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fix: correct usage of nonbond energy for close contacts #368

Merged
merged 33 commits into from Mar 17, 2023
Merged

fix: correct usage of nonbond energy for close contacts #368

merged 33 commits into from Mar 17, 2023

Commits on Feb 22, 2023

  1. unify function and variable names

    @DaniBodor
    DaniBodor committed Feb 22, 2023
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  2. function to get atoms within covalent distance 3

    @DaniBodor
    DaniBodor committed Feb 22, 2023
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  3. make function more generic

    @DaniBodor
    DaniBodor committed Feb 22, 2023
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  4. clean up intra partner function

    @DaniBodor
    DaniBodor committed Feb 22, 2023
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  5. single array output for _get_vdw_energy, taking intra partner into ac… 

    …count
    @DaniBodor
    DaniBodor committed Feb 22, 2023
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  6. update feature assignment to new format

    @DaniBodor
    DaniBodor committed Feb 22, 2023
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  7. minor code hygeine

    @DaniBodor
    DaniBodor committed Feb 22, 2023
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  8. Merge branch 'main' into 357_vanderwaals_HiLo_fix_dbodor

    @DaniBodor
    DaniBodor committed Feb 22, 2023
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Commits on Feb 24, 2023

  1. Merge branch 'main' into 357_vanderwaals_HiLo_fix_dbodor

    @DaniBodor
    DaniBodor committed Feb 24, 2023
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  2. covalent distance to domain

    @DaniBodor
    DaniBodor committed Feb 24, 2023
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  3. initial _intra_partner test

    @DaniBodor
    DaniBodor committed Feb 24, 2023
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Commits on Feb 26, 2023

  1. improve assert messages

    @DaniBodor
    DaniBodor committed Feb 26, 2023
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  2. add test for very close connections

    @DaniBodor
    DaniBodor committed Feb 26, 2023
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  3. remove unused imports

    @DaniBodor
    DaniBodor committed Feb 26, 2023
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Commits on Mar 8, 2023

  1. notebook to calculate cutoff distances

    @DaniBodor
    DaniBodor committed Mar 8, 2023
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  2. update test notebook

    @DaniBodor
    DaniBodor committed Mar 8, 2023
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Commits on Mar 13, 2023

  1. remove intra partners function

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  2. add 1-4 cutoff to vdw function

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  3. add 1-3 cutoff to vdw function

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  4. add 1-3 cutoff to electrostatic

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  5. improve docstrings

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  6. adjust cutoff distances for 1-3 and 1-4 pairing

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  7. Merge branch 'main' into 357_vanderwaals_HiLo_fix_dbodor

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  8. minor changes to test_contact.py

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  9. adjust contact tests

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  10. remove test_intra_partners

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  11. remove inter/intra nomenclature

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  12. remove notebook from repo

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  13. covalent definition to features/contact.py

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  14. minor adjustments to test

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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  15. improve spacing in test

    @DaniBodor
    DaniBodor committed Mar 13, 2023
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Commits on Mar 16, 2023

  1. fuse potential energy functions

    @DaniBodor
    DaniBodor committed Mar 16, 2023
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  2. Merge branch 'main' into 357_vanderwaals_HiLo_fix_dbodor

    @DaniBodor
    DaniBodor committed Mar 16, 2023
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