<jupyter_start><jupyter_text>Buried factors<jupyter_code>buried_factors_receptor, buried_factors_ligand, labels_receptor, labels_ligand = \
oin.buried_factors(molecular_system, 'component_index==0', 'component_index==1')
view = nv.show_molsysmt(molecular_system)
view.clear()
buried_factors_all = np.hstack([buried_factors_receptor, buried_factors_ligand])
msm.nglview.show_colored_surface_by_scalar_residue_values(view, buried_factors_all[0,:])
view
view = nv.show_molsysmt(molecular_system, selection="component_index==0")
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, buried_factors_receptor[0,:])
view
view = nv.show_molsysmt(molecular_system, selection="component_index==1")
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, buried_factors_ligand[0,:])
view<jupyter_output><empty_output><jupyter_text>Contact map and connectivity Contact map<jupyter_code>contact_map, labels_receptor, labels_ligand = \
oin.contact_map(molecular_system,'component_index==0', 'component_index==1')
plt.imshow(contact_map[0], cmap='Greys', origin='lower')
plt.show()<jupyter_output><empty_output><jupyter_text>Connectivity<jupyter_code>connectivity_receptor, connectivity_ligand, labels_receptor, labels_ligand = \
oin.connectivity(molecular_system, 'component_index==0', 'component_index==1')
plt.scatter(connectivity_ligand[0], buried_factors_ligand[0])
plt.show()
plt.scatter(connectivity_receptor[0], buried_factors_receptor[0])
plt.show()
view = nv.show_molsysmt(molecular_system)
view.clear()
connectivity_all = np.hstack([connectivity_receptor, connectivity_ligand])
msm.nglview.show_colored_surface_by_scalar_residue_values(view, connectivity_all[0,:])
view
view = nv.show_molsysmt(molecular_system, selection="component_index==0")
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, connectivity_receptor[0,:])
view
view = nv.show_molsysmt(molecular_system, selection="component_index==1")
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, connectivity_ligand[0,:])
view<jupyter_output><empty_output><jupyter_text>Nearby Connectivity<jupyter_code>nearby_connectivity_receptor, nearby_connectivity_ligand, labels_receptor, labels_ligand = \
oin.connectivity(molecular_system, 'component_index==0', 'component_index==1')
view = nv.show_molsysmt(molecular_system, selection="component_index==0")
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, nearby_connectivity_receptor[0,:])
view
view = nv.show_molsysmt(molecular_system, selection="component_index==1")
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, nearby_connectivity_ligand[0,:])
view<jupyter_output><empty_output><jupyter_text>Contacting residues<jupyter_code>residues_rec, residues_lig = oin.contacting_residues(molecular_system, 'component_index==0', 'component_index==1')
residues_rec
residues_lig
n_residues_rec = msm.get(molecular_system, selection='component_index==0', n_groups=True)
n_residues_lig = msm.get(molecular_system, selection='component_index==1', n_groups=True)
pinto_contactos = np.zeros(n_residues_rec)
pinto_contactos[residues_rec]=1.0
view = nv.show_molsysmt(molecular_system, selection='component_index==0')
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, pinto_contactos)
view
pinto_contactos = np.zeros(n_residues_lig)
pinto_contactos[residues_lig-367]=1.0
view = nv.show_molsysmt(molecular_system, selection='component_index==1')
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, pinto_contactos)
view<jupyter_output><empty_output><jupyter_text>SASA buried<jupyter_code>oin.sasa_buried(molecular_system, 'component_index==0', 'component_index==1')<jupyter_output><empty_output><jupyter_text>Surface polarity<jupyter_code>polarity = msm.physchem.get_polarity(molecular_system, selection='component_index==0', target='group', polarity_type='grantham')
view = nv.show_molsysmt(molecular_system, selection='component_index==0')
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, np.array(polarity))
view
polarity = msm.physchem.get_polarity(molecular_system, selection='component_index==1', target='group', polarity_type='grantham')
view = nv.show_molsysmt(molecular_system, selection='component_index==1')
view.clear()
msm.nglview.show_colored_surface_by_scalar_residue_values(view, np.array(polarity))
view
msm.physchem.get_radii(molecular_system, selection=[0,0,0,0,1,2,3], target='atom', radius_type='vdw')<jupyter_output><empty_output>
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