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

java.lang.Object
- chemaxon.naming.document.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()

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
```
    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).
    
    See Also:
    
    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.
    
    See Also:
    
    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)
```

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

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