chemaxon.naming.document

Class DocumentToStructure

java.lang.Object

chemaxon.naming.document.DocumentToStructure

Direct Known Subclasses:

DocumentToStructure

@PublicAPI
public class DocumentToStructure
extends java.lang.Object

A convenience class for dealing with String-based documents, such as TXT, HTML, or XML files. Also contains a number of property keys which can typically be extracted from documents and made available on the resulting molecules.

See the constructors of MolImporter for more general and common document to structure operations.

Since:

5.9

Author:

Daniel Bonniot

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BYTE For internal usage only.
static java.lang.String	CHARACTER Molecule property key on results: key of the molecule property which contains the starting character offset since the beginning of the document, for text formats (html, xml, txt).
static java.lang.String	CONFIDENCE Molecule property key on results: the confidence that the structure is correct.
static java.lang.String	CONTEXT Molecule property key on results: the context of the structure recognized in the text.
static java.lang.String	CONTEXT_INDEX Molecule property key on results: index of the hit inside the context.
static java.lang.String	DOC_AUTHOR Molecule property key on results: name of the principal author(s) of a document.
static java.lang.String	DOC_CREATION_DATE Molecule property key on results: the date on which the document was created.
static java.lang.String	DOC_LAST_AUTHOR Molecule property key on results: name of the last (most recent) author of a document.
static java.lang.String	DOC_PATENT_ASSIGNEES Molecule property key on results: the assignees of the patent, separated by newline characters.
static java.lang.String	DOC_PATENT_ID Molecule property key on results: the patent identifier.
static java.lang.String	DOC_PATENT_INVENTORS Molecule property key on results: the inventors of the patent, separated by newline characters.
static java.lang.String	DOC_PATENT_IPC Molecule property key on results: the IPC classification(s) for the patent, separated by newline characters.
static java.lang.String	DOC_PATENT_IPCR Molecule property key on results: the IPCR classification(s) for the patent, separated by newline characters.
static java.lang.String	DOC_TITLE Molecule property key on results: the title of the document.
static java.lang.String	DOCUMENT Molecule property key on results: the file name of the source document.
static java.lang.String	END_CHARACTER Molecule property key on results: key of the molecule property which contains the ending character offset since the beginning of the document, for text formats (html, xml, txt).
static java.lang.String	IDENTIFIER
static java.lang.String	PAGE Molecule property key on results: the page number, if applicable (e.g.
static java.lang.String	SECTION Molecule property key on results: the section of the document where the structure was found.
static java.lang.String	SOURCE_TEXT Molecule property key on results: the source text, as it appears in the original document.
static java.lang.String	TYPE Molecule property key on results: the type of source for the structure.
static java.lang.String	TYPE_CAS Possible value for the TYPE property: the source is a CAS Registry Number®.
static java.lang.String	TYPE_CDX Possible value for the TYPE property: the source is an embedded ChemDraw structure.
static java.lang.String	TYPE_COMMON Possible value for the TYPE property: the source is a common name.
static java.lang.String	TYPE_EC Possible value for the TYPE property: the source is an EC Number.
static java.lang.String	TYPE_GENERIC Possible value for the TYPE property: the source is a generic name, for instance "C1-C4 alkyl".
static java.lang.String	TYPE_INCHI Possible value for the TYPE property: the source is an InChI string.
static java.lang.String	TYPE_ION Possible value for the TYPE property: the source is an ion abbreviation, for instance K+ or Ca2+.
static java.lang.String	TYPE_MRV Possible value for the TYPE property: the source is an embedded ChemAxon MRV structure.
static java.lang.String	TYPE_OSR Possible value for the TYPE property: the source is a structure image recognized by Optical Structure Recognition.
static java.lang.String	TYPE_PEPTIDE Possible value for the TYPE property: the source is a peptide notation, for instance Val-Gly-Ser-Ala.
static java.lang.String	TYPE_SMILES Possible value for the TYPE property: the source is a SMILES string.
static java.lang.String	TYPE_SYMYX Possible value for the TYPE property: the source is an embedded Symyx/ISIS draw structure.
static java.lang.String	TYPE_SYSTEMATIC Possible value for the TYPE property: the source is a systematic name.

Constructor Summary

Constructors

Constructor and Description
DocumentToStructure()

Method Summary

Modifier and Type	Method and Description
static boolean	isMetadataMol(Molecule m)
static MolImporter	process(java.lang.String text) Creates a MolImporter instance to import structures from a given text using the default format options.
static MolImporter	process(java.lang.String text, java.lang.String options) Creates a MolImporter instance to import structures from a given text.

Methods inherited from class java.lang.Object

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

Field Detail

SOURCE_TEXT

public static final java.lang.String SOURCE_TEXT

Molecule property key on results: the source text, as it appears in the original document.

See Also:

Constant Field Values

DOCUMENT

public static final java.lang.String DOCUMENT

Molecule property key on results: the file name of the source document.

See Also:

Constant Field Values

PAGE

public static final java.lang.String PAGE

Molecule property key on results: the page number, if applicable (e.g. for a PDF document).

See Also:

Constant Field Values

CHARACTER

public static final java.lang.String CHARACTER

Molecule property key on results: key of the molecule property which contains the starting character offset since the beginning of the document, for text formats (html, xml, txt).

See Also:

Constant Field Values

END_CHARACTER

public static final java.lang.String END_CHARACTER

Molecule property key on results: key of the molecule property which contains the ending character offset since the beginning of the document, for text formats (html, xml, txt).

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Constant Field Values

BYTE

public static final java.lang.String BYTE

For internal usage only.

See Also:

Constant Field Values

IDENTIFIER

public static final java.lang.String IDENTIFIER

See Also:

Constant Field Values

DOC_AUTHOR

public static final java.lang.String DOC_AUTHOR

Molecule property key on results: name of the principal author(s) of a document.

See Also:

Constant Field Values

DOC_LAST_AUTHOR

public static final java.lang.String DOC_LAST_AUTHOR

Molecule property key on results: name of the last (most recent) author of a document.

See Also:

Constant Field Values

DOC_TITLE

public static final java.lang.String DOC_TITLE

Molecule property key on results: the title of the document.

See Also:

Constant Field Values

DOC_CREATION_DATE

public static final java.lang.String DOC_CREATION_DATE

Molecule property key on results: the date on which the document was created.

See Also:

Constant Field Values

DOC_PATENT_ID

public static final java.lang.String DOC_PATENT_ID

Molecule property key on results: the patent identifier.

See Also:

Constant Field Values

DOC_PATENT_IPC

public static final java.lang.String DOC_PATENT_IPC

Molecule property key on results: the IPC classification(s) for the patent, separated by newline characters.

See Also:

Constant Field Values

DOC_PATENT_IPCR

public static final java.lang.String DOC_PATENT_IPCR

Molecule property key on results: the IPCR classification(s) for the patent, separated by newline characters.

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Constant Field Values

DOC_PATENT_ASSIGNEES

public static final java.lang.String DOC_PATENT_ASSIGNEES

Molecule property key on results: the assignees of the patent, separated by newline characters.

See Also:

Constant Field Values

DOC_PATENT_INVENTORS

public static final java.lang.String DOC_PATENT_INVENTORS

Molecule property key on results: the inventors of the patent, separated by newline characters.

See Also:

Constant Field Values

CONFIDENCE

public static final java.lang.String CONFIDENCE

Molecule property key on results: the confidence that the structure is correct.

0 or less means very little confidence. 1 or more means high confidence.

This is currently set on image recognition, that is Optical Structure Recognition (OSR), also known as "chemical OCR".

See Also:

Constant Field Values

SECTION

public static final java.lang.String SECTION

Molecule property key on results: the section of the document where the structure was found.

This is currently supported only for US patents in the USPTO XML format, in which case the value of the property can be "abstract", "citation", "description" or "claim N".

See Also:

Constant Field Values

CONTEXT

public static final java.lang.String CONTEXT

Molecule property key on results: the context of the structure recognized in the text.

See Also:

CONTEXT_INDEX, Constant Field Values

CONTEXT_INDEX

public static final java.lang.String CONTEXT_INDEX

Molecule property key on results: index of the hit inside the context.

See Also:

CONTEXT, Constant Field Values

TYPE

public static final java.lang.String TYPE

Molecule property key on results: the type of source for the structure.

See Also:

TYPE_SYSTEMATIC, TYPE_COMMON, TYPE_GENERIC, TYPE_SMILES, TYPE_INCHI, TYPE_CAS, TYPE_EC, TYPE_ION, TYPE_PEPTIDE, TYPE_CDX, TYPE_MRV, TYPE_SYMYX, TYPE_OSR, Constant Field Values

TYPE_SYSTEMATIC

public static final java.lang.String TYPE_SYSTEMATIC

Possible value for the TYPE property: the source is a systematic name.

See Also:

Constant Field Values

TYPE_COMMON

public static final java.lang.String TYPE_COMMON

Possible value for the TYPE property: the source is a common name.

See Also:

Constant Field Values

TYPE_GENERIC

public static final java.lang.String TYPE_GENERIC

Possible value for the TYPE property: the source is a generic name, for instance "C1-C4 alkyl".

See Also:

Constant Field Values

TYPE_SMILES

public static final java.lang.String TYPE_SMILES

Possible value for the TYPE property: the source is a SMILES string.

See Also:

Constant Field Values

TYPE_INCHI

public static final java.lang.String TYPE_INCHI

Possible value for the TYPE property: the source is an InChI string.

See Also:

Constant Field Values

TYPE_CAS

public static final java.lang.String TYPE_CAS

Possible value for the TYPE property: the source is a CAS Registry Number^®.

See Also:

Constant Field Values

TYPE_EC

public static final java.lang.String TYPE_EC

Possible value for the TYPE property: the source is an EC Number.

See Also:

Constant Field Values

TYPE_ION

public static final java.lang.String TYPE_ION

Possible value for the TYPE property: the source is an ion abbreviation, for instance K+ or Ca2+.

See Also:

Constant Field Values

TYPE_PEPTIDE

public static final java.lang.String TYPE_PEPTIDE

Possible value for the TYPE property: the source is a peptide notation, for instance Val-Gly-Ser-Ala.

See Also:

Constant Field Values

TYPE_CDX

public static final java.lang.String TYPE_CDX

Possible value for the TYPE property: the source is an embedded ChemDraw structure.

See Also:

Constant Field Values

TYPE_MRV

public static final java.lang.String TYPE_MRV

Possible value for the TYPE property: the source is an embedded ChemAxon MRV structure.

See Also:

Constant Field Values

TYPE_SYMYX

public static final java.lang.String TYPE_SYMYX

Possible value for the TYPE property: the source is an embedded Symyx/ISIS draw structure.

See Also:

Constant Field Values

TYPE_OSR

public static final java.lang.String TYPE_OSR

Possible value for the TYPE property: the source is a structure image recognized by Optical Structure Recognition.

See Also:

Constant Field Values

Constructor Detail

DocumentToStructure

public DocumentToStructure()

Method Detail

process

public static MolImporter process(java.lang.String text)

Creates a MolImporter instance to import structures from a given text using the default format options.

A shorthand for process(text, null).

process

public static MolImporter process(java.lang.String text,
                                  java.lang.String options)

Creates a MolImporter instance to import structures from a given text.

Generally, the text is treated as plain text. However, for convenience, text that starts immediately with an XML or HTML prologue is recognized as such instead of plain text. For complete documents, a direct call to a MolImporter constructor is often more appropriate than loading the whole document into a String object.

The returned MolImporter instance does no actual resource management so closing it is not necessary.

Parameters:

text - the plain text or HTML/XML to process

options - the "d2s" format options passed to MolImporter or null if the default options should be used. Starting the String with "d2s:" is optional.

Returns:

a MolImporter that can be used to read the structures found in the text.

isMetadataMol

public static boolean isMetadataMol(Molecule m)