public class SecStruc
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
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
f * q1 * q2 * scale
Q = -332 * 0.42 * 0.20 * 1000.0
q1 and q2 are partial charges which are placed on the C,O
(+q1,-q1) and N,H (-q2,+q2)
|
Constructor and Description |
---|
SecStruc() |
Modifier and Type | Method and Description |
---|---|
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 ...
|
SecStrucGroup[] |
getGroups() |
static java.math.BigDecimal |
getPreciseDistance(Atom a,
Atom b)
calculate distance between two atoms.
|
static void |
main(java.lang.String[] args) |
java.lang.String |
toString() |
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)
public static void main(java.lang.String[] args)
public void assign(Structure s) throws StructureException
s
- StructureException
public java.lang.String toString()
toString
in class java.lang.Object
public double calculateHBondEnergy(SecStrucGroup one, SecStrucGroup two) throws StructureException
StructureException
public static java.math.BigDecimal getPreciseDistance(Atom a, Atom b) throws StructureException
a
- an Atom objectb
- an Atom objectStructureException
- ...public SecStrucGroup[] getGroups()