molsysmt.structure package#

Submodules#

molsysmt.structure.align_principal_axes module#

molsysmt.structure.align_principal_axes.align_principal_axes(molecular_system, selection='all', principal_axes_of_selection=None, principal_axes_type='inertia', structure_indices='all', weights=None, axes=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], center=False, syntax='MolSysMT', engine='MolSysMT', in_place=False)[source]#

molsysmt.structure.center module#

molsysmt.structure.center.center(molecular_system, selection='all', center_of_selection='all', weights=None, center_coordinates=None, structure_indices='all', syntax='MolSysMT', engine='MolSysMT', in_place=False, skip_digestion=False)[source]#: To be written soon…

molsysmt.structure.flip module#

molsysmt.structure.flip.flip(molecular_system, vector=[0, 0, 1], point='[0,0,0] nm', selection='all', structure_indices='all', syntax='MolSysMT', in_place=False)[source]#: To be written soon…

molsysmt.structure.get_angles module#

molsysmt.structure.get_angles.get_angles(molecular_system, triplets, structure_indices='all', pbc=False, skip_digestion=False)[source]#

molsysmt.structure.get_center module#

molsysmt.structure.get_center.get_center(molecular_system, selection='all', weights=None, structure_indices='all', syntax='MolSysMT', engine='MolSysMT', skip_digestion=False)[source]#

molsysmt.structure.get_contacts module#

molsysmt.structure.get_contacts.get_contacts(molecular_system, selection=None, center_of_atoms=False, weights=None, structure_indices='all', selection_2=None, center_of_atoms_2=False, weights_2=None, structure_indices_2=None, threshold='12 angstroms', pairs=False, pbc=True, syntax='MolSysMT', output_type='numpy.ndarray', output_indices=None, skip_digestion=False)[source]#: To be written soon…

molsysmt.structure.get_dihedral_angles module#

molsysmt.structure.get_dihedral_angles.get_dihedral_angles(molecular_system, selection='all', dihedral_quartets=None, structure_indices='all', syntax='MolSysMT', pbc=False, **kwargs)[source]#: To be written soon…

molsysmt.structure.get_distances module#

molsysmt.structure.get_distances.get_distances(molecular_system, selection='all', structure_indices='all', center_of_atoms=False, weights=None, molecular_system_2=None, selection_2=None, structure_indices_2=None, center_of_atoms_2=False, weights_2=None, pairs=False, pbc=True, output_type='numpy.ndarray', output_indices=None, output_structure_indices=None, engine='MolSysMT', syntax='MolSysMT', skip_digestion=False)[source]#

To be written soon…

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Examples

Notes

molsysmt.structure.get_least_rmsd module#

molsysmt.structure.get_least_rmsd.get_least_rmsd(molecular_system, selection='atom_type!="H"', structure_indices='all', reference_molecular_system=None, reference_selection=None, reference_structure_index=0, syntax='MolSysMT', engine='MolSysMT')[source]#: To be written soon…

molsysmt.structure.get_maximum_distances module#

molsysmt.structure.get_maximum_distances.get_maximum_distances(molecular_system, selection='all', center_of_atoms=False, weights=None, as_entity=True, structure_indices='all', molecular_system_2=None, selection_2=None, center_of_atoms_2=False, weights_2=None, as_entity_2=True, structure_indices_2=None, pairs=False, pbc=False, engine='MolSysMT', syntax='MolSysMT')[source]#: To be written soon…

molsysmt.structure.get_minimum_distances module#

molsysmt.structure.get_minimum_distances.get_minimum_distances(molecular_system, selection='all', center_of_atoms=False, weights=None, as_entity=True, structure_indices='all', molecular_system_2=None, selection_2=None, center_of_atoms_2=False, weights_2=None, as_entity_2=True, structure_indices_2=None, pairs=False, pbc=False, engine='MolSysMT', syntax='MolSysMT', skip_digestion=False)[source]#: To be written soon…

molsysmt.structure.get_neighbors module#

molsysmt.structure.get_neighbors.get_neighbors(molecular_system, selection='all', structure_indices='all', center_of_atoms=False, weights=None, molecular_system_2=None, selection_2=None, structure_indices_2=None, center_of_atoms_2=False, weights_2=None, threshold=None, n_neighbors=None, pairs=False, unique_pairs=False, mutual_only=False, pbc=True, output_type='numpy.ndarray', output_indices=None, output_structure_indices=None, sorted=True, engine='MolSysMT', syntax='MolSysMT', skip_digestion=False)[source]#: To be written soon…

molsysmt.structure.get_principal_axes module#

molsysmt.structure.get_principal_axes.get_principal_axes(molecular_system, selection='all', structure_indices='all', weights=None, principal_axes_type='inertia', syntax='MolSysMT', engine='MolSysMT')[source]#

molsysmt.structure.get_radius_of_gyration module#

molsysmt.structure.get_radius_of_gyration.get_radius_of_gyration(molecular_system, selection='all', structure_indices='all', weights=None, pbc=False, engine='MolSysMT', syntax='MolSysMT')[source]#: To be written soon…

molsysmt.structure.get_rmsd module#

molsysmt.structure.get_rmsd.get_rmsd(molecular_system, selection='atom_type!="H"', structure_indices='all', reference_molecular_system=None, reference_selection=None, reference_structure_index=0, syntax='MolSysMT', engine='MolSysMT')[source]#: To be written soon…

molsysmt.structure.least_rmsd_align module#

molsysmt.structure.least_rmsd_align.least_rmsd_align(molecular_system, selection='atom_name=="CA"', structure_indices='all', reference_molecular_system=None, reference_selection=None, reference_structure_index=0, syntax='MolSysMT', engine_sequence_alignment='Biopython', engine_least_rmsd_fit='MolSysMT', in_place=False, skip_digestion=False)[source]#: To be written soon…

molsysmt.structure.least_rmsd_fit module#

molsysmt.structure.least_rmsd_fit.least_rmsd_fit(molecular_system=None, selection='all', selection_fit='atom_type!="H"', structure_indices='all', reference_molecular_system=None, reference_selection_fit=None, reference_structure_index=0, to_form=None, in_place=False, syntax='MolSysMT', engine='MolSysMT', skip_digestion=False)[source]#: To be written soon…

molsysmt.structure.move_away module#

molsysmt.structure.move_away.move_away(molecular_system, selection='all', center_of_selection='all', weights=None, structure_indices=0, reference_molecular_system=None, reference_center_of_selection='all', reference_weights=None, reference_structure_indices=None, direction=None, distance='3 angstroms', in_place=False, syntax='MolSysMT', skip_digestion=False)[source]#: To be written soon..

molsysmt.structure.principal_component_analysis module#

molsysmt.structure.principal_component_analysis.principal_component_analysis(molecular_system, selection='all', structure_indices='all', weights=None, syntax='MolSysMT', engine='MolSysMT', skip_digestion=False)[source]#

molsysmt.structure.rotate module#

molsysmt.structure.rotate.rotate(molecular_system, rotation=None, rotation_center=None, selection='all', structure_indices='all', syntax='MolSysMT', in_place=False, skip_digestion=False)[source]#: To be written soon…

molsysmt.structure.set_dihedral_angles module#

molsysmt.structure.set_dihedral_angles.set_dihedral_angles(molecular_system, dihedral_quartets=None, angles=None, blocks=None, structure_indices='all', pbc=True, in_place=False, engine='MolSysMT')[source]#: To be written soon…

molsysmt.structure.shift_dihedral_angles module#

molsysmt.structure.shift_dihedral_angles.shift_dihedral_angles(molecular_system, dihedral_quartets=None, shifts=None, blocks=None, structure_indices='all', pbc=True, in_place=False, engine='MolSysMT', skip_digestion=False)[source]#: To be written soon…

molsysmt.structure.show_contacts module#

molsysmt.structure.show_contacts.show_contacts(molecular_system, selection=None, center_of_atoms=False, weights=None, structure_indices='all', selection_2=None, center_of_atoms_2=False, weights_2=None, structure_indices_2=None, threshold='12 angstroms', pbc=False, syntax='MolSysMT', style='plotly', show=True, skip_digestion=False)[source]#

molsysmt.structure.translate module#

molsysmt.structure.translate.translate(molecular_system, translation=None, selection='all', structure_indices='all', syntax='MolSysMT', in_place=False, skip_digestion=False)[source]#: To be written soon…