org.strbio.mol.lib
Class ScoreDefay
java.lang.Object
org.strbio.mol.lib.ScoreDefay
- All Implemented Interfaces:
- ScoreFunction
- Direct Known Subclasses:
- ScoreScaledDefay
public class ScoreDefay
- extends java.lang.Object
- implements ScoreFunction
A scoring function from Tom Defay's algorithm.
Defay & Cohen, JMB 262: 314-323. 1996.
Version 1.01, 7/20/98 - changed to reflect re-coding of environment
value in VAR files from the [-4:-1] range to the [-5:-2] range.
Version 1.0, 4/1/98 - original version
- Version:
- 1.01, 7/20/98
- Author:
- JMC
Field Summary |
java.lang.String |
defaultTable
the default table comes from Tom Defay's "easy table" |
Constructor Summary |
ScoreDefay()
If no filename is specified, use the default table. |
ScoreDefay(java.lang.String filename)
|
Method Summary |
double |
score(Monomer a,
Monomer b)
This function should return a score for aligning two
monomers of a polymer, preferably with low = good, high = bad. |
double |
score(Residue a,
Residue b)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
defaultTable
public final java.lang.String defaultTable
- the default table comes from Tom Defay's "easy table"
- See Also:
- Constant Field Values
ScoreDefay
public ScoreDefay(java.lang.String filename)
throws java.io.IOException
- Throws:
java.io.IOException
ScoreDefay
public ScoreDefay()
- If no filename is specified, use the default table.
Can't call the other constructor due to stupid Java syntax.
score
public double score(Residue a,
Residue b)
score
public double score(Monomer a,
Monomer b)
- Description copied from interface:
ScoreFunction
- This function should return a score for aligning two
monomers of a polymer, preferably with low = good, high = bad.
If this is not the case, be sure to comment it as such!
If monomer order matters to your scoring function, the first
monomer should be from the sequence (unknown structure), and
the second monomer should be from the fold (known structure).
- Specified by:
score
in interface ScoreFunction