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Make scaling factor for van-der-Waals radii for fragment detection adjustable #45

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merged 4 commits into from
Sep 25, 2024
Merged

Make scaling factor for van-der-Waals radii for fragment detection adjustable #45

merged 4 commits into from
Sep 25, 2024

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marcelmbn
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  • ConfigClass entry for the vdW radii scaling parameter (up to now fixed to 4/3). Allows for tighter distance thresholds w.r.t. to fragmentation (safer elimination of single atoms with probably low bond order).
  • adjustable via mindlessgen.toml and from CLI.
  • before, the unused vdW radii were still used in Bohr; they are now converted to Angström via a SotA conversion constant
  • scaling is not done within the vdW radii arrays anymore but as a subsequent step when handling the sum of the covalent radii

Off-topic fixes

  • print out format was broken for sum formula for Molecule.__str__; introduced a new line there to correct it.

@marcelmbn
introduce scaling factor for vdw radii; correct unit conversion
59473dc 
Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
@marcelmbn
update test accordingly
8e7f9d7 
Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
@marcelmbn
correct print error (no new line between atomic numbers and sum formula)
39afc8d 
Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
@marcelmbn marcelmbn added bug Something isn't working algorithm Related to the back-end algorithm for generating the mindless molecules. labels Sep 24, 2024
@marcelmbn marcelmbn self-assigned this Sep 24, 2024
@marcelmbn
update CHANGELOG.md accordingly
029d147 
Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
@marcelmbn marcelmbn linked an issue Sep 24, 2024 that may be closed by this pull request
Distance threshold based on covalent radii for fragment detection #44
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@marcelmbn marcelmbn merged commit 376fe6b into grimme-lab:main Sep 25, 2024
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@marcelmbn marcelmbn deleted the feat/vdw_radii_scaling branch September 26, 2024 21:47
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@jonathan-schoeps jonathan-schoeps jonathan-schoeps approved these changes

@thfroitzheim thfroitzheim Awaiting requested review from thfroitzheim

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@marcelmbn marcelmbn

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Distance threshold based on covalent radii for fragment detection
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@marcelmbn @jonathan-schoeps