OEMolBuilder¶

Attention

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.

See also

OEMolBuilderOptions class
OEConfFixOptions class

The OEMolBuilder class defines the following public methods:

AddFragLib
Build
ClearFragLibs
GetForceField and SetForceField
GetOptions and SetOptions

Constructors¶

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

Default and copy constructors.

operator=¶

OEMolBuilder &operator=(const OEMolBuilder&)

Assignment operator.

AddFragLib¶

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.

See also

OEMolBuilder::ClearFragLibs method

Build¶

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.

See also

OEConfFixOptions class

ClearFragLibs¶

void ClearFragLibs()

Clears all fragment libraries from the builder.

See also

OEMolBuilder::AddFragLib method

GetForceField¶

const OEMolPotential::OEForceField& GetForceField() const

See SetForceField method.

GetOptions¶

const OEMolBuilderOptions& GetOptions() const

See SetOptions method.

SetForceField¶

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.

See also

OEForceField class
OEMMFFSheffield class

SetOptions¶

void SetOptions(const OEMolBuilderOptions&)

Sets options for building the molecule 3D-structures.

See also

OEMolBuilderOptions class