fix: map reference atoms to their residue for no_intra_molecular - #182
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fix: map reference atoms to their residue for no_intra_molecular#182galjos wants to merge 1 commit into
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The no_intra_molecular branch looked up residue_atom_indices with the atom index of the reference particle, but that list has one entry per residue, not per atom. Whenever a reference atom index was smaller than the number of residues the analysis quietly subtracted the atoms of an unrelated molecule, so a reference particle kept its own bonded partners and the intramolecular peak survived; the wrong pair count also fed the target density, misnormalising g(r). For systems where a reference index exceeded the number of residues, such as a pure water box, the lookup raised IndexError and the run aborted. This is the default path for input files that give both a restart file and a moldescriptor file. Translate the atom index through residue_numbers before indexing the per-residue list. In topologies without residues residue_numbers is the identity, so that case is unchanged.
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #182 +/- ##
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+ Coverage 93.86% 93.94% +0.07%
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Files 177 177
Lines 9215 9228 +13
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+ Hits 8650 8669 +19
+ Misses 565 559 -6
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The intramolecular exclusion indexed the per residue list of atom indices with a per atom index, so it excluded the wrong atoms or raised an index error depending on the system.
The reference atom is now mapped to the residue it belongs to before its atoms are excluded. The added test pins the exclusion against a hand computed expectation rather than against the previous output.
Present in v1.5.0. 949 tests pass in both type checking modes.