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java.lang.ObjectRdcPanda.Rotamer
public class Rotamer
This class provides data structures and functions related to rotamers. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).
Constructor Summary | |
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Rotamer()
Instantiates a new rotamer. |
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Rotamer(java.lang.String res)
Instantiates a new rotamer. |
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Rotamer(java.lang.String res,
java.util.Vector aa)
Instantiates a new rotamer. |
Method Summary | |
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java.lang.String |
getAAName()
Gets the aA name. |
java.util.Vector |
getPdbVec()
Gets the pdb vec. |
static void |
main(java.lang.String[] argv)
The main method. |
boolean |
pruneRotamers(java.util.Vector vecPdb,
java.lang.String rotSrc,
java.util.Vector noeVec,
int curNo,
int lastNo,
java.util.Vector vecEmsemblePdbSave)
prune rotamers based on: 1: collisions with backbone atoms; 2: collisions between pairwise rotamer atoms; 3: NOE constraints, including pairwise and local NOEs Note: a recurrsive approach is used. |
java.util.Vector |
readRotamer(java.lang.String rtamerFile)
Read rotamer. |
void |
setAAName(java.lang.String res)
Sets the aA name. |
void |
setAtomVec(java.util.Vector aVec)
Sets the atom vec. |
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 Rotamer()
public Rotamer(java.lang.String res)
res
- the respublic Rotamer(java.lang.String res, java.util.Vector aa)
res
- the resaa
- the aaMethod Detail |
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public java.lang.String getAAName()
public java.util.Vector getPdbVec()
public void setAAName(java.lang.String res)
res
- the new aA namepublic void setAtomVec(java.util.Vector aVec)
aVec
- the new atom vecpublic boolean pruneRotamers(java.util.Vector vecPdb, java.lang.String rotSrc, java.util.Vector noeVec, int curNo, int lastNo, java.util.Vector vecEmsemblePdbSave) throws JampackException
vecPdb
- the pdb structure including backbone and those residue in which rotamers have been decided.rotSrc
- the file path of the rotamer librarynoeVec
- vector of ALL NOE restraintscurNo
- the cur nolastNo
- the last novecEmsemblePdbSave
- the vec emsemble pdb save
JampackException
- the jampack exceptionpublic java.util.Vector readRotamer(java.lang.String rtamerFile)
rtamerFile
- the rtamer file
public static void main(java.lang.String[] argv) throws JampackException
argv
- the arguments
JampackException
- the jampack exception
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