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OBForceField Member List
This is the complete list of members for OBForceField, including all inherited members.

_constraints | OBForceField | `[protected, static]`
_cstep | OBForceField | `[protected]`
_current_conformer | OBForceField | `[protected]`
_cutoff | OBForceField | `[protected]`
_e_n1 | OBForceField | `[protected]`
_econv | OBForceField | `[protected]`
_elepairs | OBForceField | `[protected]`
_energies | OBForceField | `[protected]`
_fixAtom | OBForceField | `[protected, static]`
_grad1 | OBForceField | `[protected]`
_gradientPtr | OBForceField | `[protected]`
_id | OBPlugin | `[protected]`
_ignoreAtom | OBForceField | `[protected, static]`
_init | OBForceField | `[protected]`
_interGroup | OBForceField | `[protected]`
_interGroups | OBForceField | `[protected]`
_intraGroup | OBForceField | `[protected]`
_linesearch | OBForceField | `[protected]`
_logbuf | OBForceField | `[protected]`
_loglvl | OBForceField | `[protected]`
_logos | OBForceField | `[protected]`
_mol | OBForceField | `[protected]`
_ncoords | OBForceField | `[protected]`
_nsteps | OBForceField | `[protected]`
_origLogLevel | OBForceField | `[protected]`
_pairfreq | OBForceField | `[protected]`
_parFile | OBForceField | `[protected]`
_rele | OBForceField | `[protected]`
_rvdw | OBForceField | `[protected]`
_temp | OBForceField | `[protected]`
_timestep | OBForceField | `[protected]`
_validSetup | OBForceField | `[protected]`
_vdwpairs | OBForceField | `[protected]`
_velocityPtr | OBForceField | `[protected]`
AddGradient(double *grad, int idx) | OBForceField | `[inline, protected]`
AddInterGroup(OBBitVec &group) | OBForceField |
AddInterGroups(OBBitVec &group1, OBBitVec &group2) | OBForceField |
AddIntraGroup(OBBitVec &group) | OBForceField |
BaseFindType(PluginMapType &Map, const char *ID) | OBPlugin | `[protected, static]`
Begin(const char *PluginID) | OBPlugin | `[inline, static]`
ClearGradients() | OBForceField | `[inline, protected, virtual]`
ClearGroups() | OBForceField |
ConjugateGradients(int steps, double econv=1e-6f, int method=OBFF_ANALYTICAL_GRADIENT) | OBForceField |
ConjugateGradientsInitialize(int steps=1000, double econv=1e-6f, int method=OBFF_ANALYTICAL_GRADIENT) | OBForceField |
ConjugateGradientsTakeNSteps(int n) | OBForceField |
CorrectVelocities() | OBForceField |
Description() | OBPlugin | `[inline, virtual]`
DetectExplosion() | OBForceField |
Display(std::string &txt, const char *param, const char *ID=NULL) | OBPlugin | `[virtual]`
DistanceGeometry() | OBForceField |
E_Angle(bool gradients=true) | OBForceField | `[inline, virtual]`
E_Bond(bool gradients=true) | OBForceField | `[inline, virtual]`
E_Electrostatic(bool gradients=true) | OBForceField | `[inline, virtual]`
E_OOP(bool gradients=true) | OBForceField | `[inline, virtual]`
E_StrBnd(bool gradients=true) | OBForceField | `[inline, virtual]`
E_Torsion(bool gradients=true) | OBForceField | `[inline, virtual]`
E_VDW(bool gradients=true) | OBForceField | `[inline, virtual]`
EnableAllPairs() | OBForceField | `[inline]`
EnableCutOff(bool enable) | OBForceField | `[inline]`
End(const char *PluginID) | OBPlugin | `[inline, static]`
Energy(bool gradients=true) | OBForceField | `[inline, virtual]`
FindForceField(const std::string &ID) | OBForceField | `[inline, static]`
FindForceField(const char *ID) | OBForceField | `[inline, static]`
FirstLine(const char *txt) | OBPlugin | `[static]`
GenerateVelocities() | OBForceField |
GetAtomTypes(OBMol &mol) | OBForceField |
GetConformers(OBMol &mol) | OBForceField |
GetConstraints() | OBForceField |
GetCoordinates(OBMol &mol) | OBForceField |
GetElectrostaticCutOff() | OBForceField | `[inline]`
GetGradient(OBAtom *a, int=OBFF_ENERGY) | OBForceField | `[inline, protected, virtual]`
GetGradientPtr() | OBForceField | `[inline, protected]`
GetGrid(double step, double padding, const char *type, double pchg) | OBForceField |
GetID() const | OBPlugin | `[inline]`
GetLineSearchType() | OBForceField | `[inline]`
GetLogLevel() | OBForceField | `[inline]`
GetMap() const =0 | OBPlugin | `[pure virtual]`
GetNumPairs() | OBForceField |
GetParameter(int a, int b, int c, int d, std::vector< OBFFParameter > &parameter) | OBForceField | `[protected]`
GetParameter(const char *a, const char *b, const char *c, const char *d, std::vector< OBFFParameter > &parameter) | OBForceField | `[protected]`
GetParameterIdx(int a, int b, int c, int d, std::vector< OBFFParameter > &parameter) | OBForceField | `[protected]`
GetPartialCharges(OBMol &mol) | OBForceField |
GetPlugin(const char *Type, const char *ID) | OBPlugin | `[static]`
GetTypeMap(const char *PluginID) | OBPlugin | `[protected, static]`
GetUnit() | OBForceField | `[inline, virtual]`
GetUpdateFrequency() | OBForceField | `[inline]`
GetVDWCutOff() | OBForceField | `[inline]`
HasAnalyticalGradients() | OBForceField | `[inline, virtual]`
HasGroups() | OBForceField |
IgnoreCalculation(int a, int b) | OBForceField | `[static]`
IgnoreCalculation(int a, int b, int c) | OBForceField | `[static]`
IgnoreCalculation(int a, int b, int c, int d) | OBForceField | `[static]`
Init() | OBPlugin | `[inline, virtual]`
IsCutOffEnabled() | OBForceField | `[inline]`
IsInSameRing(OBAtom *a, OBAtom *b) | OBForceField | `[protected]`
IsSetupNeeded(OBMol &mol) | OBForceField |
LineSearch(OBAtom *atom, vector3 &direction) | OBForceField |
LineSearch(double *currentCoords, double *direction) | OBForceField |
LineSearchTakeStep(double *origCoords, double *direction, double step) | OBForceField |
List(const char *PluginID, const char *param=NULL, std::ostream *os=&std::cout) | OBPlugin | `[static]`
ListAsString(const char *PluginID, const char *param=NULL) | OBPlugin | `[static]`
ListAsVector(const char *PluginID, const char *param, std::vector< std::string > &vlist) | OBPlugin | `[static]`
MakeInstance(const std::vector< std::string > &) | OBPlugin | `[inline, virtual]`
MakeNewInstance()=0 | OBForceField | `[pure virtual]`
MolecularDynamicsTakeNSteps(int n, double T, double timestep=0.001, int method=OBFF_ANALYTICAL_GRADIENT) | OBForceField |
Newton2NumLineSearch(double *direction) | OBForceField |
NumericalDerivative(OBAtom *a, int terms=OBFF_ENERGY) | OBForceField | `[protected]`
NumericalSecondDerivative(OBAtom *a, int terms=OBFF_ENERGY) | OBForceField | `[protected]`
OBFFLog(std::string msg) | OBForceField | `[inline]`
OBFFLog(const char *msg) | OBForceField | `[inline]`
ParseParamFile() | OBForceField | `[inline, virtual]`
PluginIterator typedef | OBPlugin |
PluginMap() | OBPlugin | `[inline, protected, static]`
PluginMapType typedef | OBPlugin |
PrintFormalCharges() | OBForceField |
PrintPartialCharges() | OBForceField |
PrintTypes() | OBForceField |
PrintVector(double *i) | OBForceField | `[inline, static]`
PrintVelocities() | OBForceField |
RandomRotorSearch(unsigned int conformers, unsigned int geomSteps=2500) | OBForceField |
RandomRotorSearchInitialize(unsigned int conformers, unsigned int geomSteps=2500) | OBForceField |
RandomRotorSearchNextConformer(unsigned int geomSteps=2500) | OBForceField |
SetConformers(OBMol &mol) | OBForceField |
SetConstraints(OBFFConstraints &constraints) | OBForceField |
SetCoordinates(OBMol &mol) | OBForceField |
SetElectrostaticCutOff(double r) | OBForceField | `[inline]`
SetFixAtom(int index) | OBForceField |
SetFormalCharges() | OBForceField | `[inline, virtual]`
SetGradient(double *grad, int idx) | OBForceField | `[inline, protected]`
SetIgnoreAtom(int index) | OBForceField |
SetLineSearchType(int type) | OBForceField | `[inline]`
SetLogFile(std::ostream *pos) | OBForceField |
SetLogLevel(int level) | OBForceField |
SetParameterFile(const std::string &filename) | OBForceField | `[inline]`
SetPartialCharges() | OBForceField | `[inline, virtual]`
SetTypes() | OBForceField | `[inline, virtual]`
Setup(OBMol &mol) | OBForceField |
Setup(OBMol &mol, OBFFConstraints &constraints) | OBForceField |
SetupCalculations() | OBForceField | `[inline, virtual]`
SetUpdateFrequency(int f) | OBForceField | `[inline]`
SetupPointers() | OBForceField | `[inline, virtual]`
SetVDWCutOff(double r) | OBForceField | `[inline]`
SteepestDescent(int steps, double econv=1e-6f, int method=OBFF_ANALYTICAL_GRADIENT) | OBForceField |
SteepestDescentInitialize(int steps=1000, double econv=1e-6f, int method=OBFF_ANALYTICAL_GRADIENT) | OBForceField |
SteepestDescentTakeNSteps(int n) | OBForceField |
SystematicRotorSearch(unsigned int geomSteps=2500) | OBForceField |
SystematicRotorSearchInitialize(unsigned int geomSteps=2500) | OBForceField |
SystematicRotorSearchNextConformer(unsigned int geomSteps=2500) | OBForceField |
TypeID() | OBForceField | `[inline, virtual]`
UnsetFixAtom() | OBForceField |
UnsetIgnoreAtom() | OBForceField |
UpdateConformers(OBMol &mol) | OBForceField | `[inline]`
UpdateCoordinates(OBMol &mol) | OBForceField | `[inline]`
UpdatePairsSimple() | OBForceField |
Validate() | OBForceField | `[inline, virtual]`
ValidateConjugateGradients(int steps) | OBForceField |
ValidateGradientError(vector3 &numgrad, vector3 &anagrad) | OBForceField |
ValidateGradients() | OBForceField | `[inline, virtual]`
ValidateLineSearch(OBAtom *atom, vector3 &direction) | OBForceField |
ValidateSteepestDescent(int steps) | OBForceField |
VectorAdd(double *i, double *j, double *result) | OBForceField | `[inline, static]`
VectorAngle(double *i, double *j, double *k) | OBForceField | `[static]`
VectorAngleDerivative(double *pos_a, double *pos_b, double *pos_c, double *force_a, double *force_b, double *force_c) | OBForceField | `[static]`
VectorAngleDerivative(vector3 &a, vector3 &b, vector3 &c) | OBForceField | `[static]`
VectorBondDerivative(double *pos_a, double *pos_b, double *force_a, double *force_b) | OBForceField | `[static]`
VectorClear(double *i) | OBForceField | `[inline, static]`
VectorCopy(double *from, double *to) | OBForceField | `[inline, static]`
VectorCross(double *i, double *j, double *result) | OBForceField | `[inline, static]`
VectorDistance(double *pos_i, double *pos_j) | OBForceField | `[inline, static]`
VectorDistanceDerivative(const double *const pos_i, const double *const pos_j, double *force_i, double *force_j) | OBForceField | `[static]`
VectorDivide(double *i, double n, double *result) | OBForceField | `[inline, static]`
VectorDot(double *i, double *j) | OBForceField | `[inline, static]`
VectorLength(double *i) | OBForceField | `[inline, static]`
VectorLengthDerivative(vector3 &a, vector3 &b) | OBForceField | `[static]`
VectorMultiply(double *i, double n, double *result) | OBForceField | `[inline, static]`
VectorMultiply(const double *const i, const double n, double *result) | OBForceField | `[inline, static]`
VectorNormalize(double *i) | OBForceField | `[inline, static]`
VectorOOP(double *i, double *j, double *k, double *l) | OBForceField | `[static]`
VectorOOPDerivative(double *pos_a, double *pos_b, double *pos_c, double *pos_d, double *force_a, double *force_b, double *force_c, double *force_d) | OBForceField | `[static]`
VectorOOPDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d) | OBForceField | `[static]`
VectorSelfMultiply(double *i, double n) | OBForceField | `[inline, static]`
VectorSubtract(double *i, double *j, double *result) | OBForceField | `[inline, static]`
VectorSubtract(const double *const i, const double *const j, double *result) | OBForceField | `[inline, static]`
VectorTorsion(double *i, double *j, double *k, double *l) | OBForceField | `[static]`
VectorTorsionDerivative(double *pos_a, double *pos_b, double *pos_c, double *pos_d, double *force_a, double *force_b, double *force_c, double *force_d) | OBForceField | `[static]`
VectorTorsionDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d) | OBForceField | `[static]`
WeightedRotorSearch(unsigned int conformers, unsigned int geomSteps) | OBForceField |
~OBForceField() | OBForceField | `[inline, virtual]`
~OBPlugin() | OBPlugin | `[inline, virtual]`

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