public class ChemaxonManipulator
extends org.helm.chemtoolkit.AbstractChemistryManipulator
| Modifier and Type | Field and Description |
|---|---|
static String |
CHEMAXON_EXTENDEND_SMILES_FORMAT |
static String |
SMILES_FORMAT |
static String |
UNIQUE_SMILES_FORMAT |
| Constructor and Description |
|---|
ChemaxonManipulator() |
| 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) |
public static final String UNIQUE_SMILES_FORMAT
public static final String SMILES_FORMAT
public static final String CHEMAXON_EXTENDEND_SMILES_FORMAT
public String convert(String data, org.helm.chemtoolkit.AbstractChemistryManipulator.StType type) throws org.helm.chemtoolkit.CTKException
convert in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionpublic boolean validateSMILES(String smiles)
validateSMILES in class org.helm.chemtoolkit.AbstractChemistryManipulatorpublic org.helm.chemtoolkit.MoleculeInfo getMoleculeInfo(org.helm.chemtoolkit.AbstractMolecule aMolecule)
throws org.helm.chemtoolkit.CTKException
getMoleculeInfo in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionpublic String canonicalize(String smiles) throws org.helm.chemtoolkit.CTKException, org.helm.chemtoolkit.CTKSmilesException
canonicalize in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionorg.helm.chemtoolkit.CTKSmilesExceptionpublic byte[] renderMol(String molFile, org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType outputType, int width, int height, int rgb) throws org.helm.chemtoolkit.CTKException
renderMol in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionpublic byte[] renderSequence(String sequence, org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType outputType, int width, int height, int rgb) throws org.helm.chemtoolkit.CTKException
renderSequence in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionpublic org.helm.chemtoolkit.AbstractMolecule getMolecule(String smiles, org.helm.chemtoolkit.AttachmentList attachments) throws IOException
getMolecule in class org.helm.chemtoolkit.AbstractChemistryManipulatorIOExceptionpublic org.helm.chemtoolkit.IBondBase bindAtoms(org.helm.chemtoolkit.IAtomBase atom1,
org.helm.chemtoolkit.IAtomBase atom2)
throws org.helm.chemtoolkit.CTKException
bindAtoms in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionpublic 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
getStereoInformation in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionpublic String convertMolecule(org.helm.chemtoolkit.AbstractMolecule container, org.helm.chemtoolkit.AbstractChemistryManipulator.StType type) throws org.helm.chemtoolkit.CTKException
convertMolecule in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionchemaxon.marvin.io.MolExportExceptionprotected 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
setStereoInformation in class org.helm.chemtoolkit.AbstractChemistryManipulatororg.helm.chemtoolkit.CTKExceptionCopyright © 2016. All rights reserved.