#include <openbabel/forcefield.h>

Inheritance diagram for OBForceField:

Public Types
typedef std::map< const char , OBPlugin , CharPtrLess >	PluginMapType

typedef PluginMapType::const_iterator	PluginIterator

Public Member Functions
virtual OBForceField *	MakeNewInstance ()=0

virtual	~OBForceField ()

const char *	TypeID ()

void	SetParameterFile (const std::string &filename)

virtual std::string	GetUnit ()

virtual bool	HasAnalyticalGradients ()

bool	Setup (OBMol &mol)

bool	Setup (OBMol &mol, OBFFConstraints &constraints)

virtual bool	ParseParamFile ()

virtual bool	SetTypes ()

virtual bool	SetFormalCharges ()

virtual bool	SetPartialCharges ()

virtual bool	SetupCalculations ()

virtual bool	SetupPointers ()

bool	IsSetupNeeded (OBMol &mol)

bool	GetAtomTypes (OBMol &mol)

bool	GetPartialCharges (OBMol &mol)

bool	GetCoordinates (OBMol &mol)

bool	UpdateCoordinates (OBMol &mol)

bool	GetConformers (OBMol &mol)

bool	UpdateConformers (OBMol &mol)

bool	SetCoordinates (OBMol &mol)

bool	SetConformers (OBMol &mol)

OBGridData *	GetGrid (double step, double padding, const char *type, double pchg)

virtual vector3	GetGradient (OBAtom *a, int=OBFF_ENERGY)

double *	GetGradientPtr ()

virtual const char *	Description ()

virtual bool	Display (std::string &txt, const char param, const char ID=NULL)

virtual OBPlugin *	MakeInstance (const std::vector< std::string > &)

virtual void	Init ()

const char *	GetID () const

virtual PluginMapType &	GetMap () const =0

Methods for specifying interaction groups
void	AddIntraGroup (OBBitVec &group)

void	AddInterGroup (OBBitVec &group)

void	AddInterGroups (OBBitVec &group1, OBBitVec &group2)

void	ClearGroups ()

bool	HasGroups ()

Methods for Cut-off distances
void	EnableCutOff (bool enable)

bool	IsCutOffEnabled ()

void	SetVDWCutOff (double r)

double	GetVDWCutOff ()

void	SetElectrostaticCutOff (double r)

double	GetElectrostaticCutOff ()

void	SetDielectricConstant (double epsilon)

double	GetDielectricConstant ()

void	SetUpdateFrequency (int f)

int	GetUpdateFrequency ()

void	UpdatePairsSimple ()

unsigned int	GetNumPairs ()

unsigned int	GetNumElectrostaticPairs ()

unsigned int	GetNumVDWPairs ()

void	EnableAllPairs ()

Methods for energy evaluation
virtual double	Energy (bool gradients=true)

virtual double	E_Bond (bool gradients=true)

virtual double	E_Angle (bool gradients=true)

virtual double	E_StrBnd (bool gradients=true)

virtual double	E_Torsion (bool gradients=true)

virtual double	E_OOP (bool gradients=true)

virtual double	E_VDW (bool gradients=true)

virtual double	E_Electrostatic (bool gradients=true)

Methods for logging
void	PrintTypes ()

void	PrintFormalCharges ()

void	PrintPartialCharges ()

void	PrintVelocities ()

bool	SetLogFile (std::ostream *pos)

bool	SetLogLevel (int level)

int	GetLogLevel ()

void	OBFFLog (std::string msg)

void	OBFFLog (const char *msg)

Methods for structure generation
void	DistanceGeometry ()

void	SystematicRotorSearch (unsigned int geomSteps=2500, bool sampleRingBonds=false)

int	SystematicRotorSearchInitialize (unsigned int geomSteps=2500, bool sampleRingBonds=false)

bool	SystematicRotorSearchNextConformer (unsigned int geomSteps=2500)

void	RandomRotorSearch (unsigned int conformers, unsigned int geomSteps=2500, bool sampleRingBonds=false)

void	RandomRotorSearchInitialize (unsigned int conformers, unsigned int geomSteps=2500, bool sampleRingBonds=false)

bool	RandomRotorSearchNextConformer (unsigned int geomSteps=2500)

void	WeightedRotorSearch (unsigned int conformers, unsigned int geomSteps, bool sampleRingBonds=false)

int	FastRotorSearch (bool permute=true)

Methods for energy minimization
void	SetLineSearchType (int type)

int	GetLineSearchType ()

vector3	LineSearch (OBAtom *atom, vector3 &direction)

double	LineSearch (double currentCoords, double direction)

double	Newton2NumLineSearch (double *direction)

void	LineSearchTakeStep (double origCoords, double direction, double step)

void	SteepestDescent (int steps, double econv=1e-6f, int method=OBFF_ANALYTICAL_GRADIENT)

void	SteepestDescentInitialize (int steps=1000, double econv=1e-6f, int method=OBFF_ANALYTICAL_GRADIENT)

bool	SteepestDescentTakeNSteps (int n)

void	ConjugateGradients (int steps, double econv=1e-6f, int method=OBFF_ANALYTICAL_GRADIENT)

void	ConjugateGradientsInitialize (int steps=1000, double econv=1e-6f, int method=OBFF_ANALYTICAL_GRADIENT)

bool	ConjugateGradientsTakeNSteps (int n)

Methods for molecular dynamics
void	GenerateVelocities ()

void	CorrectVelocities ()

void	MolecularDynamicsTakeNSteps (int n, double T, double timestep=0.001, int method=OBFF_ANALYTICAL_GRADIENT)

Methods for forcefield validation
bool	DetectExplosion ()

vector3	ValidateLineSearch (OBAtom *atom, vector3 &direction)

void	ValidateSteepestDescent (int steps)

void	ValidateConjugateGradients (int steps)

virtual bool	Validate ()

virtual bool	ValidateGradients ()

vector3	ValidateGradientError (vector3 &numgrad, vector3 &anagrad)

Static Public Member Functions
static OBForceField *	FindForceField (const std::string &ID)

static OBForceField *	FindForceField (const char *ID)

static OBPlugin *	GetPlugin (const char Type, const char ID)

static bool	ListAsVector (const char PluginID, const char param, std::vector< std::string > &vlist)

static void	List (const char PluginID, const char param=NULL, std::ostream *os=&std::cout)

static std::string	ListAsString (const char PluginID, const char param=NULL)

static std::string	FirstLine (const char *txt)

static PluginIterator	Begin (const char *PluginID)

static PluginIterator	End (const char *PluginID)

static void	LoadAllPlugins ()

Methods for vector analysis (used by OBFFXXXXCalculationYYYY)
static double	VectorBondDerivative (double pos_a, double pos_b, double force_a, double force_b)

static double	VectorDistanceDerivative (const double const pos_i, const double const pos_j, double force_i, double force_j)

static double	VectorLengthDerivative (vector3 &a, vector3 &b)

static double	VectorAngleDerivative (double pos_a, double pos_b, double pos_c, double force_a, double force_b, double force_c)

static double	VectorAngleDerivative (vector3 &a, vector3 &b, vector3 &c)

static double	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)

static double	VectorOOPDerivative (vector3 &a, vector3 &b, vector3 &c, vector3 &d)

static double	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)

static double	VectorTorsionDerivative (vector3 &a, vector3 &b, vector3 &c, vector3 &d)

static void	VectorSubtract (double i, double j, double *result)

static void	VectorSubtract (const double const i, const double const j, double *result)

static void	VectorAdd (double i, double j, double *result)

static void	VectorDivide (double i, double n, double result)

static void	VectorMultiply (double i, double n, double result)

static void	VectorMultiply (const double const i, const double n, double result)

static void	VectorSelfMultiply (double *i, double n)

static void	VectorNormalize (double *i)

static void	VectorCopy (double from, double to)

static double	VectorLength (double *i)

static double	VectorDistance (double pos_i, double pos_j)

static double	VectorAngle (double i, double j, double *k)

static double	VectorTorsion (double i, double j, double k, double l)

static double	VectorOOP (double i, double j, double k, double l)

static void	VectorClear (double *i)

static double	VectorDot (double i, double j)

static void	VectorCross (double i, double j, double *result)

static void	PrintVector (double *i)

Protected Member Functions
OBFFParameter *	GetParameter (int a, int b, int c, int d, std::vector< OBFFParameter > &parameter)

OBFFParameter *	GetParameter (const char a, const char b, const char c, const char d, std::vector< OBFFParameter > &parameter)

int	GetParameterIdx (int a, int b, int c, int d, std::vector< OBFFParameter > &parameter)

vector3	NumericalDerivative (OBAtom *a, int terms=OBFF_ENERGY)

vector3	NumericalSecondDerivative (OBAtom *a, int terms=OBFF_ENERGY)

void	SetGradient (double *grad, int idx)

void	AddGradient (double *grad, int idx)

virtual void	ClearGradients ()

bool	IsInSameRing (OBAtom a, OBAtom b)

Static Protected Member Functions
static PluginMapType &	PluginMap ()

static PluginMapType &	GetTypeMap (const char *PluginID)

static OBPlugin *	BaseFindType (PluginMapType &Map, const char *ID)

Protected Attributes
OBMol	_mol

bool	_init

std::string	_parFile

bool	_validSetup

double *	_gradientPtr

std::ostream *	_logos

char	_logbuf [BUFF_SIZE+1]

int	_loglvl

int	_origLogLevel

int	_current_conformer

std::vector< double >	_energies

double	_econv

double	_gconv

double	_e_n1

int	_cstep

int	_nsteps

double *	_grad1

unsigned int	_ncoords

int	_linesearch

double	_timestep

double	_temp

double *	_velocityPtr

bool	_cutoff

double	_rvdw

double	_rele

double	_epsilon

OBBitVec	_vdwpairs

OBBitVec	_elepairs

int	_pairfreq

std::vector< OBBitVec >	_intraGroup

std::vector< OBBitVec >	_interGroup

std::vector< std::pair< OBBitVec, OBBitVec > >	_interGroups

const char *	_id

Static Protected Attributes
static OBFFConstraints	_constraints = OBFFConstraints()

static unsigned int	_fixAtom = 0

static unsigned int	_ignoreAtom = 0

static int	AllPluginsLoaded = 0

Methods for constraints
OBFFConstraints &	GetConstraints ()

void	SetConstraints (OBFFConstraints &constraints)

void	SetFixAtom (int index)

void	UnsetFixAtom ()

void	SetIgnoreAtom (int index)

void	UnsetIgnoreAtom ()

static bool	IgnoreCalculation (int a, int b)

static bool	IgnoreCalculation (int a, int b, int c)

static bool	IgnoreCalculation (int a, int b, int c, int d)

Detailed Description

Base class for molecular mechanics force fields.

The OBForceField class is the base class for molecular mechanics in Open Babel. Classes derived from the OBForceField implement specific force fields (Ghemical, MMFF94, UFF, ...).Other classes such as OBFFParameter, OBFFConstraint, OBFFCalculation and its derived classes are only for internal use. As a user interested in using the available force fields in Open Babel, you don't need these classes. The rest of this short introduction is aimed at these users. For information on how to implement additional force fields, see the wiki pages or post your questions to the openbabel-devel mailing list.

Before we can start using a force field, we must first select it and set it up. This is illustrated in the first example below. The Setup procedure assigns atom types, charges and parameters. There are several reasons why this may fail, a log message will be written to the logfile before Setup() returns false.

The force field classes use their own logging functions. You can set the logfile using SetLogFile() and set the log level using SetLogLevel(). If needed you can also write to the logfile using OBFFLog(). There are four log levels: BFF_LOGLVL_NONE, OBFF_LOGLVL_LOW, OBFF_LOGLVL_MEDIUM, OBFF_LOGLVL_HIGH. See the API documentation to know what kind of output each function writes to the logfile for the different log levels.

Below are two examples which explain the basics.

This piece of code will output a list of available forcefields to cout:

OBPlugin::List("forcefields");

Calculate the energy for the structure in mol using the Ghemical forcefield.

#include <openbabel/forcefield.h>
#include <openbabel/mol.h>
// See OBConversion class to fill the mol object.
OBMol mol;
// Select the forcefield, this returns a pointer that we
// will later use to access the forcefield functions.
OBForceField* pFF = OBForceField::FindForceField("MMFF94");
// Make sure we have a valid pointer
if (!pFF)
// exit...
// Set the logfile (can also be &cout or &cerr)
pFF->SetLogFile(&cerr);
// Set the log level. See indivual functions to know
// what kind of output each function produces for the
// different log levels.
pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
// We need to setup the forcefield before we can use it. Setup()
// returns false if it failes to find the atom types, parameters, ...
if (!pFF->Setup(mol)) {
cerr << "ERROR: could not setup force field." << endl;
}
// Calculate the energy. The output will be written to the
// logfile specified by SetLogFile()
pFF->Energy();

Minimize the structure in mol using conjugate gradients.

#include <openbabel/forcefield.h>
#include <openbabel/mol.h>
OBMol mol;
OBForceField* pFF = OBForceField::FindForceField("MMFF94");
// Make sure we have a valid pointer
if (!pFF)
// exit...
pFF->SetLogFile(&cerr);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
if (!pFF->Setup(mol)) {
cerr << "ERROR: could not setup force field." << endl;
}
// Perform the actual minimization, maximum 1000 steps
pFF->ConjugateGradients(1000);

Minimize the structure in mol using steepest descent and fix the position of atom with index 1.

#include <openbabel/forcefield.h>
#include <openbabel/mol.h>
OBMol mol;
OBForceField* pFF = OBForceField::FindForceField("MMFF94");
// Make sure we have a valid pointer
if (!pFF)
// exit...
pFF->SetLogFile(&cerr);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
// Set the constraints
OBFFConstraints constraints;
constraints.AddAtomConstraint(1);
// We pass the constraints as argument for Setup()
if (!pFF->Setup(mol, constraints)) {
cerr << "ERROR: could not setup force field." << endl;
}
// Perform the actual minimization, maximum 1000 steps
pFF->ConjugateGradients(1000);

Minimize a ligand molecule in a binding pocket.

#include <openbabel/forcefield.h>
#include <openbabel/mol.h>
OBMol mol;
//
// Read the pocket + ligand (initial guess for position) into mol...
//
OBBitVec pocket; // set the bits with atoms indexes for the pocket to 1...
OBBitVec ligand; // set the bits with atoms indexes for the ligand to 1...
OBForceField* pFF = OBForceField::FindForceField("MMFF94");
// Make sure we have a valid pointer
if (!pFF)
// exit...
pFF->SetLogFile(&cerr);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
// Fix the binding pocket atoms
OBFFConstraints constraints;
FOR_ATOMS_OF_MOL (a, mol) {
if (pocket.BitIsSet(a->GetIdx())
constraints.AddAtomConstraint(a->GetIdx());
}
// Specify the interacting groups. The pocket atoms are fixed, so there
// is no need to calculate intra- and inter-molecular interactions for
// the binding pocket.
pFF->AddIntraGroup(ligand); // bonded interactions in the ligand
pFF->AddInterGroup(ligand); // non-bonded between ligand-ligand atoms
pFF->AddInterGroups(ligand, pocket); // non-bonded between ligand and pocket atoms
// We pass the constraints as argument for Setup()
if (!pFF->Setup(mol, constraints)) {
cerr << "ERROR: could not setup force field." << endl;
}
// Perform the actual minimization, maximum 1000 steps
pFF->ConjugateGradients(1000);

Examples:: obforcefield_energy.cpp.

Constructor & Destructor Documentation

◆ ~OBForceField()

virtual ~OBForceField ( )

inlinevirtual

Destructor.

Member Function Documentation

◆ GetParameter() [1/2]

OBFFParameter * GetParameter	(	int	a,
		int	b,
		int	c,
		int	d,
		std::vector< OBFFParameter > &	parameter
	)

protected

Get the correct OBFFParameter from a OBFFParameter vector.

vector<OBFFParameter> parameters;

this vector is filled with entries (as OBFFParameter) from a parameter file. This happens in the Setup() function.

GetParameter(a, 0, 0, 0, parameters);

returns the first OBFFParameter from vector<OBFFParameter> parameters where: pa = a (pa = parameter.a)

use: vdw parameters, ...

GetParameter(a, b, 0, 0, parameters);

returns the first OBFFParameter from vector<OBFFParameter> parameters where: pa = a & pb = b (ab) or: pa = b & pb = a (ba)

use: bond parameters, vdw parameters (pairs), ...

GetParameter(a, b, c, 0, parameters);

returns the first OBFFParameter from vector<OBFFParameter> parameters where: pa = a & pb = b & pc = c (abc) or: pa = c & pb = b & pc = a (cba)

use: angle parameters, ...

GetParameter(a, b, c, d, parameters);

returns the first OBFFParameter from vector<OBFFParameter> parameters where: pa = a & pb = b & pc = c & pd = d (abcd) or: pa = d & pb = b & pc = c & pd = a (dbca) or: pa = a & pb = c & pc = b & pd = d (acbd) or: pa = d & pb = c & pc = b & pd = a (dcba)

use: torsion parameters, ...

◆ GetParameter() [2/2]

OBFFParameter * GetParameter	(	const char *	a,
		const char *	b,
		const char *	c,
		const char *	d,
		std::vector< OBFFParameter > &	parameter
	)

protected

see GetParameter(int a, int b, int c, int d, std::vector<OBFFParameter> &parameter)

◆ GetParameterIdx()

int GetParameterIdx	(	int	a,
		int	b,
		int	c,
		int	d,
		std::vector< OBFFParameter > &	parameter
	)

protected

Get index for vector<OBFFParameter> ...

◆ NumericalDerivative()

vector3 NumericalDerivative	(	OBAtom *	a,
		int	terms = `OBFF_ENERGY`
	)

protected

Calculate the potential energy function derivative numerically with repect to the coordinates of atom with index a (this vector is the gradient)

Parameters

a	provides coordinates
terms	OBFF_ENERGY, OBFF_EBOND, OBFF_EANGLE, OBFF_ESTRBND, OBFF_ETORSION, OBFF_EOOP, OBFF_EVDW, OBFF_ELECTROSTATIC

Returns: the negative gradient of atom a

◆ NumericalSecondDerivative()

vector3 NumericalSecondDerivative	(	OBAtom *	a,
		int	terms = `OBFF_ENERGY`
	)

protected

OB 3.0.

◆ SetGradient()

void SetGradient	(	double *	grad,
		int	idx
	)

inlineprotected

Set the gradient for atom with index idx to grad

◆ AddGradient()

void AddGradient	(	double *	grad,
		int	idx
	)

inlineprotected

Add grad to the gradient for atom with index idx

◆ ClearGradients()

virtual void ClearGradients ( )

inlineprotectedvirtual

Set all gradients to zero

◆ IsInSameRing()

bool IsInSameRing	(	OBAtom *	a,
		OBAtom *	b
	)

protected

Check if two atoms are in the same ring. [NOTE: this function uses SSSR, this means that not all rings are found for bridged rings. This causes some problems with the MMFF94 validation.]

Parameters

a	atom a
b	atom b

Returns: true if atom a and b are in the same ring

◆ MakeNewInstance()

virtual OBForceField* MakeNewInstance ( )

pure virtual

Clone the current instance. May be desirable in multithreaded environments, Should be deleted after use

◆ TypeID()

const char* TypeID ( )

inlinevirtual

Returns: Plugin type ("forcefields")

Reimplemented from OBPlugin.

◆ FindForceField() [1/2]

static OBForceField* FindForceField ( const std::string & ID )

inlinestatic

Parameters

ID	forcefield id (Ghemical, MMFF94, UFF, ...).

Returns: A pointer to a forcefield (the default if ID is empty), or NULL if not available.

◆ FindForceField() [2/2]

static OBForceField* FindForceField ( const char * ID )

inlinestatic

Parameters

ID	forcefield id (Ghemical, MMFF94, UFF, ...).

Returns: A pointer to a forcefield (the default if ID is empty), or NULL if not available.

◆ SetParameterFile()

void SetParameterFile ( const std::string & filename )

inline

◆ GetUnit()

virtual std::string GetUnit ( )

inlinevirtual

Returns: The unit (kcal/mol, kJ/mol, ...) in which the energy is expressed as std::string.

Examples:: obforcefield_energy.cpp.

◆ HasAnalyticalGradients()

virtual bool HasAnalyticalGradients ( )

inlinevirtual

◆ Setup() [1/2]

bool Setup ( OBMol & mol )

Setup the forcefield for mol (assigns atom types, charges, etc.). Keep current constraints.

Parameters

mol	The OBMol object that contains the atoms and bonds.

Returns: True if succesfull.

Examples:: obforcefield_energy.cpp.

Referenced by OBEnergyConformerScore::Score(), OBMinimizingEnergyConformerScore::Score(), and OBMinimizingRMSDConformerScore::Score().

◆ Setup() [2/2]

bool Setup	(	OBMol &	mol,
		OBFFConstraints &	constraints
	)

Setup the forcefield for mol (assigns atom types, charges, etc.). Use new constraints.

Parameters

mol	The OBMol object that contains the atoms and bonds.
constraints	The OBFFConstraints object that contains the constraints.

Returns: True if succesfull.

◆ ParseParamFile()

virtual bool ParseParamFile ( )

inlinevirtual

Load the parameters (this function is overloaded by the individual forcefields, and is called autoamically from OBForceField::Setup()).

◆ SetTypes()

virtual bool SetTypes ( )

inlinevirtual

Set the atom types (this function is overloaded by the individual forcefields, and is called autoamically from OBForceField::Setup()).

◆ SetFormalCharges()

virtual bool SetFormalCharges ( )

inlinevirtual

Set the formal charges (this function is overloaded by the individual forcefields, and is called autoamically from OBForceField::Setup()).

◆ SetPartialCharges()

virtual bool SetPartialCharges ( )

inlinevirtual

Set the partial charges (this function is overloaded by the individual forcefields, and is called autoamically from OBForceField::Setup()).

◆ SetupCalculations()

virtual bool SetupCalculations ( )

inlinevirtual

Setup the calculations (this function is overloaded by the individual forcefields, and is called autoamically from OBForceField::Setup()).

◆ SetupPointers()

virtual bool SetupPointers ( )

inlinevirtual

Setup the pointers to the atom positions in the OBFFCalculation objects. This method will iterate over all the calculations and call SetupPointers for each one. (This function should be implemented by the individual force field implementations).

◆ IsSetupNeeded()

bool IsSetupNeeded ( OBMol & mol )

Compare the internal forcefield OBMol object to mol. If the two have the same number of atoms and bonds, and all atomic numbers are the same, this function returns false, and no call to Setup is needed.

Returns: True if Setup needs to be called.

◆ GetAtomTypes()

bool GetAtomTypes ( OBMol & mol )

Get the force atom types. The atom types will be added to the atoms of mol as OBPairData. The attribute will be "FFAtomType".

...
pFF->Setup(&mol);
pFF->GetAtomTypes(&mol);
FOR_ATOMS_OF_MOL (atom, mol) {
  OBPairData *type = (OBPairData*) atom->GetData("FFAtomType");
  if (type)
    cout << "atom " << atom->GetIdx() << " : " << type->GetValue() << endl;
}
...

◆ GetPartialCharges()

bool GetPartialCharges ( OBMol & mol )

Get the force field formal charges. The formal charges will be added to the atoms of mol as OBPairData. The attribute will be "FFPartialCharge".

...
pFF->Setup(&mol);
pFF->GetPartialCharges(&mol);
FOR_ATOMS_OF_MOL (atom, mol) {
  OBPairData *chg = (OBPairData*) atom->GetData("FFPartialCharge");
  if (chg)
    cout << "atom " << atom->GetIdx() << " : " << chg->GetValue() << endl;
}
...

◆ GetCoordinates()

bool GetCoordinates ( OBMol & mol )

Get coordinates for current conformer and attach OBConformerData with energies, forces, ... to mol.

Parameters

mol	The OBMol object to copy the coordinates to (from OBForceField::_mol).

Returns: True if succesfull.

◆ UpdateCoordinates()

bool UpdateCoordinates ( OBMol & mol )

inline

Deprecated:: Use GetCooordinates instead.

◆ GetConformers()

bool GetConformers ( OBMol & mol )

Get coordinates for all conformers and attach OBConformerData with energies, forces, ... to mol.

Parameters

mol	The OBMol object to copy the coordinates to (from OBForceField::_mol).

Returns: True if succesfull.

◆ UpdateConformers()

bool UpdateConformers ( OBMol & mol )

inline

Deprecated:: Use GetConformers instead.

◆ SetCoordinates()

bool SetCoordinates ( OBMol & mol )

Set coordinates for current conformer.

Parameters

mol	the OBMol object to copy the coordinates from (to OBForceField::_mol).

Returns: true if succesfull.

◆ SetConformers()

bool SetConformers ( OBMol & mol )

Set coordinates for all conformers.

Parameters

mol	The OBMol object to copy the coordinates from (to OBForceField::_mol).

Returns: True if succesfull.

◆ GetGrid()

OBGridData * GetGrid	(	double	step,
		double	padding,
		const char *	type,
		double	pchg
	)

Create a grid with spacing step and padding. Place a probe atom of type probe at every grid point, calculate the energy and store it in the grid. These grids can then be used to create isosurfaces to identify locations where the probe atom has favourable interactions with the molecule.

Parameters

step	The grid step size in A..
padding	The padding for the grid in A.
type	The force field atom type for the probe.
pchg	The partial charge for the probe atom.

Returns: Pointer to the grid constaining the results.

◆ AddIntraGroup()

void AddIntraGroup ( OBBitVec & group )

Enable intra-molecular interactions for group (bonds, angles, strbnd, torsions, oop). This function should be called before Setup().

Parameters

group OBBitVec with bits set for the indexes of the atoms which make up the group.

◆ AddInterGroup()

void AddInterGroup ( OBBitVec & group )

Enable inter-molecular interactions for group (non-bonded: vdw & ele). This function should be called before Setup().

Parameters

group OBBitVec with bits set for the indexes of the atoms which make up the group.

◆ AddInterGroups()

void AddInterGroups	(	OBBitVec &	group1,
		OBBitVec &	group2
	)

Enable inter-molecular interactions between group1 and group2 (non-bonded: vdw & ele). Note that this function doesn't enable bonded interactions in either group. Non-bonded interactions in the groups itself are also not enabled. This function should be called before Setup().

Parameters

group1	OBBitVec with bits set for the indexes of the atoms which make up the first group.
group2	OBBitVec with bits set for the indexes of the atoms which make up the second group.

◆ ClearGroups()

void ClearGroups ( )

Clear all previously specified groups.

◆ HasGroups()

bool HasGroups ( )

Returns: true if there are groups.

◆ EnableCutOff()

void EnableCutOff ( bool enable )

inline

Enable or disable Cut-offs. Cut-offs are disabled by default.

Parameters

enable Enable when true, disable when false.

◆ IsCutOffEnabled()

bool IsCutOffEnabled ( )

inline

Returns: True if Cut-off distances are used.

◆ SetVDWCutOff()

void SetVDWCutOff ( double r )

inline

Set the VDW cut-off distance to r. Note that this does not enable cut-off distances.

Parameters

r	The VDW cut-off distance to be used in A.

◆ GetVDWCutOff()

double GetVDWCutOff ( )

inline

Get the VDW cut-off distance.

Returns: The VDW cut-off distance in A.

◆ SetElectrostaticCutOff()

void SetElectrostaticCutOff ( double r )

inline

Set the Electrostatic cut-off distance to r. Note that this does not enable cut-off distances.

Parameters

r	The electrostatic cut-off distance to be used in A.

◆ GetElectrostaticCutOff()

double GetElectrostaticCutOff ( )

inline

Get the Electrostatic cut-off distance.

Returns: The electrostatic cut-off distance in A.

◆ SetDielectricConstant()

void SetDielectricConstant ( double epsilon )

inline

Set the dielectric constant for electrostatic SetupCalculations

Parameters

epsilon The relative permittivity to use (default = 1.0)

◆ GetDielectricConstant()

double GetDielectricConstant ( )

inline

◆ SetUpdateFrequency()

void SetUpdateFrequency ( int f )

inline

Set the frequency by which non-bonded pairs are updated. Values from 10 to 20 are recommended. Too low will decrease performance, too high will cause non-bonded interactions within cut-off not to be calculated.

Parameters

f	The pair list update frequency.

◆ GetUpdateFrequency()

int GetUpdateFrequency ( )

inline

Get the frequency by which non-bonded pairs are updated.

Returns: The pair list update frequency.

◆ UpdatePairsSimple()

void UpdatePairsSimple ( )

Set the bits in _vdwpairs and _elepairs to 1 for interactions that are within cut-off distance. This function is called in minimizing algorithms such as SteepestDescent and ConjugateGradients.

Todo:: set the criteria as squared values

◆ GetNumPairs()

unsigned int GetNumPairs ( )

Get the number of non-bonded pairs in _mol.

Returns: The number of atom pairs (ignores cutoff)

◆ GetNumElectrostaticPairs()

unsigned int GetNumElectrostaticPairs ( )

Get the number of enabled electrostatic pairs in _mol.

Returns: The number of pairs currently enabled (within cut-off distance)

◆ GetNumVDWPairs()

unsigned int GetNumVDWPairs ( )

Get the number of enabled VDW pairs in _mol.

Returns: The number of pairs currently enabled (within cut-off distance)

◆ EnableAllPairs()

void EnableAllPairs ( )

inline

Set bits in range 0..._numpairs-1 to 1. Using this means there will be no cut-off. (not-working: see code for more information.

◆ GetGradient()

virtual vector3 GetGradient	(	OBAtom *	a,
		int	= `OBFF_ENERGY`
	)

inlinevirtual

Get the pointer to the gradients

◆ GetGradientPtr()

double* GetGradientPtr ( )

inline

Get the pointer to the gradients

◆ Energy()

virtual double Energy ( bool gradients = true )

inlinevirtual

Parameters

gradients Set to true when the gradients need to be calculated (needs to be done before calling GetGradient()).

Returns: Total energy.

Output to log:: OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: none
OBFF_LOGLVL_MEDIUM: energy for individual energy terms
OBFF_LOGLVL_HIGH: energy for individual energy interactions

Examples:: obforcefield_energy.cpp.

Referenced by OBEnergyConformerScore::Score(), OBMinimizingEnergyConformerScore::Score(), and OBMinimizingRMSDConformerScore::Score().

◆ E_Bond()

virtual double E_Bond ( bool gradients = true )

inlinevirtual

Parameters

gradients Set to true when the gradients need to be calculated (needs to be done before calling GetGradient()).

Returns: Bond stretching energy.

Output to log:: see Energy()

◆ E_Angle()

virtual double E_Angle ( bool gradients = true )

inlinevirtual

Parameters

gradients Set to true when the gradients need to be calculated (needs to be done before calling GetGradient()).

Returns: Angle bending energy.

Output to log:: see Energy()

◆ E_StrBnd()

virtual double E_StrBnd ( bool gradients = true )

inlinevirtual

Parameters

gradients Set to true when the gradients need to be calculated (needs to be done before calling GetGradient()).

Returns: Stretch bending energy.

Output to log:: see Energy()

◆ E_Torsion()

virtual double E_Torsion ( bool gradients = true )

inlinevirtual

Parameters

gradients Set to true when the gradients need to be calculated (needs to be done before calling GetGradient()).

Returns: Torsional energy.

Output to log:: see Energy()

◆ E_OOP()

virtual double E_OOP ( bool gradients = true )

inlinevirtual

Parameters

gradients Set to true when the gradients need to be calculated (needs to be done before calling GetGradient()).

Returns: Out-Of-Plane bending energy.

Output to log:: see Energy()

◆ E_VDW()

virtual double E_VDW ( bool gradients = true )

inlinevirtual

Parameters

gradients Set to true when the gradients need to be calculated (needs to be done before calling GetGradient()).

Returns: Van der Waals energy.

Output to log:: see Energy()

◆ E_Electrostatic()

virtual double E_Electrostatic ( bool gradients = true )

inlinevirtual

Parameters

gradients Set to true when the gradients need to be calculated (needs to be done before calling GetGradient()).

Returns: Electrostatic energy.

Output to log:: see Energy()

◆ PrintTypes()

void PrintTypes ( )

Print the atom types to the log.

◆ PrintFormalCharges()

void PrintFormalCharges ( )

Print the formal charges to the log (atom.GetPartialCharge(), MMFF94 FC's are not always int).

◆ PrintPartialCharges()

void PrintPartialCharges ( )

Print the partial charges to the log.

◆ PrintVelocities()

void PrintVelocities ( )

Print the velocities to the log.

◆ SetLogFile()

bool SetLogFile ( std::ostream * pos )

Set the stream for logging (can also be &cout for logging to screen).

Parameters

pos	Stream (when pos is 0, std::cout wil be used).

Returns: True if succesfull.

◆ SetLogLevel()

bool SetLogLevel ( int level )

Set the log level (OBFF_LOGLVL_NONE, OBFF_LOGLVL_LOW, OBFF_LOGLVL_MEDIUM, OBFF_LOGLVL_HIGH). Inline if statements for logging are available:

#define IF_OBFF_LOGLVL_LOW    if(_loglvl >= OBFF_LOGLVL_LOW)
#define IF_OBFF_LOGLVL_MEDIUM if(_loglvl >= OBFF_LOGLVL_MEDIUM)
#define IF_OBFF_LOGLVL_HIGH   if(_loglvl >= OBFF_LOGLVL_HIGH)

example:

SetLogLevel(OBFF_LOGLVL_MEDIUM);
IF_OBFF_LOGLVL_HIGH {
  OBFFLog("this text will NOT be logged...\n");
}
IF_OBFF_LOGLVL_LOW {
  OBFFLog"this text will be logged...\n");
}
IF_OBFF_LOGLVL_MEDIUM {
  OBFFLog("this text will also be logged...\n");
}

◆ GetLogLevel()

int GetLogLevel ( )

inline

Returns: The log level.

◆ OBFFLog() [1/2]

void OBFFLog ( std::string msg )

inline

Print msg to the logfile.

Parameters

msg	The message to print.

◆ OBFFLog() [2/2]

void OBFFLog ( const char * msg )

inline

Print msg to the logfile.

Parameters

msg	The message to print.

◆ DistanceGeometry()

void DistanceGeometry ( )

Generate coordinates for the molecule (distance geometry)

Deprecated:: Use OBDistanceGeometry class instead

◆ SystematicRotorSearch()

void SystematicRotorSearch	(	unsigned int	geomSteps = `2500`,
		bool	sampleRingBonds = `false`
	)

Generate conformers for the molecule (systematicaly rotating torsions).

The initial starting structure here is important, this structure should be minimized for the best results. SystematicRotorSearch works by rotating around the rotatable bond in a molecule (see OBRotamerList class). This rotating generates multiple conformers. The energy for all these conformers is then evaluated and the lowest energy conformer is selected.

Parameters

geomSteps	The number of steps to take during geometry optimization.
sampleRingBonds	Whether to sample ring torsions.

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for this function will interfere with the output for this function.

OBFF_LOGLVL_NONE: None.
OBFF_LOGLVL_LOW: Number of rotatable bonds, energies for the conformers, which one is the lowest, ...
OBFF_LOGLVL_MEDIUM: See note above.
OBFF_LOGLVL_HIGH: See note above.

◆ SystematicRotorSearchInitialize()

int SystematicRotorSearchInitialize	(	unsigned int	geomSteps = `2500`,
		bool	sampleRingBonds = `false`
	)

Generate conformers for the molecule by systematicaly rotating torsions. To be used in combination with SystematicRotorSearchNexConformer().

example:

// pFF is a pointer to a OBForceField class
pFF->SystematicRotorSearchInitialize(300);
while (pFF->SystematicRotorSearchNextConformer(300)) {
  // do some updating in your program (show last generated conformer, ...)
}

If you don't need any updating in your program, SystematicRotorSearch() is recommended.

Parameters

geomSteps	The number of steps to take during geometry optimization.
sampleRingBonds	Whether to sample ring torsions.

Returns: The number of conformers.

◆ SystematicRotorSearchNextConformer()

bool SystematicRotorSearchNextConformer ( unsigned int geomSteps = 2500 )

Evaluate the next conformer.

Parameters

geomSteps The number of steps to take during geometry optimization.

Returns: True if there are more conformers.

◆ RandomRotorSearch()

void RandomRotorSearch	(	unsigned int	conformers,
		unsigned int	geomSteps = `2500`,
		bool	sampleRingBonds = `false`
	)

Generate conformers for the molecule (randomly rotating torsions).

The initial starting structure here is important, this structure should be minimized for the best results. RandomRotorSearch works by randomly rotating around the rotatable bonds in a molecule (see OBRotamerList class). This rotating generates multiple conformers. The energy for all these conformers is then evaluated and the lowest energy conformer is selected.

Parameters

conformers	The number of random conformers to consider during the search.
geomSteps	The number of steps to take during geometry optimization for each conformer.
sampleRingBonds	Whether to sample ring torsions.

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for this function will interfere with the output for this function.

OBFF_LOGLVL_NONE: None.
OBFF_LOGLVL_LOW: Number of rotatable bonds, energies for the conformers, which one is the lowest, ...
OBFF_LOGLVL_MEDIUM: See note above.
OBFF_LOGLVL_HIGH: See note above.

◆ RandomRotorSearchInitialize()

void RandomRotorSearchInitialize	(	unsigned int	conformers,
		unsigned int	geomSteps = `2500`,
		bool	sampleRingBonds = `false`
	)

Generate conformers for the molecule by randomly rotating torsions. To be used in combination with RandomRotorSearchNexConformer().

example:

// pFF is a pointer to a OBForceField class
pFF->RandomRotorSearchInitialize(300);
while (pFF->RandomRotorSearchNextConformer(300)) {
  // do some updating in your program (show last generated conformer, ...)
}

If you don't need any updating in your program, RandomRotorSearch() is recommended.

Parameters

conformers	The number of random conformers to consider during the search
geomSteps	The number of steps to take during geometry optimization
sampleRingBonds	Whether to sample ring torsions.

◆ RandomRotorSearchNextConformer()

bool RandomRotorSearchNextConformer ( unsigned int geomSteps = 2500 )

Evaluate the next conformer.

Parameters

geomSteps The number of steps to take during geometry optimization.

Returns: True if there are more conformers.

◆ WeightedRotorSearch()

void WeightedRotorSearch	(	unsigned int	conformers,
		unsigned int	geomSteps,
		bool	sampleRingBonds = `false`
	)

Generate conformers for the molecule (randomly rotating torsions).

The initial starting structure here is important, this structure should be minimized for the best results. WeightedRotorSearch works by randomly rotating around the rotatable bonds in a molecule (see OBRotamerList class). Unlike RandomRotorSearch() the random choice of torsions is reweighted based on the energy of the generated conformer. Over time, the generated conformers for each step should become increasingly better. The lowest energy conformer is selected.

Parameters

conformers	The number of random conformers to consider during the search.
geomSteps	The number of steps to take during geometry optimization for each conformer.
sampleRingBonds	Whether to sample ring torsions.

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for this function will interfere with the output for this function.

OBFF_LOGLVL_NONE: None.
OBFF_LOGLVL_LOW: Number of rotatable bonds, energies for the conformers, which one is the lowest, ...
OBFF_LOGLVL_MEDIUM: See note above.
OBFF_LOGLVL_HIGH: See note above.

◆ FastRotorSearch()

int FastRotorSearch ( bool permute = true )

A fast rotor search to find low energy conformations.

Iterate over each of the rotors, and set the torsion angle to that which minimizes the energy (while keeping the rest of the molecule fixed). In general (for molecules with more than one rotatable bond), this procedure will not find the global minimum, but it will at least get rid of any bad clashes, and it do so quickly.

Torsions closer to the center of the molecule will be optimized first as these most likely to generate large clashes.

One possible use of this procedure is to prepare a reasonable 3D structure of a molecule for viewing. Another is to prepare the starting structure for a more systematic rotor search (in which case you should geometry optimize the final structure).

Parameters

permute Whether or not to permute the order of the 4 most central rotors. Default is true. This does a more thorough search, but takes 4! = 24 times as long.

Since: version 2.4

◆ SetLineSearchType()

void SetLineSearchType ( int type )

inline

Set the LineSearchType. The default type is LineSearchType::Newton2Num.

Parameters

type	The LineSearchType to be used in SteepestDescent and ConjugateGradients.

◆ GetLineSearchType()

int GetLineSearchType ( )

inline

Get the LineSearchType.

Returns: The current LineSearchType.

◆ LineSearch() [1/2]

vector3 LineSearch	(	OBAtom *	atom,
		vector3 &	direction
	)

Perform a linesearch starting at atom in direction direction.

Deprecated:: Current code should use LineSearch(double *, double*) instead.

◆ LineSearch() [2/2]

double LineSearch	(	double *	currentCoords,
		double *	direction
	)

Perform a linesearch for the entire molecule in direction direction. This function is called when using LineSearchType::Simple.

Parameters

currentCoords	Start coordinates.
direction	The search direction.

Returns: alpha, The scale of the step we moved along the direction vector.

Output to log:: OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: none
OBFF_LOGLVL_MEDIUM: none
OBFF_LOGLVL_HIGH: none

◆ Newton2NumLineSearch()

double Newton2NumLineSearch ( double * direction )

Perform a linesearch for the entire molecule. This function is called when using LineSearchType::Newton2Num.

Parameters

direction The search direction.

Returns: alpha, The scale of the step we moved along the direction vector.

Output to log:: OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: none
OBFF_LOGLVL_MEDIUM: none
OBFF_LOGLVL_HIGH: none

◆ LineSearchTakeStep()

void LineSearchTakeStep	(	double *	origCoords,
		double *	direction,
		double	step
	)

Set the coordinates of the atoms to origCoord + step.

Parameters

origCoords	Start coordinates.
direction	The search direction.
step	The step to take.

◆ SteepestDescent()

void SteepestDescent	(	int	steps,
		double	econv = `1e-6f`,
		int	method = `OBFF_ANALYTICAL_GRADIENT`
	)

Perform steepest descent optimalization for steps steps or until convergence criteria is reached.

Parameters

steps	The number of steps.
econv	Energy convergence criteria. (defualt is 1e-6)
method	Deprecated. (see HasAnalyticalGradients())

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for the minimization will interfere with the list of energies for succesive steps.

OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: header including number of steps and first step
OBFF_LOGLVL_MEDIUM: see note above
OBFF_LOGLVL_HIGH: see note above

◆ SteepestDescentInitialize()

void SteepestDescentInitialize	(	int	steps = `1000`,
		double	econv = `1e-6f`,
		int	method = `OBFF_ANALYTICAL_GRADIENT`
	)

Initialize steepest descent optimalization, to be used in combination with SteepestDescentTakeNSteps().

example:

// pFF is a pointer to a OBForceField class
pFF->SteepestDescentInitialize(100, 1e-5f);
while (pFF->SteepestDescentTakeNSteps(5)) {
  // do some updating in your program (redraw structure, ...)
}

If you don't need any updating in your program, SteepestDescent() is recommended.

Parameters

steps	The number of steps.
econv	Energy convergence criteria. (defualt is 1e-6)
method	Deprecated. (see HasAnalyticalGradients())

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for the minimization will interfere with the list of energies for succesive steps.

OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: header including number of steps
OBFF_LOGLVL_MEDIUM: see note above
OBFF_LOGLVL_HIGH: see note above

◆ SteepestDescentTakeNSteps()

bool SteepestDescentTakeNSteps ( int n )

Take n steps in a steepestdescent optimalization that was previously initialized with SteepestDescentInitialize().

Parameters

n	The number of steps to take.

Returns: False if convergence or the number of steps given by SteepestDescentInitialize() has been reached.

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for the minimization will interfere with the list of energies for succesive steps.

OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: step number, energy and energy for the previous step
OBFF_LOGLVL_MEDIUM: see note above
OBFF_LOGLVL_HIGH: see note above

◆ ConjugateGradients()

void ConjugateGradients	(	int	steps,
		double	econv = `1e-6f`,
		int	method = `OBFF_ANALYTICAL_GRADIENT`
	)

Perform conjugate gradient optimalization for steps steps or until convergence criteria is reached.

Parameters

steps	The number of steps.
econv	Energy convergence criteria. (defualt is 1e-6)
method	Deprecated. (see HasAnalyticalGradients())

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for the minimization will interfere with the list of energies for succesive steps.

OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: information about the progress of the minimization
OBFF_LOGLVL_MEDIUM: see note above
OBFF_LOGLVL_HIGH: see note above

Referenced by OBMinimizingEnergyConformerScore::Score(), and OBMinimizingRMSDConformerScore::Score().

◆ ConjugateGradientsInitialize()

void ConjugateGradientsInitialize	(	int	steps = `1000`,
		double	econv = `1e-6f`,
		int	method = `OBFF_ANALYTICAL_GRADIENT`
	)

Initialize conjugate gradient optimalization and take the first step, to be used in combination with ConjugateGradientsTakeNSteps().

example:

// pFF is a pointer to a OBForceField class
pFF->ConjugateGradientsInitialize(100, 1e-5f);
while (pFF->ConjugateGradientsTakeNSteps(5)) {
  // do some updating in your program (redraw structure, ...)
}

If you don't need any updating in your program, ConjugateGradients() is recommended.

Parameters

steps	The number of steps.
econv	Energy convergence criteria. (defualt is 1e-6)
method	Deprecated. (see HasAnalyticalGradients())

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for the minimization will interfere with the list of energies for succesive steps.

OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: header including number of steps and first step
OBFF_LOGLVL_MEDIUM: see note above
OBFF_LOGLVL_HIGH: see note above

◆ ConjugateGradientsTakeNSteps()

bool ConjugateGradientsTakeNSteps ( int n )

Take n steps in a conjugate gradient optimalization that was previously initialized with ConjugateGradientsInitialize().

Parameters

n	The number of steps to take.

Returns: False if convergence or the number of steps given by ConjugateGradientsInitialize() has been reached.

Output to log:: This function should only be called with the log level set to OBFF_LOGLVL_NONE or OBFF_LOGLVL_LOW. Otherwise too much information about the energy calculations needed for the minimization will interfere with the list of energies for succesive steps.

OBFF_LOGLVL_NONE: none
OBFF_LOGLVL_LOW: step number, energy and energy for the previous step
OBFF_LOGLVL_MEDIUM: see note above
OBFF_LOGLVL_HIGH: see note above

◆ GenerateVelocities()

void GenerateVelocities ( )

Generate starting velocities with a Maxwellian distribution.

◆ CorrectVelocities()

void CorrectVelocities ( )

Correct the velocities so that the following is true:

      3N
     ----
0.5  \    m_i * v_i^2 = 0.5 * Ndf * R * T = E_kin
     /
     ----
     i=1
E_kin : kinetic energy
m_i : mass of atom i
v_i : velocity of atom i
Ndf : number of degrees of freedom (3 * number of atoms)
R : gas constant
T : temperature

◆ MolecularDynamicsTakeNSteps()

void MolecularDynamicsTakeNSteps	(	int	n,
		double	T,
		double	timestep = `0.001`,
		int	method = `OBFF_ANALYTICAL_GRADIENT`
	)

Take n steps at temperature T. If no velocities are set, they will be generated.

example:

// pFF is a pointer to a OBForceField class
while (pFF->MolecularDynamicsTakeNSteps(5, 300)) {
  // do some updating in your program (redraw structure, ...)
}

Parameters

n	The number of steps to take.
T	Absolute temperature in Kelvin.
timestep	The time step in picoseconds. (10e-12 s)
method	OBFF_ANALYTICAL_GRADIENTS (default) or OBFF_NUMERICAL_GRADIENTS

◆ GetConstraints()

OBFFConstraints & GetConstraints ( )

Get the current constraints.

Returns: The current constrains stored in the force field.

◆ SetConstraints()

void SetConstraints ( OBFFConstraints & constraints )

Set the constraints.

Parameters

constraints The new constraints to be used.

◆ SetFixAtom()

void SetFixAtom ( int index )

Fix the atom position until UnsetFixAtom() is called. This function can be used in programs that allow the user to interact with a molecule that is being minimized without having to check if the atom is already fixed in the constraints set by Setup() or SetConstraints(). Using this makes sure the selected atom follows the mouse cursur.

Parameters

index The index for the atom to fix.

◆ UnsetFixAtom()

void UnsetFixAtom ( )

Undo last SetFixAtom. This function will not remove the fix atom constraint for this atom if set by Setup() or SetConstraints().

◆ SetIgnoreAtom()

void SetIgnoreAtom ( int index )

Ignore the atom until UnsetIgnoreAtom() is called. This function can be used in programs that allow the user to interact with a molecule that is being minimized without having to check if the atom is already ignored in the constraints set by Setup() or SetConstraints(). Using this makes sure, in drawing mode, you can close rings without your newly created puching the other atoms away.

Parameters

index The index for the atom to ignore.

◆ UnsetIgnoreAtom()

void UnsetIgnoreAtom ( )

Undo last SetIgnoreAtom. This function will not remove the ignore atom constraint for this atom if set by Setup() or SetConstraints().

◆ IgnoreCalculation() [1/3]

bool IgnoreCalculation	(	int	a,
		int	b
	)

static

internal function

◆ IgnoreCalculation() [2/3]

bool IgnoreCalculation	(	int	a,
		int	b,
		int	c
	)

static

internal function

◆ IgnoreCalculation() [3/3]

bool IgnoreCalculation	(	int	a,
		int	b,
		int	c,
		int	d
	)

static

internal function

◆ DetectExplosion()

bool DetectExplosion ( )

(debugging)

◆ ValidateLineSearch()

vector3 ValidateLineSearch	(	OBAtom *	atom,
		vector3 &	direction
	)

(debugging)

◆ ValidateSteepestDescent()

void ValidateSteepestDescent ( int steps )

(debugging)

◆ ValidateConjugateGradients()

void ValidateConjugateGradients ( int steps )

(debugging)

◆ Validate()

virtual bool Validate ( )

inlinevirtual

Validate the force field implementation (debugging)

◆ ValidateGradients()

virtual bool ValidateGradients ( )

inlinevirtual

Validate the analytical gradients by comparing them to numerical ones. This function has to be implemented force field specific. (debugging)

◆ ValidateGradientError()

vector3 ValidateGradientError	(	vector3 &	numgrad,
		vector3 &	anagrad
	)

Calculate the error of the analytical gradient (debugging)

Returns: error = fabs(numgrad - anagrad) / anagrad * 100%

◆ VectorBondDerivative()

double VectorBondDerivative	(	double *	pos_a,
		double *	pos_b,
		double *	force_a,
		double *	force_b
	)

static

Calculate the derivative of a vector length. The vector is given by a - b, the length of this vector rab = sqrt(ab.x^2 + ab.y^2 + ab.z^2).

Parameters

pos_a	atom a (coordinates)
pos_b	atom b (coordinates)
force_a	- return value for the force on atom a
force_b	- return value for the force on atom b

Returns: The distance between a and b (bondlength for bond stretching, separation for vdw, electrostatic)

◆ VectorDistanceDerivative()

double VectorDistanceDerivative	(	const double *const	pos_i,
		const double *const	pos_j,
		double *	force_i,
		double *	force_j
	)

static

To be used for VDW or Electrostatic interactions. This is faster than VectorBondDerivative, but does no error checking.

◆ VectorLengthDerivative()

double VectorLengthDerivative	(	vector3 &	a,
		vector3 &	b
	)

static

Deprecated:

◆ VectorAngleDerivative() [1/2]

double VectorAngleDerivative	(	double *	pos_a,
		double *	pos_b,
		double *	pos_c,
		double *	force_a,
		double *	force_b,
		double *	force_c
	)

static

Calculate the derivative of a angle a-b-c. The angle is given by dot(ab,cb)/rab*rcb. Used for harmonic (cubic) angle potentials.

Parameters

pos_a	atom a (coordinates)
pos_b	atom b (coordinates)
pos_c	atom c (coordinates)
force_a	- return value for the force on atom a
force_b	- return value for the force on atom b
force_c	- return value for the force on atom c

Returns: The angle between a-b-c

◆ VectorAngleDerivative() [2/2]

double VectorAngleDerivative	(	vector3 &	a,
		vector3 &	b,
		vector3 &	c
	)

static

Deprecated:

◆ VectorOOPDerivative() [1/2]

double 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
	)

static

Calculate the derivative of a OOP angle a-b-c-d. b is the central atom, and a-b-c is the plane. The OOP angle is given by 90° - arccos(dot(corss(ab,cb),db)/rabbc*rdb).

Parameters

pos_a	atom a (coordinates)
pos_b	atom b (coordinates)
pos_c	atom c (coordinates)
pos_d	atom d (coordinates)
force_a	- return value for the force on atom a
force_b	- return value for the force on atom b
force_c	- return value for the force on atom c
force_d	- return value for the force on atom d

Returns: The OOP angle for a-b-c-d

◆ VectorOOPDerivative() [2/2]

double VectorOOPDerivative	(	vector3 &	a,
		vector3 &	b,
		vector3 &	c,
		vector3 &	d
	)

static

Deprecated:

◆ VectorTorsionDerivative() [1/2]

double 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
	)

static

Calculate the derivative of a torsion angle a-b-c-d. The torsion angle is given by arccos(dot(corss(ab,bc),cross(bc,cd))/rabbc*rbccd).

Parameters

pos_a	atom a (coordinates)
pos_b	atom b (coordinates)
pos_c	atom c (coordinates)
pos_d	atom d (coordinates)
force_a	- return value for the force on atom a
force_b	- return value for the force on atom b
force_c	- return value for the force on atom c
force_d	- return value for the force on atom d

Returns: The tosion angle for a-b-c-d

◆ VectorTorsionDerivative() [2/2]

double VectorTorsionDerivative	(	vector3 &	a,
		vector3 &	b,
		vector3 &	c,
		vector3 &	d
	)

static

Deprecated:

◆ VectorSubtract() [1/2]

static void VectorSubtract	(	double *	i,
		double *	j,
		double *	result
	)

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
j	pointer to j[3]
result	pointer to result[3], will be set to i - j

◆ VectorSubtract() [2/2]

static void VectorSubtract	(	const double *const	i,
		const double *const	j,
		double *	result
	)

inlinestatic

◆ VectorAdd()

static void VectorAdd	(	double *	i,
		double *	j,
		double *	result
	)

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
j	pointer to j[3]
result	pointer to result[3], will be set to i + j

◆ VectorDivide()

static void VectorDivide	(	double *	i,
		double	n,
		double *	result
	)

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
n	divide x,y,z with n
result	pointer to result[3]

◆ VectorMultiply() [1/2]

static void VectorMultiply	(	double *	i,
		double	n,
		double *	result
	)

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
n	multiply x,y,z with n
result	pointer to result[3]

◆ VectorMultiply() [2/2]

static void VectorMultiply	(	const double *const	i,
		const double	n,
		double *	result
	)

inlinestatic

◆ VectorSelfMultiply()

static void VectorSelfMultiply	(	double *	i,
		double	n
	)

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3], multiply this vector by n and set this vector to the result.
n	the scalar value to be multipled

◆ VectorNormalize()

static void VectorNormalize ( double * i )

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3] to be normalized

◆ VectorCopy()

static void VectorCopy	(	double *	from,
		double *	to
	)

inlinestatic

inline fuction to speed up minimization speed

Parameters

from	pointer to i[3] to be copied from
to	pointer to j[3] to be copied to

◆ VectorLength()

static double VectorLength ( double * i )

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]

Returns: the vector length

◆ VectorDistance()

static double VectorDistance	(	double *	pos_i,
		double *	pos_j
	)

inlinestatic

◆ VectorAngle()

double VectorAngle	(	double *	i,
		double *	j,
		double *	k
	)

static

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
j	pointer to j[3]
k	pointer to k[3]

Returns: the vector angle ijk (deg)

◆ VectorTorsion()

double VectorTorsion	(	double *	i,
		double *	j,
		double *	k,
		double *	l
	)

static

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
j	pointer to j[3]
k	pointer to k[3]
l	pointer to l[3]

Returns: the vector torson ijkl (deg)

◆ VectorOOP()

double VectorOOP	(	double *	i,
		double *	j,
		double *	k,
		double *	l
	)

static

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
j	pointer to j[3]
k	pointer to k[3]
l	pointer to l[3]

Returns: the vector torson ijkl (deg)

◆ VectorClear()

static void VectorClear ( double * i )

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3], will set x,y,z to 0,0,0

◆ VectorDot()

static double VectorDot	(	double *	i,
		double *	j
	)

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
j	pointer to j[3]

Returns: the dot product

◆ VectorCross()

static void VectorCross	(	double *	i,
		double *	j,
		double *	result
	)

inlinestatic

inline fuction to speed up minimization speed

Parameters

i	pointer to i[3]
j	pointer to j[3]
result	the dot product (as a return value double[3])

◆ PrintVector()

static void PrintVector ( double * i )

inlinestatic

Member Data Documentation

◆ _mol

OBMol _mol

protected

Molecule to be evaluated or minimized.

◆ _init

bool _init

protected

Used to make sure we only parse the parameter file once, when needed.

◆ _parFile

std::string _parFile

protected

◆ _validSetup

bool _validSetup

protected

< parameter file name

was the last call to Setup succesfull

◆ _gradientPtr

double* _gradientPtr

protected

pointer to the gradients (used by AddGradient(), minimization functions, ...)

◆ _logos

std::ostream* _logos

protected

Output for logfile.

◆ _logbuf

char _logbuf[BUFF_SIZE+1]

protected

Temporary buffer for logfile output.

◆ _loglvl

int _loglvl

protected

Log level for output.

◆ _origLogLevel

int _origLogLevel

protected

◆ _current_conformer

int _current_conformer

protected

used to hold i for current conformer (needed by UpdateConformers)

◆ _energies

std::vector<double> _energies

protected

used to hold the energies for all conformers

◆ _econv

double _econv

protected

◆ _gconv

double _gconv

protected

◆ _e_n1

double _e_n1

protected

Used for conjugate gradients and steepest descent(Initialize and TakeNSteps)

◆ _cstep

int _cstep

protected

◆ _nsteps

int _nsteps

protected

Used for conjugate gradients and steepest descent(Initialize and TakeNSteps)

◆ _grad1

double* _grad1

protected

Used for conjugate gradients and steepest descent(Initialize and TakeNSteps)

◆ _ncoords

unsigned int _ncoords

protected

Number of coordinates for conjugate gradients.

◆ _linesearch

int _linesearch

protected

LineSearch type.

◆ _timestep

double _timestep

protected

Molecular dynamics time step in picoseconds.

◆ _temp

double _temp

protected

Molecular dynamics temperature in Kelvin.

◆ _velocityPtr

double* _velocityPtr

protected

pointer to the velocities

◆ _constraints

OBFFConstraints _constraints = OBFFConstraints()

staticprotected

Constraints.

◆ _fixAtom

unsigned int _fixAtom = 0

staticprotected

SetFixAtom()/UnsetFixAtom()

◆ _ignoreAtom

unsigned int _ignoreAtom = 0

staticprotected

SetIgnoreAtom()/UnsetIgnoreAtom()

◆ _cutoff

bool _cutoff

protected

true = cut-off enabled

◆ _rvdw

double _rvdw

protected

VDW cut-off distance.

◆ _rele

double _rele

protected

Electrostatic cut-off distance.

◆ _epsilon

double _epsilon

protected

Dielectric constant for electrostatics.

◆ _vdwpairs

OBBitVec _vdwpairs

protected

VDW pairs that should be calculated.

◆ _elepairs

OBBitVec _elepairs

protected

Electrostatic pairs that should be calculated.

◆ _pairfreq

int _pairfreq

protected

The frequence to update non-bonded pairs.

◆ _intraGroup

std::vector<OBBitVec> _intraGroup

protected

groups for which intra-molecular interactions should be calculated

◆ _interGroup

std::vector<OBBitVec> _interGroup

protected

groups for which intra-molecular interactions should be calculated

◆ _interGroups

std::vector<std::pair<OBBitVec, OBBitVec> > _interGroups

protected

groups for which intra-molecular interactions should be calculated

The documentation for this class was generated from the following files:

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Methods for constraints

Detailed Description

Constructor & Destructor Documentation

◆ ~OBForceField()

Member Function Documentation

◆ GetParameter() [1/2]

◆ GetParameter() [2/2]

◆ GetParameterIdx()

◆ NumericalDerivative()

◆ NumericalSecondDerivative()

◆ SetGradient()

◆ AddGradient()

◆ ClearGradients()

◆ IsInSameRing()

◆ MakeNewInstance()

◆ TypeID()

◆ FindForceField() [1/2]

◆ FindForceField() [2/2]

◆ SetParameterFile()

◆ GetUnit()

◆ HasAnalyticalGradients()

◆ Setup() [1/2]

◆ Setup() [2/2]

◆ ParseParamFile()

◆ SetTypes()

◆ SetFormalCharges()

◆ SetPartialCharges()

◆ SetupCalculations()

◆ SetupPointers()

◆ IsSetupNeeded()

◆ GetAtomTypes()

◆ GetPartialCharges()

◆ GetCoordinates()

◆ UpdateCoordinates()

◆ GetConformers()

◆ UpdateConformers()

◆ SetCoordinates()

◆ SetConformers()

◆ GetGrid()

◆ AddIntraGroup()

◆ AddInterGroup()

◆ AddInterGroups()

◆ ClearGroups()

◆ HasGroups()

◆ EnableCutOff()

◆ IsCutOffEnabled()

◆ SetVDWCutOff()

◆ GetVDWCutOff()

◆ SetElectrostaticCutOff()

◆ GetElectrostaticCutOff()

◆ SetDielectricConstant()

◆ GetDielectricConstant()

◆ SetUpdateFrequency()

◆ GetUpdateFrequency()

◆ UpdatePairsSimple()

◆ GetNumPairs()

◆ GetNumElectrostaticPairs()

◆ GetNumVDWPairs()

◆ EnableAllPairs()

◆ GetGradient()

◆ GetGradientPtr()

◆ Energy()

◆ E_Bond()

◆ E_Angle()

◆ E_StrBnd()

◆ E_Torsion()

◆ E_OOP()

◆ E_VDW()

◆ E_Electrostatic()

◆ PrintTypes()

◆ PrintFormalCharges()

◆ PrintPartialCharges()

◆ PrintVelocities()