OEMCMolBase

class OEMCMolBase : public OEMolBase

The OEMCMolBase class provides the basic multi-conformer molecule in OEChem. It is an abstract base class which defines the interface for multi-conformer molecule 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. OEMCMolBase have an interface which allow access to conformers in a modal (OEMCMolBase.GetActive) or a non-modal manner (OEMCMolBase.GetConfs).

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 OEMolBase only in Java:

GetAtomList

GetBondList

GetGroupList

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=

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

Assignment operator of multi-conformer molecules via this abstract base class.

ClearBase

void ClearBase()=0

Clear the generic data from the OEBase base class of this object. Equivalent to just calling OEBase.Clear without actually clearing away molecule data like atoms, bonds, and conformers.

ClearMCMol

void ClearMCMol()=0

Clears molecule data like atoms, bonds, and conformers without clearing away the OEBase generic data.

ClearMolBase

void ClearMolBase()=0

Equivalent to calling OEMolBase.Clear.

DeleteConf

bool DeleteConf(OEConfBase *)=0

Deletes the conformer which is passed in from the OEMCMolBase object.

DeleteConfs

void DeleteConfs()=0

Warning

OEMCMolBase.DeleteConfs leaves the OEMCMolBase object in an unstable state. It should be used with care and followed shortly with a call to OEMCMolBase.NewConf.

Deletes all of the conformers from the OEMCMolBase object. This is a very useful function for creating a new transformed OEMCMolBase from an untransformed molecule.

See also

Listing 3 code example in the Conformer Creation section

GetActive

OEConfBase *GetActive() const =0

Returns the currently active conformer of the OEMCMolBase object.

Note

The OEMCMolBase.GetActive and OEMCMolBase.SetActive methods are often sufficient for accessing conformations in multi-conformer molecules.

See also

GetConf

OEConfBase * GetConf(
     const OESystem::OEUnaryPredicate<OEChem::OEConfBase > &) const =0

Returns the first conformer in the molecule for which the predicate passed in returns true.

GetConfs

OESystem::OEIterBase<OEConfBase > *GetConfs() const =0
OESystem::OEIterBase<OEConfBase > *GetConfs(
     const OESystem::OEUnaryPredicate<OEChem::OEConfBase > &) const =0

Returns an iterator over the conformers in the multi-conformer molecule. The return value of this function should always be assigned to an OEIter object. The function which takes no arguments returns an iterator over all of the conformers. The function which takes a predicate returns an iterator which only contains conformers for which the predicate returns true.

GetConfList

java.util.List<OEConfBase> GetConfList()

Returns a List of conformers in order of creation. Note that removing a conformer from the list will not remove it from the molecule.

GetMaxConfIdx

unsigned int GetMaxConfIdx() const =0

Returns the maximum conformer index of the OEMCMolBase object. Similar to OEMolBase.GetMaxAtomIdx and OEMolBase.GetMaxBondIdx this method is useful for creating temporary external data structures which can hold information that can be referenced via the OEConfBase.GetIdx method.

GetMCMolTitle

const char *GetMCMolTitle() const =0

Return the title for the parent molecule, don’t fall back to a conformer title like OEConfBase.GetTitle.

IsDeleted

bool IsDeleted(OEConfBase *) const =0

Returns whether the passed in conformer has already been deleted.

See also

NewConf

OEConfBase *NewConf()=0
OEConfBase *NewConf(const OEPlatform::OEHalfFloat *)=0
OEConfBase *NewConf(const float *)=0
OEConfBase *NewConf(const double *)=0
OEConfBase *NewConf(const long double *)=0
OEConfBase *NewConf(const OEMolBase *)=0
OEConfBase *NewConf(const OEConfBase *)=0
OEConfBase *NewConf(const OEConfBase *, const OETrans &)=0
OEConfBase *NewConf(const OEConfBase *,
                             OETYPENAME std::vector<OETorsion> &t)=0

These methods generate a new conformer that is owned by the current OEMCMolBase. Each of the methods will return a pointer to the newly created conformer. The OEMCMolBase.NewConf methods act as virtual constructors of the OEConfBase objects. OEMCMolBase.NewConf constructs a conformer with its default constructor. NewConf(const OEMolBase *) and NewConf(const OEConfBase *) copy construct a new conformer with the coordinates from the object passed into the function. The objects passed in must have the same graph as the current OEMCMolBase. NewConf that takes a OEHalfFloat, float, double, or long double pointer constructs a new conformer with the coordinates passed in as coords. The array must be of length GetMaxAtomIdx() * 3, and the coordinates for each atom in the new conformer should be the dimension values in the array starting at coords[atom->GetIdx() * 3].

Passing a NULL to any of these methods will effectively do nothing and just return a NULL OEConfBase pointer.

Warning

The dimension of the conformer will be set to 0 for the NewConf default constructor. The NewConf methods that create conformers from coordinates will set the dimension of the conformer to 3. The NewConf methods that copy construct will copy the dimension from the source.

NumConfs

unsigned int NumConfs() const =0

Returns the number of conformers contained in the OEMCMolBase object.

OrderConfs

bool OrderConfs(const OETYPENAME std::vector<OEConfBase *> &)=0

Reorders the conformers in the molecule to the order specified in the vector argument. If the vector contains an incomplete list, the remaining conformers will come at the end. This function call changes the order in which the conformers are returned by OEMCMolBase.GetConfs, but does not change the conformer indices.

PopActive

void PopActive()=0

The OEMCMolBase.PopActive method along with the OEMCMolBase.PushActive method allow to maintain a stack of active conformers.

The OEMCMolBase.PopActive method removes the top active conformer from the active stack and makes the next highest conformer in the stack active.

See also

PushActive

bool PushActive(OEConfBase *)=0

The OEMCMolBase.PushActive method along with the OEMCMolBase.PopActive method allow to maintain a stack of active conformers.

The OEMCMolBase.PushActive method makes the new conformer the active one and pushes the previous active conformer down the stack.

See also

SetActive

bool SetActive(OEConfBase *)=0

Makes the conformer passed in become the active conformer. The conformer passed in must already be a member of the OEMCMolBase object.

Note

The OEMCMolBase.GetActive and OEMCMolBase.SetActive methods are often sufficient for accessing conformations in multi-conformer molecules.

See also

SweepConfs

bool SweepConfs()=0

Cleans up unused memory and objects which may be associated with the conformers of the OEMCMolBase. Renumber the conformer indices sequentially. This function invalidates the conformer indices of all conformers in a molecule. Note that this function doesn’t guarantee that all conformer indices are sequential upon completion (some molecule implementations may treat OEMolBase.Sweep as a no-op).