DocumentToStructure (Marvin API documentation (c) 1998-2014 ChemAxon Ltd.)

java.lang.Object
- chemaxon.naming.DocumentToStructure

public class DocumentToStructure
extends Object

Since:: 5.9
Author:: Daniel Bonniot

Field Summary

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

Constructor Summary

Constructors
Constructor and Description

DocumentToStructure()

Constructors
Constructor and Description
`DocumentToStructure()`

Method Summary

Methods
Modifier and Type	Method and Description
`static MolImporter`	`process(String text)`
`static MolImporter`	`process(String text, 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 String SOURCE_TEXT
```
    The source text, as it appears in the original document.
    
    See Also:
    Constant Field Values
  - DOCUMENT
```
public static final String DOCUMENT
```
    The file name of the source document.
    
    See Also:
    Constant Field Values
  - PAGE
```
public static final String PAGE
```
    The page number, if applicable (e.g. for a PDF document).
    
    See Also:
    Constant Field Values
  - CHARACTER
```
public static final String CHARACTER
```
    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 String END_CHARACTER
```
    The ending character offset since the beginning of the document, for text formats (html, xml, txt).
    
    See Also:
    Constant Field Values
  - BYTE
```
public static final String BYTE
```
    See Also:
    Constant Field Values
  - DOC_AUTHOR
```
public static final String DOC_AUTHOR
```
    See Also:
    Constant Field Values
  - DOC_LAST_AUTHOR
```
public static final String DOC_LAST_AUTHOR
```
    See Also:
    Constant Field Values
  - DOC_TITLE
```
public static final String DOC_TITLE
```
    See Also:
    Constant Field Values
  - DOC_CREATION_DATE
```
public static final String DOC_CREATION_DATE
```
    See Also:
    Constant Field Values
  - DOC_PATENT_ID
```
public static final String DOC_PATENT_ID
```
    See Also:
    Constant Field Values
  - DOC_PATENT_IPC
```
public static final String DOC_PATENT_IPC
```
    The IPC classification(s) for the patent, separated by newline characters.
    
    See Also:
    Constant Field Values
  - DOC_PATENT_IPCR
```
public static final String DOC_PATENT_IPCR
```
    The IPCR classification(s) for the patent, separated by newline characters.
    
    See Also:
    Constant Field Values
  - DOC_PATENT_ASSIGNEES
```
public static final String DOC_PATENT_ASSIGNEES
```
    The assignees of the patent, separated by newline characters.
    
    See Also:
    Constant Field Values
  - DOC_PATENT_INVENTORS
```
public static final String DOC_PATENT_INVENTORS
```
    The inventors of the patent, separated by newline characters.
    
    See Also:
    Constant Field Values
  - DOCUMENT_METADATA
```
public static final String DOCUMENT_METADATA
```
    See Also:
    Constant Field Values
  - CONFIDENCE
```
public static final 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
  - SECTION
```
public static final 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".
    
    See Also:
    Constant Field Values
  - CONTEXT
```
public static final String CONTEXT
```
    The context of the structure recognized in the text.
    
    See Also:
    Constant Field Values
  - CONTEXT_INDEX
```
public static final String CONTEXT_INDEX
```
    Index of the hit inside the context.
    
    See Also:
    Constant Field Values
  - TYPE
```
public static final 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 String TYPE_SYSTEMATIC
```
    Systematic name.
    
    See Also:
    Constant Field Values
  - TYPE_COMMON
```
public static final String TYPE_COMMON
```
    Common name.
    
    See Also:
    Constant Field Values
  - TYPE_GENERIC
```
public static final String TYPE_GENERIC
```
    Generic name, for instance "C1-C4 alkyl".
    
    See Also:
    Constant Field Values
  - TYPE_SMILES
```
public static final String TYPE_SMILES
```
    SMILES string.
    
    See Also:
    Constant Field Values
  - TYPE_INCHI
```
public static final String TYPE_INCHI
```
    InChI string.
    
    See Also:
    Constant Field Values
  - TYPE_CAS
```
public static final String TYPE_CAS
```
    CAS number.
    
    See Also:
    Constant Field Values
  - TYPE_ION
```
public static final String TYPE_ION
```
    Ion abbreviation, for instance K+ or Ca2+.
    
    See Also:
    Constant Field Values
  - TYPE_PEPTIDE
```
public static final String TYPE_PEPTIDE
```
    Peptide notation, for instance Val-Gly-Ser-Ala.
    
    See Also:
    Constant Field Values
  - TYPE_CDX
```
public static final String TYPE_CDX
```
    Embedded ChemDraw structure.
    
    See Also:
    Constant Field Values
  - TYPE_MRV
```
public static final String TYPE_MRV
```
    Embedded ChemAxon MRV structure.
    
    See Also:
    Constant Field Values
  - TYPE_SYMYX
```
public static final String TYPE_SYMYX
```
    Embedded Symyx/ISIS draw structure.
    
    See Also:
    Constant Field Values
  - TYPE_OSR
```
public static final 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(String text)
```
  - process
```
public static MolImporter process(String text,
                  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.

Class DocumentToStructure

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SOURCE_TEXT

DOCUMENT

PAGE

CHARACTER

END_CHARACTER

BYTE

DOC_AUTHOR

DOC_LAST_AUTHOR

DOC_TITLE

DOC_CREATION_DATE

DOC_PATENT_ID

DOC_PATENT_IPC

DOC_PATENT_IPCR

DOC_PATENT_ASSIGNEES

DOC_PATENT_INVENTORS

DOCUMENT_METADATA

CONFIDENCE

SECTION

CONTEXT

CONTEXT_INDEX

TYPE

TYPE_SYSTEMATIC

TYPE_COMMON

TYPE_GENERIC

TYPE_SMILES

TYPE_INCHI

TYPE_CAS

TYPE_ION

TYPE_PEPTIDE

TYPE_CDX

TYPE_MRV

TYPE_SYMYX

TYPE_OSR

Constructor Detail

DocumentToStructure

Method Detail

process

process