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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
_epsilon | OBForceField | protected
_fixAtom | OBForceField | protected static
_gconv | OBForceField | protected
_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 |
AllPluginsLoaded | OBPlugin | protected static
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=nullptr) | 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
FastRotorSearch(bool permute=true) | OBForceField |
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 |
GetDielectricConstant() | OBForceField | inline
GetElectrostaticCutOff() | OBForceField | inline
GetGradient(OBAtom *a, int=OBFF_ENERGY) | OBForceField | inline virtual
GetGradientPtr() | OBForceField | inline
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
GetNumElectrostaticPairs() | OBForceField |
GetNumPairs() | OBForceField |
GetNumVDWPairs() | 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=nullptr, std::ostream *os=&std::cout) | OBPlugin | static
ListAsString(const char *PluginID, const char *param=nullptr) | OBPlugin | static
ListAsVector(const char *PluginID, const char *param, std::vector< std::string > &vlist) | OBPlugin | static
LoadAllPlugins() | 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, bool sampleRingBonds=false) | OBForceField |
RandomRotorSearchInitialize(unsigned int conformers, unsigned int geomSteps=2500, bool sampleRingBonds=false) | OBForceField |
RandomRotorSearchNextConformer(unsigned int geomSteps=2500) | OBForceField |
SetConformers(OBMol &mol) | OBForceField |
SetConstraints(OBFFConstraints &constraints) | OBForceField |
SetCoordinates(OBMol &mol) | OBForceField |
SetDielectricConstant(double epsilon) | OBForceField | inline
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, bool sampleRingBonds=false) | OBForceField |
SystematicRotorSearchInitialize(unsigned int geomSteps=2500, bool sampleRingBonds=false) | 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, bool sampleRingBonds=false) | OBForceField |
~OBForceField() | OBForceField | inline virtual
~OBPlugin() | OBPlugin | inline virtual