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java.lang.ObjectRdcPanda.RdcPanda
public class RdcPanda
This class implements the main function of RDC-Panda. Written by Jianyang (Michael) Zeng (2005-2009)
Field Summary | |
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java.lang.String |
rotLibName
The path of rot lib location. |
Constructor Summary | |
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RdcPanda()
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Method Summary | |
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static boolean |
deleteDir(java.io.File dir)
Delete a directory. |
void |
doAddRandomLoops(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
add random loops to an ensemble of packed SSE structures (i.e. |
void |
doAddSideChains(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
* add the side chains and prune steic clahes. |
void |
doCalAlignmentTensor(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
calculate the alignment tensor. |
void |
doCheckPackingSym(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
check the packing symmetry that best fit the noe restraints (namely with minimum NOE RMSD). |
void |
doMergeNCluster(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
* merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. |
void |
doMergeNClusterAll(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
* merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. |
void |
doRdcExactHelix(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
RDC-EXACT for two RDCs (CH and NH RDCs), and for long helix Co-Ca and Co-N RDCs are optional. |
void |
doRdcExactHelixWOAT(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
RDC-EXACT without alignment tensor for two RDCs (CH and NH RDCs), and for long helix. |
void |
doReadPDBEnergy(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
Read the engergy value from xplor PDB, and output the top structures with lowest energies. |
void |
doRefineRdcExact(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
refine the half start and end residues of pdb backbone solved from RDC-EXACT. |
void |
doRefineRdcExactMiddle(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
refine the middle residues of pdb backbone solved from RDC-EXACT. |
void |
doRunXplor(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
call Xplor as a subroutine given a script file. |
void |
doSSEPacking(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
Pack SSEs using sparse inter-SSE NOE restraints. |
static void |
main(java.lang.String[] args)
The main method. |
void |
outputProgInfo()
Output prog info. |
void |
parse(java.lang.String[] args)
Parses the. |
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 java.lang.String rotLibName
Constructor Detail |
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public RdcPanda()
Method Detail |
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public static void main(java.lang.String[] args) throws JampackException, java.lang.InterruptedException
args
- the arguments
JampackException
- the jampack exception
java.lang.InterruptedException
- the interrupted exceptionpublic void parse(java.lang.String[] args) throws JampackException, java.lang.InterruptedException
args
- the args
JampackException
- the jampack exception
java.lang.InterruptedException
- the interrupted exceptionpublic void doRunXplor(java.lang.String src, java.lang.String strOut, java.lang.String strInput) throws JampackException, java.lang.InterruptedException
src
- location of the input filestrOut
- location of the output filestrInput
- input file name
JampackException
- the jampack exception
java.lang.InterruptedException
- the interrupted exceptionpublic void doSSEPacking(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 void doMergeNCluster(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 void doAddSideChains(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 void doMergeNClusterAll(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 void doAddRandomLoops(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 void doReadPDBEnergy(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 void doCheckPackingSym(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 void doCalAlignmentTensor(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 void doRefineRdcExact(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 void doRefineRdcExactMiddle(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 void doRdcExactHelix(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 void doRdcExactHelixWOAT(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 void outputProgInfo()
public static boolean deleteDir(java.io.File dir)
dir
- the dir
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