chemaxon.naming

Class DocumentToStructure

java.lang.Object

chemaxon.naming.DocumentToStructure

@PublicAPI
public class DocumentToStructure
extends java.lang.Object

Since:

5.9

Author:

Daniel Bonniot

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BYTE
static java.lang.String	CHARACTER The starting character offset since the beginning of the document, for text formats (html, xml, txt).
static java.lang.String	CONFIDENCE The confidence that the structure is correct.
static java.lang.String	CONTEXT The context of the structure recognized in the text.
static java.lang.String	CONTEXT_INDEX Index of the hit inside the context.
static java.lang.String	DOC_AUTHOR
static java.lang.String	DOC_CREATION_DATE
static java.lang.String	DOC_LAST_AUTHOR
static java.lang.String	DOC_PATENT_ASSIGNEES The assignees of the patent, separated by newline characters.
static java.lang.String	DOC_PATENT_ID
static java.lang.String	DOC_PATENT_INVENTORS The inventors of the patent, separated by newline characters.
static java.lang.String	DOC_PATENT_IPC The IPC classification(s) for the patent, separated by newline characters.
static java.lang.String	DOC_PATENT_IPCR The IPCR classification(s) for the patent, separated by newline characters.
static java.lang.String	DOC_TITLE
static java.lang.String	DOCUMENT The file name of the source document.
static java.lang.String	DOCUMENT_METADATA
static java.lang.String	END_CHARACTER 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 The page number, if applicable (e.g.
static java.lang.String	SECTION The section of the document where the structure was found.
static java.lang.String	SOURCE_TEXT The source text, as it appears in the original document.
static java.lang.String	TYPE The type of source for the structure.
static java.lang.String	TYPE_CAS CAS Registry Number®.
static java.lang.String	TYPE_CDX Embedded ChemDraw structure.
static java.lang.String	TYPE_COMMON Common name.
static java.lang.String	TYPE_EC EC Number.
static java.lang.String	TYPE_GENERIC Generic name, for instance "C1-C4 alkyl".
static java.lang.String	TYPE_INCHI InChI string.
static java.lang.String	TYPE_ION Ion abbreviation, for instance K+ or Ca2+.
static java.lang.String	TYPE_MRV Embedded ChemAxon MRV structure.
static java.lang.String	TYPE_OSR Structure image recognized by Optical Structure Recognition.
static java.lang.String	TYPE_PEPTIDE Peptide notation, for instance Val-Gly-Ser-Ala.
static java.lang.String	TYPE_SMILES SMILES string.
static java.lang.String	TYPE_SYMYX Embedded Symyx/ISIS draw structure.
static java.lang.String	TYPE_SYSTEMATIC 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)
static MolImporter	process(java.lang.String text, java.lang.String options) Creates a MolImporter instance to import structures for 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

The source text, as it appears in the original document.

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Constant Field Values

DOCUMENT

public static final java.lang.String DOCUMENT

The file name of the source document.

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Constant Field Values

PAGE

public static final java.lang.String PAGE

The page number, if applicable (e.g. for a PDF document).

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Constant Field Values

CHARACTER

public static final java.lang.String CHARACTER

The starting character offset since the beginning of the document, for text formats (html, xml, txt).

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Constant Field Values

END_CHARACTER

public static final java.lang.String END_CHARACTER

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

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Constant Field Values

IDENTIFIER

public static final java.lang.String IDENTIFIER

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Constant Field Values

DOC_AUTHOR

public static final java.lang.String DOC_AUTHOR

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Constant Field Values

DOC_LAST_AUTHOR

public static final java.lang.String DOC_LAST_AUTHOR

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Constant Field Values

DOC_TITLE

public static final java.lang.String DOC_TITLE

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Constant Field Values

DOC_CREATION_DATE

public static final java.lang.String DOC_CREATION_DATE

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Constant Field Values

DOC_PATENT_ID

public static final java.lang.String DOC_PATENT_ID

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Constant Field Values

DOC_PATENT_IPC

public static final java.lang.String DOC_PATENT_IPC

The IPC classification(s) for the patent, separated by newline characters.

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Constant Field Values

DOC_PATENT_IPCR

public static final java.lang.String DOC_PATENT_IPCR

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

The assignees of the patent, separated by newline characters.

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Constant Field Values

DOC_PATENT_INVENTORS

public static final java.lang.String DOC_PATENT_INVENTORS

The inventors of the patent, separated by newline characters.

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Constant Field Values

DOCUMENT_METADATA

public static final java.lang.String DOCUMENT_METADATA

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Constant Field Values

CONFIDENCE

public static final java.lang.String CONFIDENCE

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".

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Constant Field Values

SECTION

public static final java.lang.String SECTION

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".

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Constant Field Values

CONTEXT

public static final java.lang.String CONTEXT

The context of the structure recognized in the text.

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Constant Field Values

CONTEXT_INDEX

public static final java.lang.String CONTEXT_INDEX

Index of the hit inside the context.

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Constant Field Values

TYPE

public static final java.lang.String TYPE

The type of source for the structure.

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TYPE_SYSTEMATIC, TYPE_COMMON, TYPE_GENERIC, TYPE_SMILES, TYPE_INCHI, TYPE_CAS, Constant Field Values

TYPE_SYSTEMATIC

public static final java.lang.String TYPE_SYSTEMATIC

Systematic name.

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Constant Field Values

TYPE_COMMON

public static final java.lang.String TYPE_COMMON

Common name.

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Constant Field Values

TYPE_GENERIC

public static final java.lang.String TYPE_GENERIC

Generic name, for instance "C1-C4 alkyl".

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Constant Field Values

TYPE_SMILES

public static final java.lang.String TYPE_SMILES

SMILES string.

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Constant Field Values

TYPE_INCHI

public static final java.lang.String TYPE_INCHI

InChI string.

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Constant Field Values

TYPE_CAS

public static final java.lang.String TYPE_CAS

CAS Registry Number^®.

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Constant Field Values

TYPE_EC

public static final java.lang.String TYPE_EC

EC Number.

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Constant Field Values

TYPE_ION

public static final java.lang.String TYPE_ION

Ion abbreviation, for instance K+ or Ca2+.

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Constant Field Values

TYPE_PEPTIDE

public static final java.lang.String TYPE_PEPTIDE

Peptide notation, for instance Val-Gly-Ser-Ala.

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Constant Field Values

TYPE_CDX

public static final java.lang.String TYPE_CDX

Embedded ChemDraw structure.

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Constant Field Values

TYPE_MRV

public static final java.lang.String TYPE_MRV

Embedded ChemAxon MRV structure.

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Constant Field Values

TYPE_SYMYX

public static final java.lang.String TYPE_SYMYX

Embedded Symyx/ISIS draw structure.

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Constant Field Values

TYPE_OSR

public static final java.lang.String TYPE_OSR

Structure image recognized by Optical Structure Recognition.

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Constant Field Values

Constructor Detail

DocumentToStructure

public DocumentToStructure()

Method Detail

process

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

process

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

Creates a MolImporter instance to import structures for 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.

Returns:

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

isMetadataMol

public static final boolean isMetadataMol(Molecule m)