%load_ext autoreload
%autoreload 2
#%matplotlib widget

import molsysmt as msm
import nglview as nv
#import warnings
#warnings.filterwarnings('ignore')

Working with NGLView#

molecular_system = msm.convert([nv.datafiles.GRO, nv.datafiles.XTC], to_form='molsysmt.MolSys')

nv.show_molsysmt(molecular_system)

view = msm.view(molecular_system, standard=True)
view

contact_map = msm.structure.get_contacts(view, selection='molecule_type=="protein" and atom_name=="CA"', threshold='12 angstroms')

CA_labels = msm.get_label(view, selection='molecule_type=="protein" and atom_name=="CA"', string='{group_name}-{group_id}')

print(CA_labels[100])

GLY-101

import plotly.express as px

fig = px.imshow(~contact_map, animation_frame=0, binary_string=True, height=600, origin='lower')

fig.update_layout(
    xaxis = dict(
        tickmode = 'array',
        tickvals = list(range(0,contact_map.shape[1],25)),
        ticktext = CA_labels[::25],
        tickangle = 45
    ),
    yaxis = dict(
        tickmode = 'array',
        tickvals = list(range(0,contact_map.shape[1],25)),
        ticktext = CA_labels[::25],
        tickangle = 45
    )
)

fig.show()

msm.convert(view, to_form='string:aminoacids3')

'AceMetAsnGlyThrGluGlyProAsnPheTyrValProPheSerAsnLysThrGlyValValArgSerProPheGluAlaProGlnTyrTyrLeuAlaGluProTrpGlnPheSerMetLeuAlaAlaTyrMetPheLeuLeuIleMetLeuGlyPheProIleAsnPheLeuThrLeuTyrValThrValGlnHisLysLysLeuArgThrProLeuAsnTyrIleLeuLeuAsnLeuAlaValAlaAspLeuPheMetValPheGlyGlyPheThrThrThrLeuTyrThrSerLeuHisGlyTyrPheValPheGlyProThrGlyCysAsnLeuGluGlyPhePheAlaThrLeuGlyGlyGluIleAlaLeuTrpSerLeuValValLeuAlaIleGluArgTyrValValValCysLysProMetSerAsnPheArgPheGlyGluAsnHisAlaIleMetGlyValAlaPheThrTrpValMetAlaLeuAlaCysAlaAlaProProLeuValGlyTrpSerArgTyrIleProGluGlyMetGlnCysSerCysGlyIleAspTyrTyrThrProHisGluGluThrAsnAsnGluSerPheValIleTyrMetPheValValHisPheIleIleProLeuIleValIlePhePheCysTyrGlyGlnLeuValPheThrValLysGluAlaAlaAlaGlnGlnGlnGluSerAlaThrThrGlnLysAlaGluLysGluValThrArgMetValIleIleMetValIleAlaPheLeuIleCysTrpLeuProTyrAlaGlyValAlaPheTyrIlePheThrHisGlnGlySerAspPheGlyProIlePheMetThrIleProAlaPhePheAlaLrtThrSerAlaValTyrAsnProValIleTyrIleMetMetAsnLysGlnPheArgAsnCysMetValThrThrLeuYplYplGlyLysAsnProLeuGlyAspAspGluAlaSerThrThrValSerLysThrGluThrSerGlnValAlaProAla'

molsys_A = msm.build.build_peptide('AceAlaNME')
molsys_B = msm.structure.translate(molsys_A, translation='[0.5, 0.0, 0.0] nm')

view1 = msm.convert(molsys_A, to_form='nglview.NGLWidget')
view2 = msm.view(molsys_B)

view = msm.merge([view1, view2])

msm.info(view)
form n_atoms n_groups n_components n_chains n_molecules n_entities n_peptides n_structures
nglview.NGLWidget 44 6 2 2 2 1 2 1 
msm.structure.get_geometric_center(view, selection='molecule_index==0')
Magnitude
[[[0.44929119636363635 0.485347455 -0.022366771363636358]]]
Unitsnanometer
msm.structure.get_geometric_center(view, selection='molecule_index==1')
Magnitude
[[[0.9492911963636362 0.485347455 -0.022366771363636358]]]
Unitsnanometer
msm.structure.get_distances(view, selection='molecule_index==0', selection_2='molecule_index==1',
                            group_behavior='geometric center', group_behavior_2='geometric center')
Magnitude
[[[0.4999999999999999]]]
Unitsnanometer