SBStructuralModelGrid#

This class is a base class to perform neighbor search between atoms. Internally, the neighbor search algorithm uses a grid to efficiently determine neighbors.

You can get a neighbor indxer for an atom:

# get a neighbor list for a atom with an index 0
neighborIndexer = grid.getNeighborIndexer(0)

# get a neighbor list for an atom
neighborIndexer = grid.getNeighborIndexer(atom)

To update the neighbor list execute:

grid.update()

See also

SAMSON SDK: SBMStructuralModelGrid

class samson.SBStructuralModelGrid(self: samson.SBStructuralModelGrid, arg0: samson.SBNodeIndexer, arg1: samson.SBQuantity.unitsSI)#

Bases: SBReferenceTarget

This class describes a grid-based neighbor search algorithm that can be applied to atoms.

areNeighbors(*args, **kwargs)#

Overloaded function.

  1. areNeighbors(self: samson.SBStructuralModelGrid, i: int, j: int) -> bool

Returns whether particles with indices i and j are neighbors

  1. areNeighbors(self: samson.SBStructuralModelGrid, atomI: SBMStructuralModelNodeAtom, atomJ: SBMStructuralModelNodeAtom) -> bool

Returns whether atoms atomI and atomJ are neighbors

getNeighborVector(*args, **kwargs)#

Overloaded function.

  1. getNeighborVector(self: samson.SBStructuralModelGrid, i: int) -> std::vector<SBMStructuralModelNodeAtom * __ptr64,std::allocator<SBMStructuralModelNodeAtom * __ptr64> >

Returns the neighbor indexer of atom i

  1. getNeighborVector(self: samson.SBStructuralModelGrid, atom: SBMStructuralModelNodeAtom) -> std::vector<SBMStructuralModelNodeAtom * __ptr64,std::allocator<SBMStructuralModelNodeAtom * __ptr64> >

Returns the neighbor indexer of atom atom

getNeighbors(*args, **kwargs)#

Overloaded function.

  1. getNeighbors(self: samson.SBStructuralModelGrid, position: samson.SBPhysicalVector3, radius: samson.SBQuantity.unitsSI) -> std::vector<SBMStructuralModelNodeAtom * __ptr64,std::allocator<SBMStructuralModelNodeAtom * __ptr64> >

Returns vector of all atoms that are at a distance smaller than or equal to radius from the specified position

  1. getNeighbors(self: samson.SBStructuralModelGrid, box: samson.SBPhysicalIAVector3) -> std::vector<SBMStructuralModelNodeAtom * __ptr64,std::allocator<SBMStructuralModelNodeAtom * __ptr64> >

Returns vector of all atoms inside the box

update(self: samson.SBStructuralModelGrid) → None#

Updates the grid and neighbor lists