DocumentToStructure (Marvin API documentation (c) 1998-2021 ChemAxon Ltd.)

java.lang.Object
- chemaxon.naming.document.DocumentToStructure

Direct Known Subclasses:

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()

Constructors
Constructor and Description
`DocumentToStructure()`

Method Summary

All Methods Static Methods Concrete Methods
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
```
    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 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
```
    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 java.lang.String BYTE
```
    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
```
    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
  - DOC_PATENT_ID
```
public static final java.lang.String DOC_PATENT_ID
```
    See Also:
    
    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.
    
    See Also:
    
    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.
    
    See Also:
    
    Constant Field Values
  - DOC_PATENT_ASSIGNEES
```
public static final java.lang.String DOC_PATENT_ASSIGNEES
```
    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
```
    The inventors of the patent, separated by newline characters.
    
    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
  - 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".
    
    See Also:
    
    Constant Field Values
  - CONTEXT
```
public static final java.lang.String CONTEXT
```
    The context of the structure recognized in the text.
    
    See Also:
    
    Constant Field Values
  - CONTEXT_INDEX
```
public static final java.lang.String CONTEXT_INDEX
```
    Index of the hit inside the context.
    
    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 Registry Number^®.
    
    See Also:
    
    Constant Field Values
  - TYPE_EC
```
public static final java.lang.String TYPE_EC
```
    EC 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)
```
    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)
```

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

IDENTIFIER

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_EC

TYPE_ION

TYPE_PEPTIDE

TYPE_CDX

TYPE_MRV

TYPE_SYMYX

TYPE_OSR

Constructor Detail

DocumentToStructure

Method Detail

process

process

isMetadataMol