MDReader (JChem Base API documentation (c) 1998-2020 ChemAxon Ltd.)

java.lang.Object
- chemaxon.descriptors.MDReader

Direct Known Subclasses:

MDArrayReader, MDDBReader, MDFileReader
```
@PublicAPI
public abstract class MDReader
extends java.lang.Object
```
Base class definitions for MDSet input streams. Different descriptors types (as fingerprints, pharmacophore fingerprints) are handled in the same, a transparent manner. Derived classes may differ in the source of initial data they handle: standard molecular structure file, chemical descriptor set file (written by an MDWrite derivative), or database.
Each element read can either get a unique identifier (ID) from the source it comes from, or alternatively an ID can also be generated by the reader.
An MDSet object is returned by the reader in each call. This set can either be re-used or a new instance can be created. This behaviour is determined by setCloneResult( boolean ).

Since:

JChem 2.0

Author:

Miklos Vargyas

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`cloneResult` indicates if mdSet is cloned or not in `next()`
`protected int`	`firstId` starting value of id
`protected boolean`	`generateDescriptor` Generates descriptor from molecule if true, direct read otherwise.
`protected boolean`	`generateId` generate unique identifiers
`protected int`	`id` unique identifier (ID) of the current element read
`protected java.lang.String`	`idTagName` name of the tag in the SDfile input which stored the unique structure id
`protected Molecule`	`lastReadMolecule` the molecule last read from the structure table
`protected MDSet`	`mdSet` the schema mdSet if descriptors are generated on-the-fly
`protected java.util.List<java.lang.String>`	`takeTags` names of tags that have to be taken from the input Molecule

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`MDReader()` Creates an new, empty object.
`protected`	`MDReader(MDSet mdSet)` Creates a molecular structure file or database table reader.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`abstract void`	`close()` Closes down the descriptor stream.
`protected void`	`createMDSetComponent(int i, java.lang.String type, java.lang.String settings)` Creates and sets the given component of the internal `MDSet` object of the given type and specified parameter settings.
`boolean`	`getCloneResult()` Gets the current value of the cloning policy flag.
`MDSet`	`getMDSet()` Gets the molecular descriptor set.
`Molecule`	`getMolecule()` Gets the current molecular structure as read from the input file (that is before any transformation were applied).
`abstract MDSet`	`next()` Reads the next element from the input and stores it in the `MDSet` object passed as parameter.
`void`	`reset()` Initializes the `MDSet` input stream.
`void`	`setCloneResult(boolean cloneResult)` Sets the cloning policy of the `next()` method.
`void`	`setFirstId(int firstId)` Sets the ID of the first `MDSet`.
`void`	`setGenerateId(boolean generateId)` Sets whether ID-s are generated or not.
`void`	`setIdTagName(java.lang.String tagName)` Sets the name of the ID tag in the SDfile.
`void`	`setTakeTag(int cdSetComponent, java.lang.String tagName)` Sets the tag name of a `MDSet` component.

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

- Field Detail
  - id
```
protected int id
```
    unique identifier (ID) of the current element read
  - firstId
```
protected int firstId
```
    starting value of id
  - generateId
```
protected boolean generateId
```
    generate unique identifiers
  - generateDescriptor
```
protected boolean generateDescriptor
```
    Generates descriptor from molecule if true, direct read otherwise.
  - lastReadMolecule
```
protected Molecule lastReadMolecule
```
    the molecule last read from the structure table
  - mdSet
```
protected MDSet mdSet
```
    the schema mdSet if descriptors are generated on-the-fly
  - cloneResult
```
protected boolean cloneResult
```
    indicates if mdSet is cloned or not in next()
  - takeTags
```
protected java.util.List<java.lang.String> takeTags
```
    names of tags that have to be taken from the input Molecule
  - idTagName
```
protected java.lang.String idTagName
```
    name of the tag in the SDfile input which stored the unique structure id
- Constructor Detail
  - MDReader
```
protected MDReader(MDSet mdSet)
```
    Creates a molecular structure file or database table reader. The reader generates descriptors from the molecule read according to the MDSet parameter passed.
    
    Parameters:
    
    mdSet - a sample MDSet object that defines what should be read from the input source
  - MDReader
```
protected MDReader()
```
    Creates an new, empty object.
- Method Detail
  - setGenerateId
```
public void setGenerateId(boolean generateId)
```
    Sets whether ID-s are generated or not. Generated ID-s are positive integers.
    
    Parameters:
    
    generateId - ID-s are generated if true, otherwise ID-s are read from the input source
  - setTakeTag
```
public void setTakeTag(int cdSetComponent,
                       java.lang.String tagName)
```
    Sets the tag name of a MDSet component. If the name is not null, the value of the tag is taken from an SDfile input, otherwise, or in the case when the tag named does not exists in the input file, the desciptor of the specified component is generated.
    
    Parameters:
    
    cdSetComponent - index of a component of the MDSet
    
    tagName - name of the tag to take the value of the descriptor from
  - setIdTagName
```
public void setIdTagName(java.lang.String tagName)
```
    Sets the name of the ID tag in the SDfile. Unique indentifier is read from that tag if exists, otherwise the value of the identifier is undefined.
    
    Parameters:
    
    tagName - name of the ID tag
  - setFirstId
```
public void setFirstId(int firstId)
```
    Sets the ID of the first MDSet. If not set, ID numeration starts from 1.
    
    Parameters:
    
    firstId - value of the of the ID of the first MDSet
  - setCloneResult
```
public void setCloneResult(boolean cloneResult)
```
    Sets the cloning policy of the next() method. If set to true returned MDSet objects are new ones, otherswise always the same object is reused and returned (typically, this is passed in the constructor of the class derived from MDReader). By default, cloning policy is set to true. This is the safer option, though it might result in slower operation.
    
    Parameters:
    
    cloneResult - indicates cloning behaviour
  - getCloneResult
```
public boolean getCloneResult()
```
    Gets the current value of the cloning policy flag.
    
    Returns:
    
    indicator of cloning policy
  - getMDSet
```
public MDSet getMDSet()
```
    Gets the molecular descriptor set. This method is provided in order to allow the used intervene into descriptor generation (for instance by overriding parameter settings).
    
    Returns:
    
    the MDSet object
  - reset
```
public void reset()
           throws MDReaderException
```
    Initializes the MDSet input stream. If the stream is not empty, the subsequent call to next( MDSet cds ) returns the first element.
    
    Throws:
    
    MDReaderException - when failed to reset the reader
  - next
```
public abstract MDSet next()
                    throws MDReaderException
```
    Reads the next element from the input and stores it in the MDSet object passed as parameter. This method should be called by the next( ) method of the derived class as the first statement. It clones the internal MDSet instance if needed and increments the id (if id-s are generated).
    
    Returns:
    
    the MDSet to be filled in with the next descriptor
    
    Throws:
    
    MDReaderException - when failed reading the next descriptor set
  - getMolecule
```
public Molecule getMolecule()
                     throws MDReaderException
```
    Gets the current molecular structure as read from the input file (that is before any transformation were applied). Not all MDReader subclasses can implement this method in a meaningful way, therefore it is not an abstract method (just for the sake of ease).
    
    Returns:
    
    always null, see subclasses for meaningful implementation
    
    Throws:
    
    MDReaderException - when failed reading the next descriptor set
  - close
```
public abstract void close()
                    throws MDReaderException
```
    Closes down the descriptor stream. After this, no more operation is permitted on the stream.
    
    Throws:
    
    MDReaderException - when failed to close the input stream
  - createMDSetComponent
```
protected void createMDSetComponent(int i,
                                    java.lang.String type,
                                    java.lang.String settings)
                             throws MDParametersException
```
    Creates and sets the given component of the internal MDSet object of the given type and specified parameter settings.
    
    Parameters:
    
    i - index of the component
    
    type - class name of the component
    
    settings - parameter settings
    
    Throws:
    
    MDParametersException

Class MDReader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

id

firstId

generateId

generateDescriptor

lastReadMolecule

mdSet

cloneResult

takeTags

idTagName

Constructor Detail

MDReader

MDReader

Method Detail

setGenerateId

setTakeTag

setIdTagName

setFirstId

setCloneResult

getCloneResult

getMDSet

reset

next

getMolecule

close

createMDSetComponent