ambit2.smarts

Class ChemObjectFactory

java.lang.Object

ambit2.smarts.ChemObjectFactory

public class ChemObjectFactory
extends Object

Utilities for generation of different types of chemical objects: molecules, fragments, queries

Field Summary

Fields

Modifier and Type	Field and Description
List<SequenceElement>	sequence

Constructor Summary

Constructors

Constructor and Description
ChemObjectFactory(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
ArrayList<String>	attachGroupToAllStructures(String groupSmiles, int groupAttachPos, ArrayList<String> inputSmiles, int strDefaultPos)
org.openscience.cdk.interfaces.IAtomContainer	condenseStructures(org.openscience.cdk.interfaces.IAtomContainer str1, int str1At0, int str1At1, org.openscience.cdk.interfaces.IAtomContainer str2, int str2At0, int str2At1)
org.openscience.cdk.interfaces.IAtomContainer	condenseStructures(String smiles1, int str1At0, int str1At1, String smiles2, int str2At0, int str2At1)
org.openscience.cdk.interfaces.IAtomContainer	connectStructures_Spiro(org.openscience.cdk.interfaces.IAtomContainer str1, int numAt1, org.openscience.cdk.interfaces.IAtomContainer str2, int numAt2, org.openscience.cdk.interfaces.IBond.Order order)
org.openscience.cdk.interfaces.IAtomContainer	connectStructures(org.openscience.cdk.interfaces.IAtomContainer str1, int numAt1, org.openscience.cdk.interfaces.IAtomContainer str2, int numAt2, org.openscience.cdk.interfaces.IBond.Order order)
org.openscience.cdk.interfaces.IAtomContainer	connectStructures(String smiles1, int numAt1, String smiles2, int numAt2, org.openscience.cdk.interfaces.IBond.Order order)
org.openscience.cdk.interfaces.IChemObjectBuilder	getBuilder()
org.openscience.cdk.interfaces.IAtomContainer	getCarbonSkelleton(List<QuerySequenceElement> sequence)
org.openscience.cdk.interfaces.IAtomContainer	getFragmentFromSequence(int numSteps)
ArrayList<String>	loadSmilesStringsFromFile(String smilesFile)
ArrayList<ArrayList<String>>	loadSmilesTuplesFromFile(String smilesFile)
void	performStructureStatistics(String smilesFile, String mdlFile, int portionSize, int nUsedStr, String outFile)
void	produceRandomStructsFromMDL(String mdlFile, int maxNumSeqSteps, int minGenStrSize, int maxNumRecord, List<StructInfo> vStr, String outFile)
void	produceStructsFromMDL(String mdlFile, int maxNumSeqSteps, int maxNumRecord, int maxStrSize, List<StructInfo> vStr, String outFile)
void	produceStructuresExhaustively(org.openscience.cdk.interfaces.IAtomContainer mol, List<StructInfo> vStr, int maxNumSeqSteps, int maxStrSize)
void	produceStructuresRandomly(org.openscience.cdk.interfaces.IAtomContainer mol, List<StructInfo> vStr, int maxNumSeqSteps, int numStructs, int minGenStrSize)
void	saveSmilesToFile(ArrayList<String> smiles, String fName)
void	saveSmilesTuplesToFile(ArrayList<ArrayList<String>> smilesTuples, String fName)
void	setAtomSequence(org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.interfaces.IAtom startAtom)
void	setBuilder(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Methods inherited from class java.lang.Object

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

Field Detail

sequence

public List<SequenceElement> sequence

Constructor Detail

ChemObjectFactory

public ChemObjectFactory(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Detail

getBuilder

public org.openscience.cdk.interfaces.IChemObjectBuilder getBuilder()

setBuilder

public void setBuilder(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

setAtomSequence

public void setAtomSequence(org.openscience.cdk.interfaces.IAtomContainer target,
                            org.openscience.cdk.interfaces.IAtom startAtom)

getFragmentFromSequence

public org.openscience.cdk.interfaces.IAtomContainer getFragmentFromSequence(int numSteps)

getCarbonSkelleton

public org.openscience.cdk.interfaces.IAtomContainer getCarbonSkelleton(List<QuerySequenceElement> sequence)

produceStructuresExhaustively

public void produceStructuresExhaustively(org.openscience.cdk.interfaces.IAtomContainer mol,
                                          List<StructInfo> vStr,
                                          int maxNumSeqSteps,
                                          int maxStrSize)
                                   throws Exception

Throws:

Exception

produceStructuresRandomly

public void produceStructuresRandomly(org.openscience.cdk.interfaces.IAtomContainer mol,
                                      List<StructInfo> vStr,
                                      int maxNumSeqSteps,
                                      int numStructs,
                                      int minGenStrSize)

produceStructsFromMDL

public void produceStructsFromMDL(String mdlFile,
                                  int maxNumSeqSteps,
                                  int maxNumRecord,
                                  int maxStrSize,
                                  List<StructInfo> vStr,
                                  String outFile)
                           throws Exception

Throws:

Exception

produceRandomStructsFromMDL

public void produceRandomStructsFromMDL(String mdlFile,
                                        int maxNumSeqSteps,
                                        int minGenStrSize,
                                        int maxNumRecord,
                                        List<StructInfo> vStr,
                                        String outFile)
                                 throws Exception

Throws:

Exception

performStructureStatistics

public void performStructureStatistics(String smilesFile,
                                       String mdlFile,
                                       int portionSize,
                                       int nUsedStr,
                                       String outFile)
                                throws Exception

Throws:

Exception

connectStructures

public org.openscience.cdk.interfaces.IAtomContainer connectStructures(org.openscience.cdk.interfaces.IAtomContainer str1,
                                                                       int numAt1,
                                                                       org.openscience.cdk.interfaces.IAtomContainer str2,
                                                                       int numAt2,
                                                                       org.openscience.cdk.interfaces.IBond.Order order)
                                                                throws Exception

Throws:

Exception

connectStructures

public org.openscience.cdk.interfaces.IAtomContainer connectStructures(String smiles1,
                                                                       int numAt1,
                                                                       String smiles2,
                                                                       int numAt2,
                                                                       org.openscience.cdk.interfaces.IBond.Order order)
                                                                throws Exception

Throws:

Exception

connectStructures_Spiro

public org.openscience.cdk.interfaces.IAtomContainer connectStructures_Spiro(org.openscience.cdk.interfaces.IAtomContainer str1,
                                                                             int numAt1,
                                                                             org.openscience.cdk.interfaces.IAtomContainer str2,
                                                                             int numAt2,
                                                                             org.openscience.cdk.interfaces.IBond.Order order)
                                                                      throws Exception

Throws:

Exception

condenseStructures

public org.openscience.cdk.interfaces.IAtomContainer condenseStructures(String smiles1,
                                                                        int str1At0,
                                                                        int str1At1,
                                                                        String smiles2,
                                                                        int str2At0,
                                                                        int str2At1)
                                                                 throws Exception

Throws:

Exception

condenseStructures

public org.openscience.cdk.interfaces.IAtomContainer condenseStructures(org.openscience.cdk.interfaces.IAtomContainer str1,
                                                                        int str1At0,
                                                                        int str1At1,
                                                                        org.openscience.cdk.interfaces.IAtomContainer str2,
                                                                        int str2At0,
                                                                        int str2At1)
                                                                 throws Exception

Throws:

Exception

loadSmilesStringsFromFile

public ArrayList<String> loadSmilesStringsFromFile(String smilesFile)
                                            throws Exception

Throws:

Exception

saveSmilesToFile

public void saveSmilesToFile(ArrayList<String> smiles,
                             String fName)
                      throws Exception

Throws:

Exception

loadSmilesTuplesFromFile

public ArrayList<ArrayList<String>> loadSmilesTuplesFromFile(String smilesFile)
                                                      throws Exception

Throws:

Exception

saveSmilesTuplesToFile

public void saveSmilesTuplesToFile(ArrayList<ArrayList<String>> smilesTuples,
                                   String fName)
                            throws Exception

Throws:

Exception

attachGroupToAllStructures

public ArrayList<String> attachGroupToAllStructures(String groupSmiles,
                                                    int groupAttachPos,
                                                    ArrayList<String> inputSmiles,
                                                    int strDefaultPos)
                                             throws Exception

Throws:

Exception