Open Babel: OBForceField Class Reference

Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Static Protected Member Functions | Protected Attributes | Static Protected Attributes

# OBForceField Class Reference

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

`#include <openbabel/forcefield.h>`

Inheritance diagram for OBForceField:

List of all members.

## 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 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 | SetUpdateFrequency (int f)
int | GetUpdateFrequency ()
void | UpdatePairsSimple ()
unsigned int | GetNumPairs ()
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)
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 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)
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 vector3 | GetGradient (OBAtom *a, int=OBFF_ENERGY)
double * | GetGradientPtr ()
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 | _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
## 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->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);

Examples:

  obforcefield_energy.cpp.

## Member Typedef Documentation

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

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

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

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]`

Get the pointer to the gradients

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, virtual]`

Returns:
  Plugin type ("forcefields")

Reimplemented from OBPlugin.

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.

Examples:
  obforcefield_energy.cpp.

virtual bool HasAnalyticalGradients | ( | ) | `[inline, virtual]`

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().

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()).

virtual bool SetTypes | ( | ) | `[inline, virtual]`

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

virtual bool SetPartialCharges | ( | ) | `[inline, virtual]`

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

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).

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.

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.

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.

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 | gradients = `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 individual energy terms
  OBFF_LOGLVL_HIGH: energy for individual energy interactions

Examples:
  obforcefield_energy.cpp.

Referenced by OBEnergyConformerScore::Score().

virtual double E_Bond | ( | bool | gradients = `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()

virtual double E_Angle | ( | bool | gradients = `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()

virtual double E_StrBnd | ( | bool | gradients = `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()

virtual double E_Torsion | ( | bool | gradients = `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()

virtual double E_OOP | ( | bool | gradients = `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()

virtual double E_VDW | ( | bool | gradients = `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()

virtual double E_Electrostatic | ( | bool | gradients = `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()

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 | ( | std::string | msg ) | `[inline]`

Print msg to the logfile.

Parameters:

  msg | The message to print.

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.

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.

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

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.

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.

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

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.

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

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

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

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

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

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

void GenerateVelocities | ( | ) |

Generate starting velocities with a Maxwellian distribution.

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

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

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
| ) |  |

(debugging)

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]`

Deprecated:

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

double VectorAngleDerivative | ( | vector3 & | a,
|  | vector3 & | b,
|  | vector3 & | c
| ) |  | `[static]`

Deprecated:

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]`

Deprecated:

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

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

Deprecated:

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

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

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]

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]

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

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

inline fuction to speed up minimization speed

Parameters:

  i | pointer to i[3] to be normalized

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]`

inline fuction to speed up minimization speed

Parameters:

  i | pointer to i[3]

Returns:
  the vector length

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

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

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])

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

## Member Data Documentation

OBMol _mol`[protected]`

Molecule to be evaluated or minimized.

bool _init`[protected]`

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

std::string _parFile`[protected]`

bool _validSetup`[protected]`

< parameter file name

was the last call to Setup succesfull

double* _gradientPtr`[protected]`

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

std::ostream* _logos`[protected]`

Output for logfile.

char _logbuf[BUFF_SIZE+1]`[protected]`

Temporary buffer for logfile output.

int _loglvl`[protected]`

Log level for output.

int _origLogLevel`[protected]`

int _current_conformer`[protected]`

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

std::vector<double> _energies`[protected]`

used to hold the energies for all conformers

double _econv`[protected]`

double _e_n1`[protected]`

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

int _cstep`[protected]`

int _nsteps`[protected]`

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

double* _grad1`[protected]`

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

unsigned int _ncoords`[protected]`

Number of coordinates for conjugate gradients.

int _linesearch`[protected]`

LineSearch type.

double _timestep`[protected]`

Molecular dynamics time step in picoseconds.

double _temp`[protected]`

Molecular dynamics temperature in Kelvin.

double* _velocityPtr`[protected]`

pointer to the velocities

OBFFConstraints _constraints = OBFFConstraints()`[static, protected]`

Constraints.

int _fixAtom = 0`[static, protected]`

SetFixAtom()/UnsetFixAtom()

int _ignoreAtom = 0`[static, protected]`

SetIgnoreAtom()/UnsetIgnoreAtom()

bool _cutoff`[protected]`

true = cut-off enabled

double _rvdw`[protected]`

VDW cut-off distance.

double _rele`[protected]`

Electrostatic cut-off distance.

OBBitVec _vdwpairs`[protected]`

VDW pairs that should be calculated.

OBBitVec _elepairs`[protected]`

Electrostatic pairs that should be calculated.

int _pairfreq`[protected]`

The frequence to update non-bonded pairs.

std::vector<OBBitVec> _intraGroup`[protected]`

groups for which intra-molecular interactions should be calculated

std::vector<OBBitVec> _interGroup`[protected]`

groups for which intra-molecular interactions should be calculated

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:

- forcefield.h
- forcefield.cpp

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