- class Collapser(step_size=0.1, distance_threshold=1.5, scale_steps=True)
Performs rigid-body collapse of molecules .
import stk bb1 = stk.BuildingBlock('NCCN', [stk.PrimaryAminoFactory()]) bb2 = stk.BuildingBlock('O=CCC=O', [stk.AldehydeFactory()]) polymer = stk.ConstructedMolecule( topology_graph=stk.polymer.Linear( building_blocks=(bb1, bb2), repeating_unit='AB', num_repeating_units=2, optimizer=stk.Collapser(), ), )
The open-source optimization code
MCHammerspecializes in the collapsing of molecules with long bonds like those constructed by
stk. This code is entirely nonphysical and is, therefore, completely general to any chemistry.
Optimize the structure of a molecule under construction.
- __init__(step_size=0.1, distance_threshold=1.5, scale_steps=True)
Initialize an instance of
float, optional) – The relative size of the step to take during collapse in Angstrom.
float, optional) – Distance between distinct building blocks to use as threshold for halting collapse in Angstrom.
bool, optional) – Whether to scale the step of each distinct building block by its relative distance from the molecules centroid.