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// SPDX-License-Identifier: LGPL-3.0-or-later
// Author: Kristian Lytje
#pragma once
#include <settings/ExportMacro.h>
namespace ausaxs::settings {
struct EXPORT molecule {
static bool center; // Decides if the structure will be centered at origo.
static bool throw_on_unknown_atom; // Decides whether an exception will be thrown if an unknown atom is encountered.
static bool implicit_hydrogens; // Decides whether implicit hydrogens will be added to the structure.
static bool use_occupancy; // Decides whether the occupancy of the atoms will be ignored.
enum class ExvSet {
Traube, // Traube 1895 as used by CRYSOL, Pepsi-SAXS & FoXS
Voronoi_implicit_H, // Voronoi volume with implicit hydrogens from Schaefer et al.
Voronoi_explicit_H, // Voronoi volume with explicit hydrogens from Schaefer et al.
MinimumFluctutation_implicit_H, // Minimum fluctuation volume with implicit hydrogens from Schaefer et al.
MinimumFluctutation_explicit_H, // Minimum fluctuation volume with explicit hydrogens from Schaefer et al.
vdw, // Volumes calculated from the van der Waals radii
//? Custom displaced volume set. Make sure to define it first with form_factor::storage::detail::set_custom_displaced_volume_set
Custom,
//! Remember to update constants::displaced_volume::standard if this is changed
Default = MinimumFluctutation_implicit_H // Default displaced volume set
};
static ExvSet exv_set;
};
struct EXPORT hydrate {
enum class HydrationStrategy {
// This strategy attempts to place water molecules along each axis of every atom
AxesStrategy,
// This strategy is a generalization of the AxesStrategy, where water molecules are placed along radial lines from each atom
RadialStrategy,
// This is a simple strategy where the entire grid is scanned for empty positions
JanStrategy,
// This is a mimic of the Pepsi hydration method
PepsiStrategy,
// No hydration molecules will be placed with this strategy
NoStrategy
};
static HydrationStrategy hydration_strategy;
enum class CullingStrategy {
// Every N molecule is removed from the list of possible waters to achieve the target number of molecules
CounterStrategy,
// Molecules are removed from the list of possible waters in an attempt to make a more uniform distribution
OutlierStrategy,
// Identical to the CounterStrategy, except the list of possible waters is randomized
RandomCounterStrategy,
// Identical to the BodyCounterStrategy, except the list of possible waters is randomized
RandomOutlierStrategy,
// No molecules will be removed with this strategy
NoStrategy
};
static CullingStrategy culling_strategy;
// Correction added to the sum of van der Waals radii when calculating the distance to the placed water molecules.
// By default this is tuned to roughly match MD density profiles.
static double shell_correction;
};
}
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