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java.lang.Object org.strbio.mol.lib.Sippl90
public class Sippl90
Sippl scoring method, from JMB 90 papers.
Identification of Native Protein Folds Amongst a Large Number of Incorrect Models Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, and Sippl M 1990 J Mol Biol 216: 167-180and also:
Calculation of Conformational Ensembles from Potentials of Mean Force Sippl M 1990 J Mol Biol 213: 859-883Energy is a function of 4 parameters: 2 amino acid types (not symmetric; the first is the more N-terminal of the 2), topological separation k (starting at 1 for adjacent amino acids),and CB-CB (or CA for glycine) distance d. In practice, k from 1 to 10 are treated separately; 11-30 are combined into 1 category (medium range), and there are 4 long range categories: 31-60, 61-100, 101-150, and 151-200.
Even though k values are counted 1-10 (and 11 for MR, 12-15 for LR1-4), they are stored internally in this code starting at 0. Look things up at k-1, not k.
Version 1.0, 1/3/00 - original version
Constructor Summary | |
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Sippl90()
Don't initialize anything. |
Method Summary | |
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double |
deltaE(char a,
char b,
int k,
double d)
Returns the deltaE(a,b,k,d). |
double |
getMaxDistance(int k)
get the maximum distance for toplogical level k |
double |
getMinDistance(int k)
get the minimum distance for toplogical level k |
IVector |
getRaw(char a,
char b,
int k)
Returns a vector of raw N(a,b,k) |
DVector |
getTabulated(char a,
char b,
int k)
Returns a vector of deltaE(a,b,k). |
void |
load(java.io.BufferedReader infile)
Load tabulated values from an open BufferedReader. |
void |
load(java.lang.String filename)
Loads tabulated values from a text file. |
void |
loadRaw(java.io.BufferedReader infile)
Load tabulated values from an open BufferedReader. |
void |
loadRaw(java.lang.String filename)
Loads raw values from a text file. |
static void |
main(java.lang.String[] argv)
Use proteins in a file to parameterize the function. |
void |
save(Printf outfile)
Saved tabulated values to a file. |
void |
save(java.lang.String filename)
Saves to a new text file. |
void |
saveRaw(Printf outfile)
Saved raw values to a file. |
void |
saveRaw(java.lang.String filename)
Saves raw values to a new text file. |
double |
selfEnergy(Protein p)
return the total self energy for a protein. |
double |
selfEnergy(Protein p,
int kMin,
int kMax)
return the self-energy for a protein for a range of k's (including both ends of the range) |
double |
selfEnergyLR1(Protein p)
return the long range (1) energy for a protein (k=31..60) |
double |
selfEnergyLR2(Protein p)
return the long range (2) energy for a protein (k=61..100) |
double |
selfEnergyLR3(Protein p)
return the long range (3) energy for a protein (k=101..150) |
double |
selfEnergyLR4(Protein p)
return the long range (4) energy for a protein (k=151+) |
double |
selfEnergyMR(Protein p)
return the medium range energy for a protein (k=11..30) |
double |
selfEnergySR(Protein p)
return the short range energy for a protein (k=1..10) |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Sippl90()
Method Detail |
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public DVector getTabulated(char a, char b, int k)
public IVector getRaw(char a, char b, int k)
public double getMinDistance(int k)
public double getMaxDistance(int k)
public double selfEnergy(Protein p, int kMin, int kMax)
public double selfEnergySR(Protein p)
public double selfEnergyMR(Protein p)
public double selfEnergyLR1(Protein p)
public double selfEnergyLR2(Protein p)
public double selfEnergyLR3(Protein p)
public double selfEnergyLR4(Protein p)
public double selfEnergy(Protein p)
public double deltaE(char a, char b, int k, double d)
public void save(Printf outfile) throws java.io.IOException
java.io.IOException
public void saveRaw(Printf outfile) throws java.io.IOException
java.io.IOException
public void load(java.io.BufferedReader infile) throws java.io.IOException
java.io.IOException
BufferedReader
public void loadRaw(java.io.BufferedReader infile) throws java.io.IOException
java.io.IOException
BufferedReader
public void save(java.lang.String filename) throws java.io.IOException
filename
- the file name.
java.io.IOException
public void load(java.lang.String filename) throws java.io.IOException
filename
- the file name.
java.io.IOException
public void saveRaw(java.lang.String filename) throws java.io.IOException
filename
- the file name.
java.io.IOException
public void loadRaw(java.lang.String filename) throws java.io.IOException
filename
- the file name.
java.io.IOException
public static final void main(java.lang.String[] argv)
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