org.helm.chemtoolkit.chemaxon

Class ChemaxonManipulator

java.lang.Object

org.helm.chemtoolkit.AbstractChemistryManipulator

org.helm.chemtoolkit.chemaxon.ChemaxonManipulator

public class ChemaxonManipulator
extends org.helm.chemtoolkit.AbstractChemistryManipulator

Author:

chistyakov

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

Modifier and Type	Field and Description
static String	CHEMAXON_EXTENDEND_SMILES_FORMAT
static String	SMILES_FORMAT
static String	UNIQUE_SMILES_FORMAT

Fields inherited from class org.helm.chemtoolkit.AbstractChemistryManipulator

SMILES_EXTENSION_SEPARATOR_REGEX

Constructor Summary

Constructors

Constructor and Description
ChemaxonManipulator()

Method Summary

Methods

Modifier and Type	Method and Description
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)
org.helm.chemtoolkit.AbstractMolecule	getMolecule(String smiles, org.helm.chemtoolkit.AttachmentList attachments)
org.helm.chemtoolkit.MoleculeInfo	getMoleculeInfo(org.helm.chemtoolkit.AbstractMolecule aMolecule)
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)
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

Field Detail

UNIQUE_SMILES_FORMAT

public static final String UNIQUE_SMILES_FORMAT

See Also:

Constant Field Values

SMILES_FORMAT

public static final String SMILES_FORMAT

See Also:

Constant Field Values

CHEMAXON_EXTENDEND_SMILES_FORMAT

public static final String CHEMAXON_EXTENDEND_SMILES_FORMAT

See Also:

Constant Field Values

Constructor Detail

ChemaxonManipulator

public ChemaxonManipulator()

Method Detail

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

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

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 smiles,
                                                org.helm.chemtoolkit.AttachmentList attachments)
                                                  throws IOException

Specified by:

getMolecule in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

IOException

bindAtoms

public 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

public 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)
                                                             throws org.helm.chemtoolkit.CTKException

Specified by:

getStereoInformation in class org.helm.chemtoolkit.AbstractChemistryManipulator

Throws:

org.helm.chemtoolkit.CTKException

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

chemaxon.marvin.io.MolExportException

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