Frag

class optking.frag.Frag(Z, geom, masses, intcos=None, frozen=False)[source]

Bases: object

Attributes Summary

Z

frozen

geom

intcos

masses

natom

num_intcos

Methods Summary

Bmat()

add_cartesian_intcos()

add_h_bonds()

Prepend h_bonds because that's where optking 2 places them

add_intcos_from_connectivity([connectivity])

connectivity_from_distances()

fix_bend_axes()

freeze()

from_dict(D)

get_atom_symbol_list()

is_atom()

is_linear()

print_intcos()

q()

q_array()

q_show()

q_show_array()

show_geom()

to_dict()

unfix_bend_axes()

update_dihedral_orientations()

Update orientation of each dihedrals/tors coordinate This saves an indicator if dihedral is slightly less than pi, or slighly more than -pi.

Attributes Documentation

Z
frozen
geom
intcos
masses
natom
num_intcos

Methods Documentation

Bmat()[source]
add_cartesian_intcos()[source]
add_h_bonds()[source]

Prepend h_bonds because that’s where optking 2 places them

add_intcos_from_connectivity(connectivity=None)[source]
connectivity_from_distances()[source]
fix_bend_axes()[source]
freeze()[source]
classmethod from_dict(D)[source]
get_atom_symbol_list()[source]
is_atom()[source]
is_linear()[source]
print_intcos()[source]
q()[source]
q_array()[source]
q_show()[source]
q_show_array()[source]
show_geom()[source]
to_dict()[source]
unfix_bend_axes()[source]
update_dihedral_orientations()[source]

Update orientation of each dihedrals/tors coordinate This saves an indicator if dihedral is slightly less than pi, or slighly more than -pi. Subsequently, computation of values can be greater than pi or less than -pi to enable computation of Delta(q) when q passed through pi.