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Limit to element_composition #63

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hoelzerC opened this issue Oct 15, 2024 · 2 comments · Fixed by #95
Closed

Limit to element_composition #63

hoelzerC opened this issue Oct 15, 2024 · 2 comments · Fixed by #95
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algorithm Related to the back-end algorithm for generating the mindless molecules. bug Something isn't working enhancement New feature or request

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@hoelzerC
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Allow limiting the output only to elements denoted in element_composition.

Some Options

  1. Extra Flag fix_element_composition
  2. Allow for forbidden_elements = "1-*" hack, i.e. forbid everything and overrule by element_composition. Currently raising a ValueError due to an empty multiprocess pool.
  3. Set this option per default.

Current workaround:
Manually forbid all elements that are not within your choice of element_composition (inconvenient).

@hoelzerC hoelzerC added enhancement New feature or request algorithm Related to the back-end algorithm for generating the mindless molecules. labels Oct 15, 2024
@marcelmbn
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Thanks for the feedback!
The forbidden_elements = "1-*" "hack" should work and thus, this is also partially a bug. Other than that, also a "fix_element_composition" flag or similar might be useful.

@marcelmbn marcelmbn added the bug Something isn't working label Oct 15, 2024
@marcelmbn
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marcelmbn commented Oct 17, 2024

Let's implement this feature, as it would also simplify the access to isomers (-> if fix_element_composition is true, we would get isomers only anyway). Brought up by @gasevic.

Points to consider

  • Charge should not be set randomly, because for true structural isomers, we don't want IP/EA comparisons but only structural differences
  • For the special case, that people want isomers but randomized charges, we can still implement a flag (--random-charges) with which people can turn the random charge assignment on and off and maybe optionally give a preference for closed-shell and open-shell cases (e.g., 0 and 1 (IMHO most default ones))
  • We would also get rid of this kinda dirty "trick" that if element_composition is set, AND min_num_atoms and max_num_atoms is in an appropriate range, we take the composition is fixed. This is way to complicated (even though it's now documented better, thanks to @jonathan-schoeps README.md changes).

@marcelmbn marcelmbn linked a pull request Dec 13, 2024 that will close this issue
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3 participants