OEMakeFragLib

Attention

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 OEMakeFragLib

This class defines interface for generating a fragments library. The builder allows to build either a partial or a complete fragments library by controlling the content of the fraglib currently loaded in the builder.

Code Examples

The OEMakeFragLib class defines the following public methods:

Constructors

OEMakeFragLib()
OEMakeFragLib(const OEFragBuilderOptions&)
OEMakeFragLib(const OEMakeFragLib&)

Default and copy constructors. The default constructor instantiates the class with OEFragBuilderOptions with the OEFragBuilderMode::Strict mode.

operator=

OEMakeFragLib &operator=(const OEMakeFragLib&)

Assignment operator.

AddFrag

void AddFrag(const OEChem::OEMCMolBase&)

Adds the specified fragment to the currently loaded fragment library.

See also

AddFragLib

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

Adds a fragment 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 fragment library does not load until either OEMakeFragLib::GetMissingFrags or OEMakeFragLib::GenerateMissingFrags 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

ClearFragLibs

void ClearFragLibs()

Clears all fragment libraries from the builder.

See also

GenerateMissingFrags

void GenerateMissingFrags(OEChem::oemolistream& , OEChem::oemolostream&);
void GenerateMissingFrags(const OEChem::OEMolBase&, OEChem::oemolostream&);

Finds the missing fragments corresponding to the given input file stream or molecule, generates 3D structures of the fragments and adds those to the output file stream.

GetForceField

const OEMolPotential::OEForceField& GetForceField() const

See SetForceField method.

GetMissingFrags

OESystem::OEIterBase<OEChem::OEMCMolBase>* GetMissingFrags(OEChem::oemolistream&)
OESystem::OEIterBase<OEChem::OEMCMolBase>* GetMissingFrags(const OEChem::OEMolBase&);

Finds the missing fragments corresponding to the given input file stream or molecule, and returns a collection of the fragments. This method does not generate 3D structures of the fragments.

SetForceField

void SetForceField(OEMolPotential::OEForceField&)

Sets the forcefield for building the fragment coordinates, when the fragment is not available in the fragments library.

Default: OEMMFFSheffield with OEMMFFSheffieldFFType::MMFF94Smod_NOESTAT mode.

See also