Remove overlapping molecules#

import molsysmt as msm
from molsysmt import pyunitwizard as puw
import numpy as np

box = np.zeros((3,3))
box[0,0] = 3.0
box[1,1] = 3.0
box[2,2] = 3.0
box = msm.pyunitwizard.quantity(box, 'nm')

water_box = msm.build.make_water_box(box)

peptide = msm.build.build_peptide('ACEALAALANME')
peptide = msm.structure.center(peptide, center_coordinates=0.5*box.diagonal())

molsys = msm.merge([water_box, peptide])

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_peptides	n_structures
molsysmt.MolSys	2729	903	900	2	900	2	899	1	1

new_molsys = msm.build.remove_overlapping_molecules(molsys, selection='molecule_type=="water"')

msm.get(new_molsys, n_waters=True)

new_molsys = msm.build.remove_overlapping_molecules(molsys, selection='atom_type!="H" and molecule_type=="water"',
                                                    selection_2='atom_type!="H" and molecule_type=="peptide"',
                                                    threshold='3 angstroms')

msm.get(new_molsys, n_waters=True)

contact_map = msm.structure.get_contacts(new_molsys, selection='atom_type!="H" and molecule_type=="water"',
                                         selection_2='atom_type!="H" and molecule_type=="peptide"',
                                         threshold='3 angstroms', pbc=True)

np.any(contact_map)

False