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Description
RAIChu cannot produce a spaghetti for a the following cluster, which contains two NON_ELONGATION_PYR trans-AT KS domains:
Drawing up to failing spaghetti:
The problem arises from the fact that the second cyclisation happens on top of an already existing cyclisation.
RAIChU cannot currently linearise the resulting type of structure:
(raichu) barbara@Barbaras-MBP raichu % python validation/rerun_cluster.py cluster_863
Traceback (most recent call last):
File "/Users/barbara/Documents/PhD/tools/raichu/validation/rerun_cluster.py", line 10, in <module>
draw_cluster(cluster, out_file)
File "/opt/anaconda3/envs/raichu/lib/python3.9/site-packages/raichu/run_raichu.py", line 126, in draw_cluster
return cluster.draw_cluster(as_string=False, out_file=out_file, colour_by_module=colour_by_module)
File "/opt/anaconda3/envs/raichu/lib/python3.9/site-packages/raichu/cluster/modular_cluster.py", line 218, in draw_cluster
drawings, widths = self.get_spaghettis()
File "/opt/anaconda3/envs/raichu/lib/python3.9/site-packages/raichu/cluster/modular_cluster.py", line 184, in get_spaghettis
drawing = RaichuDrawer(structure, dont_show=True)
File "/opt/anaconda3/envs/raichu/lib/python3.9/site-packages/raichu/drawing/drawer.py", line 53, in __init__
super().__init__(structure, options=None, coords_only=coords_only)
File "/opt/anaconda3/envs/raichu/lib/python3.9/site-packages/pikachu/drawing/drawing.py", line 371, in __init__
self.draw(coords_only=coords_only)
File "/opt/anaconda3/envs/raichu/lib/python3.9/site-packages/raichu/drawing/drawer.py", line 299, in draw
self.linearise()
File "/opt/anaconda3/envs/raichu/lib/python3.9/site-packages/raichu/drawing/drawer.py", line 995, in linearise
self.fix_rings(rings, backbone, backbone_to_placement)
File "/opt/anaconda3/envs/raichu/lib/python3.9/site-packages/raichu/drawing/drawer.py", line 813, in fix_rings
assert first_atom_cycle
AssertionError
Suggested fix is to not allow these type of double cyclisations to happen, as they have not yet been observed in nature. Should we find an example in nature, revisit this issue.
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