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Fix hydrogen bond detection across fragment orderings - #5207
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…eepchem#5194) is_hydrogen_bond indexed frag1 coordinates with the frag2 loop counter, returned after checking only the first candidate hydrogen, and compute_hbonds_in_range passed the angle cutoff positionally so it landed in the unused distance parameter. Donor-in-frag1 contacts were never found and the per-bin angle cutoff was always the default.
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Closes #5194.
Whether
compute_hydrogen_bondsfound a valid bond depended on theorder fragments and hydrogens were passed.
frag1_xyz[i]indexed withthe frag2 loop counter, placing frag1 hydrogens at frag2 coordinates.
The hydrogen-candidate loop broke out after the first candidate
instead of examining all of them.
hbond_angle_cutofflanded in thedistance parameter positionally, so the caller's angle bound never
applied.
Indexing is corrected. Every candidate is visited and the cutoff
passes by keyword. The previously empty
test_compute_hydrogen_bondsnow covers all four orderings plus a bent geometry where a tight
cutoff rejects and a loose one accepts.