OBConformerSearch Class Reference

#include <openbabel/conformersearch.h>

Public Member Functions
	OBConformerSearch ()
	~OBConformerSearch ()
bool	Setup (const OBMol &mol, int numConformers=30, int numChildren=5, int mutability=5, int convergence=25)
void	SetNumConformers (int numConformers)
void	SetNumChildren (int numChildren)
void	SetMutability (int mutability)
void	SetConvergence (int convergence)
void	SetFixedBonds (const OBBitVec &fixedBonds)
void	SetFilter (OBConformerFilter *filter)
void	SetScore (OBConformerScore *score)
void	PrintRotors (bool printrotors)
void	Search ()
const RotorKeys &	GetRotorKeys () const
void	GetConformers (OBMol &mol)
void	SetLogStream (std::ostream *sptr)
void	SetSharing (bool value=true)
int	GetNbNiches ()
void	SetNbNiches (int value)
double	GetNicheRadius ()
void	SetNicheRadius (double value)
double	GetAlphaSharing ()
void	SetAlphaSharing (double value)
double	GetSigmaSharing ()
void	SetSigmaSharing (double value)
double	GetCrossoverProbability ()
void	SetCrossoverProbability (double value)
double	GetNicheMating ()
void	SetNicheMating (double value)
void	SetLocalOptRate (int value)
int	SetLocalOptRate ()

Detailed Description

Conformer searching using genetic algorithm. See Conformer Searching.

Since

2.3

Examples:

obconformersearch_default.cpp.

Constructor & Destructor Documentation

OBConformerSearch()

OBConformerSearch

(

)

~OBConformerSearch()

~OBConformerSearch

(

)

Member Function Documentation

Setup()

bool Setup	(	const OBMol &	mol,
		int	numConformers = 30,
		int	numChildren = 5,
		int	mutability = 5,
		int	convergence = 25
	)

Setup this instance with the specified molecule.

Parameters

mol	The molecule with initial conformer.
numConformers	The number of conformers that should be generated. This is also the number of conformers selected for each generation.
numChildren	When a new generation is generated, for each of the numConformers conformers, numChildren children are created.
mutability	The mutability determines how frequent a permutation occurs when generating the next generation.
convergence	The number of identical generations before considering the process converged.

Examples:

obconformersearch_default.cpp.

SetNumConformers()

void SetNumConformers ( int  numConformers )

inline

Set the number of conformers.

SetNumChildren()

void SetNumChildren ( int  numChildren )

inline

Set the number of children generated for each parent.

SetMutability()

void SetMutability ( int  mutability )

inline

Set the mutability.

SetConvergence()

void SetConvergence ( int  convergence )

inline

Set the convergence (i.e. number of generations that did not change the score before considering the iteration converged).

SetFixedBonds()

void SetFixedBonds ( const OBBitVec &  fixedBonds )

inline

Set the bonds to be fixed.

SetFilter()

void SetFilter ( OBConformerFilter *  filter )

inline

Set the filter method used to check if a newly generated is acceptable. Typical examples are a steric filter or electrostatic energy filter. The filters make a binary selection and one group will be scored in the next step. A number of filters are provided by default but implementing a custom filter is easy.

There is also a OBConformerFilters class to make it easy to use multiple filters.

SetScore()

void SetScore ( OBConformerScore *  score )

inline

All acceptable conformers are scored to select the fittest conformers from the population. A higher score means the conformer is desired in the final set or next generation. Typical scoring would be force field energy to find the lowest energy conformer. Another example is the highest RMSD between conformer i and the closest conformer to create a diverse set of conformers. Diversity could also be expressed in other ways and implementing a scoring class is easy.

PrintRotors()

void PrintRotors ( bool  printrotors )

inline

Set whether or not you want rotors to be printed prior to the conformer search.

Search()

void Search

(

)

Perform conformer search using a genetic algorithm.

Examples:

obconformersearch_default.cpp.

GetRotorKeys()

const RotorKeys& GetRotorKeys ( ) const

inline

Examples:

obconformersearch_default.cpp.

GetConformers()

void GetConformers

(

OBMol &

mol

)

Examples:

obconformersearch_default.cpp.

SetLogStream()

void SetLogStream ( std::ostream *  sptr )

inline

SetSharing()

void SetSharing ( bool  value = true )

inline

GetNbNiches()

int GetNbNiches ( )

inline

SetNbNiches()

void SetNbNiches ( int  value )

inline

GetNicheRadius()

double GetNicheRadius ( )

inline

SetNicheRadius()

void SetNicheRadius ( double  value )

inline

GetAlphaSharing()

double GetAlphaSharing ( )

inline

SetAlphaSharing()

void SetAlphaSharing ( double  value )

inline

GetSigmaSharing()

double GetSigmaSharing ( )

inline

SetSigmaSharing()

void SetSigmaSharing ( double  value )

inline

GetCrossoverProbability()

double GetCrossoverProbability ( )

inline

SetCrossoverProbability()

void SetCrossoverProbability ( double  value )

inline

GetNicheMating()

double GetNicheMating ( )

inline

SetNicheMating()

void SetNicheMating ( double  value )

inline

SetLocalOptRate() [1/2]

void SetLocalOptRate ( int  value )

inline

SetLocalOptRate() [2/2]

int SetLocalOptRate ( )

inline

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

• conformersearch.h
• conformersearch.cpp