public class ForceFieldConfigurator extends Object
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...)
Constructor and Description |
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ForceFieldConfigurator()
Constructor for the ForceFieldConfigurator object
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Modifier and Type | Method and Description |
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IRingSet |
assignAtomTyps(IAtomContainer molecule)
Method assigns atom types to atoms (calculates sssr and aromaticity)
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boolean |
checkForceFieldType(String ffname)
Sets the forceFieldType attribute of the ForceFieldConfigurator object
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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
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IAtom |
configureMMFF94BasedAtom(IAtom atom,
String hoseCode,
boolean isInHetRing)
Configures an atom to a mmff94 based atom type
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List<IAtomType> |
getAtomTypes()
Gets the atomTypes attribute of the ForceFieldConfigurator object
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String[] |
getFfTypes()
gives a list of possible force field types
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Map<String,Object> |
getParameterSet()
Gets the parameterSet attribute of the ForceFieldConfigurator object
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String |
removeAromaticityFlagsFromHoseCode(String hoseCode) |
void |
setAtomTypes(List<IAtomType> atomtypes)
Sets the atomTypes attribute of the ForceFieldConfigurator object
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void |
setForceFieldConfigurator(String ffname,
IChemObjectBuilder builder)
Constructor for the ForceFieldConfigurator object
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void |
setInputStream(InputStream ins)
Sets the inputStream attribute of the ForceFieldConfigurator object
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void |
setMM2Parameters(IChemObjectBuilder builder)
Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
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void |
setMMFF94Parameters(IChemObjectBuilder builder) |
void |
setParameters(Map<String,Object> parameterset)
Sets the parameters attribute of the ForceFieldConfigurator object
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public ForceFieldConfigurator()
public void setInputStream(InputStream ins)
ins
- The new inputStream valuepublic String[] getFfTypes()
public boolean checkForceFieldType(String ffname)
ffname
- The new forceFieldType namepublic void setForceFieldConfigurator(String ffname, IChemObjectBuilder builder) throws CDKException
ffname
- name of the force field data fileCDKException
public void setAtomTypes(List<IAtomType> atomtypes)
atomtypes
- The new atomTypespublic void setParameters(Map<String,Object> parameterset)
parameterset
- The new parameter valuespublic void setMM2Parameters(IChemObjectBuilder builder) throws CDKException
CDKException
public void setMMFF94Parameters(IChemObjectBuilder builder) throws Exception
Exception
public List<IAtomType> getAtomTypes()
public Map<String,Object> getParameterSet()
public IRingSet assignAtomTyps(IAtomContainer molecule) throws CDKException
CDKException
- Problems detecting aromaticity or making hose codes.public IAtom configureAtom(IAtom atom, String hoseCode, boolean _boolean) throws CDKException
CDKException
public IAtom configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing) throws NoSuchAtomTypeException
atom
- atom to be configuredhoseCode
- the 4 sphere hose code of the atomNoSuchAtomTypeException
- atomType is not knownpublic String removeAromaticityFlagsFromHoseCode(String hoseCode)
public IAtom configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing) throws NoSuchAtomTypeException
atom
- atom to be configuredhoseCode
- the 4 sphere hose code of the atomNoSuchAtomTypeException
- atomType is not knownCopyright © 2021. All rights reserved.