Class ProteinFolding

java.lang.Object

org.episteme.natural.biology.ProteinFolding

public final class ProteinFolding
extends Object

Advanced protein secondary structure prediction and energy-based folding simulation. Uses a simplified force field with Lennard-Jones potentials and hydrogen bonding energy.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final record	ProteinFolding.Residue
static enum	ProteinFolding.Structure

Constructor Summary

Constructors

Constructor	Description
ProteinFolding(List<ProteinFolding.Residue> initialChain)

Method Summary

Modifier and Type	Method	Description
Real	calculateTotalEnergy()
List<ProteinFolding.Residue>	getChain()
static ProteinFolding.Structure	predictAa(String aa)
void	step(double tempDecrease)

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ProteinFolding

public ProteinFolding(List<ProteinFolding.Residue> initialChain)

Method Details

step

public void step(double tempDecrease)

calculateTotalEnergy

public Real calculateTotalEnergy()

predictAa

public static ProteinFolding.Structure predictAa(String aa)

getChain

public List<ProteinFolding.Residue> getChain()