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WIP implementing generic scan functions #498

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Jun 10, 2024
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WIP implementing generic scan functions #498

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4 changes: 4 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -108,3 +108,7 @@ venv.bak/
bin/
build/
lib/

# ignore sela repo
sella-repo/

9 changes: 9 additions & 0 deletions automol/geom/_conv.py
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Expand Up @@ -920,6 +920,15 @@ def set_distance(
assert len(dist_idxs) == 2
idx1, idx2 = dist_idxs
gra = gra if gra is not None else graph_without_stereo(geo)

# For TS graphs, cut the branch of a reacting ring at the appropriate place
# (It would be better to have a more systematic approach to this to handle all rings
# in the graph...)
ts_rng_keys = graph_base.vmat.ts_zmatrix_starting_ring_keys(gra)
if ts_rng_keys is not None:
drop_bkey = (ts_rng_keys[0], ts_rng_keys[-1])
gra = graph_base.remove_bonds(gra, [drop_bkey])

dist_val = dist_val if not angstrom else dist_val * phycon.ANG2BOHR
idxs = graph_base.branch_atom_keys(gra, idx1, idx2)

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