ambit2.smarts

Class Screening

java.lang.Object

ambit2.smarts.Screening

public class Screening
extends Object

Constructor Summary

Constructors

Constructor and Description
Screening(boolean useStrKeys) Fingerprints screening is on always
Screening(org.openscience.cdk.interfaces.IChemObjectBuilder builder) Screening by fingerprints and structural keys
Screening(List<String> externalSmartsKeys) structural keys by external file

Method Summary

Modifier and Type	Method and Description
boolean	bitSetCheck(BitSet query, BitSet target) Every bit set on in the query shouldbe present inthe target but the target can have more bits set on compared to the query
boolean	bitSetCheck(BitSet query, BitSet target, int nBits)
boolean	checkTarget(ScreeningData targetSD) PreScreening - run this after the query is set
String	getBitSetString(BitSet bs)
ScreeningData	getScreeningDataForTarget(org.openscience.cdk.interfaces.IAtomContainer ac) The ScreeningData for the target structure
BitSet	getStructureKeyBits(org.openscience.cdk.interfaces.IAtomContainer ac)
String	queryKeysToString()
void	setQuery(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query) obtained by SmartsParser - might not work by other QueryAtomContainer
BitSet	stringToBitSet(String s)
String	strKeysToString(BitSet bs)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Screening

public Screening(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
          throws Exception

Screening by fingerprints and structural keys

Throws:

Exception

Screening

public Screening(boolean useStrKeys)
          throws Exception

Fingerprints screening is on always

Parameters:

useStrKeys - whether to screen by structural keys

Throws:

Exception

Screening

public Screening(List<String> externalSmartsKeys)
          throws EmptyMoleculeException

structural keys by external file

Parameters:

externalSmartsKeys -

Throws:

EmptyMoleculeException

Method Detail

setQuery

public void setQuery(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
              throws Exception

obtained by SmartsParser - might not work by other QueryAtomContainer

Parameters:

query - search for this query

Throws:

Exception

checkTarget

public boolean checkTarget(ScreeningData targetSD)

PreScreening - run this after the query is set

Parameters:

targetSD -

Returns:

bitSetCheck

public boolean bitSetCheck(BitSet query,
                           BitSet target)

Every bit set on in the query shouldbe present inthe target but the target can have more bits set on compared to the query

Parameters:

query -

target -

Returns:

bitSetCheck

public boolean bitSetCheck(BitSet query,
                           BitSet target,
                           int nBits)

getScreeningDataForTarget

public ScreeningData getScreeningDataForTarget(org.openscience.cdk.interfaces.IAtomContainer ac)
                                        throws Exception

The ScreeningData for the target structure

Parameters:

ac -

Returns:

Throws:

Exception

getStructureKeyBits

public BitSet getStructureKeyBits(org.openscience.cdk.interfaces.IAtomContainer ac)

strKeysToString

public String strKeysToString(BitSet bs)

getBitSetString

public String getBitSetString(BitSet bs)

stringToBitSet

public BitSet stringToBitSet(String s)

queryKeysToString

public String queryKeysToString()