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java.lang.ObjectRdcPanda.vdw
public class vdw
A class for computing the vdw repellsion. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).
Nested Class Summary | |
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static class |
vdw.VdwComparator
The Class VdwComparator. |
static class |
vdw.VdwNoeComparator
The Class VdwNoeComparator. |
Constructor Summary | |
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vdw()
Instantiates a new vdw. |
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vdw(java.lang.String id2,
double[] coord2)
Instantiates a new vdw. |
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vdw(java.util.Vector vecPp,
double sc)
Instantiates a new vdw. |
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vdw(java.util.Vector vecPp,
double sc,
double noe_sc)
Instantiates a new vdw. |
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vdw(java.util.Vector vecPp,
double sc,
double nhRms,
double chRms,
int enID,
int modID)
Instantiates a new vdw. |
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vdw(java.util.Vector vecPp,
double sc,
double noe_sc,
int modID)
Instantiates a new vdw. |
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vdw(java.util.Vector vecPp,
double sc,
double noe_sc,
int modID,
java.lang.String id)
Instantiates a new vdw. |
Method Summary | |
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boolean |
checkStericClash(java.util.Vector vdwVec,
double[] vdwValue,
double vdwLevel,
boolean printVDWViolation,
boolean isHelix,
double stericThreshold,
int numThreshold,
int[] clashIndex)
check the steric clashes, if the number of steric clashes is larger than some threshold, ruturn true, else return false. |
double |
checkVDW(java.lang.String atom1,
java.lang.String atom2,
double distance,
boolean isHbond)
Check vdw. |
boolean |
computeVDW(java.util.Vector vdwVec,
double[] vdwValue,
boolean isHelix)
Compute the vdw energy. |
boolean |
computeVDW(java.util.Vector vdwVec,
double[] vdwValue,
double vdwLevel,
boolean printVDWViolation)
Compute the vdw energy. |
boolean |
computeVDW(java.util.Vector vdwVec,
double[] vdwValue,
double vdwLevel,
boolean printVDWViolation,
boolean isHelix)
Compute the vdw energy. |
java.util.Vector |
convert2VDW(Pdb[] pdbVec)
To convert the PDB coordinates into a flat structure for speed. |
java.util.Vector |
convert2VDW(java.util.Vector pdbVec)
To convert the PDB coordinates into a flat structure for speed. |
int |
countStericClash(java.util.Vector vdwVec,
double[] vdwValue,
double vdwLevel,
boolean printVDWViolation,
boolean isHelix,
double stericThreshold)
count the number of steric clash, given the threshold of penetration, ruturn true, else return false. |
int |
countStericClashBetweenTwo(java.util.Vector vdwVec,
java.util.Vector vdwVec2,
double[] vdwValue,
double vdwLevel,
boolean printVDWViolation,
boolean isHelix,
double stericThreshold)
count the number of steric clash between two structures, given the threshold of penetration, ruturn true, else return false. |
double |
getChRmsd()
Gets the ch rmsd. |
double[] |
getCoord()
Gets the coord. |
double |
getEnsembleID()
Gets the ensemble id. |
java.lang.String |
getID()
Gets the iD. |
double |
getModelID()
Gets the model id. |
double |
getNhRmsd()
Gets the nh rmsd. |
double |
getNoeRmsd()
Gets the noe rmsd. |
java.util.Vector |
getPDB()
Gets the pDB. |
java.lang.String |
getStringID()
Gets the string id. |
double |
getVdwScore()
Gets the vdw score. |
double[] |
internuclearVec(double[] n1,
double[] n2)
Internuclear vec. |
boolean |
isBonded(int no1,
int no2,
java.lang.String atom1,
java.lang.String atom2)
Only for polyalanine. |
boolean |
isBonded(java.lang.String resid,
int no1,
int no2,
java.lang.String atom1,
java.lang.String atom2)
Checks if is bonded. |
double |
length(double[] v1)
Length. |
static void |
main(java.lang.String[] argv)
The main method. |
void |
measureVDW4Ensemble()
Measure vd w4 ensemble. |
void |
mergeAndCluster(java.lang.String src,
java.lang.String srcOut,
java.lang.String strPreEnsemb,
int maxStr,
int maxEnsemSize,
double resolution,
java.lang.String strNewEnsemb,
java.lang.String strDelimit)
merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. |
void |
mergeAndClusterAll(java.lang.String src,
java.lang.String srcOut,
double resolution,
java.lang.String strNewEnsemb)
similar to "mergeAndCluster", but cluster all structures in one directory as an ensemble merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. |
int |
OutputStericClashResidues(java.util.Vector vdwVec,
double[] vdwValue,
double vdwLevel,
boolean printVDWViolation,
boolean isHelix,
double stericThreshold,
int numThreshold,
boolean[] resClash,
boolean isPrint)
check the steric clashes, if the number of steric clashes is larger than some threshold, ruturn true, else return false. |
void |
setCoord(double[] coord2)
Sets the coord. |
void |
setID(java.lang.String id2)
Sets the iD. |
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 vdw()
public vdw(java.util.Vector vecPp, double sc)
vecPp
- the vec ppsc
- the scpublic vdw(java.util.Vector vecPp, double sc, double noe_sc)
vecPp
- the vec ppsc
- the scnoe_sc
- the noe_scpublic vdw(java.util.Vector vecPp, double sc, double noe_sc, int modID)
vecPp
- the vec ppsc
- the scnoe_sc
- the noe_scmodID
- the mod idpublic vdw(java.util.Vector vecPp, double sc, double noe_sc, int modID, java.lang.String id)
vecPp
- the vec ppsc
- the scnoe_sc
- the noe_scmodID
- the mod idid
- the idpublic vdw(java.util.Vector vecPp, double sc, double nhRms, double chRms, int enID, int modID)
vecPp
- the vec ppsc
- the scnhRms
- the nh rmschRms
- the ch rmsenID
- the en idmodID
- the mod idpublic vdw(java.lang.String id2, double[] coord2)
id2
- the id2coord2
- the coord2Method Detail |
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public java.util.Vector getPDB()
public double getVdwScore()
public double getNoeRmsd()
public double getEnsembleID()
public double getModelID()
public java.lang.String getStringID()
public double getNhRmsd()
public double getChRmsd()
public java.lang.String getID()
public double[] getCoord()
public void setID(java.lang.String id2)
id2
- the new iDpublic void setCoord(double[] coord2)
coord2
- the new coordpublic double length(double[] v1)
v1
- the v1
public double[] internuclearVec(double[] n1, double[] n2)
n1
- the n1n2
- the n2
public java.util.Vector convert2VDW(java.util.Vector pdbVec)
pdbVec
- the pdb vec
public java.util.Vector convert2VDW(Pdb[] pdbVec)
pdbVec
- the pdb vec
public boolean computeVDW(java.util.Vector vdwVec, double[] vdwValue, boolean isHelix)
vdwVec
- coordinate object in a flat formvdwValue
- for returning the computed vdwEnergyisHelix
- is a boolean for treating specifically the H-bond for a helix
public boolean computeVDW(java.util.Vector vdwVec, double[] vdwValue, double vdwLevel, boolean printVDWViolation)
vdwVec
- coordinate object in a flat formvdwValue
- for returning the computed vdwEnergyvdwLevel
- if the vdwEnergy > vdwLevel and printVDWViolation
is true, print out the violation for checkingprintVDWViolation
- whether to print the vdw violation
public boolean computeVDW(java.util.Vector vdwVec, double[] vdwValue, double vdwLevel, boolean printVDWViolation, boolean isHelix)
vdwVec
- coordinate object in a flat formvdwValue
- for returning the computed vdwEnergyvdwLevel
- if the vdwEnergy > vdwLevel and printVDWViolation
is true, print out the violation for checkingprintVDWViolation
- whether to print the vdw violationisHelix
- the is helix
public int OutputStericClashResidues(java.util.Vector vdwVec, double[] vdwValue, double vdwLevel, boolean printVDWViolation, boolean isHelix, double stericThreshold, int numThreshold, boolean[] resClash, boolean isPrint)
vdwVec
- coordinate object in a flat formvdwValue
- for returning the computed vdwEnergyvdwLevel
- if the vdwEnergy > vdwLevel and printVDWViolation
is true, print out the violation for checkingprintVDWViolation
- whether to print the vdw violationisHelix
- whether it is helixstericThreshold
- the distance threshold for checking steric clash (default:0.6A)numThreshold
- the number threshold for reporting steric clashes(default:1)resClash
- store the residue indexes of steric clash, true if the residue envolves in steric clashisPrint
- the is print
public boolean checkStericClash(java.util.Vector vdwVec, double[] vdwValue, double vdwLevel, boolean printVDWViolation, boolean isHelix, double stericThreshold, int numThreshold, int[] clashIndex)
vdwVec
- coordinate object in a flat formvdwValue
- for returning the computed vdwEnergyvdwLevel
- if the vdwEnergy > vdwLevel and printVDWViolation
is true, print out the violation for checkingprintVDWViolation
- whether to print the vdw violationisHelix
- whether it is helixstericThreshold
- the distance threshold for checking steric clash (default:0.6A)numThreshold
- the number threshold for reporting steric clashes(default:1)clashIndex
- store the residue indexes of steric clash
public int countStericClash(java.util.Vector vdwVec, double[] vdwValue, double vdwLevel, boolean printVDWViolation, boolean isHelix, double stericThreshold)
vdwVec
- coordinate object in a flat formvdwValue
- for returning the computed vdwEnergyvdwLevel
- if the vdwEnergy > vdwLevel and printVDWViolation
is true, print out the violation for checking. Not used here.printVDWViolation
- whether to print the vdw violation. Not used here.isHelix
- whether it is helixstericThreshold
- the distance threshold for checking steric clash (default:0.6A)
public int countStericClashBetweenTwo(java.util.Vector vdwVec, java.util.Vector vdwVec2, double[] vdwValue, double vdwLevel, boolean printVDWViolation, boolean isHelix, double stericThreshold)
vdwVec
- coordinate object in a flat formvdwValue
- for returning the computed vdwEnergyvdwLevel
- if the vdwEnergy > vdwLevel and printVDWViolation
is true, print out the violation for checking. Not used here.printVDWViolation
- whether to print the vdw violation. Not used here.isHelix
- whether it is helixstericThreshold
- the distance threshold for checking steric clash (default:0.6A)vdwVec2
- the vdw vec2
public boolean isBonded(int no1, int no2, java.lang.String atom1, java.lang.String atom2)
no1
- the no1no2
- the no2atom1
- the atom1atom2
- the atom2
public boolean isBonded(java.lang.String resid, int no1, int no2, java.lang.String atom1, java.lang.String atom2)
resid
- the residno1
- the no1no2
- the no2atom1
- the atom1atom2
- the atom2
public double checkVDW(java.lang.String atom1, java.lang.String atom2, double distance, boolean isHbond)
atom1
- the atom1atom2
- the atom2distance
- the distanceisHbond
- the is hbond
public void mergeAndCluster(java.lang.String src, java.lang.String srcOut, java.lang.String strPreEnsemb, int maxStr, int maxEnsemSize, double resolution, java.lang.String strNewEnsemb, java.lang.String strDelimit) throws JampackException
src
- current input directorystrPreEnsemb
- the common name in the old ensembles
Note: the prvious ensemble ID and structure ID are assumely delimited by "000"strNewEnsemb
- the new name of the clutered ensemblesresolution
- the resolution for the clustering step.maxStr
- max number of structures in previous each ensemblemaxEnsemSize
- max number of in previous ensemblesstrDelimit
- the delimited string between enesmble and structure IDssrcOut
- the src out
JampackException
- the jampack exceptionpublic void mergeAndClusterAll(java.lang.String src, java.lang.String srcOut, double resolution, java.lang.String strNewEnsemb) throws JampackException
src
- the input directory of all structures in the ensemblestrNewEnsemb
- the new name of the clutered ensemblesresolution
- the resolution for the clustering step.srcOut
- the src out
JampackException
- the jampack exceptionpublic static void main(java.lang.String[] argv) throws JampackException
argv
- the arguments
JampackException
- the jampack exceptionpublic void measureVDW4Ensemble()
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