org.helm.chemtoolkit

Class AbstractChemistryManipulator

java.lang.Object

org.helm.chemtoolkit.AbstractChemistryManipulator

public abstract class AbstractChemistryManipulator
extends Object

Author:

chistyakov

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractChemistryManipulator.OutputType OutputType image type
static class	AbstractChemistryManipulator.StType StType chemical notation type

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	SMILES_EXTENSION_SEPARATOR_REGEX

Constructor Summary

Constructors

Constructor and Description
AbstractChemistryManipulator()

Method Summary

Methods

Modifier and Type	Method and Description
protected abstract IBondBase	bindAtoms(IAtomBase atom1, IAtomBase atom2)
abstract String	canonicalize(String data) returns canonical smiles
abstract String	convert(String data, AbstractChemistryManipulator.StType type) convert input notation to another
String	convertExtendedSmiles(String data) convert extended smiles format to smiles with atom mappings
abstract String	convertMolecule(AbstractMolecule container, AbstractChemistryManipulator.StType type) produces chemical notation for input molecule
protected String	getExtension(String smiles)
abstract AbstractMolecule	getMolecule(String smiles, AttachmentList attachments) returns a molecule i)nstance of AbstractMolecule
abstract MoleculeInfo	getMoleculeInfo(AbstractMolecule container) returns molecule info like molecular formula,exact mass and molecular weight
protected IAtomBase	getNeighborAtom(IAtomBase rgroup)
protected List<String>	getRGroupsFromExtendedSmiles(String smiles)
protected abstract IStereoElementBase	getStereoInformation(AbstractMolecule container, IAtomBase rGroup, IAtomBase atom1, IAtomBase atom2)
AbstractMolecule	merge(AbstractMolecule firstContainer, IAtomBase firstRgroup, AbstractMolecule secondContainer, IAtomBase secondRgroup) merges second molecule to first using given rGroups
protected AttachmentList	mergeAttachments(AbstractMolecule container, AbstractMolecule secondContainer)
abstract byte[]	renderMol(String molFile, AbstractChemistryManipulator.OutputType outputType, int width, int height, int rgb) renders a image of given molecule
abstract byte[]	renderSequence(String sequence, AbstractChemistryManipulator.OutputType outputType, int width, int height, int rgb) renders a image of molecule
protected boolean	setStereoInformation(AbstractMolecule firstContainer, IAtomBase firstRgroup, AbstractMolecule secondContainer, IAtomBase secondRgroup, IAtomBase atom1, IAtomBase atom2) recycles and set stereo information on firstContaner
abstract boolean	validateSMILES(String smiles)

Methods inherited from class java.lang.Object

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

Field Detail

SMILES_EXTENSION_SEPARATOR_REGEX

protected static final String SMILES_EXTENSION_SEPARATOR_REGEX

See Also:

Constant Field Values

Constructor Detail

AbstractChemistryManipulator

public AbstractChemistryManipulator()

Method Detail

convertMolecule

public abstract String convertMolecule(AbstractMolecule container,
                     AbstractChemistryManipulator.StType type)
                                throws CTKException

produces chemical notation for input molecule

Parameters:

molecule -

type - of chemical notation

Returns:

String that represents input molecule

Throws:

CTKException

convert

public abstract String convert(String data,
             AbstractChemistryManipulator.StType type)
                        throws CTKException

convert input notation to another

Parameters:

data - chemical notation to convert

type - type of input data instance of AbstractChemistryManipulator.StType

Returns:

chemical notation

Throws:

CTKException

convertExtendedSmiles

public String convertExtendedSmiles(String data)

convert extended smiles format to smiles with atom mappings

Parameters:

data - chemical notation to convert

Returns:

chemical notation

validateSMILES

public abstract boolean validateSMILES(String smiles)

Parameters:

smiles - to validate

Returns:

true if smiles valid

getMoleculeInfo

public abstract MoleculeInfo getMoleculeInfo(AbstractMolecule container)
                                      throws CTKException

returns molecule info like molecular formula,exact mass and molecular weight

Parameters:

molecule - input AbstractMolecule

Returns:

org.helm.chemtoolkit.MoleculeInfo object

Throws:

CTKException - general ChemToolKit exception passed to HELMToolKit

canonicalize

public abstract String canonicalize(String data)
                             throws CTKException,
                                    CTKSmilesException

returns canonical smiles

Parameters:

smiles - to canonicalize

Returns:

canonicalized smiles

Throws:

CTKException - general ChemToolkit exception passed to HELMToolkit

CTKSmilesException

renderMol

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

renders a image of given molecule

Parameters:

molFile - for rendering

outputType - a image type instance of AbstractChemistryManipulator.OutputType

width - the image width

height - the image height

rgb - a color code of image background

Returns:

image

Throws:

CTKException

renderSequence

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

renders a image of molecule

Parameters:

sequence - for rendering

outputType - a image type instance of AbstractChemistryManipulator.OutputType

width - the image width

height - the image height

rgb - a color code of image background

Returns:

image

Throws:

CTKException

getMolecule

public abstract AbstractMolecule getMolecule(String smiles,
                           AttachmentList attachments)
                                      throws IOException,
                                             CTKException

returns a molecule i)nstance of AbstractMolecule

Parameters:

smiles - smiles string

attachments - instance of AttachmentList

Returns:

molecule instance of AbstractMolecule

Throws:

IOException

CTKException

merge

public AbstractMolecule merge(AbstractMolecule firstContainer,
                     IAtomBase firstRgroup,
                     AbstractMolecule secondContainer,
                     IAtomBase secondRgroup)
                       throws CTKException

merges second molecule to first using given rGroups

Parameters:

firstContainer - a first molecule to merge instance of AbstractMolecule

firstRgroup - atom of first molecule to be removed, the connected atom is used for merging, instance of IAtomBase

secondContainer - a second molecule to merge, instance of AbstractMolecule

secondRgroup - of second molecule to be removed, the connected atom is used for merging, instance of IAtomBase

Returns:

merged molecule instance of AbstractMolecule

Throws:

CTKException

setStereoInformation

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

recycles and set stereo information on firstContaner

Parameters:

firstContainer - a first molecule instance of AbstractMolecule

firstRgroup - atom to remove, instance of IAtomBase

secondContainer - a second molecule, instance of AbstractMolecule

secondRgroup - atom to remove, instance of IAtomBase

atom1 - atom connected to firstGroup

atom2 - atom connected to secondGroup

Throws:

CTKException

getRGroupsFromExtendedSmiles

protected List<String> getRGroupsFromExtendedSmiles(String smiles)

Parameters:

extendedSmiles -

Returns:

getNeighborAtom

protected IAtomBase getNeighborAtom(IAtomBase rgroup)
                             throws CTKException

Throws:

CTKException

getExtension

protected String getExtension(String smiles)

bindAtoms

protected abstract IBondBase bindAtoms(IAtomBase atom1,
                  IAtomBase atom2)
                                throws CTKException

Parameters:

atom1 -

atom2 -

Returns:

Throws:

CTKException

mergeAttachments

protected AttachmentList mergeAttachments(AbstractMolecule container,
                              AbstractMolecule secondContainer)
                                   throws CTKException

Parameters:

first -

second -

Returns:

Throws:

CTKException

getStereoInformation

protected abstract IStereoElementBase getStereoInformation(AbstractMolecule container,
                                      IAtomBase rGroup,
                                      IAtomBase atom1,
                                      IAtomBase atom2)
                                                    throws CTKException

Parameters:

molecule -

rGroup -

atom -

Returns:

Throws:

CTKException