OverlapAnalysisContextFactory (overlap-examples-cli-dist 0.3.5 API)

java.lang.Object
- com.chemaxon.overlap.OverlapAnalysisContextFactory

@Beta
public final class OverlapAnalysisContextFactory
extends Object

Collections of overlap analysis contexts.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`DEFAULT_PHARMA_CALC_CONFIG_XML` Default configuration XML for pharma-calc fingerprints.
`static String`	`DEFAULT_PHARMA_FRAG_CONFIG_XML` Default configuration XML for pharma-frag fingerprints.
`static String`	`STANDARDIZER_DEFAULTAROMA_CONFIG_XML` Standardizer configuration XML for default aromatization.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static String`	`collectContextNames()` Collect applicable names.
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createMaccs166Context()` Maccs-166 implementation.
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleCfp10Context()`
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleCfp4Context()` Simple CFP-4-1 based context.
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleCfp5Context()`
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleCfp6Context()`
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleCfp7Context()`
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleCfp8Context()`
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleCfp9Context()`
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleEcfp10Context()` Simple ECFP-10 based context;
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleEcfp4Context()` Simple ECFP-4 based context;
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleEcfp6Context()` Simple ECFP-6 based context;
`static OverlapAnalysisContext<BinaryVectorDescriptor,long[]>`	`createSimpleEcfp8Context()` Simple ECFP-8 based context;
`static OverlapAnalysisContext<FloatVectorDescriptor,Serializable>`	`createSimplePharmaCalcContext()` Simple default PharmaCalc based context;
`static OverlapAnalysisContext`	`createtContextByName(String contextName)` Get context by name.
`static OverlapAnalysisContext<ShapeDescriptor,byte[]>`	`screen3d()` 3D alignment based shape descriptor context with default parameters.
`static OverlapAnalysisContext<DRShapeDescriptor,byte[]>`	`screen3dr()` Distance range assisted 3D alignment based shape descriptor context with default parameters.

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

- Field Detail
  - STANDARDIZER_DEFAULTAROMA_CONFIG_XML
```
public static final String STANDARDIZER_DEFAULTAROMA_CONFIG_XML
```
    Standardizer configuration XML for default aromatization.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_PHARMA_FRAG_CONFIG_XML
```
public static final String DEFAULT_PHARMA_FRAG_CONFIG_XML
```
    Default configuration XML for pharma-frag fingerprints.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_PHARMA_CALC_CONFIG_XML
```
public static final String DEFAULT_PHARMA_CALC_CONFIG_XML
```
    Default configuration XML for pharma-calc fingerprints.
    
    See Also:
    
    Constant Field Values
- Method Detail
  - screen3d
```
public static OverlapAnalysisContext<ShapeDescriptor,byte[]> screen3d()
```
    3D alignment based shape descriptor context with default parameters.
    
    Returns:
    
    the created context
  - screen3dr
```
public static OverlapAnalysisContext<DRShapeDescriptor,byte[]> screen3dr()
```
    Distance range assisted 3D alignment based shape descriptor context with default parameters.
    
    Returns:
    
    the created context
  - createMaccs166Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createMaccs166Context()
```
    Maccs-166 implementation.
    
    Returns:
    
    The created context
  - createSimpleCfp4Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleCfp4Context()
```
    Simple CFP-4-1 based context.
    
    Returns:
    
    Context for CFP-4-1 based overlap analysis
  - createSimpleCfp5Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleCfp5Context()
```
  - createSimpleCfp6Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleCfp6Context()
```
  - createSimpleCfp7Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleCfp7Context()
```
  - createSimpleCfp8Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleCfp8Context()
```
  - createSimpleCfp9Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleCfp9Context()
```
  - createSimpleCfp10Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleCfp10Context()
```
  - createSimpleEcfp4Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleEcfp4Context()
```
    Simple ECFP-4 based context;
    
    Returns:
    
    Context for ECFP-4 based overlap analysis
  - createSimpleEcfp6Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleEcfp6Context()
```
    Simple ECFP-6 based context;
    
    Returns:
    
    Context for ECFP-6 based overlap analysis
  - createSimpleEcfp8Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleEcfp8Context()
```
    Simple ECFP-8 based context;
    
    Returns:
    
    Context for ECFP-8 based overlap analysis
  - createSimpleEcfp10Context
```
public static OverlapAnalysisContext<BinaryVectorDescriptor,long[]> createSimpleEcfp10Context()
```
    Simple ECFP-10 based context;
    
    Returns:
    
    Context for ECFP-10 based overlap analysis
  - createSimplePharmaCalcContext
```
public static OverlapAnalysisContext<FloatVectorDescriptor,Serializable> createSimplePharmaCalcContext()
```
    Simple default PharmaCalc based context;
    
    Returns:
    
    Context for Pharma-calc based overlap analysis
  - createtContextByName
```
public static OverlapAnalysisContext createtContextByName(String contextName)
                                                   throws IllegalArgumentException
```
    Get context by name.
    This is a simple wrapper method for using reflection to invoke the factory method specified by the argument string.
    
    Parameters:
    
    contextName - Context name to create; use "createSimpleEcfp4Context" to invoke createSimpleEcfp4Context() or "createSimplePharmaCalcContext" to invoke createSimplePharmaCalcContext(). Alternatively context parameterization is also available here, consult ParameterizedContextFactory.createContext(String) for details.
    
    Returns:
    
    Created context
    
    Throws:
    
    IllegalArgumentException - when instantiation failed
  - collectContextNames
```
public static String collectContextNames()
```
    Collect applicable names.
    
    Returns:
    
    Applicable names in a human readable

Class OverlapAnalysisContextFactory

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

STANDARDIZER_DEFAULTAROMA_CONFIG_XML

DEFAULT_PHARMA_FRAG_CONFIG_XML

DEFAULT_PHARMA_CALC_CONFIG_XML

Method Detail

screen3d

screen3dr

createMaccs166Context

createSimpleCfp4Context

createSimpleCfp5Context

createSimpleCfp6Context

createSimpleCfp7Context

createSimpleCfp8Context

createSimpleCfp9Context

createSimpleCfp10Context

createSimpleEcfp4Context

createSimpleEcfp6Context

createSimpleEcfp8Context

createSimpleEcfp10Context

createSimplePharmaCalcContext

createtContextByName

collectContextNames