OEConfBase

class OEConfBase : public OEMolBase

OEConfBase is the generic conformer base class. It is an abstract base class which defines the interface for conformer implementations. Coordinates can be stored in OEHalfFloat (16-bit), float (32-bit), double (64-bit), or long double (>= 64-bit). The precision is determined by the constructor argument given to OEMol, taken from the OEMCMolType namespace. The default is 32-bit float.

The following methods are publicly inherited from OEMolBase:

operator=	GetDimension	NumBonds
operator bool	GetEnergy	NumGroups
Clear	GetGroup	OrderAtoms
ClearCoords	GetGroups	OrderBonds
Compress	GetMaxAtomIdx	ResetPerceived
Count	GetMaxBondIdx	SetCoords
CreateCopy	GetTitle	SetDimension
DeleteAtom	HasPerceived	SetEnergy
DeleteBond	IsDataType	SetPerceived
DeleteGroup	IsDeleted	SetRxn
GetAtom	IsRxn	SetTitle
GetAtoms	NewAtom	Sweep
GetBond	NewBond	UnCompress
GetBonds	NewGroup
GetCoords	NumAtoms

The following methods are publicly inherited from OEBase:

operator=	GetData	IsDataType
operator+=	GetDataIter	SetBaseData
AddBaseData	GetDataType	SetBoolData
AddData	GetDoubleData	SetData
Clear	GetFloatData	SetDoubleData
CreateCopy	GetIntData	SetFloatData
DeleteData	GetStringData	SetIntData
GetBoolData	HasData	SetStringData

operator=

OEConfBase &operator=(const OEMolBase &rhs)
OEConfBase &operator=(const OEConfBase &rhs)

Conformer assignment either from another conformer or OEMolBase.

AddAtom

void AddAtom(OEAtomBase *atom)=0
void AddAtom(const OEAtomBase *rhs, OEAtomBase *atom)=0

OEConfBase.AddAtom is a helper method that the OEMCMolBase can call as an adjunct to OEMolBase.NewAtom on the molecule which contains the conformers.

Warning

This should not be called by a primary user.

AddBond

void AddBond(OEBondBase *bond)=0

OEConfBase.AddBond is a helper method that the OEMCMolBase can call as an adjunct to OEMolBase.NewBond on the molecule which contains the conformers.

Warning

This should not be called by a primary user.

Delete

void Delete()=0

The OEConfBase.Delete method is equivalent to call OEMCMolBase.DeleteConf from the parent molecule. It removes the current conformer from the OEMCMolBase object containing it. These functions do not invalidate current OEIter objects, and all calls to OEMCMolBase.GetConfs called after the call to OEConfBase.Delete will not contain the deleted conformer.

GetCoordsPtr

unsigned int GetCoordsPtr(const void *&ptr) const = 0;
unsigned int GetCoordsPtr(void *&ptr) = 0;

Use with care, this provides direct access to the coordinates pointer of this conformer. Returns a constant from the OECoordsType namespace specifying the type of data ptr will point to. OECoordsType_Undefined is returned if the underlying implementation does not allow direct memory access. If access is allowed, a pointer to the memory storing the coordinates is returned as ptr. That pointer is considered owned by this class, and may be invalidated by other non-const methods on the OEConfBase or OEMCMolBase.

Warning

Users should avoid using this method directly. Use OEConstCoords or OEMutableCoords instead.

ClearCoords

bool ClearCoords() const =0

Clears the coordinates, clears perception flags and sets the coordinate dimension to 0

See also

• OEConfBase.GetCoords

• OEConfBase.SetCoords

GetCoords

GetCoords() -> {idx : (x_0, y_0, z_0), ... }

Returns a Python dictionary of the coordinates of this molecule. The dictionary is keyed off the index of the OEAtomBase as returned by OEAtomBase.GetIdx. The values will always be a 3-element tuple of floating point values. Note, the dictionary will not contain entries for deleted atoms, making it significantly easier to use than the following OEFloatArray overloads. This also means the keys of the dictionary are not always guaranteed to be contiguous integers.

Note

The overload that returns a dictionary is for convenience over performance as it is significantly more pythonic. However, if the floating point values are not needed in Python and just being passed to another OpenEye toolkit function, using the following overloads with OEFloatArray objects will be significantly faster.

bool GetCoords(OEPlatform::OEHalfFloat *) const =0
bool GetCoords(float *) const =0
bool GetCoords(double *) const =0
bool GetCoords(long double *) const =0

Fills the array passed into the function with a copy of the coordinates of the conformer. The array passed in should be at least of length OEConfBase.GetMaxAtomIdx * 3. The coordinates of each atom in the conformer will begin at coords[atom->GetIdx()*3] in the array. Changes made to the array after this function call will have no effect on the conformer.

bool GetCoords(const OEAtomBase *, OEPlatform::OEHalfFloat *coords) const =0
bool GetCoords(const OEAtomBase *, float *coords) const =0
bool GetCoords(const OEAtomBase *, double *coords) const =0
bool GetCoords(const OEAtomBase *, long double *coords) const =0

Fills the coords array with the coordinates of the OEAtomBase object. The coords array should be at least of length 3. Changes made to the coord array after this function call will have no effect on the conformer.

See also

• OEConfBase.SetCoords

• OEConfBase.ClearCoords

GetIdx

unsigned int GetIdx() const =0

Returns the index of the conformer. This value is assigned by OEChem when a conformer is created. The conformer index is unique for the conformation of a given molecule, and is stable (not reused) for the lifetime of that OEMCMolBase. These values may not be assigned sequentially, and may contain gaps. Conformer indices are guaranteed to be less than OEMCMolBase.GetMaxConfIdx. Conformer indices are typically only used for efficiently storing data in arrays externally to the OEMCMolBase. The arrays can be conveniently indexed via OEConfBase.GetIdx. For iterating across the conformers of a molecule, use OEMCMolBase.GetConfs and for keeping track of a particular conformer use the conformer pointer OEConfBase*.

GetMCMol

const OEMCMolBase &GetMCMol() const =0
      OEMCMolBase &GetMCMol()       =0

Returns the associated multi-conformer molecule that is serving as the container for the OEConfBase.

GetTitle

const char *GetTitle() const =0

OEConfBase objects can have their own title. However, if they do not, they will report the title of their parent OEMCMolBase when the OEConfBase.GetTitle method is called.

See also

• OEConfBase.HasTitle

GetTorsion

double GetTorsion(OETorsion &) const =0
double GetTorsion(const OEAtomBase *a, const OEAtomBase *b, const OEAtomBase *c,
                  const OEAtomBase *d) const =0

Returns the torsion value in the conformer. The torsion can be defined by either an OETorsion object, or by four OEAtomBase objects.

See also

• OEConfBase.SetTorsion

GetTransform

const OETrans &GetTransform() const =0

Returns an OETrans, which is a container of all the transformations which have been applied to the OEConfBase. This function is particularly useful when the internal representation of coordinates may not be Cartesian.

HasTitle

bool HasTitle() const =0

Returns whether this conformer has a title set.

See also

• OEConfBase.GetTitle

IsDeleted

bool IsDeleted() const =0

OEConfBase.IsDeleted is a helper function which assists other classes in maintaining functionality after an OEConfBase has been deleted.

See also

• OEMolBase.IsDeleted methods inherited from the OEMolBase class. That method has the purpose of identifying deleted atoms and bonds.

RemoveAtom

bool RemoveAtom(OEAtomBase *atom)=0

OEConfBase.RemoveAtom is a helper function which the OEMCMolBase can call as an adjunct to OEMolBase.DeleteAtom on the molecule which contains the conformers.

Warning

This should not be called by a primary user.

RemoveBond

bool RemoveBond(OEBondBase *bond)=0

OEConfBase.RemoveBond is a helper function which the OEMCMolBase can call as an adjunct to OEMolBase.DeleteBond on the molecule which contains the conformers.

Warning

This should not be called by a primary user.

SetCoords

bool SetCoords(const OEPlatform::OEHalfFloat *coords)=0
bool SetCoords(const float *coords)=0
bool SetCoords(const double *coords)=0
bool SetCoords(const long double *coords)=0

Sets the coordinates of a conformer. The coords parameter is expected to be an array of size OEConfBase.GetMaxAtomIdx * 3. This array should contain 3 coordinates for each atom, and they should be located in the array passed in at coords[atom->GetIdx() * 3 + i], where i ranges from 0 to 3. An internal copy of the coordinates is stored in the OEConfBase that is independent of the coords array.

bool SetCoords(const OEAtomBase *, const OEPlatform::OEHalfFloat *coords)=0
bool SetCoords(const OEAtomBase *, const float *coords)=0
bool SetCoords(const OEAtomBase *, const double *coords)=0
bool SetCoords(const OEAtomBase *, const long double *coords)=0

Sets to coordinates of a single atom in the OEConfBase. The array passed in should be of length 3 and should contain the new coordinates of the atom. An internal copy of the coordinates is stored in the OEConfBase which is independent of the coords array.

See also

• OEConfBase.GetCoords

• OEConfBase.ClearCoords

SetTorsion

void SetTorsion(OETorsion &)=0
void SetTorsion(OEAtomBase *a, OEAtomBase *b, OEAtomBase *c, OEAtomBase *d,
                double radians)=0

Sets torsion value in the conformer. The torsion can be defined by either an OETorsion object, or by four OEAtomBase objects

See also

• OEConfBase.GetTorsion

Transform

void Transform(const OETrans &)=0
void Transform(const OETransBase *)=0

Applies the geometric transformation specified in the OETransBase object or the series of geometric transformations specified in the OETrans container to the OEConfBase. These functions permanently change the coordinates of the OEConfBase.