org.openscience.cdk.modeling.builder3d

Class ForceFieldConfigurator

java.lang.Object

org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

public class ForceFieldConfigurator
extends Object

Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable Therefore, it uses the class MM2BasedParameterSetReader. private Hashtable parameterSet; key=nameofdatafield+atomid1+;atomid2;atomxid

MM2 and MMFF94 force field are implemented With force field data it configures the cdk atom (assign atomtype, van der Waals radius, charge...)

Author:

chhoppe

Created on:

2004-09-07

Constructor Summary

Constructors

Constructor and Description
ForceFieldConfigurator() Constructor for the ForceFieldConfigurator object

Method Summary

Methods

Modifier and Type	Method and Description
IRingSet	assignAtomTyps(IMolecule molecule) Method assigns atom types to atoms (calculates sssr and aromaticity)
boolean	checkForceFieldType(String ffname) Sets the forceFieldType attribute of the ForceFieldConfigurator object
IAtom	configureAtom(IAtom atom, String hoseCode, boolean _boolean)
IAtom	configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing) Configures an atom to a mm2 based atom type
IAtom	configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing) Configures an atom to a mmff94 based atom type
List<IAtomType>	getAtomTypes() Gets the atomTypes attribute of the ForceFieldConfigurator object
String[]	getFfTypes() gives a list of possible force field types
Map<String,Object>	getParameterSet() Gets the parameterSet attribute of the ForceFieldConfigurator object
String	removeAromaticityFlagsFromHoseCode(String hoseCode)
void	setAtomTypes(List<IAtomType> atomtypes) Sets the atomTypes attribute of the ForceFieldConfigurator object
void	setForceFieldConfigurator(String ffname) Constructor for the ForceFieldConfigurator object
void	setInputStream(InputStream ins) Sets the inputStream attribute of the ForceFieldConfigurator object
void	setMM2Parameters() Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
void	setMMFF94Parameters()
void	setParameters(Map<String,Object> parameterset) Sets the parameters attribute of the ForceFieldConfigurator object

Methods inherited from class java.lang.Object

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

Constructor Detail

ForceFieldConfigurator

public ForceFieldConfigurator()

Constructor for the ForceFieldConfigurator object

Method Detail

setInputStream

public void setInputStream(InputStream ins)

Sets the inputStream attribute of the ForceFieldConfigurator object

Parameters:

ins - The new inputStream value

getFfTypes

public String[] getFfTypes()

gives a list of possible force field types

Returns:

the list

checkForceFieldType

public boolean checkForceFieldType(String ffname)

Sets the forceFieldType attribute of the ForceFieldConfigurator object

Parameters:

ffname - The new forceFieldType name

setForceFieldConfigurator

public void setForceFieldConfigurator(String ffname)
                               throws CDKException

Constructor for the ForceFieldConfigurator object

Parameters:

ffname - name of the force field data file

Throws:

CDKException

setAtomTypes

public void setAtomTypes(List<IAtomType> atomtypes)

Sets the atomTypes attribute of the ForceFieldConfigurator object

Parameters:

atomtypes - The new atomTypes

setParameters

public void setParameters(Map<String,Object> parameterset)

Sets the parameters attribute of the ForceFieldConfigurator object

Parameters:

parameterset - The new parameter values

setMM2Parameters

public void setMM2Parameters()
                      throws CDKException

Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field

Throws:

CDKException

setMMFF94Parameters

public void setMMFF94Parameters()
                         throws Exception

Throws:

Exception

getAtomTypes

public List<IAtomType> getAtomTypes()

Gets the atomTypes attribute of the ForceFieldConfigurator object

Returns:

The atomTypes vector

getParameterSet

public Map<String,Object> getParameterSet()

Gets the parameterSet attribute of the ForceFieldConfigurator object

Returns:

The parameterSet hashtable

assignAtomTyps

public IRingSet assignAtomTyps(IMolecule molecule)
                        throws CDKException

Method assigns atom types to atoms (calculates sssr and aromaticity)

Returns:

sssrf set

Throws:

CDKException - Problems detecting aromaticity or making hose codes.

configureAtom

public IAtom configureAtom(IAtom atom,
                  String hoseCode,
                  boolean _boolean)
                    throws CDKException

Throws:

CDKException

configureMM2BasedAtom

public IAtom configureMM2BasedAtom(IAtom atom,
                          String hoseCode,
                          boolean hetRing)
                            throws NoSuchAtomTypeException

Configures an atom to a mm2 based atom type

Parameters:

atom - atom to be configured

hoseCode - the 4 sphere hose code of the atom

Returns:

atom

Throws:

NoSuchAtomTypeException - atomType is not known

removeAromaticityFlagsFromHoseCode

public String removeAromaticityFlagsFromHoseCode(String hoseCode)

configureMMFF94BasedAtom

public IAtom configureMMFF94BasedAtom(IAtom atom,
                             String hoseCode,
                             boolean isInHetRing)
                               throws NoSuchAtomTypeException

Configures an atom to a mmff94 based atom type

Parameters:

atom - atom to be configured

hoseCode - the 4 sphere hose code of the atom

Returns:

atom

Throws:

NoSuchAtomTypeException - atomType is not known