Package 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
Source code:
main
Belongs to CDK module:
forcefield
Created on:
2004-09-07

  • Constructor Details

    • ForceFieldConfigurator

      public ForceFieldConfigurator()
      Constructor for the ForceFieldConfigurator object

  • Method Details

    • 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, IChemObjectBuilder builder) 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(IChemObjectBuilder builder) throws CDKException
      Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
      Throws:
      CDKException

    • setMMFF94Parameters

      public void setMMFF94Parameters(IChemObjectBuilder builder) 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(IAtomContainer 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