chemaxon.naming
Class DocumentToStructure

java.lang.Object
  chemaxon.naming.DocumentToStructure

public class DocumentToStructure
extends java.lang.Object

Since:

5.9

Author:

Daniel Bonniot

Field Summary

static java.lang.String	BYTE
static java.lang.String	CHARACTER The 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. 0 or less means very little confidence. 1 or more means high confidence.
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_TITLE
static java.lang.String	DOCUMENT The file name of the source document.
static java.lang.String	DOCUMENT_METADATA
static java.lang.String	PAGE The page number, if applicable (e.g. for a PDF document).
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 number.
static java.lang.String	TYPE_CDX Embedded ChemDraw structure.
static java.lang.String	TYPE_COMMON Common name.
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

DocumentToStructure()

Method Summary

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.

See Also:

Constant Field Values

DOCUMENT

public static final java.lang.String DOCUMENT

The file name of the source document.

See Also:

Constant Field Values

PAGE

public static final java.lang.String PAGE

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

See Also:

Constant Field Values

CHARACTER

public static final java.lang.String CHARACTER

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

See Also:

Constant Field Values

BYTE

public static final java.lang.String BYTE

See Also:

Constant Field Values

DOC_AUTHOR

public static final java.lang.String DOC_AUTHOR

See Also:

Constant Field Values

DOC_LAST_AUTHOR

public static final java.lang.String DOC_LAST_AUTHOR

See Also:

Constant Field Values

DOC_TITLE

public static final java.lang.String DOC_TITLE

See Also:

Constant Field Values

DOC_CREATION_DATE

public static final java.lang.String DOC_CREATION_DATE

See Also:

Constant Field Values

DOCUMENT_METADATA

public static final java.lang.String DOCUMENT_METADATA

See Also:

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".

See Also:

Constant Field Values

TYPE

public static final java.lang.String TYPE

The type of source for the structure.

See Also:

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.

See Also:

Constant Field Values

TYPE_COMMON

public static final java.lang.String TYPE_COMMON

Common name.

See Also:

Constant Field Values

TYPE_GENERIC

public static final java.lang.String TYPE_GENERIC

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

See Also:

Constant Field Values

TYPE_SMILES

public static final java.lang.String TYPE_SMILES

SMILES string.

See Also:

Constant Field Values

TYPE_INCHI

public static final java.lang.String TYPE_INCHI

InChI string.

See Also:

Constant Field Values

TYPE_CAS

public static final java.lang.String TYPE_CAS

CAS number.

See Also:

Constant Field Values

TYPE_ION

public static final java.lang.String TYPE_ION

Ion abbreviation, for instance K+ or Ca2+.

See Also:

Constant Field Values

TYPE_PEPTIDE

public static final java.lang.String TYPE_PEPTIDE

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

See Also:

Constant Field Values

TYPE_CDX

public static final java.lang.String TYPE_CDX

Embedded ChemDraw structure.

See Also:

Constant Field Values

TYPE_MRV

public static final java.lang.String TYPE_MRV

Embedded ChemAxon MRV structure.

See Also:

Constant Field Values

TYPE_SYMYX

public static final java.lang.String TYPE_SYMYX

Embedded Symyx/ISIS draw structure.

See Also:

Constant Field Values

TYPE_OSR

public static final java.lang.String TYPE_OSR

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)

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.