PRELIMINARY-IMAGE This is a preliminary API until 2019.Oct and may be improved based on user feedback. It is currently available in C++ and Python.

class OEMolBuilder

This class defines an interface for generating an initial 3D structure of a molecule, by connecting pre-generated fragment coordinates that constitutes the molecule. Building 3D structure of a molecule with this builder is fast when all the fragments constituting a molecule are available in the fraglib associated with the builder. This builder makes no effort to obtain a low energy conformer of the molecule.

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The OEMolBuilder class defines the following public methods:


OEMolBuilder(const OEMolBuilderOptions&)
OEMolBuilder(const OEMolBuilder&)

Default and copy constructors.


OEMolBuilder &operator=(const OEMolBuilder&)

Assignment operator.


void AddFragLib()
void AddFragLib(const std::string &)
void AddFragLib(OEPlatform::oeistream &)

Adds a fragments library to be used for pre-generated fragment coordinates during molecule building. When the OEMolBuilder::AddFragLib is called without a parameter, the built-in fragments library is loaded immediately. By default, the built-in fragments library does not load until OEMolBuilder::Build is called for the first time.

The string and oeistream versions of OEMolBuilder::AddFragLib can be used to add external fragments libraries. These external libraries are used in addition to the built-in one.

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bool Build(OEChem::OEMCMolBase&)
bool Build(OEChem::OEMCMolBase&, const OEConfFixOptions&)

Generates 3D structure for a molecule. Returns true if the process succeeds. The second argument provided with appropriate options can be used to fix part of a molecule structure to predefined coordinates.

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void ClearFragLibs()

Clears all fragment libraries from the builder.

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const OEMolPotential::OEForceField& GetForceField() const

See SetForceField method.


const OEMolBuilderOptions& GetOptions() const

See SetOptions method.


void SetForceField(OEMolPotential::OEForceField&)

Sets the forcefield for building the fragment coordinates, when not available in the fragments library. Default: OEMMFFSheffield with OEMMFFSheffieldFFType::MMFF94Smod_NOESTAT mode.

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void SetOptions(const OEMolBuilderOptions&)

Sets options for building the molecule 3D-structures.

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