MDGenerator (Marvin API documentation (c) 1998-2020 ChemAxon Ltd.)

java.lang.Object
- chemaxon.descriptors.MDGenerator

Direct Known Subclasses:

BCUTGenerator, CFGenerator, ECFPGenerator, PFGenerator, RFGenerator, ShapeGenerator
```
@PublicAPI
public abstract class MDGenerator
extends java.lang.Object
```
Base class for all kinds of MolecularDescriptor generators. Its main purpose is two-fold: (1) defines an interface for all generator classes (that is, what methods should be implemented), (2) implements function for gather statistical data on descriptor generated and retrieval functions for these statistics.

Since:

JChem 2.1

Author:

Miklos Vargyas

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`createStatistics` indicates if statistical data has to be gathered during generation
`protected int[]`	`density`
`protected int[]`	`freqCount`
`protected int`	`maxNonEmptyId`
`protected float`	`maxNonEmptyPercent`
`protected int`	`minNonEmptyId`
`protected float`	`minNonEmptyPercent`
`protected int`	`molCount` variables to collect statistical data in
`protected float`	`sumNonEmptyPercent`

Constructor Summary

Constructors
Constructor and Description

MDGenerator()
Created an object.

Constructors
Constructor and Description
`MDGenerator()` Created an object.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`protected int`	`calcFreqCount(MolecularDescriptor d)` Calculate and store in `freqCount[]` absolute frequency counts per cells.
`abstract java.lang.String[]`	`generate(Molecule m, MolecularDescriptor d)` Generates the molecular descriptor for the given molecule.
`float`	`getAverageNonZeroRatio()` Gets the average percentage of cells that have non-zero value taken all descriptors generated since the initialization of the generator into account.
`int`	`getBrightestMolId()` Gets the id of that molecule which had the maximum number of non-zero cells among all descriptors generated since the initialization of the generator object.
`int`	`getDarkestMolId()` Gets the id of that molecule which had the minimum number of non-zero cells among all descriptors generated since the initialization of the generator object.
`int[]`	`getDensityCounts()` Gets the array of bit density.
`int[]`	`getFrequencyCounts()` Gets the absolute frequence count array for all descriptors generated.
`float`	`getMaximumBitRatio()` Gets the maximum percentage of non-zero cells in descriptors generated.
`float`	`getMinimumBitRatio()` Gets the minimum percentage of non-zero cells in descriptors generated.
`int`	`getMoleculeCount()` Gets the number of molecules processed (that is, the number of descriptors generated) since the initialization of the object.
`void`	`setCreateStatistics(boolean createStatistics)` Toggles the create statistics flag.
`protected void`	`updateStatistics(MolecularDescriptor d)` Updates statistics gathered on fingerprints generated.

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

- Field Detail
  - createStatistics
```
protected boolean createStatistics
```
    indicates if statistical data has to be gathered during generation
  - molCount
```
protected int molCount
```
    variables to collect statistical data in
  - minNonEmptyPercent
```
protected float minNonEmptyPercent
```
  - minNonEmptyId
```
protected int minNonEmptyId
```
  - maxNonEmptyPercent
```
protected float maxNonEmptyPercent
```
  - maxNonEmptyId
```
protected int maxNonEmptyId
```
  - sumNonEmptyPercent
```
protected float sumNonEmptyPercent
```
  - freqCount
```
protected int[] freqCount
```
  - density
```
protected int[] density
```
- Constructor Detail
  - MDGenerator
```
public MDGenerator()
```
    Created an object.
- Method Detail
  - generate
```
public abstract java.lang.String[] generate(Molecule m,
                                            MolecularDescriptor d)
                                     throws MDGeneratorException
```
    Generates the molecular descriptor for the given molecule. The MolecularDescriptor provided is updated (thus it has to be allocated and initialized by the client of this class).
    
    Parameters:
    
    m - molecule for which the descriptor is created
    
    d - the generated descriptor
    
    Returns:
    
    names of tags (properties) added
    
    Throws:
    
    MDGeneratorException - in the case of any failures to generate the descriptor
  - setCreateStatistics
```
public void setCreateStatistics(boolean createStatistics)
```
    Toggles the create statistics flag.
    
    Parameters:
    
    createStatistics - new value for the create statistics flag
    
    Since:
    
    JChem 2.1
  - updateStatistics
```
protected void updateStatistics(MolecularDescriptor d)
```
    Updates statistics gathered on fingerprints generated.
    
    Parameters:
    
    d - newly generated MolecularDescriptor
    
    Since:
    
    JChem 2.1
  - calcFreqCount
```
protected int calcFreqCount(MolecularDescriptor d)
```
    Calculate and store in freqCount[] absolute frequency counts per cells. Also gets number of non-zero cells in the descriptor.
    
    Parameters:
    
    d - descriptor in which non-zero cells should be counted
    
    Returns:
    
    number of non-zero cells
  - getMoleculeCount
```
public int getMoleculeCount()
```
    Gets the number of molecules processed (that is, the number of descriptors generated) since the initialization of the object.
    
    Returns:
    
    number of molecules processed
  - getAverageNonZeroRatio
```
public float getAverageNonZeroRatio()
```
    Gets the average percentage of cells that have non-zero value taken all descriptors generated since the initialization of the generator into account.
    
    Returns:
    
    relative number of bits set in descriptors
  - getMaximumBitRatio
```
public float getMaximumBitRatio()
```
    Gets the maximum percentage of non-zero cells in descriptors generated.
    
    Returns:
    
    maximum bits set, relative to descriptor length
  - getBrightestMolId
```
public int getBrightestMolId()
```
    Gets the id of that molecule which had the maximum number of non-zero cells among all descriptors generated since the initialization of the generator object.
    
    Returns:
    
    unique molecule identifier (a consequtive index from zero)
  - getMinimumBitRatio
```
public float getMinimumBitRatio()
```
    Gets the minimum percentage of non-zero cells in descriptors generated.
    
    Returns:
    
    minimum bits set, relative to descriptor length
  - getDarkestMolId
```
public int getDarkestMolId()
```
    Gets the id of that molecule which had the minimum number of non-zero cells among all descriptors generated since the initialization of the generator object.
    
    Returns:
    
    unique molecule identifier (a consequtive index from zero)
  - getDensityCounts
```
public int[] getDensityCounts()
```
    Gets the array of bit density. The array can be indexed from 0 to 10. Index i returns the number of descriptors in which the ratio non-zero cells is between 10 * i and 10 * i + 10.
    
    Returns:
    
    array of density counts
  - getFrequencyCounts
```
public int[] getFrequencyCounts()
```
    Gets the absolute frequence count array for all descriptors generated. Each element of the array stores the number of descriptors in which the corresponding cell had non-zero value.
    
    Returns:
    
    per-cell frequency count array

Class MDGenerator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

createStatistics

molCount

minNonEmptyPercent

minNonEmptyId

maxNonEmptyPercent

maxNonEmptyId

sumNonEmptyPercent

freqCount

density

Constructor Detail

MDGenerator

Method Detail

generate

setCreateStatistics

updateStatistics

calcFreqCount

getMoleculeCount

getAverageNonZeroRatio

getMaximumBitRatio

getBrightestMolId

getMinimumBitRatio

getDarkestMolId

getDensityCounts

getFrequencyCounts