cct.modelling
Class FFMolecule

java.lang.Object
  extended by cct.modelling.FFMolecule

public class FFMolecule
extends java.lang.Object

Title:

Description:

Copyright: Copyright (c) 2006

Company: ANU


Field Summary
protected  java.lang.Object[] AngleBendInteractions
           
protected  java.lang.Object[] BondStretchInteractions
           
protected  boolean Calculate_1_4
           
static float defaultFk
           
static int HARMONIC_BOND_TERM
           
protected  MoleculeInterface Molecule
           
(package private)  java.util.ArrayList nonbodedPairs
           
(package private)  Nonbonded15Table nonbondedTable
           
(package private)  java.util.ArrayList oneFourInteractions
           
(package private)  float SCEE
           
(package private)  float SCNB
           
(package private)  java.util.ArrayList torsionInteractions
           
(package private)  java.util.ArrayList Torsions
           
 
Constructor Summary
FFMolecule(MoleculeInterface molec)
           
 
Method Summary
 void applyForceField(ForceFieldInterface ff)
           
static java.util.ArrayList find14Interactions(MoleculeInterface molec, java.util.ArrayList torsions)
           
static AngleBendsArray findDynamicAngles(MoleculeInterface molec)
          Finds all valent angles where at least one atom forming angle is dynamic
static java.util.ArrayList findDynamicTorsions(MoleculeInterface molec)
          Finds all regular torsions in molecule
static java.util.ArrayList findNonbondedPairs(MoleculeInterface molec, Nonbonded15Table nbTable)
           
 int formAngleBendInteractions(int paramType, AngleBendsArray angles)
           
 int formBondStretchInteractions(int paramType, int intType)
           
 void formFFParameters()
           
 java.util.ArrayList formTorsionInteractions(int paramType, java.util.ArrayList torsions)
           
 java.util.ArrayList get14Interactions()
           
 java.lang.Object[] getAngleBendInteractions()
           
 java.lang.Object[] getBondStretchInteractions()
           
 MoleculeInterface getMolecule()
           
 java.util.ArrayList getNonbondInteractions()
           
 java.util.ArrayList getTorsionInteractions()
           
 boolean isCalculate14()
           
static void main(java.lang.String[] args)
           
 void setupNonbondedInteractions(int paramType, java.util.ArrayList nonbonded)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

HARMONIC_BOND_TERM

public static final int HARMONIC_BOND_TERM
See Also:
Constant Field Values

defaultFk

public static float defaultFk

Molecule

protected MoleculeInterface Molecule

BondStretchInteractions

protected java.lang.Object[] BondStretchInteractions

AngleBendInteractions

protected java.lang.Object[] AngleBendInteractions

Calculate_1_4

protected boolean Calculate_1_4

Torsions

java.util.ArrayList Torsions

torsionInteractions

java.util.ArrayList torsionInteractions

oneFourInteractions

java.util.ArrayList oneFourInteractions

nonbodedPairs

java.util.ArrayList nonbodedPairs

nonbondedTable

Nonbonded15Table nonbondedTable

SCNB

float SCNB

SCEE

float SCEE
Constructor Detail

FFMolecule

public FFMolecule(MoleculeInterface molec)
Method Detail

applyForceField

public void applyForceField(ForceFieldInterface ff)

isCalculate14

public boolean isCalculate14()

get14Interactions

public java.util.ArrayList get14Interactions()

getTorsionInteractions

public java.util.ArrayList getTorsionInteractions()

getNonbondInteractions

public java.util.ArrayList getNonbondInteractions()

getBondStretchInteractions

public java.lang.Object[] getBondStretchInteractions()

getAngleBendInteractions

public java.lang.Object[] getAngleBendInteractions()

getMolecule

public MoleculeInterface getMolecule()

formFFParameters

public void formFFParameters()
                      throws java.lang.Exception
Throws:
java.lang.Exception

formBondStretchInteractions

public int formBondStretchInteractions(int paramType,
                                       int intType)
                                throws java.lang.Exception
Parameters:
paramType - int
intType - int- type of bond stretch interactions: 0 - harmonic K*(r-r0)
Returns:
int - number of bond stretch interactions
Throws:
java.lang.Exception

setupNonbondedInteractions

public void setupNonbondedInteractions(int paramType,
                                       java.util.ArrayList nonbonded)
                                throws java.lang.Exception
Throws:
java.lang.Exception

formAngleBendInteractions

public int formAngleBendInteractions(int paramType,
                                     AngleBendsArray angles)
                              throws java.lang.Exception
Throws:
java.lang.Exception

formTorsionInteractions

public java.util.ArrayList formTorsionInteractions(int paramType,
                                                   java.util.ArrayList torsions)
                                            throws java.lang.Exception
Throws:
java.lang.Exception

findDynamicAngles

public static AngleBendsArray findDynamicAngles(MoleculeInterface molec)
Finds all valent angles where at least one atom forming angle is dynamic

Parameters:
molec - MoleculeInterface - Molecule
Returns:
AngleBendsArray

findDynamicTorsions

public static java.util.ArrayList findDynamicTorsions(MoleculeInterface molec)
Finds all regular torsions in molecule

Parameters:
molec - MoleculeInterface - Molecule
Returns:
ArrayList - array of class Torsion

find14Interactions

public static java.util.ArrayList find14Interactions(MoleculeInterface molec,
                                                     java.util.ArrayList torsions)

findNonbondedPairs

public static java.util.ArrayList findNonbondedPairs(MoleculeInterface molec,
                                                     Nonbonded15Table nbTable)

main

public static void main(java.lang.String[] args)