public class ForceField
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
protected boolean |
swigCMemOwn |
Modifier | Constructor and Description |
---|---|
|
ForceField() |
|
ForceField(ForceField other) |
|
ForceField(long dimension) |
protected |
ForceField(long cPtr,
boolean cMemoryOwn) |
Modifier and Type | Method and Description |
---|---|
double |
calcEnergy() |
double |
calcEnergy(Double_Vect contribs) |
double |
calcEnergy(SWIGTYPE_p_double pos) |
void |
calcGrad(SWIGTYPE_p_double forces) |
void |
calcGrad(SWIGTYPE_p_double pos,
SWIGTYPE_p_double forces) |
FF_Contrib_Vect |
contribs() |
void |
delete() |
long |
dimension() |
double |
distance(long i,
long j) |
double |
distance(long i,
long j,
SWIGTYPE_p_double pos) |
protected void |
finalize() |
Int_Vect |
fixedPoints() |
protected static long |
getCPtr(ForceField obj) |
void |
initialize() |
int |
minimize() |
int |
minimize(long maxIts) |
int |
minimize(long maxIts,
double forceTol) |
int |
minimize(long maxIts,
double forceTol,
double energyTol) |
int |
minimize(long snapshotFreq,
SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t snapshotVect) |
int |
minimize(long snapshotFreq,
SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t snapshotVect,
long maxIts) |
int |
minimize(long snapshotFreq,
SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t snapshotVect,
long maxIts,
double forceTol) |
int |
minimize(long snapshotFreq,
SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t snapshotVect,
long maxIts,
double forceTol,
double energyTol) |
static ForceField |
MMFFGetMoleculeForceField(ROMol mol) |
static ForceField |
MMFFGetMoleculeForceField(ROMol mol,
java.lang.String mmffVariant) |
static ForceField |
MMFFGetMoleculeForceField(ROMol mol,
java.lang.String mmffVariant,
double nonBondedThresh) |
static ForceField |
MMFFGetMoleculeForceField(ROMol mol,
java.lang.String mmffVariant,
double nonBondedThresh,
int confId) |
static ForceField |
MMFFGetMoleculeForceField(ROMol mol,
java.lang.String mmffVariant,
double nonBondedThresh,
int confId,
boolean ignoreInterfragInteractions) |
static boolean |
MMFFHasAllMoleculeParams(ROMol mol) |
static int |
MMFFOptimizeMolecule(ROMol mol) |
static int |
MMFFOptimizeMolecule(ROMol mol,
java.lang.String mmffVariant) |
static int |
MMFFOptimizeMolecule(ROMol mol,
java.lang.String mmffVariant,
int maxIters) |
static int |
MMFFOptimizeMolecule(ROMol mol,
java.lang.String mmffVariant,
int maxIters,
double nonBondedThresh) |
static int |
MMFFOptimizeMolecule(ROMol mol,
java.lang.String mmffVariant,
int maxIters,
double nonBondedThresh,
int confId) |
static int |
MMFFOptimizeMolecule(ROMol mol,
java.lang.String mmffVariant,
int maxIters,
double nonBondedThresh,
int confId,
boolean ignoreInterfragInteractions) |
long |
numPoints() |
Point3D_Vect |
positions3D() |
static void |
UFFAddAtomChargeFlags(Atom atom,
SWIGTYPE_p_std__string atomKey) |
static void |
UFFAddAtomChargeFlags(Atom atom,
SWIGTYPE_p_std__string atomKey,
boolean tolerateChargeMismatch) |
static java.lang.String |
UFFGetAtomLabel(Atom atom) |
static Flagged_Atomic_Params_Vect |
UFFGetAtomTypes(ROMol mol) |
static Flagged_Atomic_Params_Vect |
UFFGetAtomTypes(ROMol mol,
java.lang.String paramData) |
static ForceField |
UFFGetMoleculeForceField(ROMol mol) |
static ForceField |
UFFGetMoleculeForceField(ROMol mol,
double vdwThresh) |
static ForceField |
UFFGetMoleculeForceField(ROMol mol,
double vdwThresh,
int confId) |
static ForceField |
UFFGetMoleculeForceField(ROMol mol,
double vdwThresh,
int confId,
boolean ignoreInterfragInteractions) |
static boolean |
UFFHasAllMoleculeParams(ROMol mol) |
static int |
UFFOptimizeMolecule(ROMol mol) |
static int |
UFFOptimizeMolecule(ROMol mol,
int maxIters) |
static int |
UFFOptimizeMolecule(ROMol mol,
int maxIters,
double vdwThresh) |
static int |
UFFOptimizeMolecule(ROMol mol,
int maxIters,
double vdwThresh,
int confId) |
static int |
UFFOptimizeMolecule(ROMol mol,
int maxIters,
double vdwThresh,
int confId,
boolean ignoreInterfragInteractions) |
protected ForceField(long cPtr, boolean cMemoryOwn)
public ForceField(long dimension)
public ForceField()
public ForceField(ForceField other)
protected static long getCPtr(ForceField obj)
protected void finalize()
finalize
in class java.lang.Object
public void delete()
public void initialize()
public double calcEnergy(Double_Vect contribs)
public double calcEnergy()
public double calcEnergy(SWIGTYPE_p_double pos)
public void calcGrad(SWIGTYPE_p_double forces)
public void calcGrad(SWIGTYPE_p_double pos, SWIGTYPE_p_double forces)
public int minimize(long snapshotFreq, SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t snapshotVect, long maxIts, double forceTol, double energyTol)
public int minimize(long snapshotFreq, SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t snapshotVect, long maxIts, double forceTol)
public int minimize(long snapshotFreq, SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t snapshotVect, long maxIts)
public int minimize(long snapshotFreq, SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t snapshotVect)
public int minimize(long maxIts, double forceTol, double energyTol)
public int minimize(long maxIts, double forceTol)
public int minimize(long maxIts)
public int minimize()
public FF_Contrib_Vect contribs()
public double distance(long i, long j, SWIGTYPE_p_double pos)
public double distance(long i, long j)
public long dimension()
public long numPoints()
public Int_Vect fixedPoints()
public Point3D_Vect positions3D()
public static int UFFOptimizeMolecule(ROMol mol, int maxIters, double vdwThresh, int confId, boolean ignoreInterfragInteractions)
public static int UFFOptimizeMolecule(ROMol mol, int maxIters, double vdwThresh, int confId)
public static int UFFOptimizeMolecule(ROMol mol, int maxIters, double vdwThresh)
public static int UFFOptimizeMolecule(ROMol mol, int maxIters)
public static int UFFOptimizeMolecule(ROMol mol)
public static ForceField UFFGetMoleculeForceField(ROMol mol, double vdwThresh, int confId, boolean ignoreInterfragInteractions)
public static ForceField UFFGetMoleculeForceField(ROMol mol, double vdwThresh, int confId)
public static ForceField UFFGetMoleculeForceField(ROMol mol, double vdwThresh)
public static ForceField UFFGetMoleculeForceField(ROMol mol)
public static boolean UFFHasAllMoleculeParams(ROMol mol)
public static void UFFAddAtomChargeFlags(Atom atom, SWIGTYPE_p_std__string atomKey, boolean tolerateChargeMismatch)
public static void UFFAddAtomChargeFlags(Atom atom, SWIGTYPE_p_std__string atomKey)
public static java.lang.String UFFGetAtomLabel(Atom atom)
public static Flagged_Atomic_Params_Vect UFFGetAtomTypes(ROMol mol, java.lang.String paramData)
public static Flagged_Atomic_Params_Vect UFFGetAtomTypes(ROMol mol)
public static int MMFFOptimizeMolecule(ROMol mol, java.lang.String mmffVariant, int maxIters, double nonBondedThresh, int confId, boolean ignoreInterfragInteractions)
public static int MMFFOptimizeMolecule(ROMol mol, java.lang.String mmffVariant, int maxIters, double nonBondedThresh, int confId)
public static int MMFFOptimizeMolecule(ROMol mol, java.lang.String mmffVariant, int maxIters, double nonBondedThresh)
public static int MMFFOptimizeMolecule(ROMol mol, java.lang.String mmffVariant, int maxIters)
public static int MMFFOptimizeMolecule(ROMol mol, java.lang.String mmffVariant)
public static int MMFFOptimizeMolecule(ROMol mol)
public static ForceField MMFFGetMoleculeForceField(ROMol mol, java.lang.String mmffVariant, double nonBondedThresh, int confId, boolean ignoreInterfragInteractions)
public static ForceField MMFFGetMoleculeForceField(ROMol mol, java.lang.String mmffVariant, double nonBondedThresh, int confId)
public static ForceField MMFFGetMoleculeForceField(ROMol mol, java.lang.String mmffVariant, double nonBondedThresh)
public static ForceField MMFFGetMoleculeForceField(ROMol mol, java.lang.String mmffVariant)
public static ForceField MMFFGetMoleculeForceField(ROMol mol)
public static boolean MMFFHasAllMoleculeParams(ROMol mol)