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Big smiles #358

Closed
wants to merge 25 commits into from
Closed

Big smiles #358

wants to merge 25 commits into from

Commits on Jan 19, 2024

  1. infrastructure for big smile parsing

    @fgrunewald
    fgrunewald committed Jan 19, 2024
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  2. optional dep. for pysmiles

    @fgrunewald
    fgrunewald committed Jan 19, 2024
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  3. add a processor that reads a big smile string and returns a full meta… 

    …molecule including edges.
    @fgrunewald
    fgrunewald committed Jan 19, 2024
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Commits on Jan 20, 2024

  1. atest-big-smile parsing part I

    @fgrunewald
    fgrunewald committed Jan 20, 2024
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Commits on Jan 22, 2024

  1. fix hcount for single atom; fix nexted branches

    @fgrunewald
    fgrunewald committed Jan 22, 2024
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  2. tests for smile iter and test nested branches

    @fgrunewald
    fgrunewald committed Jan 22, 2024
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  3. add pysmiles to test requrm.

    @fgrunewald
    fgrunewald committed Jan 22, 2024
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  4. add tests for bonding descriptor evaluation

    @fgrunewald
    fgrunewald committed Jan 22, 2024
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Commits on Jan 23, 2024

  1. add tests for big smile molecule prc

    @fgrunewald
    fgrunewald committed Jan 23, 2024
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  2. allow multiple bonding per atom; fix bugs

    @fgrunewald
    fgrunewald committed Jan 23, 2024
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Commits on Jan 24, 2024

  1. remove mpl import

    @fgrunewald
    fgrunewald committed Jan 24, 2024
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  2. add changed tests for multiple bonding per atom

    @fgrunewald
    fgrunewald committed Jan 24, 2024
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  3. delete old processor file

    @fgrunewald
    fgrunewald committed Jan 24, 2024
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Commits on Mar 3, 2024

  1. add H and ] as special characters in big smile parser

    @fgrunewald
    fgrunewald committed Mar 3, 2024
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  2. account for explicit hydrogen in the smiles string input

    @fgrunewald
    fgrunewald committed Mar 3, 2024
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  3. test accounting for explicit hydrogen in the smiles string input

    @fgrunewald
    fgrunewald committed Mar 3, 2024
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Commits on Mar 4, 2024

  1. adjust doc string

    @fgrunewald
    fgrunewald committed Mar 4, 2024
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Commits on Mar 6, 2024

  1. parse force-field in molprocessor, adjust hydrogen reconstruction

    @fgrunewald
    fgrunewald committed Mar 6, 2024
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  2. fix tests

    @fgrunewald
    fgrunewald committed Mar 6, 2024
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  3. Apply suggestions from code review 

    Co-authored-by: Peter C Kroon <pckroon@users.noreply.github.com>
    @fgrunewald @pckroon
    fgrunewald and pckroon authored Mar 6, 2024
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Commits on Mar 7, 2024

  1. allow nested branch expansion

    @fgrunewald
    fgrunewald committed Mar 7, 2024
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  2. test branch expansion

    @fgrunewald
    fgrunewald committed Mar 7, 2024
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  3. add comments all over residue expansion functions

    @fgrunewald
    fgrunewald committed Mar 7, 2024
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  4. address comments

    @fgrunewald
    fgrunewald committed Mar 7, 2024
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  5. allow for ionic bonds with . syntax

    @fgrunewald
    fgrunewald committed Mar 7, 2024
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