OBForceField Member List

This is the complete list of members for OBForceField, including all inherited members.
_constraintsOBForceField [protected, static]
_cstepOBForceField [protected]
_current_conformerOBForceField [protected]
_cutoffOBForceField [protected]
_e_n1OBForceField [protected]
_econvOBForceField [protected]
_elepairsOBForceField [protected]
_energiesOBForceField [protected]
_fixAtomOBForceField [protected, static]
_grad1OBForceField [protected]
_gradientPtrOBForceField [protected]
_idOBPlugin [protected]
_ignoreAtomOBForceField [protected, static]
_initOBForceField [protected]
_interGroupOBForceField [protected]
_interGroupsOBForceField [protected]
_intraGroupOBForceField [protected]
_linesearchOBForceField [protected]
_logbufOBForceField [protected]
_loglvlOBForceField [protected]
_logosOBForceField [protected]
_molOBForceField [protected]
_ncoordsOBForceField [protected]
_nstepsOBForceField [protected]
_origLogLevelOBForceField [protected]
_pairfreqOBForceField [protected]
_parFileOBForceField [protected]
_releOBForceField [protected]
_rvdwOBForceField [protected]
_tempOBForceField [protected]
_timestepOBForceField [protected]
_validSetupOBForceField [protected]
_vdwpairsOBForceField [protected]
_velocityPtrOBForceField [protected]
AddGradient(double *grad, int idx)OBForceField [inline, protected]
AddInterGroup(OBBitVec &group)OBForceField
AddInterGroups(OBBitVec &group1, OBBitVec &group2)OBForceField
AddIntraGroup(OBBitVec &group)OBForceField
AllPluginsLoadedOBPlugin [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=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 =0OBPlugin [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=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]
LoadAllPlugins()OBPlugin [protected, static]
MakeInstance(const std::vector< std::string > &)OBPlugin [inline, virtual]
MakeNewInstance()=0OBForceField [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 typedefOBPlugin
PluginMap()OBPlugin [inline, protected, static]
PluginMapType typedefOBPlugin
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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