Add bulk water back into the mask/map. More...
|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::GCoord >||boundingBox (const loos::AtomicGroup &)|
|Calculate the appropriate bounding box (given the molecule) |
|Calculate the volume of the region we can pick waters from... |
|Public Member Functions inherited from loos::DensityTools::WaterFilterDecorator|
|WaterFilterDecorator (WaterFilterBase *p)|
|Protected Attributes inherited from loos::DensityTools::WaterFilterBase|
|std::vector< loos::GCoord >||bdd_|
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.