A configuration object for distance geometry runs with sane defaults. More...

#include <Conformers.h>

Data Fields
Partiality	partiality {Partiality::FourAtom}
	Choose for how many atoms to re-smooth the distance bounds after a distance choice. More...

unsigned	refinementStepLimit {10000}
	Limit the maximum number of refinement steps. More...

double	refinementGradientTarget {1e-5}
	Sets the gradient at which a refinement is considered complete. More...

double	spatialModelLoosening {1.0}
	Sets the loosening of the spatial model. More...

std::vector< std::pair < AtomIndex, Utils::Position > >	fixedPositions
	Set fixed positions for a subset of atoms. More...

Detailed Description

A configuration object for distance geometry runs with sane defaults.

Field Documentation

std::vector< std::pair<AtomIndex, Utils::Position> > Scine::Molassembler::DistanceGeometry::Configuration::fixedPositions

Set fixed positions for a subset of atoms.

By default does not set any fixed positions.

Precondition: Any fixed atom must have zero, one or all binding sites fully fixed. No individual ligand sites may be partially fixed (i.e. the atoms constituting a haptic ligand binding site must be either completely unfixed or fixed and may not be mixed).

Note: Remember Utils::Positions are in bohr length units!

Partiality Scine::Molassembler::DistanceGeometry::Configuration::partiality {Partiality::FourAtom}

Choose for how many atoms to re-smooth the distance bounds after a distance choice.

FourAtom partiality is default because incurring more refinement steps costs less than resmoothing the distance bounds matrix after each successive distance choice.

double Scine::Molassembler::DistanceGeometry::Configuration::refinementGradientTarget {1e-5}

Sets the gradient at which a refinement is considered complete.

The default value is fairly tight, and can be loosened if faster results are desired and looser local shapes are tolerable.

unsigned Scine::Molassembler::DistanceGeometry::Configuration::refinementStepLimit {10000}

Limit the maximum number of refinement steps.

The default value is typically enough for medium-sized systems, but may need to be incremented for large systems.

double Scine::Molassembler::DistanceGeometry::Configuration::spatialModelLoosening {1.0}

Sets the loosening of the spatial model.

If a molecule's distortions are not well encompassed in the spatial model, spatial modeling may claim a molecular graph is impossible to represent in three dimensions. Custom loosening of all bounds (distances, angles and dihedrals) may enable molassembler to generate conformers.

The default value does not add in any loosening. It is suggested to stay below 2.0.

The documentation for this struct was generated from the following file:

Molassembler/Conformers.h

Data Fields

Detailed Description

Field Documentation