OEConfFixOptions

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 OEConfFixOptions

This class provides an interface to setup options required for constraining a part of a molecule during conformational search.

See also

The OEConfFixOptions class defines the following public methods:

Constructors

OEConfFixOptions()
OEConfFixOptions(const OEConfFixOptions &)

Default and copy constructors.

operator=

OEConfFixOptions &operator=(const OEConfFixOptions &)

Assignment operator.

ClearFixFile

void ClearFixFile()

See SetFixFile method.

GetFixDeleteH

bool GetFixDeleteH() const

See SetFixDeleteH method.

GetFixMaxMatch

unsigned int GetFixMaxMatch() const

See SetFixMaxMatch method.

GetFixMol

const OEChem::OEMolBase& GetFixMol() const

See SetFixMol method.

GetFixPredicate

const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>* GetFixPredicate() const

See SetFixPredicate method.

GetFixRMS

double GetFixRMS() const

See SetFixRMS method.

GetFixSmarts

const std::string& GetFixSmarts() const

See SetFixSmarts method.

GetFixSubSearch

const OEChem::OESubSearch &GetFixSubSearch() const

Returns the substructure search (:oe:cls`OEChem::OESubSearch`) for fixed fragments.

GetFixUniqueMatch

bool GetFixUniqueMatch() const

See SetFixUniqueMatch method.

HasFixPattern

bool HasFixPattern() const

Method checks if a criterion for fixing a potion of the molecule, during conformation search, is currently set.

SetFixDeleteH

void SetFixDeleteH(const bool)

Sets whether hydrogens should be stripped from the fix file molecule before it is used to match input structures. Default: True.

SetFixFile

void SetFixFile(OEChem::oemolistream&,
     unsigned int atomOpts = OEChem::OEExprOpts::DefaultAtoms,
     unsigned int bondOpts = OEChem::OEExprOpts::DefaultBonds)

Sets the substructure of the input molecules of which coordinates could be fixed during conformation search. Only the first molecule from the input oemolistream is used.

See also

SetFixMaxMatch

void SetFixMaxMatch(const unsigned int)

Sets the maximum number of different substructure search matches used. This limit only used if the SetFixFile method specifies has more than one substructure search match in the input molecules. Default: 1.

SetFixMol

void SetFixMol(const OEChem::OEMolBase&,
     unsigned int atomOpts = OEChem::OEExprOpts::DefaultAtoms,
     unsigned int bondOpts = OEChem::OEExprOpts::DefaultBonds)

Sets the substructure of the input molecules of which coordinates could be fixed during conformation search. Default: None.

See also

SetFixPredicate

void SetFixPredicate(const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>&)

Uses the atom predicate to define which atom should be kept fixed during conformation search. Default: None.

SetFixRMS

void SetFixRMS(const double)

Sets the RMS distance (Root Mean Square (RMS) Cartesian) below which two atom positions are treated as identical. Default: 0.15.

SetFixSmarts

void SetFixSmarts(const std::string&)

Uses the SMARTS pattern to define which potion of the molecule should be kept fixed during conformation search. Default: None.

SetFixSubSearch

void SetFixSubSearch(const OEChem::OESubSearch&)

Uses the substructure search (OESubSearch) to define which potion of the molecule should be kept fixed during conformation search. Default: None.

SetFixUniqueMatch

void SetFixUniqueMatch(const bool)

Sets whether only the unique substructure matches of the SetFixMol to be used for coordinate replacement. Default: True.