpdbBBVec
- the PDB backbone structureasgVec
- resonace listrotSrc
- the path of rotmaer libraryNoesyVec
- Noe vector including both ha and hn noesdistBound
- the distance bound for back computing distance pattern for each rotamerresIndex
- residue index to be analizedcsErrN
- the cs err ncsErrCA
- the cs err capickNum
- the pick num
JampackException
- the jampack exceptionpublic java.util.Vector RefineRotamerSelection(java.util.Vector vecGrowPdb, java.util.Vector vecRot4AllResidues, int[] rotID)
vecGrowPdb
- previous structure after placing rotmaers into the backbonevecRot4AllResidues
- vector of rotamers at each residuerotID
- store the rotamer that is current in the residue
public java.util.Vector RefineRotamerSelectionRandom(java.util.Vector vecGrowPdb, java.util.Vector vecRot4AllResidues, int[] rotID)
vecGrowPdb
- previous structure after placing rotmaers into the backbonevecRot4AllResidues
- vector of rotamers at each residuerotID
- store the rotamer that is current in the residue
public java.util.Vector RefineRotamerSelectionSearch(java.util.Vector vecGrowPdb, int resNo, java.lang.String rotSrc, int depth)
vecGrowPdb
- previous structure after placing rotmaers into the backboneresNo
- the res norotSrc
- the rot srcdepth
- the depth
public boolean RefineRotamerSelectionRecur(java.util.Vector vecGrowPdb, java.util.Vector vecRot4AllResidues, int resInd, java.util.Vector vecSavePdb, boolean[] resNoeIndex)
vecGrowPdb
- previous structure after placing rotmaers into the backbonevecRot4AllResidues
- vector of rotamers at each residuevecSavePdb
- vector to save returing pdbsresInd
- the res indresNoeIndex
- the res noe index
public java.util.Vector AssembleTwoSSEs(java.util.Vector vecSSEPdb1, java.util.Vector vecSSEPdb2, int brkResNo, java.util.Vector<Dipolar> rdcVecNh, java.util.Vector<Dipolar> rdcVecCh, double Syy, double Szz) throws JampackException
vecSSEPdb1
- the first ssevecSSEPdb2
- the second sserdcVecNh
- a vector of NH RDC valuesrdcVecCh
- a vector of CH RDC valuesSzz
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsbrkResNo
- the brk res no
JampackException
- the jampack exceptionpublic java.util.Vector LoopComputFromNOEPatterns(double csErrH, double csErrN, double csErrCA, java.util.Vector seqVec, java.util.Vector vecPdbBbSSE, java.util.Vector asgVec, java.lang.String rotSrc, java.util.Vector NoesyVec, double distBound, int firstResNo, int secondResNo)
csErrH
- csErrN csErrCA error window size at each dimensionseqVec
- vector of protein sequencevecPdbBbSSE
- the secondary structure backbone structure solved from RDC-EXACTasgVec
- resonace listrotSrc
- the path of rotmaer libraryNoesyVec
- Noe vector including both ha and hn noesdistBound
- the distance bound for back computing distance pattern for each rotamerfirstResNo
- the first residue no of the loopsecondResNo
- the first residue no of the loopcsErrN
- the cs err ncsErrCA
- the cs err ca
public boolean measureDisFromRotam(java.util.Vector pdbVec, java.util.Vector rotamVecA, java.util.Vector rotamVecB, int noA, java.lang.String residueA, java.lang.String nucleusA, int noB, java.lang.String residueB, java.lang.String nucleusB, double[] distance)
pdbVec
- the PDB structurenoA
- the residue NO of nucleus AresidueA
- the residue type of nucleus AnucleusA
- the name of the nucleus of residue AnoB
- the residue NO of nucleus AresidueB
- the residue type of nucleus BnucleusB
- the name of the nucleus of residue Bdistance
- save the back-computed NOE distancerotamVecA
- the rotam vec arotamVecB
- the rotam vec b
public void statsOfSixAngles(java.lang.String pdbLists)
pdbLists
- the pdb listspublic java.util.Vector radiiFromCb(java.util.Vector pdbVec, java.lang.String residue, java.lang.String hAtom)
pdbVec
- is an array of PDB objectresidue
- the type of residuehAtom
- the h atom
public java.util.Vector radiiFromNH(java.util.Vector pdbVec, java.lang.String residue, java.lang.String hAtom)
pdbVec
- is an array of PDB objectresidue
- the type of residuehAtom
- the h atom
public java.util.Vector sixAngles(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public void printToFile(java.util.Vector pdbVec, java.lang.String fileName, java.io.PrintWriter out)
pdbVec
- a vector of Pdb objectfileName
- the file nameout
- the outpublic void print(java.util.Vector pdbVec)
pdbVec
- a vector of Pdb objectpublic void h1Distance(java.lang.String pdbLists, java.lang.String aaType, java.lang.String nucType)
pdbLists
- the pdb listsaaType
- the aa typenucType
- the nuc typepublic static void main0(java.lang.String[] argv)
argv
- the argv
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