LOOS  v2.3.2
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. More...
 
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. More...
 
virtual std::string help () const
 Returns a slice of the example command-line in the help output. More...
 

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.
 
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::WaterFilterBasefilter_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.

Definition at line 55 of file DensityOptions.hpp.

Member Function Documentation

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.

Definition at line 86 of file DensityOptions.hpp.


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