java.lang.Object
- com.actelion.research.chem.reaction.ReactionEncoder

public class ReactionEncoder
extends java.lang.Object

Field Summary

Fields
Modifier and Type	Field	Description
`static char`	`CATALYST_DELIMITER`
`static int`	`INCLUDE_ALL`
`static int`	`INCLUDE_CATALYSTS`
`static int`	`INCLUDE_COORDS`
`static int`	`INCLUDE_DEFAULT`
`static int`	`INCLUDE_DRAWING_OBJECTS`
`static int`	`INCLUDE_MAPPING`
`static int`	`INCLUDE_RXN_CODE_ONLY`
`static char`	`MOLECULE_DELIMITER`
`static java.lang.String`	`MOLECULE_DELIMITER_STRING`
`static char`	`OBJECT_DELIMITER`
`static java.lang.String`	`OBJECT_DELIMITER_STRING`
`static char`	`PRODUCT_IDENTIFIER`
`static int`	`RETAIN_REACTANT_AND_PRODUCT_ORDER`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static Reaction`	`decode(byte[] rxnCode, byte[] rxnMapping, byte[] rxnCoords, java.lang.String rxnObjects, byte[] rxnCatalysts, boolean ensureCoordinates)`	Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
`static Reaction`	`decode(java.lang.String s, boolean ensureCoordinates)`
`static Reaction`	`decode(java.lang.String s, boolean ensureCoordinates, Reaction rxn)`	Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class and are passed OBJECT_DELIMITER-delimited within one string.
`static Reaction`	`decode(java.lang.String s, int includeOptions, Reaction rxn)`	Creates a Reaction object by interpreting a reaction string encoded by this class.
`static Reaction`	`decode(java.lang.String rxnCode, java.lang.String rxnMapping, java.lang.String rxnCoords, java.lang.String rxnObjects, java.lang.String rxnCatalysts, boolean ensureCoordinates, Reaction rxn)`	Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
`static StereoMolecule[]`	`decodeCatalysts(byte[] rxnBytes)`	Generates an array of all catalysts of the encoded reaction string as bytes.
`static StereoMolecule[]`	`decodeMolecules(byte[] rxnBytes, byte[] coords, byte[] mapping, boolean includeReactants, boolean includeProducts)`	Generates an array of all reactants and/or products of the encoded reaction string as bytes.
`static StereoMolecule[]`	`decodeMolecules(java.lang.String s, boolean includeCoords, boolean includeMapping, boolean includeReactants, boolean includeProducts)`	Generates an array of all reactants and/or products of the encoded reaction string as bytes.
`static java.lang.String[]`	`encode(Reaction reaction, boolean keepAbsoluteCoordinates)`	Creates a String containing a unique reaction code by creating idcodes of every reactant and product and concatenating them in lexical order.
`static java.lang.String`	`encode(Reaction reaction, boolean keepAbsoluteCoordinates, int mode)`	Creates a String containing a reaction code by creating idcodes of every reactant and product and concatenating them in original (if mode includes RETAIN_REACTANT_AND_PRODUCT_ORDER) or in lexical order.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MOLECULE_DELIMITER
```
public static final char MOLECULE_DELIMITER
```
    See Also:
    
    Constant Field Values
  - PRODUCT_IDENTIFIER
```
public static final char PRODUCT_IDENTIFIER
```
    See Also:
    
    Constant Field Values
  - CATALYST_DELIMITER
```
public static final char CATALYST_DELIMITER
```
    See Also:
    
    Constant Field Values
  - OBJECT_DELIMITER
```
public static final char OBJECT_DELIMITER
```
    See Also:
    
    Constant Field Values
  - MOLECULE_DELIMITER_STRING
```
public static final java.lang.String MOLECULE_DELIMITER_STRING
```
    See Also:
    
    Constant Field Values
  - OBJECT_DELIMITER_STRING
```
public static final java.lang.String OBJECT_DELIMITER_STRING
```
    See Also:
    
    Constant Field Values
  - INCLUDE_MAPPING
```
public static final int INCLUDE_MAPPING
```
    See Also:
    
    Constant Field Values
  - INCLUDE_COORDS
```
public static final int INCLUDE_COORDS
```
    See Also:
    
    Constant Field Values
  - INCLUDE_DRAWING_OBJECTS
```
public static final int INCLUDE_DRAWING_OBJECTS
```
    See Also:
    
    Constant Field Values
  - INCLUDE_CATALYSTS
```
public static final int INCLUDE_CATALYSTS
```
    See Also:
    
    Constant Field Values
  - INCLUDE_ALL
```
public static final int INCLUDE_ALL
```
    See Also:
    
    Constant Field Values
  - INCLUDE_RXN_CODE_ONLY
```
public static final int INCLUDE_RXN_CODE_ONLY
```
    See Also:
    
    Constant Field Values
  - INCLUDE_DEFAULT
```
public static final int INCLUDE_DEFAULT
```
    See Also:
    
    Constant Field Values
  - RETAIN_REACTANT_AND_PRODUCT_ORDER
```
public static final int RETAIN_REACTANT_AND_PRODUCT_ORDER
```
    See Also:
    
    Constant Field Values
- Method Detail
  - encode
```
public static java.lang.String[] encode(Reaction reaction,
                                        boolean keepAbsoluteCoordinates)
```
    Creates a String containing a unique reaction code by creating idcodes of every reactant and product and concatenating them in lexical order. If mapping information is available this will be encoded in a 2nd string. Otherwise this will be null. Coordinates, if available, will be encoded in a 3rd string. If there are drawing objects assigned to this reaction then these are encoded in a 4th string.
    
    Returns:
    
    String[5] with reaction code, mapping, coordinates, drawing objects, catalysts
  - encode
```
public static java.lang.String encode(Reaction reaction,
                                      boolean keepAbsoluteCoordinates,
                                      int mode)
```
    Creates a String containing a reaction code by creating idcodes of every reactant and product and concatenating them in original (if mode includes RETAIN_REACTANT_AND_PRODUCT_ORDER) or in lexical order. In the latter case this string is a canonical reaction encoding. If mapping information is available this will be encoded in a 2nd string. Coordinates, if available, will be encoded in a 3rd string. If there are drawing objects assigned to this reaction then these are encoded in a 4th string.
    
    Returns:
    
    One String with reaction code, coordinates, mapping, drawing objects as defined by mode.
  - decode
```
public static Reaction decode(java.lang.String rxnCode,
                              java.lang.String rxnMapping,
                              java.lang.String rxnCoords,
                              java.lang.String rxnObjects,
                              java.lang.String rxnCatalysts,
                              boolean ensureCoordinates,
                              Reaction rxn)
```
    Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class. If rxnCoords are relative or null, and if ensureCoordinates==true then all reactants and products are placed automatically along a horizontal line.
    
    Returns:
    
    Reaction
  - decode
```
public static Reaction decode(byte[] rxnCode,
                              byte[] rxnMapping,
                              byte[] rxnCoords,
                              java.lang.String rxnObjects,
                              byte[] rxnCatalysts,
                              boolean ensureCoordinates)
```
    Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class. If rxnCoords are relative or null, and if ensureCoordinates==true then all reactants and products are placed automatically along a horizontal line.
    
    Returns:
    
    Reaction
  - decode
```
public static Reaction decode(java.lang.String s,
                              boolean ensureCoordinates)
```
  - decode
```
public static Reaction decode(java.lang.String s,
                              boolean ensureCoordinates,
                              Reaction rxn)
```
    Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class and are passed OBJECT_DELIMITER-delimited within one string. If rxnCoords are relative or null, and if ensureCoordinates==true then all reactants and products are placed automatically along a horizontal line.
    
    Returns:
    
    Reaction
  - decode
```
public static Reaction decode(java.lang.String s,
                              int includeOptions,
                              Reaction rxn)
```
    Creates a Reaction object by interpreting a reaction string encoded by this class. Include options define whether mapping, coordinates, catalysts, and drawing objects # are included in the reaction object.
    
    Parameters:
    
    s -
    
    includeOptions -
    
    Returns:
    
    Reaction
  - decodeMolecules
```
public static StereoMolecule[] decodeMolecules(java.lang.String s,
                                               boolean includeCoords,
                                               boolean includeMapping,
                                               boolean includeReactants,
                                               boolean includeProducts)
```
    Generates an array of all reactants and/or products of the encoded reaction string as bytes. If the string includes atom coordinates or if they are explicitly, these are used. At least one of includeReactants and includeProducts must be true.
    
    Parameters:
    
    s - encoded reaction
    
    includeReactants -
    
    includeProducts -
    
    includeMapping -
    
    Returns:
    
    null (if reactants or products are missing) or StereoMolecule array with at least one molecule
  - decodeMolecules
```
public static StereoMolecule[] decodeMolecules(byte[] rxnBytes,
                                               byte[] coords,
                                               byte[] mapping,
                                               boolean includeReactants,
                                               boolean includeProducts)
```
    Generates an array of all reactants and/or products of the encoded reaction string as bytes. If the string includes atom coordinates or if they are explicitly, these are used. At least one of includeReactants and includeProducts must be true.
    
    Parameters:
    
    rxnBytes - may contain atom coordinates
    
    coords - may be null
    
    mapping - may be null
    
    includeReactants -
    
    includeProducts -
    
    Returns:
    
    null (if reactants or products are missing) or StereoMolecule array with at least one molecule
  - decodeCatalysts
```
public static StereoMolecule[] decodeCatalysts(byte[] rxnBytes)
```
    Generates an array of all catalysts of the encoded reaction string as bytes. If the string includes atom coordinates, these are used.
    
    Parameters:
    
    rxnBytes -
    
    Returns:
    
    null or StereoMolecule array with at least one molecule

Class ReactionEncoder

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MOLECULE_DELIMITER

PRODUCT_IDENTIFIER

CATALYST_DELIMITER

OBJECT_DELIMITER

MOLECULE_DELIMITER_STRING

OBJECT_DELIMITER_STRING

INCLUDE_MAPPING

INCLUDE_COORDS

INCLUDE_DRAWING_OBJECTS

INCLUDE_CATALYSTS

INCLUDE_ALL

INCLUDE_RXN_CODE_ONLY

INCLUDE_DEFAULT

RETAIN_REACTANT_AND_PRODUCT_ORDER

Method Detail

encode

encode

decode

decode

decode

decode

decode

decodeMolecules

decodeMolecules

decodeCatalysts