public class DistanceGeom
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
protected boolean |
swigCMemOwn |
Modifier | Constructor and Description |
---|---|
|
DistanceGeom() |
protected |
DistanceGeom(long cPtr,
boolean cMemoryOwn) |
Modifier and Type | Method and Description |
---|---|
static boolean |
ComputeInitialCoords(DoubleSymmMatrix distmat,
Point3D_Vect positions) |
static boolean |
ComputeInitialCoords(DoubleSymmMatrix distmat,
Point3D_Vect positions,
boolean randNegEig) |
static boolean |
ComputeInitialCoords(DoubleSymmMatrix distmat,
Point3D_Vect positions,
boolean randNegEig,
long numZeroFail) |
static ForceField |
ConstructForceField(BoundsMatrix mmat,
Point_Vect positions,
SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets) |
static ForceField |
ConstructForceField(BoundsMatrix mmat,
Point_Vect positions,
SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets,
double weightChiral) |
static ForceField |
ConstructForceField(BoundsMatrix mmat,
Point_Vect positions,
SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets,
double weightChiral,
double weightFourthDim) |
static ForceField |
ConstructForceField(BoundsMatrix mmat,
Point_Vect positions,
SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets,
double weightChiral,
double weightFourthDim,
SWIGTYPE_p_std__mapT_std__pairT_boost__int32_t_int_t_double_t extraWeights) |
static ForceField |
ConstructForceField(BoundsMatrix mmat,
Point_Vect positions,
SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets,
double weightChiral,
double weightFourthDim,
SWIGTYPE_p_std__mapT_std__pairT_boost__int32_t_int_t_double_t extraWeights,
double basinSizeTol) |
void |
delete() |
static int |
EmbedMolecule(ROMol mol) |
static int |
EmbedMolecule(ROMol mol,
EmbedParameters params) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs,
boolean useBasicKnowledge) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
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) |
static int |
EmbedMolecule(ROMol mol,
long maxIterations,
int seed,
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) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
EmbedParameters params) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh,
Int_Point3D_Map coordMap) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh,
Int_Point3D_Map coordMap,
double optimizerForceTol) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs,
boolean useBasicKnowledge) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs,
boolean useBasicKnowledge,
boolean verbose) |
static Int_Vect |
EmbedMultipleConfs(ROMol mol,
long numConfs,
long maxIterations,
int seed,
boolean clearConfs,
boolean useRandomCoords,
double boxSizeMult,
boolean randNegEig,
long numZeroFail,
double pruneRmsThresh,
Int_Point3D_Map coordMap,
double optimizerForceTol,
boolean ignoreSmoothingFailures,
boolean enforceChirality,
boolean useExpTorsionAnglePrefs,
boolean useBasicKnowledge,
boolean verbose,
double basinThresh) |
protected void |
finalize() |
protected static long |
getCPtr(DistanceGeom obj) |
static void |
SetTopolBounds(ROMol mol,
BoundsMatrix mmat) |
static void |
SetTopolBounds(ROMol mol,
BoundsMatrix mmat,
boolean set15bounds) |
static void |
SetTopolBounds(ROMol mol,
BoundsMatrix mmat,
boolean set15bounds,
boolean scaleVDW) |
protected DistanceGeom(long cPtr, boolean cMemoryOwn)
public DistanceGeom()
protected static long getCPtr(DistanceGeom obj)
protected void finalize()
finalize
in class java.lang.Object
public void delete()
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, 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)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, 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)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs, boolean useBasicKnowledge)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap, double optimizerForceTol)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, Int_Point3D_Map coordMap)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed, boolean clearConfs)
public static int EmbedMolecule(ROMol mol, long maxIterations, int seed)
public static int EmbedMolecule(ROMol mol, long maxIterations)
public static int EmbedMolecule(ROMol mol)
public static int EmbedMolecule(ROMol mol, EmbedParameters params)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs, boolean useBasicKnowledge, boolean verbose, double basinThresh)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs, boolean useBasicKnowledge, boolean verbose)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs, boolean useBasicKnowledge)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality, boolean useExpTorsionAnglePrefs)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures, boolean enforceChirality)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh, Int_Point3D_Map coordMap, double optimizerForceTol, boolean ignoreSmoothingFailures)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh, Int_Point3D_Map coordMap, double optimizerForceTol)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh, Int_Point3D_Map coordMap)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail, double pruneRmsThresh)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig, long numZeroFail)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult, boolean randNegEig)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords, double boxSizeMult)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs, boolean useRandomCoords)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed, boolean clearConfs)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations, int seed)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, long maxIterations)
public static Int_Vect EmbedMultipleConfs(ROMol mol, long numConfs, EmbedParameters params)
public static void SetTopolBounds(ROMol mol, BoundsMatrix mmat, boolean set15bounds, boolean scaleVDW)
public static void SetTopolBounds(ROMol mol, BoundsMatrix mmat, boolean set15bounds)
public static void SetTopolBounds(ROMol mol, BoundsMatrix mmat)
public static ForceField ConstructForceField(BoundsMatrix mmat, Point_Vect positions, SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets, double weightChiral, double weightFourthDim, SWIGTYPE_p_std__mapT_std__pairT_boost__int32_t_int_t_double_t extraWeights, double basinSizeTol)
public static ForceField ConstructForceField(BoundsMatrix mmat, Point_Vect positions, SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets, double weightChiral, double weightFourthDim, SWIGTYPE_p_std__mapT_std__pairT_boost__int32_t_int_t_double_t extraWeights)
public static ForceField ConstructForceField(BoundsMatrix mmat, Point_Vect positions, SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets, double weightChiral, double weightFourthDim)
public static ForceField ConstructForceField(BoundsMatrix mmat, Point_Vect positions, SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets, double weightChiral)
public static ForceField ConstructForceField(BoundsMatrix mmat, Point_Vect positions, SWIGTYPE_p_std__vectorT_boost__shared_ptrT_DistGeom__ChiralSet_t_t csets)
public static boolean ComputeInitialCoords(DoubleSymmMatrix distmat, Point3D_Vect positions, boolean randNegEig, long numZeroFail)
public static boolean ComputeInitialCoords(DoubleSymmMatrix distmat, Point3D_Vect positions, boolean randNegEig)
public static boolean ComputeInitialCoords(DoubleSymmMatrix distmat, Point3D_Vect positions)