#include <openbabel/rotamer.h>

Inheritance diagram for OBRotamerList:

Public Member Functions
	OBRotamerList ()

virtual OBGenericData *	Clone (OBBase *parent) const

	~OBRotamerList ()

void	Setup (OBMol &, OBRotorList &)

void	Setup (OBMol &mol, unsigned char *ref, int nrotors)

unsigned int	NumRotors () const

unsigned int	NumRotamers () const

void	AddRotamer (double *)

void	AddRotamer (int *key)

void	AddRotamer (std::vector< int > key)

void	AddRotamer (unsigned char *key)

void	AddRotamers (unsigned char *arr, int nconf)

void	GetReferenceArray (unsigned char *) const

std::vector< double * >	CreateConformerList (OBMol &mol)

void	ExpandConformerList (OBMol &mol, std::vector< double *> &confs)

bool	SetCurrentCoordinates (OBMol &mol, std::vector< int > arr)

void	SetBaseCoordinateSets (OBMol &mol)

void	SetBaseCoordinateSets (std::vector< double *> bc, unsigned int N)

unsigned int	NumBaseCoordinateSets () const

double *	GetBaseCoordinateSet (unsigned int i) const

unsigned int	NumAtoms () const

void	SetAttribute (const std::string &v)

void	SetOrigin (const DataOrigin s)

virtual const std::string &	GetAttribute () const

unsigned int	GetDataType () const

virtual const std::string &	GetValue () const

virtual DataOrigin	GetOrigin () const

Iterator methods
std::vector< unsigned char * >::iterator	BeginRotamer ()

std::vector< unsigned char * >::iterator	EndRotamer ()

Protected Attributes
std::string	_attr

unsigned int	_type

DataOrigin	_source

Detailed Description

Supports a set of rotamer coordinate sets for some number of potentially rotatable bonds.

A high-level class for rotamer / conformer generation, intended mainly for use with the related class OBRotorList and the OBRotorRules database

Rotamers represent conformational isomers formed simply by rotation of dihedral angles. On the other hand, conformers may include geometric relaxation (i.e., slight modification of bond lengths, bond angles, etc.)

The following shows an example of generating 2 conformers using different rotor states. Similar code could be used for systematic or Monte Carlo conformer sampling when combined with energy evaluation (molecular mechanics or otherwise).

OBRotorList rl; // used to sample all rotatable bonds via the OBRotorRules data
// If you want to "fix" any particular atoms (i.e., freeze them in space)
// then set up an OBBitVec of the fixed atoms and call
// rl.SetFixAtoms(bitvec);
rl.Setup(mol);
// How many rotatable bonds are there?
cerr << " Number of rotors: " << rl.Size() << endl;
// indexed from 1, rotorKey[0] = 0
std::vector<int> rotorKey(rl.Size() + 1, 0);
// each entry represents the configuration of a rotor
// e.g. indexes into OBRotor::GetResolution() -- the different angles
//   to sample for a rotamer search
for (unsigned int i = 0; i < rl.Size() + 1; ++i)
rotorKey[i] = 0; // could be anything from 0 .. OBRotor->GetResolution().size()
// -1 is for no rotation
// The OBRotamerList can generate conformations (i.e., coordinate sets)
OBRotamerList rotamers;
rotamers.SetBaseCoordinateSets(mol);
rotamers.Setup(mol, rl);
rotamers.AddRotamer(rotorKey);
rotorKey[1] = 2; // switch one rotor
rotamers.AddRotamer(rotorKey);
rotamers.ExpandConformerList(mol, mol.GetConformers());
// change the molecule conformation
mol.SetConformer(0); // rotorKey 0, 0, ...
conv.Write(&mol);
mol.SetConformer(1); // rotorKey 0, 2, ...

Constructor & Destructor Documentation

◆ OBRotamerList()

OBRotamerList ( )

inline

◆ ~OBRotamerList()

~OBRotamerList ( )

Member Function Documentation

◆ Clone()

OBGenericData * Clone ( OBBase * parent ) const

virtual

Reimplemented from OBGenericData.

◆ Setup() [1/2]

void Setup	(	OBMol &	mol,
		OBRotorList &	rl
	)

Set up a rotamer list based on an already created OBRotorList.

Referenced by OBRotamerList::Clone(), OBForceField::FastRotorSearch(), OBConformerSearch::GetConformers(), OBForceField::RandomRotorSearchInitialize(), OBConformerSearch::Setup(), OBForceField::SystematicRotorSearchInitialize(), OpenBabel::UpdateConformersFromTree(), and OBForceField::WeightedRotorSearch().

◆ Setup() [2/2]

void Setup	(	OBMol &	mol,
		unsigned char *	ref,
		int	nrotors
	)

Set up a rotamer list based on the supplied reference atoms and the number of rotors

Parameters

mol	The molecule to evaluate
ref	An array of the 4 dihedral atoms for each rotor
nrotors	The number of rotors (i.e., the size of ref / 4)

◆ NumRotors()

unsigned int NumRotors ( ) const

inline

Returns: the number of rotatable bonds considered

◆ NumRotamers()

unsigned int NumRotamers ( ) const

inline

Returns: the number of rotamer (conformation) coordinate sets

◆ AddRotamer() [1/4]

void AddRotamer ( double * c )

Add a rotamer to the list based on the supplied coordinate set as a double*.

Referenced by OBConformerSearch::GetConformers(), OBForceField::RandomRotorSearchInitialize(), OBConformerSearch::Setup(), and OBForceField::SystematicRotorSearchInitialize().

◆ AddRotamer() [2/4]

void AddRotamer ( int * key )

Add a rotamer to the list based on key as a configuration of the individual rotor bonds.

◆ AddRotamer() [3/4]

void AddRotamer ( std::vector< int > key )

Add a rotamer to the list based on key as a configuration of the individual rotor bonds.

◆ AddRotamer() [4/4]

void AddRotamer ( unsigned char * key )

Add a rotamer to the list based on key as a configuration of the individual rotor bonds.

◆ AddRotamers()

void AddRotamers	(	unsigned char *	arr,
		int	nconf
	)

Add nconf rotamers based on as an array of configurations much like AddRotamer()

Referenced by OBRotamerList::Clone().

◆ GetReferenceArray()

void GetReferenceArray ( unsigned char * ref ) const

Returns: A reference array (as used by AddRotamer() as a configuration of the individual rotor bonds

◆ BeginRotamer()

std::vector<unsigned char*>::iterator BeginRotamer ( )

inline

◆ EndRotamer()

std::vector<unsigned char*>::iterator EndRotamer ( )

inline

◆ CreateConformerList()

vector< double * > CreateConformerList ( OBMol & mol )

Create a conformer list using the internal base set of coordinates.

Returns: The set of coordinates by rotating the bonds in each rotamer

◆ ExpandConformerList()

void ExpandConformerList	(	OBMol &	mol,
		std::vector< double *> &	confs
	)

Create a conformer list using the internal base set of coordinates.

Returns: The set of coordinates as a reference in confs

Referenced by OBConformerSearch::GetConformers(), OBForceField::RandomRotorSearchInitialize(), OBConformerSearch::Setup(), and OBForceField::SystematicRotorSearchInitialize().

◆ SetCurrentCoordinates()

bool SetCurrentCoordinates	(	OBMol &	mol,
		std::vector< int >	arr
	)

Change the current coordinate set

Since: version 2.2

Referenced by OBForceField::FastRotorSearch(), OpenBabel::UpdateConformersFromTree(), and OBForceField::WeightedRotorSearch().

◆ SetBaseCoordinateSets() [1/2]

void SetBaseCoordinateSets ( OBMol & mol )

Copies the mol's conformers (the coordinates, NOT the pointers) into the object as base coordinates.

Referenced by OBRotamerList::Clone(), OBForceField::FastRotorSearch(), OBConformerSearch::GetConformers(), OBForceField::RandomRotorSearchInitialize(), OBConformerSearch::Setup(), OBForceField::SystematicRotorSearchInitialize(), OpenBabel::UpdateConformersFromTree(), and OBForceField::WeightedRotorSearch().

◆ SetBaseCoordinateSets() [2/2]

void SetBaseCoordinateSets	(	std::vector< double *>	bc,
		unsigned int	N
	)

Copies the coordinates in bc, NOT the pointers, into this object.

Parameters

bc	The conformer set for the molecule
N	The number of atoms in the molecule

◆ NumBaseCoordinateSets()

unsigned int NumBaseCoordinateSets ( ) const

inline

Returns: The number of "base" coordinate sets (i.e., the number of conformers in the base OBMol)

◆ GetBaseCoordinateSet()

double* GetBaseCoordinateSet ( unsigned int i ) const

inline

Get a pointer to a specific base pointer (i.e., specific conformer)

◆ NumAtoms()

unsigned int NumAtoms ( ) const

inline

Returns: The number of atoms in the base OBMol

◆ SetAttribute()

void SetAttribute ( const std::string & v )

inlineinherited

Set the attribute (key), which can be used to retrieve this data.

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::ComparePairSecond(), OBMol::DoTransformations(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBForceField::GetAtomTypes(), OBMol::GetFormula(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

◆ SetOrigin()

void SetOrigin ( const DataOrigin s )

inlineinherited

Set the origin of this data, which can be used to filter the data.

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::ComparePairSecond(), OBMol::DoTransformations(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

◆ GetAttribute()

virtual const std::string& GetAttribute ( ) const

inlinevirtualinherited

Returns: The attribute (key), which can be used to retrieve this data

Referenced by OpenBabel::extract_thermochemistry(), and OBMoleculeFormat::MakeCombinedMolecule().

◆ GetDataType()

unsigned int GetDataType ( ) const

inlineinherited

Returns: the data type for this object as defined in OBGenericDataType

◆ GetValue()

virtual const std::string& GetValue ( ) const

inlinevirtualinherited

Base class returns a default value (the attribute type) but should never be called.

Reimplemented in OBPairData, and OBCommentData.

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OBDescriptor::FilterCompare(), and OBDescriptor::GetValues().

◆ GetOrigin()

virtual DataOrigin GetOrigin ( ) const

inlinevirtualinherited

Member Data Documentation

◆ _attr

std::string _attr

protectedinherited

attribute tag (e.g., "UnitCell", "Comment" or "Author")

Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().

◆ _type

unsigned int _type

protectedinherited

attribute type – declared for each subclass

Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().

◆ _source

DataOrigin _source

protectedinherited

source of data for accounting

Referenced by OBConformerData::operator=(), OBSymmetryData::operator=(), OBTorsionData::operator=(), and OBAngleData::operator=().

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

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OBRotamerList()

◆ ~OBRotamerList()

Member Function Documentation

◆ Clone()

◆ Setup() [1/2]

◆ Setup() [2/2]

◆ NumRotors()

◆ NumRotamers()

◆ AddRotamer() [1/4]

◆ AddRotamer() [2/4]

◆ AddRotamer() [3/4]

◆ AddRotamer() [4/4]

◆ AddRotamers()

◆ GetReferenceArray()

◆ BeginRotamer()

◆ EndRotamer()

◆ CreateConformerList()

◆ ExpandConformerList()

◆ SetCurrentCoordinates()

◆ SetBaseCoordinateSets() [1/2]

◆ SetBaseCoordinateSets() [2/2]

◆ NumBaseCoordinateSets()

◆ GetBaseCoordinateSet()

◆ NumAtoms()

◆ SetAttribute()

◆ SetOrigin()

◆ GetAttribute()

◆ GetDataType()

◆ GetValue()

◆ GetOrigin()

Member Data Documentation

◆ _attr

◆ _type

◆ _source