%load_ext autoreload
%autoreload 2

import molsysmt as msm

Move away#

molecular_system_1 = msm.convert(msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm'])
molecular_system_2 = msm.convert(msm.systems['valine dipeptide']['valine_dipeptide.h5msm'])

molecular_system_1 = msm.structure.center(molecular_system_1)

molecular_system_2 = msm.structure.move_away(molecular_system_2, reference_molecular_system=molecular_system_1,
                                             direction=[1,0,0], distance='1 nanometer')

msm.view([molecular_system_1, molecular_system_2])

print(msm.structure.get_center(molecular_system_1))
print(msm.structure.get_center(molecular_system_2))

[[[5.0464682937507114e-17 -1.5139404881252134e-17 -2.523234146875356e-18]]] nanometer

[[[1.0000000000000004 -4.3615904538845435e-17 0.0]]] nanometer

molecular_system_2 = msm.structure.move_away(molecular_system_2, reference_molecular_system=molecular_system_1,
                                             distance='1 nanometer')

msm.view([molecular_system_1, molecular_system_2])

print(msm.structure.get_center(molecular_system_1))
print(msm.structure.get_center(molecular_system_2))

[[[5.0464682937507114e-17 -1.5139404881252134e-17 -2.523234146875356e-18]]] nanometer

[[[1.999999999999999 -6.344131569286608e-17 1.2390881971262907e-19]]] nanometer

molsys1 = msm.convert(msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm'])
molsys2 = msm.convert(msm.systems['valine dipeptide']['valine_dipeptide.h5msm'])

msm.structure.center(molsys1, in_place=True)

molsys2 = msm.structure.move_away(molsys2, reference_molecular_system=molsys1,
                                      direction=[1,0,0], distance='1 nanometer')

center1 = msm.structure.get_center(molsys1)
center2 = msm.structure.get_center(molsys2)

center1
Magnitude
[[[5.0464682937507114e-17 -1.5139404881252134e-17 -2.523234146875356e-18]]]
Unitsnanometer
center2
Magnitude
[[[1.0000000000000004 -4.3615904538845435e-17 0.0]]]
Unitsnanometer