Visualize Topologies

Hexala

from kimmdy.parsing import read_top
from kimmdy.topology.topology import Topology
from pathlib import Path
from kimmdy.tools import write_top_as_dot
ala_top = read_top(Path('../../tests/test_files/test_topology/urea.top'), use_gmx_dir=False)
top = Topology(ala_top)

write_top_as_dot(top, "ala-top.dot")
G 1 C 1 C 2 O 2 O 1 C–2 O 3 N 3 N 1 C–3 N 6 N 6 N 1 C–6 N 4 H 4 H 3 N–4 H 5 H 5 H 3 N–5 H 7 H 7 H 6 N–7 H 8 H 8 H 6 N–8 H
Figure 1: A diagram of the ala topology
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