Accumulate Traces

Description

Accumulate traces (accumulated positions) for specific atoms in a sequence of time steps. The accumulator is an uniformly subdivided volume. For each time step (as determined by the start, end, increment and step inputs) the cells containig selected atoms are incremented. Also the positions of the atoms are saved to create the lines of evolution of each atom.

Basically the module can work with two modalities:

  1. Immediate: at each step both the accumulator size and counts are updated.
  2. Deferred: first the positions of the atoms are saved in a run, then in another run the accumulator is updated.

Input Ports

molecule MolecularDataType Molecular data.
start int Loop start value of the sequence of positions.
end int Loop end value of the sequence of positions.
increment int Loop increment value for the sequence.
step int Loop current step value.

Parameters

Select atoms to trace multi select list The list of atoms contained in the molecule.
Deselect All button Deselect all the entries in the Select atoms to trace list.
Select All button Select all the entries in the Select atoms to trace list.
Selection type radio buttons Select the kind of operation:
pass all selected
Pass to output only the atoms selected in the list
remove all selected
Remove from the molecule only the atoms selected in the list
pass all similar
Pass to output the atoms with names that starts like to the ones selected in the list
remove all similar
Remove from the molecule the atoms with names that starts like to the ones selected in the list
Select operation radio buttons The operation to be performed. It can be:
inactive
do nothing.
immediate
for each step update the accumulator.
accumulate
for each step accumulate only the atoms positions. This is useful when the accumulator limits are not know.
playback
use the accumulate positions to update the accumulator.
Clear button Empties the accumulator.
Accumulator side numeric field The number of cells on each side of the accumulator.
use manual limits toggle For the accumulator volume use the limits entered below. If not set the volume limits are computed by the module and show in the fields below.
X, Y, Z min numeric fields Lower coordinates values for the volume.
X, Y, Z max numeric fields Upper coordinates values for the volume.

Output Ports

out_occupancy Field_Unif The accumulator. Each node contains a count of the accumulated presences of the traced atoms in the corresponding accumulator cell.
out_trace Mesh For each traced atom this field contains a polyline passing through all its visited positions .
obj_trace DefaultObject The renderable version of out_trace.

See also