loos::OptionsFramework::BasicWater Class Reference

Options specific to tools that work with water/internal-water. More...

#include <DensityOptions.hpp>

Inheritance diagram for loos::OptionsFramework::BasicWater:

Collaboration diagram for loos::OptionsFramework::BasicWater:

Public Member Functions
void	addGeneric (po::options_description &opts)
	Appends generic options (those that the user can see)
bool	postConditions (po::variables_map &map)
	Post-processing of options returning true if there were no problems, otherwise false.
std::string	print () const
	Returns a string listing the encapsulated options, suitable for logging.
Public Member Functions inherited from loos::OptionsFramework::OptionsPackage
virtual void	addHidden (po::options_description &opts)
	Appends hidden options (these generally match positional)
virtual void	addPositional (po::positional_options_description &opts)
	Appends positional options.
virtual bool	check (po::variables_map &map)
	Validates passed options, returning true if there is a problem or false if not.
virtual std::string	help () const
	Returns a slice of the example command-line in the help output.

Public Attributes
double	zmin
	Parameters sent to various decorators.
double	zmax
double	pad
	Extra padding for water.
double	radius
	Optional parameter used in by the WaterFilter.
uint	contacts
std::string	water_string
	User-specified strings.
std::string	prot_string
std::string	grid_name
std::string	filter_mode
std::string	bulked_spec
	User-specified strings (used internally by the WaterFilter decorators)
std::string	zrange_spec
DensityTools::WaterFilterBase *	filter_func
	Filter for determining internal waters.
DensityTools::DensityGrid< int >	the_grid
	Grid mask for internal waters.

Detailed Description

Options specific to tools that work with water/internal-water.

Allows definition of water, protein, padding, among others. Also includes a "factory" for setting how internal waters are defined (selected).

Mode can be: axis (distance from principal axis), box (a bounding box), and grid (grid-mask).

Decorations include Z-range (clamping to a set-zrange), and "bulked", which adds back in the entire system above and below a z-plane.

Member Function Documentation

addGeneric()

void loos::OptionsFramework::BasicWater::addGeneric ( po::options_description & opts )

inlinevirtual

Appends generic options (those that the user can see)

Reimplemented from loos::OptionsFramework::OptionsPackage.

postConditions()

bool loos::OptionsFramework::BasicWater::postConditions ( po::variables_map & map )

inlinevirtual

Post-processing of options returning true if there were no problems, otherwise false.

postConditions() is called after options parsing and validation is complete. This is a mechanism for a subclass to do additional processing with the options it has been provided. For example, a model option subclass might read in the specified model and copy coordinates from an optionally specified file.

Note that the return value from postConditions() is the opposite of check(). Here, a true is returned if there are no problems.

Reimplemented from loos::OptionsFramework::OptionsPackage.

print()

std::string loos::OptionsFramework::BasicWater::print ( ) const

inlinevirtual

Returns a string listing the encapsulated options, suitable for logging.

Reimplemented from loos::OptionsFramework::OptionsPackage.

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

• Packages/DensityTools/DensityOptions.hpp