io.reader
Class RandomAccessMDLReader

java.lang.Object
  extended by io.reader.RandomAccessMDLReader

public class RandomAccessMDLReader
extends java.lang.Object


Nested Class Summary
 class RandomAccessMDLReader.ParseThread
          this thread reads a molecule
 
Constructor Summary
RandomAccessMDLReader(java.io.File sdf)
          opens a buffered reader on mdl sd file
 
Method Summary
 java.util.Set<java.lang.String> getAllLabelClasses(java.lang.String label)
          returns all possible labels for this data set
 java.lang.String getLabel(int index, java.lang.String label)
          returns the mdl sd tag for the ith molecule
 java.lang.String getMDLMolString(int index)
          returns the ith molecule in the random access file as plain mol file (e.g. to display it with Marvin)
 org.openscience.cdk.Molecule getMol(int index)
          returns the ith molecule in the random access file
 int getSize()
          returns the number of structures contained in the MDL SD file
 boolean isRemoveHydrogens()
           
 void setRemoveHydrogens(boolean removeHydrogens)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

RandomAccessMDLReader

public RandomAccessMDLReader(java.io.File sdf)
                      throws java.io.IOException
opens a buffered reader on mdl sd file

Parameters:
sdf -
Throws:
java.io.IOException
Method Detail

getMDLMolString

public java.lang.String getMDLMolString(int index)
returns the ith molecule in the random access file as plain mol file (e.g. to display it with Marvin)

Parameters:
index -
Returns:

getLabel

public java.lang.String getLabel(int index,
                                 java.lang.String label)
returns the mdl sd tag for the ith molecule

Parameters:
index -
Returns:

getAllLabelClasses

public java.util.Set<java.lang.String> getAllLabelClasses(java.lang.String label)
returns all possible labels for this data set

Parameters:
label -
Returns:

getMol

public org.openscience.cdk.Molecule getMol(int index)
returns the ith molecule in the random access file

Parameters:
index -

getSize

public int getSize()
returns the number of structures contained in the MDL SD file

Returns:

isRemoveHydrogens

public boolean isRemoveHydrogens()

setRemoveHydrogens

public void setRemoveHydrogens(boolean removeHydrogens)