pele.angleaxis.aasystem

AASystem.get_takestep()

Source

def get_takestep(self, **kwargs):

return the takestep object for use in basinhopping, etc.

default is random displacement with adaptive step size adaptive temperature

See also

pele.takestep

RBSystem.load_coords_pymol()

Source

def load_coords_pymol(
    self, coordslist, oname, index=1
):

load the coords into pymol

the new object must be named oname so we can manipulate it later

Parameters:

coordslistlist of arrays

onamestr

the new pymol object must be named oname so it can be manipulated later

indexint

we can have more than one molecule on the screen at one time. index tells which one to draw. They are viewed at the same time, so should be visually distinct, e.g. different colors. accepted values are 1 or 2

Notes

the implementation here is a bit hacky. we create a temporary xyz file from coords and load the molecule in pymol from this file.