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
double (64-bit), or
long double (>= 64-bit). The precision
is determined by the constructor argument given to
OEMol, taken from the
namespace. OEMCMolBase have an interface which
allow access to conformers in a modal
OEMCMolBase.GetActive) or a non-modal manner
The following methods are publicly inherited from OEMolBase:
The following methods are publicly inherited from OEBase:
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.
Clears molecule data like atoms, bonds, and conformers without clearing away the OEBase generic data.
bool DeleteConf(OEConfBase *)=0
Deletes the conformer which is passed in from the OEMCMolBase object.
OEConfBase *GetActive() const =0
Returns the currently active conformer of the OEMCMolBase object.
OEConfBase * GetConf( const OESystem::OEUnaryPredicate<OEChem::OEConfBase > &) const =0
Returns the first conformer in the molecule for which the predicate passed
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
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
unsigned int GetMaxConfIdx() const =0
Returns the maximum conformer index of the OEMCMolBase
OEMolBase.GetMaxBondIdx this method
is useful for creating temporary external data structures which can hold
information that can be referenced via the
const char *GetMCMolTitle() const =0
Return the title for the parent molecule, don’t fall back to a
conformer title like
bool IsDeleted(OEConfBase *) const =0
Returns whether the passed in conformer has already been deleted.
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
OEMCMolBase.NewConf constructs a
conformer with its default constructor.
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,
long double pointer constructs a
new conformer with the coordinates passed in as coords. The
array must be of length
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].
NULL to any of these methods will effectively do
nothing and just return a
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
3. The NewConf methods that copy construct
will copy the dimension from the source.
unsigned int NumConfs() const =0
Returns the number of conformers contained in the OEMCMolBase object.
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
OEMCMolBase.GetConfs, but does
not change the conformer indices.
OEMCMolBase.PopActive method removes the top active
conformer from the active stack and makes the next highest conformer
in the stack active.
bool PushActive(OEConfBase *)=0
OEMCMolBase.PushActive method makes the new conformer
the active one and pushes the previous active conformer down the stack.
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.
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
OEMolBase.Sweep as a no-op).