Package org.helm.chemtoolkit.cdk

Class CDKManipulator

java.lang.Object

org.helm.chemtoolkit.AbstractChemistryManipulator

org.helm.chemtoolkit.cdk.CDKManipulator

public class CDKManipulator
extends org.helm.chemtoolkit.AbstractChemistryManipulator

Nested Class Summary

Nested classes/interfaces inherited from class org.helm.chemtoolkit.AbstractChemistryManipulator

org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType, org.helm.chemtoolkit.AbstractChemistryManipulator.StType

Field Summary

Fields inherited from class org.helm.chemtoolkit.AbstractChemistryManipulator

SMILES_EXTENSION_SEPARATOR_REGEX

Constructor Summary

Constructors

Constructor	Description
CDKManipulator()

Method Summary

Modifier and Type	Method	Description
protected org.helm.chemtoolkit.IBondBase	bindAtoms(org.helm.chemtoolkit.IAtomBase atom1, org.helm.chemtoolkit.IAtomBase atom2)
String	canonicalize(String smiles)
String	convert(String data, org.helm.chemtoolkit.AbstractChemistryManipulator.StType type)
String	convertMolecule(org.helm.chemtoolkit.AbstractMolecule container, org.helm.chemtoolkit.AbstractChemistryManipulator.StType type)
String	convertMolIntoSmilesWithAtomMapping(String molfile)
org.helm.chemtoolkit.AbstractMolecule	getMolecule(String data, org.helm.chemtoolkit.AttachmentList attachments)
org.helm.chemtoolkit.MoleculeInfo	getMoleculeInfo(org.helm.chemtoolkit.AbstractMolecule aMolecule)
protected org.helm.chemtoolkit.IStereoElementBase	getStereoInformation(org.helm.chemtoolkit.AbstractMolecule molecule, org.helm.chemtoolkit.IAtomBase rGroup, org.helm.chemtoolkit.IAtomBase atom1, org.helm.chemtoolkit.IAtomBase atom2)
boolean	isConnected(String molfile)
byte[]	renderMol(String molFile, org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType outputType, int width, int height, int rgb)
byte[]	renderSequence(String sequence, org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType outputType, int width, int height, int rgb)
protected boolean	setStereoInformation(org.helm.chemtoolkit.AbstractMolecule firstContainer, org.helm.chemtoolkit.IAtomBase firstRgroup, org.helm.chemtoolkit.AbstractMolecule secondContainer, org.helm.chemtoolkit.IAtomBase secondRgroup, org.helm.chemtoolkit.IAtomBase atom1, org.helm.chemtoolkit.IAtomBase atom2)
boolean	validateSMILES(String smiles)

Methods inherited from class org.helm.chemtoolkit.AbstractChemistryManipulator

convertExtendedSmiles, getExtension, getNeighborAtom, getRGroupsFromExtendedSmiles, merge, mergeAttachments

Methods inherited from class java.lang.Object

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

Constructor Detail

CDKManipulator

public CDKManipulator()

Method Detail

validateSMILES

public boolean validateSMILES(String smiles)

Specified by:

validateSMILES in class org.helm.chemtoolkit.AbstractChemistryManipulator

getMoleculeInfo

public org.helm.chemtoolkit.MoleculeInfo getMoleculeInfo(org.helm.chemtoolkit.AbstractMolecule aMolecule)
                                                  throws org.helm.chemtoolkit.CTKException

Specified by:

getMoleculeInfo in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

convertMolIntoSmilesWithAtomMapping

public String convertMolIntoSmilesWithAtomMapping(String molfile)
                                           throws org.helm.chemtoolkit.CTKException

Specified by:

convertMolIntoSmilesWithAtomMapping in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

isConnected

public boolean isConnected(String molfile)
                    throws org.helm.chemtoolkit.CTKException

Specified by:

isConnected in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

convert

public String convert(String data,
                      org.helm.chemtoolkit.AbstractChemistryManipulator.StType type)
               throws org.helm.chemtoolkit.CTKException

Specified by:

convert in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

canonicalize

public String canonicalize(String smiles)
                    throws org.helm.chemtoolkit.CTKException,
                           org.helm.chemtoolkit.CTKSmilesException

Specified by:

canonicalize in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

org.helm.chemtoolkit.CTKSmilesException

renderMol

public byte[] renderMol(String molFile,
                        org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType outputType,
                        int width,
                        int height,
                        int rgb)
                 throws org.helm.chemtoolkit.CTKException

Specified by:

renderMol in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

renderSequence

public byte[] renderSequence(String sequence,
                             org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType outputType,
                             int width,
                             int height,
                             int rgb)
                      throws org.helm.chemtoolkit.CTKException

Specified by:

renderSequence in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

getMolecule

public org.helm.chemtoolkit.AbstractMolecule getMolecule(String data,
                                                         org.helm.chemtoolkit.AttachmentList attachments)
                                                  throws org.helm.chemtoolkit.CTKException

Specified by:

getMolecule in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

bindAtoms

protected org.helm.chemtoolkit.IBondBase bindAtoms(org.helm.chemtoolkit.IAtomBase atom1,
                                                   org.helm.chemtoolkit.IAtomBase atom2)
                                            throws org.helm.chemtoolkit.CTKException

Specified by:

bindAtoms in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

getStereoInformation

protected org.helm.chemtoolkit.IStereoElementBase getStereoInformation(org.helm.chemtoolkit.AbstractMolecule molecule,
                                                                       org.helm.chemtoolkit.IAtomBase rGroup,
                                                                       org.helm.chemtoolkit.IAtomBase atom1,
                                                                       org.helm.chemtoolkit.IAtomBase atom2)

Specified by:

getStereoInformation in class org.helm.chemtoolkit.AbstractChemistryManipulator

Parameters:

molecule - given molecule

rGroup - given rgroup

atom1 - given atom1

atom2 - given atom2

Returns:

IStereoElementBase

convertMolecule

public String convertMolecule(org.helm.chemtoolkit.AbstractMolecule container,
                              org.helm.chemtoolkit.AbstractChemistryManipulator.StType type)
                       throws org.helm.chemtoolkit.CTKException

Specified by:

convertMolecule in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

setStereoInformation

protected boolean setStereoInformation(org.helm.chemtoolkit.AbstractMolecule firstContainer,
                                       org.helm.chemtoolkit.IAtomBase firstRgroup,
                                       org.helm.chemtoolkit.AbstractMolecule secondContainer,
                                       org.helm.chemtoolkit.IAtomBase secondRgroup,
                                       org.helm.chemtoolkit.IAtomBase atom1,
                                       org.helm.chemtoolkit.IAtomBase atom2)
                                throws org.helm.chemtoolkit.CTKException

Overrides:

setStereoInformation in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException