AtomsTopologyMixin

class sknano.core.atoms.AtomsTopologyMixin

Bases: object

Mixin Atoms topology class.

Attributes

all_angles	Angles.
all_bonds	Bonds.
all_dihedrals	Dihedrals.
all_impropers	Impropers.
angles	Angles.
angles_in_degrees	bool setting for returning angles in degrees.
bonds	Bonds.
dihedrals	Dihedrals.
impropers	Impropers.
topology_stats	dict of topology statistics.

Methods

get_angle(*triplet[, check_operands, degrees])	Compute bond angles.
get_angles([neighbors_only, unique, ids_only])	Return list of bond angles.
get_bond(*pair[, check_operands, degrees])	Compute bond lengths.
get_bonds([neighbors_only, unique, ids_only])	Return list of bonds.
get_dihedral(*ids[, check_operands, degrees])	Compute dihedral angles.
get_dihedrals([neighbors_only, unique, ids_only])	Return list of Dihedrals
get_improper(*ids[, check_operands, degrees])	Compute improper angles.
get_impropers([neighbors_only, unique, ids_only])	Return list of Improperss
update_attrs([topology])	Update AtomsTopologyMixin class attributes.

Attributes Summary

all_angles	Angles.
all_bonds	Bonds.
all_dihedrals	Dihedrals.
all_impropers	Impropers.
angles	Angles.
angles_in_degrees	bool setting for returning angles in degrees.
bonds	Bonds.
dihedrals	Dihedrals.
impropers	Impropers.
topology_stats	dict of topology statistics.

Methods Summary

get_angle(*triplet[, check_operands, degrees])	Compute bond angles.
get_angles([neighbors_only, unique, ids_only])	Return list of bond angles.
get_bond(*pair[, check_operands, degrees])	Compute bond lengths.
get_bonds([neighbors_only, unique, ids_only])	Return list of bonds.
get_dihedral(*ids[, check_operands, degrees])	Compute dihedral angles.
get_dihedrals([neighbors_only, unique, ids_only])	Return list of Dihedrals
get_improper(*ids[, check_operands, degrees])	Compute improper angles.
get_impropers([neighbors_only, unique, ids_only])	Return list of Improperss
update_attrs([topology])	Update AtomsTopologyMixin class attributes.

Attributes Documentation

all_angles

Angles.

all_bonds

Bonds.

all_dihedrals

Dihedrals.

all_impropers

Impropers.

angles

Angles.

angles_in_degrees

bool setting for returning angles in degrees.

bonds

Bonds.

dihedrals

Dihedrals.

impropers

Impropers.

topology_stats

dict of topology statistics.

Methods Documentation

get_angle(*triplet, check_operands=True, degrees=False)

Compute bond angles.

Parameters:

• triplet (list of ints.) – list of ids
• check_operands (bool, optional) –
• degrees (bool, optional) –

Returns:

Return type:

float

Raises:

• TypeError – if triplet is not a list of ids
• ValueError – if len(triplet) != 3.

get_angles(neighbors_only=False, unique=False, ids_only=False)

Return list of bond angles.

get_bond(*pair, check_operands=True, degrees=False)

Compute bond lengths.

Parameters:

• pair (list of ints.) – list of ids
• check_operands (bool, optional) –
• degrees (bool, optional) –

Returns:

Return type:

float

Raises:

• TypeError – if pair is not a list of ids
• ValueError – if len(pair) != 2.

get_bonds(neighbors_only=False, unique=False, ids_only=False)

Return list of bonds.

get_dihedral(*ids, check_operands=True, degrees=False)

Compute dihedral angles.

get_dihedrals(neighbors_only=False, unique=False, ids_only=False)

Return list of Dihedrals

get_improper(*ids, check_operands=True, degrees=False)

Compute improper angles.

get_impropers(neighbors_only=False, unique=False, ids_only=False)

Return list of Improperss

update_attrs(topology=True, **kwargs)

Update AtomsTopologyMixin class attributes.