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java.lang.Objectorg.biojava.bio.structure.secstruc.SecStruc
public class SecStruc
Assign secondary structure to a Structure object. tries to use the rules as defined by DSSP Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637. original DSSP article see at : dssp.pdf some bits also taken from T.E.Creighton Proteins - Structure and Molecular Properties 2nd Edition, Freeman 1994
Field Summary | |
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static int |
CA_MIN_DIST
the minimal distance of two CA atoms if H-bonds are allowed to form. |
static double |
HBONDHIGHENERGY
higher limit for H-bond energy |
static int |
HBONDLOWENERGY
Minimal H-bond energy in cal / mol |
static double |
MINDIST
the minimal distance between two residues |
static double |
Q
constant for electrostatic energy |
Constructor Summary | |
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SecStruc()
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Method Summary | |
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void |
assign(Structure s)
assigns the secondary structure to the groups in this Structure object and set the results in the group properties. |
double |
calculateHBondEnergy(SecStrucGroup one,
SecStrucGroup two)
calculate HBond energy of two groups in cal/mol ... |
static BigDecimal |
getPreciseDistance(Atom a,
Atom b)
calculate distance between two atoms. |
static void |
main(String[] args)
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String |
toString()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static double MINDIST
public static int CA_MIN_DIST
public static int HBONDLOWENERGY
public static double HBONDHIGHENERGY
public static double Q
f * q1 * q2 * scale Q = -332 * 0.42 * 0.20 * 1000.0q1 and q2 are partial charges which are placed on the C,O (+q1,-q1) and N,H (-q2,+q2)
Constructor Detail |
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public SecStruc()
Method Detail |
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public static void main(String[] args)
public void assign(Structure s) throws StructureException
s
-
StructureException
public String toString()
toString
in class Object
public double calculateHBondEnergy(SecStrucGroup one, SecStrucGroup two) throws StructureException
StructureException
public static BigDecimal getPreciseDistance(Atom a, Atom b) throws StructureException
a
- an Atom objectb
- an Atom object
StructureException
- ...
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