OESliceEnsembleOptions

Attention

PRELIMINARY-IMAGE This is a preliminary API until 2020.Apr and may be improved based on user feedback. It is currently available in C++ and Python.

class OESliceEnsembleOptions

This class provides an interface to setup options required for reducing a molecule conformer ensemble, by removing duplicates and high energy conformers.

See also

The OESliceEnsembleOptions class defines the following public methods:

Constructors

OESliceEnsembleOptions()
OESliceEnsembleOptions(const OESliceEnsembleOptions &)

Default and copy constructors.

operator=

OESliceEnsembleOptions &operator=(const OESliceEnsembleOptions &)

Assignment operator.

GetEnergyWindow

double GetEnergyWindow() const
double GetEnergyWindow(const unsigned int numRotors) const

See SetEnergyWindow method. The second variation of the method returns the value of energy widnow that is in effect for a given molecule with specified number of rotors.

GetEnergyRange

std::vector<double> GetEnergyRange() const

See SetEnergyRange method.

GetEnergyThreshold

double GetEnergyThreshold() const

See SetEnergyRange method.

GetMaxConfs

unsigned int GetMaxConfs() const
unsigned int GetMaxConfs(const unsigned int numRotors) const

See SetMaxConfs method. The second variation of the method returns the value of maximum conformers that is in effect for a given molecule with specified number of rotors.

GetMaxConfRange

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

See SetMaxConfRange method.

GetMaxTerminalHeavy

unsigned GetMaxTerminalHeavy() const

See SetMaxConfRange method.

GetRangeIncrement

unsigned int GetRangeIncrement() const

See SetRangeIncrement method.

GetRMSThreshold

double GetRMSThreshold() const
double GetRMSThreshold(const unsigned int numRotors) const

See SetRMSThreshold method. The second variation of the method returns the value of RMS threshold that is in effect for a given molecule with specified number of rotors.

GetRMSRange

std::vector<double> GetRMSRange() const

See SetRMSRange method.

GetSliceByEnergy

bool GetSliceByEnergy() const

See SetRMSRange method.

SetEnergyWindow

void SetEnergyWindow(const double)

Sets the maximum allowable energy difference between the lowest and the highest energy conformers, in units of kcal/mol. Default: 10.0 kcal/mol.

SetEnergyRange

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

Sets the energy range that allows to define a varying EnergyWindow energy window in conjunction with the RangeIncrement. Defining the range overrides the singly defined energy widnow value.

SetEnergyThreshold

void SetEnergyThreshold(const double)

Sets the Energy threshold (Difference between energies) below which two conformers are treated as duplicates. This value is only meaningful when SetSliceByEnergy is set to true. Default: 0.01.

SetMaxConfs

void SetMaxConfs(const unsigned int)

Sets the maximum number of conformers to be kept. Default: 200.

SetMaxConfRange

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

Sets the maximum number of conformers range that allows to define a varying number of MaxConfs in conjunction with the RangeIncrement. Defining the range overrides the singly defined max confs value.

SetMaxTerminalHeavy

void SetMaxTerminalHeavy(const unsigned int)

Sets the maximum number of terminal heavy atoms that should be allowed in calculating RMSD between conformers. If the number of terminal heavy atoms in the molecule accedes the specified limit, all terminal heavy atoms are ignored in RMSD calculation. If the number is set to 0, this values is treated as not set. Default: 0.

SetRangeIncrement

void SetRangeIncrement(const unsigned int)

Sets the number of rotatable bonds range to be used when the OEOmegaOptions.SetEnergyRange, OEOmegaOptions.SetRMSRange, and OEOmegaOptions.SetMaxConfRange are defines in terms of ranges. Default: 5.

SetRMSThreshold

void SetRMSThreshold(const double)

Sets the RMS threshold (Root Mean Square Cartesian distance) below which two conformers are treated as duplicates. Default: 0.5.

SetRMSRange

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

Sets the RMS range that allows to define a varying RMSThreshold in conjunction with the RangeIncrement. Defining the range overrides the singly defined RMS threshold value.

SetSliceByEnergy

void SetSliceByEnergy(const bool)

Sets flag if energy of the conformers should be used for slicing of conformers. This flag should be turned on if energies are optimized energies of the conformers. Default: False