%load_ext autoreload
%autoreload 2

import molsysmt as msm
import numpy as np
import matplotlib.pyplot as plt

Wrapping to the minimum image

Atoms are wrapped independently by default. Set keep_covalent_bonds=True when bonded blocks must first be reconstructed and then translated as complete units.

molecular_system = msm.convert('1VII', to_form='molsysmt.MolSys')
molecular_system = msm.remove(molecular_system, selection='atom_type=="H"')
molecular_system = msm.build.add_missing_terminal_cappings(molecular_system,
                                                           N_terminal='ACE', C_terminal='NME')
molecular_system = msm.build.add_missing_hydrogens(molecular_system, pH=7.4)

molecular_system = msm.build.solvate(molecular_system, box_shape='truncated octahedral',
                         clearance='14.0 angstroms', engine='PDBFixer')

msm.get(molecular_system, element='system', box_shape=True)

'truncated octahedral'

molecular_system = msm.pbc.wrap_to_mic(molecular_system, center_of_selection='molecule_type=="peptide"', keep_covalent_bonds=True)

msm.view(molecular_system, standard=True, with_water_as='surface')