LOOS  v2.3.2
loos::DensityTools::BulkedWaterFilter Class Reference

Add bulk water back into the mask/map. More...

#include <internal-water-filter.hpp>

Inheritance diagram for loos::DensityTools::BulkedWaterFilter:
Collaboration diagram for loos::DensityTools::BulkedWaterFilter:

Public Member Functions

 BulkedWaterFilter (WaterFilterBase *p, const double pad, const double zmin, const double zmax)
std::string name (void) const
 Just states the name of the filter/picker.
std::vector< int > filter (const loos::AtomicGroup &, const loos::AtomicGroup &)
 Given a molecule and a set of waters, pick which waters are inside. More...
std::vector< loos::GCoordboundingBox (const loos::AtomicGroup &)
 Calculate the appropriate bounding box (given the molecule)
double volume (void)
 Calculate the volume of the region we can pick waters from...
- Public Member Functions inherited from loos::DensityTools::WaterFilterDecorator
 WaterFilterDecorator (WaterFilterBase *p)

Additional Inherited Members

- Protected Attributes inherited from loos::DensityTools::WaterFilterBase
std::vector< loos::GCoordbdd_

Detailed Description

Add bulk water back into the mask/map.

When using a water filter, particularly with the ZClipped decorator, you will end up with internal waters that don't necessarily connect to bulk (for pore-like proteins). You will also not get bulk water layers if you're simulating a membrane system. To make it obvious that you've got water in there, use the Bulked decorator. This decorator examines waters not picked by the internal filters. If the water lies within the molecule's bounding box (plus pad), and is higher or lower than the given z-bounds, it is accepted as an "internal" water. This will give you a nice plane of bulk water over your protein/membrane.

Definition at line 260 of file internal-water-filter.hpp.

Member Function Documentation

vector< int > loos::DensityTools::BulkedWaterFilter::filter ( const loos::AtomicGroup ,
const loos::AtomicGroup  

Given a molecule and a set of waters, pick which waters are inside.

The result is a map of which waters are inside (1 = inside, 0 = not)

Reimplemented from loos::DensityTools::WaterFilterDecorator.

Definition at line 401 of file internal-water-filter.cpp.

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