atom_mask Class Reference

Radial shell flat solvent mask and structure factors. More...

#include <mmtbx/masks/atom_mask.h>

List of all members.

Public Member Functions
	atom_mask (const cctbx::uctbx::unit_cell &unit_cell, const cctbx::sgtbx::space_group &group_, const grid_t::index_type &gridding_n_real, double solvent_radius_, double shrink_truncation_radius_)
	Allocates memory for mask calculation.
	atom_mask (const cctbx::uctbx::unit_cell &unit_cell, const cctbx::sgtbx::space_group &group_, double resolution, double grid_step_factor=4.0, double solvent_radius_=1.11, double shrink_truncation_radius_=0.9)
	Allocates memory for mask calculation.
void	compute (const coord_array_t &sites_frac, const double_array_t &atom_radii, const shells_array_t &shells=shells_array_t())
	Clears current, and calculates new mask based on atomic data.
const mask_array_t &	get_mask () const
scitbx::af::shared < std::complex< double > >	structure_factors (const scitbx::af::const_ref< cctbx::miller::index<> > &indices, unsigned char layer=0)
	Computes mask structure factors.
scitbx::int3	grid_size () const
	Returns x,y,z dimensions of the full cell grid.
size_t	grid_size_1d () const
size_t	n_asu_atoms () const
	Returns estimated number of atoms intersecting with the asu.
unsigned char	n_solvent_layers ()
	Returns number of solvent layers for which mask has been computed.
void	xplor_write_map (std::string const &file_name, unsigned char layer=0, bool invert=false)
	Saves asymmetric part of the mask in xplor format.
Public Attributes
const double	solvent_radius
const double	shrink_truncation_radius
double	accessible_surface_fraction
	Solvent volume, if atom radius = vdw_radius + solvent_radius.
double	contact_surface_fraction
	Solvent volume.
long	debug_mask_asu_time
long	debug_atoms_to_asu_time
long	debug_accessible_time
long	debug_contact_time
long	debug_fft_time
bool	debug_has_enclosed_box

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Detailed Description

Radial shell flat solvent mask and structure factors.

This mask will have valid values only inside asymmetric unit. Outside they will be zero. Inside the asu 0 - means macromolecule, non-zero - solvent.

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Constructor & Destructor Documentation

atom_mask	(	const cctbx::uctbx::unit_cell &	unit_cell,
		const cctbx::sgtbx::space_group &	group_,
		const grid_t::index_type &	gridding_n_real,
		double	solvent_radius_,
		double	shrink_truncation_radius_
	)			[inline]

Allocates memory for mask calculation.

gridding_n_real must be compatible with the space_group. At least the following must be true: every grid point has to be transformed into grid point by every symmetry operator of the group.

References MMTBX_ASSERT, and space_group::order_z().

atom_mask	(	const cctbx::uctbx::unit_cell &	unit_cell,
		const cctbx::sgtbx::space_group &	group_,
		double	resolution,
		double	grid_step_factor = 4.0,
		double	solvent_radius_ = 1.11,
		double	shrink_truncation_radius_ = 0.9
	)			[inline]

Allocates memory for mask calculation.

This constructor will calculate grid size appropriate for the spacegroup based on resolution and grid_step_factor.

References MMTBX_ASSERT, and space_group::order_z().

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Member Function Documentation

void compute	(	const coord_array_t &	sites_frac,
		const double_array_t &	atom_radii,
		const shells_array_t &	shells = shells_array_t()
	)

Clears current, and calculates new mask based on atomic data.

Number of masks produced is equal to shells.size() + 1.

Parameters:

	sites_frac	array of atoms coordinates
	atom_radii	array of atoms radii
	shells	array of widths of radial masks

scitbx::af::shared< std::complex<double> > structure_factors	(	const scitbx::af::const_ref< cctbx::miller::index<> > &	indices,
		unsigned char	layer = 0
	)

Computes mask structure factors.

Parameters:

	indices	array of miller indices
	layer	mask layer for wich structure factors will be caculated. Range: [1,n_solvent_layers()]. 1 - closest to the atoms; n_solvent_layers() - fartherst from the atoms.

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

• mmtbx/masks/atom_mask.h