OBForceField Class Reference

Base class for molecular mechanics force fields. More...

#include <openbabel/forcefield.h>

Inheritance diagram for OBForceField:

List of all members.

Methods for constraints

OBFFConstraintsGetConstraints ()
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)

Public Types

typedef std::map< const char
*, OBPlugin *, CharPtrLess
PluginMapType
typedef
PluginMapType::const_iterator 
PluginIterator

Public Member Functions

virtual OBForceFieldMakeNewInstance ()=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)
OBGridDataGetGrid (double step, double padding, const char *type, double pchg)
virtual const char * Description ()
virtual bool Display (std::string &txt, const char *param, const char *ID=NULL)
virtual OBPluginMakeInstance (const std::vector< std::string > &)
const char * GetID () const
virtual PluginMapTypeGetMap () 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 SetUpdateFrequency (int f)
int GetUpdateFrequency ()
void UpdatePairsSimple ()
unsigned int GetNumPairs ()
void EnableAllPairs ()
Methods for energy evaluation
virtual double Energy (bool=true)
virtual double E_Bond (bool=true)
virtual double E_Angle (bool=true)
virtual double E_StrBnd (bool=true)
virtual double E_Torsion (bool=true)
virtual double E_OOP (bool=true)
virtual double E_VDW (bool=true)
virtual double E_Electrostatic (bool=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)
int SystematicRotorSearchInitialize (unsigned int geomSteps=2500)
bool SystematicRotorSearchNextConformer (unsigned int geomSteps=2500)
void RandomRotorSearch (unsigned int conformers, unsigned int geomSteps=2500)
void RandomRotorSearchInitialize (unsigned int conformers, unsigned int geomSteps=2500)
bool RandomRotorSearchNextConformer (unsigned int geomSteps=2500)
void WeightedRotorSearch (unsigned int conformers, unsigned int geomSteps)
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 OBForceFieldFindForceField (const std::string &ID)
static OBForceFieldFindForceField (const char *ID)
static OBPluginGetPlugin (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)
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

OBFFParameterGetParameter (int a, int b, int c, int d, std::vector< OBFFParameter > &parameter)
OBFFParameterGetParameter (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 vector3 GetGradient (OBAtom *a, int=OBFF_ENERGY)
double * GetGradientPtr ()
virtual void ClearGradients ()
bool IsInSameRing (OBAtom *a, OBAtom *b)

Static Protected Member Functions

static PluginMapTypePluginMap ()
static PluginMapTypeGetTypeMap (const char *PluginID)
static OBPluginBaseFindType (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 _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
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 int _fixAtom = 0
static int _ignoreAtom = 0


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->SteepestDescent(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.BitIsOn(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->SteepestDescent(1000);

Member Typedef Documentation

typedef std::map<const char*, OBPlugin*, CharPtrLess> PluginMapType [inherited]

typedef PluginMapType::const_iterator PluginIterator [inherited]


Constructor & Destructor Documentation

virtual ~OBForceField (  )  [inline, virtual]

Destructor.


Member Function Documentation

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, ...

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

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

Get index for vector<OBFFParameter> ...

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

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::MolecularDynamicsTakeNSteps(), and OBForceField::SteepestDescentTakeNSteps().

vector3 NumericalSecondDerivative ( OBAtom a,
int  terms = OBFF_ENERGY 
) [protected]

OB 3.0.

void SetGradient ( double *  grad,
int  idx 
) [inline, protected]

Set the gradient for atom with index idx to grad

void AddGradient ( double *  grad,
int  idx 
) [inline, protected]

Add grad to the gradient for atom with index idx

virtual vector3 GetGradient ( OBAtom a,
int  = OBFF_ENERGY 
) [inline, protected, virtual]

double* GetGradientPtr (  )  [inline, protected]

Get the pointer to the gradients

virtual void ClearGradients (  )  [inline, protected, virtual]

Set all gradients to zero

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

virtual OBForceField* MakeNewInstance (  )  [pure virtual]

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

const char* TypeID (  )  [inline]

Returns:
Plugin type ("forcefields")

static OBForceField* FindForceField ( const std::string &  ID  )  [inline, static]

Parameters:
ID forcefield id (Ghemical, MMFF94, UFF, ...).
Returns:
A pointer to a forcefield (the default if ID is empty), or NULL if not available.

static OBForceField* FindForceField ( const char *  ID  )  [inline, static]

Parameters:
ID forcefield id (Ghemical, MMFF94, UFF, ...).
Returns:
A pointer to a forcefield (the default if ID is empty), or NULL if not available.

void SetParameterFile ( const std::string &  filename  )  [inline]

virtual std::string GetUnit (  )  [inline, virtual]

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

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.

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.

virtual bool ParseParamFile (  )  [inline, virtual]

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

Referenced by OBForceField::Setup().

virtual bool SetTypes (  )  [inline, virtual]

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

Referenced by OBForceField::GetGrid(), and OBForceField::Setup().

virtual bool SetFormalCharges (  )  [inline, virtual]

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

Referenced by OBForceField::Setup().

virtual bool SetPartialCharges (  )  [inline, virtual]

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

Referenced by OBForceField::Setup().

virtual bool SetupCalculations (  )  [inline, virtual]

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

Referenced by OBForceField::GetGrid(), OBForceField::SetConstraints(), and OBForceField::Setup().

virtual bool SetupPointers (  )  [inline, virtual]

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).

Referenced by OBForceField::RandomRotorSearchNextConformer(), OBForceField::SetConformers(), OBForceField::SystematicRotorSearchNextConformer(), and OBForceField::WeightedRotorSearch().

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.

Referenced by OBForceField::Setup().

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;
  }
  ...

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;
  }
  ...

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.

bool UpdateCoordinates ( OBMol mol  )  [inline]

Deprecated:
Use GetCooordinates instead.

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.

bool UpdateConformers ( OBMol mol  )  [inline]

Deprecated:
Use GetConformers instead.

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.

Referenced by OBForceField::Setup().

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.

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.

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.

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.

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.

void ClearGroups (  ) 

Clear all previously specified groups.

bool HasGroups (  ) 

Returns:
true if there are groups.

void EnableCutOff ( bool  enable  )  [inline]

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

Parameters:
enable Enable when true, disable when false.

bool IsCutOffEnabled (  )  [inline]

Returns:
True if Cut-off distances are used.

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.

double GetVDWCutOff (  )  [inline]

Get the VDW cut-off distance.

Returns:
The VDW cut-off distance in A.

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.

double GetElectrostaticCutOff (  )  [inline]

Get the Electrostatic cut-off distance.

Returns:
The electrostatic cut-off distance in A.

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.

int GetUpdateFrequency (  )  [inline]

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

Returns:
The pair list update frequency.

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.

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::SteepestDescentInitialize(), and OBForceField::SteepestDescentTakeNSteps().

unsigned int GetNumPairs (  ) 

Get the number of non-bonded pairs in _mol.

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

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.

virtual double Energy ( bool  = true  )  [inline, virtual]

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 indivudual energy terms
OBFF_LOGLVL_HIGH: energy for individual energy interactions

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::LineSearch(), OBForceField::MolecularDynamicsTakeNSteps(), OBForceField::Newton2NumLineSearch(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OBForceField::RandomRotorSearchNextConformer(), OBForceField::SteepestDescentInitialize(), OBForceField::SteepestDescentTakeNSteps(), OBForceField::SystematicRotorSearchNextConformer(), and OBForceField::WeightedRotorSearch().

virtual double E_Bond ( bool  = true  )  [inline, virtual]

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()

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

virtual double E_Angle ( bool  = true  )  [inline, virtual]

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()

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

virtual double E_StrBnd ( bool  = true  )  [inline, virtual]

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()

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

virtual double E_Torsion ( bool  = true  )  [inline, virtual]

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()

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

virtual double E_OOP ( bool  = true  )  [inline, virtual]

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()

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

virtual double E_VDW ( bool  = true  )  [inline, virtual]

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()

Referenced by OBForceField::GetGrid(), OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

virtual double E_Electrostatic ( bool  = true  )  [inline, virtual]

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()

Referenced by OBForceField::GetGrid(), OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

void PrintTypes (  ) 

Print the atom types to the log.

void PrintFormalCharges (  ) 

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

void PrintPartialCharges (  ) 

Print the partial charges to the log.

void PrintVelocities (  ) 

Print the velocities to the log.

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.

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");
  }

int GetLogLevel (  )  [inline]

Returns:
The log level.

void OBFFLog ( const char *  msg  )  [inline]

Print msg to the logfile.

Parameters:
msg The message to print.

void DistanceGeometry (  ) 

Generate coordinates for the molecule (distance geometry). (OB 3.0).

void SystematicRotorSearch ( unsigned int  geomSteps = 2500  ) 

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.
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.

int SystematicRotorSearchInitialize ( unsigned int  geomSteps = 2500  ) 

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.
Returns:
The number of conformers.

Referenced by OBForceField::SystematicRotorSearch().

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.

Referenced by OBForceField::SystematicRotorSearch().

void RandomRotorSearch ( unsigned int  conformers,
unsigned int  geomSteps = 2500 
)

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.
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.

void RandomRotorSearchInitialize ( unsigned int  conformers,
unsigned int  geomSteps = 2500 
)

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

Referenced by OBForceField::RandomRotorSearch().

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.

Referenced by OBForceField::RandomRotorSearch().

void WeightedRotorSearch ( unsigned int  conformers,
unsigned int  geomSteps 
)

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.
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.

void SetLineSearchType ( int  type  )  [inline]

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

Parameters:
type The LineSearchType to be used in SteepestDescent and ConjugateGradients.

int GetLineSearchType (  )  [inline]

Get the LineSearchType.

Returns:
The current LineSearchType.

vector3 LineSearch ( OBAtom atom,
vector3 direction 
)

Perform a linesearch starting at atom in direction direction.

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

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), and OBForceField::SteepestDescentTakeNSteps().

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

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

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), and OBForceField::SteepestDescentTakeNSteps().

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.

Referenced by OBForceField::Newton2NumLineSearch().

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

Referenced by OBForceField::WeightedRotorSearch().

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

Referenced by OBForceField::SteepestDescent().

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

Referenced by OBForceField::SteepestDescent().

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 OBForceField::RandomRotorSearchInitialize(), OBForceField::RandomRotorSearchNextConformer(), OBForceField::SystematicRotorSearchInitialize(), OBForceField::SystematicRotorSearchNextConformer(), and OBForceField::WeightedRotorSearch().

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

Referenced by OBForceField::ConjugateGradients().

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

Referenced by OBForceField::ConjugateGradients().

void GenerateVelocities (  ) 

Generate starting velocities with a Maxwellian distribution.

Referenced by OBForceField::MolecularDynamicsTakeNSteps().

void CorrectVelocities (  ) 

Correct the velocities so that the following is true:

        3N
       ----
  0.5  \    m_i * v_i^2 = 0.5 * Ndf * kB * 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)
  kB : Boltzmann's constant
  T : temperature

Referenced by OBForceField::GenerateVelocities(), and OBForceField::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

OBFFConstraints & GetConstraints (  ) 

Get the current constraints.

Returns:
The current constrains stored in the force field.

void SetConstraints ( OBFFConstraints constraints  ) 

Set the constraints.

Parameters:
constraints The new constraints to be used.

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.

void UnsetFixAtom (  ) 

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

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.

void UnsetIgnoreAtom (  ) 

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

bool IgnoreCalculation ( int  a,
int  b 
) [static]

internal function

Referenced by OBForceField::IgnoreCalculation().

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

internal function

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

internal function

bool DetectExplosion (  ) 

(debugging)

vector3 ValidateLineSearch ( OBAtom atom,
vector3 direction 
)

void ValidateSteepestDescent ( int  steps  ) 

(debugging)

void ValidateConjugateGradients ( int  steps  ) 

(debugging)

virtual bool Validate (  )  [inline, virtual]

Validate the force field implementation (debugging).

virtual bool ValidateGradients (  )  [inline, virtual]

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

vector3 ValidateGradientError ( vector3 numgrad,
vector3 anagrad 
)

Calculate the error of the analytical gradient (debugging)

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

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)

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.

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]

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

Referenced by OBFFConstraints::GetConstraintEnergy().

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]

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

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]

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

Referenced by OBFFConstraints::GetConstraintEnergy().

double VectorTorsionDerivative ( vector3 a,
vector3 b,
vector3 c,
vector3 d 
) [static]

static void VectorSubtract ( double *  i,
double *  j,
double *  result 
) [inline, static]

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

Referenced by OBForceField::VectorAngle(), OBForceField::VectorAngleDerivative(), OBForceField::VectorBondDerivative(), OBForceField::VectorDistanceDerivative(), OBForceField::VectorOOP(), OBForceField::VectorOOPDerivative(), OBForceField::VectorTorsion(), and OBForceField::VectorTorsionDerivative().

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

static void VectorAdd ( double *  i,
double *  j,
double *  result 
) [inline, static]

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

Referenced by OBForceField::VectorAngleDerivative(), OBForceField::VectorOOPDerivative(), and OBForceField::VectorTorsionDerivative().

static void VectorDivide ( double *  i,
double  n,
double *  result 
) [inline, static]

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]

Referenced by OBForceField::VectorAngle(), OBForceField::VectorAngleDerivative(), OBForceField::VectorBondDerivative(), OBForceField::VectorOOP(), OBForceField::VectorOOPDerivative(), OBForceField::VectorTorsion(), and OBForceField::VectorTorsionDerivative().

static void VectorMultiply ( double *  i,
double  n,
double *  result 
) [inline, static]

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]

Referenced by OBForceField::VectorBondDerivative(), OBForceField::VectorDistanceDerivative(), OBForceField::VectorOOPDerivative(), and OBForceField::VectorTorsionDerivative().

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

static void VectorSelfMultiply ( double *  i,
double  n 
) [inline, static]

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

Referenced by OBForceField::VectorAngleDerivative(), OBForceField::VectorDistanceDerivative(), and OBForceField::VectorOOPDerivative().

static void VectorNormalize ( double *  i  )  [inline, static]

inline fuction to speed up minimization speed

Parameters:
i pointer to i[3] to be normalized

Referenced by OBForceField::VectorAngleDerivative().

static void VectorCopy ( double *  from,
double *  to 
) [inline, static]

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

static double VectorLength ( double *  i  )  [inline, static]

static double VectorDistance ( double *  pos_i,
double *  pos_j 
) [inline, static]

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)

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)

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)

static void VectorClear ( double *  i  )  [inline, static]

inline fuction to speed up minimization speed

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

Referenced by OBForceField::VectorAngleDerivative(), OBForceField::VectorOOPDerivative(), and OBForceField::VectorTorsionDerivative().

static double VectorDot ( double *  i,
double *  j 
) [inline, static]

inline fuction to speed up minimization speed

Parameters:
i pointer to i[3]
j pointer to j[3]
Returns:
the dot product

Referenced by OBForceField::VectorAngle(), OBForceField::VectorAngleDerivative(), OBForceField::VectorOOP(), OBForceField::VectorOOPDerivative(), OBForceField::VectorTorsion(), and OBForceField::VectorTorsionDerivative().

static void VectorCross ( double *  i,
double *  j,
double *  result 
) [inline, static]

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])

Referenced by OBForceField::VectorAngle(), OBForceField::VectorAngleDerivative(), OBForceField::VectorOOP(), OBForceField::VectorOOPDerivative(), OBForceField::VectorTorsion(), and OBForceField::VectorTorsionDerivative().

static void PrintVector ( double *  i  )  [inline, static]

virtual const char* Description (  )  [inline, virtual, inherited]

Required description of a sub-type.

Reimplemented in OBFormat, OBGroupContrib, and OpTransform.

Referenced by OBPlugin::Display(), and OBOp::OpOptions().

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

Write information on a plugin class to the string txt. Return false if not written. The default implementation outputs: the ID, a tab character, and the first line of the Description. The param string can be used in derived types to provide different outputs.

Reimplemented in OBDescriptor, and OBFormat.

Referenced by OBDescriptor::Display().

virtual OBPlugin* MakeInstance ( const std::vector< std::string > &   )  [inline, virtual, inherited]

Make a new instance of the class. See OpTransform, OBGroupContrib, SmartsDescriptor classes for derived versions. Usually, the first parameter is the classname, the next three are parameters(ID, filename, description) for a constructor, and the rest data.

Reimplemented in OBGroupContrib, and OpTransform.

Referenced by OBConversion::LoadFormatFiles().

static OBPlugin* GetPlugin ( const char *  Type,
const char *  ID 
) [inline, static, inherited]

Get a pointer to a plugin from its type and ID. Return NULL if not found. Not cast to Type*.

Referenced by OBConversion::LoadFormatFiles().

const char* GetID (  )  const [inline, inherited]

Return the ID of the sub-type instance.

Referenced by OBPlugin::Display(), OBFormat::Display(), and OBDescriptor::PredictAndSave().

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

Output a list of sub-type classes of the the type PluginID, or, if PluginID is "plugins" or empty, a list of the base types. If PluginID is not recognized or is NULL, the base types are output and the return is false.

Referenced by OBConversion::GetSupportedInputFormat(), OBConversion::GetSupportedOutputFormat(), and OBPlugin::List().

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

As ListAsVector but sent to an ostream with a default of cout if not specified.

Referenced by OBPlugin::ListAsString().

string ListAsString ( const char *  PluginID,
const char *  param = NULL 
) [static, inherited]

As ListAsVector but returns a string containing the list.

string FirstLine ( const char *  txt  )  [static, inherited]

Utility function to return only the first line of a string.

Referenced by OBPlugin::Display(), OBFormat::Display(), and OBOp::OpOptions().

static PluginIterator Begin ( const char *  PluginID  )  [inline, static, inherited]

Return an iterator at the start of the map of the plugin types PluginID or, if there is no such map, the end of the top level plugin map.

Referenced by OBConversion::GetNextFormat(), and OBOp::OpOptions().

static PluginIterator End ( const char *  PluginID  )  [inline, static, inherited]

virtual PluginMapType& GetMap (  )  const [pure virtual, inherited]

Returns the map of the subtypes.

Referenced by OBFormat::RegisterFormat().

static PluginMapType& PluginMap (  )  [inline, static, protected, inherited]

Returns a reference to the map of the plugin types. Is a function rather than a static member variable to avoid initialization problems.

Referenced by OBPlugin::GetTypeMap(), OBPlugin::ListAsVector(), and OBFormat::RegisterFormat().

OBPlugin::PluginMapType & GetTypeMap ( const char *  PluginID  )  [static, protected, inherited]

Returns the map of a particular plugin type, e.g. GetMapType("fingerprints").

static OBPlugin* BaseFindType ( PluginMapType Map,
const char *  ID 
) [inline, static, protected, inherited]

Returns the type with the specified ID, or NULL if not found. Will be cast to the appropriate class in the calling routine.


Member Data Documentation

bool _init [protected]

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

Referenced by OBForceField::Setup().

std::string _parFile [protected]

bool _validSetup [protected]

< parameter file name

was the last call to Setup succesfull

Referenced by OBForceField::SetConstraints(), and OBForceField::Setup().

std::ostream* _logos [protected]

Output for logfile.

Referenced by OBForceField::SetLogFile().

int _nsteps [protected]

double* _grad1 [protected]

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

Referenced by OBForceField::ConjugateGradientsInitialize(), and OBForceField::ConjugateGradientsTakeNSteps().

double _timestep [protected]

Molecular dynamics time step in picoseconds.

Referenced by OBForceField::MolecularDynamicsTakeNSteps().

double _temp [protected]

double _rvdw [protected]

VDW cut-off distance.

Referenced by OBForceField::UpdatePairsSimple().

double _rele [protected]

Electrostatic cut-off distance.

Referenced by OBForceField::UpdatePairsSimple().

OBBitVec _vdwpairs [protected]

VDW pairs that should be calculated.

Referenced by OBForceField::UpdatePairsSimple().

OBBitVec _elepairs [protected]

Electrostatic pairs that should be calculated.

Referenced by OBForceField::UpdatePairsSimple().

int _pairfreq [protected]

The frequence to update non-bonded pairs.

Referenced by OBForceField::ConjugateGradientsTakeNSteps(), and OBForceField::SteepestDescentTakeNSteps().

std::vector<OBBitVec> _intraGroup [protected]

groups for which intra-molecular interactions should be calculated

Referenced by OBForceField::AddIntraGroup(), OBForceField::ClearGroups(), and OBForceField::HasGroups().

std::vector<OBBitVec> _interGroup [protected]

groups for which intra-molecular interactions should be calculated

Referenced by OBForceField::AddInterGroup(), OBForceField::ClearGroups(), and OBForceField::HasGroups().

std::vector<std::pair<OBBitVec, OBBitVec> > _interGroups [protected]

groups for which intra-molecular interactions should be calculated

Referenced by OBForceField::AddInterGroups(), OBForceField::ClearGroups(), and OBForceField::HasGroups().

const char* _id [protected, inherited]


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