Improve MolecularContainer.top_up_conformations

[speleo3]

Top up from all conformations, not just first.

Fixes https://github.com/jensengroup/propka/issues/147

[codecov[bot]]

Codecov Report

Patch coverage: 90.00% and project coverage change: +0.08% :tada:

Comparison is base (fd7b155) 73.08% compared to head (0d6dbfa) 73.17%.

:exclamation: Current head 0d6dbfa differs from pull request most recent head 7d78aca. Consider uploading reports for the commit 7d78aca to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #167 +/- ## ========================================== + Coverage 73.08% 73.17% +0.08% ========================================== Files 25 25 Lines 3972 3977 +5 ========================================== + Hits 2903 2910 +7 + Misses 1069 1067 -2 ``` | [Files Changed](https://app.codecov.io/gh/jensengroup/propka/pull/167?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=jensengroup) | Coverage Δ | | |---|---|---| | [propka/conformation\_container.py](https://app.codecov.io/gh/jensengroup/propka/pull/167?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=jensengroup#diff-cHJvcGthL2NvbmZvcm1hdGlvbl9jb250YWluZXIucHk=) | `84.97% <85.71%> (-0.05%)` | :arrow_down: | | [propka/molecular\_container.py](https://app.codecov.io/gh/jensengroup/propka/pull/167?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=jensengroup#diff-cHJvcGthL21vbGVjdWxhcl9jb250YWluZXIucHk=) | `92.52% <100.00%> (-0.07%)` | :arrow_down: | ... and [2 files with indirect coverage changes](https://app.codecov.io/gh/jensengroup/propka/pull/167/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=jensengroup)

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