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java.lang.ObjectRdcPanda.Model
public class Model
This class provides functions that compute backbone from RDC-EXACT algorithm. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009)
Constructor Summary | |
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Model()
Instantiates a new model. |
Method Summary | |
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java.util.Vector |
BackonbeRotation(java.util.Vector pdbAll,
java.util.Vector pdbBB)
rotate the whole protein according to the reference backbone such that the backbone coordinates are the same (both should have the same residues). |
java.util.Vector |
BackonbeRotationAtResidue(java.util.Vector pdbAll,
java.util.Vector pdbBB,
int resNo)
rotate the whole protein according to the reference backbone at specific residue, such that the backbone coordinates are the same (both should have the same residues). |
void |
doRdcExactSheet(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
compute the beta sheet using RDC-EXACT. |
static void |
main(java.lang.String[] argv)
The main method for testing. |
static void |
main1(java.lang.String[] argv)
Main function for testing. |
java.util.Vector |
parameterReader(java.lang.String fileName)
Parameter reader. |
java.util.Vector |
sheetModel(java.util.Vector eRdc1Vec,
java.util.Vector eRdc2Vec,
double Syy,
double Szz,
java.util.Vector HbondVec,
java.util.Vector paraVec,
java.util.Vector[] orderVec,
boolean printEulerSearch)
Compute s beta-sheet with the order specified by orderVec. |
java.util.Vector |
sheetModel2(java.util.Vector pdbVec,
java.util.Vector eRdc1Vec,
java.util.Vector eRdc2Vec,
double Syy,
double Szz,
java.util.Vector HbondVec,
java.util.Vector paraVec,
java.util.Vector[] orderVec,
boolean printEulerSearch)
Compute s beta-sheet with the order specified by orderVec. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Model()
Method Detail |
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public java.util.Vector parameterReader(java.lang.String fileName)
fileName
- the file name
public java.util.Vector BackonbeRotation(java.util.Vector pdbAll, java.util.Vector pdbBB) throws JampackException
pdbAll
- pdb to be rotatedpdbBB
- reference backbone pdb
JampackException
- the jampack exceptionpublic java.util.Vector BackonbeRotationAtResidue(java.util.Vector pdbAll, java.util.Vector pdbBB, int resNo) throws JampackException
pdbAll
- pdb to be rotatedpdbBB
- reference backbone pdbresNo
- the res no
JampackException
- the jampack exceptionpublic void doRdcExactSheet(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 java.util.Vector sheetModel(java.util.Vector eRdc1Vec, java.util.Vector eRdc2Vec, double Syy, double Szz, java.util.Vector HbondVec, java.util.Vector paraVec, java.util.Vector[] orderVec, boolean printEulerSearch)
eRdc1Vec
- RDC of medium 1 for all the strands of the sheeteRdc2Vec
- RDC of medium 2 for all the strands of the sheetHbondVec
- the Hbonds between the strandsparaVec
- the set of parameters used to compute each strands including the 1st oneprintEulerSearch
- if true it will print out the the detail of rotation searchSyy
- the syySzz
- the szzorderVec
- the order vec
public java.util.Vector sheetModel2(java.util.Vector pdbVec, java.util.Vector eRdc1Vec, java.util.Vector eRdc2Vec, double Syy, double Szz, java.util.Vector HbondVec, java.util.Vector paraVec, java.util.Vector[] orderVec, boolean printEulerSearch)
eRdc1Vec
- RDC of medium 1 for all the strands of the sheeteRdc2Vec
- RDC of medium 2 for all the strands of the sheetHbondVec
- the Hbonds between the strandsparaVec
- the set of parameters used to compute each strands including the 1st oneprintEulerSearch
- if true it will print out the the detail of rotation searchpdbVec
- the pdb vecSyy
- the syySzz
- the szzorderVec
- the order vec
public static void main(java.lang.String[] argv) throws JampackException
argv
- the arguments
JampackException
- the jampack exceptionpublic static void main1(java.lang.String[] argv) throws JampackException
argv
- the argv
JampackException
- the jampack exception
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