molsysmt.lib package

Subpackages

• molsysmt.lib.pbc package
  • Submodules
  • molsysmt.lib.pbc.box_is_orthogonal module
    • box_is_orthogonal()
    • box_is_orthogonal_single_structure()
  • molsysmt.lib.pbc.get_angles_from_box module
    • get_angles_from_box()
    • get_angles_from_box_single_structure()
  • molsysmt.lib.pbc.get_box_from_lengths_and_angles module
    • get_box_from_lengths_and_angles()
    • get_box_from_lengths_and_angles_single_structure()
  • molsysmt.lib.pbc.get_lengths_and_angles_from_box module
    • get_lengths_and_angles_from_box()
    • get_lengths_and_angles_from_box_single_structure()
  • molsysmt.lib.pbc.get_lengths_from_box module
    • get_lengths_from_box()
    • get_lengths_from_box_single_structure()
  • molsysmt.lib.pbc.unwrap module
    • unwrap()
  • molsysmt.lib.pbc.wrap_to_mic module
    • wrap_to_mic()
    • wrap_to_mic_vector_single_structure()
  • molsysmt.lib.pbc.wrap_to_pbc module
    • wrap_to_pbc()
    • wrap_to_pbc_center()
    • wrap_to_pbc_center_vector_single_structure()
    • wrap_to_pbc_vector_single_structure()
  • Module contents
• molsysmt.lib.structure package
  • Submodules
  • molsysmt.lib.structure.flip module
    • flip()
    • flip_single_structure()
  • molsysmt.lib.structure.get_angles module
    • get_angles()
    • get_angles_single_structure()
  • molsysmt.lib.structure.get_center module
    • get_center()
    • get_center_groups_of_atoms()
    • get_center_groups_of_atoms_single_structure()
    • get_center_single_structure()
  • molsysmt.lib.structure.get_dihedral_angles module
    • get_dihedral_angles()
    • get_dihedral_angles_single_structure()
  • molsysmt.lib.structure.get_distances module
    • get_distance_two_points_single_structure()
    • get_distances()
    • get_distances_pairs()
    • get_distances_pairs_single_structure()
    • get_distances_single_structure()
    • get_distances_single_system()
    • get_distances_single_system_single_structure()
  • molsysmt.lib.structure.get_least_rmsd module
    • get_least_rmsd()
    • get_least_rmsd_single_structure()
    • get_least_rmsd_with_single_reference_structure()
  • molsysmt.lib.structure.get_least_rmsd_rotation_and_translation module
    • get_least_rmsd_rotation_and_translation()
    • get_least_rmsd_rotation_and_translation_single_structure()
    • get_least_rmsd_rotation_and_translation_with_single_reference_structure()
  • molsysmt.lib.structure.get_mic_angles module
    • get_mic_angles()
    • get_mic_angles_single_structure()
  • molsysmt.lib.structure.get_mic_dihedral_angles module
    • get_mic_dihedral_angles()
    • get_mic_dihedral_angles_single_structure()
  • molsysmt.lib.structure.get_mic_distances module
    • get_mic_distance_two_points_single_structure()
    • get_mic_distances()
    • get_mic_distances_pairs()
    • get_mic_distances_pairs_single_structure()
    • get_mic_distances_single_structure()
    • get_mic_distances_single_system()
    • get_mic_distances_single_system_single_structure()
  • molsysmt.lib.structure.get_principal_geometric_axes module
    • get_principal_geometric_axes()
    • get_principal_geometric_axes_single_structure()
  • molsysmt.lib.structure.get_principal_inertia_axes module
    • get_principal_inertia_axes()
    • get_principal_inertia_axes_single_structure()
  • molsysmt.lib.structure.get_rmsd module
    • get_rmsd()
    • get_rmsd_single_structure()
    • get_rmsd_with_single_reference_structure()
  • molsysmt.lib.structure.principal_component_analysis module
    • principal_component_analysis()
  • molsysmt.lib.structure.set_dihedral_angles module
    • set_dihedral_angles()
    • set_dihedral_angles_single_structure()
  • molsysmt.lib.structure.set_mic_dihedral_angles module
    • set_mic_dihedral_angles()
    • set_mic_dihedral_angles_single_structure()
  • molsysmt.lib.structure.shift_dihedral_angles module
    • shift_dihedral_angles()
    • shift_dihedral_angles_single_structure()
  • molsysmt.lib.structure.shift_mic_dihedral_angles module
    • shift_mic_dihedral_angles()
    • shift_mic_dihedral_angles_single_structure()
  • Module contents

Submodules

molsysmt.lib.make_numba_signature module

molsysmt.lib.make_numba_signature.make_numba_signature(arguments=None, output=None)

molsysmt.lib.math module

molsysmt.lib.math.angle(vect0, vect1)

molsysmt.lib.math.cross_product(a, b)

molsysmt.lib.math.dihedral_angle(vect0, vect1, vect2)

molsysmt.lib.math.dot_product(a, b)

molsysmt.lib.math.inverse_matrix_3x3(m)

molsysmt.lib.math.matmul(m, v)

molsysmt.lib.math.norm_vector(a)

molsysmt.lib.math.normalize_vector(a)

molsysmt.lib.math.quaternion_to_rotation_matrix(q)

molsysmt.lib.math.rodrigues_rotation(vector, unit_vector, angle)

molsysmt.lib.math.transpmatmul(m, v)

molsysmt.lib.series module

molsysmt.lib.series.chunks_to_serie(starts, chunk_size)

molsysmt.lib.series.occurrence_order(serie)

molsysmt.lib.series.occurrence_order_sorted_serie(serie)

class molsysmt.lib.series.serialized_lists(item=None, dtype=None)

Bases: object

molsysmt.lib.series.serie_to_chunks(serie)

Module contents