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java.lang.ObjectRdcPanda.PdbRmsd
public class PdbRmsd
A program for determining the relative positions of a helix and a beta sheet based on the NOE distances between them. The main idea is: (1) Compute the centers of the two groups of nuclei with NOEs. Compute the RMSD between two PDBs based on SVD. In the simple case their AA sequence are the same except that one can be only a partial of the other (shorter than the other). When do the rotation the center is very important so we need to compute the center first as in the algorithm. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).
Field Summary | |
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boolean |
isSkipOutEnsembe
The is skip out ensembe. |
Constructor Summary | |
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PdbRmsd()
Instantiates a new pdb rmsd. |
Method Summary | |
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java.util.Vector |
calcMinPackingRms(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE)
calculate the minimum rms between two sses, for checking packing symmetry In both SSEs, all rotamers are places. |
double[] |
centerCal(double[][] pdbVec)
compute the center of a PDB coordinates when the coordinates are represented as an array of nx3. |
double[] |
centerCal(java.util.Vector pdbVec)
compute the center of a PDB object (the 3D coordinates). |
double[] |
centerCalNew(java.util.Vector vecCC)
compute the center of a PDB coordinates when the coordinates are represented as an array of nx3. |
double |
centerFit(java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
java.util.Vector hbVec,
boolean debug)
compute the H-bond energy term between the two paired strands. |
java.util.Vector |
centerFitVec(java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
java.util.Vector hbVec,
boolean debug)
compute the H-bond energy term between the two paired strands. |
double[] |
dirCos(double[] vec)
cal the directioal cosines of the vector vec. |
java.util.Vector |
getPdbVecA()
Gets the pdb vec a. |
java.util.Vector |
getPdbVecB()
Gets the pdb vec b. |
double |
interAngle(double[] v1,
double[] v2)
calculate the angles between two vectors v1 and v2 The returned angle is in the [0,Pi] range or the cosine itself. |
java.util.Vector |
positionByAmbiNOEAllRotamers(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE,
java.lang.String strPass,
java.util.Vector vecSeq,
double resol_cluster)
pack two SSEs based on Amgibuous NOE restratints. |
java.util.Vector |
positionByNOE_old(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE)
use heavy atom to replace pseduo protons Compute the new center of atoms involved in NOE distances. |
java.util.Vector |
positionByNOE(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE)
use exact name for pseduo protons Compute the new center of atoms involved in NOE distances. |
java.util.Vector |
positionByNOEAllRotamers(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE,
java.lang.String strPass,
java.util.Vector vecSeq,
double resol_cluster)
pack two SSEs based on NOE restratints In both SSEs, all rotamers are placed. |
java.util.Vector |
positionByNOEAllRotamersGrid(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE)
pack two SSEs based on NOE restratints In both SSEs, all rotamers are places. |
java.util.Vector |
positionByNOEAllRotamersSaved(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE,
java.lang.String strPass,
java.util.Vector vecSeq)
Position by noe all rotamers saved. |
java.util.Vector |
positionByNOENew(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE)
Note: all rotamers are put in both structures. |
java.util.Vector |
positionByNOEPatterns(java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
java.util.Vector assignVec,
java.util.Vector NoesyVec,
double csErrH,
double csErrN,
double csErrCA,
double distBound,
int pickNum,
double[] max_score)
pack two sses based on back-computed NOE patterns. |
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 boolean isSkipOutEnsembe
Constructor Detail |
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public PdbRmsd()
Method Detail |
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public java.util.Vector getPdbVecA()
public java.util.Vector getPdbVecB()
public double interAngle(double[] v1, double[] v2)
v1
- the v1v2
- the v2
public double[] dirCos(double[] vec)
vec
- the vec
public double[] centerCal(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public double[] centerCal(double[][] pdbVec)
pdbVec
- the pdb vec
public double[] centerCalNew(java.util.Vector vecCC)
vecCC
- the vec cc
public double centerFit(java.util.Vector pdbVecA, java.util.Vector pdbVecB, java.util.Vector hbVec, boolean debug)
pdbVecA
- strand ApdbVecB
- strand B, A's partnerhbVec
- the vector of Hbond informationdebug
- if true it print the information for debuging
public java.util.Vector centerFitVec(java.util.Vector pdbVecA, java.util.Vector pdbVecB, java.util.Vector hbVec, boolean debug)
pdbVecA
- strand ApdbVecB
- strand B, A's partnerhbVec
- the vector of Hbond informationdebug
- the debug
public java.util.Vector positionByNOENew(java.util.Vector noeVec, java.util.Vector pdbVecA, java.util.Vector pdbVecB, double[] noeRms, boolean debugNOE, java.util.Vector vecUpdateNOE)
noeVec
- the NOE distance restraints between the fragment A and BpdbVecA
- one fragmentpdbVecB
- another fragmentnoeRms
- saving the min NOE rmsddebugNOE
- if true it will print out the NOE fitting RmsdsvecUpdateNOE
- the vec update noe
public java.util.Vector positionByNOE_old(java.util.Vector noeVec, java.util.Vector pdbVecA, java.util.Vector pdbVecB, double[] noeRms, boolean debugNOE, java.util.Vector vecUpdateNOE)
noeVec
- the NOE distance restraints between the fragment A and BpdbVecA
- one fragmentpdbVecB
- another fragmentnoeRms
- saving the NOE rmsddebugNOE
- if true it will print out the NOE fitting RmsdsvecUpdateNOE
- the vec update noe
public java.util.Vector positionByNOE(java.util.Vector noeVec, java.util.Vector pdbVecA, java.util.Vector pdbVecB, double[] noeRms, boolean debugNOE, java.util.Vector vecUpdateNOE)
noeVec
- the NOE distance restraints between the fragment A and BpdbVecA
- one fragmentpdbVecB
- another fragmentnoeRms
- saving the NOE rmsddebugNOE
- if true it will print out the NOE fitting RmsdsvecUpdateNOE
- the vec update noe
public java.util.Vector positionByNOEAllRotamers(java.util.Vector noeVec, java.util.Vector pdbVecA, java.util.Vector pdbVecB, double[] noeRms, boolean debugNOE, java.util.Vector vecUpdateNOE, java.lang.String strPass, java.util.Vector vecSeq, double resol_cluster) throws JampackException
noeVec
- the NOE distance restraints between the fragment A and BpdbVecA
- one fragmentpdbVecB
- another fragmentnoeRms
- saving the NOE rmsddebugNOE
- if true it will print out the NOE fitting RmsdsvecSeq
- sequence of residue namesresol_cluster
- the resolution of each clustervecUpdateNOE
- the vec update noestrPass
- the str pass
JampackException
- the jampack exceptionpublic java.util.Vector positionByAmbiNOEAllRotamers(java.util.Vector noeVec, java.util.Vector pdbVecA, java.util.Vector pdbVecB, double[] noeRms, boolean debugNOE, java.util.Vector vecUpdateNOE, java.lang.String strPass, java.util.Vector vecSeq, double resol_cluster) throws JampackException
noeVec
- the NOE distance restraints between the fragment A and BpdbVecA
- one fragmentpdbVecB
- another fragmentnoeRms
- saving the NOE rmsddebugNOE
- if true it will print out the NOE fitting RmsdsvecSeq
- sequence of residue namesresol_cluster
- the resolution of each clustervecUpdateNOE
- the vec update noestrPass
- the str pass
JampackException
- the jampack exceptionpublic java.util.Vector positionByNOEAllRotamersSaved(java.util.Vector noeVec, java.util.Vector pdbVecA, java.util.Vector pdbVecB, double[] noeRms, boolean debugNOE, java.util.Vector vecUpdateNOE, java.lang.String strPass, java.util.Vector vecSeq) throws JampackException
noeVec
- the noe vecpdbVecA
- the pdb vec apdbVecB
- the pdb vec bnoeRms
- the noe rmsdebugNOE
- the debug noevecUpdateNOE
- the vec update noestrPass
- the str passvecSeq
- the vec seq
JampackException
- the jampack exceptionpublic java.util.Vector positionByNOEAllRotamersGrid(java.util.Vector noeVec, java.util.Vector pdbVecA, java.util.Vector pdbVecB, double[] noeRms, boolean debugNOE, java.util.Vector vecUpdateNOE) throws JampackException
noeVec
- the NOE distance restraints between the fragment A and BpdbVecA
- one fragmentpdbVecB
- another fragmentnoeRms
- saving the NOE rmsddebugNOE
- if true it will print out the NOE fitting RmsdsvecUpdateNOE
- the vec update noe
JampackException
- the jampack exceptionpublic java.util.Vector positionByNOEPatterns(java.util.Vector pdbVecA, java.util.Vector pdbVecB, java.util.Vector assignVec, java.util.Vector NoesyVec, double csErrH, double csErrN, double csErrCA, double distBound, int pickNum, double[] max_score)
pdbVecA
- one fragmentpdbVecB
- another fragmentassignVec
- vector of resonane assignment listNoesyVec
- vector of experimental NOESY peak listdistBound
- NOE upper distance limitpickNum
- size of packing ensemblemax_score
- store the maximum score in the ensemble of packingscsErrH
- the cs err hcsErrN
- the cs err ncsErrCA
- the cs err ca
public java.util.Vector calcMinPackingRms(java.util.Vector noeVec, java.util.Vector pdbVecA, java.util.Vector pdbVecB, double[] noeRms, boolean debugNOE) throws JampackException
noeVec
- the NOE distance restraints between the fragment A and BpdbVecA
- one fragmentpdbVecB
- another fragmentnoeRms
- saving the NOE rmsddebugNOE
- if true it will print out the NOE fitting Rmsds
JampackException
- the jampack exception
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |