public class EmbedParameters
extends java.lang.Object
Modifier and Type | Field and Description |
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protected boolean |
swigCMemOwn |
Modifier | Constructor and Description |
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EmbedParameters() |
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EmbedParameters(EmbedParameters other) |
protected |
EmbedParameters(long cPtr,
boolean cMemoryOwn) |
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EmbedParameters(long maxIterations,
int numThreads,
int randomSeed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs,
boolean useBasicKnowledge,
boolean verbose,
double basinThresh,
double pruneRmsThresh,
boolean onlyHeavyAtomsForRMS) |
|
EmbedParameters(long maxIterations,
int numThreads,
int randomSeed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs,
boolean useBasicKnowledge,
boolean verbose,
double basinThresh,
double pruneRmsThresh,
boolean onlyHeavyAtomsForRMS,
long ETversion) |
|
EmbedParameters(long maxIterations,
int numThreads,
int randomSeed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs,
boolean useBasicKnowledge,
boolean verbose,
double basinThresh,
double pruneRmsThresh,
boolean onlyHeavyAtomsForRMS,
long ETversion,
BoundsMatrix boundsMat) |
|
EmbedParameters(long maxIterations,
int numThreads,
int randomSeed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs,
boolean useBasicKnowledge,
boolean verbose,
double basinThresh,
double pruneRmsThresh,
boolean onlyHeavyAtomsForRMS,
long ETversion,
BoundsMatrix boundsMat,
boolean embedFragmentsSeparately) |
protected EmbedParameters(long cPtr, boolean cMemoryOwn)
public EmbedParameters()
public EmbedParameters(long maxIterations, int numThreads, int randomSeed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs, boolean useBasicKnowledge, boolean verbose, double basinThresh, double pruneRmsThresh, boolean onlyHeavyAtomsForRMS, long ETversion, BoundsMatrix boundsMat, boolean embedFragmentsSeparately)
public EmbedParameters(long maxIterations, int numThreads, int randomSeed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs, boolean useBasicKnowledge, boolean verbose, double basinThresh, double pruneRmsThresh, boolean onlyHeavyAtomsForRMS, long ETversion, BoundsMatrix boundsMat)
public EmbedParameters(long maxIterations, int numThreads, int randomSeed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs, boolean useBasicKnowledge, boolean verbose, double basinThresh, double pruneRmsThresh, boolean onlyHeavyAtomsForRMS, long ETversion)
public EmbedParameters(long maxIterations, int numThreads, int randomSeed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs, boolean useBasicKnowledge, boolean verbose, double basinThresh, double pruneRmsThresh, boolean onlyHeavyAtomsForRMS)
public EmbedParameters(EmbedParameters other)
protected static long getCPtr(EmbedParameters obj)
protected void finalize()
finalize
in class java.lang.Object
public void delete()
public void setMaxIterations(long value)
public long getMaxIterations()
public void setNumThreads(int value)
public int getNumThreads()
public void setRandomSeed(int value)
public int getRandomSeed()
public void setClearConfs(boolean value)
public boolean getClearConfs()
public void setUseRandomCoords(boolean value)
public boolean getUseRandomCoords()
public void setBoxSizeMult(double value)
public double getBoxSizeMult()
public void setRandNegEig(boolean value)
public boolean getRandNegEig()
public void setNumZeroFail(long value)
public long getNumZeroFail()
public void setCoordMap(Int_Point3D_Map value)
public Int_Point3D_Map getCoordMap()
public void setOptimizerForceTol(double value)
public double getOptimizerForceTol()
public void setIgnoreSmoothingFailures(boolean value)
public boolean getIgnoreSmoothingFailures()
public void setEnforceChirality(boolean value)
public boolean getEnforceChirality()
public void setUseExpTorsionAnglePrefs(boolean value)
public boolean getUseExpTorsionAnglePrefs()
public void setUseBasicKnowledge(boolean value)
public boolean getUseBasicKnowledge()
public void setVerbose(boolean value)
public boolean getVerbose()
public void setBasinThresh(double value)
public double getBasinThresh()
public void setPruneRmsThresh(double value)
public double getPruneRmsThresh()
public void setOnlyHeavyAtomsForRMS(boolean value)
public boolean getOnlyHeavyAtomsForRMS()
public void setETversion(long value)
public long getETversion()
public void setBoundsMat(SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_const_t value)
public SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_const_t getBoundsMat()
public void setEmbedFragmentsSeparately(boolean value)
public boolean getEmbedFragmentsSeparately()