OEOmegaOptions

class OEOmegaOptions

Constructors

OEOmegaOptions(const unsigned int sampling = OEOmegaSampling::Sparse)
OEOmegaOptions(const OEOmegaOptions &)

Default and copy constructors.

operator=

OEOmegaOptions &operator=(const OEOmegaOptions &)

ClearFixFile

void ClearFixFile()

Clears out the fragment that has been restrained. This allows the OEOmega object to be used in an unrestrained manner after it had previously been used with a fixed fragment.

GetBuildForceField

unsigned int GetBuildForceField() const

Returns the force field type currently set for building structures from 1D/2D to 3D, as an unsigned int from the OEOmegaForceFieldType namespace.

GetCanonOrder

bool GetCanonOrder() const

Returns the state of the canon order flag. If true, the OEOmega instance will order atoms into canonical order before any other calculations.

GetCommentEnergy

bool GetCommentEnergy() const

Gets the state of the comment energy flag. If true, OEOmega will place conformer energy in kcal/mol into the comments that appear if the output is written to a MOL2 file.

GetDielectric

double GetDielectric() const

Gets the dielectric applied to the Coulomb term of the force field.

GetEnergyRange

std::vector<double> GetEnergyRange() const

Returns a vector of the energies used in conjunction with the range increment for a varying energy window. All energies are in units of kcal/mol.

GetEnergyWindow

double GetEnergyWindow() const

Returns the energy window in kcal/mol.

GetEnumNitrogen

unsigned int GetEnumNitrogen() const

Returns the nitrogen enumeration setting as an unsigned int from the OENitrogenEnumeration namespace.

GetEnumRing

bool GetEnumRing() const

Gets the state of the enum ring flag. If true, Omega will enumerate alternate ring conformations as part of the conformer search.

GetExponent

double GetExponent() const

Gets the exponent applied to the inverse distance calculation of the Coulomb term of the force field.

GetFixDeleteH

bool GetFixDeleteH() const

Gets the state of the fix delete H flag. If true, hydrogens will be stripped from the fix file molecule before it is used to match input structures.

GetFixMaxMatch

unsigned int GetFixMaxMatch() const

Gets the state of the fix max match flag. This value controls the max number of different substructure search matches will be used. Only matters if the fixfile has more than one subsearch match in the input molecules.

GetFixMol

const OEChem::OEMolBase &GetFixMol() const

Gets the molecule used to specify the coordinates for a substructure of the input molecules.

GetFixRMS

double GetFixRMS() const

Gets the RMS superposition criteria.

GetFixSubSearch

const OEChem::OESubSearch &GetFixSubSearch() const

Gets the substructure search for fixed fragments.

GetFixUniqueMatch

bool GetFixUniqueMatch() const

Gets whether only the unique substructure matches of the fixfile/fixmol are used for coordinate replacement.

GetFromCT

bool GetFromCT() const

Gets whether the algorithm should generate an initial set of 3D coordinates using only the connection table of the input molecule.

GetIncludeInput

bool GetIncludeInput() const

Gets whether the input conformer will be included in the output file.

GetMaxConfRange

std::vector<unsigned int> GetMaxConfRange() const

Gets the maximum number of conformers to be output for a structure based on the number of rotatable bonds in the structure.

GetMaxConfs

unsigned int GetMaxConfs() const

Returns the maximum number of conformers to be returned by OEOmega.operator().

GetMaxRotors

int GetMaxRotors() const

Gets the maximum number of rotatable bonds cutoff.

GetMaxSearchTime

double GetMaxSearchTime() const

Gets the time limit (in seconds) for generating conformers for each molecule.

GetRMSRange

std::vector<double> GetRMSRange() const

Gets the RMS cutoff used for duplicate conformer removal based on the number of rotatable bonds in the structure.

GetRMSThreshold

double GetRMSThreshold() const

Gets the minimum Root Mean Square (RMS) Cartesian distance below which two conformers are duplicates.

GetRangeIncrement

unsigned int GetRangeIncrement() const

Get the number of rotatable bonds range used with the OEOmegaOptions.SetMaxConfRange, OEOmegaOptions.SetRMSRange, and OEOmegaOptions.SetEnergyRange.

GetRotorOffset

bool GetRotorOffset() const

Returns true if rotor offset compress is turned on, returns false if it is turned off.

GetSampleHydrogens

bool GetSampleHydrogens() const

Returns true if hydrogen sampling is turned on, returns false if it is turned off.

GetSDEnergy

bool GetSDEnergy() const

Returns true if the energy is set to be written in an SD tag.

GetSearchForceField

unsigned int GetSearchForceField() const

Returns the force field type currently set to calculate strain energies of conformers generated during a torsion search, as an unsigned int from the OEOmegaForceFieldType namespace.

GetStrictAtomTypes

bool GetStrictAtomTypes() const

Returns the setting for strict atomtyping in the forcefield.

GetStrictStereo

bool GetStrictStereo() const

Returns the setting for the strict stereochemistry requirement.

GetTorLib

const OETorLib &GetTorLib() const

Retrieves a constant reference to the OETorLib instance as currently set.

GetTorsionDrive

bool GetTorsionDrive() const

Gets whether to assign torsion from OEOmegaOptions.GetTorLib to input molecules.

GetWarts

bool GetWarts() const

Gets whether to generate unique titles for conformers.

SetBuildForceField

bool SetBuildForceField(const unsigned int)

Sets the force field used for constructing fragments that are assembled to build an initial model of the input structure using an unsigned int from the OEOmegaForceFieldType namespace. Method returns false when the invalid selection is chosen, true otherwise.

SetCanonOrder

void SetCanonOrder(const bool)

Sets the state of the canon order flag. If true, the OEOmega instance will order atoms into canonical order before any other calculations.

SetCommentEnergy

void SetCommentEnergy(const bool)

Sets the state of the comment energy flag. If true, the energy is written in kcal/mol in a comment field of the molecule.

SetDielectric

void SetDielectric(const double)

Sets the dielectric applied to the Coulomb term of the force field.

SetEnergyRange

void SetEnergyRange(const std::vector<double> &)
void SetEnergyRange(const std::string &rangeString)

This sets the energy cutoff in kcal/mol used as an accept or reject criteria for conformers depending on the number of rotatable bonds in the structure. Any conformer that has a calculated strain energy less than the sum of the energy window and the energy of the global minimum conformer will be accepted. Conformers with strain energies above this threshold are rejected. The energy range is given as a comma separated list of values that correspond to the range increment setting. For example, “5.0, 10.0, 15.0, 20.0” used with a range increment of 3 sets the energy window to 5.0 kcal/mol for structures with zero to two rotatable bonds, 10.0 kcal/mol for structures with three to five rotatable bonds, and so on. The energy window for structures with more rotors than the highest energy range value specified will be taken as the highest specified value.

SetEnergyWindow

void SetEnergyWindow(const double)

This sets the energy window in kcal/mol used as an accept or reject criteria for conformers. Any conformer that has a calculated strain energy less than the sum of the energy window and the energy of the global minimum conformer will be accepted. Conformers with strain energies above this threshold are rejected.

SetEnumNitrogen

bool SetEnumNitrogen(const unsigned int)

Sets nitrogen enumeration using an unsigned int from the OENitrogenEnumeration namespace. Method returns false when the invalid selection is chosen, true otherwise.

SetEnumRing

void SetEnumRing(const bool)

Sets the state of the enum ring flag. If true, Omega will enumerate alternate ring conformations as part of the conformer search.

SetExponent

void SetExponent(const double)

Sets the exponent applied to the inverse distance calculation of the Coulomb term of the force field.

SetFixDeleteH

void SetFixDeleteH(const bool)

Sets the state of the fix delete H flag. If true, hydrogens will be stripped from the fix file molecule before it is used to match input structures.

SetFixFile

void SetFixFile(OEChem::oemolistream &,
                unsigned int aopts=OEChem::OEExprOpts::DefaultAtoms,
                unsigned int bopts=OEChem::OEExprOpts::DefaultBonds)

Sets a molecule file for fixed fragments.

SetFixMaxMatch

void SetFixMaxMatch(const unsigned int)

Sets the state of the fix max match flag. This value controls the max number of different substructure search matches will be used. Only matters if the fixfile has more than one subsearch match in the input molecules.

SetFixMol

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

Sets a molecule used to specify the coordinates for a substructure of the input molecules. The substructure will be fixed during conformation search.

SetFixQuery

void SetFixQuery(const OEChem::OESubSearch &)

Sets the substructure search for fixed fragments.

SetFixRMS

void SetFixRMS(const double)

Sets the RMS superposition criteria. It can be loosened to allow suboptimal superpositions to succeed in spite of the poor geometric complementarity.

SetFixSmarts

void SetFixSmarts(const std::string &)

This method sets a string for SMARTS pattern matching to fix a portion of the molecule. 3D coordinates must be available from either the input file with OEOmegaOptions.SetFromCT set to false or from having OEOmegaOptions.SetFixMol set.

SetFixUniqueMatch

void SetFixUniqueMatch(const bool)

Sets whether only the unique substructure matches of the fixfile/fixmol are used for coordinate replacement. A unique substructure match is defined as a match that does not cover the identical set of target atoms as any other substructure match in a set.

SetFromCT

void SetFromCT(const bool)

Sets whether the algorithm should generate an initial set of 3D coordinates using only the connection table of the input molecule.

SetIncludeInput

void SetIncludeInput(const bool)

Sets whether the input conformer will be included in the output file.

SetMaxConfRange

void SetMaxConfRange(const std::string &rangeString)
void SetMaxConfRange(const std::vector<unsigned int> &)

Sets the maximum number of conformers to be output for a structure based on the number of rotatable bonds in the structure.

SetMaxConfs

bool SetMaxConfs(const unsigned int)

This method sets the maximum number of conformers to be returned by OEOmega.operator().

SetMaxRotors

void SetMaxRotors(const unsigned int)

Sets the maximum number of rotatable bonds cutoff. The algorithm will not search for conformers of molecules that have more rotors than the cutoff.

SetMaxSearchTime

void SetMaxSearchTime(const double)

Sets a time limit (in seconds) for generating conformers for each molecule.

SetRMSRange

void SetRMSRange(const std::vector<double> &)
void SetRMSRange(const std::string &rangeString)

Sets the RMS cutoff used for duplicate conformer removal based on the number of rotatable bonds in the structure.

SetRMSThreshold

void SetRMSThreshold(const double)

Sets the minimum RMS Cartesian distance below which two conformers are duplicates

SetRangeIncrement

void SetRangeIncrement(const unsigned int)

Set the number of rotatable bonds range used with the OEOmegaOptions.SetMaxConfRange, OEOmegaOptions.SetRMSRange, and OEOmegaOptions.SetEnergyRange.

SetRotorOffset

void SetRotorOffset(const bool)

Passing in a value of true will turn on rotor offset compress and passing in a value of false will turn it off. The default value is set to false for Omega TK and set to true in the OMEGA application. It is safe to have this compression algorithm turned on when molecules are passed directly to OEWriteMolecule; however, handling the coordinates of molecules after running Omega is not safe in the toolkits so the default is false.

SetRotorPredicate

void
  SetRotorPredicate(const OESystem::OEUnaryPredicate<OEChem::OEBondBase> &pred)

Sets a predicate to decide whether a bond is rotatable.

SetSampleHydrogens

void SetSampleHydrogens(const bool)

Sets whether hydrogens will be sampled. This option will enable sampling of hydrogen locations for -OH, -SH, and amines.

SetSDEnergy

void SetSDEnergy(const bool)

Sets whether the energy in kcal/mol is to be written in an SD tag.

SetSearchForceField

bool SetSearchForceField(const unsigned int)

Sets the force field used to calculate strain energies of conformers generated during a torsion search using an unsigned int from the OEOmegaForceFieldType namespace. Method returns false when the invalid selection is chosen, true otherwise.

SetStrictAtomTypes

void SetStrictAtomTypes(const bool)

Starting in version 2.4.0 the default is for a molecule to fail if any atom does not have a valid MMFF atom type. Calling this method with false will allow the atom typer to look for a different atom type of the same element and replace the failing atom type with a valid one that is “close enough”.

SetStrictStereo

void SetStrictStereo(const bool)

Starting in version 2.4.0, by default OMEGA will fail any molecule with unspecified stereochemistry, with the exception of unspecified invertible nitrogens. Setting this to false will induce the previous behavior of choosing a random set of stereochemistry for the molecule.

SetTorLib

bool SetTorLib(const OETorLib &torlib)

Sets the torsion library by passing in an OETorLib instance.

SetTorsionDrive

void SetTorsionDrive(const bool)

Sets whether to assign torsion from OEOmegaOptions.GetTorLib to input molecules.

SetWarts

void SetWarts(const bool)

Sets whether to generate unique titles for conformers.